bluuebunny/crossref_metadata_2025 huggingface dataset:
Dimension of the facial bone wall in the anterior maxilla: a cone‐beam computed tomography study
Authors: Januário Alessandro Lourenço , Duarte Wagner Rodrigues , Barriviera Mauricio , Mesti Juliana Cristina , Araújo Mauricio Guimarães , Lindhe Jan
Published: February 2011

Objective: To determine the thickness of the facial bone wall in the anterior dentition of the maxilla and at different locations apical to the cemento‐enamel junction (CEJ).

Material and methods: Two‐hundred and fifty subjects, aged between 17 and 66 years, with all maxillary front teeth present were included. Written informed consents were obtained. Cone‐beam computed tomography scans were performed with the iCAT unit. This examination included all tooth and edentulous sites in the dentition. The images were acquired by means of the iCAT software and processed by a computer. Measurements of the (i) distance between the CEJ and the facial bone crest and (ii) the thickness of the facial bone wall were performed. The bone wall dimensions were assessed at three different positions in relation to the facial bone crest, i.e., at distances of 1, 3, and 5 mm apical to the crest.

Results: The measurements demonstrated that (i) the distance between the CEJ and the facial bone crest varied between 1.6 and 3 mm and (ii) the facial bone wall in most locations in all tooth sites examined was ≤1 mm thick and that close to 50% of sites had a bone wall thickness that was ≤0.5 mm.

Conclusion: Most tooth sites in the anterior maxilla have a thin facial bone wall. Such a thin bone wall may undergo marked dimensional diminution following tooth extraction. This fact must be considered before tooth removal and the planning of rehabilitation in the anterior segment of the dentition in the maxilla.

To cite this article:
 Januário AL, Duarte WR, Barriviera M, Mesti JC, Araújo MG, Lindhe J. Dimension of the facial bone wall in the anterior maxilla: a cone‐beam computed tomography study. Clin. Oral Impl. Res. 22, 2011; 1168–1171 doi: 10.1111/j.1600‐0501.2010.02086.x. 10.1111/j.1600‐0501.2010.02086.x
Relationships among invasive common carp, native fishes and physicochemical characteristics in upper Midwest (USA) lakes
Authors: Weber Michael J. , Brown Michael L.
Published: February 2011

Abstract –  Common carp Cyprinus carpio is a widespread invasive species that, in high abundance, can impose numerous deleterious effects in aquatic ecosystems. Common carp increase turbidity and nutrient availability while reducing invertebrate prey resources and aquatic macrophytes, transforming shallow lakes from the clear‐ to turbid‐water state. However, potential effects of common carp on native fish communities have received limited attention. We evaluated the relationships among relative abundances of nine native fishes and common carp for 81 lakes in eastern South Dakota and their associated physicochemical characteristics. Inverse threshold relationships among relative abundances of native fishes and common carp were identified for black bullhead Ameiurus melas, black crappie Pomoxis nigromaculatus, bluegill Lepomis macrochirus, white bass Morone chrysops and northern pike Esox lucius, while marginally significant relationships were detected for largemouth bass Micropterus salmoides and smallmouth bass M. dolomieu. Lakes where common carp relative abundance exceeded 0.6 fish per net night had low abundance of native fishes, whereas lower abundance of common carp resulted in variable abundance of native fishes. Lakes with abundance of common carp surpassing 0.6 fish per net night were also characterised by larger surface areas and watersheds and impaired water quality (higher dissolved solids and chlorophyll a concentrations and lower secchi depth). Our results are consistent with the biotic‐abiotic constraining hypothesis that proposes biotic factors can regulate fish populations regardless of abiotic conditions. Thus, common carp abundance may need to be reduced and sustained below ecological thresholds to improve water quality and increase abundance of native fishes.
Retracted: Neonatal Pulse oximetry screening: A National Survey
Authors: Kang SL , Tobin S , Kelsall W
Published: February 2011

Retraction: The following article from Acta Paediatrica; ‘Neonatal pulse oximetry screening: A national survey’ by Sok‐Leng Kang, Suzanne Tobin and Wilf Kelsall, posted online on 18 February 2011 in a format yet to undergo copy‐editing and proof correction, in Wiley Online Library (http://www.onlinelibrary.wiley.com), has been retracted by agreement between the authors, the Editor‐in‐Chief, Hugo Lagercrantz, and Blackwell Publishing Ltd. The retraction has been agreed due to overlap between this article and the following article published in Archives of Disease Fetal & Neonatal Edition; ‘Neonatal pulse oximetry screening: A national survey’, published online on 19 February 2011 in its final format, but in advance of the print journal.
Comparing sleep measures of infants derived from parental reports in sleep diaries and acceleration sensors
Authors: Asaka Yoko , Takada Satoshi
Published: February 2011

Aim:  Comparing sleep measures of infants derived from two data collection methods, acceleration sensors and sleep diaries, and identify the clinical application for each data collection method.

Methods:  The participants were 52 pairs of infants and mothers. Infant sleep measures were obtained through the actigraphs (Micro‐mini RC, Ambulatory Monitoring Inc., Ardsley, NY, USA) and sleep diaries for over a period of 7 days.

Results:  The results showed that the concordance in sleep measures derived from two methods showed decreases in the following order: sleep offset time [r = 0.91 (p = 0.00)], sleep onset time r = 0.89 (p = 0.00), nocturnal sleep duration [r = 0.75 (p = 0.00)], the number of night wakings [r = 0.46 (p < 0.01)] and WASO [r = 0.34 (p < 0.05)]. It was revealed that the accuracy of sleep diary records was affected by the sleeping place and varied throughout the study period.

