bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Determinants of PI(4,5)P2 and PI(3,4,5)P3 Regulation of the Epithelial Na+ Channel
Authors: Pochynyuk Oleh , Tong Qiusheng , Medina Jorge , Vandewalle Alain , Staruschenko Alexander , Bugaj Vladislav , Stockand James D.
Published: September 2007

Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) are physiologically important second messengers. These molecules bind effector proteins to modulate activity. Several types of ion channels, including the epithelial Na+ channel (ENaC), are phosphoinositide effectors capable of directly interacting with these signaling molecules. Little, however, is known of the regions within ENaC and other ion channels important to phosphoinositide binding and modulation. Moreover, the molecular mechanism of this regulation, in many instances, remains obscure. Here, we investigate modulation of ENaC by PI(3,4,5)P3 and PI(4,5)P2 to begin identifying the molecular determinants of this regulation. We identify intracellular regions near the inner membrane interface just following the second transmembrane domains in β- and γ- but not α-ENaC as necessary for PI(3,4,5)P2 but not PI(4,5)P2 modulation. Charge neutralization of conserved basic amino acids within these regions demonstrated that these polar residues are critical to phosphoinositide regulation. Single channel analysis, moreover, reveals that the regions just following the second transmembrane domains in β- and γ-ENaC are critical to PI(3,4,5)P3 augmentation of ENaC open probability, thus, defining mechanism. Unexpectedly, intracellular domains within the extreme N terminus of β- and γ-ENaC were identified as being critical to down-regulation of ENaC activity and Po in response to depletion of membrane PI(4,5)P2. These regions of the channel played no identifiable role in a PI(3,4,5)P3 response. Again, conserved positive-charged residues within these domains were particularly important, being necessary for exogenous PI(4,5)P2 to increase open probability. We conclude that β and γ subunits bestow phosphoinositide sensitivity to ENaC with distinct regions of the channel being critical to regulation by PI(3,4,5)P3 and PI(4,5)P2. This argues that these phosphoinositides occupy distinct ligand-binding sites within ENaC to modulate open probability.
Uniform spaces and weak slice spaces
Authors: Buckley Stephen , Herron David
Published: September 2007

We characterize uniform spaces in terms of a slice condition. We also establish the Gehring–Osgood–Väisälä theorem for uniformity in the metric space context.
New opportunities and emerging themes of research in microwave spectroscopy
Authors: Walker Nicholas R
Published: September 2007

It is easy to set a frisbee spinning but hard to flip a javelin end-over-end. The properties of a rotating body are determined by its moment of inertia. Changes in the energy associated with the rotation of a single molecule are incremental, or quantized, in contrast with the everyday examples of the frisbee and the javelin. Only photons with energies that correspond to specific discrete frequencies of electromagnetic radiation can be absorbed or emitted to cause transitions between different rotational energy levels. Photons that cause rotational transitions generally have microwave or millimetre-wave frequencies. Microwave spectroscopy thus provides a basis for exploring molecular structure through studies of molecular rotation. The first experiments involving microwave spectroscopy exploited technology developed for radio detection and ranging during the Second World War. Microwave spectroscopy is now being applied to study chemical reactions significant in atmospheric chemistry and to probe superfluidity in He

n

clusters. This article reviews the research themes that were the focus of the past 50 years and surveys new opportunities.
Computers getting the drift
Authors: McCarthy Diana
Published: September 2007

Natural language processing is the study of computer programs that can understand and produce human language. An important goal in the research to produce such technology is identifying the right meaning of words and phrases. In this paper, we give an overview of current research in three areas: (i) inducing word meaning; (ii) distinguishing different meanings of words used in context; and (iii) determining when the meaning of a phrase cannot straightforwardly be obtained from its parts. Manual construction of resources is labour intensive and costly and furthermore may not reflect the meanings that are useful for the task or data at hand. For this reason, we focus particularly on systems that use samples of language data to learn about meanings, rather than examples annotated by humans.
In vitro ability of Staphylococcus aureus isolates from bacteraemic patients with and without metastatic complications to invade vascular endothelial cells
Authors: Park Wan Beom , Kim Sung Han , Kang Cheol-in , Cho Jae Hyun , Bang Ji Whan , Park Kyoung Wha , Lee Yeong Seon , Kim Nam Joong , Oh Myoung-don , Kim Hong Bin , Won Choe Kang
Published: September 2007

Invasion of vascular endothelial cells is thought to be a critical step in the development of metastatic infections in patients withStaphylococcus aureusbacteraemia. This study was designed to evaluate the association between the ability to invade endothelial cells and metastatic infection byS. aureus. Patients with metastatic infection were identified among those with community-acquiredS. aureusbacteraemia in a tertiary referral hospital. Patients with simple bacteraemia caused byS. aureusover the same period served as the control group. The ability of each clinical isolate to invade endothelial cells was evaluated by counting the number of intracellular organisms 1 h after inoculation onto human umbilical vein endothelial cellsin vitro. The cytotoxic activity of intracellularS. aureuswas determined 24 h after internalization, and expressed as the percentage of cells killed. The clinical isolates varied in invasiveness and cytotoxicity. The median invasiveness, relative toS. aureusreference strain ATCC 29213, was 145  % in the cases (n=10) [interquartile range (IQR) 103–160] and 153  % (IQR 111–173) in the controls (n=11;P=0.44). The median cytotoxicity was 59.4  % (IQR 47–68) in the cases and 65.2  % (IQR 50–74) in the controls (P=0.44). Differences in the ability ofS. aureusto invade and destroy vascular endothelial cellsin vitrowere not associated with the development of metastatic complications in patients withS. aureusbacteraemia. This implies that the invasiveness and toxicity ofS. aureusfor endothelial cells may not be major determinants of metastatic infection.
Negative impact of Aspergillus galactomannan and DNA detection in the diagnosis of fungal rhinosinusitis
Authors: Kostamo Katriina , Richardson Malcolm , Eerola Erkki , Rantakokko-Jalava Kaisu , Meri Taru , Malmberg Henrik , Toskala Elina
Published: September 2007

