bluuebunny/crossref_metadata_2025 huggingface dataset:
Epidermal growth factor receptor immunoexpression evaluation in malignant salivary gland tumours
Authors: Monteiro L. S. , Bento M. J. , Palmeira C. , Lopes C.
Published: July 2009

Objective:  The aim of this study was to determine epidermal growth factor receptor (EGFR) expression in malignant salivary gland tumours and its possible relationships with clinical and morphological findings, disease course and prognosis.

Patients and methods:  The study sample comprised 88 patients diagnosed and treated for primary malignant salivary gland tumours between January 1992 and December 2002. We analysed EGFR expression using immunohistochemistry on formalin‐fixed, paraffin embedded surgical specimens of all patients. Statistical analysis was used to investigate possible relationships between EGFR expression and clinical findings, histological findings, disease course and patients survival.

Results:  Of all cases, 32 (36.4%) were EGFR positive. There was a statistically significant correlation between EGFR expression and histological grade. No other variable was correlated with EGFR expression including the overall and disease‐free survival. Stage classification was the only parameter in multivariate analysis that was an independent predictor of low overall and disease‐free survival.

Conclusion:  EGFR is not a useful indicator of prognosis in malignant salivary gland tumours. However, the EGFR expression in salivary gland cancers like adenocarcinomas, undifferentiated carcinomas, mucoepidermoid carcinomas or salivary duct carcinomas suggests that these tumours may be a candidate for therapy investigation directed at EGFR.
EMMPRIN expression in tongue squamous cell carcinoma
Authors: Huang Zhiquan , Huang Hongzhang , Li Haigang , Chen Weiliang , Pan Chaobin
Published: July 2009

Background:  Extracellular matrix metalloproteinase inducer (EMMPRIN) is identified as a tumor‐cell membrane protein that stimulates matrix metalloproteinases (MMPs) production. Several studies have shown that higher EMMPRIN expression is associated with shorter survival time and correlated significantly with more advanced clinico‐parameters of cancer. The aim of this study was to investigate the relationship between clinico‐pathologic characteristics and EMMPRIN, and prognostic significance of EMMPRIN expression in human tongue squamous cell carcinoma.

Methods:  Extracellular MMP inducer expression was examined immunohistochemically on paraffin‐embedded tissue specimens from 68 patients with tongue squamous cell carcinoma and who underwent radical surgeries from 1996 to 2006. The 68 patients were followed up from 1 to 119 months, with an average of 27.5 months. Nonparametric tests were performed for the comparison of EMMPRIN expression between two independent groups. Survival analysis was performed to find the prognostic significance of EMMPRIN expression.

Results:  We found that EMMPRIN expression in tongue squamous cell carcinoma is significantly higher than that in non‐cancerous epithelium adjacent to carcinoma of tongue. In addition, EMMPRIN expression is significantly associated with tumor diameter and clinical stage in the samples, but did not correlate with gender, age, tumor metastasis, and pathological grade. Finally, survival analysis indicates that EMMPRIN overexpression correlates significantly with poor overall survival in the patient cohort.

Conclusion:  These results suggest that EMMPRIN might represent an attractive target for immunotherapeutic approaches in a subgroup of patients with tongue squamous cell carcinoma.
Outcome of oral dysplasia: a retrospective hospital‐based study of 207 patients with a long follow‐up
Authors: Arduino Paolo G. , Surace Antonio , Carbone Mario , Elia Alessandra , Massolini Gianluca , Gandolfo Sergio , Broccoletti Roberto
Published: July 2009

The aim of this retrospective hospital‐based study was to review and evaluate the long‐term outcome of patients with oral epithelial dysplasia (OED), with or without surgical intervention, to identify factors affecting clinical course and malignant evolution. Patients with a follow‐up of at least 12 months were included. Data collected were statistically analyzed. The mean age was 63.58 years for women (n = 100) and 64.17 years for men (n = 107). One hundred and thirty‐five of the patients had lesions with histopathological features of mild OED, 50 had moderate OED and 22 had severe OED. Gender and risk factors seemed not to be related with the development of OED. One hundred and thirty‐three patients underwent active treatment. During the period considered, 39.4% of the 207 lesions disappeared; 19.66% remained stable and 33.7% of the total cases showed a new dysplastic event after treatment. Fifteen (7.24%) out of 207 developed a squamous cell carcinoma during follow‐up. Our data showed that speckled lesions are more often associated with high histological grade. The risk of malignant development does not seem to be predictable. Surrounded by the limitations of the retrospective designs, we have showed that there is no eminent benefit of surgical intervention of OED in preventing recurrences and malignant development.
Impact of PI and NNRTI HAART‐based therapy on oral lesions of Brazilian HIV‐infected patients
Authors: Ortega Karem L. , Vale Daniela A. , Magalhães Marina H. C. G.
Published: July 2009

Background:  The incidence of oral lesions related to human immunodeficiency virus (HIV) infection have been investigated after treatment with highly active antiretroviral therapy (HAART) including protease inhibitors (PI) but no data are available on the effect of non‐nucleoside reverse transcriptase inhibitor (NNRTI)‐based therapy on incidence of acquired immunodeficiency syndrome (AIDS) oral manifestations or impact of HAART on oral manifestations of HIV infection in Brazil. The aim of this study was to describe the effects of anti‐HIV therapy on the incidence of oral lesions during 17 years of AIDS epidemics in a Brazilian population.

