bluuebunny/crossref_metadata_2025 huggingface dataset:
The Market for Mergers and the Boundaries of the Firm
Authors: RHODES‐KROPF MATTHEW , ROBINSON DAVID T.
Published: May 2008

We relate the property rights theory of the firm to empirical regularities in the market for mergers and acquisitions. We first show that high market‐to‐book acquirers typically do not purchase low market‐to‐book targets. Instead, mergers pair together firms with similar ratios. We then build a continuous‐time model of investment and merger activity combining search, scarcity, and asset complementarity to explain this like buys like result. We test the model by relating like‐buys‐like to search frictions. Search frictions and assortative matching vary inversely, supporting the model over standard explanations.
The Price of Immediacy
Authors: CHACKO GEORGE C. , JUREK JAKUB W. , STAFFORD ERIK
Published: May 2008

This paper models transaction costs as the rents that a monopolistic market maker extracts from impatient investors who trade via limit orders. We show that limit orders are American options. The limit prices inducing immediate execution of the order are functionally equivalent to bid and ask prices and can be solved for various transaction sizes to characterize the market maker's entire supply curve. We find considerable empirical support for the model's predictions in the cross‐section of NYSE firms. The model produces unbiased, out‐of‐sample forecasts of abnormal returns for firms added to the S&P 500 index.
Loan Sales and Relationship Banking
Authors: PARLOUR CHRISTINE A. , PLANTIN GUILLAUME
Published: May 2008

Firms raise money from banks and the bond market. Banks sell loans in a secondary market to recycle their funds or to trade on private information. Liquidity in the loan market depends on the relative likelihood of each motive for trade and affects firms' optimal financial structure. The endogenous degree of liquidity is not always socially optimal: There is excessive trade in highly rated names, and insufficient liquidity in riskier bonds. We provide testable implications for prices and quantities in primary and secondary loan markets, and bond markets. Further, we posit that risk‐based capital requirements may be socially desirable.
Hypertrophic Cardiomyopathy with Preexcitation: Insights from Noninvasive Electrocardiographic Imaging (ECGI) and Catheter Mapping
Authors: GHOSH SUBHAM , AVARI JENNIFER N. , RHEE EDWARD K. , WOODARD PAMELA K. , RUDY YORAM
Published: May 2008

Introduction: Fasciculoventricular pathway has been described as an unusual variant of preexcitation. Electrocardiographic imaging (ECGI) is a novel imaging modality for noninvasive electroanatomic mapping of epicardial activation and repolarization.

Case: We present a case of an 18‐year‐old male with hypertrophic cardiomyopathy (HCM) and an electrocardiogram (ECG)‐based diagnosis of Wolff‐Parkinson‐White (WPW) syndrome, who underwent a noninvasive ECGI study to image ventricular activation, followed by an electrophysiology study (EPS). The ECGI electroanatomic isochrone map showed early activation of the epicardial aspect of the atrioventricular (A‐V) groove and an aberrant posterior‐base‐to‐apex progression of activation in the left ventricular (LV) epicardium. The EPS showed a likely fasciculoventricular pathway (FVP) without any inducible tachycardia.

Conclusion: While FVP has been described before, this is the first report of detailed quantitative three‐dimensional characterization of electrical activation sequence of a heart with this type of preexcitation, using a novel noninvasive imaging modality (ECGI). In spite of abnormal ventricular activation, the EPS demonstrated that the FVP is not capable of supporting reentrant supraventricular tachycardia or rapidly conducted atrial fibrillation.
Changes in child safety restraint use and parental driving behaviours in Italy
Authors: Collarile Paolo , Valent Francesca , Di Bartolomeo Stefano , Barbone Fabio
Published: May 2008

Aim: To evaluate the changes in prevalence of child‐restraint correct use, level of parental information and parental driving behaviours in a population of North‐Eastern Italy 2 years after a previous survey.

Methods: A mail survey of 514 families with children <12 years. We examined the prevalence of child restraint correct use, level of parental information, parental driving behaviours and the concordance between the responses to the current and previous survey. Multivariable logistic regression was used to identify factors influencing correct restraint use.

Results: Habitual restraint use was reported for 92.5% of children. The frequency of habitual use decreased with increasing child's age (p = 0.0143). Among children 3–7 years, correct restraint use was lower than in the previous survey (p = 0.0039). Increased child's age was associated with decreased likelihood of correct restraint use. Previous correct restraint use and parental information on child restraints, and current parental seat belt use were positively associated with correct use. In the last 2 years, only 17.5% of families have received information on transport safety. Most parents declared to comply with traffic regulations.

Conclusion: In our study area, the use of child restraints is common, although non‐habitual use is reported, especially among older children. The information on transport safety is insufficient. Law enforcement and information campaigns could further enhance parental compliance with traffic regulations.
Insights into and speculations about snake venom metalloproteinase (SVMP) synthesis, folding and disulfide bond formation and their contribution to venom complexity
Authors: Fox Jay W. , Serrano Solange M. T.
Published: May 2008