A proportion of patients with chronic rhinosinusitis, especially if nasal polyps are present, have a diagnosis of fungal rhinosinusitis. The diagnosis is difficult to establish because the symptoms and clinical and radiological signs are non-specific. Also current diagnostic methods, i.e. histology, fungal staining and culture, are insensitive. The performance of theAspergillusgalactomannan (GM) ELISA and real-time PCR forAspergillus fumigatusmitochondrial DNA was evaluated for the detection ofAspergillusin sinus mucus samples from 25 patients with chronic rhinosinusitis with nasal polyposis. The results were compared with those from nasal lavage fluid from 19 healthy volunteers. Seven patients (28 %) were diagnosed as having fungal rhinosinusitis according to the presence of filaments in histology or direct microscopy using Calcofluor white. All fungal rhinosinusitis patients were negative in the GM ELISA. GM ELISA was positive in five patients whose samples were negative using conventional methods andA. fumigatusPCR. Two out of seven patients with fungal rhinosinusitis were positive byA. fumigatusPCR: one also had a positiveA. fumigatusculture, and one had hyphae consistent withAspergillusin histology. One additional patient had a weak positive PCR result, but other fungal tests were negative. In control subjects, the GM ELISA was positive in 21 %, whereas direct microscopy, culture andA. fumigatusPCR were negative in all samples. Direct microscopy and culture together with histology remain pivotal in defining fungal rhinosinusitis diagnosis.A. fumigatusPCR may have additional value in allowing the diagnosis to be made sooner, whereas the GM ELISA is not reliable in diagnosingAspergillusinfection of the paranasal sinuses.
A virulent genotype of Microsporum canis is responsible for the majority of human infections
Authors: Sharma Rahul , de Hoog S. , Presber Wolfgang , Gräser Yvonne
Published: September 2007

The zoophilic dermatophyte speciesMicrosporum canisbelongs to theArthroderma otaecomplex and is known to mate with tester strains of that teleomorph species, at least in the laboratory. Human infections are likely to be acquired from the fur of cats, dogs and horses. Epidemiological studies to reveal sources and routes of infection have been hampered by a lack of polymorphic molecular markers. Human cases mainly concern moderately inflammatory tinea corporis and tinea capitis, but, as cases of highly inflammatory ringworm are also observed, the question arises as to whether all lineages ofM. canisare equally virulent to humans. In this study, two microsatellite markers were developed and used to analyse a global set of 101M. canisstrains to reveal patterns of genetic variation and dispersal. Using a Bayesian and a distance approach for structuring theM. canissamples, three populations could be distinguished, with evidence of recombination in one of them (III). This population contained 44 % of the animal isolates and only 9 % of the human strains. Population I, with strictly clonal reproduction (comprising a single multilocus genotype), contained 74 % of the global collection of strains from humans, but only 23 % of the animal strains. From these findings, it was concluded that population differentiation inM. canisis not allopatric, but rather is due to the emergence of a (virulent) genotype that has a high potential to infect the human host. Adaptation of genotypes resulting in a particular clinical manifestation was not evident. Furthermore, isolates from horses did not show a monophyletic clustering.
Virulence characteristics and the molecular epidemiology of enteroaggregative Escherichia coli isolates from travellers to developing countries
Authors: Huang David B. , Mohamed Jamal A. , Nataro James P. , DuPont Herbert L. , Jiang Zhi-Dong , Okhuysen Pablo C.
Published: September 2007

Enteroaggregative Escherichia coli (EAEC) is associated with diarrhoea among travellers to developing countries. EAEC virulence properties predisposing to illness are not clear. Sixty-four EAEC strains identified by a HEp-2 cell assay and isolated from faecal samples from US and European travellers to developing countries were studied for the prevalence of 11 putative virulence genes by PCR: 49 EAEC strains from adults with acute diarrhoea and 15 EAEC strains from adults without diarrhoea. E. coli strains from the stools of healthy travellers to the same region were used as controls. EAEC carrying aggR, aap, astA and set1A were identified individually more often in the stools of subjects with diarrhoea compared with those without diarrhoea (P<0.05). EAEC isolates with two or three of these genes were associated with diarrhoea compared with EAEC isolates without the presence of these genes (P<0.05). Subjects with diarrhoea who shed EAEC isolates positive for these genes were more likely than subjects shedding EAEC negative for these genes to pass stools with gross mucus (57 vs 14 %) and faecal leukocytes (40 vs 7 %) (P<0.05). This study shows the heterogeneity of gene profiles of EAEC strains found in the stools of international travellers and suggests that the presence of aggR, aap, astA or set1A, the number of genes present and stool characteristics may be markers for more virulent EAEC strains.
Simultaneous direct detection of toxigenic and non-toxigenic Vibrio cholerae from rectal swabs and environmental samples by sandwich ELISA
Authors: Tuteja Urmil , Kumar Sanjay , Shukla Jyoti , Kingston Joseph , Batra Harsh V.
Published: September 2007

