bluuebunny/crossref_metadata_2025 huggingface dataset:
“EMOTIONAL INTELLIGENCE” IN THE CLASSROOM? AN ARISTOTELIAN CRITIQUE
Authors: Kristjánsson Kristján
Published: February 2006

Abstract A recent trend in moral education, social and emotional learning, incorporates the mantra of emotional intelligence (EI) as a key element in an extensive program of character building. In making his famous claim that the good life would have to include appropriate emotions, Aristotle obviously considered the schooling of emotions to be an indispensable part of moral education. However, in this essay Kristján Kristjánsson casts doubt on the assumption that Aristotelians should approve of the clarion call for EI, as understood by Daniel Goleman and the proponents of social and emotional learning, in the classroom. Various marked differences between EI and Aristotelian emotional virtue are highlighted and explored. Kristjánsson argues that the claims of EI lack moral ballast and that when this fact is added to an existing heap of educational problems attached to the implementation of EI programs, educators had better rethink their reliance on EI as a model of emotion cultivation, and perhaps revert to the teachings of Aristotle himself.
DEWEY’S EPISTEMOLOGY: AN ARGUMENT FOR WARRANTED ASSERTIONS, KNOWING, AND MEANINGFUL CLASSROOM PRACTICE
Authors: Boyles Deron R.
Published: February 2006

Abstract In an effort to navigate the treacherous path between professionalism and social relevancy, this essay takes up an area of professional philosophy — epistemology — with the intention of reclaiming the integrative role John Dewey held for philosophy and classroom practice. Deron Boyles asserts that epistemology can and should represent an area of inquiry that is relevant and useful for philosophy of education, especially as it develops classroom practices that foster inquiry. He specifically seeks to revive Dewey’s conception of warranted assertibility in an effort to show the value of fallibilist epistemology in practical and social teaching and learning contexts. By highlighting the distinctions between traditional epistemology and Dewey’s conception of knowing, Boyles demonstrates that epistemology has value insofar as it highlights a more useful, instrumentalist theory of knowing that is applicable to classroom practice.
THE “KINGDOM OF GOD ON EARTH” AND EARLY CHICAGO PRAGMATISM
Authors: Tröhler Daniel
Published: February 2006

Abstract Pragmatism has been rediscovered in recent years and presented as emblematic of modern thinking. At the center of this worldwide interest in late‐nineteenth century Pragmatism stood, first, a rejection of the traditional dualistic construction of the world in philosophy and psychology; second, a distinguishing of the findings of learning theory from those of evolutionary theory; and, third, a consideration of industrial democracy as the context of modern thinking and action. In this essay Daniel Tröhler shows that these innovations were far less secular than has generally been assumed. Underlying early Chicago Pragmatism is a reformed (Calvinist) Protestant mentality that was shaped by a vision of a common mission: realizing the “kingdom of God on earth”— a mentality that responded critically to the provocations of modernity (specifically, industrialization and capitalism) and, through this response, developed a distinctive discourse that came to be called “Pragmatism.”
Review of morbidity and mortality associated with falls from heights among patients presenting to a major trauma centre
Authors: Kent Alison , Pearce Andrew
Published: February 2006

Objective:  To compare differences in demographics and injuries of patients presenting after falls from heights at home and at work.

Method:  A retrospective case series review of patients treated by the Royal Adelaide Hospital (RAH) Trauma Service following a fall from a ladder, scaffold, building, or tree between July 2000 and December 2003.

Results:  Two hundred and eighty‐two patients fulfilled study criteria. The 162 (57.4%, 95% confidence interval [CI] 48.9–60.5) injured at home were significantly (P < 0.001) older (mean age 53.9 years, 95% CI 51.3–56.7) than those injured at work (mean age 41.2 years, 95% CI 38.6–43.8). Injury severity score (ISS) was similar in the two groups. Those injured at home were more likely to be admitted to hospital and have significantly longer hospital stays (P = 0.003). Thirteen deaths were recorded, eight (61.5%) from home, all over 49 years old. Ladders were implicated in seven (53.8%, 95% CI 26.7–80.9) of the deaths. A 67% (95% CI 55.4–79.0) increase in the number of presentations following falls at home over the study period was significantly greater than the 12.2% (95% CI 10.7–13.7) increase in total trauma presentations during this time (P = 0.0007).

Conclusions:  Injuries resulting from falls at home are increasing. This group tends to be elderly and at risk of significant injury and prolonged hospital stays. Causes are multifactorial and might be related to increased popularity of home renovations. Ladders are implicated in many of these accidents. As emergency physicians we should target this population to educate them in safe ladder use.
Ketamine for rapid sequence induction in patients with head injury in the emergency department
Authors: Sehdev Rajesh S , Symmons David AD , Kindl Korana
Published: February 2006

Objective:  To examine the evidence regarding the use of ketamine for induction of anaesthesia in patients with head injury in the ED.

Method:  A literature review using the key words ketamine, head injury and intracranial pressure.

Results:  Advice from early literature guiding against the use of ketamine in head injury has been met with widespread acceptance, as reflected by current practice. That evidence is conflicting and inconclusive in regards to the safety of using ketamine in head injury. A review of the literature to date suggests that ketamine could be a safe and useful addition to our available treatment modalities. The key to this argument rests on specific pharmacological properties of ketamine, and their effects on the cerebral haemodynamics and cellular physiology of brain tissue that has been exposed to traumatic injury.

