bluuebunny/crossref_metadata_2025 huggingface dataset:
Friction stir processing of 316L stainless steel plate
Authors: Chen Y. C. , Fujii H. , Tsumura T. , Kitagawa Y. , Nakata K. , Ikeuchi K. , Matsubayashi K. , Michishita Y. , Fujiya Y. , Katoh J.
Published: April 2009

316L stainless steel plates were friction stir processed using polycrystalline cubic boron nitride tools. Mechanical properties and microstructure evolution of the friction stir processing (FSP) zone were investigated. Tensile test results showed that the tensile strengths of the defect free FSP zones were equal to those of base metals. All the samples fractured at the base metal side. Microstructural observation results showed that the grains in the FSP zone were refined by the tool. The FSP zone was a roughly equiaxed grain structure and the grain size was in the range of 10–30 μm, which was smaller than that in the base metal (30–80 μm). Moreover, transmission electron microscopy observation revealed that sigma phases formed in this zone during FSP.
Effect of contamination on microstructure in friction stir spot welded DP590 steel
Authors: Ohashi R. , Fujimoto M. , Mironov S. , Sato Y. S. , Kokawa H.
Published: April 2009

In this study, FSSW of DP590 steel was performed using both bare and TiC/TiN coated Si3N4 tool with Ar shielding, and effect of contamination on the microstructure during FSSW was examined. Defect free welds were successfully obtained at all welding conditions. Si, N and O contaminations were clearly found in the weld when bare Si3N4 tool was used without Ar shielding, but the coated tool and Ar shielding could suppress the contaminations. The contaminations caused higher hardness in the vicinity of the pin hole and reduced the weld strength. The present study showed that the prevention of the contaminations could improve the weld strength, especially the cross-tension strength, in FSSW of DP590 steel using Si3N4 tool.
Microstructural and mechanical characterisation of friction stir welded 15-5PH steel
Authors: Weinberger T. , Enzinger N. , Cerjak H.
Published: April 2009

Martensitic precipitation hardening steels are characterised by high strength which is achieved by a martensitic matrix and precipitates. The material also shows a good ductility and toughness if properly heat treated. But welding of these steel types is often problematic and requires a special procedure (e.g. post-weld heat treatment) in order to achieve satisfactory results. In this contribution, the solid state welding process – friction stir welding was used to weld 15-5PH and the results of the investigations are shown. The butt welds for 2·6 mm thick steel sheets have been carried out at Institute for Materials Science and Welding at Graz University of Technology using tungsten based tools, different welding speeds and tool rotational rates. Temperature measurements using thermocouples have been performed on the advancing and retreating sides of the weld. Detailed microstructural observations were performed for base material, heat affected zone, thermomechanically affected zone and stir zone. The appearance of retained austenite, which reduces the strength of the material, has been studied for the distinct regions of the friction stir weld. A quantitative spot analysis by energy dispersive spectroscopy was performed to identify tool remanents in the stir zone of the weld. For further characterisation, hardness profiles of the weld have been created. Tensile tests and surface fracture analysis using scanning electron microscopy have been performed. Welds with low energy input have shown better results than welds with high energy input. Additionally, effects of post-weld heat treatment on microstructure and properties of the joint have been analysed.
Conventional and bobbin friction stir welding of 12% chromium alloy steel using composite refractory tool materials
Authors: Thomas W. M. , Wiesner C. S. , Marks D. J. , Staines D. G.
Published: April 2009

The use of matching tapers to provide a hot friction drive coupling for composite refractory tools for conventional and bobbin friction stir welding of 12% chromium alloy steel is described. The feasibility of using self-reacting (Bobbin) friction stir welding for steel has been demonstrated and the resulting microstructures have been evaluated.
Critical assessment: Friction stir welding of steels
Authors: Bhadeshia H. K. D. H. , DebRoy T.
Published: April 2009

The level of activity in research on the friction stir welding of steels is dwarfed when compared with that on aluminium alloys. There are good reasons for this. The relative weakness of aluminium makes it ideally suited for a process which requires, at high strain rates, the permanent flow and mixing of material without melting. In contrast, there are in general no cost effective tools available for steel. The purpose of this article and the associated papers in this special issue of Science and Technology of Welding and Joining is to assess the state of the art, focusing on the knowledge base in the open literature.
Plerixafor and G-CSF versus placebo and G-CSF to mobilize hematopoietic stem cells for autologous stem cell transplantation in patients with multiple myeloma
Authors: DiPersio John F. , Stadtmauer Edward A. , Nademanee Auayporn , Micallef Ivana N. M. , Stiff Patrick J. , Kaufman Jonathan L. , Maziarz Richard T. , Hosing Chitra , Früehauf Stefan , Horwitz Mitchell , Cooper Dennis , Bridger Gary , Calandra Gary ,   for the 3102 Investigators
Published: April 2009