A mAb-based simple, specific and rapid two-tip dipstick ELISA was developed for simultaneous detection of toxin- and non-toxin-producing strains ofVibrio cholerae, and for direct detection ofV. choleraefrom rectal swabs of patients and from environmental water samples. Rabbit polyclonal antibodies and murine mAbs were raised against recombinant protein (r-protein) antigens of cholera toxin B (CtxB) and outer membrane protein W (OmpW). Rabbit polyclonal antibodies to both r-proteins were coated individually onto the tips of nitrocellulose (NC) membranes of a two-tipped NC dipstick as capture antibodies and a mixture of two mAbs was used for the detecting antibodies. The test was found to be specific forV. choleraestrains O1, O139, non-O1 and non-O139, and did not show any cross-reaction to closely related bacterial strains. The test was evaluated on rectal swabs collected at the bedside of 75 hospitalized diarrhoeal patients and on 50 environmental water samples after enrichment for 4 h in alkaline peptone water. The mAb two-tip dipstick ELISA detectedV. choleraein 52/75 rectal swabs and 2/50 environmental water samples for CtxB antigen, and in 1/50 environmental water samples for the non-toxin OmpW antigen ofV. choleraewithin 1.5 h. These findings were identical to those observed using PCR and conventional culture methods. Thus, this mAb-based two-tip dipstick ELISA could be used for early and reliable simultaneous detection of toxigenic and non-toxigenic strains ofV. choleraefrom clinical and environmental water samples.
Role of caspases in cleavage of lamin A/C and PARP during apoptosis in macrophages infected with a periodontopathic bacterium
Authors: Okinaga Toshinori , Kasai Hironori , Tsujisawa Toshiyuki , Nishihara Tatsuji
Published: September 2007

The periodontopathic bacterium Actinobacillus actinomycetemcomitans has been implicated in the pathogenesis of periodontal diseases. It has been reported previously that infection with the organism induced apoptosis in the mouse macrophage cell line J774.1. In the present study, the role of caspases during apoptosis in A. actinomycetemcomitans-infected J774.1 cells was examined. A large number of apoptotic cells was detected by flow cytometric analysis in infected J774.1 cells; however, inhibitors of caspase-9, -6 and -3/7 completely blocked the induction of apoptosis. Expression of the cleaved forms of caspase-6 and -7 was detected during apoptosis in infected J774.1 cells. Immunoblot analysis revealed that the caspase-9 inhibitor blocked expression of the cleaved forms of caspase-6 and -7, whilst the caspase-3 inhibitor blocked expression of the cleaved form of caspase-7, but not caspase-6. It is known that lamin A/C and poly(ADP-ribose) polymerase (PARP) are essential nuclear components for maintaining normal cell function and viability, and both were found to be cleaved in the infected J774.1 cells. Immunoblot analysis also revealed that the caspase-6 inhibitor blocked the cleavage of lamin A/C, whilst the caspase-3/7 inhibitor blocked the cleavage of PARP. Taken together, these results suggest that activation of caspases and the subsequent cleavage of lamin A/C and PARP are involved in the morphological changes of apoptotic macrophages infected with A. actinomycetemcomitans.
Multiplex PCR for direct identification of Campylobacter spp. in human and chicken stools
Authors: Al Amri Aisha , Senok Abiola C. , Ismaeel Abdulrahman Yusuf , Al-Mahmeed Ali E. , Botta Giuseppe A.
Published: September 2007

Differentiation between Campylobacter jejuni and Campylobacter coli is problematic in clinical specimens due to fastidious growth requirements and limited biochemical tests. This study describes a rapid, multiplex PCR protocol for the direct detection and differentiation of C. jejuni and C. coli in stools. An evaluation was carried out of this multiplex protocol based on the detection of cadF (genus specific), and hipO (C. jejuni) and asp (C. coli) genes, using stool from patients with Campylobacter enteritis and chicken. Protocol sensitivity was assessed and specificity determined using a panel of enteric bacteria, and evaluation of 30 diarrhoeic stool specimens culture negative for Campylobacter. Of the 114 specimens (54 human and 60 chicken) evaluated by the protocol, 70 (61.4 %) were identified as C. jejuni, 35 (30.7 %) as C. coli and 9 (7.9 %) as a mixed infection/colonization with both species. All mixed infections were identified as C. jejuni by culture. Among the stool specimens that were culture negative for Campylobacter, two (6.7 %) were C. jejuni positive by multiplex PCR. The protocol sensitivity limit was 0.015–0.016 ng C. jejuni and C. coli DNA μl−1 in the specimen. There was no cross-reaction with the reference strains assessed. Comparison of hippurate test and multiplex PCR demonstrated 17 isolates with false-positive hippurate enzymic activity and 7 with false-negative activity. This rapid protocol (turnaround time 6 h) is highly sensitive and specific for direct evaluation of stool for these pathogens. It has significant application for routine clinical diagnostic and epidemiological purposes.
Development of a real-time PCR assay for the detection and identification of Staphylococcus capitis, Staphylococcus haemolyticus and Staphylococcus warneri
Authors: Iwase Tadayuki , Seki Keiko , Shinji Hitomi , Mizunoe Yoshimitsu , Masuda Shogo
Published: September 2007

