bluuebunny/crossref_metadata_2025 huggingface dataset:
The Outlook for Applied Entomology
Authors: Riley C. V.
Published: October 2006

I have thus touched, gentlemen, upon a few of the many subjects that crowd upon the mind for consideration on an occasion like this, — a few gleanings from a field which is passing rich in promise and possibility. It is a field that some of us have cultivated for many years, and yet have only scratched the surface; and, if I have ventured to suggest or admonish, it is with the feeling that my own labors in this field are ere long about to end, and that I may not have another occasion. At no time in the history of the world has there, I trow, been gathered together such a body of devoted and capable workers in applied entomology. It marks an era in our calling, and, looking back at the progress of the past fifteen years, we may well ponder the possibilities of the next fifteen. They will be fruitful of grand results in proportion as we persistently and combinedly pursue the yet unsolved problems, and are not tempted to the immediate presentation of separate facts, which are so innumerable and so easily observed that their very wealth becomes an element of weakness. Epoch-making discoveries result only from this power of following up unswervingly any given problem or any fixed ideal. The kerosene emulsion; the cyclone nozzle; the history of Phylloxera vastatrix, of Phorodon humuli, of Vedalia cardinalis,— are illustrations in point: and, while we may not expect frequent results as striking or of as wide application as these, there is no end of important problems yet to be solved, and from the solution of which we may look for similar beneficial results. Applied entomology is often considered a sordid pursuit; but it only becomes so when the object is sordid. When pursued with unselfish enthusiasm born of the love of investigation and the delight in benefiting our fellow-men, it is inspiring; and there are few pursuits more deservedly so, considering the vast losses to our farmers from insect injury and the pressing need that the distressed husbandman has for every aid that can be given him. Our work is elevating in its sympathies for the struggles and sufferings of others. Our standard should be high,— the pursuit of knowledge for the advancement of agriculture. No official entomologist should lower it by sordid aims.

During the recent political campaign the farmer must have been sorely puzzled to know whether his interests needed protection or not. On the abstract question of tariff protection to his products, we, as entomologists, may no more agree than do the politicians, or than does the farmer himself; but ours is a case of protection from injurious insects, and upon that there can nowhere be division of opinion. It is our duty to see that be gets it with as little tax for the means as possible. Gentlemen, I thank you.
Cultivation-Independent Examination of Horizontal Transfer and Host Range of an IncP-1 Plasmid among Gram-Positive and Gram-Negative Bacteria Indigenous to the Barley Rhizosphere
Authors: Musovic Sanin , Oregaard Gunnar , Kroer Niels , Sørensen Søren J.
Published: October 2006

The host range and transfer frequency of an IncP-1 plasmid (pKJK10) among indigenous bacteria in the barley rhizosphere was investigated. A new flow cytometry-based cultivation-independent method for enumeration and sorting of transconjugants for subsequent 16S rRNA gene classification was used. Indigenous transconjugant rhizosphere bacteria were collected by fluorescence-activated cell sorting and identified by cloning and sequencing of 16S rRNA genes from the sorted cells. The host range of the pKJK10 plasmid was exceptionally broad, as it included not only bacteria belonging to the alpha, beta, and gamma subclasses of theProteobacteria, but alsoArthrobactersp., a gram-positive member of theActinobacteria. The transfer frequency (transconjugants per donor) from thePseudomonas putidadonor to the indigenous bacteria was 7.03 × 10−2± 3.84 × 10−2. This is the first direct documentation of conjugal transfer between gram-negative donor and gram-positive recipient bacteria in situ.
Eukaryotic Lipid Body Proteins in Oleogenous Actinomycetes and Their Targeting to Intracellular Triacylglycerol Inclusions: Impact on Models of Lipid Body Biogenesis
Authors: Hänisch Jan , Wältermann Marc , Robenek Horst , Steinbüchel Alexander
Published: October 2006

Bacterial neutral lipid inclusions are structurally related to eukaryotic lipid bodies. These lipid inclusions are composed of a matrix of triacylglycerols (TAGs) or wax esters surrounded by a monolayer of phospholipids. Whereas the monolayers of lipid bodies from animal and plant cells harbor specific classes of proteins which are involved in the structure of the inclusions and lipid homoestasis, no such proteins are known to be associated with bacterial lipid inclusions. The present study was undertaken to reveal whether the mammalian lipid body proteins perilipin A, adipose differentiation-related protein, and tail-interacting protein of 47 kDa (TIP47), which comprise the so called PAT family proteins, and the maize (
Zea mays
L.) oleosin are targeted to prokaryotic TAG bodies in vivo. When fused to enhanced green fluorescent protein, all proteins except the oleosin were mainly located at the surfaces of lipid inclusions when heterologously expressed in the recombinant actinomycetes
Rhodococcus opacus
PD630 and
Mycobacterium smegmatis
mc
2
155. A more detailed intracellular distribution analysis of TIP47 in recombinant
R. opacus
cells by immunocytochemical labeling of ultrathin cryosections and freeze fracture replicas revealed a substantial amount of TIP47 protein also pervading the cores of the inclusions. We discuss the impact of these results on the current model of lipid body biogenesis in prokaryotes.
Babesia
spp. Identified by PCR in Ticks Collected from Domestic and Wild Ruminants in Southern Switzerland
Authors: Hilpertshauser Heidi , Deplazes Peter , Schnyder Manuela , Gern Lise , Mathis Alexander
Published: October 2006