Conclusion:  It was confirmed that the sleep measures indicating sleep schedule reported from the sleep diaries had high concordances compared with the data from the actigraphs. Using the sleep diary was recommended to understand behaviours when focusing on infant’s daily rhythms. In terms of accuracy and stability of recording throughout the study period, understanding sleep quality and independence of sleeping places, the choice of actigraph was recommended.
High prevalence of BCR‐ABL fusion transcripts with poor prognostic impact among adult ALL patients: report from Pakistan
Authors: FAIZ Mariam , IQBAL Qazi Javed , QURESHI Asif
Published: February 2011

Aim:  Philadelphia (Ph) chromosome positive acute lymphoblastic leukemia (ALL) is a common cytogenetic abnormality associated with poor outcome in adults. This preliminary study, in the absence of substantial evidence, reported the prevalence of the BCR‐ABL gene fusion in ALL patients by RT‐PCR in Pakistan. Moreover, the prognostic significance of BCR‐ABL fusion along with other characteristics was also ascertained.

Methods:  One hundred forty six newly diagnosed ALL patients treated at our center between 2005 and 2008 comprised the study group. The patients were treated with a Children and Leukemia Group B induction regimen.

Results:  Among these patients, BCR‐ABL fusion oncogene was present in 43 of 78 patients (55%). A statistically significant difference in BCR‐ABL‐positivity within three age groups (<20 years, 20–50 years, >50 years) was observed (P= 0.001). The median age was significantly higher in the BCR‐ABL+ group (30 vs 19 years; P= 0.001). BCR‐ABL+ patients were also characterized by higher median WBC counts (96 000/µL vs 23 000//µL, P= 0.002). Complete remission was achieved in 74% BCR‐ABL− patients and 35% BCR‐ABL+ patients (P= 0.001). Only 10% of BCR‐ABL− patients achieved continued complete remission (CR). None of the BCR‐ABL+ patients maintained a CR further to induction therapy. With the available therapeutic protocol, the presence of a BCR‐ABL fusion predicted a lower survival (P= 0.001).

Conclusion:  A high prevalence of BCR‐ABL gene fusion was observed that appeared as a poor prognostic factor. Identification of this genetic entity at diagnosis is crucial for understanding the nature of adult ALL and for deciding optimal treatment.
Calibrating emission lines as quasar bolometers
Authors: Punsly Brian , Zhang Shaohua
Published: February 2011

Historically, emission lines have been considered a valuable tool for estimating the bolometric thermal luminosity of the accretion flow in active galactic nucleus, Lbol. We study the reliability of this method by comparing line strengths to the optical/ultraviolet continuum luminosity of Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) radio-quiet quasars with 0.4 < z < 0.8. We find formulae for Lbol as a function of single line strengths for the broad components of Hβ and Mg ii, as well as the narrow lines of [O iii] and [O ii]. We determine the standard errors of the formulae that are fitted to the data. Our new estimators are shown to be more accurate than archival line strength estimations in the literature. It is demonstrated that broad lines are superior estimators of the continuum luminosity (and Lbol) with Hβ being the most reliable. The fidelity of each of the estimators is determined in the context of the SDSS DR7 radio-loud quasars as an illustrative application of our results. In general, individual researchers can use our results as a tool to decide if a particular line strength provides an adequate estimate of Lbol for their purposes. Finally, it is shown that considering all four line strengths, simultaneously, can yield information on both Lbol and the radio jet power.
Competition, cooperation, and corporate culture
Authors: Kosfeld Michael , von Siemens Ferdinand A.
Published: February 2011

Cooperation between workers can be of substantial value to a firm, yet its level often varies substantially between firms. We show that these differences can unfold in a competitive labor market if workers have heterogeneous social preferences and preferences are private information. In our model, workers differ in their willingness to cooperate voluntarily. We show that there always exists a separating equilibrium in which workers self‐select into firms that differ in their monetary incentives as well as their level of worker cooperation. Our model highlights the role of sorting and worker heterogeneity in the emergence of heterogeneous corporate cultures. It also provides a new explanation for the coexistence of nonprofit and for‐profit firms.

“Here you don’t communicate. And sometimes you end up not knowing things. … Everyone says we need effective communication. But it’s a low priority in action. … The hardest thing at the gates when flights are delayed is to get information.”

Customer service supervisor, American Airlines

“There is constant communication between service and the ramp. When planes have to be switched and bags must be moved, customer service will advise the ramp directly or through operations. If there’s an aircraft swap operations keeps everyone informed. … It happens smoothly.”

Customer service supervisor, Southwest Airlines1
The Results of the National Heritage Language Survey: Implications for Teaching, Curriculum Design, and Professional Development
Authors: Carreira Maria , Kagan Olga
Published: February 2011

Abstract:This article reports on a survey of heritage language learners (HLLs) across different heritage languages (HLs) and geographic regions in the United States. A general profile of HLLs emerges as a student who (1) acquired English in early childhood, after acquiring the HL; (2) has limited exposure to the HL outside the home; (3) has relatively strong aural and oral skills but limited literacy skills; (4) has positive HL attitudes and experiences; and (5) studies the HL mainly to connect with communities of speakers in the United States and to gain insights into his or her roots. We argue that a community‐based curriculum represents an effective way to harness the wealth of knowledge and experiences that HLLs bring to the classroom and to respond to their goals for their HL.
Qualitative and Quantitative Measures of Second Language Writing: Potential Outcomes of Informal Target Language Learning Abroad
Authors: Brown N. Anthony , Solovieva Raissa V. , Eggett Dennis L.
Published: February 2011