Methods:  From 1989 to 2006, we collected data from 1595 consecutive HIV patients at the Special Care Dentistry Center, São Paulo, Brazil. We compared the effect of PI‐ and NNRTI‐based antiretroviral therapy (ARVT) on the annual incidence of Kaposi sarcoma (KS), oral candidiasis (OC) and hairy leukoplakia (HL). The chi‐squared test was used to test the association between oral lesions and therapeutic regimen (P < 0.05).

Results:  None of patients on ARVT presented with KS. Patients who used (nucleoside reverse transcriptase inhibitors) NRTI + PI were 0.9 times as likely to present with HL as those who used NRTI + NNRTI. This finding, however, was not statistically significant (P = 0.5). The relative risk for OC was 0.8 in patients with PI‐based HAART. The increased risk among those on PIs was statistically significant (P = 0.004).

Conclusions:  The superiority of NNRTI regimens in decreasing OC incidence is consistent with current therapeutic guidelines which recommend NNRTI‐based therapy as the treatment of choice for initial ARVT.
A clinico‐pathologic study of 311 intra‐oral salivary gland tumors in Thais
Authors: Dhanuthai Kittipong , Boonadulyarat Mingkwun , Jaengjongdee Thitipa , Jiruedee Kanyarat
Published: July 2009

Background:  There have been several epidemiologic studies on intra‐oral salivary gland tumors in several countries, but little is known of these tumors in Thailand.

Objectives:  To determine the relative frequency and distribution of various types of intra‐oral salivary gland tumors in the Thai population.

Methods:  The files of the Department of Oral Pathology, Faculty of Dentistry, Chulalongkorn University, from 1969 to 2007 were searched for intra‐oral salivary gland tumors. Histopathologic slides were reviewed and reclassified according to the 2005 WHO Classification of Head and Neck Tumors. The age, gender, race, and anatomical distribution of the tumors were collected from the patients’ records.

Results:  Of the 16,358 accessioned cases, 311 cases (1.90%) were diagnosed as intra‐oral salivary gland tumors. One hundred and forty‐seven cases (47.27%) were benign tumors, while 164 cases (52.73%) were malignant tumors. The mean age of the patient ± SD = 41.57 ± 16.65 years. Females outnumbered male patients by a ratio of M:F = 1:1.38. Almost all except one patient were Thais. Pleomorphic adenoma was the most common intra‐oral salivary gland tumor. The majority of cases occurred at the palate.

Conclusions:  Pleomorphic adenoma is the most common intra‐oral salivary gland tumor and the most common benign intra‐oral salivary gland tumor, while mucoepidermoid carcinoma is the most common malignant intra‐oral salivary gland tumor. Intra‐oral salivary gland tumors in Thailand elicit similar trend as in previous studies, with only minor differences such as the ranking of some tumors, the higher incidence of intra‐bony location, and the lower incidence of polymorphous low‐grade adenocarcinoma.
Heart Failure in ALLHAT: Did Blood Pressure Medication at Study Entry Influence Outcome?
Authors: Grimm Richard H. , Davis Barry R. , Piller Linda B. , Cutler Jeffrey A. , Margolis Karen L. , Barzilay Joshua , Dart Richard A. , Graumlich James F. , Murden Robert A. , Randall Otelio S. ,   for the ALLHAT Collaborative Research Group
Published: July 2009

Lower heart failure (HF) rates in individuals taking chlorthalidone vs amlodipine, lisinopril, or doxazosin were unanticipated in the Antihypertensive and Lipid‐Lowering Treatment to Prevent Heart Attack Trial (ALLHAT). HF differences appeared early, leading to questions about the possible influence of pre‐enrollment antihypertensive drugs. A post hoc study evaluated hospitalized HF events. During year 1479 individuals had HF, with pre‐entry antihypertensive medication data obtained on 301 patients (63%). Case‐only analysis examined interactive effects (interaction odds ratio [OR, ratio of ORs]) of previous medication and ALLHAT treatment on HF outcomes, eg, did treatment effect differ by pre‐entry antihypertensive class? Among cases, 39%, 37%, 17%, and 47% were taking pre‐entry diuretics, angiotensin‐converting enzyme inhibitors, β‐blockers, and calcium channel blockers, respectively. Interaction OR for year 1 HF for amlodipine vs chlorthalidone for patients taking vs not taking diuretics pre‐entry was 1.08 (95% confidence interval [CI], 0.53–2.21; P=.83); for lisinopril vs chlorthalidone, 1.33 (95% CI, 0.65–2.74; P=.44); and for doxazosin vs chlorthalidone, 1.13 (95% CI, 0.57–2.25; P=.73). Controlling for other pre‐entry antihypertensives yielded similar results. There was no significant evidence that pre‐entry drug type explained observed hospitalized HF differences by ALLHAT treatment.
A Home Blood Pressure Monitor Equipped With a Graphic Function Facilitates Faster Blood Pressure Control than the Conventional Home Blood Pressure Monitor
Authors: Kabutoya Tomoyuki , Ishikawa Joji , Hoshide Satoshi , Eguchi Kazuo , Shimada Kazuyuki , Kario Kazuomi
Published: July 2009