Concurrent infections with vector-borne pathogens affected a cattle herd in Switzerland, and one of the pathogens was identified as
Babesia bigemina
, which had never been observed in this country before. Therefore, a survey of the occurrence of ruminant
Babesia
spp. and their tick vectors in Switzerland was conducted. A total of 2,017 ticks were collected from sheep, goats, cattle, and wild ruminants (deer, roe deer, and chamois) in southern parts of Switzerland and identified morphologically. The vast majority of the ticks (99.2%) were
Ixodes ricinus
, but 14 ticks from sheep and goats were identified as
Dermacentor marginatus
and two ticks from wild ruminants were identified as
Hemaphysalis punctata
. PCR analyses of 700 ticks revealed the presence of
Babesia divergens
(
n
= 6),
Babesia
sp. genotype EU1 (
n
= 14), and
B. major
(
n
= 2), whose suggested occurrence was confirmed in this study by molecular analysis, and the presence of novel
Babesia
sp. genotype CH1 (
n
= 4), which is closely related to
B. odocoilei
and to
Babesia
sp. genotype RD61 reported from North America. The identification of
B. divergens
and
B. major
in ticks collected from wild ruminants cast doubt on the postulated strict host specificity of these bovine
Babesia
species. Furthermore, the zoonotic
Babesia
sp. genotype EU1 was detected in ticks collected from domestic animals but was obtained predominantly from ticks collected from wild ruminants. More than one tick containing DNA of different
Babesia
spp. were collected from two red deer. Hence, the role of these game animals as reservoir hosts of
Babesia
spp. seems to be important but requires further investigation.
The AauR-AauS Two-Component System Regulates Uptake and Metabolism of Acidic Amino Acids in
Pseudomonas putida
Authors: Sonawane Avinash M. , Singh Birendra , Röhm Klaus-Heinrich
Published: October 2006

Pseudomonas putida
KT2440 metabolizes a wide range of carbon and nitrogen sources, including many amino acids. In this study, a σ
54
-dependent two-component system that controls the uptake and metabolism of acidic amino acids was identified. The system (designated
aau
, for
a
cidic
a
mino acid
u
tilization) involves a sensor histidine kinase, AauS, encoded by PP1067, and a response regulator, AauR, encoded by PP1066.
aauR
and
aauS
deletion mutants were unable to efficiently utilize aspartate (Asp), glutamate (Glu), and glutamine (Gln) as sole sources of carbon and nitrogen. Growth of the mutants was partially restored when the above-mentioned amino acids were supplemented with glucose or succinate as an additional carbon source. Uptake of Gln, Asp, and asparagine (Asn) by the
aauR
mutant was moderately reduced, while Glu uptake was severely impaired. In the absence of glucose, the
aauR
mutant even secreted Glu into the medium. Furthermore, disruption of
aauR
affected the activities of several key enzymes of Glu and Asp metabolism, leading to the intracellular accumulation of Glu and greatly reduced survival times under conditions of nitrogen starvation. By a proteomics approach, four major proteins were identified that are downregulated during growth of the
aauR
mutant on Glu. Two of these were identified as periplasmic glutaminase/asparaginase and the solute-binding protein of a Glu/Asp transporter. Transcriptional analysis of
lacZ
fusions containing the putative promoter regions of these genes confirmed that their expression is indeed affected by the
aau
system. Three further periplasmic solute-binding proteins were strongly expressed during growth of the
aauR
deletion mutant on Glu but downregulated during cultivation on glucose/NH
4
+
. These systems may be involved in amino acid efflux.
General Model, Based on Two Mixed Weibull Distributions of Bacterial Resistance, for Describing Various Shapes of Inactivation Curves
Authors: Coroller L. , Leguerinel I. , Mettler E. , Savy N. , Mafart P.
Published: October 2006

Cells of
Listeria monocytogenes
or
Salmonella enterica
serovar Typhimurium taken from six characteristic stages of growth were subjected to an acidic stress (pH 3.3). As expected, the bacterial resistance increased from the end of the exponential phase to the late stationary phase. Moreover, the shapes of the survival curves gradually evolved as the physiological states of the cells changed. A new primary model, based on two mixed Weibull distributions of cell resistance, is proposed to describe the survival curves and the change in the pattern with the modifications of resistance of two assumed subpopulations. This model resulted from simplification of the first model proposed. These models were compared to the Whiting's model. The parameters of the proposed model were stable and showed consistent evolution according to the initial physiological state of the bacterial population. Compared to the Whiting's model, the proposed model allowed a better fit and more accurate estimation of the parameters. Finally, the parameters of the simplified model had biological significance, which facilitated their interpretation.
Mineralization of Paraoxon and Its Use as a Sole C and P Source by a Rationally Designed Catabolic Pathway in
Pseudomonas putida
Authors: de la Peña Mattozzi Matthew , Tehara Sundiep K. , Hong Thomas , Keasling Jay D.
Published: October 2006

Organophosphate compounds, which are widely used as pesticides and chemical warfare agents, are cholinesterase inhibitors. These synthetic compounds are resistant to natural degradation and threaten the environment. We constructed a strain of
Pseudomonas putida
that can efficiently degrade a model organophosphate, paraoxon, and use it as a carbon, energy, and phosphorus source. This strain was engineered with the
pnp
operon from
Pseudomonas
sp. strain ENV2030, which encodes enzymes that transform
p
-nitrophenol into β-ketoadipate, and with a synthetic operon encoding an organophosphate hydrolase (encoded by
opd
) from
Flavobacterium
sp. strain ATCC 27551, a phosphodiesterase (encoded by
pde
) from
Delftia acidovorans
, and an alkaline phosphatase (encoded by
phoA
) from
Pseudomonas aeruginosa
HN854 under control of a constitutive promoter. The engineered strain can efficiently mineralize up to 1 mM (275 mg/liter) paraoxon within 48 h, using paraoxon as the sole carbon and phosphorus source and an inoculum optical density at 600 nm of 0.03. Because the organism can utilize paraoxon as a sole carbon, energy, and phosphorus source and because one of the intermediates in the pathway (
p
-nitrophenol) is toxic at high concentrations, there is no need for selection pressure to maintain the heterologous pathway.
Effect on Components of the Intestinal Microflora and Plasma Neuropeptide Levels of Feeding
Lactobacillus delbrueckii
,
Bifidobacterium lactis
, and Inulin to Adult and Elderly Rats
Authors: Lesniewska Violetta , Rowland Ian , Cani Patrice D. , Neyrinck Audrey M. , Delzenne Nathalie M. , Naughton Patrick J.
Published: October 2006