Conclusion:  In the modern acute management of head‐injured patients, ketamine might be a suitable agent for induction of anaesthesia, particularly in those patients with potential cardiovascular instability.
The case for venous rather than arterial blood gases in diabetic ketoacidosis
Authors: Kelly Anne‐Maree
Published: February 2006

Objectives:  For patients with diabetic ketoacidosis (DKA), arterial blood gas (BG) sampling for measurement of pH and bicarbonate has been considered an essential part of initial evaluation and monitoring of progress. There is growing evidence that venous values can be clinically acceptable alternatives to arterial measurements. This article summarizes the recent evidence regarding the validity of venous BG sampling in DKA.

Methods:  Medline search for the years 1995 to present, hand search of reference lists, search of on‐line evidence‐based medicine sites.

Results:  In patients with DKA the weighted average difference between arterial and venous pH was 0.02 pH units (95% limits of agreement −0.009 to +0.021 pH units) and between arterial and venous bicarbonate was −1.88 mEq/L.

Conclusions:  There is reasonable evidence that venous and arterial pH have sufficient agreement as to be clinically interchangeable in patients with DKA who are haemodynamically stable and without respiratory failure. There is some evidence that venous and arterial bicarbonate also agree closely in DKA but this requires confirmation.
Paediatric lap‐belt injury: A 7 year experience
Authors: Shepherd Michael , Hamill James , Segedin Elizabeth
Published: February 2006

Objective:  To highlight the injuries that result from lap‐belt use and make recommendations for prevention, the recent experience of a regional paediatric trauma centre was reviewed.

Methods:  Retrospective review of admissions to Starship Children's Hospital from 1996 to 2003, with significant injury following involvement in a motor vehicle crash, while wearing a lap‐belt. Patients were identified from two prospectively collected databases and discharge coding data.

Results:  In total, 19 patients were identified over the 7 year period. The morbidity sustained includes 15 patients with hollow viscus injury, 13 laparotomies, 7 spinal fractures, 2 paraplegia and 1 fatality. A total of 11 patients required laparotomy with a median delay of 24 h. Of patients in the present series, 58% were aged less than 8 years and thus were inappropriately restrained.

Conclusions:  Lap‐belt use can result in a range of life‐threatening injuries or permanent disability in the paediatric population. The incidence of serious lap‐belt injury does not appear to be decreasing. Morbidity and mortality could be reduced by the use of three‐point restraints, age appropriate restraints and booster seats.
Ethnic and Socioeconomic Comparisons of Fitness, Activity Levels, and Barriers to Exercise in High School Females
Authors: Fahlman Mariane M. , Hall Heather L. , Lock Robyn
Published: February 2006

Abstract: The purpose of this study was to determine if high school females differed in individual measures of health‐related physical fitness, barriers to exercise, or activity level based on ethnicity or socioeconomic status. A cross‐sectional sample consisting of African American (28%), Hispanic (23%), and white (49%) female high school students, 46% from low socioeconomic groups and 54% from moderate or high socioeconomic groups (n = 1314, age = 16.2 ± 0.9) participated in this study. A 15‐question survey instrument assessed barriers to exercise and activity level. The FITNESSGRAM fitness test assessed aerobic capacity and body mass index (BMI), and skinfold calipers were used to assess percent body fat. Significant differences between African Americans, Hispanics, and whites were found on the following dependent variables: BMI, percent fat, mile run, perceived barriers to exercise, and activity level. Significant differences between socioeconomic groups were found on the following dependent variables: percent fat, mile run, activity level, and perceived barriers to exercise. These results suggest that students of minority and low socioeconomic groups should be given separate and different interventions regarding health‐related fitness. (J Sch Health. 2006;76(1):12‐17)
Modes and models of GABAAreceptor gating
Authors: Lema Gareth M. C. , Auerbach Anthony
Published: February 2006

Upon activation by agonist, the type A γ‐aminobutyric acid receptor (GABAR) ‘gates’, allowing chloride ions to permeate membranes and produce fast inhibition of neurons. There is no consensus kinetic model for the GABAR gating mechanism. We expressed human α1β1γ2SGABARs in HEK 293 cells and recorded single channel currents in the cell‐attached configuration using various GABA concentrations (50–5000 μm). Closed and open events occurred individually and in clusters that had at least three different modes that were distinguishable by open probability (PO): High (PO= 0.73), Mid (PO= 0.50), and Low (PO= 0.21). We used a critical time to isolate shorter bursts of openings and to thus eliminate long‐lived, desensitized events. Bursts from all three modes contained three closed and three open components. We employed maximum likelihood fitting, autocorrelation analysis and macroscopic current simulation to distinguish kinetic schemes. The ‘core’ gating scheme for most models contained two closed states that preceded an open state (C1⇌ C2⇌ O1). The two best‐fitting models had a third closed state connected to C1and a second open state (O2) connected to C2. The third open state, whose occupancy varied greatly between modes, could be connected either to O2or C2. We estimated rate constants for two identical, independent GABA binding steps by globally fitting data across GABA concentrations ranging from 50 to 1000 μm. For the most highly ranked model the binding rate constants were:k+= 3 μm−1s−1andk–= 272 s−1(KD= 91 μm).
Glutamate uptake block triggers deadly rhythmic bursting of neonatal rat hypoglossal motoneurons
Authors: Sharifullina Elina , Nistri Andrea
Published: February 2006

