bluuebunny/crossref_metadata_2025 huggingface dataset:
Democracy and Diversity
Authors: Reilly Benjamin
Published: February 2007

This book shows how political reformers across the Asia-Pacific region have responded to the reality of their internal diversity by deliberate, innovative, and often highly ambitious forms of political engineering. Harking back to the success of the East Asian ‘Tigers’ and their unorthodox but successful interventions in the economic arena, many democratizing Northeast Asian, Southeast Asian, and Pacific Island states are now seeking to manage political change by far-reaching reforms to their electoral, parliamentary, and party systems. This book is part of the Oxford Studies in Democratization, a series for scholars and students of comparative politics and related disciplines. Volumes concentrate on the comparative study of the democratization process that accompanied the decline and termination of the cold war. The geographical focus of the series is primarily Latin America, the Caribbean, Southern and Eastern Europe, and relevant experiences in Africa and Asia.
3 Diversity, Democracy, and Development in the Asia‐Pacific
Authors: Reilly Benjamin
Published: February 2007

This chapter examines the impact of social diversity on state development across the Asia-Pacific region. It argues that variation in ethnic structure both between and within states helps to explain some of the distinctive features of political and economic development across the region. However, these vary across different dimensions of governance. With regards to public policy, highly diverse societies almost inevitably face difficulties of government coordination and policy implementation due to competing ethnoregional demands. On the other hand, in certain situations such diversity may also assist democratic continuity by necessitating cross-ethnic power-sharing and making challenges to the existing order difficult to organize and sustain.
The Coordination of the European Union
Authors: Jordan Andrew , Schout Adriaan
Published: February 2007

As the traditional mode of coordinating — essentially issuing regulation — no longer commands sufficient political support, the EU has turned to what are increasingly termed soft or ‘new’ modes of governance, which rely upon different actors working together in relatively non-hierarchical networks. New modes of governance are in vogue because they appear to provide the EU with a new way to add value to national level activities without the slow process of agreeing new legislation or the cost associated with building new administrative capacities in Brussels. This analysis provides the first book-length account of the effectiveness of network-based modes at addressing problems that simultaneously demand greater horizontal and vertical coordination. Taking as an example the thirty-year struggle to build environmental thinking into all areas and levels of EU policy making, it systematically explores the steps that two major EU institutions (the European Commission and the European Parliament), and three member states (Germany, the Netherlands, and the UK) have (not) taken to build effective networked governance. By blending state of the art theories with new empirical findings, it offers a stark reminder that networked governance is not and has never been a panacea. Coordinating networks do not spontaneously ‘self organize’ in the EU; they have to be carefully designed as part of a repertoire of different coordinating instruments. The book concludes that the EU urgently needs to devote more of its time to the more mundane but important task of auditing and managing networks, which, paradoxically, is an exercise in hierarchy. In so doing, this book helps to strip away some of the rhetorical claims made about the novelty and appeal of new modes, to reveal a much more sober and realistic appraisal of their coordinating potential.
1 POLITICAL AMBITIONS AND COORDINATION CAPACITIES: THE MANAGEMENT OF HORIZONTAL AND VERTICAL INTERDEPENDENCE
Authors: Jordan Andrew , Schout Adriaan
Published: February 2007

This chapter aims to explore the role — both real and potential — of one particular family of coordinating devices that have come to be known as ‘new’ modes of governing. In particular, it addresses what is needed to ensure these new modes function effectively at national and at European levels. It analyses the terms coordination and governance, then shows why the coordination of a cross-sectoral, boundary spanning challenge like environmental protection is especially difficult to achieve in a complex multi-levelled governance system such as the EU. The three most widely known and intensively studied modes of coordination are described: hierarchy, markets, and networks, and are related to the steps taken by the EU to achieve greater environmental coordination at EU level.
Crisis of Doubt
Authors: Larsen Timothy
Published: February 2007

