bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor Tu and F-ATPase β-subunit
Authors: Paradis Sonia , Boissinot Maurice , Paquette Nancy , Bélanger Simon D. , Martel Eric A. , Boudreau Dominique K. , Picard François J. , Ouellette Marc , Roy Paul H. , Bergeron Michel G.
Published: September 2005

The phylogeny of enterobacterial species commonly found in clinical samples was analysed by comparing partial sequences of their elongation factor Tu gene (tuf) and of their F-ATPase β-subunit gene (atpD). An 884 bp fragment for tuf and an 884 or 871 bp fragment for atpD were sequenced for 96 strains representing 78 species from 31 enterobacterial genera. The atpD sequence analysis exhibited an indel specific to Pantoea and Tatumella species, showing, for the first time, a tight phylogenetic affiliation between these two genera. Comprehensive tuf and atpD phylogenetic trees were constructed and are in agreement with each other. Monophyletic genera are Cedecea, Edwardsiella, Proteus, Providencia, Salmonella, Serratia, Raoultella and Yersinia. Analogous trees based on 16S rRNA gene sequences available from databases were also reconstructed. The tuf and atpD phylogenies are in agreement with the 16S rRNA gene sequence analysis, and distance comparisons revealed that the tuf and atpD genes provide better discrimination for pairs of species belonging to the family Enterobacteriaceae. In conclusion, phylogeny based on tuf and atpD conserved genes allows discrimination between species of the Enterobacteriaceae.
Reclassification of Nonomuraea flexuosa (Meyer 1989) Zhang et al. 1998 as Thermopolyspora flexuosa gen. nov., comb. nov., nom. rev.
Authors: Goodfellow Michael , Maldonado Luis A. , Quintana Erika T.
Published: September 2005

A polyphasic study was undertaken to clarify the taxonomic position of Nonomuraea flexuosa DSM 41386T. The distinct 16S rRNA gene sequence phyletic branch formed by this strain was equated with nine related monophyletic clades composed of representatives of the genera classified in the family Streptosporangiaceae. The organism produced a PCR product characteristic of this taxon when examined using a set of oligonucleotide primers specific for members of the family Streptosporangiaceae. Strain DSM 41386T could also be distinguished from representatives of the nine genera assigned to this family using a combination of chemotaxonomic, morphological and physiological properties. It is evident from the genotypic and phenotypic data that strain DSM 41386T is misclassified in the genus Nonomuraea and merits recognition as a monospecific genus within the family Streptosporangiaceae. It is proposed that the name Thermopolyspora flexuosa gen. nov., comb. nov., nom. rev. be used for this purpose, with the type strain DSM 41386T (=NRRL B-24348T).
Staphylococcus simiae sp. nov., isolated from South American squirrel monkeys
Authors: Pantůček Roman , Sedláček Ivo , Petráš Petr , Koukalová Dagmar , Švec Pavel , Štětina Vlastimil , Vancanneyt Marc , Chrastinová Lenka , Vokurková Jitka , Růžičková Vladislava , Doškař Jiří , Swings Jean , Hájek Václav
Published: September 2005

Eight coagulase-negative, oxidase-negative and novobiocin-susceptible staphylococcal strains were isolated from the gastrointestinal tracts of South American squirrel monkeys (Saimiri sciureus L.). These strains were differentiated from known staphylococcal species on the basis of 16S rRNA gene and hsp60 gene sequencing, and from the most closely related species by using DNA–DNA hybridization, ribotyping, whole-cell protein profiles and biotyping. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that these strains are members of the Staphylococcus aureus species group (99 % similarity) but are biochemically similar to Staphylococcus piscifermentans, from which they can be phenotypically distinguished by resistance to polymyxin B, acid production from d-mannitol, the inability to hydrolyse aesculin and DNA and the absence of α-glucosidase. On the basis of these analyses, a novel species of the genus Staphylococcus is described, for which the name Staphylococcus simiae sp. nov. is proposed, with CCM 7213T (=LMG 22723T) as the type strain.
Tetrathiobacter kashmirensis gen. nov., sp. nov., a novel mesophilic, neutrophilic, tetrathionate-oxidizing, facultatively chemolithotrophic betaproteobacterium isolated from soil from a temperate orchard in Jammu and Kashmir, India
Authors: Ghosh Wriddhiman , Bagchi Angshuman , Mandal Sukhendu , Dam Bomba , Roy Pradosh
Published: September 2005

Twelve chemolithotrophic strains were isolated from temperate orchard soil on reduced sulfur compounds as energy and electron sources and characterized on the basis of their physiological properties and ability to oxidize various reduced sulfur compounds. The new isolates could oxidize tetrathionate as well as thiosulfate, and oxidation of the latter involved conversion of thiosulfate to tetrathionate followed by its accumulation and eventual oxidation to sulfate, manifested in the production of acid. The mesophilic, neutrophilic, Gram-negative and coccoid bacteria had a respiratory metabolism. Physiologically and biochemically, all the strains were more or less similar, differing only in their growth rates and ability to utilize a few carbon compounds as single heterotrophic substrates. 16S rRNA gene sequence analysis was performed with five representative strains, which revealed a high degree of similarity (⩾99 %) among them and placed the cluster in the ‘Betaproteobacteria’. The strains showed low levels (93·5–95·3 %) of 16S rRNA gene sequence similarity toPigmentiphaga kullae,Achromobacter xylosoxidans,Pelistega europaeaand species belonging to the generaAlcaligenes,TaylorellaandBordetella. The taxonomic coherence of the new isolates was confirmed by DNA–DNA hybridization. On the basis of their uniformly low 16S rRNA gene sequence similarities to species of all the closest genera, unique fatty acid profile, distinct G+C content (54–55·2 mol%) and phenotypic characteristics that include efficient chemolithotrophic utilization of tetrathionate, the organisms were classified in a new genus,Tetrathiobactergen. nov. In the absence of any significant discriminatory phenotypic or genotypic characteristics, all the new isolates are considered to constitute a single species, for which the nameTetrathiobacter kashmirensissp. nov. (type strain WT001T=LMG 22695T=MTCC 7002T) is proposed.
Marinococcus halotolerans sp. nov., isolated from Qinghai, north-west China
Authors: Li Wen-Jun , Schumann Peter , Zhang Yu-Qin , Chen Guo-Zhong , Tian Xin-Peng , Xu Li-Hua , Stackebrandt Erko , Jiang Cheng-Lin
Published: September 2005

