bluuebunny/crossref_metadata_2025 huggingface dataset:
Alignment-independent bilinear multivariate modelling (AIBIMM) for global analyses of 16S rRNA gene phylogeny
Authors: Rudi Knut , Zimonja Monika , Næs Tormod
Published: July 2006

Alignment-independent phylogenetic methods have interesting properties for global phylogenetic reconstructions, particularly with respect to speed and accuracy. Here, we present a novel multimer-based alignment-independent bilinear mathematical modelling (AIBIMM) approach for global 16S rRNA gene phylogenetic analyses. In AIBIMM, jackknife cross-validated principal component analyses (PCA) are used to explain the variance in nucleotide n-mer frequency data. We compared AIBIMM with alignment-based distance, maximum-parsimony and maximum-likelihood phylogenetic methods, analysing taxa belonging to the Proteobacteria (n=82), Actinobacteria (n=30) and Archaea (n=7). These analyses indicated an attraction between the Actinobacteria and Archaea for the traditional methods, with the two taxa Acidimicrobium and Rubrobacter at the root of the tree. AIBIMM, on the other hand, showed that the Actinobacteria was tightly clustered, with Acidimicrobium and Rubrobacter within a distinct subgroup of the Actinobacteria. The application of AIBIMM was further evaluated, analysing full-length 16S rRNA gene sequences for 2818 taxa representing the prokaryotic domains. We obtained a highly structured description of the prokaryote diversity. Sample-to-model (Si) distances were also determined for taxa included in our work. We determined Si distances for models of the six major subgroups of taxa detected in the global analyses, in addition to nested subgroups within the Alphaproteobacteria. The Si-distance evaluation showed a very good separation of the taxa within the models from those outside. We conclude that AIBIMM represents a novel phylogenetic framework suitable for accommodating the current exponential growth of 16S rRNA gene sequences in the public domain.
Rhodovulum marinum sp. nov., a novel phototrophic purple non-sulfur alphaproteobacterium from marine tides of Visakhapatnam, India
Authors: Srinivas T. N. R. , Kumar P. Anil , Sasikala Ch. , Ramana Ch. V. , Süling J. , Imhoff J. F.
Published: July 2006

A yellowish-brown bacterium was isolated from enrichment cultures inoculated with seawater samples from the eastern coast of India (Visakhapatnam) under photoheterotrophic conditions. Enrichment and isolation in a medium containing 2 % NaCl (w/v) yielded strain JA128T, which has ovoid to rod-shaped cells, also forms chains and is non-motile. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA128T clusters with the Alphaproteobacteria and the sequence similarity with its closest relatives, Rhodovulum iodosum and Rhodovulum sulfidophilum, was 95 %. Strain JA128T contained vesicular intracytoplasmic membranes, bacteriochlorophyll a and carotenoids of the spheroidene series. Strain JA128T was mesophilic, slightly acidophilic, slightly halophilic and grew photoheterotrophically with a number of organic compounds as carbon source and electron donor. It was unable to grow photoautotrophically, chemoautotrophically or by fermentative modes. It did not utilize sulfide, thiosulfate or hydrogen as electron donors. Thiamine was required as a growth factor. Based on the 16S rRNA gene sequence analysis, morphological and physiological characteristics, strain JA128T was significantly different from other species of the genus Rhodovulum and was recognized as a novel species for which the name Rhodovulum marinum sp. nov. is proposed. The type strain is JA128T (=ATCC BAA 1215T=CCUG 52183T=JCM 13300T).
Paenibacillus pasadenensis sp. nov. and Paenibacillus barengoltzii sp. nov., isolated from a spacecraft assembly facility
Authors: Osman Shariff , Satomi Masataka , Venkateswaran Kasthuri
Published: July 2006

Two novel spore-forming, Gram-positive, mesophilic, heterotrophic bacteria representing two novel species were isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility (JPL-SAF) at Pasadena, CA, USA. The incidence of similar strains was examined by screening the growing collection of isolates (~400 strains) obtained from the JPL-SAF using species-specific PCR primer sets designed from the 16S rRNA gene sequences of strains SAFN-016Tand SAFN-007T. Phylogenetic analysis of 16S rRNA gene sequences placed these novel isolates within the genusPaenibacillus. Two strains, SAFN-016Tand SAFN-125, shared 98 % 16S rRNA gene sequence similarity withPaenibacillus timonensisand 97 % similarity withPaenibacillus macerans. Strain SAFN-007Tshowed 95.2 % 16S rRNA gene sequence similarity withPaenibacillus kobensis, its nearest phylogenetic neighbour. The results of DNA–DNA hybridization, physiological tests and biochemical analysis allowed genotypic and phenotypic differentiation of the isolates from currently recognizedPaenibacillusspecies. Strain SAFN-007Tand strains SAFN-016Tand SAFN-125 are representatives of two separate novel species, for which the namesPaenibacillus pasadenensissp. nov. (type strain SAFN-007T=ATCC BAA-1211T=NBRC 101214T) andPaenibacillus barengoltziisp. nov. (type strain SAFN-016T=ATCC BAA-1209T=NBRC 101215T) are proposed.
Rickettsia tamurae sp. nov., isolated from Amblyomma testudinarium ticks
Authors: Fournier Pierre-Edouard , Takada Nobuhiro , Fujita Hiromi , Raoult Didier
Published: July 2006