As more data are generated from proteome and transcriptome analyses of snake venoms, we are gaining an appreciation of the complexity of the venoms and, to some degree, the various sources of such complexity. However, our knowledge is still far from complete. The translation of genetic information from the snake genome to the transcriptome and ultimately the proteome is only beginning to be appreciated, and will require significantly more investigation of the snake venom genomic structure prior to a complete understanding of the genesis of venom composition. Venom complexity, however, is derived not only from the venom genomic structure but also from transcriptome generation and translation and, perhaps most importantly, post‐translation modification of the nascent venom proteome. In this review, we examine the snake venom metalloproteinases, some of the predominant components in viperid venoms, with regard to possible synthesis and post‐translational mechanisms that contribute to venom complexity. The aim of this review is to highlight the state of our knowledge on snake venom metalloproteinase post‐translational processing and to suggest testable hypotheses regarding the cellular mechanisms associated with snake venom metalloproteinase complexity in venoms.
Transcription factor human Skn‐1a enhances replication of human papillomavirus DNA through the direct binding to two sites near the viral replication origin
Authors: Kukimoto Iwao , Mori Seiichiro , Sato Hidetaka , Takeuchi Takamasa , Kanda Tadahito
Published: May 2008

Human papillomavirus type 16 (HPV16) DNA replication, which requires two viral proteins E1 and E2, occurs only in the differentiating epithelium. Besides the general factors necessary for cellular DNA synthesis, other unidentified cellular factors are assumed to be involved in the regulation of HPV DNA replication. In the present study, we found that the POU‐domain transcription factor human Skn‐1a, which induces the terminal differentiation of keratinocytes and activates the HPV16 late promoter, enhanced the transient replication of a plasmid containing the HPV16 replication origin in HEK293 cells when co‐transfected with a plasmid expressing E1 and E2. An electrophoretic mobility shift assay with a bacterially expressed human Skn‐1a or an extract of HeLa cells over‐expressing human Skn‐1a revealed the presence of two human Skn‐1a binding sites that are distinct from the known three sites, near the replication origin. A chromatin immunoprecipitation analysis showed that human Skn‐1a bound to these sites in cells. Nucleotide substitutions in the sites abolished the binding of human Skn‐1a and the human Skn‐1a‐mediated replication enhancement. The data strongly suggest that, through the binding to the two sites, human Skn‐1a enhances HPV DNA replication.
A Conceptual Model for Nursing Information
Authors: Hughes Rodney , Lloyd David , Clark Dame June
Published: May 2008

PURPOSE.  This Conceptual Model for Nursing Information describes the core activities of nursing, the collection of information about these activities, and argues that these activities must be described using standardized nursing languages.

DATA SOURCES.  Relevant literature, both national and international, was reviewed and summarized.

DATA SYNTHESIS.  A maximum data set for nursing was developed.

CONCLUSIONS.  In the United Kingdom, a new and radical approach to the process of nursing is required; one that demonstrates that nursing is the decision‐making that takes place in all core activities of nursing.

IMPLICATIONS FOR NURSING PRACTICE.  Unless nurses have a clear view of what the profession requires from technological solutions for the recording of nursing activities, less than optimal solutions will be forced upon the profession.
The Developmental Processes for NANDA International Nursing Diagnoses
Authors: Scroggins Leann M.
Published: May 2008

PURPOSE.  This study aims to provide a step‐by‐step procedural guideline for the development of a nursing diagnosis that meets the necessary criteria for inclusion in the NANDA International and NNN classification systems.

DATA SOURCES.  The guideline is based on the processes developed by the Diagnosis Development Committee of NANDA International and includes the necessary processes for development of Actual, Wellness, Health Promotion, and Risk nursing diagnoses.

DATA SYNTHESIS.  Definitions of Actual, Wellness, Health Promotion, and Risk nursing diagnoses along with inclusion criteria and taxonomy rules have been incorporated into the guideline to streamline the development and review processes for submitted diagnoses.

CONCLUSIONS.  A step‐by‐step procedural guideline will assist the submitter to move efficiently and effectively through the submission process, resulting in increased submissions and enhancement of the NANDA International and NNN classification systems.
New Zealand cookbooks as a reflection of nutritional knowledge, 1940–1969
Authors: MITCHELL Janet
Published: May 2008

New Zealanders have been exposed to nutritional information from health professionals, government and non‐government bodies for at least 100 years. The present study analyses both community and national cookbooks published in New Zealand from 1940 to 1969 to ascertain if nutritional information and/or recipes with special nutritional significance are transmitted to the community via this medium. During the war years and rationing, it was found that food shortages limited food choice; therefore, it was important to choose food carefully to obtain the required nutrients to maintain good health. Cookbooks published during the 1940s that dealt with rationing, therefore, proved to be an important source of information about nutrition. After the war, as the food supply returned to normal, New Zealanders returned to their traditional diet which led to over consumption and a focus on slimming diets. Cookbooks examined in the present study illustrated nutrition concerns during the period and changes in our culinary culture.
Enhancing nutritional research within an aged care facility
Authors: NOWSON Caryl , JARMAN Heather , HERD Angela
Published: May 2008

Aim:  The present study examined the barriers to the implementation of a nutritional intervention project and sought ways to enhance future projects.

Methods:  The study, utilising a qualitative approach, included participants from key areas involved in the project and who were employed by either the university or regional aged care facility.

Results:  Through analysis the themes ‘successes’, ‘stumbling blocks’ and ‘solutions’ emerged. Within these themes descriptive stories of what worked, what did not work and suggestions for future projects are depicted.