This phase 3, multicenter, randomized (1:1), double-blind, placebo-controlled study evaluated the safety and efficacy of plerixafor with granulocyte colony-stimulating factor (G-CSF) in mobilizing hematopoietic stem cells in patients with multiple myeloma. Patients received G-CSF (10 μg/kg) subcutaneously daily for up to 8 days. Beginning on day 4 and continuing daily for up to 4 days, patients received either plerixafor (240 μg/kg) or placebo subcutaneously. Starting on day 5, patients began daily apheresis for up to 4 days or until more than or equal to 6 × 106 CD34+ cells/kg were collected. The primary endpoint was the percentage of patients who collected more than or equal to 6 × 106 CD34+ cells/kg in less than or equal to 2 aphereses. A total of 106 of 148 (71.6%) patients in the plerixafor group and 53 of 154 (34.4%) patients in the placebo group met the primary endpoint (P < .001). A total of 54% of plerixafor-treated patients reached target after one apheresis, whereas 56% of the placebo-treated patients required 4 aphereses to reach target. The most common adverse events related to plerixafor were gastrointestinal disorders and injection site reactions. Plerixafor and G-CSF were well tolerated, and significantly more patients collected the optimal CD34+ cell/kg target for transplantation earlier compared with G-CSF alone. This study is registered at www.clinicaltrials.gov as #NCT00103662.
Impaired development of human Th1 cells in patients with deficient expression of STAT4
Authors: Chang Hua-Chen , Han Ling , Goswami Ritobrata , Nguyen Evelyn T. , Pelloso David , Robertson Michael J. , Kaplan Mark H.
Published: April 2009

IL-12 activates STAT4, which is a critical regulator of inflammation and T helper type I (Th1) lineage development in murine systems. The requirement for STAT4 in the generation of human Th1 cells has not been examined thoroughly. Compared with control Th1 cultures, expression of the Th1 genes IFNγ, IL-12Rβ2, and TNFα is greatly reduced in Th1 cultures of CD4 T cells isolated from lymphoma patients after autologous stem cell transplantation who have acquired STAT4 deficiency. Moreover, IL-4 and IL-5 production is increased in patient Th1 cultures though there are no defects in the development of Th2 cells. Reconstitution of STAT4 in patient T cells allowed recovery of IFNγ and IL-12Rβ2 expression, whereas ectopic expression of IL-12Rβ2 did not rescue STAT4 expression, and increased IFNγ production only to levels intermediate between control and patient samples. These results demonstrate that, as in murine systems, STAT4 is required for optimal human Th1 lineage development.
The 2008 revision of the World Health Organization (WHO) classification of myeloid neoplasms and acute leukemia: rationale and important changes
Authors: Vardiman James W. , Thiele Jüergen , Arber Daniel A. , Brunning Richard D. , Borowitz Michael J. , Porwit Anna , Harris Nancy Lee , Le Beau Michelle M. , Hellström-Lindberg Eva , Tefferi Ayalew , Bloomfield Clara D.
Published: April 2009

Recently the World Health Organization (WHO), in collaboration with the European Association for Haematopathology and the Society for Hematopathology, published a revised and updated edition of the WHO Classification of Tumors of the Hematopoietic and Lymphoid Tissues. The 4th edition of the WHO classification incorporates new information that has emerged from scientific and clinical studies in the interval since the publication of the 3rd edition in 2001, and includes new criteria for the recognition of some previously described neoplasms as well as clarification and refinement of the defining criteria for others. It also adds entities—some defined principally by genetic features—that have only recently been characterized. In this paper, the classification of myeloid neoplasms and acute leukemia is highlighted with the aim of familiarizing hematologists, clinical scientists, and hematopathologists not only with the major changes in the classification but also with the rationale for those changes.
Mortality in bronchiectasis: a long-term study assessing the factors influencing survival
Authors: Loebinger M. R. , Wells A. U. , Hansell D. M. , Chinyanganya N. , Devaraj A. , Meister M. , Wilson R.
Published: April 2009

There is little literature about the mortality associated with bronchiectasis. The aim of the present study was to investigate factors affecting mortality in patients with bronchiectasis.

In total, 91 patients were examined for aetiology, pulmonary function tests, high-resolution computed tomography, sputum microbiology and quality of life scores and were then followed over 13 yrs.

Overall, 29.7% of the patients died. On multivariate analysis, age, St George’s Respiratory Questionnaire activity score,Pseudomonas aeruginosainfection, total lung capacity (TLC), residual volume/TLC and the transfer factor coefficient were all independently associated with mortality.

In patients with moderate to severe bronchiectasis, mortality is associated with a degree of restrictive and obstructive disease, poor gas transfer and chronic pseudomonas infection. These features should guide future research into disease progression, and identify those patients needing intensive treatment.
Cryptogenic haemoptysis in smokers: angiography and results of embolisation in 35 patients
Authors: Menchini L. , Remy-Jardin M. , Faivre J-B. , Copin M-C. , Ramon P. , Matran R. , Deken V. , Duhamel A. , Remy J.
Published: April 2009

The aim of the present study was to describe angiographic findings and embolisation results in smokers with haemoptysis.

We retrospectively reviewed the clinical data and angiographic findings from 35 patients with smoking-related bronchopulmonary disease and no associated comorbidity, who were referred for embolisation for mild (n = 6), moderate (n = 14) and severe (n = 15) haemoptysis. Spirometric classification subdivided our population into: 16 patients with chronic bronchitis but no airflow limitation; and 19 patients with chronic obstructive pulmonary disease (COPD) (stage I: n = 12; stage II: n = 5; stage III: n = 2).

Bronchoscopy depicted focal submucosal vascular abnormalities in three patients and only endobronchial inflammation in 32 (91%) patients. Bronchial artery angiography revealed moderate (n = 18) or severe (n = 10) hypervascularisation in 28 (80%) patients, and normal vascularisation in seven (20%). No statistically significant difference was observed between the angiographic findings and the severity of COPD, tobacco consumption or the amount of bleeding. Cessation of bleeding was obtained by embolisation in 29 out of the 34 technically successful procedures (85%), requiring surgery in three out of five patients with recurrence. Follow-up (mean duration 7 yrs) demonstrated no recurrence of bleeding in 32 (94%) out of 34 patients and excluded late endobronchial malignancy.