In this study, we evaluated whether antihypertensive therapy using a home blood pressure monitor (HBPM) equipped with a graphic display of weekly and monthly averaged blood pressure (BP) can obtain better BP control than the conventional HBPM. Sixty‐five hypertensive outpatients who had HBP >135/85 mm Hg were enrolled by 8 doctors in 2 different hospitals. The patients were randomly assigned either a graph‐equipped HBPM (graph‐equipped HBPM group; n=33) or an HBPM without the graph function (conventional HBPM group; n=32). The patients were treated with antihypertensive medications targeting HBP <135/85 mm Hg. After 2 months, the home systolic BP level was lower in the graph‐equipped HBPM group than in the conventional HBPM group (141.3±15.4 vs 147.7±10.8 mm Hg; P<.05); its reduction was significantly larger in the former group (11.9 vs 5.6 mm Hg; P<.05). Using an HBP device with a graphic display could accelerate the achievement of BP control.
A PSYCHOSIS MORE ORDINARY: A LACANIAN TREATMENT OF PARANOIA
Authors: Schwartz Susan
Published: July 2009

abstract

Many patients who are diagnosed as borderline within psychiatric discourse are, within the Lacanian orientation, more likely to be considered to have a psychotic structure even though there has been no psychotic break. The concept of ‘ordinary psychosis’ was developed by Jacques‐Alain Miller to describe a psychosis that has not been triggered, or has been triggered and has since stabilized. This is not a diagnostic category but rather an epistemic one; it provides a way of thinking about and treating patients who are not clearly neurotic but do not present with any obvious psychotic phenomena.
LE DÉSIR DE VIVRE: AN INTRODUCTION TO THE LIFE AND WORK OF FRANÇOISE DOLTO
Authors: Hall Guy
Published: July 2009

abstract

This paper serves as a brief introduction into the life and works of the French psychoanalyst, Françoise Dolto. Although acclaimed around the world, she is almost unknown in the United Kingdom as most of her books are not available in translation. It is suggested that this omission is largely due to the complicated post‐war politics amongst Parisian psychoanalytic organizations and with the IPA. With reference to four questions, it is hoped that this paper will stimulate a greater interest into her life, her theoretical ideas and her clinical work, so that they become better known and her contribution to psychoanalysis can receive the recognition it deserves.
THE FUTURE OF THE TRANSFERENCE‐BASED THERAPIES
Authors: Murdin Lesley
Published: July 2009

abstract

Much demonology has grown up round the acronym IAPT. This paper considers the current state of its effect on the discipline in which we practise. The paper sets out the current landscape and begins to address the implications for those who are practising models of psychotherapy other than the cognitive–behavioural model. The outlook may not be a disaster but we need to heed the warnings and gather our thoughts so that we can ensure not only the continued existence of our model but its continued availability for those who need us.
TEACHING AND TRANSFORMATION: A PSYCHOANALYTIC PERSPECTIVE ON PSYCHOTHERAPEUTIC TRAINING
Authors: Rizq Rosemary
Published: July 2009

abstract

While there has been much recent interest in the impact of organizational structures underpinning psychotherapeutic training (e.g. Davies 2008; Kernberg 2006), there has been curiously little interest in the impact of interpersonal dynamics on the process of teaching psychotherapy. In this paper, I draw on my experience as a university lecturer and tutor on a postgraduate counselling and psychotherapy training programme to explore some of the unconscious dynamics underpinning the psychotherapy trainee's development towards a mature professional identity. The implicit expectations that trainee psychotherapists hold at the start of their training are initially discussed; I then turn to psychoanalytic writers such as Bollas, Winnicott and Jessica Benjamin in an attempt to articulate and explore how trainees may progress from relating, to constructive use of their tutors in their quest for personal transformation and professional recognition.
PSYCHOANALYSIS AS AN ART FORM
Authors: Williams Meg Harris
Published: July 2009

abstract

This paper takes Bion's question ‘What sort of artists can we be?’ and begins the quest for an answer. In the light of the later aesthetic model posited by Bion and Meltzer, I consider first the nature and properties of symbols as containers for meaning, then the problem of how symbols are formed and metabolized by means of the transference–countertransference. Finally attention is drawn to the musical resonances of the ‘countertransference dream’ which have traditionally been overshadowed by verbal and visual considerations.
‘And the beat goes on’ The cardiac conduction system: the wiring system of the heart
Authors: Boyett Mark R.
Published: July 2009

The cardiac conduction system (CCS), consisting of the sino‐atrial node, atrioventricular node and His–Purkinje system, is responsible for the initiation and co‐ordination of the heart beat. In the last decade, our understanding of the CCS has been transformed. Immunohistochemistry, used in conjunction with anatomical techniques, has transformed our understanding of its anatomy; arguably, we now understand the position of the sino‐atrial node (not the same as in medical textbooks), and our new understanding of the atrioventricular node anatomy means that we can compute its physiological and pathophysiological behaviour. Ion channel expression in the CCS has been shown to be fundamentally different from that in the working myocardium. Dysfunction of the CCS has previously been attributed to fibrosis, but it is now clear that remodelling of ion channels plays an important role in dysfunction during ageing, heart failure and atrial fibrillation. Differences in ion channel expression may even be responsible for the bradycardia in the athlete and differences in heart rate among different species (such as humans and mice). Recent work has highlighted less well‐known components of the CCS, including tricuspid, mitral and aortic rings and even a third (retro‐aortic) node. These additional tissues do not participate in the initiation and co‐ordination of the heart beat and instead they are likely to be the source of various life‐threatening arrhythmias. During embryological development, all parts of the CCS have been shown to develop from the primary myocardium of the linear heart tube, partly under the influence of the transcription factor, Tbx3.
A simple automated stimulator of mechanically induced arrhythmias in the isolated rat heart
Authors: Huang Haixia , Wei Hua , Liu Ping , Wang Wei , Sachs Frederick , Niu Weizhen
Published: July 2009