Staphylococcus capitis, Staphylococcus haemolyticus and Staphylococcus warneri are coagulase-negative staphylococci. Each species has different characteristics, and a difference in pathology is also seen in compromised hosts. Therefore, the development of a species-specific simple detection method for the identification of these staphylococci is important. Here, a species-specific real-time PCR assay is reported that targets the superoxide dismutase A-encoding gene of these bacteria. Primers were designed with a base that was non-complementary with regard to the other bacteria. This base was at the 3′ end of the primer (3′ mismatch primer) and conferred high specificity. These primers were then evaluated using real-time PCR. They reacted only with the target bacterium. In addition, stable quantitative reactions were observed when experiments were performed using genomic DNA extracted from varying numbers of staphylococci cells (101–107 cells). These results indicate that this method is useful for the identification and quantitative analysis of S. capitis, S. haemolyticus and S. warneri.
Endophthalmitis due to Williamsia muralis
Authors: Murray Ronan J. , Aravena-Román Max , Kämpfer Peter
Published: September 2007

A case of endophthalmitis caused by Williamsia muralis is described. The infection occurred following a procedure known as intravitreal triamcinolone acetonide injection for the treatment of diabetic maculopathy. This is the first report of W. muralis as a causative agent of endophthalmitis.
Distribution of staphylococcal cassette chromosome mec (SCCmec) types I, II, III and IV in coagulase-negative staphylococci from patients attending a tertiary hospital in southern Brazil
Authors: Mombach Pinheiro Machado Alice Beatriz , Reiter Keli Cristine , Paiva Rodrigo Minuto , Barth Afonso Luis
Published: September 2007

Coagulase-negative staphylococci (CoNS) are now recognized as the aetiological agents of an important range of infections in humans. Most developed countries have reported an increase in CoNS infections in hospitalized patients that are resistant to meticillin and other antibiotics. Staphylococcal cassette chromosome mec (SCCmec) typing is essential for understanding the molecular epidemiology of meticillin-resistant Staphylococcus strains. SCCmec elements are currently classified into types I to VI based on the characteristics of the mec and ccr gene complexes and are further classified into subtypes according to their ‘junkyard DNA’ region. We evaluated the distribution of SCCmec types in CoNS from patients attending the Hospital de Clínicas de Porto Alegre over the period August 2004–December 2005. Among the 129 bloodstream isolates, 36 (27.9 %) harboured SCCmec type I, 4 (3.0 %) harboured SCCmec type II, 67 (52 %) harboured SCCmec type III, 1 (0.8 %) harboured SCCmec type IV and 4 (3.0 %) harboured SCCmec types I and III. Seventeen isolates were not typable. Identification of CoNS at the species level indicated that Staphylococcus
epidermidis was the most common species, with 87 isolates, followed by Staphylococcus
haemolyticus (15), Staphylococcus
hominis (13), Staphylococcus
capitis (12) and Staphylococcus
sciuri (1). SCCmec type III was the most prevalent among isolates of S. epidermidis (52 %). Among these strains, 30 (23 %) harboured a modified SCCmec type III which contained an additional dcs region in comparison with regular type III. SCCmec type III was also highly prevalent (75 %) among S. capitis isolates. The predominant SCCmec type found among S. haemolyticus isolates was type I. However, all four isolates harbouring SCCmec type II belonged to S. haemolyticus. Our results indicate that SCCmec type III was the most prevalent among the CoNS. Isolates with SCCmec type III were more resistant to non-β-lactam antimicrobials than isolates harbouring SCCmec types I, II and IV, although the increase in resistance was statistically significant only for clindamycin (P=0.021), rifampicin (P=0.010) and levofloxacin (P=0.005).
Phospholipase, proteinase and haemolytic activities of Candida albicans isolated from oral cavities of patients with type 2 diabetes mellitus
Authors: Tsang C. S. P. , Chu F. C. S. , Leung W. K. , Jin L. J. , Samaranayake L. P. , Siu S. C.
Published: September 2007

The aim of this study was to biotype and characterize phospholipase, proteinase and haemolytic activities of oral Candida albicans isolates from 210 Chinese patients with type 2 diabetes mellitus (DM) and 210 age- and sex-matched healthy controls. Seventy-six and 50 C. albicans isolates were obtained from type 2 DM patients and controls, respectively, using the oral rinse technique. The isolates were characterized with a biotyping system based on enzyme profiles, carbohydrate assimilation patterns and boric acid resistance of the yeasts, and the isolates were further tested for in vitro phospholipase, proteinase and haemolytic activities. The major biotypes of C. albicans isolates from the type 2 DM and control groups were A1R (42.1 %) and J1R (36.0 %), respectively. Significantly higher proteinase and haemolytic activities were found in the isolates from the type 2 DM group (P<0.05). Proteinase activity was higher in isolates from patients with ≥10 years of DM history than those with <10 years (P<0.05). Haemolytic activity was significantly higher in isolates from female DM patients than in those from male counterparts (P<0.05). These data provide evidence of increased extracellular enzyme activity in Candida isolates taken from DM patients.
The type III secretion system of Proteus mirabilis HI4320 does not contribute to virulence in the mouse model of ascending urinary tract infection
Authors: Pearson Melanie M. , Mobley Harry L. T.
Published: September 2007