An aerobic bacterium was isolated from saline soil located in Qinghai, north-west China. The bacterium, designated YIM 70157T, was investigated using a polyphasic taxonomic approach. The Gram reaction of the organism was positive. Comparative 16S rRNA gene sequence analysis demonstrated the isolate to be a member of the genus Marinococcus, the closest phylogenetic neighbour of the unknown bacterium being Marinococcus halophilus DSM 20408T with a similarity of 99·4 %. The peptidoglycan type of YIM 70157T was A1γ, with meso-diaminopimelic acid as diagnostic diamino acid. The major fatty acids were ai-C15 : 0, ai-C17 : 0 and i-C16 : 0. The menaquinones were MK-7 and MK-6. The phospholipids were diphosphatidylglycerol and phosphatidylinositol. The G+C content of total DNA was 48·5 mol%. On the basis of phylogenetic and phenotypic evidence and DNA–DNA hybridization data, this isolate should be classified as a novel species of Marinococcus, for which the name Marinococcus halotolerans sp. nov. is proposed. The type strain is YIM 70157T (=DSM 16375T=KCTC 19045T).
Thalassobacter stenotrophicus Macián et al. 2005 is a later synonym of Jannaschia cystaugens Adachi et al. 2004, with emended description of the genus Thalassobacter
Authors: Pujalte M. J. , Macián M. C. , Arahal D. R. , Garay E.
Published: September 2005

The type strains of Jannaschia cystaugens (LMG 22015T) and Thalassobacter stenotrophicus (CECT 5294T) were analysed by means of genomic DNA–DNA hybridization, comparison of 16S rRNA gene sequences and phenotypic properties determined under the same methodological conditions. J. cystaugens LMG 22015T showed DNA–DNA relatedness levels of 72 % when hybridized with the genomic DNA of T. stenotrophicus CECT 5294T. Sequence comparisons revealed that the 16S rRNA genes of the two strains had a similarity of 99·8 %. The cellular fatty acid and polar lipid compositions of the two strains and their DNA mol% G+C contents were almost identical. Bacteriochlorophyll a (Bchl a) and polyhydroxybutyrate were produced by both strains under the same culture conditions. Their closest phylogenetic neighbours were Jannaschia helgolandensis and Jannaschia rubra; however, the low sequence similarity values (95·7–95·9 %) and several important differences in phenotypic traits (ionic requirements, Bchl a production and polar lipids) support the distinction between the genera Thalassobacter and Jannaschia. Thus, we propose the unification of J. cystaugens (LMG 22015T) and T. stenotrophicus (CECT 5294T) as Thalassobacter stenotrophicus (type strain, CECT 5294T=DSM 16310T). An emended description of the genus Thalassobacter is also presented.
Roseivirga echinicomitans sp. nov., a novel marine bacterium isolated from the sea urchin Strongylocentrotus intermedius, and emended description of the genus Roseivirga
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Lysenko Anatoly M. , Park Myung Soo , Mikhailov Valery V. , Bae Kyung Sook , Park Ho Yong
Published: September 2005

A novel strictly aerobic, heterotrophic, pink-pigmented, non-motile, Gram-negative, oxidase-, catalase-, β-galactosidase- and alkaline phosphatase-positive marine bacterium, designated strain KMM 6058T, was isolated from the sea urchin Strongylocentrotus intermedius and studied using a polyphasic taxonomic approach. The G+C content of the DNA of the isolate was 41·3 mol%. The predominant fatty acids were i15 : 1, i15 : 0, a15 : 0 and i17 : 0 3-OH. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KMM 6058T formed a monophyletic clade with Roseivirga ehrenbergii, with 99 % similarity. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the novel bacterium should be assigned to the genus Roseivirga as Roseivirga echinicomitans sp. nov. The type strain is KMM 6058T (=KCTC 12370T=LMG 22587T).
Agromyces subbeticus sp. nov., isolated from a cave in southern Spain
Authors: Jurado Valme , Groth Ingrid , Gonzalez Juan M. , Laiz Leonila , Saiz-Jimenez Cesareo
Published: September 2005

An actinomycete, strain Z33T, was isolated from a cyanobacterial biofilm in the Cave of Bats, near Zuheros (Cordoba, southern Spain). 16S rRNA gene sequence analysis showed that strain Z33T formed a distinct phyletic line within the genus Agromyces. This isolate could be readily distinguished from representatives of all recognized Agromyces species on the basis of a broad range of phenotypic characteristics and DNA–DNA relatedness data. Genotypic and phenotypic properties indicate that strain Z33T represents a novel species, for which the name Agromyces subbeticus sp. nov. is proposed. The type strain is Z33T (=HKI 0340T=DSM 16689T=NCIMB 14025T).
The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov.
Authors: Lee Kyung-Bum , Liu Chi-Te , Anzai Yojiro , Kim Hongik , Aono Toshihiro , Oyaizu Hiroshi
Published: September 2005