In the brain the extracellular concentration of glutamate is controlled by glial transporters that restrict the neurotransmitter action to synaptic sites and avoid excitotoxicity. Impaired transport of glutamate occurs in many cases of amyotrophic lateral sclerosis, a devastating motoneuron disease. Motoneurons of the brainstem nucleus hypoglossus are among the most vulnerable, giving early symptoms like slurred speech and dysphagia. However, the direct consequences of extracellular glutamate build‐up, due to uptake block, on synaptic transmission and survival of hypoglossal motoneurons remain unclear and have been studied using the neonatal rat brainstem slice preparation as a model. Patch clamp recording from hypoglossal motoneurons showed that, in about one‐third of these cells, inhibition of glutamate transport with the selective blocker dl‐threo‐β‐benzyloxyaspartate (TBOA; 50 μm) unexpectedly led to the emergence of rhythmic bursting consisting of inward currents of long duration with superimposed fast oscillations and synaptic events. Synaptic inhibition block facilitated bursting. Bursts had a reversal potential near 0 mV, and were blocked by tetrodotoxin, the gap junction blocker carbenoxolone, or antagonists of AMPA, NMDA or mGluR1 glutamate receptors. Intracellular Ca2+ imaging showed bursts as synchronous discharges among motoneurons. Synergy of activation of distinct classes of glutamate receptor plus gap junctions were therefore essential for bursting. Ablating the lateral reticular formation preserved bursting, suggesting independence from propagated network activity within the brainstem. TBOA significantly increased the number of dead motoneurons, an effect prevented by the same agents that suppressed bursting. Bursting thus represents a novel hallmark of motoneuron dysfunction triggered by glutamate uptake block.
Bidirectional modulation of GABAergic transmission by cholecystokinin in hippocampal dentate gyrus granule cells of juvenile rats
Authors: Deng Pan‐Yue , Lei Saobo
Published: February 2006

Cholecystokinin (CCK) interacts with two types of G protein‐coupled receptors in the brain: CCK‐A and CCK‐B receptors. Both CCK and CCK‐B receptors are widely distributed in the hippocampal formation, but the functions of CCK there have been poorly understood. In the present study, we initially examined the effects of CCK on GABAAreceptor‐mediated synaptic transmission in the hippocampal formation and then explored the underlying cellular mechanisms by focusing on the dentate gyrus region, where the highest levels of CCK‐binding sites have been detected. Our results indicate that activation of CCK‐B receptors initially and transiently increased spontaneous IPSC (sIPSC) frequency, followed by a persistent reduction. The effects of CCK were more evident in juvenile rats, suggesting that they are developmentally regulated. Cholecystokinin failed to modulate the miniature IPSCs recorded in the presence of TTX and the amplitude of the evoked IPSCs, but produced a transient increase followed by a reduction in action potential firing frequency recorded from GABAergic interneurons, suggesting that CCK acts by modulating the excitability of the interneurons to regulate GABA release. Cholecystokinin reduced the amplitude of the after‐hyperpolarization of the action potentials, and application of paxilline or charybdotoxin considerably reduced CCK‐mediated modulation of sIPSC frequency, suggesting that the effects of CCK are related to the inhibition of Ca2+‐activated K+currents (IK(Ca)). The effects of CCK were independent of the functions of phospholipase C, intracellular Ca2+release, protein kinase C or phospholipase A2, suggesting a direct coupling between the G proteins of CCK‐B receptors andIK(Ca). Our results provide a novel mechanism underlying CCK‐mediated modulation of GABA release.
Recent observations on the regulation of fetal metabolism by glucose
Authors: Hay William W.
Published: February 2006

Glucose is the principal energy substrate for the the fetus and is essential for normal fetal metabolism and growth. Fetal glucose metabolism is directly dependent on the fetal plasma glucose concentration. Fetal glucose utilization is augmented by insulin produced by the developing fetal pancreas in increasing amounts as gestation proceeds, which enhances glucose utilization among the insulin‐sensitive tissues (skeletal muscle, liver, heart, adipose tissue) that increase in mass and thus glucose need during late gestation. Glucose‐stimulated insulin secretion increases over gestation. Both insulin secretion and insulin action are affected by prevailing glucose concentrations and the amount and activity of tissue glucose transporters. In cases of intrauterine growth restriction (IUGR), fetal weight‐specific tissue glucose uptake rates and glucose transporters are maintained or increased, while synthesis of amino acids into protein and corresponding insulin–IGF signal transduction proteins are decreased. These observations demonstrate the mixed phenotype of the IUGR fetus that includes enhanced glucose utilization capacity, but diminished protein synthesis and growth. Thus, the fetus has considerable capacity to adapt to changes in glucose supply by relatively common and understandable mechanisms that regulate fetal metabolism and growth and could underlie certain later life metabolic disorders such as insulin resistance, obesity and diabetes mellitus.
Late Precambrian Oxygenation; Inception of the Clay Mineral Factory
Authors: Kennedy Martin , Droser Mary , Mayer Lawrence M. , Pevear David , Mrofka David
Published: February 2006

An enigmatic stepwise increase in oxygen in the late Precambrian is widely considered a prerequisite for the expansion of animal life. Accumulation of oxygen requires organic matter burial in sediments, which is largely controlled by the sheltering or preservational effects of detrital clay minerals in modern marine continental margin depocenters. Here, we show mineralogical and geochemical evidence for an increase in clay mineral deposition in the Neoproterozoic that immediately predated the first metazoans. Today most clay minerals originate in biologically active soils, so initial expansion of a primitive land biota would greatly enhance production of pedogenic clay minerals (the “clay mineral factory”), leading to increased marine burial of organic carbon via mineral surface preservation.
Cellular Senescence in Aging Primates
Authors: Herbig Utz , Ferreira Mark , Condel Laura , Carey Dee , Sedivy John M.
Published: February 2006