Rickettsiasp. strain AT-1Twas isolated fromAmblyomma testudinariumticks in Japan in 1993. Comparative analysis of sequences obtained from 16S rRNA,gltA,ompA,ompBandsca4gene fragments demonstrated those from AT-1Tto be markedly different from those of other members of the spotted fever group. Using mouse serotyping, it was also observed thatRickettsiasp. strain AT-1Twas different from otherRickettsiaspecies with validly published names. Such genotypic and phenotypic characteristics warrant its classification as a representative of a novel species, for which the nameRickettsia tamuraesp. nov. is proposed, with the type strain AT-1T(=CSUR R1T).
Chryseobacterium wanjuense sp. nov., isolated from greenhouse soil in Korea
Authors: Weon Hang-Yeon , Kim Byung-Yong , Yoo Seung-Hee , Kwon Soon-Wo , Cho Yang-Hee , Go Seung-Joo , Stackebrandt Erko
Published: July 2006

A taxonomic study was performed on strain R2A10-2T, isolated from greenhouse soil cultivated with lettuce (Lactuca sativa L.), collected in Wanju Province, Korea. The bacterial cells were Gram-negative, aerobic, short rods. The growth temperature and pH were 5–35 °C and 5.0–9.0, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this isolate had 93.3–97.7 % similarity to Chryseobacterium species: the highest sequence similarities were to the type strains of Chryseobacterium daecheongense (97.7 %), Chryseobacterium formosense (97.1 %) and Chryseobacterium defluvii (96.9 %). Low levels of DNA–DNA relatedness were found between strain R2A10-2T and the type strains of these three species (<28 %). Differences in phenotypic properties were found with respect to Chryseobacterium species with validly published names. The predominant cellular fatty acids were iso-15 : 0 (40.0 %), iso-17 : 0 3-OH (21.9 %), iso-17 : 1ω9c (11.7 %) and summed feature 4 (iso-15 : 0 2-OH and/or 16 : 1ω7c/t, 11.0 %). Menaquinone MK-6 was detected as the sole respiratory quinone. The G+C content of the genomic DNA was 37.8 mol%. On the basis of the genomic and phenotypic evidence, this isolate represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium wanjuense sp. nov. is proposed. The type strain is R2A10-2T (=KACC 11468T=DSM 17724T).
Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field
Authors: Tanaka Reiji , Kawaichi Satoshi , Nishimura Hiroshi , Sako Yoshihiko
Published: July 2006

A novel thermophilic bacterium, strain KW1T, was isolated from a coastal hydrothermal field on the Satsuma Peninsula, Kagoshima Prefecture, Japan. The variably Gram-stained cells were motile rods with flagella, did not form spores and proliferated at 52–78 °C (optimum, 70 °C), pH 5–8 (optimum, pH 7) and 0–4.5 % NaCl (optimum, 1.0 %). The novel isolate was a strictly aerobic heterotroph that utilized complex proteinaceous substrates as well as a variety of carboxylic acids and amino acids. The G+C content of the genomic DNA was 70.8 mol%. Analysis of 16S rRNA gene sequences indicated that strain KW1Tis closely related toThermaerobacter subterraneusC21T(98.4 % sequence similarity). However, the DNA–DNA hybridization value for strain KW1TandT. subterraneusATCC BAA-137Twas below 46 %. On the basis of the molecular and physiological traits of strain KW1T, it represents a novel species of the genusThermaerobacter, for which the nameThermaerobacter litoralissp. nov. is proposed. The type strain is KW1T(=JCM 13210T=DSM 17372T).
Leeuwenhoekiella blandensis sp. nov., a genome-sequenced marine member of the family Flavobacteriaceae
Authors: Pinhassi Jarone , Bowman John P. , Nedashkovskaya Olga I. , Lekunberri Itziar , Gomez-Consarnau Laura , Pedrós-Alió Carlos
Published: July 2006

Bacteria in the family Flavobacteriaceae are increasingly recognized to play important roles in the degradation of organic matter during and following algal blooms. A novel heterotrophic, rod-shaped, aerobic, yellow-pigmented and gliding bacterium was isolated from a seawater sample collected in the Bay of Blanes in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that the bacterium was closely related to members of the genus Leeuwenhoekiella within the family Flavobacteriaceae, phylum Bacteroidetes. Phenotypic, genotypic, chemotaxonomic and phylogenetic analyses supported the creation of a novel species to accommodate this bacterium, for which the name Leeuwenhoekiella blandensis sp. nov. is proposed. The type strain is MED 217T (=CECT 7118T=CCUG 51940T).
Halorubrum ezzemoulense sp. nov., a halophilic archaeon isolated from Ezzemoul sabkha, Algeria
Authors: Kharroub Karima , Quesada Teresa , Ferrer Raquel , Fuentes Susana , Aguilera Margarita , Boulahrouf Abdrahmane , Ramos-Cormenzana Alberto , Monteoliva-Sánchez Mercedes
Published: July 2006

A novel extremely halophilic archaeon was isolated from Ezzemoul sabkha, Algeria. The strain, designated 5.1T, was neutrophilic, motile and Gram-negative. At least 15 % (w/v) NaCl was required for growth. The isolate grew at pH 6.5–9.0, with optimum growth at pH 7.0–7.5. Mg2+ was required for growth. Polar lipids were C20C20 derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, and phosphatidylglycerol sulfate and sulfated diglycosyl diether. The genomic DNA G+C content of strain 5.1T was 61.9 mol% (T
m). Phylogenetic analysis based on comparison of 16S rRNA gene sequences revealed that strain 5.1T clustered with Halorubrum species. The results of DNA–DNA hybridization and biochemical tests allowed genotypic and phenotypic differentiation of strain 5.1T from other Halorubrum species. The name Halorubrum ezzemoulense sp. nov. (type strain 5.1T=CECT 7099T=DSM 17463T) is proposed.
Halostagnicola larsenii gen. nov., sp. nov., an extremely halophilic archaeon from a saline lake in Inner Mongolia, China
Authors: Castillo A. M. , Gutiérrez M. C. , Kamekura M. , Xue Y. , Ma Y. , Cowan D. A. , Jones B. E. , Grant W. D. , Ventosa A.
Published: July 2006