Transient stretching of the ventricle can trigger arrhythmias and evoke ventricular fibrillation, especially when the stimulation occurs in the vulnerable period. To explore the sensitivity of small hearts we used a commercial pressure servo to study the kinetic relationship of left ventricular pressure to excitability and arrhythmias in the rat heart. Stimulation protocols were readily composed on the computer and programmed to vary the stimulus amplitude and timing relative to pacing. The pressure‐induced premature ventricular excitations were similar to those observed in larger hearts, but the convenience of using small hearts allows the use of inexpensive transgenic animals to explore the molecular basis of transduction.
Glucose ingestion during endurance training in men attenuates expression of myokine receptor
Authors: Akerstrom Thorbjorn C. A. , Krogh‐Madsen Rikke , Petersen Anne Marie Winther , Pedersen Bente Klarlund
Published: July 2009

Glucose ingestion during exercise attenuates the release of the myokine interleukin‐6 (IL‐6) from working skeletal muscle, which results in a diminished increase in plasma IL‐6. Interleukin‐6 receptor α (IL‐6Rα) expression in skeletal muscle is induced by acute exercise, mediated in part by an increased IL‐6 concentration in the bloodstream. We hypothesized that endurance training would increase the density of IL‐6Rα in skeletal muscle and that glucose ingestion would attenuate the effect. Nine subjects performed 10 weeks of one‐legged knee‐extensor training. They trained one leg (Glc‐leg) while ingesting a glucose solution (Glc) and ingested a placebo (Plc) while training the other leg (Plc‐leg). Endurance training increased peak power by ∼14% and reduced the exercise‐induced gene expression of IL‐6 and IL‐6Rα in skeletal muscle and IL‐6 plasma concentration. The IL‐6Rα density increased to a lesser extent in the Glc‐leg, suggesting that glucose ingestion attenuates the effect of training on IL‐6Rα by blunting the IL‐6 response. We conclude that glucose ingestion during endurance training attenuates the increase in IL‐6Rα density.
Role of Flagella in Virulence of the Coral Pathogen
Vibrio coralliilyticus
Authors: Meron Dalit , Efrony Rotem , Johnson Wesley R. , Schaefer Amy L. , Morris Pamela J. , Rosenberg Eugene , Greenberg E. Peter , Banin Ehud
Published: July 2009

A recently available transposition system was utilized to isolate a nonmotile mutant of the coral-bleaching pathogen
Vibrio coralliilyticus
. The mutation was localized to the
fhlA
gene, and the mutant lacked flagella. The
flhA
mutant was unable to exhibit chemotaxis toward coral mucus or to adhere to corals and subsequently cause infection.
Overproduction of Geranylgeraniol by Metabolically Engineered
Saccharomyces cerevisiae
Authors: Tokuhiro Kenro , Muramatsu Masayoshi , Ohto Chikara , Kawaguchi Toshiya , Obata Shusei , Muramoto Nobuhiko , Hirai Masana , Takahashi Haruo , Kondo Akihiko , Sakuradani Eiji , Shimizu Sakayu
Published: July 2009

(
E
,
E
,
E
)-Geranylgeraniol (GGOH) is a valuable starting material for perfumes and pharmaceutical products. In the yeast
Saccharomyces cerevisiae
, GGOH is synthesized from the end products of the mevalonate pathway through the sequential reactions of farnesyl diphosphate synthetase (encoded by the
ERG20
gene), geranylgeranyl diphosphate synthase (the
BTS1
gene), and some endogenous phosphatases. We demonstrated that overexpression of the diacylglycerol diphosphate phosphatase (
DPP1
) gene could promote GGOH production. We also found that overexpression of a
BTS1
-
DPP1
fusion gene was more efficient for producing GGOH than coexpression of these genes separately. Overexpression of the hydroxymethylglutaryl-coenzyme A reductase (
HMG1
) gene, which encodes the major rate-limiting enzyme of the mevalonate pathway, resulted in overproduction of squalene (191.9 mg liter
−1
) rather than GGOH (0.2 mg liter
−1
) in test tube cultures. Coexpression of the
BTS1
-
DPP1
fusion gene along with the
HMG1
gene partially redirected the metabolic flux from squalene to GGOH. Additional expression of a
BTS1
-
ERG20
fusion gene resulted in an almost complete shift of the flux to GGOH production (228.8 mg liter
−1
GGOH and 6.5 mg liter
−1
squalene). Finally, we constructed a diploid prototrophic strain coexpressing the
HMG1
,
BTS1
-
DPP1
, and
BTS1
-
ERG20
genes from multicopy integration vectors. This strain attained 3.31 g liter
−1
GGOH production in a 10-liter jar fermentor with gradual feeding of a mixed glucose and ethanol solution. The use of bifunctional fusion genes such as the
BTS1
-
DPP1
and
ERG20
-
BTS1
genes that code sequential enzymes in the metabolic pathway was an effective method for metabolic engineering.
Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology
Authors: Caron David A. , Countway Peter D. , Savai Pratik , Gast Rebecca J. , Schnetzer Astrid , Moorthi Stefanie D. , Dennett Mark R. , Moran Dawn M. , Jones Adriane C.
Published: July 2009

DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.
Quantitative PCR for Genetic Markers of Human Fecal Pollution
Authors: Shanks Orin C. , Kelty Catherine A. , Sivaganesan Mano , Varma Manju , Haugland Richard A.
Published: July 2009

Assessment of health risk and fecal bacterial loads associated with human fecal pollution requires reliable host-specific analytical methods and a rapid quantification approach. We report the development of quantitative PCR assays for quantification of two recently described human-specific genetic markers targeting
Bacteroidales
-like cell surface-associated genes. Each assay exhibited a range of quantification from 10 to 1 × 10
6
copies of target DNA. For each assay, internal amplification controls were developed to detect the presence or absence of amplification inhibitors. The assays predominantly detected human fecal specimens and exhibited specificity levels greater than 97% when tested against 265 fecal DNA extracts from 22 different animal species. The abundance of each human-specific genetic marker in primary effluent wastewater samples collected from 20 geographically distinct locations was measured and compared to quantities estimated by real-time PCR assays specific for rRNA gene sequences from total
Bacteroidales
and enterococcal fecal microorganisms. Assay performances combined with the prevalence of DNA targets in sewage samples provide experimental evidence supporting the potential application of these quantitative methods for monitoring fecal pollution in ambient environmental waters.
Quantitative PCR for Determining the Infectivity of Bacteriophage MS2 upon Inactivation by Heat, UV-B Radiation, and Singlet Oxygen: Advantages and Limitations of an Enzymatic Treatment To Reduce False-Positive Results
Authors: Pecson Brian M. , Martin Luisa Valério , Kohn Tamar
Published: July 2009

Health risks posed by waterborne viruses are difficult to assess because it is tedious or impossible to determine the infectivity of many viruses. Recent studies hypothesized that quantitative PCR (qPCR) could selectively quantify infective viruses if preceded by an enzymatic treatment (ET) to reduce confounding false-positive signals. The goal of this study was to determine if ET with qPCR (ET-qPCR) can be used to accurately quantify the infectivity of the human viral surrogate bacteriophage MS2 upon partial inactivation by three treatments (heating at 72°C, singlet oxygen, and UV radiation). Viruses were inactivated in buffered solutions and a lake water sample and assayed with culturing, qPCR, and ET-qPCR. To ensure that inactivating genome damage was fully captured, primer sets that covered the entire coding region were used. The susceptibility of different genome regions and the maximum genomic damage after each inactivating treatment were compared. We found that (i) qPCR alone caused false-positive results for all treatments, (ii) ET-qPCR significantly reduced (up to >5.2 log units) but did not eliminate the false-positive signals, and (iii) the elimination of false-positive signals differed between inactivating treatments. By assaying the whole coding region, we demonstrated that genome damage only partially accounts for virus inactivation. The possibility of achieving complete accordance between culture- and PCR-based assays is therefore called into doubt. Despite these differences, we postulate that ET-qPCR can track infectivity, given that decreases in infectivity were always accompanied by dose-dependent decreases in ET-qPCR signal. By decreasing false-positive signals, ET-qPCR improved the detection of infectivity loss relative to qPCR.
Quantitative Physiology of
Saccharomyces cerevisiae
at Near-Zero Specific Growth Rates
Authors: Boender Léonie G. M. , de Hulster Erik A. F. , van Maris Antonius J. A. , Daran-Lapujade Pascale A. S. , Pronk Jack T.
Published: July 2009

Growth at near-zero specific growth rates is a largely unexplored area of yeast physiology. To investigate the physiology of
Saccharomyces cerevisiae
under these conditions, the effluent removal pipe of anaerobic, glucose-limited chemostat culture (dilution rate, 0.025 h
−1
) was fitted with a 0.22-μm-pore-size polypropylene filter unit. This setup enabled prolonged cultivation with complete cell retention. After 22 days of cultivation, specific growth rates had decreased below 0.001 h
−1
(doubling time of >700 h). Over this period, viability of the retentostat cultures decreased to ca. 80%. The viable biomass concentration in the retentostats could be accurately predicted by a maintenance coefficient of 0.50 mmol of glucose g
−1
of biomass h
−1
calculated from anaerobic, glucose-limited chemostat cultures grown at dilution rates of 0.025 to 0.20 h
−1
. This indicated that, in contrast to the situation in several prokaryotes, maintenance energy requirements in
S. cerevisiae
do not substantially change at near-zero specific growth rates. After 22 days of retentostat cultivation, glucose metabolism was predominantly geared toward alcoholic fermentation to meet maintenance energy requirements. The strict correlation between glycerol production and biomass formation observed at higher specific growth rates was not maintained at the near-zero growth rates reached in the retentostat cultures. In addition to glycerol, the organic acids acetate,
d
-lactate, and succinate were produced at low rates during prolonged retentostat cultivation. This study identifies robustness and by-product formation as key issues in attempts to uncouple growth and product formation in
S. cerevisiae
.
Absence of
Escherichia coli
Phylogenetic Group B2 Strains in Humans and Domesticated Animals from Jeonnam Province, Republic of Korea
Authors: Unno Tatsuya , Han Dukki , Jang Jeonghwan , Lee Sun-Nim , Ko GwangPyo , Choi Ha Young , Kim Joon Ha , Sadowsky Michael J. , Hur Hor-Gil
Published: July 2009