Conclusions:  Communication was the connecting element of each theme, suggesting effective verbal and written communication that ensures ownership by all involved is essential for successful clinical research projects. Strategies to enhance this process have been included to assist future researchers.
Di‐ and Triorganotin(IV) Esters of 3,4‐Methylenedioxyphenylpropenoic Acid: Synthesis, Spectroscopic Characterization and Biological Screening for Antimicrobial, Cytotoxic and Antitumor Activities
Authors: Ahmad Muhammad Sheeraz , Hussain Mukhtiar , Hanif Muhammad , Ali Saqib , Qayyum Mazhar , Mirza Bushra
Published: May 2008

Nine biologically significant organotin(IV) esters of 3,4‐Methylenedioxyphenylpropenoic acid (L) were synthesized with the general formulae [R2SnL2], where R includes Me(1), Et(3), But(4), Oct(5), Ph(8), and [R3SnL], in which R is Me(2), Cy(6), Ph(7), and But(9). The acid and its compounds were characterized by basic analytical techniques comprising elemental analysis, FTIR and mass spectrometry in solid state and by Multinuclear (1H, 13C and 119Sn) NMR in solution form, which provides some important information about the different coordination behaviors of metal in both solid and solution. Methylenedioxy moiety in these compounds enhances the biological activity of these compounds. These compounds were screened for a range of biological activities. Antibacterial activities were determined against six pathogenic bacterial strains, three gram‐positive and three gram‐negative, the activities were measured in terms of inhibition zones (mm). Results demonstrate that diorganotin derivatives are more active than triorganotin derivatives and ligand acid. Antifungal activity was determined against six pathogenic fungal strains, cytotoxicity by the brine shrimp lethality assay, and antitumor activity by crown gall tumor inhibition (potato disc) assay. Results for antifungal activity, cytotoxicity, and antitumor activity of these compounds demonstrate that triorganotin derivatives are more active than diorganotin derivatives and ligand. Finally, the results were compared with similar reports in the literature.
Histological evaluation of the effect of three medicaments; trichloracetic acid, formocresol and mineral trioxide aggregate on pulpotomised teeth of dogs
Authors: Karami Babak , Khayat Akbar , Moazami Fariborz , Pardis Soheil , Abbott Paul
Published: May 2008

The aim of this study was to use clinical, radiographic and histological examinations to compare the dental pulp response in 162 premolar roots of eight dogs when trichloracetic acid (TCA), formocresol, mineral trioxide aggregate (MTA) and zinc oxide eugenol were used as pulpotomy agents. The teeth were divided into four groups. Following pulpotomy, the teeth were restored with amalgam. The animals were sacrificed at 48 h, 2, 4 and 8 weeks (two dogs at each interval). Histological evaluation indicated no cases with necrosis. After 8 weeks follow up, dentine bridge formation was evident in 20%, 50% and 91.7% of formocresol, TCA and MTA cases respectively. The first signs of bridge formation were seen for MTA at 2 weeks and for TCA at 4 weeks. MTA was superior to formocresol and TCA in treating pulps in dogs. However, bridge formation was seen in 50% of TCA cases after 8 weeks which is a desirable finding in pulpotomy procedures.
Estimating age of harbor seals (Phoca vitulina) with incisor teeth and morphometrics
Authors: Blundell Gail M. , Pendleton Grey W.
Published: May 2008

Abstract

We compared annuli counts from sets of canine, postcanine, and incisor teeth from 450 subsistence‐harvested harbor seals, submitted blind to a laboratory. Postcanine and incisor ages were highly correlated with canine age estimates (r= 0.985 andr= 0.984, respectively), as were postcanine and incisor teeth (r= 0.984). Age estimates from teeth of 23 known‐aged seals were highly correlated; canine teethr= 0.987; postcaniner= 0.996; incisorr= 0.992, although age for all tooth‐types was underestimated for a 29‐yr‐old seal. Incisor estimates were variable; comparison of age estimates from two incisors/individual (n= 42) wasr= 0.992 if only high‐quality age estimates were used andr= 0.705 if lower‐quality estimates were used. Morphometrics and incisor‐based ages of 164 live‐captured seals were explored to derive a method of estimating ages of harbor seals when age estimates are needed immediately; 39 seals were of known age. Curvilinear length, mass, and axial girth were most predictive of age for females, and curvilinear length and mass for males (equations for morphometrically calculating ages are given). Morphometric‐based age estimates were highly correlated with known ages (r= 0.896) and incisor‐based estimates (r= 0.904) and discrepancies between known and morphometric‐based ages were small for younger seals. Morphometric‐based age estimates also accurately distinguished between young and mature individuals.
Oestrogen changed cardiomyocyte contraction and β‐adrenoceptor expression in rat hearts subjected to ischaemia–reperfusion
Authors: Wu Qin , Zhao Zhi , Sun Hong , Hao Yan‐ling , Yan Chang‐dong , Gu Shu‐ling
Published: May 2008

Women with functional ovaries have a lower cardiovascular risk than men and postmenopausal women. However, oestrogen replacement therapy remains controversial. This study examined the effect of ovarian hormone deficiency and oestrogen replacement on ventricular myocyte contractile function and expression of β‐adrenoceptors (β‐ARs). Female Sprague–Dawley rats were subjected to bilateral ovariectomy (OVX) or sham operation (Sham). A subgroup of OVX rats received oestrogen (E2) replacement (40 μg kg−1 day−1) for 4 weeks. Cardiomyocyte shortening was evaluated in basal conditions and in the presence of isoprenaline (ISO). The expression of β‐ARs was assessed by Western blotting. The presence of lactate dehydrogenase (LDH) activity in the coronary effluent was determined. Ovariectomy promoted body weight gain associated with reduced serum E2 and uterine weight, all of which were abolished by treatment with E2. Ovariectomy increased the amplitude of both basal and ISO‐stimulated contractions, increased LDH release, upregulated β1‐AR expression and downregulated β2‐AR expression, all of which were restored by treatment with E2. A β1‐AR antagonist, CGP20712A, but not a β2‐AR antagonist, ICI118,551, significantly decreased the amplitude of ventricular myocyte shortening. Oestrogen decreased cardiomyocyte contraction and the expression of β1‐AR, and increased expression of β2‐AR, and all these effects were abolished by the E2 receptor antagonist, ICI182,780. These data suggest that oestrogen plays a cardioprotective role in female rat hearts subjected to ischaemia–reperfusion injury, and the effects of oestrogen are associated with decreased cardiomyocyte contraction and expression of β1‐AR, and increased expression of β2‐AR.
Analysis of cardiac mitochondrial Na+–Ca2+ exchanger kinetics with a biophysical model of mitochondrial Ca2+ handing suggests a 3: 1 stoichiometry
Authors: Dash Ranjan K. , Beard Daniel A.
Published: May 2008