The aging of organisms is characterized by a gradual functional decline of all organ systems. Mammalian somatic cells in culture display a limited proliferative life span, at the end of which they undergo an irreversible cell cycle arrest known as replicative senescence. Whether cellular senescence contributes to organismal aging has been controversial. We investigated telomere dysfunction, a recently discovered biomarker of cellular senescence, and found that the number of senescent fibroblasts increases exponentially in the skin of aging baboons, reaching >15% of all cells in very old individuals. In addition, the same cells contain activated ataxia-telangiectasia mutated kinase and heterochromatinized nuclei, confirming their senescent status.
MOSFET-Embedded Microcantilevers for Measuring Deflection in Biomolecular Sensors
Authors: Shekhawat Gajendra , Tark Soo-Hyun , Dravid Vinayak P.
Published: February 2006

A promising approach for detecting biomolecules follows their binding to immobilized probe molecules on microfabricated cantilevers; binding causes surface stresses that bend the cantilever. We measured this deflection, which is on the order of tens of nanometers, by embedding a metal-oxide semiconductor field-effect transistor (MOSFET) into the base of the cantilever and recording decreases in drain current with deflections as small as 5 nanometers. The gate region of the MOSFET responds to surface stresses and thus is embedded in silicon nitride so as to avoid direct contact with the sample solution. This approach, which offers low noise, high sensitivity, and direct readout, was used to detect specific binding events with biotin and antibodies.
In Vitro Kinetic Analysis of Oligofructose Consumption by
Bacteroides
and
Bifidobacterium
spp. Indicates Different Degradation Mechanisms
Authors: Van der Meulen Roel , Makras Lefteris , Verbrugghe Kristof , Adriany Tom , De Vuyst Luc
Published: February 2006

The growth of pure cultures of
Bacteroides thetaiotaomicron
LMG 11262 and
Bacteroides fragilis
LMG 10263 on fructose and oligofructose was examined and compared to that of
Bifidobacterium longum
BB536 through in vitro laboratory fermentations. Gas chromatography (GC) analysis was used to determine the different fractions of oligofructose and their degradation during the fermentation process. Both
B. thetaiotaomicron
LMG 11262 and
B. fragilis
LMG 10263 were able to grow on oligofructose as fast as on fructose, succinic acid being the major metabolite produced by both strains.
B. longum
BB536 grew slower on oligofructose than on fructose. Acetic acid and lactic acid were the main metabolites produced when fructose was used as the sole energy source. Increased amounts of formic acid and ethanol were produced when oligofructose was used as an energy source at the cost of lactic acid. Detailed kinetic analysis revealed a preferential metabolism of the short oligofructose fractions (e.g., F
2
and F
3
) for
B. longum
BB536. After depletion of the short fractions, the larger oligofructose fractions (e.g., F
4
, GF
4
, F
5
, GF
5
, and F
6
) were metabolized, too. Both
Bacteroides
strains did not display such a preferential metabolism and degraded all oligofructose fractions simultaneously, transiently increasing the fructose concentration in the medium. This suggests a different mechanism for oligofructose breakdown between the strain of
Bifidobacterium
and both strains of
Bacteroides
, which helps to explain the bifidogenic nature of inulin-type fructans.
Nitrous Oxide Reductase Genes (
nosZ
) of Denitrifying Microbial Populations in Soil and the Earthworm Gut Are Phylogenetically Similar
Authors: Horn Marcus A. , Drake Harold L. , Schramm Andreas
Published: February 2006

Earthworms emit nitrous oxide (N
2
O) and dinitrogen (N
2
). It has been hypothesized that the in situ conditions of the earthworm gut activates ingested soil denitrifiers during gut passage and leads to these in vivo emissions (M. A. Horn, A. Schramm, and H. L. Drake, Appl. Environ. Microbiol.
69:
1662-1669, 2003). This hypothesis implies that the denitrifiers in the earthworm gut are not endemic to the gut but rather are regular members of the soil denitrifier population. To test this hypothesis, the denitrifier populations of gut and soil from three different sites were comparatively assessed by sequence analysis of
nosZ
, the gene for the terminal enzyme in denitrification, N
2
O reductase. A total of 182 and 180
nosZ
sequences were retrieved from gut and soil, respectively; coverage of gene libraries was 79 to 100%. Many of the
nosZ
sequences were heretofore unknown, clustered with known soil-derived sequences, or were related to N
2
O reductases of the genera
Bradyrhizobium
,
Brucella
,
Dechloromonas
,
Flavobacterium
,
Pseudomonas
,
Ralstonia
, and
Sinorhizobium
. Although the numbers of estimators for genotype richness of sequence data from the gut were higher than those of soil, only one gut-derived
nosZ
sequence did not group phylogenetically with any of the soil-derived
nosZ
sequences. Thus, the phylogenies of
nosZ
from gut and soil were not dissimilar, indicating that gut denitrifiers are soil derived.
Effect of Ammonia Production by
Colletotrichum gloeosporioides
on
pelB
Activation, Pectate Lyase Secretion, and Fruit Pathogenicity
Authors: Kramer-Haimovich H. , Servi E. , Katan T. , Rollins J. , Okon Y. , Prusky D.
Published: February 2006