Strain XH-48Twas isolated from the sediment of Lake Xilinhot, a saline lake in Inner Mongolia (China). The organism is pleomorphic, neutrophilic and requires at least 2.5 M (15 %) NaCl, but not MgCl2, for growth; it exhibits optimal growth at 3.4 M (20 %) NaCl. The G+C content of its DNA is 61 mol%. 16S rRNA gene sequence analysis revealed that strain XH-48Tis a member of the familyHalobacteriaceae, but there were low levels of similarity with other members of this family. The highest sequence similarity values (94.5 and 93.3 %) were obtained with the 16S rRNA genes ofNatrialba aegyptiacaandNatrialba asiatica, respectively. Polar lipid analyses revealed that strain XH-48Tcontains phosphatidylglycerol and phosphatidylglyceromethylphosphate, derived from both C20C20and C20C25glycerol diethers, and two unidentified glycolipids. On the basis of the data obtained, the novel isolate cannot be classified within any recognized genus. Strain XH-48Tshould be placed within a novel genus and species within the familyHalobacteriaceae, orderHalobacteriales, for which the nameHalostagnicola larseniigen. nov., sp. nov. is proposed. The type strain ofHalostagnicola larseniiis strain XH-48T(=DSM 17691T=CGMCC 1.5338T=JCM 13463T=CECT 7116T).
Tenacibaculum aestuarii sp. nov., isolated from a tidal flat sediment in Korea
Authors: Jung Seo-Youn , Oh Tae-Kwang , Yoon Jung-Hoon
Published: July 2006

A novel Tenacibaculum-like bacterial strain, SMK-4T, was isolated from a tidal flat sediment in Korea. Strain SMK-4T was Gram-negative, pale yellow-pigmented and rod-shaped. It grew optimally at 30–37 °C and in the presence of 2–3 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C16 : 0 3-OH and C16 : 1
ω7c and/or iso-C15 : 0 2-OH as the major fatty acids (>10 % of total fatty acids). The DNA G+C content was 33.6 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strain SMK-4T fell within the evolutionary radiation encompassed by the genus Tenacibaculum. Strain SMK-4T exhibited 16S rRNA gene sequence similarity levels of 95.2–98.6 % with respect to the type strains of recognized Tenacibaculum species. DNA–DNA relatedness levels and differential phenotypic properties made it possible to categorize strain SMK-4T as a species that is separate from previously described Tenacibaculum species. On the basis of phenotypic properties and phylogenetic and genetic distinctiveness, strain SMK-4T (=KCTC 12569T=JCM 13491T) should be classified as a novel Tenacibaculum species, for which the name Tenacibaculum aestuarii sp. nov. is proposed.
Crystal structures of native and xylosaccharide‐bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG‐27: Structural insights into alkalophilicity and implications for adaptation to polyextreme conditions
Authors: Manikandan Karuppasamy , Bhardwaj Amit , Gupta Naveen , Lokanath Neratur K. , Ghosh Amit , Reddy Vanga Siva , Ramakumar Suryanarayanarao
Published: July 2006

Crystal structures are known for several glycosyl hydrolase family 10 (GH10) xylanases. However, none of them is from an alkalophilic organism that can grow in alkaline conditions. We have determined the crystal structures at 2.2 Å of a GH10 extracellular endoxylanase (BSX) from an alkalophilic Bacillus sp. NG‐27, for the native and the complex enzyme with xylosaccharides. The industrially important enzyme is optimally active and stable at 343 K and at a pH of 8.4. Comparison of the structure of BSX with those of other thermostable GH10 xylanases optimally active at acidic or close to neutral pH showed that the solvent‐exposed acidic amino acids, Asp and Glu, are markedly enhanced in BSX, while solvent‐exposed Asn was noticeably depleted. The BSX crystal structure when compared with putative three‐dimensional homology models of other extracellular alkalophilic GH10 xylanases from alkalophilic organisms suggests that a protein surface rich in acidic residues may be an important feature common to these alkali thermostable enzymes. A comparison of the surface features of BSX and of halophilic proteins allowed us to predict the activity of BSX at high salt concentrations, which we verified through experiments. This offered us important lessons in the polyextremophilicity of proteins, where understanding the structural features of a protein stable in one set of extreme conditions provided clues about the activity of the protein in other extreme conditions. The work brings to the fore the role of the nature and composition of solvent‐exposed residues in the adaptation of enzymes to polyextreme conditions, as in BSX.
Highly efficient selenomethionine labeling of recombinant proteins produced in mammalian cells
Authors: Barton William A. , Tzvetkova‐Robev Dorothea , Erdjument‐Bromage Hediye , Tempst Paul , Nikolov Dimitar B.
Published: July 2006

The advent of the multiwavelength anomalous diffraction phasing method has significantly accelerated crystal structure determination and has become the norm in protein crystallography. This method allows researchers to take advantage of the anomalous signal from diverse atoms, but the dominant method for derivative preparation is selenomethionine substitution. Several generally applicable, high‐efficiency labeling protocols have been developed for use in the bacterial, yeast, and baculovirus/insect cell expression systems but not for mammalian tissue culture. As a large number of proteins of biomedical importance can only be produced in yields sufficient for X‐ray diffraction experiments in mammalian expression systems, it becomes all the more important to develop such protocols. We therefore evaluated several variables that play roles in determining incorporation levels and report here a simple protocol for selenomethionine modification of proteins in mammalian cells routinely yielding >90% labeling efficiency.
Assessment of effects of an additional dietary natural mineral water uptake on skin hydration in healthy subjects by dynamic barrier function measurements and clinic scoring
Authors: Mac‐Mary S. , Creidi P. , Marsaut D. , Courderot‐Masuyer C. , Cochet V. , Gharbi T. , Guidicelli‐Arranz D. , Tondu F. , Humbert P.
Published: July 2006

Background/aims: The skin protects the body's organs and tissues from damage and physical, chemical and bacteriological injuries. It also prevents the transcutaneous loss of water. The present study was conducted to assess the effects of additional dietary natural mineral water uptake on skin hydration and cutaneous well‐being in subjects with dry skin.