The aim of this study was to compare the effects of the mixture of
Lactobacillus delbrueckii
subsp.
rhamnosus
strain GG,
Bifidobacterium lactis
Bb12, and inulin on intestinal populations of lactobacilli, bifidobacteria, and enterobacteria in adult and elderly rats fed the same (in quality and quantity) diet. The portal plasma levels of two neuropeptides, neuropeptide Y (NPY) and peptide YY (PYY), were also evaluated to assess the physiological consequences of the synbiotic treatment for the gastrointestinal (GI) tracts of rats of different ages. Adult (
n
= 24) and elderly (
n
= 24) male rats were fed the AIN-93 M maintenance diet. After 2 weeks of adaptation, the diet of 12 rats of each age group was supplemented with 8% inulin and with strains GG and Bb12 to provide 2.2 × 10
9
CFU of each strain g
−1
of the diet. Blood and different regions of the GI tract were sampled from all rats after 21 days of the treatment. Treatment with the mixture of strain GG, strain BB12, and inulin induced significantly different changes in the numbers of lactobacilli, bifidobacteria, and enterobacteria of the stomach, small intestine, cecum, and colon microflora. Moreover, the GG, BB12, and inulin mixture increased the concentrations of NPY and PYY for adult rats. For the elderly animals, the PYY concentration was not changed, while the NPY concentration was decreased by treatment with the GG, BB12, and inulin mixture. The results of the present study indicate that the physiological status of the GI tract, and not just diet, has a major role in the regulation of important groups of the GI bacteria community, since even the outcome of the dietary modification with synbiotics depends on the ages of the animals.
Changes in Active Bacterial Communities before and after Dredging of Highly Polluted Baltic Sea Sediments
Authors: Edlund Anna , Jansson Janet K.
Published: October 2006

Bacteria residing in sediments have key functions in the marine food web. However, it has been difficult to correlate the identity and activity of bacteria in sediments due to lack of appropriate methods beyond cultivation-based techniques. Our aim was to use a combination of molecular approaches, bromodeoxyuridine incorporation and immunocapture, terminal restriction fragment length polymorphism, and cloning and sequencing of 16S rRNA genes to assess the composition of growing bacteria in Baltic Sea sediments. The study site was a highly polluted area off the Swedish coast. The sediments were sampled in two consecutive years, before and after remediation, by dredging of the top sediments. Levels of polyaromatic hydrocarbons (PAHs), mercury, and polychlorinated biphenyls were dramatically reduced as a result of the cleanup project. The compositions of growing members of the communities were significantly different at the two sampling periods. In particular, members from the class
Deltaproteobacteria
and genus
Spirochaeta
were more dominant before dredging, but members of the classes
Gammaproteobacteria
and the
Flavobacteria
represented the most dominant growing populations after dredging. We also cultivated isolates from the polluted sediments that could transform the model PAH compound, phenanthrene. Some of these isolates were confirmed as dominant growing populations by the molecular methods as well. This suite of methods enabled us to link the identity and activity of the members of the sediment communities.
Response of the Microaerophilic
Bifidobacterium
Species,
B. boum
and
B. thermophilum
, to Oxygen
Authors: Kawasaki Shinji , Mimura Tsuyoshi , Satoh Takumi , Takeda Kouji , Niimura Youichi
Published: October 2006

We investigated the effects of O
2
on
Bifidobacterium
species using liquid shaking cultures under various O
2
concentrations. Although most of the
Bifidobacterium
species we selected showed O
2
sensitivity, two species,
B. boum
and
B. thermophilum
, demonstrated microaerophilic profiles. The growth of
B. bifidum
and
B. longum
was inhibited under high-O
2
conditions accompanied by the accumulation of H
2
O
2
in the medium, and growth was restored by adding catalase to the medium.
B. boum
and
B. thermophilum
grew well even under 20% O
2
conditions without H
2
O
2
accumulation, and growth was stimulated compared to anoxic growth. H
2
O-forming NADH oxidase activities were detected dominantly in cell extracts of
B. boum
and
B. thermophilum
under acidic reaction conditions (pH 5.0 to 6.0).
Novel Method To Identify Source-Associated Phylogenetic Clustering Shows thatListeria monocytogenesIncludes Niche-Adapted Clonal Groups with Distinct Ecological Preferences
Authors: Nightingale K. K. , Lyles K. , Ayodele M. , Jalan P. , Nielsen R. , Wiedmann M.
Published: October 2006