The Gram-negative enteric bacterium Proteus mirabilis is a frequent cause of urinary tract infections (UTIs) in individuals with long-term indwelling catheters or with complicated urinary tracts. The recent release of the P. mirabilis strain HI4320 genome sequence has facilitated identification of potential virulence factors in this organism. Genes appearing to encode a type III secretion system (TTSS) were found in a low GC-content pathogenicity island in the P. mirabilis chromosome. This island contains 24 intact genes that appear to encode all components necessary to assemble a TTSS needle complex, plus at least two putative secreted effector proteins and their chaperones. The genetic organization of the TTSS genes is very similar to that of the TTSS of Shigella flexneri. RT-PCR analysis indicated that these genes are expressed at low levels in vitro. However, insertional mutation of two putative TTSS genes, encoding the requisite ATPase and a possible negative regulator, resulted in no change in either the growth rate of the mutant or the secreted protein profile compared to wild-type. Furthermore, there was no difference in quantitative cultures of urine, bladder and kidney between the ATPase mutant and the wild-type strain in the mouse model of ascending UTI in either independent challenge or co-challenge experiments. The role of the P. mirabilis TTSS, if any, is yet to be determined.
Virulence properties of Campylobacter jejuni isolates of poultry and human origin
Authors: Van Deun Kim , Haesebrouck Freddy , Heyndrickx Marc , Favoreel Herman , Dewulf Jeroen , Ceelen Liesbeth , Dumez Linn , Messens Winy , Leleu Saskia , Van Immerseel Filip , Ducatelle Richard , Pasmans Frank
Published: September 2007

Campylobacter jejuni is one of the leading causes of food-borne gastroenteritis. Because of the high prevalence of C. jejuni in poultry, poultry meat is considered a major source of C. jejuni infections for humans. However, it is not known whether all poultry-associated C. jejuni strains are capable of causing disease in humans. Four different virulence properties of C. jejuni strains were compared between 20 poultry isolates and 24 human isolates. Strains were chosen based on their PFGE pattern to represent a heterogeneous population. The isolates were compared for their ability to invade and induce interleukin-8 (IL-8) production in T84 cells, their production of functional cytolethal distending toxin (CDT) using HEp-2 cells, and their sodium deoxycholate resistance. All four virulence factors were present among strains of human and poultry origin, with strong differences observed among strains. For invasion and IL-8 induction, no difference was observed between the two populations. However, on average, human isolates arrested more HEp-2 cells in their cell cycle than did the poultry isolates (P=0.041), suggesting higher CDT production by the former. The ability to survive 16 000 μg sodium deoxycholate ml−1 was significantly more pronounced (P=0.006) among human isolates than poultry isolates, although all strains possessed the cmeABC operon. These data suggest that all four virulence properties are widespread among C. jejuni isolates, but that a higher degree of bile-salt resistance and more pronounced CDT production are associated with strains causing enteritis in humans.
Rapid screening of clarithromycin resistance in Helicobacter pylori by pyrosequencing
Authors: Moder Karen-Anja , Layer Franziska , König Wolfgang , König Brigitte
Published: September 2007

Helicobacter pylori infections can be effectively treated with clarithromycin, a macrolide, in combination with other antibiotics, such as amoxicillin, tetracycline or metronidazole. The failure of H. pylori eradication is mainly associated with macrolide-resistant strains. Three point mutations (A2142G/C, A2143G, T2182C) in the peptidyltransferase region of domain V of the 23S rRNA have been described as being associated with clarithromycin resistance. Therefore, the determination of clarithromycin resistance by pyrosequencing was evaluated. H. pylori from 81 gastric biopsies was cultured and clarithromycin resistance was determined by Etest, as well as by pyrosequencing technology (PSQ 96 system; Biotage). The respective mutations were set in relation to the MIC measured in μg ml−1 by Etest. In this study, point mutations in positions 2142 and 2143 were associated with clarithromycin resistance. Mutations in position 2182 did not contribute to clarithromycin resistance. In addition, from 22 out of the 81 biopsies, clarithromycin resistance was determined directly without culturing H. pylori to save additional time. Identical results were obtained as compared to resistance testing with pure H. pylori strains. All results obtained by pyrosequencing were evaluated by Sanger sequencing. The data show that pyrosequencing to detect point mutation is a fast and reliable method for determining clarithromycin resistance in H. pylori, and provides the same results as the Etest.
Purpura fulminans in a child secondary to Panton–Valentine leukocidin-producing Staphylococcus aureus
Authors: Hussain Abid , Robinson Gisela , Malkin Joanne , Duthie Mark , Kearns Angela , Perera Nelun
Published: September 2007

A case of purpura fulminans (PF) in a child secondary to infection with meticillin-sensitive Staphylococcus aureus (MSSA) encoding the Panton–Valentine leukocidin (PVL) toxin genes is presented. Occasional cases of PF have been documented secondary to S. aureus infection in adults, but, to the authors' knowledge, not in children. Here the first UK case of MSSA-PVL leading to PF is presented.
Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicity
Authors: Holladay Nathan B. , Kinch Lisa N. , Grishin Nick V.
Published: September 2007

X‐ray crystallographic protein structures often contain disordered regions that are observed as missing electron density. Diffraction data may give little or no direct evidence as to the specific nature of disordered regions. We have developed a weighted window‐based disorder predictor optimized using crystallographic data. Performance of a predictor is strongly influenced by chain termini. Optimized score adjustment values for amino‐ and carboxy‐terminal positions demonstrate a simple, monotonic relationship between disorder and residue distance from termini. This optimized disorder predictor performs similarly to DISOPRED2 on crystallographically disordered regions. Data‐optimized residue disorder propensities show strong linear correlation with experimentally determined amino acid transfer energies between water and hydrogen‐bonding organic solvents, which primarily reflect residue hydrophobicity (exemplified by the Nozaki‐Tanford hydrophobicity scale). Disorder propensities do not correlate as well with transfer energies between water and apolar solvents, which primarily reflect a different hydropathic property: residue hydrophilicity (also reflected by the Kyte‐Doolittle hydropathy scale). Our results suggest that while hydrophobic side‐chain interactions are primarily involved in determining stability of the folded conformation, hydrogen bonding, and similar polar interactions are primarily involved in conformational and interaction specificity.
Structural biology of transmembrane domains: Efficient production and characterization of transmembrane peptides by NMR
Authors: Hu Jian , Qin Huajun , Li Conggang , Sharma Mukesh , Cross Timothy A. , Gao Fei Philip
Published: September 2007