Multiplex PCR analyses of DNAs from genotypically unique
Escherichia coli
strains isolated from the feces of 138 humans and 376 domesticated animals from Jeonnam Province, South Korea, performed using primers specific for the
chuA
and
yjaA
genes and an unknown DNA fragment, TSPE4.C2, indicated that none of the strains belonged to
E. coli
phylogenetic group B2. In contrast, phylogenetic group B2 strains were detected in about 17% (8 of 48) of isolates from feces of 24 wild geese and in 3% (3 of 96) of isolates obtained from the Yeongsan River in Jeonnam Province, South Korea. The distribution of
E. coli
strains in phylogenetic groups A, B1, and D varied depending on the host examined, and there was no apparent seasonal variation in the distribution of strains in phylogenetic groups among the Yeongsan River isolates. The distribution of four virulence genes (
eaeA
,
hlyA
,
stx
1
, and
stx
2
) in isolates was also examined by using multiplex PCR. Virulence genes were detected in about 5% (38 of 707) of the total group of unique strains examined, with 24, 13, 13, and 9 strains containing
hlyA
,
eaeA
,
stx
2
, and
stx
1
, respectively. The virulence genes were most frequently present in phylogenetic group B1 strains isolated from beef cattle. Taken together, results of these studies indicate that
E. coli
strains in phylogenetic group B2 were rarely found in humans and domesticated animals in Jeonnam Province, South Korea, and that the majority of strains containing virulence genes belonged to phylogenetic group B1 and were isolated from beef cattle. Results of this study also suggest that the relationship between the presence and types of virulence genes and phylogenetic groupings may differ among geographically distinct
E. coli
populations.
Large Sequence Polymorphisms Unveil the Phylogenetic Relationship of Environmental and Pathogenic Mycobacteria Related to
Mycobacterium ulcerans
Authors: Käser Michael , Hauser Julia , Small Pamela , Pluschke Gerd
Published: July 2009

Mycolactone is an immunosuppressive cytotoxin responsible for the clinical manifestation of Buruli ulcer in humans. It was believed to be confined to its etiologic agent,
Mycobacterium ulcerans
. However, the identification of other mycolactone-producing mycobacteria (MPMs) in other species, including
Mycobacterium marinum
, indicated a more complex taxonomic relationship. This highlighted the need for research on the biology, evolution, and distribution of such emerging and potentially infectious strains. The reliable genetic fingerprinting analyses presented here aim at both the unraveling of phylogenetic relatedness and of dispersal between environmental and pathogenic mycolactone producers and the identification of genetic prerequisites that enable lateral gene transfer of such plasmids. This will allow for the identification of environmental reservoirs of virulence plasmids that encode enzymes required for the synthesis of mycolactone. Based on dynamic chromosomal loci identified earlier in
M. ulcerans
, we characterized large sequence polymorphisms for the phylogenetic analysis of MPMs. Here, we identify new insertional-deletional events and single-nucleotide polymorphisms that confirm and redefine earlier strain differentiation markers. These results support other data showing that all MPMs share a common ancestry. In addition, we found unique genetic features specific for
M. marinum
strain M, the genome sequence strain which is used widely in research.
Extracellular Iron Biomineralization by Photoautotrophic Iron-Oxidizing Bacteria
Authors: Miot Jennyfer , Benzerara Karim , Obst Martin , Kappler Andreas , Hegler Florian , Schädler Sebastian , Bouchez Camille , Guyot François , Morin Guillaume
Published: July 2009

Iron oxidation at neutral pH by the phototrophic anaerobic iron-oxidizing bacterium
Rhodobacter
sp. strain SW2 leads to the formation of iron-rich minerals. These minerals consist mainly of nano-goethite (α-FeOOH), which precipitates exclusively outside cells, mostly on polymer fibers emerging from the cells. Scanning transmission X-ray microscopy analyses performed at the C K-edge suggest that these fibers are composed of a mixture of lipids and polysaccharides or of lipopolysaccharides. The iron and the organic carbon contents of these fibers are linearly correlated at the 25-nm scale, which in addition to their texture suggests that these fibers act as a template for mineral precipitation, followed by limited crystal growth. Moreover, we evidence a gradient of the iron oxidation state along the mineralized fibers at the submicrometer scale. Fe minerals on these fibers contain a higher proportion of Fe(III) at cell contact, and the proportion of Fe(II) increases at a distance from the cells. All together, these results demonstrate the primordial role of organic polymers in iron biomineralization and provide first evidence for the existence of a redox gradient around these nonencrusting, Fe-oxidizing bacteria.
New Design Strategy for Development of Specific Primer Sets for PCR-Based Detection ofChlorophyceaeandBacillariophyceaein Environmental Samples
Authors: Valiente Moro Claire , Crouzet Olivier , Rasconi Séréna , Thouvenot Antoine , Coffe Gérard , Batisson Isabelle , Bohatier Jacques
Published: July 2009