While phylogenetic and cluster analyses are often used to define clonal groups within bacterial species, the identification of clonal groups that are associated with specific ecological niches or host species remains a challenge. We usedListeria monocytogenes, which causes invasive disease in humans and different animal species and which can be isolated from a number of environments including food, as a model organism to develop and implement a two-step statistical approach to the identification of phylogenetic clades that are significantly associated with different source populations, including humans, animals, and food. If the null hypothesis that the genetic distances for isolates within and between source populations are identical can be rejected (SourceCluster test), then particular clades in the phylogenetic tree with significant overrepresentation of sequences from a given source population are identified (TreeStats test). Analysis of sequence data for 120L. monocytogenesisolates revealed evidence of clustering between isolates from the same source, based on the phylogenies inferred fromactAandinlA(P= 0.02 andP= 0.07, respectively; SourceCluster test). Overall, the TreeStats test identified 10 clades with significant (P< 0.05) or marginally significant (P< 0.10) associations with defined sources, including human-, animal-, and food-associated clusters. Epidemiological and virulence phenotype data supported the fact that the source-associated clonal groups identified here are biologically valid. Overall, our data show that (i) the SourceCluster and TreeStats tests can identify biologically meaningful source-associated phylogenetic clusters and (ii)L. monocytogenesincludes clonal groups that have adapted to infect specific host species or colonize nonhost environments.
Use of PCR and Reverse Line Blot Hybridization Macroarray Based on 16S-23S rRNA Gene Internal Transcribed Spacer Sequences for Rapid Identification of 34
Mycobacterium
Species
Authors: Xiong Likuan , Kong Fanrong , Yang Yingzhou , Cheng Jinquan , Gilbert Gwendolyn L.
Published: October 2006

The aim of this study was to develop a PCR and reverse line blot hybridization (PCR-RLB) macroarray assay based on 16S-23S rRNA gene internal transcribed spacer sequences for the identification and differentiation of 34 mycobacterial species or subspecies. The performance of the PCR-RLB assay was assessed and validated by using 78 reference strains belonging to 55
Mycobacterium
species, 219 clinical isolates which had been identified as mycobacteria by high-performance liquid chromatography or gas chromatography, three skin biopsy specimens from patients with suspected leprosy which had been shown to contain acid-fast bacilli, and isolates of 14 nonmycobacterial species. All mycobacteria were amplified in the PCR and hybridized with a genus-specific probe (probe MYC). The 34 species-specific probes designed in this study hybridized only with the corresponding
Mycobacterium
species. The mycobacterial PCR-RLB assay is an efficient tool for the identification of clinical isolates of mycobacteria; it can reliably identify mixed mycobacterial cultures and
M. leprae
in skin biopsy specimens.
Preparation of His-Tagged Armored RNA Phage Particles as a Control for Real-Time Reverse Transcription-PCR Detection of Severe Acute Respiratory Syndrome Coronavirus
Authors: Cheng Yangjian , Niu Jianjun , Zhang Yongyou , Huang Jianwei , Li Qingge
Published: October 2006

Armored RNA has been increasingly used as both an external and internal positive control in nucleic acid-based assays for RNA virus. In order to facilitate armored RNA purification, a His6tag was introduced into the loop region of the MS2 coat protein, which allows the exposure of multiple His tags on the surface during armored RNA assembly. The His-tagged armored RNA particles were purified to homogeneity and verified to be free of DNA contamination in a single run of affinity chromatography. A fragment of severe acute respiratory syndrome coronavirus (SARS-CoV) genome targeted for SARS-CoV detection was chosen for an external positive control preparation. A plant-specific gene sequence was chosen for a universal noncompetitive internal positive control preparation. Both controls were purified by Co2+affinity chromatography and were included in a real-time reverse transcription-PCR assay for SARS-CoV. The noncompetitive internal positive control can be added to clinical samples before RNA extraction and enables the identification of potential inhibitive effects without interfering with target amplification. The external control could be used for the quantification of viral loads in clinical samples.
Comparison of Subtyping Methods for Differentiating
Salmonella enterica
Serovar Typhimurium Isolates Obtained from Food Animal Sources
Authors: Foley Steven L. , White David G. , McDermott Patrick F. , Walker Robert D. , Rhodes Bobbie , Fedorka-Cray Paula J. , Simjee Shabbir , Zhao Shaohua
Published: October 2006

Molecular characterization (e.g., DNA-based typing methods) of
Salmonella
isolates is frequently employed to compare and distinguish clinical isolates recovered from animals and from patients with food-borne disease and nosocomial infections. In this study, we compared the abilities of different phenotyping and genotyping methods to distinguish isolates of
Salmonella enterica
serovar Typhimurium from different food animal sources. One hundred twenty-eight
S. enterica
serovar Typhimurium strains isolated from cattle, pigs, chickens, and turkeys or derived food products were characterized using pulsed-field gel electrophoresis (PFGE), repetitive element PCR (Rep-PCR), multilocus sequence typing (MLST), plasmid profiling, and antimicrobial susceptibility testing. Among the 128
Salmonella
isolates tested, we observed 84 Rep-PCR profiles, 86 PFGE patterns, 89 MLST patterns, 36 plasmid profiles, and 38 susceptibility profiles. The molecular typing methods, i.e., PFGE, MLST, and Rep-PCR, demonstrated the best discriminatory power among
Salmonella
isolates. However, no apparent correlation was evident between the results of one molecular typing method and those of the others, suggesting that a combination of multiple methods is needed to differentiate
S. enterica
serovar Typhimurium isolates that genetically cluster according to one particular typing method.
Use of a Single-Nucleotide Polymorphism Genotyping System To Demonstrate the Unique Epidemiology of Methicillin-Resistant
Staphylococcus aureus
in Remote Aboriginal Communities
Authors: McDonald Malcolm , Dougall Annette , Holt Deborah , Huygens Flavia , Oppedisano Frances , Giffard Philip M. , Inman-Bamber John , Stephens Alex J. , Towers Rebecca , Carapetis Jonathan R. , Currie Bart J.
Published: October 2006