The accumulation of ammonia and associated tissue alkalinization predispose avocado fruit to attack by
Colletotrichum gloeosporioides
. Secretion of ammonia by
C. gloeosporioides
in the presence of KNO
3
was induced by decreasing the pH from 7.0 to 4.0. When the fungus was grown at pH 4.0 or 6.0 in the absence of a nitrogen source, ammonia did not accumulate, and neither
pelB
(encoding pectate lyase) transcription nor pectate lyase secretion was detected. Under these nitrogen starvation conditions, only transcriptional activation of
areA
, which encodes the global nitrogen regulator, was detected.
pelB
transcription and pectate lyase secretion were both detected when
C. gloeosporioides
was grown at pH 6.0 in the presence of ammonia accumulated from different nitrogen sources. The early accumulation of ammonia induced early
pelB
expression and pectate lyase secretion. As the external pH increased from 4.0 to 6.0, transcripts of
pac1
, the
C. gloeosporioides pacC
homolog, also could be detected. Nit mutants of
C. gloeosporioides
, which cannot utilize KNO
3
as a nitrogen source, did not secrete ammonia, alkalinize the medium, or secrete pectate lyase. If Nit mutants were grown at pH 6.0 in the presence of glutamate, then pectate lyase secretion was induced. Infiltration of 0.1 M ammonium hydroxide at pH 10 into ripening avocado fruits enhanced the activation of quiescent infection and symptom development by
C. gloeosporioides
. These results suggest that ambient pH alkalinization resulting from ammonia accumulation and the availability of ammonia as a nitrogen source independently regulate
pelB
expression, pectate lyase secretion, and virulence of
C. gloeosporioides
. These data suggest that alkalinization during
C. gloeosporioides
infection is important for its transformation from the quiescent biotrophic stage to the necrotrophic stage of fungal colonization in the fruit host.
Specific Detection of
Xanthomonas axonopodis
pv. dieffenbachiae in Anthurium (
Anthurium andreanum
) Tissues by Nested PCR
Authors: Robène-Soustrade Isabelle , Laurent Philippe , Gagnevin Lionel , Jouen Emmanuel , Pruvost Olivier
Published: February 2006

Efficient control of
Xanthomonas axonopodis
pv. dieffenbachiae, the causal agent of anthurium bacterial blight, requires a sensitive and reliable diagnostic tool. A nested PCR test was developed from a sequence-characterized amplified region marker identified by randomly amplified polymorphic DNA PCR for the detection of
X. axonopodis
pv. dieffenbachiae. Serological and pathogenicity tests were performed concurrently with the nested PCR test with a large collection of
X. axonopodis
pv. dieffenbachiae strains that were isolated worldwide and are pathogenic to anthurium and/or other aroids. The internal primer pair directed amplification of the expected product (785 bp) for all 70
X. axonopodis
pv. dieffenbachiae strains pathogenic to anthurium tested and for isolates originating from syngonium and not pathogenic to anthurium. This finding is consistent with previous studies which indicated that there is a high level of relatedness between strains from anthurium and strains from syngonium. Strains originating from the two host genera can be distinguished by restriction analysis of the amplification product. No amplification product was obtained with 98 strains of unrelated phytopathogenic bacteria or saprophytic bacteria from the anthurium phyllosphere, except for a weak signal obtained for one
X. axonopodis
pv. allii strain. Nevertheless, restriction enzyme analysis permitted the two pathovars to be distinguished. The detection threshold obtained with pure cultures or plant extracts (10
3
CFU ml
−1
) allowed detection of the pathogen from symptomless contaminated plants. This test could be a useful diagnostic tool for screening propagation stock plant material and for monitoring international movement of
X. axonopodis
pv. dieffenbachiae.
The Naphthalene Catabolic (
nag
) Genes of
Polaromonas naphthalenivorans
CJ2: Evolutionary Implications for Two Gene Clusters and Novel Regulatory Control
Authors: Jeon Che Ok , Park Minjeong , Ro Hyun-Su , Park Woojun , Madsen Eugene L.
Published: February 2006

Polaromonas naphthalenivorans
CJ2, found to be responsible for the degradation of naphthalene in situ at a coal tar waste-contaminated site (C.-O. Jeon et al., Proc. Natl. Acad. Sci. USA 100:13591-13596, 2003), is able to grow on mineral salts agar media with naphthalene as the sole carbon source. Beginning from a 484-bp
nagAc
-like region, we used a genome walking strategy to sequence genes encoding the entire naphthalene degradation pathway andadditional flanking regions. We found that the naphthalene catabolic genes in
P. naphthalenivorans
CJ2 were divided into one large and one small gene cluster, separated by an unknown distance. The large gene cluster (
nagRAaGHAbAcAdBFCQEDJI′ORF1tnpA
) is bounded by a LysR-type regulator (
nagR
). The small cluster (
nagR2ORF2I"KL
) is bounded by a MarR-type regulator (
nagR2
). The catabolic genes of
P. naphthalenivorans
CJ2 were homologous to many of those of
Ralstonia
U2, which uses the gentisate pathway to convert naphthalene to central metabolites. However, three open reading frames (
nagY
,
nagM
, and
nagN
), present in
Ralstonia
U2, were absent. Also,
P. naphthalenivorans
carries two copies of gentisate dioxygenase (
nagI
) with 77.4% DNA sequence identity to one another and 82% amino acid identity to their homologue in
Ralstonia
sp. strain U2. Investigation of the operons using reverse transcription PCR showed that each cluster was controlled independently by its respective promoter. Insertional inactivation and lacZ reporter assays showed that
nagR2
is a negative regulator and that expression of the small cluster is not induced by naphthalene, salicylate, or gentisate. Association of two putative
Azoarcus
-related transposases with the large cluster and one
Azoarcus
-related putative salicylate 5-hydroxylase gene (
ORF2
) in the small cluster suggests that mobile genetic elements were likely involved in creating the novel arrangement of catabolic and regulatory genes in
P. naphthalenivorans
.
Novel Genetic Variants of
Anaplasma phagocytophilum
,
Anaplasma bovis
,
Anaplasma centrale
, and a Novel
Ehrlichia
sp. in Wild Deer and Ticks on Two Major Islands in Japan
Authors: Kawahara Makoto , Rikihisa Yasuko , Lin Quan , Isogai Emiko , Tahara Kenji , Itagaki Asao , Hiramitsu Yoshimichi , Tajima Tomoko
Published: February 2006