Smokers with various stages of COPD severity may suffer from haemoptysis that is efficiently treatable by endovascular treatment.
Present and future costs of COPD in Iceland and Norway: results from the BOLD study
Authors: Nielsen R. , Johannessen A. , Benediktsdottir B. , Gislason T. , Buist A. S. , Gulsvik A. , Sullivan S. D. , Lee T. A.
Published: April 2009

The Burden of Obstructive Lung Disease (BOLD) initiative provides standardised estimates of the burden of chronic obstructive pulmonary disease (COPD) worldwide. We estimate the current and future economic burden of COPD in Reykjavik, Iceland and Bergen, Norway using data from the BOLD initiative.

Data on utilisation of healthcare resources were gathered from the BOLD survey, existing literature and unit costs from national sources. Economic data were applied to a Markov model using transition probabilities derived from Framingham data. Sensitivity analyses were conducted varying unit costs, utilisation and prevalence of disease.

The cost of COPD was \#8364;478 per patient per yr in Iceland and \#8364;284 per patient per yr in Norway. The estimated cumulative costs of COPD for the population aged ≥40 yrs, were \#8364;130 million and \#8364;1,539 million for the following 10 yrs in Iceland and Norway, respectively. Costs of COPD accounted for 1.2 and 0.7% of healthcare budgets in Iceland and Norway, respectively. Sensitivity analyses showed estimates were most sensitive to changes in exacerbation frequency.

COPD has a significant economic burden in both Iceland and Norway and will grow in the future. Interventions aimed at avoiding exacerbations will have the most impact on costs of COPD over the next 20 yrs.
Growth hormone excess and sternohyoid muscle mechanics in rats
Authors: Attal P. , Claes V. , Bobin S. , Chanson P. , Kamenicky P. , Zizzari P. , Lecarpentier Y.
Published: April 2009

In vitroisotonic and isometric mechanical properties of the sternohyoid (SH) muscle, an upper airway dilator muscle, were studied in rats with a growth hormone (GH)-secreting tumour (GH tumour group; n = 10). The effects of muscle fatigue were also studied.

Stress and shortening were measured in muscles contracting from zero load up to isometric load under tetanic conditions. Isometric stress and maximum unloaded shortening velocity were determined and compared with values obtained from control rats (n = 10). Crossbridge kinetics and energetics and mechanical efficiency were calculated from Huxley’s equations.

Compared with controls, isometric stress, mechanical efficiency, crossbridge number and crossbridge single force were lower in the GH tumour group. The probability of crossbridge being in the power stroke configuration was lower in the GH tumour group than in controls. Muscle fatigue significantly impaired maximal muscle efficiency and crossbridge single force in the GH tumour group but not in controls.

In conclusion, mechanical and energetic properties of the SH muscle and crossbridge properties were worse in the GH tumour group than in controls. This may partly account for impairment of the upper airway dilator muscle function and the increased occurrence of obstructive sleep apnoea in acromegaly.
Distinct clinical phenotypes of airways disease defined by cluster analysis
Authors: Weatherall M. , Travers J. , Shirtcliffe P. M. , Marsh S. E. , Williams M. V. , Nowitz M. R. , Aldington S. , Beasley R.
Published: April 2009

Airways disease is currently classified using diagnostic labels such as asthma, chronic bronchitis and emphysema. The current definitions of these classifications may not reflect the phenotypes of airways disease in the community, which may have differing disease processes, clinical features or responses to treatment. The aim of the present study was to use cluster analysis to explore clinical phenotypes in a community population with airways disease.

A random population sample of 25–75-yr-old adults underwent detailed investigation, including a clinical questionnaire, pulmonary function tests, nitric oxide measurements, blood tests and chest computed tomography. Cluster analysis was performed on the subgroup with current respiratory symptoms or obstructive spirometric results.

Subjects with a complete dataset (n = 175) were included in the cluster analysis. Five clusters were identified with the following characteristics: cluster 1: severe and markedly variable airflow obstruction with features of atopic asthma, chronic bronchitis and emphysema; cluster 2: features of emphysema alone; cluster 3: atopic asthma with eosinophilic airways inflammation; cluster 4: mild airflow obstruction without other dominant phenotypic features; and cluster 5: chronic bronchitis in nonsmokers.

Five distinct clinical phenotypes of airflow obstruction were identified. If confirmed in other populations, these findings may form the basis of a modified taxonomy for the disorders of airways obstruction.
Prediction of guide strand of microRNAs from its sequence and secondary structure
Authors: Ahmed Firoz , Ansari Hifzur Rahman , Raghava Gajendra PS
Published: April 2009

Background

MicroRNAs (miRNAs) are produced by the sequential processing of a long hairpin RNA transcript by Drosha and Dicer, an RNase III enzymes, and form transitory small RNA duplexes. One strand of the duplex, which incorporates into RNA-induced silencing complex (RISC) and silences the gene expression is called guide strand, or miRNA; while the other strand of duplex is degraded and called the passenger strand, or miRNA*. Predicting the guide strand of miRNA is important for better understanding the RNA interference pathways.