Structural characterization of transmembrane peptides (TMPs) is justified because transmembrane domains of membrane proteins appear to often function independently of the rest of the protein. However, the challenge in obtaining milligrams of isotopically labeled TMPs to study these highly hydrophobic peptides by nuclear magnetic resonance (NMR) is significant. In the present work, a protocol is developed to produce, isotopically label, and purify TMPs in high yield as well as to initially characterize the TMPs with CD and both solution and solid‐state NMR. Six TMPs from three integral membrane proteins, CorA, M2, and KdpF, were studied. CorA and KdpF are from Mycobacterium tuberculosis, while M2 is from influenza A virus. Several milligrams of each of these TMPs ranging from 25 to 89 residues were obtained per liter of M9 culture. The initial structural characterization results showed that these peptides were well folded in both detergent micelles and lipid bilayer preparations. The high yield, the simplicity of purification, and the convenient protocol represents a suitable approach for NMR studies and a starting point for characterizing the transmembrane domains of membrane proteins.
WrbA bridges bacterial flavodoxins and eukaryotic NAD(P)H:quinone oxidoreductases
Authors: Carey Jannette , Brynda Jiri , Wolfová Julie , Grandori Rita , Gustavsson Tobias , Ettrich Rüdiger , Smatanová Ivana Kutá
Published: September 2007

The crystal structure of the flavodoxin‐like protein WrbA with oxidized FMN bound reveals a close relationship to mammalian NAD(P)H:quinone oxidoreductase, Nqo1. Structural comparison of WrbA, flavodoxin, and Nqo1 indicates how the twisted open‐sheet fold of flavodoxins is elaborated to form multimers that extend catalytic function from one‐electron transfer between protein partners using FMN to two‐electron reduction of xenobiotics using FAD. The structure suggests a novel physiological role for WrbA and Nqo1.
Analysis of a secondary contact between divergent lineages of brown trout Salmo trutta L. from Duero basin using microsatellites and mtDNA RFLPs
Authors: Martínez P. , Bouza C. , Castro J. , Hermida M. , Pardo B. G. , Sánchez L.
Published: September 2007

The analysis of 12 microsatellite loci in 16 native populations of Salmo trutta from Duero basin evidenced a strong genetic differentiation in accordance with the existence of two divergent Atlantic mtDNA lineages, Atlantic (AT) and Duero (DU). These lineages were observed spatially segregated mainly in the Lower‐course and in the inner part of the basin. Unlike previous isozyme information, microsatellite data suggested a more downstream location of the sharpest genetic divergence in Duero basin and a more complex structure in the inward area. Putative hybrid populations evidenced higher Hardy–Weinberg and gametic disequilibria than pure ones (Pisuerga, Lower‐course), not explained by mixture due to differential immigration pattern across the basin. Hybridization indexes suggested a bimodal pattern of hybridization and a higher weight of Pisuerga region in the genetic composition of hybrid samples in accordance with mtDNA data. The results suggested a limited introgression between AT and DU lineages. Taking into account the time of divergence between both lineages, selection and/or genetic incompatibility appeared necessary to explain the genetic structure observed and the ancient location of DU lineage restricted to this area.
Mitochondrial cytochrome b analysis reveals two invasive lionfish species with strong founder effects in the western Atlantic
Authors: Hamner R. M. , Freshwater D. W. , Whitfield P. E.
Published: September 2007

Lionfish (Scorpaenidae, Pteroinae) are venomous predatory fish that are native to the Indo‐Pacific region and have recently become established in the western Atlantic Ocean. Since the invasion was first documented in 2000, the number of lionfish in the Atlantic has increased substantially and spurred a series of investigations regarding their biology and potential impacts on the ecosystem. The present study uses haplotypes from the mitochondria‐encoded cytochrome b (cyt b) locus to determine the number of lionfish species involved in the Atlantic invasion and the decrease in genetic diversity that accompanied the invasion. The cyt b data reveal that Pterois volitans along with a small number of Pterois miles are present in the Atlantic Ocean and that a strong founder effect has resulted in a large decrease in genetic diversity compared with native lionfish populations.
Substantial loss of genetic variation in a single generation of Senegalese sole (Solea senegalensis) culture: implications in the domestication process
Authors: Porta J. , Maria Porta J , Cañavate P. , Martínez‐Rodríguez G. , Carmen Alvarez M
Published: September 2007