Phylogenetic analysis of the class ‘Alphaproteobacteria’, including physiologically diverse species, was conducted by using small-subunit rRNA gene sequences. The 16S rRNA gene sequences of 261 species in the class ‘Alphaproteobacteria’ were obtained from GenBank/EMBL/DDBJ for constructing a phylogenetic tree by using maximum-likelihood analysis. In the resulting tree, members of the class ‘Alphaproteobacteria’ were subdivided into five major clusters, which were compared with the taxonomic outline ofBergey's Manual of Systematic Biologyand thearbtree. Based on this phylogenetic tree, three novel families are proposed:Hyphomonadaceaefam. nov. to accommodate the bacterial generaHyphomonas,Hirschia,MaricaulisandOceanicaulis,Xanthobacteraceaefam. nov. to include the generaXanthobacter,Azorhizobium,Ancylobacter,LabrysandStarkeya, andErythrobacteraceaefam. nov. to accommodate the generaErythrobacter,PorphyrobacterandErythromicrobium. The phylogenetic tree of 16S rRNA gene sequences established in this study may provide a sound basis for future taxonomic reconstruction of the class ‘Alphaproteobacteria’.
Kazachstania aquatica sp. nov. and Kazachstania solicola sp. nov., novel ascomycetous yeast species
Authors: Wu Zuo-Wei , Bai Feng-Yan
Published: September 2005

The unidentified strains AS 2.0706T, preserved in the China General Microbiological Culture Collection Center (CGMCC), Academia Sinica, Beijing, China, and CBS 6904T, preserved in the Centraalbureau voor Schimmelcultures (CBS), Utrecht, The Netherlands, were shown to represent two novel ascomycetous yeast species of the genus Kazachstania by 18S rDNA, internal transcribed spacer (ITS) region (including 5·8S rDNA) and 26S rDNA D1/D2 domain sequence analysis and electrophoretic karyotype comparison. The names Kazachstania aquatica sp. nov. and Kazachstania solicola sp. nov. are proposed for strains AS 2.0706T and CBS 6904T, respectively. Phylogenetically, the two novel species are closely related to Kazachstania aerobia, Kazachstania servazzii and Kazachstania unispora.
Microbacterium xylanilyticum sp. nov., a xylan-degrading bacterium isolated from a biofilm
Authors: Kim Kwang Kyu , Park Hye Yoon , Park Wooshin , Kim In S. , Lee Sung-Taik
Published: September 2005

A novel xylan-degrading bacterium, S3-ET, was isolated from the biofilm of a membrane bioreactor. The cells of this strain were Gram-positive, non-motile, non-spore-forming rods, produced primary branches and formed yellow colonies on nutrient agar. The strain had chemotaxonomic markers that were consistent with classification in the genusMicrobacterium, i.e. MK-12, MK-11 and MK-13 as the major menaquinones, predominant iso- and anteiso-branched cellular fatty acids, glucose and galactose as the cell-wall sugars, peptidoglycan-type B2βwith glycolyl residues and a DNA G+C content of 69·7 mol%. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that strain S3-ETis most similar toMicrobacterium hominisIFO 15708TandMicrobacterium foliorumDSM 12966T(97·6 and 97·4 % sequence similarity, respectively), and that it forms a separate lineage withM. hominisin the genusMicrobacterium. DNA–DNA hybridization results and phenotypic properties showed that strain S3-ETcould be distinguished from all knownMicrobacteriumspecies and represented a novel species, for which the nameMicrobacterium xylanilyticumsp. nov. is proposed; the type strain is S3-ET(=DSM 16914T=KCTC 19079T).
Gaetbulibacter saemankumensis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat sediment in Korea
Authors: Jung Seo-Youn , Kang So-Jung , Lee Mi-Hwa , Lee Soo-Young , Oh Tae-Kwang , Yoon Jung-Hoon
Published: September 2005

Three Gram-negative, yellow-pigmented, rod-shaped bacterial strains, SMK-12T, SMK-36 and SMK-45, were isolated from a tidal flat sediment of the Yellow Sea in Korea, and their taxonomic positions were investigated by a polyphasic approach. The three strains grew optimally at 25–30 °C and in the presence of 2–3 % (w/v) NaCl. They contained MK-6 as the predominant menaquinone. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1, anteiso-C15 : 0, iso-C15 : 0 3-OH and C16 : 1
ω7c and/or iso-C15 : 0 2-OH. The DNA G+C contents of the three strains were 34·7–34·9 mol%. The phylogenetic tree based on 16S rRNA gene sequences revealed that the three strains form one distinct evolutionary lineage supported by a bootstrap value of 100 % within the family Flavobacteriaceae. The three strains exhibited 16S rRNA gene sequence similarity levels of 93·8–94·9 % to the nearest phylogenetic neighbours, the genera Algibacter, Bizionia and Formosa. On the basis of differences in phenotypic characteristics and phylogenetic distinctiveness, strains SMK-12T, SMK-36 and SMK-45 were classified in a novel genus and species, for which the name Gaetbulibacter saemankumensis gen. nov., sp. nov. is proposed. The type strain for the novel species is SMK-12T (=KCTC 12379T=DSM 17032T).
Enterococcus canintestini sp. nov., from faecal samples of healthy dogs
Authors: Naser Sabri M. , Vancanneyt Marc , De Graef Evelyne , Devriese Luc A. , Snauwaert Cindy , Lefebvre Karen , Hoste Bart , Švec Pavel , Decostere Annemie , Haesebrouck Freddy , Swings Jean
Published: September 2005