Abstract: This research describes a method applied at a U.S. university in a third‐year Russian language course designed to facilitate Advanced and Superior second language writing proficiency through the forum of argumentation and debate. Participants had extensive informal language experience living in a Russian‐speaking country but comparatively little formal language instruction, especially with regard to writing. The authors quantitatively analyzed weekly position papers and ACTFL pre– and post–Written Proficiency Test compositions using prescribed complexity measures and compared them with qualitative ACTFL proficiency ratings. Preliminary findings underscore the value to both the writer and instructor of applying both quantitative and qualitative measures; they likewise point out challenges associated with teaching students whose language has become automatized, albeit oftentimes error‐full, in part owing to the nature of past language study.
Teaching About Women and Islam in North Africa: Integrating Postcolonial Feminist Theory in the Classroom
Authors: Zayzafoon Lamia Ben Youssef
Published: February 2011

Abstract: Using postcolonial feminist theory, the researcher attempts in this article to redefine the interpretive framework through which courses on Islam and North African women are being taught in American undergraduate classes. Several conceptual limitations have been identified: inadequate knowledge of the geography and history of North Africa; the discursive dichotomy between East and West; the production of the Muslim woman as a single category; the tendency to de‐historicize Islam and Eastern cultures in general into unchanging and closed systems of religious practices and beliefs; the uncritical adoption of Islamic exegesis as an explanatory prism to understand all the woes of the Islamic world; and the cultural essentialism underlying the discourse of multiculturalism in American textbooks. To each one of these limitations, the author proposes alternative teaching strategies such as the historicization of all discourses on Muslim women; inclusion of the scholarship of Maghrebian women scholars in the classroom; role‐playing; cross‐cultural comparisons; and the integration of medieval maps and Renaissance drawings as well as audiovisual materials produced in North Africa and the Middle East ranging from political cartoons and commercials to youth programs like “Star Academy.”
The effectiveness of biofield therapies for decreasing symptoms of pain and anxiety, and improving QoL
Authors: Wesa K , Cassileth B , Jain S
Published: February 2011

Jain S, Mills PJ.

Biofield therapies: helpful or full of hype? A best evidence synthesis.

Int J Behav Med 2010; 17: 1–16.
Massage therapy after heart surgery: possibly pleasant, but not effective
Authors: Baxter GD , Albert NM
Published: February 2011

Albert NM, Gillinov AM, Lytle BW, Feng J, Cwynar R, Blackstone EH.

A randomized trial of massage therapy after heart surgery.

Heart Lung 2009; 38: 480–90.
Discovering bipartite substructure in directed networks
Authors: Taylor Alan , Vass J. Keith , Higham Desmond J.
Published: February 2011

Bipartivity is an important network concept that can be applied to nodes, edges and communities. Here we focus on directed networks and look for subnetworks made up of two distinct groups of nodes, connected by ‘one-way’ links. We show that a spectral approach can be used to find hidden substructures of this form. Theoretical support is given for the idealized case where there is limited overlap between subnetworks. Numerical experiments show that the approach is robust to spurious and missing edges. A key application of this work is in the analysis of high-throughput gene expression data, and we give an example where a biologically meaningful directed bipartite subnetwork is found from a cancer microarray dataset.
Minimal alterations in T‐type calcium channel gating markedly modify physiological firing dynamics
Authors: Tscherter A. , David F. , Ivanova T. , Deleuze C. , Renger J. J. , Uebele V. N. , Shin H‐S. , Bal T. , Leresche N. , Lambert R. C.
Published: February 2011

Non‐technical summary  Voltage‐dependant calcium channels constitute a heterogeneous group playing ubiquitous roles in excitable cells. Among them the low‐voltage activated T‐type channels generate a family of currents that differ in their biophysical properties reflecting structural or neuromodulatory diversity. These T‐type calcium channels are highly expressed in neurons located in the thalamus, a brain structure considered as the gateway to the cortex. Thalamic T‐type calcium channels are critically involved in oscillatory neuronal activities associated with sleep or epilepsy and may contribute to sensory processing. Using injections of computer‐simulated T‐type conductances (a real time mimicry of ionic currents) in biological thalamic neurons, we dissect how the diversity in T‐type currents impact on the output of thalamic neurons. We show that very subtle modifications in the properties of the T current that were overlooked so far affect drastically the physiological output of the thalamic neurons and therefore condition the dynamics of thalamo‐cortical information integration.
Stochastic Stability of Coupled Oscillators With One Asymptotically Stable and One Critical Mode
Authors: Sri Namachchivaya N. , Vedula Lalit , Onu Kristjan
Published: February 2011

An analytic explanation is given for the experimental results reported by Popp and Romberg (2001, “Influence of Stochastic Effects on Flow Induced Vibrations in Tube Bundles,” IUTAM Symposium on Nonlinearity and Stochastic Structural Dynamics (Solid Mechanics and Its Applications), S. Narayanan and R. N. Iyengar, eds., Kluwer Academic, Dordrecht, Vol. 85, pp. 197–208) on fluid flow over tube bundles by using the concept of the maximal Lyapunov exponent. The motion of one tube in the bundle is modeled as a two-degree-of-freedom (four dimensional) system with one critical mode and one asymptotically stable mode driven by a small intensity stochastic process. We obtain a general asymptotic approximation for the maximal Lyapunov exponent for this four dimensional system and explain how the stochastic components that couple the critical and stable modes play an important role in determining whether a noisy excitation can stabilize or destabilize the oscillatory critical mode.
Splitting Water and Carbon Dioxide via the Heterogeneous Oxidation of Zinc Vapor: Thermodynamic Considerations
Authors: Venstrom Luke J. , Davidson Jane H.
Published: February 2011