Community-acquired methicillin-resistant
Staphylococcus aureus
(CA-MRSA) has emerged as a major public health problem in Australia, as in many other parts of the world. High rates of CA-MRSA skin and soft tissue infection have been reported from Aboriginal communities. We used a single-nucleotide polymorphism (SNP) genotyping typing system based on the multilocus sequence type (MLST) database to investigate the epidemiology of CA-MRSA and methicillin-sensitive
S. aureus
(MSSA) over a 12-month period in three remote Aboriginal communities of Northern Australia. This was supplemented by real-time PCR for Panton-Valentine leukocidin (PVL) genes, staphylococcal cassette chromosome
mec
(SCC
mec
) typing, and antimicrobial susceptibility testing.
S. aureus
was recovered from pyoderma lesions on 221 occasions and throat swabs on 44 occasions. The median monthly recovery rate of
S. aureus
from skin sores was 58% (interquartile range, 62 to 78%), and there was no seasonal variation. Twenty-three percent of isolates were CA-MRSA; the proportion was similar across the communities and did not vary over the study period. Erythromycin resistance was found in 47% of CA-MRSA and 21% of MSSA. SNP-based typing identified 14 different clonal complexes (cc); however, cc75 was predominant, accounting for 71% of CA-MRSA isolates. These were confirmed as ST75-like by using an additional SNP and MLST of selected isolates. All but one of the cc75 isolates had SSC
mec
type IV (one had type V), and all were PVL negative. Monthly tracking of SNP-based cc types showed a highly dynamic process. ST75-MRSA-IV appears to be unique to the region and probably evolved de novo in remote Aboriginal communities.
Molecular Identification of Black-Grain Mycetoma Agents
Authors: Desnos-Ollivier Marie , Bretagne Stéphane , Dromer Françoise , Lortholary Olivier , Dannaoui Eric
Published: October 2006

Black-grain mycetomas are subcutaneous devastating chronic infections due to several dematiaceous fungi. They are diagnosed mostly in tropical countries. Identification of these fungi with standard mycological procedures is difficult because of their poor or delayed sporulation. The aim of this study was thus to assess the accuracy of molecular identification of these fungi. A total of 54 strains, mostly of clinical origin, were used, including 15Madurella mycetomatis, 6Madurella grisea, 12Leptosphaeria senegalensis, 4Leptosphaeria tompkinsii, 6Pyrenochaetaspp., 4Curvularia lunata, and 7Exophiala jeanselmeistrains. The internal transcribed spacer 1 (ITS1)-5.8S-ITS2 DNA region was amplified by using universal fungal primers and sequenced. Both intra- and interspecies sequence similarities were assessed.Madurella mycetomatisappeared to be a homogeneous species. More intraspecies variations were found forC. lunataandE. jeanselmei, leading, in some instances, to changes in the initial identification.L. senegalensisandL. tompkinsiishowed intraspecies similarities of >99%, but similarity between the two species was <88%. Intergenera and interspecies variations were important, with sequence homologies of <81% between genera. In contrast,Pyrenochaeta romeroiandM. griseaappeared to be heterogeneous, with intraspecies similarities of 40 to 100% and 53 to 100%, respectively, which suggest either erroneous identification or the need for taxonomic revision. Epidemiological and therapeutic studies could benefit from a precise identification of the fungi responsible for black-grain mycetoma based not only on phenotypical characteristics but also on ITS sequencing.
Candida guilliermondii
, an Opportunistic Fungal Pathogen with Decreased Susceptibility to Fluconazole: Geographic and Temporal Trends from the ARTEMIS DISK Antifungal Surveillance Program
Authors: Pfaller M. A. , Diekema D. J. , Mendez M. , Kibbler C. , Erzsebet P. , Chang S.-C. , Gibbs D. L. , Newell V. A. ,   the Global Antifungal Surveillance Group
Published: October 2006

Although a rare cause of invasive candidiasis,
Candida guilliermondii
has been reported to exhibit decreased susceptibility to antifungal agents. Aside from case reports and small surveys, there is little information regarding the epidemiology and antifungal susceptibility profile of
C. guilliermondii
. We report geographic and temporal trends in the isolation and antifungal susceptibilities of 1,029
C. guilliermondii
clinical isolates collected from 127 medical centers as part of the ARTEMIS DISK Antifungal Surveillance Program. In addition, we report the in vitro susceptibility of 132 bloodstream isolates of
C. guilliermondii
to caspofungin.
C. guilliermondii
represented 1.4% of the 75,761 isolates collected from 2001 to 2003 and was most common among isolates from Latin America (3.7% versus 0.6 to 1.1%). Decreased susceptibility to fluconazole was noted (75% susceptible; range, 68 to 77% across regions), and voriconazole was more active in vitro against
C. guilliermondii
than fluconazole (91% susceptible; range, 88 to 93% across regions). Fluconazole was least active against isolates from dermatology (58%) and surgical (69%) services and against isolates associated with skin and soft tissue infection (68%, compared to 85% susceptible for bloodstream isolates). There was no evidence of increasing azole resistance over time among
C. guilliermondii
isolates tested from 2001 to 2003. Of 132 bloodstream isolates of
C. guilliermondii
tested against caspofungin, most were inhibited by ≤2 μg/ml (96%; MIC
50
/MIC
90
, 0.5/1.0 μg/ml).
C. guilliermondii
, a species that exhibits reduced susceptibility to fluconazole, is the sixth most frequently isolated
Candida
species from this large survey and may be an emerging pathogen in Latin America.
Multiplex Real-Time PCR Assay for Simultaneous Detection of
Acanthamoeba
spp.,
Balamuthia mandrillaris
, and
Naegleria fowleri
Authors: Qvarnstrom Yvonne , Visvesvara Govinda S. , Sriram Rama , da Silva Alexandre J.
Published: October 2006