Results

This paper describes support vector machine (SVM) models developed for predicting the guide strands of miRNAs. All models were trained and tested on a dataset consisting of 329 miRNA and 329 miRNA* pairs using five fold cross validation technique. Firstly, models were developed using mono-, di-, and tri-nucleotide composition of miRNA strands and achieved the highest accuracies of 0.588, 0.638 and 0.596 respectively. Secondly, models were developed using split nucleotide composition and achieved maximum accuracies of 0.553, 0.641 and 0.602 for mono-, di-, and tri-nucleotide respectively. Thirdly, models were developed using binary pattern and achieved the highest accuracy of 0.708. Furthermore, when integrating the secondary structure features with binary pattern, an accuracy of 0.719 was seen. Finally, hybrid models were developed by combining various features and achieved maximum accuracy of 0.799 with sensitivity 0.781 and specificity 0.818. Moreover, the performance of this model was tested on an independent dataset that achieved an accuracy of 0.80. In addition, we also compared the performance of our method with various siRNA-designing methods on miRNA and siRNA datasets.

Conclusion

In this study, first time a method has been developed to predict guide miRNA strands, of miRNA duplex. This study demonstrates that guide and passenger strand of miRNA precursors can be distinguished using their nucleotide sequence and secondary structure. This method will be useful in understanding microRNA processing and can be implemented in RNA silencing technology to improve the biological and clinical research. A web server has been developed based on SVM models described in this studyhttp://crdd.osdd.net:8081/RISCbinder/.
Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana
Authors: Iida Kei , Jin Hailing , Zhu Jian-Kang
Published: April 2009

Background

Modifications of RNA bases have been found in some mRNAs and non-coding RNAs including rRNAs, tRNAs, and snRNAs, where modified bases are important for RNA function. Little is known about RNA base modifications in Arabidopsis thaliana.

Results

In the current work, we carried out a bioinformatics analysis of RNA base modifications in tRNAs and miRNAs using large numbers of cDNA sequences of small RNAs (sRNAs) generated with the 454 technology and the massively parallel signature sequencing (MPSS) method. We looked for sRNAs that map to the genome sequence with one-base mismatch (OMM), which indicate candidate modified nucleotides. We obtained 1,187 sites with possible RNA base modifications supported by both 454 and MPSS sequences. Seven hundred and three of these sites were within tRNA loci. Nucleotide substitutions were frequently located in the T arm (substitutions from A to U or G), upstream of the D arm (from G to C, U, or A), and downstream of the D arm (from G to U). The positions of major substitution sites corresponded with the following known RNA base modifications in tRNAs: N1-methyladenosine (m1A), N2-methylguanosine (m2G), and N2-N2-methylguanosine (m2
2G).

Conclusion

These results indicate that our bioinformatics method successfully detected modified nucleotides in tRNAs. Using this method, we also found 147 substitution sites in miRNA loci. As with tRNAs, substitutions from A to U or G and from G to C, U, or A were common, suggesting that base modifications might be similar in tRNAs and miRNAs. We suggest that miRNAs contain modified bases and such modifications might be important for miRNA maturation and/or function.
The complete mitochondrial genomes of two band-winged grasshoppers, Gastrimargus marmoratus and Oedaleus asiaticus
Authors: Ma Chuan , Liu Chunxiang , Yang Pengcheng , Kang Le
Published: April 2009

Background

The two closely related species of band-winged grasshoppers, Gastrimargus marmoratus and Oedaleus asiaticus, display significant differences in distribution, biological characteristics and habitat preferences. They are so similar to their respective congeneric species that it is difficult to differentiate them from other species within each genus. Hoppers of the two species have quite similar morphologies to that of Locusta migratoria, hence causing confusion in species identification. Thus we determined and compared the mitochondrial genomes of G. marmoratus and O. asiaticus to address these questions.

Results

The complete mitochondrial genomes of G. marmoratus and O. asiaticus are 15,924 bp and 16,259 bp in size, respectively, with O. asiaticus being the largest among all known mitochondrial genomes in Orthoptera. Both mitochondrial genomes contain a standard set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and an A+T-rich region in the same order as those of the other analysed caeliferan species, but different from those of the ensiferan species by the rearrangement of trnD and trnK. The putative initiation codon for the cox1 gene in the two species is ATC. The presence of different sized tandem repeats in the A+T-rich region leads to size variation between their mitochondrial genomes. Except for nad2, nad4L, and nad6, most of the caeliferan mtDNA genes exhibit low levels of divergence. In phylogenetic analyses, the species from the suborder Caelifera form a monophyletic group, as is the case for the Ensifera. Furthermore, the two suborders cluster as sister groups, supporting the monophyly of Orthoptera.

Conclusion

The mitochondrial genomes of both G. marmoratus and O. asiaticus harbor the typical 37 genes and an A+T-rich region, exhibiting similar characters to those of other grasshopper species. Characterization of the two mitochondrial genomes has enriched our knowledge on mitochondrial genomes of Orthoptera.
Quality of reporting internal and external validity data from randomized controlled trials evaluating stents for percutaneous coronary intervention
Authors: Ethgen Morgane , Boutron lsabelle , Steg Philippe Gabriel , Roy Carine , Ravaud Philippe
Published: April 2009

Background

Stents are commonly used to treat patients with coronary artery disease. However, the quality of reporting internal and external validity data in published reports of randomised controlled trials (RCTs) of stents has never been assessed.

The objective of our study was to evaluate the quality of reporting internal and external validity data in published reports of RCTs assessing the stents for percutaneous coronary interventions.