The heterogeneous oxidation of zinc vapor is proposed as a promising reaction path for the exothermic step in the two-step Zn/ZnO solar thermochemical water and carbon dioxide splitting cycles. This approach circumvents mass transfer limitations encountered in the oxidation of solid or liquid zinc, promising rapid hydrogen and carbon monoxide production rates concurrent with a complete conversion of zinc to zinc oxide. In this paper, a parametric thermodynamic analysis is presented to quantify the benefit of achieving a rapid and complete conversion of zinc via the heterogeneous oxidation of zinc vapor. The conversion of zinc in polydisperse aerosol reactors has been limited to 20% for reaction times on the order of a minute, resulting in a cycle efficiency of ∼6%. The benefit of completely converting zinc via the heterogeneous oxidation of zinc vapor is an increase in efficiency to 27% and 31% for water and carbon dioxide splitting, respectively. The cycle efficiency could be higher if heat recuperation is implemented.
Properties of phosphorus-doped zinc oxide films grown by pulsed laser deposition
Authors: Li Yuanjie , Liu Zilong , Ren Jiangbo
Published: February 2011

Electrical and chemical bonding properties of P-doped ZnO thin films grown by pulsed laser deposition on sapphire substrates were systematically characterized utilizing the Hall effect and x-ray photoelectron spectroscopy (XPS) measurements. Oxygen growth pressure and postannealing processing play a great role in the properties of these films. Increasing oxygen growth pressure from 5 to 20 Pa enhanced the resistivity of P-doped ZnO films by three orders of magnitude. P-doped ZnO films grown at 700 °C under 20 Pa O2 exhibited p-type conductivity with hole concentration of 5×1017 cm−3 and hole mobility of 0.3 cm2/V s. Rapid thermal annealing processing decreased the electron density in the P-doped ZnO films. XPS binding energies of P 2s and 2p peaks showed formation of P–O bonds which increased with oxygen pressure in the films. This indicates formation of defect complexes of P dopants occupying zinc sites PZn and zinc vacancies VZn in the P-doped ZnO films.
Exploring Platelet Chemokine Antimicrobial Activity: Nuclear Magnetic Resonance Backbone Dynamics of NAP-2 and TC-1
Authors: Nguyen Leonard T. , Kwakman Paulus H. S. , Chan David I. , Liu Zhihong , de Boer Leonie , Zaat Sebastian A. J. , Vogel Hans J.
Published: February 2011

The platelet chemokines neutrophil-activating peptide-2 (NAP-2) and thrombocidin-1 (TC-1) differ by only two amino acids at their carboxy-terminal ends. Nevertheless, they display a significant difference in their direct antimicrobial activities, with the longer NAP-2 being inactive and TC-1 being active. In an attempt to rationalize this difference in activity, we studied the structure and the dynamics of both proteins by nuclear magnetic resonance (NMR) spectroscopy. Using15N isotope-labeled protein, we confirmed that the two monomeric proteins essentially have the same overall structure in aqueous solution. However, NMR relaxation measurements provided evidence that the negatively charged carboxy-terminal residues of NAP-2 experience a restricted motion, whereas the carboxy-terminal end of TC-1 moves in an unrestricted manner. The same behavior was also seen in molecular dynamic simulations of both proteins. Detailed analysis of the protein motions through model-free analysis, as well as a determination of their overall correlation times, provided evidence for the existence of a monomer-dimer equilibrium in solution, which seemed to be more prevalent for TC-1. This finding was supported by diffusion NMR experiments. Dimerization generates a larger cationic surface area that would increase the antimicrobial activities of these chemokines. Moreover, these data also show that the negatively charged carboxy-terminal end of NAP-2 (which is absent in TC-1) folds back over part of the positively charged helical region of the protein and, in doing so, interferes with the direct antimicrobial activity.
Rationale-Based,
De Novo
Design of Dehydrophenylalanine-Containing Antibiotic Peptides and Systematic Modification in Sequence for Enhanced Potency
Authors: Pathak Sarika , Chauhan Virander Singh
Published: February 2011

Increased microbial drug resistance has generated a global requirement for new anti-infective agents. As part of an effort to develop new, low-molecular-mass peptide antibiotics, we used a rationale-based minimalist approach to design short, nonhemolytic, potent, and broad-spectrum antibiotic peptides with increased serum stability. These peptides were designed to attain an amphipathic structure in helical conformations. VS1 was used as the lead compound, and its properties were compared with three series of derivates obtained by (i) N-terminal amino acid addition, (ii) systematic Trp substitution, and (iii) peptide dendrimerization. The Trp substitution approach underlined the optimized sequence of VS2 in terms of potency, faster membrane permeation, and cost-effectiveness. VS2 (a variant of VS1 with two Trp substitutions) was found to exhibit good antimicrobial activity against both the Gram-negative
Escherichia coli
and the Gram-positive bacterium
Staphylococcus aureus
. It was also found to have noncytolytic activity and the ability to permeate and depolarize the bacterial membrane. Lysis of the bacterial cell wall and inner membrane by the peptide was confirmed by transmission electron microscopy. A combination of small size, the presence of unnatural amino acids, high antimicrobial activity, insignificant hemolysis, and proteolytic resistance provides fundamental information for the
de novo
design of an antimicrobial peptide useful for the management of infectious disease.
Activity of and Development of Resistance to Corallopyronin A, an Inhibitor of RNA Polymerase
Authors: Mariner Katherine , McPhillie Martin , Trowbridge Rachel , Smith Catriona , O'Neill Alex J. , Fishwick Colin W. G. , Chopra Ian
Published: February 2011