Infections caused by
Naegleria fowleri
,
Acanthamoeba
spp., and
Balamuthia mandrillaris
occur throughout the world and pose many diagnostic challenges. To date, at least 440 cases of severe central nervous system infections caused by these amebas have been documented worldwide. Rapid and specific identification of these free-living amebas in clinical samples is of crucial importance for efficient case management. We have developed a triplex real-time TaqMan PCR assay that can simultaneously identify
Acanthamoeba
spp.,
B. mandrillaris
, and
N. fowleri
in the same PCR vessel. The assay was validated with 22 well-characterized amebic strains harvested from cultures and nine clinical specimens that were previously characterized by in vitro culture and/or immunofluorescence assay. The triplex assay demonstrated high specificity and a rapid test completion time of less than 5 h from the reception of the specimen in the laboratory. This assay was able to detect one single ameba per sample analyzed, as determined with cerebrospinal fluid spiked with diluted cultured amebas. This assay could become useful for fast laboratory diagnostic assessment of amebic infections (caused by free-living amebas) in laboratories with adequate infrastructure to perform real-time PCR testing.
Evaluation of the BD Phoenix Automated Microbiology System for Identification and Antimicrobial Susceptibility Testing of
Enterobacteriaceae
Authors: Carroll Karen C. , Glanz Brian D. , Borek Anita P. , Burger Chad , Bhally Hasan S. , Henciak Susan , Flayhart Diane
Published: October 2006

We evaluated the accuracy of the BD Phoenix system for the identification (ID) and antimicrobial susceptibility testing (AST) of 251 isolates of the family
Enterobacteriaceae
representing 31 species. Organisms were inoculated onto the Phoenix panel according to the manufacturer's instructions. The results from conventional biochemical tests were used for the reference method for ID. Agar dilution, performed according to the CLSI guidelines, was the reference AST method. Essential and categorical agreements were determined. The overall levels of agreement for the genus- and species-level identifications were 95.6% and 94.4%, respectively. Fourteen isolates were incorrectly identified by the Phoenix system; 10 of these were incorrectly identified to the species level. Three of these were
Enterobacter
(
Pantoea
) species and four of these were
Shigella
spp. misidentified as
Escherichia coli
. For AST results, the essential and categorical agreements were 98.7% and 97.9%, respectively. The very major error, major error, and minor error rates were 0.38%, 0.33%, and 1.8%, respectively. Six isolates (three
E. coli
isolates and three
Klebsiella
isolates) were extended-spectrum β-lactamase producers. All six were flagged by the Phoenix system expert rules. The Phoenix system compares favorably to traditional methods for ID and AST of
Enterobacteriaceae
.
Molecular Epidemiology of Rotavirus Diarrhea among Children and Adults in Nepal: Detection of G12 Strains with P[6] or P[8] and a G11P[25] Strain
Authors: Uchida Ryuichi , Pandey Basu Dev , Sherchand Jeevan Bahadur , Ahmed Kamurddin , Yokoo Michiyo , Nakagomi Toyoko , Cuevas Luis E. , Cunliffe Nigel A. , Hart C. A. , Nakagomi Osamu
Published: October 2006

In anticipation of a rotavirus vaccine in Nepal, this study was undertaken to determine the distribution of the G and P serotypes and electropherotypes of rotaviruses in order to examine if there is any emerging serotype or unusual strain circulating in children and adults in Nepal. Of 1,315 diarrheal stool specimens, rotavirus was detected by an enzyme-linked immunosorbent assay in 116 (17%) of 666 patients less than 5 years of age, in 18 (7%) of 260 patients 5 to 14 years of age, and in 19 (5%) of 358 patients 15 years of age and older. Approximately 75% of rotavirus diarrhea occurred in children less than 5 years of age. Approximately 70% of rotaviruses found in each of the three age groups belonged to serotype G1P[8]. Interestingly, there were 29 (20%) G12 rotaviruses carrying either P[8] or P[6] and one (0.7%) G11 rotavirus carrying an unusual P[25] genotype. RNA polyacrylamide gel electrophoresis discriminated 19 strains (electropherotypes), among which there were three codominant strains carrying G1P[8] and long RNA patterns. Five electropherotypes were discriminated among G12 rotaviruses, all of which had long RNA patterns. The fact that 20% of rotaviruses were G12 strains carrying either P[8] or P[6] and had multiple electropherotypes suggest that G12 strains are not more rare strains but that they pose an emerging challenge to current and future vaccines. The presence of multiple strains as defined by electropherotypes suggests the richness of the rotavirus gene pool in Nepal, where unusual strains may continue to emerge.
Comparative Evaluation of Three Commercially Available Methodologies for Hepatitis C Virus Genotyping
Authors: Schutzbank Ted E. , Sefers Susan E. , Kahmann Nicole , Li Haijing , Tang Yi-Wei
Published: October 2006

We compared the performances of three hepatitis C virus genotyping methodologies supplied by Bayer, Abbott, and Third Wave Technologies. Genotypes were determined for 136 of 137 specimens by the Bayer method, 121 of 137 specimens by the Invader assay, and only 77 of 137 specimens by the Abbott assay. All reported genotypes were concordant by all three methods.
Comparison of Three Commercial Assays and a Modified Disk Diffusion Assay with Two Broth Microdilution Reference Assays for Testing Zygomycetes,
Aspergillus
spp.,
Candida
spp., and
Cryptococcus neoformans
with Posaconazole and Amphotericin B
Authors: Espinel-Ingroff A.
Published: October 2006