Methods

A systematic literature review was conducted. Reports of RCTs assessing stents for percutaneous coronary interventions indexed in MEDLINE and the Cochrane Central Register of Controlled Trials and published between January 2003 and September 2008 were selected. A standardized abstraction form was used to extract data. All analyses were adjusted for the effect of clustering articles by journal.

Results

132 articles were analyzed. The generation of the allocation sequence was adequate in 58.3% of the reports; treatment allocation was concealed in 34.8%. Adequate blinding was reported in one-fifth of the reports. An intention-to-treat analysis was described in 79.5%. The main outcome was a surrogate angiographic endpoint in 47.0%. The volume of interventions per center was described in two reports. Operator expertise was described in five (3.8%) reports. The quality of reporting was better in journals with high impact factors and in journals endorsing the CONSORT statement.

Conclusion

The current reporting of results of RCTs testing stents needs to be improved to allow readers to appraise the risk of bias and the applicability of the results.
A retrospective analysis of second-line chemotherapy in patients with advanced gastric cancer
Authors: Ji Sang Hoon , Lim Do Hyoung , Yi Seong Yoon , Kim Hyo Song , Jun Hyun Jung , Kim Kyoung Ha , Chang Myung Hee , Park Min Jae , Uhm Ji Eun , Lee Jeeyun , Park Se Hoon , Park Joon Oh , Park Young Suk , Lim Ho Yeong , Kang Won Ki
Published: April 2009

Background

Because treatment of advanced gastric cancer (AGC) patients after failure with first-line chemotherapy remains controversial, we performed this retrospective analysis based on the data obtained from 1455 patients registered in a first-line treatment cohort with respect to receiving or not receiving subsequent chemotherapy.

Methods

The decision for administering second-line chemotherapy was, in most cases, at the discretion of the physician. Seven-hundred twenty-five (50%) received second-line chemotherapy after first-line failure. Univariate and multivariate analyses were performed on the recognized baseline parameters for survival.

Results

At the time of initiating second-line chemotherapy, the patients' median age was 56 years (range, 22 to 86) and 139 (19%) had an Eastern Cooperative Oncology Group (ECOG) performance status of 2 or more. Seven (1%) complete and 108 (15%) partial responses to second-line chemotherapy were observed for an overall response rate of 16% (95% confidence interval [CI], 13 to 19%). The median progression-free and overall survivals, calculated from the start of second-line chemotherapy, were 2.9 months (95% CI, 2.6 to 3.3) and 6.7 months (95% CI, 5.8 to 7.5), respectively. Multivariate analysis revealed that low baseline hemoglobin level (hazard ratio [HR], 0.74; 95% CI 0.61–0.90) and a poor performance status (HR, 0.66; 95% CI, 0.52–0.83) were independent negative prognostic factors for overall survival.

Conclusion

Performance status, along with baseline hemoglobin level, could be used to identify the subgroup of patients most likely to benefit from second-line chemotherapy for AGC.
Optimization of physical factors affecting the production of thermo-stable organic solvent-tolerant protease from a newly isolated halo tolerant Bacillus subtilis strain Rand
Authors: Abusham Randa A , Rahman Raja Noor Zaliha RA , Salleh Abu Bakar , Basri Mahiran
Published: April 2009

Background

Many researchers have reported on the optimization of protease production; nevertheless, only a few have reported on the optimization of the production of organic solvent-tolerant proteases. Ironically, none has reported on thermostable organic solvent-tolerant protease to date. The aim of this study was to isolate the thermostable organic solvent-tolerant protease and identify the culture conditions which support its production. The bacteria of genus Bacillus are active producers of extra-cellular proteases, and the thermostability of enzyme production by Bacillus species has been well-studied by a number of researchers. In the present study, the Bacillus subtilis strain Rand was isolated from the contaminated soil found in Port Dickson, Malaysia.

Results

A thermostable organic solvent-tolerant protease producer had been identified as Bacillus subtilis strain Rand, based on the 16S rRNA analysis conducted, as well as the morphological characteristics and biochemical properties. The production of the thermostable organic solvent-tolerant protease was optimized by varying various physical culture conditions. Inoculation with 5.0% (v/v) of (AB600 = 0.5) inoculum size, in a culture medium (pH 7.0) and incubated for 24 h at 37°C with 200 rpm shaking, was the best culture condition which resulted in the maximum growth and production of protease (444.7 U/ml; 4042.4 U/mg). The Rand protease was not only stable in the presence of organic solvents, but it also exhibited a higher activity than in the absence of organic solvent, except for pyridine which inhibited the protease activity. The enzyme retained 100, 99 and 80% of its initial activity, after the heat treatment for 30 min at 50, 55, and 60°C, respectively.

Conclusion

Strain Rand has been found to be able to secrete extra-cellular thermostable organic solvent-tolerant protease into the culture medium. The protease exhibited a remarkable stability towards temperature and organic solvent. This unique property makes it attractive and useful to be used in industrial applications.
Massive comparative genomic analysis reveals convergent evolution of specialized bacteria
Authors: Merhej Vicky , Royer-Carenzi Manuela , Pontarotti Pierre , Raoult Didier
Published: April 2009

Background

Genome size and gene content in bacteria are associated with their lifestyles. Obligate intracellular bacteria (i.e., mutualists and parasites) have small genomes that derived from larger free-living bacterial ancestors; however, the different steps of bacterial specialization from free-living to intracellular lifestyle have not been studied comprehensively. The growing number of available sequenced genomes makes it possible to perform a statistical comparative analysis of 317 genomes from bacteria with different lifestyles.