Methods: Eighty subjects (44 women and 36 males, mean age 56±5.6 years) were included in the study, randomised per forearm and stratified by gender. Skin surface hydration, transepidermal water loss (TEWL), sorption–desorption test, skin colour, thickness and micro‐relief were evaluated on the forearms. Clinical scoring of dryness, roughness and elasticity was performed by a dermatologist.

Results: An improvement of skin hydration was observed after additional water uptake, statistically modifying the hydration level as well as TEWL, the water‐binding capacity of the uppermost layers of the stratum corneum. Improvements of softness, smoothness and skin‐moisturising effect were perceived by healthy subjects, and skin micro‐relief was improved.

Conclusion: We suggest that natural mineral water supplementation may be used in order to improve the hydration of skin dryness as a complementary cosmetic approach.
Chemoprevention of spontaneous development of hepatocellular carcinomas in fatty liver Shionogi mice by a cyclooxygenase‐2 inhibitor
Authors: Liu Weidong , Nakamura Hideji , Tsujimura Tohru , Cheng Jidong , Yamamoto Teruhisa , Iwamoto Yuna , Imanishi Hiroyasu , Shimomura Soji , Yamamoto Tetsuo , Hirasawa Tsutomu , Inagaki Shuichiro , Nishiguchi Shuhei , Hada Toshikazu
Published: July 2006

Cyclooxygenase 2 (COX‐2) and retinoid X receptor α (RXRα) are suggested to have roles in carcinogenesis. COX‐2 inhibitors have been reported to suppress growth of hepatocellular carcinoma (HCC) cell linesin vitro. However, little is known about the preventive effect of these drugs on spontaneous hepatocarcinogenesisin vivo. Etodolac exists in a racemic mixture containing S‐ and R‐etodolac. S‐etodolac is responsible for COX‐2 inhibitory activity and R‐etodolac is related to the downregulation of RXRα. Here, the effect of etodolac on spontaneous development of HCC in fatty liver Shionogi mice is evaluated. Etodolac was administered at a low (2 mg/kg) or high (10 mg/kg) dose three times a week for 16 months starting at the age of 3 months. The development of HCC was suppressed slightly in the high‐dose group, and suppressed markedly in the low‐dose group, although the development of fatty liver was not inhibited in either group. Plasma prostaglandin E2levels were also decreased significantly in the low‐dose group, consistent with the suppression of HCC. The expression of RXRα and proliferating cell nuclear antigen in non‐tumorous liver tissues was decreased significantly in both the low‐dose and high‐dose groups. These findings show that etodolac treatment at an optimum dose suppresses hepatocarcinogenesisin vivo, and may be useful for preventing the development of HCC in humans. (Cancer Sci2006; 97: 768–773)
Foster children as young adults: many motherless, fatherless or orphaned: a Swedish national cohort study
Authors: Franzén Eva , Vinnerljung Bo
Published: July 2006

We examined prevalence of parental deaths among former out‐of‐home care youths at age 18 and 25, and odds of parental loss compared with peers from similar socio‐economic childhood backgrounds. The study utilized Swedish national register data for 12 entire birth cohorts (1972–1983), 35 550 former out‐of‐home care youths and 1 138 726 cohort peers without out‐of‐home care experiences. Logistic regression models were used to compute odds ratios for parental loss through death.

It was especially common among former residents of long‐term out‐of‐home care to be motherless (11%), fatherless (11–13%) or orphaned (3–4%) at age 18, compared with non‐foster care peers (1%, 3% and 0.03%). Twenty‐six per cent had lost at least one parent (4% among non‐foster care peers). At age 25, the figures had increased considerably; 36% had lost at least one parent, compared with 7% in the majority population. Adjusted odds ratios for parental loss among long‐term care youth were strikingly high, particularly for having a deceased mother. In short‐term and intermediate care, most youths with deceased parents had suffered parental loss before entering foster care. For youth from long‐term care, parental death after start of placement was most common.
Quantifying uncertainty from large‐scale model predictions of forest carbon dynamics
Authors: MIEHLE PETER , LIVESLEY STEPHEN J. , LI CHANGSHENG , FEIKEMA PAUL M. , ADAMS MARK A. , ARNDT STEFAN K.
Published: July 2006