We compared posaconazole M27-A2 and M38-A MICs to Etest and YeastOne MICs for 92 zygomycetes, 126
Aspergillus
isolates, 110
Candida
isolates, and
Cryptococcus neoformans
. Reference MICs were also correlated with inhibition zone diameters in millimeters (modified M44-A disk and Neo-Sensitabs tablet methods). Etest MICs were obtained on solidified (1.5% agar) RPMI 1640 (2% dextrose), and zone diameters were obtained on supplemented (2% glucose and 0.5 μg/ml methylene blue [for all isolates]) and nonsupplemented Mueller-Hinton (MH; molds only) agar. MICs and zone diameters were obtained between 16 and 72 h. The overall agreement (% MIC pairs within a three-dilution range) between reference posaconazole and YeastOne MICs was 98 to 100% at 16 to 24 h for zygomycetes and yeasts and 99% at 24 to 48 h for
Aspergillus
. The overall agreement was lower between reference posaconazole and Etest MICs (94 to 97%) and by both methods with amphotericin B for all species (95 to 99.3%). For yeasts, the correlation coefficient was similar between reference posaconazole MICs and either disk (
R
, 0.810) or tablet (
R
, 0.769) zone diameter at 24 h and was superior on MH agar for molds at 16 to 48 h (
R
, 0.804 and 0.799 for disk and tablet, respectively). For amphotericin B, the best correlation between reference MICs and zone diameters was observed at 16 to 48 h for molds on MH agar (
R
, 0.736 to 0.812 and 0.765 to 0.749 for disk and tablet, respectively) and at 48 h for yeasts (
R
, 0.681 and 0.503 for disk and tablet, respectively). These data suggest the potential value of these alternative broth dilution and agar diffusion methods for testing posaconazole and amphotericin B in the clinical laboratory against the species evaluated.
Molecular Epidemiology of G9 Rotaviruses in Taiwan between 2000 and 2002
Authors: Lin Yi-Pei , Chang Sui-Yuan , Kao Chuan-Liang , Huang Li-Min , Chung Ming-Yi , Yang Jyh-Yuan , Chen Hour-Young , Taniguchi Koki , Tsai Keh-Sung , Lee Chun-Nan
Published: October 2006

Since the mid-1990s, novel G9 rotaviruses have been detected in many countries, suggesting that G9 is a globally important serotype. The molecular epidemiology of G9 rotaviruses in Taiwan from 2000 to 2002 was investigated in this study. G9 rotavirus first appeared in 2000 with 4 cases and constituted 33.8% and 54.8% of the rotavirus-positive samples in 2001 and 2002, respectively. These G9 strains belonged to P[8]G9, subgroup II, and long electropherotype, except one belonged to P[4]G9, subgroup II, and short electropherotype. Nucleotide sequencing and phylogenetic analysis of 52 Taiwanese G9 rotaviruses showed that the VP7 genes shared a high degree of identity to overseas G9 rotaviruses detected after 1993 and that the VP8* portions of the VP4 genes were more closely related to those of local rotaviruses of other G types. The two P[8]G9 strains with high nucleotide identities in the VP7 and the partial VP4 genes, 01TW591 of Taiwan from 2001 and 95H115 of Japan from 1995, varied in four genes, genes 2, 3, 7, and 8, which was revealed by RNA-RNA hybridization. Representative strains for different RNA patterns were also analyzed in the partial VP2 and VP3 genes; the nucleotide identities were high between Taiwanese G9 strains and local G3 or G2 strains. These results suggested that Taiwanese G9 rotaviruses possibly had evolved through reassortment between overseas G9 strains and circulating rotaviruses of other G types.
Coexpression of an unusual form of theEWS–WT1fusion transcript and interleukin 2/15 receptor βmRNA in a desmoplastic small round cell tumour
Authors: Nakanishi Y , Oinuma T , Sano M , Fuchinoue F , Komatsu K , Seki T , Obana Y , Tabata M , Kikuchi K , Shimamura M , Ohmori K , Nemoto N
Published: October 2006

Background:The β chain of the interleukin 2/15 receptor (IL-2/15Rβ) is induced by the expression of theEWS–WT1. A case of desmoplastic small round cell tumour (DSRCT) expressing only an unusualEWS-WT1treated by us is reported here.

Aim:To characterise an unusual form ofEWS–WT1.

Methods:Frozen tissue sections of the axillary tumour were examined using a laser-assisted microdissection technique and reverse transcriptase polymerase chain reaction.

Results:The novel fusion of exon 8 ofEWSand the defective exon 10 ofWT1(−KTS) was detected. Although it was an unusual form, the coexpression of the presentEWS–WT1,IL-2/15Rβand Janus kinase (JAK1) mRNA was detected in the tumour cells.IL-2and signal transducers and activators of transcription (STAT5) mRNA were detected in both tumour and stromal cells.

Conclusion:The induction of the IL-2/15 receptor signalling pathway may contribute to tumorigenesis in DSRCT through a paracrine or an autocrine system, even though theEWS–WT1was an unusual form.
Ovarian clear cell adenocarcinoma: a continuing enigma: Table 1
Authors: Tan David S P , Kaye Stan
Published: October 2006

Ovarian clear cell adenocarcinomas (OCCAs) account for <5% of all ovarian malignancies. Compared to other epithelial ovarian cancer (EOC) subtypes, when at an advanced stage, they are associated with a poorer prognosis and are relatively resistant to conventional platinum-based chemotherapy. By contrast, early-stage clear cell ovarian cancer carries a relatively good prognosis. Hence, there is a need to improve our understanding of its pathobiology in order to optimise currently available treatments and develop new therapeutic strategies. This review summarises the currently available literature regarding the pathogenesis of OCCA, its molecular genetic features and postulated molecular mechanisms that underlie its chemoresistant phenotype. Marked similarities with clear cell carcinomas of the kidney and endometrium have been noted by some investigators, raising interesting possibilities regarding novel therapeutic approaches. Unfortunately, most studies on OCCA have hitherto been hampered by insufficient sample sizes, leaving many key issues unresolved. It is envisaged that in the future, high-resolution genomic and gene-expression microarray studies incorporating larger sample sizes will lead to the characterisation of the key molecular players in OCCA biology, which may potentially lead to the identification of novel targets for therapeutic development.
CD56-positive haematological neoplasms of the skin: a multicentre study of the Cutaneous Lymphoma Project Group of the European Organisation for Research and Treatment of Cancer
Authors: Assaf Chalid , Gellrich Sylke , Whittaker Sean , Robson Alistair , Cerroni Lorenzo , Massone Cesare , Kerl Helmut , Rose Christian , Chott Andreas , Chimenti Sergio , Hallermann Christian , Petrella Tony , Wechsler Janine , Bagot Martine , Hummel Michael , Bullani-Kerl Katrin , Bekkenk Marcel W , Kempf Werner , Meijer Chris J L M , Willemze Rein , Sterry Wolfram
Published: October 2006