Results

Compared to free-living bacteria, host-dependent bacteria exhibit fewer rRNA genes, more split rRNA operons and fewer transcriptional regulators, linked to slower growth rates. We found a function-dependent and non-random loss of the same 100 orthologous genes in all obligate intracellular bacteria. Thus, we showed that obligate intracellular bacteria from different phyla are converging according to their lifestyle. Their specialization is an irreversible phenomenon characterized by translation modification and massive gene loss, including the loss of transcriptional regulators. Although both mutualists and parasites converge by genome reduction, these obligate intracellular bacteria have lost distinct sets of genes in the context of their specific host associations: mutualists have significantly more genes that enable nutrient provisioning whereas parasites have genes that encode Types II, IV, and VI secretion pathways.

Conclusion

Our findings suggest that gene loss, rather than acquisition of virulence factors, has been a driving force in the adaptation of parasites to eukaryotic cells. This comparative genomic analysis helps to explore the strategies by which obligate intracellular genomes specialize to particular host-associations and contributes to advance our knowledge about the mechanisms of bacterial evolution.

Reviewers

This article was reviewed by Eugene V. Koonin, Nicolas Galtier, and Jeremy Selengut.
Hypothalamic Injection of Oxyntomodulin Suppresses Circulating Ghrelin-Like Immunoreactivity
Authors: Patterson Michael , Murphy Kevin G. , Patel Sejal R. , Patel Neekhil A. , Greenwood Hannah C. , Cooke Jenny H. , Campbell Daniel , Bewick Gavin A. , Ghatei Mohammad A. , Bloom Stephen R.
Published: April 2009

Ghrelin is a gastric peptide that regulates appetite and GH secretion. Circulating ghrelin levels are elevated by fasting and suppressed postprandially. However, the mechanisms regulating circulating ghrelin levels are unclear. Oxyntomodulin is an anorexic peptide hormone released from L cells in the gut. We investigated the effects of intracerebroventricular (icv) administration of oxyntomodulin on circulating ghrelin levels. The icv administration of 1, 3, or 10 nmol oxyntomodulin reduced circulating acylated and total (acylated and des-acylated) ghrelin 60 min after icv injection. Administration of 1 nmol oxyntomodulin directly into the arcuate nucleus of the hypothalamus significantly reduced total and acylated ghrelin levels, and administration of 3 nmol oxyntomodulin into the lateral ventricle induced c-fos mRNA expression in arcuate nucleus neurons expressing the glucagon-like peptide-1 (GLP-1) receptor. In a final study, the reduction in total ghrelin observed after icv injection of 3 nmol oxyntomodulin was blocked by coadministration of the GLP-1 receptor antagonist exendin (9–39). These studies suggest oxyntomodulin reduces peripheral ghrelin levels via GLP-1 receptor-dependent hypothalamic pathways. Postprandial release of anorexic gut hormones may thus act centrally to contribute to the postprandial reduction in circulating ghrelin.
Progesterone Increases Rat Neural Progenitor Cell Cycle Gene Expression and Proliferation Via Extracellularly Regulated Kinase and Progesterone Receptor Membrane Components 1 and 2
Authors: Liu Lifei , Wang Junming , Zhao Liqin , Nilsen Jon , McClure Kelsey , Wong Karren , Brinton Roberta Diaz
Published: April 2009

Progesterone receptor (PR) expression and regulation of neural progenitor cell (NPC) proliferation was investigated using NPC derived from adult rat brain. RT-PCR revealed that PRA mRNA was not detected in rat NPCs, whereas membrane-associated PRs, PR membrane components (PGRMCs) 1 and 2, mRNA were expressed. Progesterone-induced increase in 5-bromo-2-deoxyuridine incorporation was confirmed by fluorescent-activated cell sorting analysis, which indicated that progesterone promoted rat NPC exit of G0/G1 phase at 5 h, followed by an increase in S-phase at 6 h and M-phase at 8 h, respectively. Microarray analysis of cell-cycle genes, real-time PCR, and Western blot validation revealed that progesterone increased expression of genes that promote mitosis and decreased expression of genes that repress cell proliferation. Progesterone-induced proliferation was not dependent on conversion to metabolites and was antagonized by the ERK1/2 inhibitor UO126. Progesterone-induced proliferation was isomer and steroid specific. PGRMC1 small interfering RNA treatment, together with computational structural analysis of progesterone and its isomers, indicated that the proliferative effect of progesterone is mediated by PGRMC1/2. Progesterone mediated NPC proliferation and concomitant regulation of mitotic cell cycle genes via a PGRMC/ERK pathway mechanism is a potential novel therapeutic target for promoting neurogenesis in the mammalian brain.
The B Cell Translocation Gene (BTG) Family in the Rat Ovary: Hormonal Induction, Regulation, and Impact on Cell Cycle Kinetics
Authors: Li Feixue , Liu Jing , Park Eun-Sil , Jo Misung , Curry Thomas E.
Published: April 2009