For fifty years or more, a dominant motif in 19th-century British studies has been the Victorian crisis of faith or loss of faith. From Basil Willey to A. N. Wilson, books have been written that recounted the stories of Victorians who lost their faith. This narrative has become so ingrained that it is often the principal theme presented when religion in 19th-century Britain is discussed in general histories, textbooks, and literary studies. Serving as a corrective to that tired and overblown approach, this book uncovers a new pattern: the Victorian crisis of doubt. A whole succession of freethinking or Secularist leaders in 19th-century England reconverted back to Christianity, including figures well known in social, political, and literary studies such as the radical publisher William Hone and the Chartist Thomas Cooper. As sceptics, they had read, written about, and lectured on all the latest ideas that served to undermine faith such as biblical criticism and Darwinism. Nevertheless, they went on to judge that faith was more intellectually compelling than doubt, and to defend Christian thought in their writings, lectures, and public debates with Secularists. They held an honest faith to match the familiar theme of honest doubt. This was a deep crisis in the popular, freethinking movement: again and again leading Secularist lecturers and editors defected from the cause and re-emerged as able opponents. The book explores in detail their reasons for rejecting scepticism and their responses to the intellectual challenges to faith in their day. This study serves not only to correct an exaggerated emphasis on the Victorian crisis of faith, but also to reveal the intellectual strength of Christianity in the 19th century.
3 Frederic Rowland Young
Authors: Larsen Timothy
Published: February 2007

Frederic Rowland Young was a Secularist lecturer who worked for G. J. Holyoake and wrote for his newspaper, the Reasoner; he later became a Unitarian minister. With George Sexton, he became a Christian apologist and a proponent of Spiritualism. Eventually, he became convinced of the doctrine of the Trinity and the deity of Christ and served for a time as a Congregational minister.
8 Marriage and Sexual Relationships
Authors: Holmes Andrew R.
Published: February 2007

This chapter outlines official marriage practices and attitudes, with particular reference to the established church, before examining the communal aspect of marriage and sexual relations within the context of church discipline and local community life.
10 Catechizing, Education, and Reading Practices
Authors: Holmes Andrew R.
Published: February 2007

This chapter begins by outlining how catechizing and visitation was conducted, and the impact evangelicalism had upon pastoral efficiency in the Synod of Ulster. Section two examines the provision of education through Sunday and day schools, noting the symbiotic relationship between the supply of opportunities for education on the part of voluntary societies and the demands of the laity. The chapter concludes by examining in general terms the reading practices of Presbyterians, what and how they read, and the impact evangelicalism had upon the demand for, and supply of, certain types of reading material.
8 Conclusion: Legitimizing Democracy and Democratizing Legitimacy
Authors: Deveaux Monique
Published: February 2007

In this concluding chapter, the main arguments of the book are briefly recapped and extended. Democratic legitimacy is defended as a core norm for plural, liberal democratic societies, one which should also guide deliberations about contested cultural practices. This chapter also makes the case for expanding the scope of what we understand as (legitimating) democratic activity, so as to include not only formal, institutionalized democratic practices and spaces, but also informal, everyday expressions of democratic agency. Such a shift should enable us to better see and foster women’s capacities and opportunities to resist, affirm, transform, and reinvent their cultural traditions and arrangements, which speak directly to the issue of the legitimacy of those traditions.
The Aims of Enquiry
Authors: Gaukroger Stephen
Published: February 2007

This chapter builds on the previous two to offer a more integrated account of the intersections between questions of truth, justification, objectivity, and legitimacy. The origins of philosophy in Plato's Socratic dialogues are represented as a struggle between sophism and philosopher, where the difference lies in a commitment to uncovering the truth. This concern can be traced through to the early modern period, but the 17th century witnessed a shift from notions of truth to notions of objectivity and impartiality as a guide for natural philosophical enquiry.
Corpuscularianism and the Rise of Mechanism
Authors: Gaukroger Stephen
Published: February 2007