Calcium is a key ion and is known to mediate signalling pathways between cytosol and mitochondria and modulate mitochondrial energy metabolism. To gain a quantitative, biophysical understanding of mitochondrial Ca2+ regulation, we developed a thermodynamically balanced model of mitochondrial Ca2+ handling and bioenergetics by integrating kinetic models of mitochondrial Ca2+ uniporter (CU), Na+–Ca2+ exchanger (NCE), and Na+–H+ exchanger (NHE) into an existing computational model of mitochondrial oxidative phosphorylation. Kinetic flux expressions for the CU, NCE and NHE were developed and individually parameterized based on independent data sets on flux rates measured in purified mitochondria. While available data support a wide range of possible values for the overall activity of the CU in cardiac and liver mitochondria, even at the highest estimated values, the Ca2+ current through the CU does not have a significant effect on mitochondrial membrane potential. This integrated model was then used to analyse additional data on the dynamics and steady‐states of mitochondrial Ca2+ governed by mitochondrial CU and NCE. Our analysis of the data on the time course of matrix free [Ca2+] in respiring mitochondria purified from rabbit heart with addition of different levels of Na+ to the external buffer medium (with the CU blocked) with two separate models – one with a 2: 1 stoichiometry and the other with a 3: 1 stoichiometry for the NCE – supports the hypothesis that the NCE is electrogenic with a stoichiometry of 3: 1. This hypothesis was further tested by simulating an additional independent data set on the steady‐state variations of matrix free [Ca2+] with respect to the variations in external free [Ca2+] in purified respiring mitochondria from rat heart to show that only the 3: 1 stoichiometry model predictions are consistent with the data. Based on these analyses, it is concluded that the mitochondrial NCE is electrogenic with a stoichiometry of 3: 1.
Inhibition of native TRPC6 channel activity by phosphatidylinositol 4,5‐bisphosphate in mesenteric artery myocytes
Authors: Albert Anthony P. , Saleh Sohag N. , Large William A.
Published: May 2008

The present work investigates the effect of phosphatidylinositol‐4,5‐bisphosphate (PIP2) on native TRPC6 channel activity in freshly dispersed rabbit mesenteric artery myocytes using patch clamp recording and co‐immunoprecipitation methods. Inclusion of 100 μm diC8‐PIP2 in the patch pipette and bathing solutions, respectively, inhibited angiotensin II (Ang II)‐evoked whole‐cell cation currents and TRPC6 channel activity by over 90%. In inside‐out patches diC8‐PIP2 also inhibited TRPC6 activity induced by the diacylglycerol analogue 1‐oleoyl‐2‐acetyl‐sn‐glycerol (OAG) with an IC50 of 7.6 μm. Anti‐PIP2 antibodies potentiated Ang II‐ and OAG‐evoked TRPC6 activity by about 2‐fold. Depleters of tissue PIP2 wortmannin and LY294002 stimulated TRPC6 activity, as did the polycation PIP2 scavenger poly‐l‐lysine. Wortmannin reduced Ang II‐evoked TRPC6 activity by over 75% but increased OAG‐induced TRPC6 activity by over 50‐fold. Co‐immunoprecipitation studies demonstrated association between PIP2 and TRPC6 proteins in tissue lysates. Pre‐treatment with Ang II, OAG and wortmannin reduced TRPC6 association with PIP2. These results provide for the first time compelling evidence that constitutively produced PIP2 exerts a powerful inhibitory action on native TRPC6 channels.
Phylogenetic Diversity and Molecular Detection of Bacteria in Gull Feces
Authors: Lu Jingrang , Santo Domingo Jorge W. , Lamendella Regina , Edge Thomas , Hill Stephen
Published: May 2008