We explored the properties of corallopyronin A (CorA), a poorly characterized inhibitor of bacterial RNA polymerase (RNAP). It displayed a 50% inhibitory concentration of 0.73 μM against RNAP, compared with 11.5 nM for rifampin. The antibacterial activity of CorA was also inferior to rifampin, and resistant mutants of
Staphylococcus aureus
were easily selected. The mutations conferring resistance resided in the
rpoB
and
rpoC
subunits of RNAP. We conclude that CorA is not a promising antibacterial drug candidate.
Cellulose- and Xylan-Degrading Thermophilic Anaerobic Bacteria from Biocompost
Authors: Sizova M. V. , Izquierdo J. A. , Panikov N. S. , Lynd L. R.
Published: February 2011

Nine thermophilic cellulolytic clostridial isolates and four other noncellulolytic bacterial isolates were isolated from self-heated biocompost via preliminary enrichment culture on microcrystalline cellulose. All cellulolytic isolates grew vigorously on cellulose, with the formation of either ethanol and acetate or acetate and formate as principal fermentation products as well as lactate and glycerol as minor products. In addition, two out of nine cellulolytic strains were able to utilize xylan and pretreated wood with roughly the same efficiency as for cellulose. The major products of xylan fermentation were acetate and formate, with minor contributions of lactate and ethanol. Phylogenetic analyses of 16S rRNA and glycosyl hydrolase family 48 (GH48) gene sequences revealed that two xylan-utilizing isolates were related to a
Clostridium clariflavum
strain and represent a distinct novel branch within the GH48 family. Both isolates possessed high cellulase and xylanase activity induced independently by either cellulose or xylan. Enzymatic activity decayed after growth cessation, with more-rapid disappearance of cellulase activity than of xylanase activity. A mixture of xylan and cellulose was utilized simultaneously, with a significant synergistic effect observed as a reduction of lag phase in cellulose degradation.
The Probiotic
Escherichia coli
Nissle 1917 Reduces Pathogen Invasion and Modulates Cytokine Expression in Caco-2 Cells Infected with Crohn's Disease-Associated
E. coli
LF82
Authors: Huebner Claudia , Ding Yaoyao , Petermann Ivonne , Knapp Christoph , Ferguson Lynnette R.
Published: February 2011

Increased numbers of adherent invasive
Escherichia coli
(AIEC) have been found in Crohn's disease (CD) patients. In this report, we investigate the potential of the probiotic
Escherichia coli
Nissle 1917 (EcN) to reduce features associated with AIEC pathogenicity in an already established infection with AIEC reference strain LF82.
Genetic Diversity of O-Antigen Biosynthesis Regions in
Vibrio cholerae
Authors: Aydanian Antonina , Tang Li , Morris J. Glenn , Johnson Judith A. , Stine O. Colin
Published: February 2011

O-antigen biosynthetic (
wbf
) regions for
Vibrio cholerae
serogroups O5, O8, and O108 were isolated and sequenced. Sequences were compared to those of other published
V. cholerae
O-antigen regions. These
wbf
regions showed a high degree of heterogeneity both in gene content and in gene order. Genes identified frequently showed greater similarities to polysaccharide biosynthesis genes from species other than
V. cholerae
. Our results demonstrate the plasticity of O-antigen genes in
V. cholerae
, the diversity of the genetic pool from which they are drawn, and the likelihood that new pandemic serogroups will emerge.
Marker Removal System for
Thermoanaerobacterium saccharolyticum
and Development of a Markerless Ethanologen
Authors: Shaw A. Joe , Covalla Sean F. , Hogsett David A. , Herring Christopher D.
Published: February 2011

Marker removal strategies were developed for
Thermoanaerobacterium saccharolyticum
to select against the
pyrF
gene and the
pta
and
ack
genes. The
pta
- and
ack
-based haloacetate selective strategy was subsequently used to create strain M0355, a markerless Δ
ldh
Δ
pta
Δ
ack
strain that produces ethanol at a high yield.
Temperature Adaptation Markedly Determines Evolution within the GenusSaccharomyces
Authors: Salvadó Z. , Arroyo-López F. N. , Guillamón J. M. , Salazar G. , Querol A. , Barrio E.
Published: February 2011

The present study uses a mathematical-empirical approach to estimate the cardinal growth temperature parameters (Tmin, the temperature below which growth is no longer observed;Topt, the temperature at which the μmaxequals its optimal value; μopt, the optimal value of μmax; andTmax, the temperature above which no growth occurs) of 27 yeast strains belonging to differentSaccharomycesand non-Saccharomycesspecies.S. cerevisiaewas the yeast best adapted to grow at high temperatures within theSaccharomycesgenus, with the highest optimum (32.3°C) and maximum (45.4°C) growth temperatures. On the other hand,S. kudriavzeviiandS. bayanusvar.uvarumshowed the lowest optimum (23.6 and 26.2°C) and maximum (36.8 and 38.4°C) growth temperatures, respectively, confirming that both species are more psychrophilic thanS. cerevisiae. The remainingSaccharomycesspecies (S. paradoxus,S. mikatae,S. arboricolus, andS. cariocanus) showed intermediate responses. With respect to the minimum temperature which supported growth, this parameter ranged from 1.3 (S. cariocanus) to 4.3°C (S. kudriavzevii). We also tested whether these physiological traits were correlated with the phylogeny, which was accomplished by means of a statistical orthogram method. The analysis suggested that the most important shift in the adaptation to grow at higher temperatures occurred in theSaccharomycesgenus after the divergence of theS. arboricolus,S. mikatae,S. cariocanus,S. paradoxus, andS. cerevisiaelineages from theS. kudriavzeviiandS. bayanusvar.uvarumlineages. Finally, our mathematical models suggest that temperature may also play an important role in the imposition ofS. cerevisiaeversus non-Saccharomycesspecies during wine fermentation.
Determination of Adhesin Gene Sequences in, and Biofilm Formation by, O157 and Non-O157 Shiga Toxin-ProducingEscherichia coliStrains Isolated from Different Sources
Authors: Biscola Franciele Tafarello , Abe Cecilia Mari , Guth Beatriz Ernestina Cabilio
Published: February 2011