From the early 17th century onwards, the dominant natural philosophy was mechanism: the view that all explanations must ultimately take the form of a reduction to a very economical range of features at the micro-corpuscularian level, e.g., in the paradigm case, size, speed, and direction of motion. Gassendi and Beeckman offered very different routes to mechanism: Gassendi's was a legitimatory programme that focuses on matter theory, whereas Beeckman's approach comes directly out of mechanics, which it attempted to transform into natural philosophy by fleshing it out in micro-corpuscularian terms. The crucial stage in mechanism comes with the rise of concerted attempts to integrate mechanics and matter theory into a consistent whole, at the same time offering the mechanism so devised as a complete theory of the cosmos, and it is the approaches of Hobbes, whose closest affinities are with Gassendi, and Descartes, whose closest affinities are with Beeckman, that bring out most clearly what is at issue here.
OMWSA: detection of DNA repeats using moving window spectral analysis
Authors: Du Liping , Zhou Hongxia , Yan Hong
Published: February 2007

Summary: Repetitive DNA sequences play paramount biological roles, such as gene variation and regulatory functions on gene expressions. Until now, detection of various kinds of DNA repeats accurately is still an open problem. In this article, we propose a new method and a visualization tool for detecting DNA repeats in a 2D plane of location and frequency by using optimized moving window spectral analysis. The spectrogram can display the general distribution of repetitive sequences while showing the repeat period, length and location without any prior knowledge. Experimental results demonstrate that our method is accurate and robust even under the condition of excessive mutating and interleaving.

Availability: Available on http://www.hy8.com/~tec/sw01/omwsa01.zip.

Contact:  h.yan@cityu.edu.hk

Supplementary information: Supplementary data are available at Bioinformatics online.
PROMALS: towards accurate multiple sequence alignments of distantly related proteins
Authors: Pei Jimin , Grishin Nick V.
Published: February 2007

Motivation: Accurate multiple sequence alignments are essential in protein structure modeling, functional prediction and efficient planning of experiments. Although the alignment problem has attracted considerable attention, preparation of high-quality alignments for distantly related sequences remains a difficult task.

Results: We developed PROMALS, a multiple alignment method that shows promising results for protein homologs with sequence identity below 10%, aligning close to half of the amino acid residues correctly on average. This is about three times more accurate than traditional pairwise sequence alignment methods. PROMALS algorithm derives its strength from several sources: (i) sequence database searches to retrieve additional homologs; (ii) accurate secondary structure prediction; (iii) a hidden Markov model that uses a novel combined scoring of amino acids and secondary structures; (iv) probabilistic consistency-based scoring applied to progressive alignment of profiles. Compared to the best alignment methods that do not use secondary structure prediction and database searches (e.g. MUMMALS, ProbCons and MAFFT), PROMALS is up to 30% more accurate, with improvement being most prominent for highly divergent homologs. Compared to SPEM and HHalign, which also employ database searches and secondary structure prediction, PROMALS shows an accuracy improvement of several percent.

Availability: The PROMALS web server is available at: http://prodata.swmed.edu/promals/

Contact:  jpei@chop.swmed.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
A simulation test bed for hypotheses of genome evolution
Authors: Beiko Robert G. , Charlebois Robert L.
Published: February 2007

Motivation: Microbial genomes undergo evolutionary processes such as gene family expansion and contraction, variable rates and patterns of sequence substitution and lateral genetic transfer. Simulation tools are essential for both the generation of data under different evolutionary models and the validation of analytical methods on such data. However, meaningful investigation of phenomena such as lateral genetic transfer requires the simultaneous consideration of many underlying evolutionary processes.

Results: We have developed EvolSimulator, a software package that combines non-stationary sequence and gene family evolution together with models of lateral genetic transfer, within a customizable birth–death model of speciation and extinction. Here, we examine simulated data sets generated with EvolSimulator using existing statistical techniques from the evolutionary literature, showing in detail each component of the simulation strategy.

Availability: Source code, manual and other information are freely available at www.bioinformatics.org.au/evolsim

Contact:  beiko@cs.dal.ca

Supplementary information: Supplementary data are available at Bioinformatics online.
CopyCat : cophylogenetic analysis tool
Authors: Meier-Kolthoff Jan P. , Auch Alexander F. , Huson Daniel H. , Göker Markus
Published: February 2007

Summary: We have developed the software CopyCat which provides an easy and fast access to cophylogenetic analyses. It incorporates a wrapper for the program ParaFit, which conducts a statistical test for the presence of congruence between host and parasite phylogenies. CopyCat offers various features, such as the creation of customized host–parasite association data and the computation of phylogenetic host/parasite trees based on the NCBI taxonomy.