In spite of increasing public health concerns about the potential risks associated with swimming in waters contaminated with waterfowl feces, little is known about the composition of the gut microbial community of aquatic birds. To address this, a gull 16S rRNA gene clone library was developed and analyzed to determine the identities of fecal bacteria. Analysis of 282 16S rRNA gene clones demonstrated that the gull gut bacterial community is mostly composed of populations closely related to
Bacilli
(37%),
Clostridia
(17%),
Gammaproteobacteria
(11%), and
Bacteriodetes
(1%). Interestingly, a considerable number of sequences (i.e., 26%) were closely related to
Catellicoccus marimammalium
, a gram-positive, catalase-negative bacterium. To determine the occurrence of
C. marimammalium
in waterfowl, species-specific 16S rRNA gene PCR and real-time assays were developed and used to test fecal DNA extracts from different bird (
n
= 13) and mammal (
n
= 26) species. The results showed that both assays were specific to gull fecal DNA and that
C. marimammalium
was present in gull fecal samples collected from the five locations in North America (California, Georgia, Ohio, Wisconsin, and Toronto, Canada) tested. Additionally, 48 DNA extracts from waters collected from six sites in southern California, Great Lakes in Michigan, Lake Erie in Ohio, and Lake Ontario in Canada presumed to be impacted with gull feces were positive by the
C. marimammalium
assay. Due to the widespread presence of this species in gulls and environmental waters contaminated with gull feces, targeting this bacterial species might be useful for detecting gull fecal contamination in waterfowl-impacted waters.
Bifidobacterium bifidumLacto-N-Biosidase, a Critical Enzyme for the Degradation of Human Milk Oligosaccharides with a Type 1 Structure
Authors: Wada Jun , Ando Takuro , Kiyohara Masashi , Ashida Hisashi , Kitaoka Motomitsu , Yamaguchi Masanori , Kumagai Hidehiko , Katayama Takane , Yamamoto Kenji
Published: May 2008

Breast-fed infants often have intestinal microbiota dominated by bifidobacteria in contrast to formula-fed infants. We found that several bifidobacterial strains produce a lacto-N-biosidase that liberates lacto-N-biose I (Galβ1,3GlcNAc; type 1 chain) from lacto-N-tetraose (Galβ1,3GlcNAcβ1,3Galβ1,4Glc), which is a major component of human milk oligosaccharides, and subsequently isolated the gene fromBifidobacterium bifidumJCM1254. The gene, designatedlnbB, was predicted to encode a protein of 1,112 amino acid residues containing a signal peptide and a membrane anchor at the N and C termini, respectively, and to possess the domain of glycoside hydrolase family 20, carbohydrate binding module 32, and bacterial immunoglobulin-like domain 2, in that order, from the N terminus. The recombinant enzyme showed substrate preference for the unmodified β-linked lacto-N-biose I structure. Lacto-N-biosidase activity was found in several bifidobacterial strains, but not in the other enteric bacteria, such as clostridia, bacteroides, and lactobacilli, under the tested conditions. These results, together with our recent finding of a novel metabolic pathway specific for lacto-N-biose I in bifidobacterial cells, suggest that some of the bifidobacterial strains are highly adapted for utilizing human milk oligosaccharides with a type 1 chain.
Infection Dynamics of Coexisting Beta- and Gammaproteobacteria in the Nested Endosymbiotic System of Mealybugs
Authors: Kono Marie , Koga Ryuichi , Shimada Masakazu , Fukatsu Takema
Published: May 2008

We investigated the infection dynamics of endosymbiotic bacteria in the developmental course of the mealybugs
Planococcus kraunhiae
and
Pseudococcus comstocki
. Molecular phylogenetic analyses identified a betaproteobacterium and a gammaproteobacterium from each of the mealybug species. The former bacterium was related to the β-endosymbionts of other mealybugs, i.e., “
Candidatus
Tremblaya princeps,” and formed a compact clade in the
Betaproteobacteria
. Meanwhile, the latter bacterium was related to the γ-endosymbionts of other mealybugs but belonged to distinct clades in the
Gammaproteobacteria
. Whole-mount in situ hybridization confirmed the peculiar nested formation in the endosymbiotic system of the mealybugs: the β-endosymbiont cells were present in the cytoplasm of the bacteriocytes, and the γ-endosymbiont cells were located in the β-endosymbiont cells. In nymphal and female development, a large oval bacteriome consisting of a number of bacteriocytes was present in the abdomen, wherein the endosymbionts were harbored. In male development, strikingly, the bacteriome progressively degenerated in prepupae and pupae and became almost unrecognizable in adult males. In the degeneration process, the γ-endosymbionts disappeared more rapidly than the β-endosymbionts did. Quantitative PCR analyses revealed that (i) the population dynamics of the endosymbionts in female development reflected the reproductive activity of the insects, (ii) the population dynamics of the endosymbionts were strikingly different between female development and male development, (iii) the endosymbiont populations drastically decreased in male development, and (iv) the γ-endosymbiont populations decreased more rapidly than the β-endosymbiont populations in male development. Possible mechanisms underlying the uncoupled regulation of the β- and γ-endosymbiont populations are discussed in relation to the establishment and evolution of this unique prokaryote-prokaryote endosymbiotic system.
Isolation and Characterization of Bacteriophages Infecting the Fish Pathogen
Flavobacterium psychrophilum
Authors: Stenholm Anne Rønnest , Dalsgaard Inger , Middelboe Mathias
Published: May 2008

Flavobacterium psychrophilum
is a serious pathogen in trout aquaculture, responsible for the diseases rainbow trout fry syndrome (RTFS) and cold water disease (CWD). Bacteriophage control of
F. psychrophilum
may constitute a realistic approach in the treatment of these diseases; however, a detailed understanding of the phage-host interactions is needed to evaluate the potential of
F. psychrophilum
bacteriophages for that purpose. Twenty-two
F. psychrophilum
phages from Danish rainbow trout farms were isolated and characterized. The phage genome sizes differed considerably and fell into three major size classes (8.5 to 12 kb, 48 kb, and 90 kb). The phage host ranges comprised from 5 to 23 of the 28 tested
F. psychrophilum
strains, and 18 of the phage isolates showed unique host ranges. Each bacterial strain had a unique pattern of susceptibility to the 22 phages, and individual strains also showed large variations (up to 10
7
-fold differences) in susceptibility to specific phages. Phage burst size (7 to 162 phages infected cell
−1
) and latency period (4 to 6 h) also showed pronounced differences both between phages and, for a specific phage, between host strains. In general, the characterization documented the presence of diverse
F. psychrophilum
phage communities in Danish trout farms, with highly variable patterns of infectivity. The discovery and characterization of broad-host-range phages with strong lytic potential against numerous pathogenic
F. psychrophilum
host strains thus provided the foundation for future exploration of the potential of phages in the treatment of RTFS and CWD.
Field-Based Stable Isotope Probing Reveals the Identities of Benzoic Acid-Metabolizing Microorganisms and Their In Situ Growth in Agricultural Soil
Authors: Pumphrey Graham M. , Madsen Eugene L.
Published: May 2008