The flatfish Solea senegalensis represents an important resource in modern mariculture and is largely raised in South Spain and Portugal. Substantial progress has been achieved in its domestication, though suitable reproduction and zootechnical conditions still remain unknown. Difficulties to obtain breeders from wild lead many companies to set up broodstocks with first generation (G1) progeny without genetic guidelines. To study the genetic processes underlying the early stage of domestication of this species, the genetic structure of four representative broodstocks from Southern Spain has been assessed by means of eight microsatellite loci. Data revealed a substantial reduction in levels of genetic variability on just one generation in stocks totally or partially composed of G1 individuals when compared with those solely integrated by individuals from wild. The genetic relatedness within the four stocks has been established, having detected close relationships between individuals from cultured origin, thus suggesting that the loss of variability is apparently due to setting up broodstocks by blind selecting of family related G1 individuals. The high proportion of siblings in these stocks can have negative consequences in future generations due to inbreeding effects. The relationships between the four broodstocks were traced, having found a common origin between two of them, which come from the same donor hatchery, thus enhancing the homogenization of the existent resources for S. senegalensis among the various stocks. This finding alerts about the risks in exchanging fish between hatcheries without knowing their genetic origin. From this study, the use of microsatellites is strongly recommended to control the genetic composition of S. senegalensis broodstocks, aimed to maintain standards of genetic health and improve their reproduction capacity, which is a key issue in the domestication process.
Effect of DNA extraction on ageing success in coral trout (Plectropomus leopardus) otoliths
Authors: Heath D. , Lou D. C. , Ovenden J. , Begg G. A.
Published: September 2007

To maximize the information commonly collected from otoliths, the effect of DNA extraction on the estimation of age with otoliths was evaluated by comparing sagittal otolith samples from common coral trout (Plectropomus leopardus) for clarity and ageing discrepancies in DNA‐extracted and untreated control otoliths. The DNA extraction process had no significant effect, indicating that archived otoliths can be used as a source of DNA while retaining their utility for age estimation.
Chemokine receptors in cancer metastasis and cancer cell‐derived chemokines in host immune response
Authors: Koizumi Keiichi , Hojo Shozo , Akashi Takuya , Yasumoto Kazuo , Saiki Ikuo
Published: September 2007

The chemotactic cytokines called chemokines are a superfamily of small secreted cytokines that were initially characterized through their ability to prompt the migration of leukocytes. Attention has been focused on the chemokine receptors expressed on cancer cells because cancer cell migration and metastasis show similarities to leukocyte trafficking. CXC chemokine receptor 4 (CXCR4) was first investigated as a chemokine receptor that is associated with lung metastasis of breast cancers. Recently, CXCR4 was reported to be a key molecule in the formation of peritoneal carcinomatosis in gastric cancer. In the present review, we highlight current knowledge about the role of CXCR4 in cancer metastases. In contrast to chemokine receptors expressed on cancer cells, little is known about the roles of cancer cell‐derived chemokines. Cancer tissue consists of both cancer cells and various stromal cells, and leukocytes that infiltrate into cancer are of particular importance in cancer progression. Although colorectal cancer invasion is regulated by the chemokine CCL9‐induced infiltration of immature myeloid cells into cancer, high‐level expression of cancer cell‐derived chemokine CXCL16 increases infiltrating CD8+ and CD4+ T cells into cancer tissues, and correlates with a good prognosis. We discuss the conflicting biological effects of cancer cell‐derived chemokines on cancer progression, using CCL9 and CXCL16 as examples. (Cancer Sci 2007; 98: 1652–1658)
Downregulation of microRNAs‐143 and ‐145 in B‐cell malignancies
Authors: Akao Yukihiro , Nakagawa Yoshihito , Kitade Yukio , Kinoshita Tomohiro , Naoe Tomoki
Published: September 2007

Recently, it has been found that inappropriate expression of microRNAs (miRNAs) is strongly associated with carcinogenesis. In this study, we demonstrated that the expression of miRNAs (miRs) ‐143 and ‐145, the levels of which were previously shown to be reduced in colon cancers and various kinds of established cancer cell lines, was also decreased in most of the B‐cell malignancies examined, including chronic lymphocytic leukemias (CLL), B‐cell lymphomas, Epstein‐Barr virus (EBV)‐transformed B‐cell lines, and Burkitt lymphoma cell lines. All samples from 13 CLL patients and eight of nine B‐cell lymphoma ones tested exhibited an extremely low expression of miRs‐143 and ‐145. The expression levels of miRs‐143 and ‐145 were consistently low in human Burkitt lymphoma cell lines and were inversely associated with the cell proliferation observed in the EBV‐transformed B‐cell lines. Moreover, the introduction of either precursor or mature miR‐143 and ‐145 into Raji cells resulted in a significant growth inhibition that occurred in a dose‐dependent manner and the target gene of miRNA‐143 was determined to be ERK5, as previously reported in human colon cancer DLD‐1 cells. Taken together, these findings suggest that miRs‐143 and ‐145 may be useful as biomarkers that differentiate B‐cell malignant cells from normal cells and contribute to carcinogenesis in B‐cell malignancies by a newly defined mechanism. (Cancer Sci 2007; 98: 1914–1920)
Quantitative trait loci with additive effects on palatability and fatty acid composition of meat in a Wagyu–Limousin F2 population
Authors: Alexander L. J. , MacNeil M. D. , Geary T. W. , Snelling W. M. , Rule D. C. , Scanga J. A.
Published: September 2007

A whole‐genome scan was conducted on 328 F2 progeny in a Wagyu × Limousin cross to identify quantitative trait loci (QTL) affecting palatability and fatty acid composition of beef at an age‐constant endpoint. We have identified seven QTL on five chromosomes involved in lipid metabolism and tenderness. None of the genes encoding major enzymes involved in fatty acid metabolism, such as fatty acid synthase (FASN), acetyl‐CoA carboxylase alpha (ACACA), solute carrier family 2 (facilitated glucose transporter) member 4 (SLC2A4), stearoyl‐CoA desaturase (SCD) and genes encoding the subunits of fatty acid elongase, was located in these QTL regions. The present study may lead to a better‐tasting and healthier product for consumers through improved selection for palatability and lipid content of beef.
Genomic organization of the IGF1, IGF2, MYF5, MYF6 and GRF/PACAP genes across Salmoninae genera
Authors: Moghadam H. K. , Ferguson M. M. , Rexroad C. E. , Coulibaly I. , Danzmann R. G.
Published: September 2007