Availability: CopyCat and its manual are freely available at http://www-ab.informatik.uni-tuebingen.de/software/copycat.

Contact:  auch@informatik.uni-tuebingen.de

Supplementary information: Results of the real-world example can be found at http://www-ab.informatik.uni-tuebingen.de/software/copycat or Bioinformatics online.
Ontology development for biological systems: immunology
Authors: Diehl Alexander D. , Lee Jamie A. , Scheuermann Richard H. , Blake Judith A.
Published: February 2007

Summary: We recently implemented improvements to the representation of immunology content of the biological process branch of the Gene Ontology (GO). The aims of the revision were to provide a comprehensive representation of immunological processes and to improve the organization of immunology related terms in the GO to match current concepts in the field of immunology. With these improvements, the GO will better reflect current understanding in the field of immunology and thus prove to be a more valuable resource for knowledge representation in gene annotation and analysis in the areas of immunology related to genomics and bioinformatics.

Availability:  http://www.geneontology.org

Contact:  adiehl@informatics.jax.org
Mechanisms of cardiac protection from ischemia/reperfusion injury: a role for caveolae and caveolin‐1
Authors: Patel Hemal H. , Tsutsumi Yasuo M. , Head Brian P. , Niesman Ingrid R. , Jennings Michelle , Horikawa Yousuke , Huang Diane , Moreno Ana L. , Patel Piyush M. , Insel Paul A. , Roth David M.
Published: February 2007

Caveolae, small invaginations in the plasma membrane, contain caveolins (Cav) that scaffold signaling molecules including the tyrosine kinase Src. We tested the hypothesis that cardiac protection involves a caveolin‐dependent mechanism. We usedin vitroandin vivomodels of ischemia‐reperfusion injury, electron microscopy (EM), transgenic mice, and biochemical assays to address this hypothesis. We found that Cav‐1 mRNA and protein were expressed in mouse adult cardiac myocytes (ACM). The volatile anesthetic, isoflurane, protected ACM from hypoxia‐induced cell death and increased sarcolemmal caveolae. Hearts of wild‐type (WT) mice showed rapid phosphorylation of Src and Cav‐1 after isoflurane and ischemic preconditioning. The Src inhibitor PP2 reduced phosphorylation of Src (Y416) and Cav‐1 in the heart and abolished isoflurane‐induced cardiac protection in WT mice. Infarct size (percent area at risk) was reduced by isoflurane in WT (30.5±4vs.44.2±3,n=7,P<0.05) but not Cav‐1−/−mice (46.6±5vs.41.7±3,n=7). Cav‐1−/−mice exposed to isoflurane showed significant alterations in Src phosphorylation and recruitment of C‐terminal Src kinase, a negative regulator of Src, when compared to WT mice. The results indicate that isoflurane modifies cardiac myocyte sarcolemmal membrane structure and composition and that activation of Src and phosphorylation of Cav‐1 contribute to cardiac protection. Accordingly, therapies targeted to post‐translational modification of Src and Cav‐1 may provide a novel approach for such protection.—Patel, H. H., Tsutsumi, Y. M., Head, B. P., Niesman, I. R., Jennings, M., Horikawa, Y. Huang, D., Moreno, A. L., Patel, P. M., Insel, P. A., Roth, D. M. Mechanisms of cardiac protection from ischemia/reperfusion injury: a role for caveolae and caveolin‐1.FASEB J.21, 1565–1574 (2007)
Laser Eustachian Tuboplasty: Two‐Year Results
Authors: Poe Dennis S. , Grimmer J. Fredrik , Metson Ralph
Published: February 2007

Objective/Hypothesis: Laser eustachian tuboplasty (LETP) combined with appropriate medical management will eliminate the chronic presence of middle ear effusions in selected patients.