Background:Cutaneous lymphomas expressing CD56, a neural cell adhesion molecule, are characterised in most cases by a highly aggressive clinical course and a poor prognosis. However, prognostic subsets within the CD56+ group have been difficult to identify due to the lack of uniform clinicopathological and immunophenotypical criteria.

Methods:A multicentre study was conducted by the Cutaneous Lymphoma Task Force of the European Organisation for Research and Treatment of Cancer to define prognostic parameters and establish diagnostic and therapeutic guidelines for CD56+ haematological neoplasms presenting primarily in the skin.

Results:Four different subtypes of lymphoproliferations with CD56 expression were identified: (1) haematodermic neoplasm; (2) skin infiltration as the first manifestation of CD56+ acute myeloid leukaemia; (3) nasal-type extranodal natural killer/T-cell lymphoma; and (4) “classical” cases of cutaneous T-cell lymphoma (CTCL) with co-expression of the CD56 molecule. Patients in the first three groups had a poor outcome (93% died) with a median survival rate of 11 months (95% CI 2–72 months), whereas all patients with CD56+ CTCL were alive at the last follow-up.

Conclusion:Results show that CD56+ cutaneous lymphoproliferative disorders, with the exception of CD56+ CTCL have a very poor prognosis. It is therefore clinically important to separate CD56+ CTCL from the remaining CD56+ haematological disorders.
Mitochondria play an important role in 17β-estradiol attenuation of H2O2-induced rat endothelial cell apoptosis
Authors: Lu Ailing , Frink Michael , Choudhry Mashkoor A. , Hubbard William J. , Rue Loring W. , Bland Kirby I. , Chaudry Irshad H.
Published: October 2006

Studies have shown salutary effects of 17β-estradiol following trauma-hemorrhage on different cell types. 17β-Estradiol also induces improved circulation via relaxation of the aorta and has an anti-apoptotic effect on endothelial cells. Because mitochondria play a pivotal role in apoptosis, we hypothesized that 17β-estradiol will maintain mitochondrial function and will have protective effects against H2O2-induced apoptosis in endothelial cells. Endothelial cells were isolated from rats' aorta and cultured in the presence or absence of H2O2, a potent inducer of apoptosis. In additional studies, endothelial cells were pretreated with 17β-estradiol. Flow cytometry analysis revealed H2O2-induced apoptosis in 80.9% of endothelial cells; however, prior treatment of endothelial cells with 17β-estradiol resulted in an ∼40% reduction in apoptosis. This protective effect of 17β-estradiol was abrogated when endothelial cells were cultured in the presence ICI-182780, indicating the involvement of estrogen receptor (ER). Fluorescence microscopy revealed a 17β-estradiol-mediated attenuation of H2O2-induced mitochondrial condensation. Western blot analysis demonstrated that H2O2-induced cytochrome c release from mitochondrion to cytosol and the activation of caspase-9 and -3 were decreased by 17β-estradiol. These findings suggest that 17β-estradiol attenuated H2O2-induced apoptosis via ER-dependent activation of caspase-9 and -3 in rat endothelial cells through mitochondria.
The characterization of α5-integrin expression on tubular epithelium during renal injury
Authors: White Lindsay R. , Blanchette Jason B. , Ren Li , Awn Ali , Trpkov Kiril , Muruve Daniel A.
Published: October 2006

The hallmark of progressive chronic kidney disease is the deposition of extracellular matrix proteins and tubulointerstitial fibrosis. Integrins mediate cell-extracellular matrix interaction and may play a role tubular epithelial injury. Murine primary tubular epithelial cells (TECs) express α5-integrin, a fibroblast marker and the natural receptor for fibronectin. Microscopy localized α5-integrin on E-cadherin-positive cells, confirming epithelial expression. The expression of α5-integrin increased in TECs grown on fibronectin and occurred in parallel with an upregulation of α-smooth muscle actin (αSMA), a marker of epithelial-mesenchymal transition (EMT). Exposure of TECs to transforming growth factor (TGF)-β also increased TEC α5-integrin expression in association with αSMA and EMT. Knock-down of α5-integrin expression with short interfering RNA attenuated the TGF-β induction of αSMA but did not alter morphologic EMT. Rather, α5-integrin was necessary for epithelial cell migration on fibronectin but not type IV collagen during cell spreading and epithelial wound healing in vitro. Immunohistochemistry revealed basolateral tubular epithelial α5-integrin expression in mouse kidneys after unilateral ureteric obstruction but not in contralateral control kidneys. In patient biopsies of nondiabetic kidney disease, α5-integrin expression was increased significantly in the renal interstitium. Focal basolateral staining was also detected in injured, but not in normal, tubular epithelium. In summary, these data show that TECs are induced to express α5-integrin during EMT and tubular epithelial injury in vitro and in vivo. These results increase our understanding of the biology of integrins during EMT and tubular injury in chronic kidney disease.