The taxonomic position of strain LMG 13590T, originally isolated from dog faeces and classified as Enterococcus dispar in the BCCM/LMG Bacteria Catalogue, was reinvestigated. This strain and 12 recent isolates from faecal samples of healthy dogs occupied a clearly separate position when investigated with multilocus sequence analysis (MLSA) of the genes encoding the alpha subunit of ATP synthase (atpA), RNA polymerase alpha subunit (rpoA) and phenylalanyl-tRNA synthase alpha subunit (pheS). The 16S rRNA gene sequence of one representative strain showed highest similarities of 98–99 % with E. dispar LMG 13521T, Enterococcus canis LMG 12316T and Enterococcus asini LMG 18727T. A further polyphasic taxonomic study based on whole-cell protein fingerprinting, DNA–DNA hybridization and biochemical features demonstrated that the 13 enterococcal dog faecal strains represent a single, novel Enterococcus species for which the name Enterococcus canintestini sp. nov. is proposed. The type strain is LMG 13590T (=CCM 7285T).
Structural basis for the enhancement of eIF4A helicase activity by eIF4G
Authors: Oberer Monika , Marintchev Assen , Wagner Gerhard
Published: September 2005

The eukaryotic translation initiation factors 4A (eIF4A) and 4G (eIF4G) are crucial for the assembly of the translationally active ribosome. Together with eIF4E, they form the eIF4F complex, which recruits the 40S subunit to the 5′ cap of mRNA. The two-domain RNA helicase eIF4A is a very weak helicase by itself, but the activity is enhanced upon interaction with the scaffolding protein eIF4G. Here we show that, albeit both eIF4A domains play a role in binding the middle domain of eIF4G (eIF4G-m, amino acids 745-1003), the main interaction surface is located on the C-terminal domain. We use NMR spectroscopy to define the binding site and find that the contact surface is adjacent to the RNA-, ATP-, and eIF4A-NTD-interacting regions. Mutations of interface residues abrogated binding, confirmed the interface, and showed that the N-terminal end of eIF4G-m interacts with the C-terminal domain of eIF4A. The data suggest that eIF4G-m forms a soft clamp to stabilize the closed interdomain orientation of eIF4A. This model can explain the cooperativity between all binding partners of eIF4A (eIF4G, RNA, ATP) and stimulation of eIF4A activity in the eIF4F complex.
Hox genes specify vertebral types in the presomitic mesoderm
Authors: Carapuço Marta , Nóvoa Ana , Bobola Nicoletta , Mallo Moisés
Published: September 2005

We show here that expression of Hoxa10 in the presomitic mesoderm is sufficient to confer a Hox group 10 patterning program to the somite, producing vertebrae without ribs, an effect not achieved when Hoxa10 is expressed in the somites. In addition, Hox group 11-dependent vertebral sacralization requires Hoxa11 expression in the presomitic mesoderm, while their caudal differentiation requires that Hoxa11 is expressed in the somites. Therefore, Hox gene patterning activity is different in the somites and presomitic mesoderm, the latter being very prominent for Hox gene-mediated patterning of the axial skeleton. This is further supported by our finding that inactivation of Gbx2, a homeobox-containing gene expressed in the presomitic mesoderm but not in the somites, produced Hox-like phenotypes in the axial skeleton without affecting Hox gene expression.
Ribosomal protein S6 phosphorylation is a determinant of cell size and glucose homeostasis
Authors: Ruvinsky Igor , Sharon Nitzan , Lerer Tal , Cohen Hannah , Stolovich-Rain Miri , Nir Tomer , Dor Yuval , Zisman Philip , Meyuhas Oded
Published: September 2005

The regulated phosphorylation of ribosomal protein (rp) S6 has attracted much attention since its discovery in 1974, yet its physiological role has remained obscure. To directly address this issue, we have established viable and fertile knock-in mice, whose rpS6 contains alanine substitutions at all five phosphorylatable serine residues (rpS6P-/-). Here we show that contrary to the widely accepted model, this mutation does not affect the translational control of TOP mRNAs. rpS6P-/-mouse embryo fibroblasts (MEFs) display an increased rate of protein synthesis and accelerated cell division, and they are significantly smaller than rpS6P+/+MEFs. This small size reflects a growth defect, rather than a by-product of their faster cell division. Moreover, the size of rpS6P-/-MEFs, unlike wild-type MEFs, is not further decreased upon rapamycin treatment, implying that the rpS6 is a critical downstream effector of mTOR in regulation of cell size. The small cell phenotype is not confined to embryonal cells, as it also selectively characterizes pancreatic β-cells in adult rpS6P-/-mice. These mice suffer from diminished levels of pancreatic insulin, hypoinsulinemia, and impaired glucose tolerance.
Whole-Genome Validation of High-Information-Content Fingerprinting
Authors: Nelson William M. , Bharti Arvind K. , Butler Ed , Wei Fusheng , Fuks Galina , Kim HyeRan , Wing Rod A. , Messing Joachim , Soderlund Carol
Published: September 2005

Fluorescent-based high-information-content fingerprinting (HICF) techniques have recently been developed for physical mapping. These techniques make use of automated capillary DNA sequencing instruments to enable both high-resolution and high-throughput fingerprinting. In this article, we report the construction of a whole-genome HICF FPC map for maize (Zea mays subsp. mays cv B73), using a variant of HICF in which a type IIS restriction enzyme is used to generate the fluorescently labeled fragments. The HICF maize map was constructed from the same three maize bacterial artificial chromosome libraries as previously used for the whole-genome agarose FPC map, providing a unique opportunity for direct comparison of the agarose and HICF methods; as a result, it was found that HICF has substantially greater sensitivity in forming contigs. An improved assembly procedure is also described that uses automatic end-merging of contigs to reduce the effects of contamination and repetitive bands. Several new features in FPC v7.2 are presented, including shared-memory multiprocessing, which allows dramatically faster assemblies, and automatic end-merging, which permits more accurate assemblies. It is further shown that sequenced clones may be digested in silico and located accurately on the HICF assembly, despite size deviations that prevent the precise prediction of experimental fingerprints. Finally, repetitive bands are isolated, and their effect on the assembly is studied.
A comparison of the human papillomavirus test and Papanicolaou smear as a second screening method for women with minor cytological abnormalities
Authors: Andersson Sonia , Dillner Lena , Elfgren Kristina , Mints Miriam , Persson Maria , Rylander Eva
Published: September 2005