Wild deer are one of the important natural reservoir hosts of several species of
Ehrlichia
and
Anaplasma
that cause human ehrlichiosis or anaplasmosis in the United States and Europe. The primary aim of the present study was to determine whether and what species of
Ehrlichia
and
Anaplasma
naturally infect deer in Japan. Blood samples obtained from wild deer on two major Japanese islands, Hokkaido and Honshu, were tested for the presence of
Ehrlichia
and
Anaplasma
by PCR assays and sequencing of the 16S rRNA genes, major outer membrane protein
p44
genes, and
groESL
. DNA representing four species and two genera of
Ehrlichia
and
Anaplasma
was identified in 33 of 126 wild deer (26%). DNA sequence analysis revealed novel strains of
Anaplasma phagocytophilum
, a novel
Ehrlichia
sp.,
Anaplasma centrale
, and
Anaplasma bovis
in the blood samples from deer. None of these have been found previously in deer. The new
Ehrlichia
sp.,
A. bovis
, and
A. centrale
were also detected in
Hemaphysalis longicornis
ticks from Honshu Island. These results suggest that enzootic cycles of
Ehrlichia
and
Anaplasma
species distinct from those found in the United States or Europe have been established in wild deer and ticks in Japan.
Isolation and Expression of the Lysis Genes of
Actinomyces naeslundii
Phage Av-1
Authors: Delisle Allan L. , Barcak Gerard J. , Guo Ming
Published: February 2006

Like most gram-positive oral bacteria,
Actinomyces naeslundii
is resistant to salivary lysozyme and to most other lytic enzymes. We are interested in studying the lysins of phages of this important oral bacterium as potential diagnostic and therapeutic agents. To identify the
Actinomyces
phage genes encoding these species-specific enzymes in
Escherichia coli
, we constructed a new cloning vector, pAD330, that can be used to enrich for and isolate phage holin genes, which are located adjacent to the lysin genes in most phage genomes. Cloned holin insert sequences were used to design sequencing primers to identify nearby lysin genes by using whole phage DNA as the template. From partial digestions of
A. naeslundii
phage Av-1 genomic DNA we were able to clone, in independent experiments, inserts that complemented the defective λ holin in pAD330, as evidenced by extensive lysis after thermal induction. The DNA sequence of the inserts in these plasmids revealed that both contained the complete lysis region of Av-1, which is comprised of two holin-like genes, designated
holA
and
holB
, and an endolysin gene, designated
lysA
. We were able to subclone and express these genes and determine some of the functional properties of their gene products.
Engineering Plant-Microbe Symbiosis for Rhizoremediation of Heavy Metals
Authors: Wu Cindy H. , Wood Thomas K. , Mulchandani Ashok , Chen Wilfred
Published: February 2006

The use of plants for rehabilitation of heavy-metal-contaminated environments is an emerging area of interest because it provides an ecologically sound and safe method for restoration and remediation. Although a number of plant species are capable of hyperaccumulation of heavy metals, the technology is not applicable for remediating sites with multiple contaminants. A clever solution is to combine the advantages of microbe-plant symbiosis within the plant rhizosphere into an effective cleanup technology. We demonstrated that expression of a metal-binding peptide (EC20) in a rhizobacterium,
Pseudomonas putida
06909, not only improved cadmium binding but also alleviated the cellular toxicity of cadmium. More importantly, inoculation of sunflower roots with the engineered rhizobacterium resulted in a marked decrease in cadmium phytotoxicity and a 40% increase in cadmium accumulation in the plant root. Owing to the significantly improved growth characteristics of both the rhizobacterium and plant, the use of EC20-expressing
P. putida
endowed with organic-degrading capabilities may be a promising strategy to remediate mixed organic-metal-contaminated sites.
Molecular and Genetic Characterization of a Novel Nisin Variant Produced by
Streptococcus uberis
Authors: Wirawan Ruth E. , Klesse Nikolai A. , Jack Ralph W. , Tagg John R.
Published: February 2006

Streptococcus uberis
is one of the principal causative agents of bovine mastitis. In this study, we report that
S. uberis
strain 42 produces a lantibiotic, nisin U, which is 78% identical (82% similar) to nisin A from
Lactococcus lactis
. The 15.6-kb nisin U locus comprises 11 open reading frames, similar in putative functionality but differing in arrangement from that of the nisin A biosynthetic cluster. The nisin U producer strain exhibits specific resistance (immunity) to nisin U and cross-resistance to nisin A, a finding consistent with the 55% sequence similarity of their respective immunity peptides. Homologues of the nisin U structural gene were identified in several additional
S. uberis
strains, and in each case cross-protective immunity was expressed to nisin A and to the other producers of nisin U and its variants. To our knowledge, this is the first report both of characterization of a bacteriocin by
S. uberis
, as well as of a member of the nisin family of peptides in a species other than
L. lactis
.
Differential Expression of Proteins and Genes in the Lag Phase of
Lactococcus lactis
subsp.
lactis
Grown in Synthetic Medium and Reconstituted Skim Milk
Authors: Larsen Nadja , Boye Mette , Siegumfeldt Henrik , Jakobsen Mogens
Published: February 2006