Studying aquatic microalgae is essential for monitoring biodiversity and water quality. We designed new sets of 18S rRNA PCR primers forChlorophyceaeandBacillariophyceaeby using the ARB software and implementing a virtual PCR program. The results of specificity analysis showed that most of the targeted algal families were identified and nontargeted organisms, such as fungi or ciliates, were excluded. These newly developed PCR primer sets were also able to amplify microalgal rRNA genes from environmental samples with accurate specificity. These tools could be of great interest for studying freshwater microalgal ecology and for developing bioindicators of the health status of aquatic environments.
Modified
Bacillus thuringiensis
Toxins and a Hybrid
B. thuringiensis
Strain Counter Greenhouse-Selected Resistance in
Trichoplusia ni
Authors: Franklin Michelle T. , Nieman Christal L. , Janmaat Alida F. , Soberón Mario , Bravo Alejandra , Tabashnik Bruce E. , Myers Judith H.
Published: July 2009

Resistance of greenhouse-selected strains of the cabbage looper,
Trichoplusia ni
, to
Bacillus thuringiensis
subsp.
kurstaki
was countered by a hybrid strain of
B. thuringiensis
and genetically modified toxins Cry1AbMod and Cry1AcMod, which lack helix α-1. Resistance to Cry1AbMod and Cry1AcMod was >100-fold less than resistance to native toxins Cry1Ab and Cry1Ac.
Regulatory Phenotyping Reveals Important Diversity within the Species
Lactococcus lactis
Authors: Bachmann Herwig , Starrenburg Marjo J. C. , Dijkstra Annereinou , Molenaar Douwe , Kleerebezem Michiel , Rademaker Jan L. W. , van Hylckama Vlieg Johan E. T.
Published: July 2009

The diversity in regulatory phenotypes among a collection of 84
Lactococcus lactis
strains isolated from dairy and nondairy origin was explored. The specific activities of five enzymes were assessed in cell extracts of all strains grown in two different media, a nutritionally rich broth and a relatively poor chemically defined medium. The five investigated enzymes, branched chain aminotransferase (BcaT), aminopeptidase N (PepN), X-prolyl dipeptidyl peptidase (PepX), alpha-hydroxyisocaproic acid dehydrogenase (HicDH), and esterase, are involved in nitrogen and fatty acid metabolism and catalyze key steps in the production of important dairy flavor compounds. The investigated cultures comprise 75
L. lactis
subsp.
lactis
isolates (including 7
L. lactis
subsp.
lactis
biovar diacetylactis isolates) and 9
L. lactis
subsp.
c
remoris
isolates. All
L. lactis
subsp.
cremoris
and 22
L. lactis
subsp.
lactis
(including 6
L. lactis
subsp.
lactis
biovar diacetylactis) cultures originated from a dairy environment. All other cultures originated from (fermented) plant materials and were isolated at different geographic locations. Correlation analysis of specific enzyme activities revealed significantly different regulatory phenotypes for dairy and nondairy isolates. The enzyme activities in the two investigated media were in general poorly correlated and revealed a high degree of regulatory diversity within this collection of closely related strains. To the best of our knowledge, these results represent the most extensive diversity analysis of regulatory phenotypes within a single bacterial species to date. The presented findings underline the importance of the availability of screening procedures for, e.g., industrially relevant enzyme activities in models closely mimicking application conditions. Moreover, they corroborate the notion that regulatory changes are important drivers of evolution.
Potential Applicability of Chymotrypsin-Susceptible Microcin J25 Derivatives to Food Preservation
Authors: Pomares María Fernanda , Salomón Raúl A. , Pavlova Olga , Severinov Konstantin , Farías Ricardo , Vincent Paula A.
Published: July 2009

Microcin J25 (MccJ25) is a 21-residue ribosomally synthesized lariat peptide antibiotic. MccJ25 is active against such food-borne disease-causing pathogens asSalmonellaspp.,Shigellaspp., andEscherichia coli, includingE. coliO157:H7 and non-O157 strains. MccJ25 is highly resistant to digestion by proteolytic enzymes present in the stomach and intestinal contents. MccJ25 would therefore remain active in the gastrointestinal tract, affecting normal intestinal microbiota, and this limits the potential use of MccJ25 as a food preservative. In the present paper, we describe a chymotrypsin-susceptible MccJ25 derivative with a mutation of Gly12to Tyr that retained almost full antibiotic activity and efficiently inhibited the growth of pathogenicSalmonella entericaserovar Newport andEscherichia coliO157:H7 in skim milk and egg yolk. However, unlike the wild-type MccJ25, the MccJ25(G12Y) variant was inactivated by digestive enzymes both in vitro and in vivo. To our knowledge, our results represent the first example of a rational modification of a microcin aimed at increasing its potential use in food preservation.
Complete WO Phage Sequences Reveal Their Dynamic Evolutionary Trajectories and Putative Functional Elements Required for Integration into theWolbachiaGenome
Authors: Tanaka Kohjiro , Furukawa Seiichi , Nikoh Naruo , Sasaki Tetsuhiko , Fukatsu Takema
Published: July 2009