Biofilm formation by Shiga toxin-producingEscherichia coli(STEC) has been associated with the expression of different adhesins (type 1 fimbria, curli, Ag43, Cah, and EhaA). In this study, biofilm formation and the presence of adhesin-related gene sequences were determined by PCR in 18 O157 strains and 33 non-O157 strains isolated from different sources (human, animal, food, and water). The expression of different adhesins was also assessed by reverse transcription-PCR (RT-PCR), Congo red agar plates, and mannose-sensitive hemagglutination (MSHA) assay. Biofilm formation occurred in 5/18 (28%) O157 STEC strains and 17/33 (51%) non-O157 STEC strains from different serotypes and sources, when the assays were performed at 28°C for 48 h. Among the non-O157 biofilm-producing isolates, 12/17 (71%) expressed type 1 fimbriae and 11/17 (65%) expressed curli and produced cellulose, while 8/17 (47%) were considered to be Ag43+by RT-PCR. Among O157 strains, a close correlation was observed between biofilm formation and expression of curli and cellulose. In non-O157 strains, it seems that, in addition to the presence of curli, the ability to form biofilm is associated with the presence of other factors such as type 1 fimbriae and autotransporter proteins, which may contribute to the persistence of these organisms in the environment.
Spatial Genetic Structure of a Vector-Borne Generalist Pathogen
Authors: Coletta-Filho Helvécio D. , Bittleston Leonora S. , Almeida Rodrigo P. P.
Published: February 2011

Vector-borne generalist pathogens colonize several reservoir species and are usually dependent on polyphagous arthropods for dispersal; however, their spatial genetic structure is generally poorly understood. Using fast-evolving genetic markers (20 simple sequence repeat loci, resulting in a total of 119 alleles), we studied the genetic structure of the vector-borne plant-pathogenic bacteriumXylella fastidiosain Napa Valley, CA, where it causes Pierce's disease when it is transmitted to grapevines from reservoir plants in adjacent riparian vegetation. Eighty-three differentX. fastidiosamultilocus microsatellite genotypes were found in 93 isolates obtained from five vineyards, resulting in an index of clonal fraction closer to 0 and a Simpson's genotypic diversity index (D) closer to a maximum value of 1. Moderate values of Nei's gene diversity (HNei; averageHNei= 0.41) were observed for most of theX. fastidiosapopulations. The low Wright's index of genetic diversity among populations calculated by the FSTAT software (Wright'sFSTindex) among population pairs (0.0096 to 0.1080) indicated a weak or absent genetic structure among the five populations; a panmictic population was inferred by Bayesian analyses (with the STRUCTURE and BAPS programs). Furthermore, a Mantel test showed no significant genetic isolation by distance when both Nei (r= −0.3459,P= 0.268) and linearized θ (r= −0.3106,P= 0.269) indices were used. These results suggest that the riparian vegetation from which vectors acquire the pathogen prior to inoculation of grapevines supports a diverse population ofX. fastidiosa.
Activity and Distribution of Thermophilic Prokaryotes in Hydrothermal Fluid, Sulfidic Structures, and Sheaths of Alvinellids (East Pacific Rise, 13°N)
Authors: Bonch-Osmolovskaya Elizaveta A. , Perevalova Anna A. , Kolganova Tatiana V. , Rusanov Igor I. , Jeanthon Christian , Pimenov Nikolay V.
Published: February 2011

Processes of inorganic carbon assimilation, methanogenesis, sulfate reduction, and acetate oxidation to CO
2
occurring in samples from the East Pacific Rise at 13°N were traced, using radioisotopically labeled substrates, at temperatures ranging from 65 to 100°C. Molecular hydrogen stimulated lithotrophic methanogenesis and sulfate reduction but inhibited inorganic carbon assimilation. Active mineralization of acetate was observed in an organic-rich
Alvinella
-associated system at 80°C. Members of the
Thermococcales
were the most numerous hyperthermophilic archaea in these samples, their density achieving 10
8
cells per cm
3
, while the numbers of cultured hydrogen-utilizing thermophilic lithotrophs were several orders of magnitude lower.
Construction of a Bacterial Assay for Estrogen Detection Based on an Estrogen-Sensitive Intein
Authors: Liang Rubing , Zhou Jing , Liu Jianhua
Published: February 2011

Escherichia colistrain DIER was constructed for estrogen detection by inserting an estrogen-sensitive intein (VMAERintein) into the specific site of the constitutively expressed chromosomallacZgene. This VMAERintein was generated by replacing the endonuclease region of theSaccharomyces cerevisiaeVMA intein with the estrogen binding region of the human estrogen receptor α (hERα). When there were estrogens or analogs, the splicing of the VMAERintein was induced to produce the mature LacZ protein, which was detected through a β-galactosidase colorimetric assay. Eight typical chemicals (17-β-estradiol, bisphenol A, chrysene, 6-OH-chrysene, benz[a]anthracene, pyrene, progesterone, and testosterone) were detected using this DIER strain, and the whole detection procedure was accomplished in 2 h. Their 50% effective concentrations (EC50), relative estrogenic activities, and estradiol equivalency factors were calculated and were quite consistent with those detected with the yeast estrogen screening (YES) system. Furthermore, the estrogenic activities of the synthetic musk samples extracted from the wastewater and waste sludge of a sewage treatment plant of Shanghai (China) were detected, and their results were comparable to those obtained from the YES system and gas chromatography-mass spectrometry (GC-MS). In conclusion, the DIER bioassay could fill a niche for the efficient, rapid, high-throughput screening of estrogenic compounds and has potential for the remote, near-real-time monitoring of environmental estrogens.
Pathogenicity Island Markers, Virulence Determinants
malX
and
usp
, and the Capacity of
Escherichia coli
To Persist in Infants' Commensal Microbiotas
Authors: Östblom Anna , Adlerberth Ingegerd , Wold Agnes E. , Nowrouzian Forough L.
Published: February 2011