We investigated protein and gene expression in the lag phase of
Lactococcus lactis
subsp.
lactis
CNRZ 157 and compared it to the exponential and stationary phases. By means of two-dimensional polyacrylamide gel electrophoresis, 28 highly expressed lag-phase proteins, implicated in nucleotide metabolism, glycolysis, stress response, translation, transcription, cell division, amino acid metabolism, and coenzyme synthesis, were identified. Among the identified proteins, >2-fold induction and down-regulation in the lag phase were determined for 12 proteins in respect to the exponential phase and for 18 proteins in respect to the stationary phase. Transcriptional changes of the lag-phase proteins in
L. lactis
were studied by oligonucleotide microarrays. Good correlation between protein and gene expression studies was demonstrated for several differentially expressed proteins, including nucleotide biosynthetic enzymes, adenylosuccinate synthase (PurA), IMP dehydrogenase (GuaB), and aspartate carbamoyl transferase (PyrB); heat-shock protein DnaK; serine hydroxymethyl transferase (GlyA); carbon catabolite control protein (CcpA); elongation factor G (FusA); and cell division protein (FtsZ).
Identification of QuiP, the Product of Gene PA1032, as the Second Acyl-Homoserine Lactone Acylase ofPseudomonas aeruginosaPAO1
Authors: Huang Jean J. , Petersen Ashley , Whiteley Marvin , Leadbetter Jared R.
Published: February 2006

The relevance of the acyl homoserine lactone (acyl-HSL) quorum signalsN-3-oxododecanoyl-homoserine lactone (3OC12HSL) andN-butanoyl-homoserine lactone to the biology and virulence ofPseudomonas aeruginosais well investigated. Previously,P. aeruginosawas shown to degrade long-chain, but not short-chain, acyl-HSLs as sole carbon and energy sources (J. J. Huang, J.-I. Han, L.-H. Zhang, and J. R. Leadbetter, Appl. Environ. Microbiol.69:5941-5949, 2003). A gene encoding an enzyme with acyl-HSL acylase activity,pvdQ(PA2385), was identified, but it was not required for acyl-HSL utilization. This indicated thatP. aeruginosaencodes another acyl-HSL acylase, which we identify here. A comparison of total cell proteins of cultures grown with long-acyl acyl-HSLs versus other substrates implicated the involvement of a homolog of PvdQ, the product of gene PA1032, for which we propose the name QuiP. Transposon mutants ofquiPwere defective for growth whenP. aeruginosawas cultured in medium containing decanoyl-HSL as a sole carbon and energy source. Complementation with a functional copy ofquiPrescued this growth defect. WhenP. aeruginosawas grown in buffered lysogeny broth, constitutive expression of QuiP inP. aeruginosaled to decreased accumulations of the quorum signal 3OC12HSL, relative to the wild type. Heterologous expression of QuiP was sufficient to confer long-chain acyl-HSL acylase activity uponEscherichia coli. Examination of gene expression patterns during acyl-HSL-dependent growth ofP. aeruginosafurther supported the involvement ofquiPin signal decay and revealed other genes also possibly involved. It is not yet known under which “natural” conditionsquiPis expressed or howP. aeruginosabalances the expression of its quorum-sensing systems with the expression of its acyl-HSL acylase activities.
Genetic Variance in the Composition of Two Functional Groups (Diazotrophs and Cyanobacteria) from a Hypersaline Microbial Mat
Authors: Yannarell Anthony C. , Steppe Timothy F. , Paerl Hans W.
Published: February 2006

Examination of variation in ecological communities can lead to an understanding of the forces that structure communities, the consequences of change at the ecosystem level, and the relevant scales involved. This study details spatial and seasonal variability in the composition of nitrogen-fixing and cyanobacterial (i.e., oxygenic photosynthetic) functional groups of a benthic, hypersaline microbial mat from Salt Pond, San Salvador Island, Bahamas. This system shows extreme annual variability in the salinity of the overlying water and the extent of water coverage. Analysis of molecular variance and F
ST
tests of genetic differentiation of
nifH
and cyanobacterial 16S rRNA gene clone libraries allowed for changes at multiple taxonomic levels (i.e., above, below, and at the species level) to inform the conclusions regarding these functional groups. Composition of the nitrogen-fixing community showed significant seasonal changes related to salinity, while cyanobacterial composition showed no consistent seasonal pattern. Both functional groups exhibited significant spatial variation, changing with depth in the mat and horizontally with distance from the shoreline. The patterns of change suggest that cyanobacterial composition was more insensitive to water stress, and consequently, cyanobacteria dominated the nitrogen-fixing community during dry months but gave way to a more diverse community of diazotrophs in wet months. This seasonal pattern may allow the mat community to respond quickly to water-freshening events after prolonged dry conditions (system recovery) and maintain ecosystem function in the face of disturbance during the wet season (system resilience).
Detection of Type A, B, E, and F
Clostridium botulinum
Neurotoxins in Foods by Using an Amplified Enzyme-Linked Immunosorbent Assay with Digoxigenin-Labeled Antibodies
Authors: Sharma Shashi K. , Ferreira Joseph. L. , Eblen Brian S. , Whiting Richard C.
Published: February 2006