Linking environmental computer simulation models and geographic information systems (GIS) is now a common practice to scale up simulations of complex ecosystem processes for decision support. Unfortunately, several important issues of upscaling using GIS are rarely considered; in particular scale dependency of models, availability of input data, support of input and validation data, and uncertainty in prediction including error propagation from the GIS. We linked the biogeochemical Forest‐DNDC model to a GIS database to predict growth of Eucalyptus globulus plantations at two different scales (∼0.045 ha plot−1 scale and ∼100 ha grid−1 scale) across Victoria, in south‐eastern Australia. Results showed that Forest‐DNDC was not scale dependent across the range of scales investigated. Reduced availability of input data at the larger scale may introduce severe prediction errors, but did not require adjustment of the model in this study. Differences in the support of input and validation data led to an underestimation of predictive precision but an overestimation of prediction accuracy. Increasing data support, produced a high level of prediction accuracy (−e%), but a medium level of predictive precision (r2=0.474, ME=0.318) after statistical validation. GIS error contribution could be detected but was not readily or reliably quantified. In a regional case study for 2653 ha of E. globulus plantations, the linked model GIS system estimated a total standing biomass of 95 260 t C for mid‐2003 and a net CO2 balance of −45 671 t CO2‐C yr−1 for the entire year of 2002. This study showed that regional predictions of forest growth and carbon sequestration can be produced with greater confidence after a comprehensive assessment of upscaling issues.
On linking interannual tree ring variability with observations of whole‐forest CO2flux
Authors: ROCHA ADRIAN V. , GOULDEN MICHAEL L. , DUNN ALLISON L. , WOFSY STEVEN C.
Published: July 2006

We used a 10‐year record of the CO2flux by an old growth boreal forest in central Manitoba (the Northern Old Black Spruce Site (NOBS)), a ∼150‐year‐oldPicea mariana[Mill.] stand) to determine whether and how whole‐forest CO2flux is related to tree ring width. We compared a 37‐year ring width chronology collected at NOBS to a second chronology that was collected at a nearby Black Spruce stand with a different disturbance history, and also to three measures of annual whole‐forest photosynthesis [gross ecosystem production (GEP)], two measures of annual respiration (R), and one measure of annual carbon balance [net ecosystem production (NEP)]. The year‐to‐year ring width fluctuations were well correlated between the two sites; increasing our confidence in the NOBS chronology and implying that ring width variation is driven and synchronized by the physical environment. Both chronologies exhibited serial correlation, with a fluctuation in ring width that had an apparent periodicity of ∼7 years. Neither chronology was correlated with variation in annual precipitation or temperature. Ring width and NEP increased, while R decreased from 1995 to 2004. GEP either remained constant or decreased from 1995 to 2004, depending on which measure was considered. The lack of relationship between ring width and GEP may indicate that ring growth is controlled almost entirely by something other than carbon uptake. Alternative explanations for the ring width chronologies include the possibility that wood production varies as a result of shifts in respiration, or that an unidentified aspect of the environment, rather than the balance between GEP and respiration, controls wood production. The serial correlation in ring width may be related to increases and decreases in carbohydrate pools, or to gradual changes in nutrient availability, pathogens, herbivores, soil frost or soil water table. The cause or causes of serial correlation, and the controls on the allocation of photosynthate to wood production, emerge as critical uncertainties for efforts in predicting the carbon balance of boreal ecosystems and inferring past climate from tree rings.
Influence of sodium hypochlorite on fracture properties and corrosion of ProTaper Rotary instruments
Authors: Berutti E. , Angelini E. , Rigolone M. , Migliaretti G. , Pasqualini D.
Published: July 2006

Aim  To evaluate the influence of immersion in NaOCl on resistance to cyclic fatigue fracture and corrosion of ProTaper NiTi Rotary instruments.

Methodology  A total of 120 new ProTaper NiTi Rotary files (F2) were randomized and assigned to three different groups of 40 each. Group 1 was the control group; 20 mm (excluding the shaft) of group 2 instruments were immersed in 5% NaOCl at 50 °C for 5 min; instruments in group 3 were completely immersed in 5% NaOCl at 50 °C for 5 min. All instruments were then tested for cyclic fatigue, recording the time in seconds to fracture. Data were analysed by the Kruskall–Wallis test and post‐hoc multiple comparisons (P < 0.05). Micromorphological and microchemical analyses were also completed by means of a field emission scanning electron microscopy (SEM) on those instruments in group 3 that had undergone early fracture.

Results  Instruments in group 3 had a significantly lower resistance to fracture because of cyclic fatigue than those in groups 1 and 2 (P < 0.001). In some instruments in group 3, early fracture occurred after only a few seconds of fatigue testing. SEM observations revealed evident signs of corrosion of the fractured instruments.

Conclusion  Group 3 had significantly reduced resistance to cyclic fatigue compared with instruments in groups 1 and 2. The phenomenon of early fracture may be attributed to galvanic corrosion induced by the presence of dissimilar metals, where one acts as the cathode of a galvanic couple, established when the instrument is immersed in NaOCl solution. The NiTi alloy may acts as the anode and thus undergoes corrosion.
A comparison of cyclic fatigue between used and new Mtwo Ni–Ti rotary instruments
Authors: Plotino G. , Grande N. M. , Sorci E. , Malagnino V. A. , Somma F.
Published: July 2006

Aim  To evaluate the cyclic fatigue of Mtwo Ni–Ti rotary instruments after controlled clinical use in molar teeth.

Methodology  Twenty Mtwo instruments of each size were selected and divided into two groups: group A consisted of 10 new instruments (control group); group B consisted of 10 used instruments. Each instrument in group B was used to clean and shape 10 root canals of molar teeth in patients. Cyclic fatigue testing of instruments was performed in tapered artificial canals with a 5‐mm radius of curvature and a 60° angle of curvature. In all 140, instruments were rotated until fracture and the number of cycles to failure was recorded. Data were analysed using one‐way anova, Tukey's HSD test and independent sample t‐test to determine any statistical difference; the significance was determined at the 95% confidence level.

Results  A reduction of cycles to failure between new (group A) and used (group B) instruments was apparent. A statistically significant difference (P < 0.05) was noted between instruments of groups A and B in all sizes with the exception of size 40, 0.04 taper.