The B cell translocation gene (BTG) family regulates gene transcription and cellular differentiation and inhibits proliferation. The present study investigated the spatiotemporal expression pattern of BTG members and their potential role in the rat ovary during the periovulatory period. Immature female rats (22–23 d old) were injected with pregnant mare serum gonadotropin to stimulate follicular development. Ovaries or granulosa cells were collected at various times after hCG administration (n = 3 per time point). Real-time PCR analysis revealed that mRNA for Btg1, Btg2, and Btg3 were highly induced both in intact ovaries and granulosa cells by 4–8 h after hCG treatment, although their temporal expression patterns differed. In situ hybridization analysis demonstrated that Btg1 mRNA expression was highly induced in theca cells at 4 h after hCG, primarily localized to granulosa cells at 8 h, and decreased at 24 h. Btg2 and Btg3 mRNA was also induced in granulosa cells; however, Btg2 mRNA was observed in newly forming corpora lutea. Inhibition of progesterone action and the epidermal growth factor pathway did not change Btg1 and Btg2 mRNA expression, whereas inhibition of prostaglandin synthesis or RUNX activity diminished Btg2 mRNA levels. Overexpression of BTG1 or BTG2 arrested granulosa cells at the G0/G1 phase of the cell cycle and decreased cell apoptosis. In summary, hCG induced Btg1, Btg2, and Btg3 mRNA expression predominantly in the granulosa cell compartment. Our findings suggest that the induction of the BTG family may be important for theca and granulosa cell differentiation into luteal cells by arresting cell cycle progression.
The Effects of Cycling Levels of 17β-Estradiol and Progesterone on the Magnitude of Temporomandibular Joint-Induced Nociception
Authors: Kramer P. R. , Bellinger L. L.
Published: April 2009

A greater incidence of temporomandibular joint (TMJ) pain is reported in females, suggesting that gonadal hormones may play a role in this condition. However, the exact roles of 17β-estradiol (E2) and progesterone (P4) in TMJ pain are not completely known. Two experiments were performed to determine the separate roles of E2 and P4 in TMJ nociception at various stages of the estrous cycle. Ovariectomized (OVX) rats were cycled with physiological concentrations of E2 or P4. The E2-cycled rats then received bilateral TMJ injections of saline (SAL) or complete Freund’s adjuvant (CFA) on the morning of diestrus-2 (low E2 condition) or proestrus (high E2 condition). As a control, OVX rats (no ovarian E2 and no replacement) were injected with SAL or CFA. The TMJ nociception was measured using a validated novel method in which an increase in meal duration directly correlated to the intensity of deep TMJ nociception. In the E2 experiment, CFA injection, but not SAL, increased TMJ nociception in the OVX group, but the effect was less pronounced in diestrus-2 and even less in proestrus. In the P4 experiment, the rats receiving TMJ CFA in diestrus-2 (end of minor P4 surge) did not show an increase in TMJ nociception, whereas the rats injected in proestrus (major P4 surge), estrus (low P4), and metestrus (low P4) had similar increases in TMJ nociception. The hormones’ concentration did not affect TMJ IL-1β, IL-6, C-C motif ligand 20, or C-X-C motif ligand 2 or the trigeminal ganglia calcitonin gene-related peptide. The high physiological concentrations of E2 observed at proestrus and the low P4 concentrations observed at diestrus-2 attenuated or eliminated CFA-induced TMJ nociception. The results suggest that the cyclic estrous cycle concentrations of E2 and P4 can influence CFA-induced TMJ nociception in the rat.
Identification of a Thyroid Hormone Response Element in the Mouse Krüppel-Like Factor 9 Gene to Explain Its Postnatal Expression in the Brain
Authors: Denver Robert J. , Williamson Keith E.
Published: April 2009

Brain development is critically dependent on thyroid hormone (T3). Krüppel-like factor 9 (Klf9) is a T3-inducible gene in developing rat brain, and several lines of evidence support that KLF9 plays a key role in neuronal morphogenesis. Here we extend our findings to the mouse and demonstrate the presence of a functional T3 response element (T3RE) in the 5′ flanking region of the mouse Klf9 gene. Klf9 mRNA is strongly induced in the mouse hippocampus and cerebellum in a developmental stage- and T3-dependent manner. Computer analysis identified a near optimal direct repeat 4 (DR-4) T3RE 3.8 kb upstream of the Klf9 transcription start site, and EMSAs showed that T3 receptor (TR)-retinoid X receptor heterodimers bound to the T3RE with high affinity. The T3RE acts as a strong positive response element in transfection assays using a minimal heterologous promoter. In the mouse neuroblastoma cell line N2a[TRβ1], T3 caused a dose-dependent up-regulation of Klf9 mRNA. Chromatin immunoprecipitation assays conducted with N2a[TRβ1] cells showed that TRs associated with the Klf9 T3RE, and this association was promoted by T3. Treatment of N2a[TRβ1] cells with T3 led to hyperacetylation of histones 3 and 4 at the T3RE site. Furthermore, TRs associated with the DR-4 T3RE in postnatal d 4 mouse brain, and histone 4 acetylation was greater at this site compared with other regions of the Klf9 gene. Our study identifies a functional DR-4 T3RE located in the mouse Klf9 gene to explain its regulation by T3 during mammalian brain development.
Reduced Adiposity and High-Fat Diet-Induced Adipose Inflammation in Mice Deficient for Phosphodiesterase 4B
Authors: Zhang Ren , Maratos-Flier Eleftheria , Flier Jeffrey S.
Published: April 2009