Whole‐genome duplication in the ancient ray‐finned fish and subsequent tetraploidization in the ancestor to the salmonids have complicated genomic and candidate gene studies in these organisms as many genes with multiple copies are present throughout their genomes. In an attempt to identify genes with a potential influence on growth and development, we investigated the genomic positions of insulin‐like growth factors 1 and 2 (IGF1, IGF2), myogenic factors 5 and 6 (MYF5, MYF6) and growth hormone‐releasing factor/pituitary adenylate cyclase‐activating polypeptide (GRF/PACAP) in three salmonid species: rainbow trout (Oncorhynchus mykiss), Atlantic salmon (Salmo salar) and Arctic charr (Salvelinus alpinus). Our results suggest a tight association between the IGF1, MYF5 and MYF6 genes in all three species. We further localized the duplicated copies of IGF1 to the homeologous linkage groups RT‐7/15 in rainbow trout and AC‐3/24 in Arctic charr, and the two copies of MYF6 to homeologous linkage groups AS‐22/24 in Atlantic salmon. Localization of GRF/PACAP to RT‐7, AS‐31 and AC‐27 and IGF2 to RT‐27, AS‐2 and AC‐4 in rainbow trout, Atlantic salmon and Arctic charr respectively is consistent with previously reported homologies among these chromosomal segments identified using other genetic markers. However, localization of the second copy of GRF/PACAP to RT‐19 and AC‐14 and the duplicated copy of IGF2 to AC‐19 suggest a possible new homology/homeology between these chromosomes. These results might also be an indication of a more ancient polyploidization event that occurred deep in the ray‐finned fish lineage.
The type I Lanyu pig has a maternal genetic lineage distinct from Asian and European pigs
Authors: Wu C. Y. , Jiang Y. N. , Chu H. P. , Li S. H. , Wang Y. , Li Y. H. , Chang Y. , Ju Y. T.
Published: September 2007

The Lanyu pig is an indigenous breed from Lanyu Islet, located south‐east of Taiwan, with phenotypic characteristics distinctive from other pig breeds in Asia and Europe. Based on geographic considerations, the Lanyu pig may have originated from mainland China, Austronesia or the Ryukyu Islands. In the present study, polymorphism of the mitochondrial DNA control region sequence was used to clarify phylogenetic relationships among two herds of Lanyu pigs imported before 1980 from Lanyu Islet into Taiwan and reared in isolation on two different farms. Two distinct mitochondrial control region haplotypes were found. The type I Lanyu sequence appeared independently as a unique clade different from Asian and European pig sequences, while the type II Lanyu sequence was clustered within the major Asian clade. The pairwise distances between the major Asian clade vs. the type I Lanyu and European clades were 0.01726 ± 0.00275 and 0.01975 ± 0.00212 changes per site respectively. Estimates of divergence time suggest that the type I Lanyu sequence split from the major Asian pig clade in prehistoric times. The type II Lanyu mtDNA shares a close genetic lineage with Japanese Satsuma and New Zealand Kune Kune mtDNA with pairwise distances of 0.00095 ± 0.00000 and 0.00192 ± 0.00000 respectively, indicating gene flow between Lanyu Islet, Japan and Oceania in recent times. Together these results indicate that the type I Lanyu pig has a genetic lineage separate from Asian‐type pigs, while the type II Lanyu sequence may represent a more recent introgression of modern Asian pigs.
Home administration of lanreotide Autogel® by patients with acromegaly, or their partners, is safe and effective
Authors: Bevan J. S. , Newell‐Price J. , Wass J. A. H. , Atkin S. L. , Bouloux P. M. , Chapman J. , Davis J. R. E. , Howlett T. A. , Randeva H. S. , Stewart P. M. , Viswanath A.
Published: September 2007

Objective  The introduction of ready‐to‐use lanreotide Autogel® has presented the possibility of patients receiving their acromegaly treatment at home. The objective of this study was to assess the ability of patients (or their partners) to administer repeat, unsupervised, injections of lanreotide Autogel without compromising efficacy or safety.

Design  Multicentre (10 UK regional endocrine centres), open‐label, nonrandomised, controlled study. Patients elected either to receive/administer unsupervised home injections after injection technique training (Test group) or continued to receive injections from a healthcare professional (Control group). Patients received monthly injections of lanreotide Autogel® at their established dose. Effects were monitored for up to 40 weeks.

Patients  Thirty patients (15 per treatment group) with acromegaly treated with a stable dose of lanreotide Autogel® (60, 90 or 120 mg) for ≥ 4 months before screening.

Measurements  The main outcome measure was the proportion of patients/partners who successfully administered injections throughout the study.

Results  All Test group patients/partners qualified to administer injections. Fourteen of 15 patients fulfilled all criteria for successful administration of unsupervised injections (95% confidence interval, 70%–99%). Fourteen of 15 Test and 14/15 Control patients maintained growth hormone and IGF‐1 control. Local injection tolerability was good for both treatment groups, and safety profiles were similar. All Test group patients continued with unsupervised injections after the study.

Conclusions  Patients with acromegaly or their partners were able to administer lanreotide Autogel® injections with no detrimental effect on efficacy and safety; therefore, unsupervised home injections are a viable alternative to healthcare professional injections for suitably motivated patients.