Wolbachiaendosymbionts are ubiquitously found in diverse insects including many medical and hygienic pests, causing a variety of reproductive phenotypes, such as cytoplasmic incompatibility, and thereby efficiently spreading in host insect populations. Recently,Wolbachia-mediated approaches to pest control and management have been proposed, but the application of these approaches has been hindered by the lack of genetic transformation techniques for symbiotic bacteria. Here, we report the genome and structure of active bacteriophages from aWolbachiaendosymbiont. From theWolbachiastrainwCauB infecting the mothEphestia kuehniellatwo closely related WO prophages, WOcauB2 of 43,016 bp with 47 open reading frames (ORFs) and WOcauB3 of 45,078 bp with 46 ORFs, were characterized. In each of the prophage genomes, an integrase gene and an attachment site core sequence were identified, which are putatively involved in integration and excision of the mobile genetic elements. The 3′ region of the prophages encoded genes with sequence motifs related to bacterial virulence and protein-protein interactions, which might represent effector molecules that affect cellular processes and functions of their host bacterium and/or insect. Database searches and phylogenetic analyses revealed that the prophage genes have experienced dynamic evolutionary trajectories. Genes similar to the prophage genes were found across divergent bacterial phyla, highlighting the active and mobile nature of the genetic elements. We suggest that the active WO prophage genomes and their constituent sequence elements would provide a clue to development of a genetic transformation vector forWolbachiaendosymbionts.
Inter- and Intraspecies Plasmid-Mediated Transfer of Florfenicol Resistance in
Enterobacteriaceae
Isolates from Swine
Authors: Rayamajhi Nabin , Cha Seung Bin , Kang Mi Lan , Lee Su In , Lee Hee Soo , Yoo Han Sang
Published: July 2009

Florfenicol resistance was analyzed in 230 enteric pig isolates collected between 1998 and 2006. PCR, plasmid profiling, Southern blot hybridization, and a mixed-broth conjugation assay suggested the intra- and interspecies plasmid-mediated transfer of florfenicol resistance among the isolates that exhibited MICs for florfenicol between 4 to 128 mg/liter.
Outwardly Rectifying Anionic Channel from the Plasma Membrane of the Fungus
Phycomyces blakesleeanus
Authors: Živić Miroslav , Popović Marko , Todorović Nataša , Vučinić Željko
Published: July 2009

In the present report, by using a patch clamp technique, we provide, to our knowledge, the first detailed description of an anionic channel from filamentous fungi. The characterized channel, an outwardly rectifying anionic channel (ORAC), is the most prominent feature of the cell membrane of the fungus
Phycomyces blakesleeanus
in the absence of energizing substrates. The unitary conductance of the channel is 11.3 ± 0.4 pS. It is characterized by a strong voltage dependence of the open-channel probability (
z
δ; the gating charge is 2.1 ± 0.1), and the channel is activated by depolarization. The values of the time constants for voltage-induced activation and deactivation of 28 ± 3 ms for τ

a

and 39 ± 9 ms for τ

d

show that the ORAC is characterized by fast activation/deactivation kinetics. The ORAC shows strong selectivity for anions over cations and weak selectivity among anions, with a selectivity sequence of I
−
≥ NO
3
−
> Br
−
> Cl
−
> SO
4
2−
= 4.8 > 4.4 > 2.2 > 1 > 0.55, which corresponds to Eisenman series 1. The channel is characterized by two open and two closed states, with dominant long open (τ
o2
= 35.0 ± 3.9 ms) and long closed (τ
c2
= 166 ± 28 ms) states occupying 63% ± 8% and 79% ± 3% of total open and closed times, respectively. The ORAC is insensitive to anthracene-9-carboxylic acid (<200 μM), but 2 mM malate reversibly inhibits 59% ± 12% of the channel activity. Based on the electrophysiological properties of the channel, we propose that the ORAC plays a role in anion accumulation and in membrane potential regulation through local membrane depolarization.
Swarming ofPseudomonas aeruginosaIs Controlled by a Broad Spectrum of Transcriptional Regulators, Including MetR
Authors: Yeung Amy T. Y. , Torfs Ellen C. W. , Jamshidi Farzad , Bains Manjeet , Wiegand Irith , Hancock Robert E. W. , Overhage Joerg
Published: July 2009

Pseudomonas aeruginosaexhibits swarming motility on semisolid surfaces (0.5 to 0.7% agar). Swarming is a more than just a form of locomotion and represents a complex adaptation resulting in changes in virulence gene expression and antibiotic resistance. In this study, we used a comprehensiveP. aeruginosaPA14 transposon mutant library to investigate how the complex swarming adaptation process is regulated. A total of 233P. aeruginosaPA14 transposon mutants were verified to have alterations in swarming motility. The swarming-associated genes functioned not only in flagellar or type IV pilus biosynthesis but also in processes as diverse as transport, secretion, and metabolism. Thirty-three swarming-deficient and two hyperswarming mutants had transposon insertions in transcriptional regulator genes, including genes encoding two-component sensors and response regulators; 27 of these insertions were newly identified. Of the 25 regulatory mutants whose swarming motility was highly impaired (79 to 97%), only 1 (a PA1458 mutant) had a major defect in swimming, suggesting that this regulator might influence flagellar synthesis or function. Twitching motility, which requires type IV pili, was strongly affected in only two regulatory mutants (pilHand PA2571 mutants) and was moderately affected in three other mutants (algR,ntrB, andnosRmutants). Microarray analyses were performed to compare the gene expression profile of a swarming-deficient PA3587 mutant to that of the wild-type PA14 strain under swarming conditions. PA3587 showed 63% homology tometR, which encodes a regulator of methionine biosynthesis inEscherichia coli. The observed dysregulation in themetRmutant of nine different genes required for swarming motility provided a possible explanation for the swarming-deficient phenotype of this mutant.