We used a combination of stable isotope probing (SIP), gas chromatography-mass spectrometry-based respiration, isolation/cultivation, and quantitative PCR procedures to discover the identity and in situ growth of soil microorganisms that metabolize benzoic acid. We added [
13
C]benzoic acid or [
12
C]benzoic acid (100 μg) once, four times, or five times at 2-day intervals to agricultural field plots. After monitoring
13
CO
2
evolution from the benzoic acid-dosed soil, field soils were harvested and used for nucleic acid extraction and for cultivation of benzoate-degrading bacteria. Exposure of soil to benzoate increased the number of culturable benzoate degraders compared to unamended soil, and exposure to benzoate shifted the dominant culturable benzoate degraders from
Pseudomonas
species to
Burkholderia
species. Isopycnic separation of heavy [
13
C]DNA from the unlabeled fraction allowed terminal restriction fragment length polymorphism (T-RFLP) analyses to confirm that distinct 16S rRNA genes were localized in the heavy fraction. Phylogenetic analysis of sequenced 16S rRNA genes revealed a predominance (15 of 58 clones) of
Burkholderia
species in the heavy fraction.
Burkholderia
sp. strain EBA09 shared 99.5% 16S rRNA sequence similarity with a group of clones representing the dominant RFLP pattern, and the T-RFLP fragment for strain EBA09 and a clone from that cluster matched the fragment enriched in the [
13
C]DNA fraction. Growth of the population represented by EBA09 during the field-dosing experiment was demonstrated by using most-probable-number-PCR and primers targeting EBA09 and the closely related species
Burkholderia hospita
. Thus, the target population identified by SIP not only actively metabolized benzoic acid but reproduced in the field upon the addition of the substrate.
Proteomic Analysis of Stationary Phase in the Marine Bacterium “
Candidatus
Pelagibacter ubique”
Authors: Sowell Sarah M. , Norbeck Angela D. , Lipton Mary S. , Nicora Carrie D. , Callister Stephen J. , Smith Richard D. , Barofsky Douglas F. , Giovannoni Stephen J.
Published: May 2008

“
Candidatus
Pelagibacter ubique,” an abundant marine alphaproteobacterium, subsists in nature at low ambient nutrient concentrations and may often be exposed to nutrient limitation, but its genome reveals no evidence of global regulatory mechanisms for adaptation to stationary phase. High-resolution capillary liquid chromatography coupled online to an LTQ mass spectrometer was used to build an accurate mass and time (AMT) tag library that enabled quantitative examination of proteomic differences between exponential- and stationary-phase “
Ca
. Pelagibacter ubique” cells cultivated in a seawater medium. The AMT tag library represented 65% of the predicted protein-encoding genes. “
Ca
. Pelagibacter ubique” appears to respond adaptively to stationary phase by increasing the abundance of a suite of proteins that contribute to homeostasis rather than undergoing a major remodeling of its proteome. Stationary-phase abundances increased significantly for OsmC and thioredoxin reductase, which may mitigate oxidative damage in “
Ca
. Pelagibacter,” as well as for molecular chaperones, enzymes involved in methionine and cysteine biosynthesis, proteins involved in ρ-dependent transcription termination, and the signal transduction enzyme CheY-FisH. We speculate that this limited response may enable “
Ca
. Pelagibacter ubique” to cope with ambient conditions that deprive it of nutrients for short periods and, furthermore, that the ability to resume growth overrides the need for a more comprehensive global stationary-phase response to create a capacity for long-term survival.
Characterization ofgtf, a Glucosyltransferase Gene in the Genomes ofPediococcus parvulusandOenococcus oeni, Two Bacterial Species Commonly Found in Wine
Authors: Dols-Lafargue Marguerite , Lee Hyo Young , Le Marrec Claire , Heyraud Alain , Chambat Gérard , Lonvaud-Funel Aline
Published: May 2008

“Ropiness” is a bacterial alteration in wines, beers, and ciders, caused by β-glucan-synthesizing pediococci. A single glucosyltransferase, Gtf, controls ropy polysaccharide synthesis. In this study, we show that the correspondinggtfgene is also present on the chromosomes of several strains ofOenococcus oeniisolated from nonropy wines.gtfis surrounded by mobile elements that may be implicated in its integration into the chromosome ofO. oeni. gtfis expressed in all thegtf+strains, and β-glucan is detected in the majority of these strains. Part of this β-glucan accumulates around the cells forming a capsule, while the other part is liberated into the medium together with heteropolysaccharides. Most of the time, this polymer excretion does not lead to ropiness in a model medium. In addition, we show that wild or recombinant bacterial strains harboring a functionalgtfgene (gtf+) are more resistant to several stresses occurring in wine (alcohol, pH, and SO2) and exhibit increased adhesion capacities compared to theirgtfmutant variants.
Diversity and Distribution of Ecotypes of the Aerobic Anoxygenic Phototrophy Gene
pufM
in the Delaware Estuary
Authors: Waidner Lisa A. , Kirchman David L.
Published: May 2008