The concept that obesity is an inflammatory state has changed our understanding of this condition and suggested that pharmacological interventions targeting inflammation may be useful strategies to improve metabolic complications of obesity. Phosphodiesterase 4 (PDE4) inhibitors exhibit profound antiinflammatory effects, but whether PDE4 inhibition suppresses obesity-induced inflammation is unknown. Among PDE4 isoforms, PDE4B is the major species mediating inflammatory responses. We therefore examined obesity-related phenotypes in mice deficient for PDE4B. Compared with wild-type littermates, PDE4B-null mice were leaner, with lower fat pad weights, smaller adipocytes, and decreased serum leptin levels on both chow and high-fat diets (HFDs). PDE4B deficiency suppressed TNF-α mRNA levels and macrophage infiltration in white adipose tissue in mice on HFD, but insulin sensitivity was unaltered. PDE4B-null mice on HFDs had increased locomotor activity. These results suggest a previously unappreciated role for PDE4B in the regulation of energy balance and that PDE4B inhibitors could have utility in treatment of obesity and for suppression of obesity-induced inflammation in white adipose tissue.
Fate mapping of mammalian embryonic taste bud progenitors
Authors: Thirumangalathu Shoba , Harlow Danielle E. , Driskell Amanda L. , Krimm Robin F. , Barlow Linda A.
Published: April 2009

Mammalian taste buds have properties of both epithelial and neuronal cells,and are thus developmentally intriguing. Taste buds differentiate at birth within epithelial appendages, termed taste papillae, which arise at mid-gestation as epithelial thickenings or placodes. However, the embryonic relationship between placodes, papillae and adult taste buds has not been defined. Here, using an inducible Cre-lox fate mapping approach with the ShhcreERT2 mouse line, we demonstrate that Shh-expressing embryonic taste placodes are taste bud progenitors, which give rise to at least two different adult taste cell types, but do not contribute to taste papillae. Strikingly, placodally descendant taste cells disappear early in adult life. As placodally derived taste cells are lost, we used Wnt1Cre mice to show that the neural crest does not supply cells to taste buds, either embryonically or postnatally, thus ruling out a mesenchymal contribution to taste buds. Finally, using Bdnf null mice, which lose neurons that innervate taste buds, we demonstrate that Shh-expressing taste bud progenitors are specified and produce differentiated taste cells normally,in the absence of gustatory nerve contact. This resolution of a direct relationship between embryonic taste placodes with adult taste buds, which is independent of mesenchymal contribution and nerve contact, allows us to better define the early development of this important sensory system. These studies further suggest that mammalian taste bud development is very distinct from that of other epithelial appendages.
Human oligodendrocytes from embryonic stem cells: conserved SHH signaling networks and divergent FGF effects
Authors: Hu Bao-Yang , Du Zhong-Wei , Li Xue-Jun , Ayala Melvin , Zhang Su-Chun
Published: April 2009

Human embryonic stem cells (hESCs) offer a platform to bridge what we have learned from animal studies to human biology. Using oligodendrocyte differentiation as a model system, we show that sonic hedgehog (SHH)-dependent sequential activation of the transcription factors OLIG2, NKX2.2 and SOX10 is required for sequential specification of ventral spinal OLIG2-expressing progenitors, pre-oligodendrocyte precursor cells (pre-OPCs) and OPCs from hESC-derived neuroepithelia, indicating that a conserved transcriptional network underlies OPC specification in human as in other vertebrates. However,the transition from pre-OPCs to OPCs is protracted. FGF2, which promotes mouse OPC generation, inhibits the transition of pre-OPCs to OPCs by repressing SHH-dependent co-expression of OLIG2 and NKX2.2. Thus, despite the conservation of a similar transcriptional network across vertebrates, human stem/progenitor cells may respond differently to those of other vertebrates to certain extrinsic factors.
Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants
Authors: Naramoto Satoshi , Sawa Shinichiro , Koizumi Koji , Uemura Tomohiro , Ueda Takashi , Friml Jíří , Nakano Akihiko , Fukuda Hiroo
Published: April 2009

ACAP-type ARF GTPase activating proteins (ARF-GAPs) regulate multiple cellular processes, including endocytosis, secretion, phagocytosis, cell adhesion and cell migration. However, the regulation of ACAP functions by other cellular proteins is poorly understood. We have reported previously that a plant ACAP, VAN3, plays a pivotal role in plant venation continuity. Here,we report on newly identified VAN3 regulators: the CVP2 (cotyledon vascular pattern 2) 5 PTase, which is considered to degrade IP3 and also to produce PtdIns(4)P from PtdIns(4,5)P2; and a PH domain-containing protein, VAB (VAN3 binding protein). Combinational mutations of both CVP2 and its closest homologue CVL1 (CVP2 like 1) phenocopied the strong allele of van3 mutants, showing severe vascular continuity. The phenotype of double mutants between van3,cvp2 and vab suggested that VAN3, CVP2 and VAB function in vascular pattern formation in the same pathway. Localization analysis revealed that both CVP2 and VAB colocalize with VAN3 in the trans-Golgi network (TGN),supporting their functions in the same pathway. The subcellular localization of VAN3 was dependent on its PH domain, and mislocalization of VAN3 was induced in cvp2 or vab mutants. These results suggest that CVP2 and VAB cooperatively regulate the subcellular localization of VAN3 through the interaction between its PH domain and phosphoinositides and/or inositol phosphates. In addition, PtdIns(4)P, to which VAN3 binds preferentially, enhanced the ARF-GAP activity of VAN3, whereas IP3inhibited it. These results suggest the existence of PtdIns(4)Pand/or IP3-dependent subcellular targeting and regulation of VAN3 ACAP activity that governs plant vascular tissue continuity.