Conclusions  Clinical use significantly reduced cyclic fatigue resistance of Mtwo rotary instruments when compared with an unused control group. However, all the instruments had minimal instrument fatigue when discarded after controlled clinical use.
Modulation of inflammatory response in sepsis by proteasome inhibition
Authors: Šafránek Roman , Ishibashi Nobuya , Oka Youske , Ozasa Hiroyuki , Shirouzu Kazuo , Holeček Milan
Published: July 2006

The Ubiquitin‐proteasome system has recently been shown to be involved in the regulation of cytokine expression. We tested the hypothesis of whether the in vivo administration of proteasome inhibitor MG‐132 can modulate cytokine response and mortality in sepsis. Sepsis was induced in mice by caecal ligation and puncture (CLP). Animals were divided into four groups: control, CLP, CLP and 1 μg MG‐132/g of b.w. intraperitoneally, and CLP and 10 μg MG‐132/g of b.w. Plasma levels of interleukin (IL)‐1, tumour necrosis factor‐α (TNF‐α, IL‐6 and IL‐10 were determined by ELISA 6 h after the induction of sepsis. CLP induced significant increase in plasma levels of all measured cytokines. MG‐132 treatment resulted in lower increase in IL‐1, TNF‐α and IL‐10 levels. IL‐6 was not significantly affected. A mortality study revealed prolonged survival in MG‐132 treated mice. We conclude that MG‐132 treatment decreases inflammatory response and prolongs survival in the CLP model of sepsis.
Identification of T‐cell epitopes associated with immunity within the surface protein of duck hepatitis B virus
Authors: Welschinger R. , Cossart Y. , Pouliopoulos J. , Dixon R. , Vickery K.
Published: July 2006

Summary.  Duck hepatitis is a convenient model of hepatitis B virus (HBV) infection, but the lack of immunological reagents hampers investigation of pathogenesis and vaccine development. The aim of this study was to define T‐cell epitopes in the surface peptide recognized by vaccinated immune birds. Blastogenesis assays were used to test the proliferative response of spleen mononuclear cells to synthetic peptides spanning the pre‐S/S region in 22 naïve and 13 immunized and challenged immune ducks. Roughly ≥50% of the immune ducks responded to five immunodominant peptides eliciting a statistically greater proliferative response than in naïve birds. Fewer ducks responded to an additional six peptides. No statistically significant difference could be shown for the response to 11 peptides between the immune ducks and the naïve ducks. There was no clustering of the immunodominant peptides which were located throughout the surface antigen at sites of major swings in hydrophobicity. A number of peptides which induce lymphoblastogenesis in vaccinated immune ducks have been identified. Their role in spontaneous recovery from duck hepatitis B infection merits investigation.
Quantitative detection of hepatitis E virus RNA and dynamics of viral replication in experimental infection
Authors: Li X. , Kamili S. , Krawczynski K.
Published: July 2006

Summary.  Hepatitis E virus (HEV) RNA has been detected in the stool and serum of patients with HEV infection and experimentally infected nonhuman primates. However, dynamics of HEV levels in the stool and serum during clinical and subclinical infections have not been determined. A real‐time reverse transcription polymerase chain reaction assay, using SYBR Green I in a LightCycler, was developed and optimized to allow quantification of HEV RNA in the stool and serum of both genotype 1 and 2 isolates. The specificity of the assay was confirmed by testing known HEV‐RNA‐positive and ‐negative stool and serum specimens and the sensitivity was evaluated using a synthetic HEV RNA standard. Profiles of viraemia and faecal shedding in two chimpanzees inoculated with an isolate of HEV genotype 1 showed the appearance of virus in the stools on day 4 postinoculation (5.65–6.85 log copies/mg) and in the serum on day 7 postinoculation (6.0–6.93 log copies/mL). Peak HEV RNA levels in the stool and serum coincided with peak alanine aminotransferase (ALT) levels observed on day 22 postinoculation in the two chimpanzees. At the time of detection of IgG anti‐HEV in serum, viral RNA was no longer detectable in the stool or serum and ALT values had returned to normal levels in both chimpanzees, suggesting the efficacy of the immune response in terminating viral replication. Quantitative evaluation of HEV RNA in humans may allow determining the role of virus levels in the pathogenesis and transmission of HEV.
Associations of tumour necrosis factor alpha promoter polymorphisms at position −308 and −238 with clinical characteristics of chronic hepatitis C
Authors: Dai C‐Y. , Chuang W‐L. , Lee L‐P. , Chen S‐C. , Hou N‐J. , Lin Z‐Y. , Hsieh M‐Y. , Hsieh M‐Y. , Wang L‐Y. , Chang W‐Y. , Yu M‐L.
Published: July 2006

Summary.  The aim of this study was to investigate the association between G vs A transitions in the promoter region of the tumour necrosis factor (TNF) alpha at positions −308 (TNF308.2) and −238 (TNF238.2) and clinical features of chronic hepatitis C (CHC). These two promoter TNF‐alpha variants were determined in 250 biopsy‐proven CHC patients by polymerase chain reaction amplification, followed by the Restriction Fragment Length Polymorphism (RFLP) method. The distribution of −308 and −238 TNF‐alpha promoter genotypes were TNF308.1/TNF308.1: 187 (74.8%), TNF308.1/TNF308.2: 57 (22.8%) and TNF308.2/TNF308.2: 6 (2.4%), respectively, and TNF238.1/TNF238.1: 247 (98.8%) and TNF238.1/TNF238.2: 3 (1.2%). The frequencies of the TNF308.2 and TNF238.2 promoter alleles were 13.8% and 0.6%. Increased TNF308.2 allele copy numbers were significantly associated with increased frequency of lower pretreatment hepatitis C virus (HCV) RNA levels (<800 000 IU/mL; P = 0.031) and severe fibrosis stage (F3‐F4; P = 0.006) and higher mean fibrosis score (P = 0.007). The higher cytokine production (with one or two TNF308.2 alleles) was correlated significantly with lower pretreatment HCV RNA levels with a lower mean HCV RNA level (P = 0.024) and increased frequency of lower pretreatment HCV RNA levels (<800 000 IU/mL; P = 0.017). Stepwise logistic regression showed that higher fibrosis score and low HCV RNA levels were independently related to the TNF308.2 allele [odds ratio (95% CI): 1.385 (1.127–1.702) and 0.698 (0.488–0.990)]. We conclude that inheritance of the TNF‐alpha promoter genotype at the position −308 appears to be associated with variability in severity of fibrosis and viral load in chronic HCV infection.
Isolation of a novel nodulin: a molecular marker of osmotic stress in Glycine max/Bradyrhizobium japonicum nodule
Authors: CLEMENT MATHILDE , BONCOMPAGNI ERIC , DE ALMEIDA‐ENGLER JANICE , HEROUART DIDIER
Published: July 2006