The diversity of aerobic anoxygenic phototrophic (AAP) bacteria has been examined in marine habitats, but the types of AAP bacteria in estuarine waters and distribution of ecotypes in any environment are not well known. The goal of this study was to determine the diversity of AAP bacteria in the Delaware estuary and to examine the distribution of select ecotypes using quantitative PCR (qPCR) assays for the
pufM
gene, which encodes a protein in the light reaction center of AAP bacteria. In PCR libraries from the Delaware River,
pufM
genes similar to those from
Beta
- (
Rhodoferax
-like) or
Gammaproteobacteria
comprised at least 50% of the clones, but the expressed
pufM
genes from the river were not dominated by these two groups in August 2002 (less than 31% of clones). In four transects, qPCR data indicated that the gammaproteobacterial type of
pufM
was abundant only near the mouth of the bay whereas
Rhodoferax
-like AAP bacteria were restricted to waters with a salinity of <5. In contrast, a
Rhodobacter
-like
pufM
gene was ubiquitous, but its distribution along the salinity gradient varied with the season. High fractions (12 to 24%) of all three
pufM
types were associated with particles. The data suggest that different groups of AAP bacteria are controlled by different environmental factors, which may explain current difficulties in predicting the distribution of total AAP bacteria in aquatic environments.
Characterization of Cytochrome 579, an Unusual Cytochrome Isolated from an Iron-Oxidizing Microbial Community
Authors: Singer Steven W. , Chan Clara S. , Zemla Adam , VerBerkmoes Nathan C. , Hwang Mona , Hettich Robert L. , Banfield Jillian F. , Thelen Michael P.
Published: May 2008

A novel, soluble cytochrome with an unusual visible spectral signature at 579 nm (Cyt
579
) has been characterized after isolation from several different microbial biofilms collected in an extremely acidic ecosystem. Previous proteogenomic studies of an Fe(II)-oxidizing community indicated that this abundant red cytochrome could be extracted from the biofilms with dilute sulfuric acid. Here, we found that the Fe(II)-dependent reduction of Cyt
579
was thermodynamically favorable at a pH of >3, raising the possibility that Cyt
579
acts as an accessory protein for electron transfer. The results of transmission electron microscopy of immunogold-labeled biofilm indicated that Cyt
579
is localized near the bacterial cell surface, consistent with periplasmic localization. The results of further protein analysis of Cyt
579
, using preparative chromatofocusing and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, revealed three forms of the protein that correspond to different N-terminal truncations of the amino acid sequence. The results of intact-protein analysis corroborated the posttranslational modifications of these forms and identified a genomically uncharacterized Cyt
579
variant. Homology modeling was used to predict the overall cytochrome structure and heme binding site; the positions of nine amino acid substitutions found in three Cyt
579
variants all map to the surface of the protein and away from the heme group. Based on this detailed characterization of Cyt
579
, we propose that Cyt
579
acts as an electron transfer protein, shuttling electrons derived from Fe(II) oxidation to support critical metabolic functions in the acidophilic microbial community.
Surface Plasmon Resonance Assay for Real-Time Monitoring of Somatic Coliphages in Wastewaters
Authors: García-Aljaro Cristina , Muñoz-Berbel Xavier , Jenkins A. Toby A. , Blanch Anicet R. , Muñoz Francesc Xavier
Published: May 2008

The surface plasmon resonance (SPR) technique is a well-established method for the measurement of molecules binding to surfaces and the quantification of binding constants between surface-immobilized proteins and proteins in solution. In this paper we describe an extension of the methodology to study bacteriophage-bacterium interactions. A two-channel microfluidic SPR sensor device was used to detect the presence of somatic coliphages, a group of bacteriophages that have been proposed as fecal pollution indicators in water, using their host,
Escherichia coli
WG5, as a target for their selective detection. The bacterium,
E. coli
WG5, was immobilized on gold sensor chips using avidin-biotin and bacteriophages extracted from wastewater added. The initial binding of the bacteriophage was observed at high concentrations, and a separate, time-delayed cell lysis event also was observed, which was sensitive to bacteriophage at low concentrations. As few as 1 PFU/ml of bacteriophage injected into the chamber could be detected after a phage incubation period of 120 min, which equates to an approximate limit of detection of around 10
2
PFU/ml. The bacteriophage-bacterium interaction appeared to cause a structural change in the surface-bound bacteria, possibly due to collapse of the cell, which was observed as an increase in mass density on the sensor chip. These results suggest that this methodology could be employed for future biosensor technologies and for quantification of the bacteriophage concentration.
Discovery of a Modified Transcription Factor Endowing Yeasts with Organic-Solvent Tolerance and Reconstruction of an Organic-Solvent-Tolerant
Saccharomyces cerevisiae
Strain
Authors: Matsui Ken , Teranishi Shinya , Kamon Shohei , Kuroda Kouichi , Ueda Mitsuyoshi
Published: May 2008