Methods: The study population consisted of 13 adults with otitis media with effusion (OME). Patients underwent slow‐motion video endoscopy to identify the location and extent of surgical resection. A diode or argon laser was used to vaporize areas of hypertrophic mucosa and submucosa along the cartilaginous eustachian tube. Patients were evaluated at 6, 12, and 24 months. Successful outcome was defined as absence of OME. Patients with evidence of reflux disease or allergic rhinitis were treated with medical therapy before surgery and throughout the follow‐up period as indicated.

Results: LETP combined with medical management eliminated OME in 36% (4 of 11) of patients at 6 months, 40% (4 of 10) at 1 year, and 38% (3 of 8) at 2 years. Failure of LETP correlated with presence of laryngopharyngeal reflux (P = .01) or allergic disease (P = .05) for the results at 1 year but not at 2 years.

Conclusions: LETP combined with appropriate medical management may be an effective treatment in select patients with chronic persistent eustachian tube dysfunction. A controlled trial with a larger number of subjects will be necessary to determine the efficacy of LETP and identify those factors predictive of successful outcome.
Protein Expression of the Tumor Suppressors p16INK4A and p53 and Disease Progression in Recurrent Respiratory Papillomatosis
Authors: Pham Truc T. , Ongkeko Weg M. , An Yi , Yi Eunhee S.
Published: February 2007

Background: Recurrent respiratory papillomatosis (RRP) is a benign condition that rarely metastasizes as invasive squamous cell carcinoma. Although this disease is associated with human papillomavirus, the role of this virus in tumorigenesis is unclear.

Objectives: The aim of this study is to assess the involvement of the tumor suppressors P16INK4A and p53 in RRP tumor progression.

Design: Immunohistochemistry of p16INK4A and p53 was performed on biopsies of recurrent squamous papillomas and invasive lesions in nine patients.

Results: Twenty biopsies were graded as papillomas (RP), three as papillomas with high‐grade dysplasia/carcinoma in situ (HGD/CIS), and two as invasive squamous cell carcinoma (SCCA). Forty‐five percent of RP and 60% of HGD/CIS/SCCA expressed p16INK4A. Fifty percent of RP and 100% of HGD/CIS/SCCA expressed p53. The difference in the frequency of p53‐positive staining between HGD/CIS and SCCA (100% of tissues examined) and RP (50% of tissues examined) approached statistical significance. Neither p16INK4A nor p53 was predictive of invasive transformation.

Conclusions: Expression of p16INK4A, which is a surrogate for the tumor suppressor retinoblastoma (Rb), did not immediately lead to invasive disease. There is no correlation between disease severity of RRP and level of p16INK4A.
Extracranial Head and Neck Schwannomas: A Clinical Analysis of 33 Patients
Authors: Zhang Hao , Cai Changping , Wang Shili , Liu Huiru , Ye Yanfen , Chen Xueming
Published: February 2007

Objective: To study the clinical features, diagnosis, and management of the extracranial head and neck schwannomas.

Study Design: Retrospective study.

Methods: The clinical data of 33 patients with schwannoma of the head and neck from 1996 to 2006 were studied retrospectively.

Results: Extracranial head and neck schwannomas usually presented as solitary and well‐demarcated lesions with insidious course. Although benign, the lesion can cause secondary symptoms, such as nasal obstruction, dysphasia, and hoarseness, relevant to location of the lesion. Fine needle aspiration cytology, computed tomography scans, and magnetic resonance imaging may provide limited implications in the diagnosis of schwannomas, whereas postoperative pathologic examination establishes the final diagnosis.

Conclusions: Complete surgical excisions with appropriate approaches have proven to be efficient and successful in the treatment of head and neck schwannomas.
War, Politics, and Voice: The Vocal Fold Paralysis of George Orwell
Authors: Sulica Lucian
Published: February 2007

Background: In 1936, like many individuals who felt the menace of fascism, George Orwell traveled to Spain to lend his support to the cause of the Republic, battling a right‐wing coup. Spain, during its Civil War, was an eye‐opening experience for him, yielding insights that allowed, and even compelled him to write Animal Farm and 1984. Spain was also a close brush with death. In May of 1937, in a trench on a windswept ridge near Huesca, Orwell was shot through the neck by a sniper, leaving him with a paralyzed vocal fold.