Symbiotic N2 fixation of legume crops is highly sensitive to drought, which results in a dramatic drop of N accumulation and yield. The symbiosis between soybean (Glycine max) and Bradyrhizobium japonicum, because of its extreme sensitivity to drought, was chosen as a model to analyse the response to drought stress at a molecular level. The mRNA differential display technique was performed to isolate cDNA markers differentially expressed in well‐watered [100% of N2 fixation capacity (NFC)] and drought‐stressed nodules (40% NFC). One gene noted, G93, appeared strongly down‐regulated by drought and fully recovered after rehydration. In situ hybridization showed that G93 transcripts were localized in N2‐fixing cells of mature nodules, indicating that G93 could be considered as a late nodulin. However, G93 expression was not directly correlated to N2 fixation but mainly responded to osmotic stress. Other stresses that lead to decrease of N2 fixation did not affect G93 expression. Sequence analyses showed that G93 presented a strong homology with two soybean expressed sequence tags (ESTs) and with the ZR1 protein of Medicago sativa. Putative roles of this nodulin in adaptation of soybean nodule to osmotic stress are proposed.
Isotretinoin and the controversy of psychiatric adverse effects
Authors: Strahan Jamison E. , Raimer Sharon
Published: July 2006

Isotretinoin is a synthetic oral retinoid that has great efficacy against severe, recalcitrant, nodulocystic acne. Since its introduction to the market, it has been associated with a variety of adverse psychiatric effects, including depression, psychosis, mood swings, violent behavior, suicide, and suicide attempts. A MEDLINE review was performed to compile all case reports, case series, adverse drug event reportings, and prospective and retrospective studies relating psychiatric adverse events to isotretinoin. In addition, literature linking a biological mechanism for psychiatric adverse events to retinoid signaling pathways was also reviewed. Although a variety of anecdotal and epidemiologic studies are available, the overall lack of concrete scientific data limits any conclusion that can be drawn about a causal relationship between istotretinoin and psychiatric adverse events. Several lines of evidence link retinoid signaling to theorized psychiatric pathogenesis, but are limited in their applicability to adult neurophysiology.
Are food intolerances and allergies increasing in immigrant children coming from developing countries ?
Authors: Cataldo Francesco , Accomando Salvatore , Fragapane Maria L. , Montaperto Daniela ,   SIGENP and GLNBI Working Groups on Food Intolerances
Published: July 2006

There are not available data concerning the occurrence, the clinical features and the environmental risk factors for food intolerances and allergies in immigrant children. The aim of the study was to evaluate rates, distribution, clinical features and environmental risk factors for food intolerances and allergies in immigrant children. Hospital records of 4130 patients with celiac disease (CD), cow milk protein intolerance (CMPI) and food allergies (FA) diagnosed in 24 Italian Centres from 1999 to 2001 were retrospectively reviewed, comparing immigrant patients with Italian ones. 78/4130 (1.9%) patients were immigrant: 36/1917 (1.9%) had CD, 24/1370 (1.75%) CMPI and 18/843 (2.1%) FA. They were evenly distributed across Italy and their native areas were: East Europe (23/78), Northern Africa (23/78), Southern Asia (14/78), Saharan and Sub‐Saharan Africa (9/78), Southern America (4/78), Far East (3/7), Middle East (2/78). Despite differences in their origin, the clinical features of immigrant children were similar to the ones of Italian patients and among each ethnic group. The majority of them were born in Italy (57/78) or have been residing in Italy since several years (19/78). All of them had lost dietary habits of the native countries and had acquired those of the Italian childhood population. Food intolerances and allergies are present also in children coming from developing countries, and paediatricians will need to have a full awareness of them because the number of immigrant children in Italy is quickly increasing. The clinical features of food intolerances and allergies appear the same in each ethnic group, despite differences in races. Sharing of dietary habits with the Italian childhood population seems to be an important environmental risk factor.
Angiotensin receptor antagonist vs. angiotensin‐converting enzyme inhibitor in Asian subjects with type 2 diabetes and albuminuria – a randomized crossover study
Authors: Lim S.‐C. , Koh A. F. Y. , Goh S. K. , Chua C.‐L. , Heng B.‐L. , Subramaniam T. , Sum C.‐F.
Published: July 2006

Background:  Subjects with type 2 diabetes mellitus (T2DM) and albuminuria are at risk for progressive diabetic nephropathy. The relative blood pressure lowering and antialbuminuric efficacy of angiotensin receptor antagonist (ARB) vs. angiotensin‐converting enzyme (ACE) inhibitor has not been well studied.