Background.  Of the estimated one million Papanicolaou (pap) smears performed annually in Sweden, about 4% show any degree of abnormality. Approximately, 1% of these cases contain moderate or severe atypia (high‐grade squamous intraepithelial lesions) and the rest contain low‐grade atypia. Recommendations for the management of minor abnormalities vary in various parts of Sweden. Generally, a second Pap smear is obtained 4–6 months after the first one showing low‐grade atypia. The aim of this study is to compare the sensitivity of human papilloma virus (HPV)‐DNA testing for the detection of cervical intraepithelial neoplasia (CIN) 2–3 with that of a second Pap smear in women, who had low‐grade atypia in their first Pap smear.

Methods.  Women with low‐grade atypia in the Stockholm area, detected at a population‐based cytology screening, were enrolled. A repeat Pap smear, HPV test, and colposcopically directed biopsies were obtained. For the detection of HPV, Hybrid Capture II (HC II) was used.

Results.  The HPV‐DNA test was positive in 66% of the 177 participating women. The sensitivity of the second Pap smear and HPV‐DNA test to detect CIN 2–3 was 61 (95% CI = 45–74) and 82% (95% CI = 67–91), respectively. The positive and negative predictive values of HPV testing were 27 (95% CI = 18–35) and 89% (95% CI = 80–97), respectively.

Conclusions.  In Sweden, a second Pap smear is often obtained for the follow‐up of women with low‐grade atypia. The results of our study show that compared to the second Pap smear, HPV testing with HC II is a more sensitive method for detecting high‐grade lesions.
Diclofenac pyrrolidine versus Ketoprofen for the relief of pain from episiotomy: A randomized controlled trial
Authors: Facchinetti Fabio , Luisa Casini Maria , Costabile Loredana , Malavasi Barbara , Unfer Vittorio
Published: September 2005

Background.  The treatment of pain from episiotomy or from tearing of perineal tissues during childbirth is often unapplied, although discomfort may be severe. We performed a randomized double‐blind controlled trial to compare the effectiveness and side‐effects of two analgesics in the management of postpartum perineal pain. Patient preference toward the two medications was also analyzed.

Methods.  A total of 261 women were randomly assigned to receive either Diclofenac hydroxyethyl pyrrolidine (100 mg) (n = 133) or Ketoprofen (100 mg) (n = 128), both given orally every 12 hr up to 48 hr, as necessary. Inclusion criteria were vaginal birth with episiotomy and/or a second‐ to third‐degree tear. Pain ratings were recorded before the administration of the drugs and at 1, 4, 12, and 24 hr after the first dose, according to a 10‐cm visual‐analog scale. Side‐effects and overall opinion on the two treatments were assessed at 24 hr.

Results.  Diclofenac hydroxyethyl pyrrolidine and Ketoprofen had similar analgesic properties in the first 24 hr postpartum [mean pain rating 3.1 ± 1.8 and 3.4 ± 2.0, mean number of doses in 24 hr 1.4 ± 1.4 and 1.3 ± 1.5, and proportion of treatment failures 12.8% (17/133) and 16.4% (21/128), respectively]. Significantly fewer subjects in the Diclofenac hydroxyethyl pyrrolidine group than in the Ketoprofen group experienced side‐effects (6.8% versus 15.6%; p = 0.038) with an odd risk = 0.39(95% C.I. 0.16–0.95). There were no significant differences in overall patient satisfaction between the two groups.

Conclusions.  No main differences were found concerning the relief of pain between the two treatments. Diclofenac hydroxyethyl pyrrolidine may be the preferred choice because it is associated with less adverse reactions, together with a faster action in the relief of pain.
Swedish teenager perceptions of teenage pregnancy, abortion, sexual behavior, and contraceptive habits – a focus group study among 17‐year‐old female high‐school students
Authors: Ekstrand Maria , Larsson Margareta , Von Essen Louise , Tydén Tanja
Published: September 2005

Background.  Sweden has the highest abortion numbers among the Nordic countries. Since 1995, the abortion rate among teenagers has increased by nearly 50%. We therefore undertook a study where the overall aim was to gain a deeper understanding on which factors female teenagers believe may explain the increasing numbers of teenage abortions. Teenagers' perceptions of teenage pregnancy, abortion, sexual behavior, and contraceptive habits were investigated.

Methods.  Six focus group interviews with 17‐year‐old Swedish girls were conducted. The interviews were tape‐recorded, transcribed verbatim, and analyzed by manifest content analysis.

Results.  Negative attitudes toward teenage pregnancy and supportive attitudes toward abortion were expressed. Risk‐taking behaviors such as negligence in contraceptive use and intercourse under the influence of alcohol were suggested as main reasons behind the increasing numbers of abortions among Swedish teenagers. The contemporary, sexualized, media picture was believed to influence adolescents' sexual behavior, and liberal attitudes toward casual sex were expressed. Girls were perceived as more obliged than boys in taking responsibility for contraceptive compliance and avoidance of pregnancy. The apprehension that hormonal contraceptives cause negative side‐effects was widely spread, and the participants were found to have a somewhat limited knowledge of abortion. The majority were unsatisfied with the quality of sexual education provided by the schools.