Design: A thorough review of firsthand accounts of Orwell's injury and subsequent care was made. These are presented in the context of current knowledge of ballistics, penetrating neck trauma, and vocal fold paralysis.

Results and Conclusion: Orwell survived largely because of the nature of his wounding with a high‐velocity jacketed military round. His recovery followed a course in many ways typical for patients with vocal fold paralysis. His writings leave us a unique and extraordinary account of the experience of being shot, of the medical care of the day, of the handicap of paralytic dysphonia, and of survival and heroism under extraordinary circumstances.
Effect of Surgical Treatment on Lymphoproliferation in Advanced Supraglottic Laryngeal Cancer
Authors: Conti‐Freitas Luiz Carlos , Foss‐Freitas Maria Cristina , Mamede Rui Celso Martins , Foss Norma Tiraboschi
Published: February 2007

Objectives: The capacity of cell immunity to act against tumor cells has been presented as a decisive influence in the prognosis of patients with cancer. The aim of this study was to evaluate lymphoproliferation in nonadherent peripheral blood cell cultures of patients with advanced supraglottic laryngeal cancer.

Study Design: Fourteen patients with advanced supraglottic laryngeal cancer were studied prospectively. Lymphoproliferation was quantified by adding 3H‐thymidine and measured in counts/minute using liquid scintillation spectrometry. Based on the ratio between stimulated and baseline cultures, the proliferation index was calculated before and 236 ± 18 days after the surgery.

Results: Lymphoproliferation was lower in patients than in healthy controls (P = .01) in the preoperative as well as in the late postoperative period (P = .006 and P = .02, respectively). However, there was no change from preoperative to late postoperative.

Conclusion: Pre‐ and postoperative results show that patients with advanced supraglottic laryngeal cancer present lymphoproliferation diminished before the surgery, and in the late postoperative period, there was no recovery of immune capacity evaluated by lymphoproliferation measurement.
Distress in Spouses and Patients After Treatment for Head and Neck Cancer
Authors: Verdonck‐de Leeuw Irma M. , Eerenstein Simone E. , Van der Linden Mecheline H. , Kuik Dirk J. , de Bree Remco , Leemans C. Rene
Published: February 2007

Background: The objective of this study is to obtain insight into distress in spouses and patients treated for head and neck cancer.

Methods: Forty‐one patient–spouse pairs completed the Hospital Anxiety and Depression Scale (HADS). Inclusion criteria included curative treatment for head and neck cancer. Exclusion criteria were visiting the clinic without a spouse, bad news at the routine follow‐up examination, diseases causing cognitive dysfunction, and poor understanding of the Dutch language. Next to the HADS, the assessment protocol included age, gender, health status, coping strategy, time since cancer treatment, tumor stage and site, treatment modality, functional and social impairment, and caregiving burden.

Results: A clinical level of distress was noted in 20% of the spouses and in 27% of the patients. Distress in spouses was related to the presence of a feeding tube in patients, a passive coping style, less vitality, and a disrupted daily life schedule resulting from caregiving. Distress in patients was related to the presence of a feeding tube, speech and swallowing problems, less social contacts, a passive style of coping, and nonexpression of emotions.

Conclusion: Distress is often present in spouses and patients treated for head and neck cancer. Routine screening for psychologic distress is recommended.
Effects of Halofuginone on Fibrosis Formation Secondary to Experimentally Induced Subglottic Trauma
Authors: Ertuğrul E. Eylem , Cincik Hakan , Dogru Salim , Cekin Engin , Berber Ufuk , Gungor Atila , Poyrazoğlu I. Ethem
Published: February 2007

Objective: The aim of the study was to assess the antifibrotic effect of systemically applied halofuginone after subglottic injury.

Materials and Methods: After standardized trauma to subglottic area, rats were divided into two groups: a study group that received treatment and a control group that did not. The rats were treated with 0.1 mg/kg/day intraperitoneal halofuginone injection for 30 days. The larynx specimens were examined histopathologically under light microscope for epithelization, inflammation, necrosis, and fibrosis.