An amplified enzyme-linked immunosorbent assay (ELISA) for the detection of
Clostridium botulinum
complex neurotoxins was evaluated for its ability to detect these toxins in food. The assay was found to be suitable for detecting type A, B, E, and F botulinum neurotoxins in a variety of food matrices representing liquids, solid, and semisolid food. Specific foods included broccoli, orange juice, bottled water, cola soft drinks, vanilla extract, oregano, potato salad, apple juice, meat products, and dairy foods. The detection sensitivity of the test for these botulinum complex serotypes was found to be 60 pg/ml (1.9 50% lethal dose [LD
50
]) for botulinum neurotoxin type A (BoNT/A), 176 pg/ml (1.58 LD
50
) for BoNT/B, 163 pg/ml for BoNT/E (4.5 LD
50
), and 117 pg/ml for BoNT/F (less than 1 LD
50
) in casein buffer. The test could also readily detect 2 ng/ml of neurotoxins type A, B, E, and F in a variety of food samples. For specificity studies, the assay was also used to test a large panel of type A
C. botulinum
, a smaller panel of proteolytic and nonproteolytic type B, E, and F neurotoxin-producing
Clostridia
, and nontoxigenic organisms using an overnight incubation of toxin production medium. The assay appears to be an effective tool for large-scale screening of the food supply in the event of a botulinum neurotoxin contamination event.
New Threshold and Confidence Estimates for Terminal Restriction Fragment Length Polymorphism Analysis of Complex Bacterial Communities
Authors: Osborne Catherine A. , Rees Gavin N. , Bernstein Yaniv , Janssen Peter H.
Published: February 2006

Terminal restriction fragment length polymorphism (T-RFLP) analysis has the potential to be useful for comparisons of complex bacterial communities, especially to detect changes in community structure in response to different variables. To do this successfully, systematic variations have to be detected above method-associated noise, by standardizing data sets and assigning confidence estimates to relationships detected. We investigated the use of different standardizing methods in T-RFLP analysis of PCR-amplified 16S rRNA genes to elucidate the similarities between the bacterial communities in 17 soil and sediment samples. We developed a robust method for standardizing data sets that appeared to allow detection of similarities between complex bacterial communities. We term this the variable percentage threshold method. We found that making conclusions about the similarities of complex bacterial communities from T-RFLP profiles generated by a single restriction enzyme (RE) may lead to erroneous conclusions. Instead, the use of multiple REs, each individually, to generate multiple data sets allowed us to determine a confidence estimate for groupings of apparently similar communities and at the same time minimized the effects of RE selection. In conjunction with the variable percentage threshold method, this allowed us to make confident conclusions about the similarities of the complex bacterial communities in the 17 different samples.
Rapid High-Throughput Assessment of Aerobic Bacteria in Complex Samples by Fluorescence-Based Oxygen Respirometry
Authors: O'Mahony Fiach C. , Papkovsky Dmitri B.
Published: February 2006

A simple method has been developed for the analysis of aerobic bacteria in complex samples such as broth and food homogenates. It employs commercial phosphorescent oxygen-sensitive probes to monitor oxygen consumption of samples containing bacteria using standard microtiter plates and fluorescence plate readers. As bacteria grow in aqueous medium, at certain points they begin to deplete dissolved oxygen, which is seen as an increase in probe fluorescence above baseline signal. The time required to reach threshold signal is used to either enumerate bacteria based on a predetermined calibration or to assess the effects of various effectors on the growth of test bacteria by comparison with an untreated control. This method allows for the sensitive (down to a single cell), rapid (0.5 to 12 h) enumeration of aerobic bacteria without the need to conduct lengthy (48 to 72 h) and tedious colony counts on agar plates. It also allows for screening a wide range of chemical and environmental samples for their toxicity. These assays have been validated with different bacteria, including
Escherichia coli
,
Micrococcus luteus
, and
Pseudomonas fluorescens
, with the enumeration of total viable counts in broth and industrial food samples (packaged ham, chicken, and mince meat), and comparison with established agar plating and optical-density-at-600-nm assays has been given.
Strategy for Identification of
Bacillus cereus
and
Bacillus thuringiensis
Strains Closely Related to
Bacillus anthracis
Authors: Daffonchio Daniele , Raddadi Noura , Merabishvili Maya , Cherif Ameur , Carmagnola Lorenzo , Brusetti Lorenzo , Rizzi Aurora , Chanishvili Nina , Visca Paolo , Sharp Richard , Borin Sara
Published: February 2006

Bacillus cereus
strains that are genetically closely related to
B. anthracis
can display anthrax-like virulence traits (A. R. Hoffmaster et al., Proc. Natl. Acad. Sci. USA 101:8449-8454, 2004). Hence, approaches that rapidly identify these “near neighbors” are of great interest for the study of
B. anthracis
virulence mechanisms, as well as to prevent the use of such strains for
B. anthracis
-based bioweapon development. Here, a strategy is proposed for the identification of near neighbors of
B. anthracis
based on single nucleotide polymorphisms (SNP) in the 16S-23S rRNA intergenic spacer (ITS) containing tRNA genes, characteristic of
B. anthracis
. By using restriction site insertion-PCR (RSI-PCR) the presence of two SNP typical of
B. anthracis
was screened in 126
B. cereus
group strains of different origin. Two
B. cereus
strains and one
B. thuringiensis
strain showed RSI-PCR profiles identical to that of
B. anthracis
. The sequencing of the entire ITS containing tRNA genes revealed two of the strains to be identical to
B. anthracis
. The strict relationship with
B. anthracis
was confirmed by multilocus sequence typing (MLST) of four other independent loci:
cerA
,
plcR
, AC-390, and SG-749. The relationship to
B. anthracis
of the three strains described by MLST was comparable and even higher to that of four
B. cereus
strains associated with periodontitis in humans and previously reported as the closest known strains to
B. anthracis
. SNP in ITS containing tRNA genes combined with RSI-PCR provide a very efficient tool for the identification of strains closely related to
B. anthracis
.