Conclusion.  Possible reasons for increased abortion numbers among teenagers in Sweden could be liberal attitudes toward casual sex in combination with negligence in contraceptive use, use of alcohol followed by sexual risk‐taking, fear of hormonal contraceptives, and a deterioration of sexual education in the schools.
Significance of HPV tests on women with cervical smears showing ASCUS
Authors: De Lang Anna , Wikström Ingrid , Wilander Erik
Published: September 2005

Background.  The relationship between the human papillomavirus (HPV) tests and the cytological findings was evaluated.

Methods.  Totally, 161 women participating in the organized cytological screening in the County of Uppsala and showing atypical squamous cells of uncertain significance (ASCUS) in their cervical smears were identified during 2002 and 2003. Those women were invited for a repeated examination about 3 months later. At that occasion, a smear sample was collected and used for cytological examination and a concomitant HPV test. Oncogenic HPV was identified by polymerase chain reaction and HPV deoxyribonucleoside acid (DNA) sequence analysis in 50 cases and by Hybrid Capture II in 111 cases.

Results.  Women with an ASCUS diagnosis showed a normal cytology and a negative HPV test in 30% of the cases, abnormal cytology and a positive HPV test in 32% of the cases; in 26% of the women, the HPV test was positive, whereas cytology was normal; and in 11% of the women, the HPV test was negative, whereas cytology was abnormal (ASCUS or more).

Conclusion.  The results show that HPV tests identify a larger group of women at risk to develop cervical cancer in comparison with cytological examination. As the HPV tests have a higher sensitivity than the cytological screening, it is suggested that an HPV test in conjunction with a diagnosis of ASCUS can be employed to more efficiently select women, to whom further follow up is recommended.
Trends in the incidence and mortality of ovarian cancer in Denmark 1978–2002. Comparison with other Nordic countries
Authors: Kjærbye‐Thygesen Anette , Huusom Lene Drasbek , Frederiksen Kirsten , Kjær Susanne Krüger
Published: September 2005

Background.  The Nordic countries are well‐known high‐incidence areas of ovarian cancer, but even within the Nordic countries, differences exist.

Methods.  Focus in this descriptive epidemiological study is to assess developments in incidence and mortality of ovarian cancer in Denmark 1978–2002 and to make a comparison with the development in the other Nordic countries. The results are based on data from the nationwide Danish Cancer Registry as well as the other Nordic Cancer Registries.

Results.  A total of 14 325 cases of ovarian cancer were registered from 1978 to 2002 in Denmark. In this period, the age‐standardized incidence decreased slightly from 14.3 (1978–1982) to 13.3 per 100 000 woman‐years (1998–2002). The histology‐specific time trends showed a tendency towards more specified histological diagnoses. Iceland had the highest age‐adjusted ovarian cancer incidence in the Nordic countries, whereas Denmark had the highest mortality rate. In the entire period, the Danish mortality rate declined from 10.8 (1978–1982) to 9.0 per 100 000 woman‐years (1998–1999). Only 19% of ovarian cancers in Denmark from 1978 to 2002 were localized at the time of diagnosis, while 30% had distant metastases. Older women were more likely to have advanced disease at diagnosis. The Danish distribution of stage at diagnosis seems less favorable compared to results from other countries.

Conclusions.  The Danish incidence of ovarian cancer seemed to decrease slightly from 1978 to 2002. Even though the mortality rate of ovarian cancer also declined, Denmark had the highest mortality rate of ovarian cancer in the world. Part of it may be explained by a less‐favorable distribution of stage at diagnosis.
Psychosocial Stress and Cardiovascular Risk: What is the Role of Daily Experience?
Authors: Kamarck Thomas W. , Schwartz Joseph E. , Shiffman Saul , Muldoon Matthew F. , Sutton‐Tyrrell Kim , Janicki Denise L.
Published: September 2005

Abstract
We describe an ecological momentary assessment (EMA) protocol designed to measure daily life experiences along several psychosocial dimensions (Social Conflict, Task Demand, Decisional Control, Negative Affect, and Arousal) hypothesized to be relevant for cardiovascular disease risk. In a large community sample, these assessments have been administered in conjunction with ambulatory blood pressure (ABP) monitoring and measures of subclinical cardiovascular disease. Several results have emerged that support the promise of this approach. First of all, each of these dimensions of experience appears to be a trigger for cardiovascular activation, with movement on each scale being associated with significant within‐person changes in heart rate and blood pressure in the natural environment. Second, there appear to be individual differences in physiological responsiveness to these dimensions of daily experience, with such differences being associated in some cases with laboratory‐based assessments of cardiovascular reactivity, as might be expected. Third, EMA ratings are associated in several instances with (between‐person) stable individual differences in ABP readings. And finally, we have found that some of the characteristics defined by our EMA ratings are related to measures of subclinical atherosclerosis. Such effects appear to be mediated, in part, by ABP. The advantages of using EMA measures for capturing the effects of psychosocial stressors are highlighted by comparing the predictive validity of these daily life assessments to traditional global self‐reports. We conclude by describing future plans for use of this type of assessment protocol for helping us to characterize psychosocial characteristics relevant to cardiovascular disease risk.