Virulence-associated genes in bacteria are often located on chromosomal regions, termed pathogenicity islands (PAIs). Several PAIs are found in
Escherichia coli
strains that cause extraintestinal infections, but their role in commensal bowel colonization is unknown. Resident strains are enriched in adhesins (P fimbriae and type 1 fimbriae), capsular antigens (K1 and K5), hemolysin, and aerobactin and mostly belong to phylogenetic group B2. Here, we investigated whether six pathogenicity islands and the virulence determinants
malX
and
usp
are associated with fitness of
E. coli
in the infant bowel microbiota.
E. coli
strains isolated from stools of 130 Swedish infants during the first year of life were examined for their carriage of PAI markers,
malX
, and
usp
by PCR. Carriage was related to strain persistence: long-term colonizers (≥12 months) carried significantly more of PAI II from strain CFT703 (II
CFT703
), IV
536,
and II
J96
and
malX
and
usp
than intermediate colonizers (1 to 11 months) and transient strains (<3 weeks). The accumulation of PAI markers in each individual strain correlated positively with its time of persistence in the colon. Phylogenetic group B2 accounted for 69% of long-term colonizers, 46% of intermediate colonizers and 14% of transient strains. These results support the hypothesis that some bacterial traits contributing to extraintestinal infections have in fact evolved primarily because they increase the fitness of
E. coli
in its natural niche, the colon; accordingly, they may be regarded as fitness islands in the gut.
Distribution and Diversity of
Gallionella
-Like Neutrophilic Iron Oxidizers in a Tidal Freshwater Marsh
Authors: Wang Juanjuan , Vollrath Susann , Behrends Thilo , Bodelier Paul L. E. , Muyzer Gerard , Meima-Franke Marion , Den Oudsten Frank , Van Cappellen Philippe , Laanbroek Hendrikus J.
Published: February 2011

Microbial iron oxidation is an integral part of the iron redox cycle in wetlands. Nonetheless, relatively little is known about the composition and ecology of iron-oxidizing communities in the soils and sediments of wetlands. In this study, sediment cores were collected across a freshwater tidal marsh in order to characterize the iron-oxidizing bacteria (FeOB) and to link their distributions to the geochemical properties of the sediments. We applied recently designed 16S rRNA primers targeting
Gallionella-
related FeOB by using a nested PCR-denaturing gradient gel electrophoresis (DGGE) approach combined with a novel quantitative PCR (qPCR) assay.
Gallionella
-related FeOB were detected in most of the samples. The diversity and abundance of the putative FeOB were generally higher in the upper 5 to 12 cm of sediment than in deeper sediment and higher in samples collected in April than in those collected in July and October. Oxygen supply by macrofauna appears to be a major force in controlling the spatial and temporal variations in FeOB communities. The higher abundance of
Gallionella
-related FeOB in April coincided with elevated concentrations of extractable Fe(III) in the sediments. Despite this coincidence, the distributions of FeOB did not exhibit a simple relationship to the redox zonation inferred from the geochemical depth profiles.
Inhibitory Spectra and Modes of Antimicrobial Action of Gallotannins from Mango Kernels (Mangifera indicaL.)
Authors: Engels Christina , Schieber Andreas , Gänzle Michael G.
Published: February 2011

This study investigated the antimicrobial activities and modes of action of penta-, hexa-, hepta-, octa-, nona-, and deca-O-galloylglucose (gallotannins) isolated from mango kernels. The MICs and minimum bactericidal concentrations (MBCs) against food-borne bacteria and fungi were determined using a critical dilution assay. Gram-positive bacteria were generally more susceptible to gallotannins than were Gram-negative bacteria. The MICs of gallotannins againstBacillus subtilis,Bacillus cereus,Clostridium botulinum,Campylobacter jejuni,Listeria monocytogenes, andStaphylococcus aureuswere 0.2 g liter−1or less; enterotoxigenicEscherichia coliandSalmonella entericawere inhibited by 0.5 to 1 g liter−1, and lactic acid bacteria were resistant. The use of lipopolysaccharide mutants ofS. entericaindicated that the outer membrane confers resistance toward gallotannins. Supplementation of LB medium with iron eliminated the inhibitory activity of gallotannins againstStaphylococcus aureus, and siderophore-deficient mutants ofS. entericawere less resistant toward gallotannins than was the wild-type strain. Hepta-O-galloylglucose sensitizedLactobacillus plantarumTMW1.460 to hop extract, indicating inactivation of hop resistance mechanisms, e.g., the multidrug resistance (MDR) transporter HorA. Carbohydrate metabolism ofLactococcus lactisMG1363, a conditionally respiring organism, was influenced by hepta-O-galloylglucose when grown under aerobic conditions and in the presence of heme but not under anaerobic conditions, indicating that gallotannins influence the respiratory chain. In conclusion, the inhibitory activities of gallotannins are attributable to their strong affinity for iron and likely additionally relate to the inactivation of membrane-bound proteins.
Inhibition of Predation by
Bdellovibrio bacteriovorus
and
Micavibrio aeruginosavorus
via Host Cell Metabolic Activity in the Presence of Carbohydrates
Authors: Dashiff Aliza , Keeling Thomas G. , Kadouri Daniel E.
Published: February 2011