Organic-solvent tolerance in
Saccharomyces cerevisiae
strain KK-211, which was first isolated as an organic-solvent-tolerant strain, depends on point mutation (R821S) of the transcription factor Pdr1p. The integration of the
PDR1
R821S mutation into wild-type yeast results in organic-solvent tolerance, and the
PDR1
R821S mutant can reduce carbonyl compounds in organic solvents.
Direct Interactions between the Paf1 Complex and a Cleavage and Polyadenylation Factor Are Revealed by Dissociation of Paf1 from RNA Polymerase II
Authors: Nordick Kristen , Hoffman Matthew G. , Betz Joan L. , Jaehning Judith A.
Published: May 2008

The Paf1 complex (Paf1, Ctr9, Cdc73, Rtf1, and Leo1) is normally associated with RNA polymerase II (Pol II) throughout the transcription cycle. However, the loss of either Rtf1 or Cdc73 results in the detachment of the Paf1 complex from Pol II and the chromatin form of actively transcribed genes. Using functionally tagged forms of the Paf1 complex factors, we have determined that, except for the more loosely associated Rtf1, the remaining components stay stably associated with one another in an RNase-resistant complex after dissociation from Pol II and chromatin. The loss of Paf1, Ctr9, or to a lesser extent Cdc73 or Rtf1 results in reduced levels of serine 2 phosphorylation of the Pol II C-terminal domain and in increased read through of the
MAK21
polyadenylation site. We found that the cleavage and polyadenylation factor Cft1 requires the Pol II-associated form of the Paf1 complex for full levels of interaction with the serine 5-phosphorylated form of Pol II. When the Paf1 complex is dissociated from Pol II, a direct interaction between Cft1 and the Paf1 complex can be detected. These results are consistent with the Paf1 complex providing a point of contact for recruitment of 3′-end processing factors at an early point in the transcription cycle. The lack of this connection helps to explain the defects in 3′-end formation observed in the absence of Paf1.
TheFrancisellaPathogenicity Island Protein PdpD Is Required for Full Virulence and Associates with Homologues of the Type VI Secretion System
Authors: Ludu Jagjit S. , de Bruin Olle M. , Duplantis Barry N. , Schmerk Crystal L. , Chou Alicia Y. , Elkins Karen L. , Nano Francis E.
Published: May 2008

Francisella tularensisis a highly infectious, facultative intracellular bacterial pathogen that is the causative agent of tularemia. Nearly a century ago, researchers observed that tularemia was often fatal in North America but almost never fatal in Europe and Asia. The chromosomes ofF. tularensisstrains carry two identical copies of theFrancisellapathogenicity island (FPI), and the FPIs of North America-specific biotypes contain two genes,anmKandpdpD, that are not found in biotypes that are distributed over the entire Northern Hemisphere. In this work, we studied the contribution ofanmKandpdpDto virulence by usingF. novicida, which is very closely related toF. tularensisbut which carries only one copy of the FPI. We showed thatanmKandpdpDare necessary for full virulence but not for intracellular growth. This is in sharp contrast to most other FPI genes that have been studied to date, which are required for intracellular growth. We also showed that PdpD is localized to the outer membrane. Further, overexpression of PdpD affects the cellular distribution of FPI-encoded proteins IglA, IglB, and IglC. Finally, deletions of FPI genes encoding proteins that are homologues of known components of type VI secretion systems abolished the altered distribution of IglC and the outer membrane localization of PdpD.
Lipoprotein Signal Peptides Are Processed by Lsp and Eep of
Streptococcus uberis
Authors: Denham E. L. , Ward P. N. , Leigh J. A.
Published: May 2008

Lipoprotein signal peptidase (
lsp
) is responsible for cleaving the signal peptide sequence of lipoproteins in gram-positive bacteria. Investigation of the role of Lsp in
Streptococcus uberis
, a common cause of bovine mastitis, was undertaken using the lipoprotein MtuA (a protein essential for virulence) as a marker. The
S. uberis lsp
mutant phenotype displayed novel lipoprotein processing. Not only was full-length (uncleaved) MtuA detected by Western blotting, but during late log phase, a lower-molecular-weight derivative of MtuA was evident. Similar analysis of an
S. uberis
double mutant containing insertions disrupting both
lsp
and
eep
(a homologue of the
Enterococcus faecalis
“enhanced expression of pheromone” gene) indicated a role for
eep
in cleavage of lipoproteins in the absence of Lsp. Such a function may indicate a role for
eep
in maintenance of secretion pathways during disruption of normal lipoprotein processing.
Switching Control of Expression ofptsGfrom the Mlc Regulon to the NagC Regulon
Authors: El Qaidi Samir , Plumbridge Jacqueline
Published: May 2008

The Mlc and NagC transcriptional repressors bind to similar 23-bp operators. The sequences are weakly palindromic, with just four positions totally conserved. There is no cross regulation observed between the repressors in vivo, but there are no obvious bases which could be responsible for operator site discrimination. To investigate the basis for operator recognition and to try to understand what differentiates NagC sites from Mlc sites, we have undertaken mutagenesis experiments to convertptsGfrom a gene regulated by Mlc into a gene regulated by NagC. There are two Mlc operators upstream ofptsG, and to switchptsGto the NagC regulon, it was necessary to change two different characteristics of both operators. Firstly, we replaced the AT base pair at position +/−11 from the center of symmetry of the operators with a GC base pair. Secondly, we changed the sequence of the CG base pairs in the central region of the operator (positions −4 to +4 around the center of symmetry). Our results show that changes at either of these locations are sufficient to lose regulation by Mlc but that both types of changes in both operators are necessary to convertptsGto a gene regulated by NagC. In addition, these experiments confirmed that two operators are necessary for regulation by NagC. We also show that regulation ofptsGby Mlc involves some cooperative binding of Mlc to the two operators.