Personality and social processes during daily living may have an important impact not only on psychological functioning but also on physical health and disease. In this article we review our recent work involving the assessment of daily experience as a means of better understanding the role of psychosocial stress in cardiovascular disease risk. First, we outline the rationale for our interest in daily experience sampling for examining these processes, and we describe the methods we have adopted for this purpose. Next, we review findings from a recent study in which we have used these approaches to examine the role of psychosocial stress on ABP and atherosclerosis in a community‐dwelling sample. We compare our approach to more traditional (global self‐report and laboratory‐observation) methods for examining these relationships in humans, and we discuss potential future directions for use of daily experience sampling in studies of health and behavior.
Oxidative stress in chronic venous leg ulcers
Authors: Wlaschek Meinhard , Scharffetter‐Kochanek Karin
Published: September 2005

Venous leg ulcers are common and cause considerable morbidity in the population. As healing may be slow or may never be achieved, ulcers create persistent and substantial demands on clinical resources. Great efforts have been made to accelerate tissue repair in chronic venous leg ulcers with limited success. This may at least be partly due to the limited knowledge on the microenvironment of chronic wounds. In fact, the tremendous impact of the microenvironmental conditions on the outcome of wound healing has increasingly become apparent. Oxidative stress as a consequence of an imbalance in the prooxidant‐antioxidant homeostasis in chronic wounds is thought to drive a deleterious sequence of events finally resulting in the nonhealing state. The majority of reactive oxygen species are most likely released by neutrophils and macrophages and to an unknown extent from resident fibroblasts and endothelial cells. As the inflammatory phase does not resolve in chronic wounds, the load of reactive oxygen species persists over a long period of time with subsequent continuous damage and perpetuation of the inflammation. In this article, we will critically discuss recent findings that support the role of oxidative stress in the pathophysiology of nonhealing chronic venous leg ulcers.
Modeling the economic losses from pressure ulcers among hospitalized patients in Australia
Authors: Graves Nicholas , Birrell Frances A. , Whitby Michael
Published: September 2005

The objective of this study was to predict the number of cases of pressure ulcer, the bed days lost, and the economic value of these losses at Australian public hospitals. All adults (≥ 18 years of age) with a minimum stay of 1 night and discharged from selected clinical units from all Australian public hospitals in 2001–02 were included in the study. The main outcome measures were the number of cases of pressure ulcer, bed days lost to pressure ulcer, and economic value of these losses. We predict a median of 95,695 cases of pressure ulcer with a median of 398,432 bed days lost, incurring median opportunity costs of AU$285 M. The number of cases, and so costs, were greatest in New South Wales and lowest in Australian Capitol Territory. We conclude that pressure ulcers represent a serious clinical and economic problem for a resource‐constrained public hospital system. The most cost‐effective, risk‐reducing interventions should be pursued up to a point where the marginal benefit of prevention is equalized with marginal cost. By preventing pressure ulcers, public hospitals can improve efficiency and the quality of the patient's experience and health outcome.
Expression of matrix metalloproteinases (MMP‐2 and ‐9) and tissue inhibitors of metalloproteinases (TIMP‐1 and ‐2) in acute myelogenous leukaemia blasts: comparison with normal bone marrow cells
Authors: Janowska‐Wieczorek Anna , Marquez Leah , Matsuzaki Akinobu , Hashmi Haroon , Larratt Lori , Boshkov Lynn , Turner A. , Zhang Melissa , Edwards Dylan , Kossakowska Anna
Published: September 2005

We compared the expression of matrix metalloproteinases (MMP‐2 and MMP‐9) and tissue inhibitors of metalloproteinases (TIMP‐1 and TIMP‐2) in bone marrow acute myelogenous leukaemia (AML) blasts and leukaemic cell lines (HEL, HL‐60, K‐562 and KG‐1) with their expression in normal bone marrow cells. All AML samples and leukaemic cell lines tested expressed MMP‐9 and/or MMP‐2 mRNA and, accordingly, these gelatinases were secreted into media. Moreover, TIMP‐1 and TIMP‐2 mRNA and secreted proteins were demonstrated in all the AML samples. Although all the leukaemic cell lines expressed TIMP‐1, the HL‐60 cells also expressed TIMP‐2. In contrast, normal steady‐state bone marrow immature progenitor cells (CD34+ cells) did not express or secrete either MMP‐2 or MMP‐9, but more mature mononuclear cells from normal bone marrow expressed and secreted MMP‐9. Also, normal bone marrow CD34+ cells and mononuclear cells expressed TIMP‐1 and TIMP‐2 mRNA, but these proteins were not detectable by reverse zymography. Furthermore, whereas bone marrow fibroblasts and endothelial cells secreted only latent MMP‐2, the activated form of this enzyme was found in media conditioned by cells obtained from long‐term cultures of normal and AML bone marrow adherent layers. Our finding of up‐regulated production of gelatinases, TIMP‐1 and TIMP‐2 by leukaemic cells suggests that these proteins may be implicated in the invasive phenotype of AML.
Two patients with novel BCR/ABL fusion transcripts (e8/a2 and e13/a2) resulting from translocation breakpoints within BCR exons
Authors: How G. F. , Lim L. C. , Kulkarni S. , Tan L. T. , Tan P. , Cross N. C. P.
Published: September 2005

We have identified novel BCR‐ABL mRNA fusions by RT‐PCR in two patients with Philadelphia (Ph) chromosome positive leukaemia. Sequencing revealed in‐frame fusions consisting of part of BCR exon e8 spliced to ABL exon a2 in one patient and part of BCR exon e13 spliced to ABL exon a2 in the other. The breaks within BCR exons e8 and e13 did not conform to consensus splice sites, suggesting that the aberrant fusion mRNAs may have arisen as a result of translocation breakpoints at these sites. This was confirmed by genomic DNA bubble PCR for the second patient. These data show that BCR‐ABL translocation breakpoints can occasionally occur within coding exons.
Developing services for the carers of young adults with early‐onset psychosis – listening to their experiences and needs
Authors: SIN J. , MOONE N. , WELLMAN N.
Published: September 2005