Methods:  Forty‐one ARB‐ and ACE inhibitor–naive T2DM subjects with albuminuria (>30 mg/g creatinine) were given either 50 mg of losartan (ARB) or 20 mg of quinapril (ACE inhibitor) (50% maximum dose) for 4 weeks, with a 4‐week wash‐out period in‐between interventions in a crossover fashion. The order of intervention was randomized. The primary endpoint was the reduction of blood pressure and albuminuria. Secondary endpoint was changes in plasma transforming growth factor β (TGF‐β).

Results:  Among the 41 subjects, 66% were male. The mean age (s.d.) was 52 (10) years, and duration of diabetes was 8 (14) years. Blood pressure reduction (though not statistically significant) was similar on both interventions [systolic: losartan 3 (15) vs. quinapril 2 (13) mmHg, p = 0.52; diastolic: losartan 1 (9) vs. quinapril 2 (8) mmHg, p = 0.55]. However, amelioration of albuminuria [mean (s.e.)] was significantly greater with losartan [losartan vs. quinapril: −93 (82) vs. –49 (65) mg/g, p = 0.02]. There was no change in plasma TGF‐β levels [mean (s.d.)] on either treatment, losartan [before 12.1 (8.9) vs. after 11.9 (9.6) ng/ml, p = 0.68] and quinapril [11.1 (7.9) vs. 11.1 (7.8) ng/ml, p = 0.87).

Conclusion:  In Asian subjects with T2DM and albuminuria, 4 weeks of losartan therapy at 50 mg daily appeared to have greater antialbuminuric effect than 20 mg of quinapril.
Relationships ofExodontiella, a non‐alysiine, exodont member of the family Braconidae (Insecta, Hymenoptera)
Authors: Wharton Robert A. , Yoder Matthew J. , Gillespie Joseph J. , Patton John C. , Honeycutt Rodney L.
Published: July 2006

The placement ofExodontiellaWharton is re‐examined in light of the discovery of four additional individuals. Genomic DNA was extracted from one of the individuals, the D2 expansion segment of the 28S rRNA gene was sequenced, and the sequence compared to selected taxa within the Braconidae. Based on the molecular data and the morphological study,Exodontiellais formally transferred from the Opiinae to the Gnamptodontinae. The genus and its included species are redescribed.
Enhancement of essential amino acid contents in crops by genetic engineering and protein design
Authors: Beauregard Marc , Hefford Mary Alice
Published: July 2006

The importance and urgency of providing humans and animals with quality proteins are reflected in the growing scientific and industrial interest in augmenting the nutritive value of the world's protein sources. Such nutritive value is determined by the protein content in ‘essential amino acids’, those that cannot be synthesized de novo and that must be supplied from the diet. It is the object of this review to discuss recent advances in the genetic modification of crops that aim to provide enhanced quantities of essential amino acids.
Return Migration to Eastern Kentucky and the Stem Family Concept
Authors: WHITE STEPHEN E.
Published: July 2006

This research provides a conceptual framework—based on the stem family concept—with which to explore the cyclical nature of return migration to Eastern Kentucky. A generalized six‐phase migration model is developed within a stem family/diffusion context to explain how the socioeconomic characteristics of return migrants have varied in response to economic changes outside Appalachia. The role of awareness space on channeling migration flows is also examined.

Responses from 119 households in Laurel, Pike, and Powell counties, Kentucky, are used to test hypotheses associated with the general model. The survey results support the continued existence of extreme stem family forces within Eastern Kentucky. Most inmigrants are return migrants. Return migration motives continue to be more related to sociocultural factors than they are job‐related decisions. Most returnees are well below retirement age, and even the younger and more educated among these have a strong preference for remaining in Eastern Kentucky, although their historical tendency has been to move away when economic pulls are strong enough. Maps of return migrants’awareness spaces closely conform with past outmigration patterns. As awareness spaces have been shown to correspond with migrants’destination choices, the maps suggest that future outmigrants from Eastern Kentucky will continue to bias their destination choices more toward the North than the South.
Advantages of Place as Perceived by Sunbelt Promoters
Authors: RAITZ KARL
Published: July 2006

A questionnaire was sent to 104 Chamber of Commerce executives in states and cities in the South and Southwest to evaluate the factors they perceive to be important in recruiting business and industrial migrants from the North. Eighty‐one respondents rated 33 locational factors on a scale of 1 to 5. Results show variation in the perceived importance of factors between Southeast, South Central, and Southwest states and the Border states. Patterns of perceived competition among cities reveal that Border cities view Southern cities as their most important competitors but Southern cities see their major competitors as other rapidly growing Southern cities. Large cities do not see smaller cities as competitors with the exception of the “high tech” research centers such as Raleigh, NC.
Conjoining Interindustry Linkages and Ownership Data: An Empirical Application
Authors: JACKSON RANDALL W.
Published: July 2006

Interest in the economic role of the large enterprise has led to numerous studies of economic dependency and regional economic health and performance. In this paper, an interindustry accounting framework is conjoined with Dun and Bradstreet corporate ownership data to provide a fresh perspective on the effects of external economic ownership. The aggregate level measurement method is applied to fifteen multicounty regions in the state of Illinois, and reveals considerable variation in the measures generated. High regional dependence measures are directly related to employment stability and inversely related to employment growth.

Although interindustry accounts have been used most commonly in economic impacts assessment and forecasting, a broader range of potential applications lies in their use as descriptive and explanatory measurement tools. This paper addresses the external ownership issue at the macrolevel by testing the relationship between measures of input‐output dependence and indices of regional employment growth and stability, and demonstrates, in the process, a non‐conventional use of interindustry data. The conjoining of interindustry data and the Dun and Bradstreet data produces a unique set of measures of regional economic structure.