Bdellovibrio bacteriovorus
and
Micavibrio aeruginosavorus
are highly motile Gram-negative predatory bacteria with the potential of being used as biocontrol agents or living antibiotics. It was suggested previously that sugar-binding proteins play a role in
M. aeruginosavorus
and
B. bacteriovorus
host specificity and predator-prey interactions. The effect of carbohydrates on predation was reexamined in this study. It was demonstrated that the presence of carbohydrates could indeed block predation. However, further investigation demonstrated that inhibition of predation was due to medium acidification by the metabolic activity of the host and not to a blocking of a putative sugar-binding protein. The data presented here might be of value when storing, growing, and cultivating predatory bacteria, as well as when considering environmental conditions that might influence predation in the field.
Proof of Concept for Recombinant Cellular Controls in Quantitative Molecular Pathogen Detection
Authors: Rossmanith Peter , Mester Patrick , Frühwirth Karin , Fuchs Sabine , Wagner Martin
Published: February 2011

In this study, we present the concept of internal sample process controls (ISPCs) to monitor the efficiency of an analytical chain using sample preparation and quantitative PCR (qPCR). A recombinant
Listeria monocytogenes
Δ
prfA
(targeted deletion) strain containing a competitive artificial single-copy genomic target was applied to naturally contaminated samples to demonstrate its analytical suitability as an ISPC.
Contribution of Rapid Evolution of theluxR-luxIIntergenic Region to the Diverse Bioluminescence Outputs ofVibrio fischeriStrains Isolated from Different Environments
Authors: Bose Jeffrey L. , Wollenberg Michael S. , Colton Deanna M. , Mandel Mark J. , Septer Alecia N. , Dunn Anne K. , Stabb Eric V.
Published: February 2011

Vibrio fischeriserves as a valuable model of bacterial bioluminescence, its regulation, and its functional significance. Light output varies more than 10,000-fold in wild-type isolates from different environments, yet dim and bright strains have similar organization of the light-producingluxgenes, with the activator-encodingluxRdivergently transcribed fromluxICDABEG. By comparing the genomes of bright strain MJ11 and the dimmer ES114, we found that theluxregion has diverged more than most shared orthologs, including those flankinglux. Divergence was particularly high in the intergenic sequence betweenluxRandluxI. Analysis of the intergenicluxregion from 18V. fischeristrains revealed that, with one exception, sequence divergence essentially mirrored strain phylogeny but with relatively high substitution rates. The bases conserved among intergenicluxR-luxIsequences included binding sites for known regulators, such as LuxR and ArcA, and bases of unknown significance, including a striking palindromic repeat. By using this collection of diverseluxR-luxIregions, we found that expression of PluxI-lacZbut not PluxR-lacZtranscriptional reporters correlated with the luminescence output of the strains from which the promoters originated. We also found that exchange of a small stretch of theluxI-luxRintergenic region between two strains largely reversed their relative brightness. Our results show that theluxR-luxIintergenic region contributes significantly to the variable luminescence output amongV. fischeristrains isolated from different environments, although other elements of strain backgrounds also contribute. Moreover, theluxsystem appears to have evolved relatively rapidly, suggesting unknown environment-specific selective pressures.
Synechococcus
sp. Strain PCC 7002
nifJ
Mutant Lacking Pyruvate:Ferredoxin Oxidoreductase
Authors: McNeely Kelsey , Xu Yu , Ananyev Gennady , Bennette Nicholas , Bryant Donald A. , Dismukes G. Charles
Published: February 2011

The
nifJ
gene codes for pyruvate:ferredoxin oxidoreductase (PFOR), which reduces ferredoxin during fermentative catabolism of pyruvate to acetyl-coenzyme A (acetyl-CoA). A
nifJ
knockout mutant was constructed that lacks one of two pathways for the oxidation of pyruvate in the cyanobacterium
Synechococcus
sp. strain PCC 7002. Remarkably, the photoautotrophic growth rate of this mutant increased by 20% relative to the wild-type (WT) rate under conditions of light-dark cycling. This result is attributed to an increase in the quantum yield of photosystem II (PSII) charge separation as measured by photosynthetic electron turnover efficiency determined using fast-repetition-rate fluorometry (

F
v

/

F
m

). During autofermentation, the excretion of acetate and lactate products by
nifJ
mutant cells decreased 2-fold and 1.2-fold, respectively. Although
nifJ
cells displayed higher
in vitro
hydrogenase activity than WT cells, H
2
production
in vivo
was 1.3-fold lower than the WT level. Inhibition of acetate-CoA ligase and pyruvate dehydrogenase complex by glycerol eliminated acetate production, with a resulting loss of reductant and a 3-fold decrease in H
2
production by
nifJ
cells compared to WT cells. Continuous electrochemical detection of dissolved H
2
revealed two temporally resolved phases of H
2
production during autofermentation, a minor first phase and a major second phase. The first phase was attributed to reduction of ferredoxin, because its level decreased 2-fold in
nifJ
cells. The second phase was attributed to glycolytic NADH production and decreased 20% in
nifJ
cells. Measurement of the intracellular NADH/NAD
+
ratio revealed that the reductant generated by PFOR contributing to the first phase of H
2
production was not in equilibrium with bulk NADH/NAD
+
and that the second phase corresponded to the equilibrium NADH-mediated process.