The care‐giving experience of carers of young adults with early onset psychosis is relatively unexplored. New carers are less likely to be engaged with local services for carers and families, than those more established in their caring role. Understanding the experience of these carers provides some valuable insight into the value of caring and in guiding service development. This paper reports on a study designed to explore carers’ experiences of caring for a young adult diagnosed with a first psychotic episode and their needs in relation to the development of an early intervention for psychosis service. A phenomenological approach was used. Eleven carers were given a semi‐structured interview in their own homes. All of the carers in the study had a son with early onset psychosis. The outcome revealed that all carers were providing a comprehensive range of practical, emotional and financial support for their son including initiating and sustaining engagement between them and local mental health services. Many carers were felt to be invisible and silent partners in care and felt under‐valued by mental health services.
Analysis of Xenorhabdus nematophila metabolic mutants yields insight into stages of Steinernema carpocapsae nematode intestinal colonization
Authors: Martens Eric C. , Russell Frances M. , Goodrich‐Blair Heidi
Published: September 2005

Xenorhabdus nematophila colonizes the intestinal tract of infective‐juvenile (IJ) stage Steinernema carpocapsae nematodes. During colonization, X. nematophila multiplies within the lumen of a discrete region of the IJ intestine termed the vesicle. To begin to understand bacterial nutritional requirements during multiplication in the IJ vesicle, we analysed the colonization behaviour of several X. nematophila metabolic mutants, including amino acid and vitamin auxotrophs. X. nematophila mutants defective for para‐aminobenzoate, pyridoxine or l‐threonine biosynthesis exhibit substantially decreased colonization of IJs (0.1–50% of wild‐type colonization). Analysis of gfp‐labelled variants revealed that those mutant cells that can colonize the IJ vesicle differ noticeably from wild‐type X. nematophila. One aberrant colonization phenotype exhibited by the metabolic mutants tested, but not wild‐type X. nematophila, is a spherical shape indicative of apparently non‐viable X. nematophila cells within the vesicle. Because these spherical cells appear to have initiated colonization but failed to proliferate, we term this type of colonization ‘abortive’. In a portion of IJs grown on para‐aminobenzoate auxotrophs, X. nematophila does not exhibit abortive colonization but rather reduced growth and filamentous cell morphology. Several mutants with defects in other amino acid, vitamin and nutrient metabolism pathways colonize IJs to wild‐type levels suggesting that the IJ vesicle is replete with respect to a number of nutrients.
Determinants of nitric oxide steady‐state levels during anaerobic respiration by Neisseria gonorrhoeae
Authors: Cardinale Jean A. , Clark Virginia L.
Published: September 2005

Nitric oxide (NO) is an important host defence molecule that varies its immune stimulatory effects depending on the concentrations at which it is produced, with low concentrations (< 1 µM) promoting an anti‐inflammatory host response while higher concentrations (>1 µM) lead to inflammatory responses. Neisseria gonorrhoeae grows anaerobically by anaerobic respiration using nitrite reductase (Nir) to convert nitrite to NO and nitric oxide reductase (Nor) to convert NO to nitrous oxide. As N. gonorrhoeae can both produce and degrade NO, we have begun a study of NO metabolism in this bacterium to understand how gonococcal manipulation of NO concentration may influence the inflammatory response during infection. N. gonorrhoeae has an apparent Nir Km of 33 µM nitrite and an apparent Nor Km of 1.2 µM NO. The maximum specific activities for Nir and Nor were 135 nmoles nitrite reduced per minute per OD600 (pH 6.7) and 270 nmoles NO reduced per minute per OD600 (pH 7.5) respectively. N. gonorrhoeae established a steady‐state concentration of NO after nitrite addition that was dependent on the nitrite concentration until saturation at 1 mM nitrite. The NO steady‐state level decreased as pH increased, and the ratio of activities of Nir and Nor correlated to the NO steady‐state level. When the NO donor DETA/NO was used to simulate host NO production, N. gonorrhoeae also established a NO steady‐state level. The concentration of NO at steady state was found to be a function of the concentration of NO generated by DETA/NO, with N. gonorrhoeae reducing the NO from proinflammatory (>1 µM) to anti‐inflammatory (∼100 nM) concentrations. The implications of the ability of N. gonorrhoeae to maintain an anti‐inflammatory NO concentration is discussed in relation to asymptomatic infection in women.
Turnip rape and oilseed rape are new potential food allergens in children with atopic dermatitis
Authors: Poikonen S. , Puumalainen T. J. , Kautiainen H. , Burri P. , Palosuo T. , Reunala T. , Turjanmaa K.
Published: September 2005

Background:  When skin prick testing (SPT) young children with atopic dermatitis (AD) for suspected food allergy, we frequently found positive reactions with turnip rape (Brassica rapa) and oilseed rape (Brassica napus). We performed food challenge to examine whether these children react clinically to turnip rape.

Methods:  A total of 1887 children were screened with SPTs for sensitization to turnip rape and oilseed rape. Twenty‐eight children with clearly positive SPT (≥5 mm) were first subjected to labial challenge with turnip rape seeds followed, if negative, by open oral challenge for up to 7 days. Twenty‐five children with AD but negative SPT to turnip rape and oilseed rape served as controls.

Results:  Two‐hundred and six (10.9%) children had positive SPT to turnip rape and/or oilseed rape. Twenty‐five (89%) of 28 children showed a positive challenge reaction to turnip rape. Seventeen reacted with labial whealing, and eight in oral challenge with facial urticaria, flare‐up of AD or abdominal symptoms. All 25 control children remained negative in the labial challenge.

Conclusions:  Turnip rape and oilseed rape seem to be new important food allergens in young children with AD. The modes of exposure to these allergens and the possible routes of sensitization remain to be established.