Results: The fibrosis indexes of the treated group were significantly less than those of the control group (P < .01).

Conclusions: Systemically applied halofuginone hydrobromide decreases fibrosis/scar tissue formation secondary to experimentally induced acute subglottic trauma.
Shewanella donghaensis sp. nov., a psychrophilic, piezosensitive bacterium producing high levels of polyunsaturated fatty acid, isolated from deep-sea sediments
Authors: Yang Sung-Hyun , Lee Jung-Hyun , Ryu Ji-Sun , Kato Chiaki , Kim Sang-Jin
Published: February 2007

A Gram-negative, motile, rod-shaped, psychrophilic bacterium, LT17T, was isolated from deep-sea sediments (3300 m depth) of the East Sea (Sea of Japan). Optimal growth of LT17Trequires the presence of 2.5 % (w/v) NaCl, a pH of 7.0–7.5 and a temperature of 17 °C. The isolate grows optimally under a hydrostatic pressure of 10 MPa and growth is possible between 0.1 and <30 MPa. The novel strain is positive in tests for catalase, oxidase, lipase,β-glucosidase and gelatinase activities and reduces nitrate to nitrate. The predominant cellular fatty acids are iso-C13 : 0, iso-C15 : 0, C16 : 0, C16 : 1ω7 and C20 : 5ω3. The DNA G+C content of strain LT17Tis 38.8 mol%. Phylogenetic analysis of 16S rRNA gene sequences places this bacterium in the classGammaproteobacteria, within the genusShewanella. The closest relatives of strain LT17TareShewanella japonica(97.8 % gene sequence similarity),Shewanella pacifica(97.5 %),Shewanella olleyana(96.8 %),Shewanella frigidimarina(96.5 %) andShewanella gelidimarina(95.4 %). The DNA–DNA hybridization levels between the novel isolate and its closest known phylogenetic relatives,S. japonicaandS. pacifica, are lower than 14 %. On the basis of this polyphasic evidence, strain LT17Trepresents a novel species of the genusShewanella, for which the nameShewanella donghaensissp. nov. is proposed. The type strain is LT17T(=KCTC 10635BPT=JCM 12524T).
Thalassospira xiamenensis sp. nov. and Thalassospira profundimaris sp. nov.
Authors: Liu Chenli , Wu Yehui , Li Li , Ma Yingfei , Shao Zongze
Published: February 2007

Two bacterial strains, M-5Tand WP0211T, were isolated from the surface water of a waste-oil pool in a coastal dock and from a deep-sea sediment sample from the West Pacific Ocean, respectively. Analysis of 16S rRNA gene sequences indicated that both strains belonged to the classAlphaproteobacteriaand were closely related toThalassospira lucentensis(96.1 and 96.2 %, gene sequence similarity, respectively). Based on the results of physiological and biochemical tests, as well as DNA–DNA hybridization experiments, it is suggested that these isolates represent two novel species of the genusThalassospira. Various traits allow both novel strains to be differentiated fromThalassospira lucentensis, including oxygen requirement, nitrate reduction and denitrification abilities and major fatty acid profiles, as well as their ability to utilize six different carbon sources. Furthermore, the novel strains may be readily distinguished from each other by differences in their motility, flagellation, growth at 4 °C and 40 °C, their ability to hydrolyse Tween 40 and Tween 80, their utilization of 19 different carbon sources and by quantitative differences in their fatty acid contents. It is proposed that the isolates represent two novel species for which the namesThalassospira xiamenensissp. nov. (type strain, M-5T=DSM 17429T=CGMCC 1.3998T) andThalassospira profundimarissp. nov. (type strain, WP0211T=DSM 17430T=CGMCC 1.3997T) are proposed.
Methylobacterium oryzae sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic, 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from rice
Authors: Madhaiyan Munusamy , Kim Byung-Yong , Poonguzhali Selvaraj , Kwon Soon-Wo , Song Myung-Hee , Ryu Jeoung-Hyun , Go Seung-Joo , Koo Bon-Sung , Sa Tong-Min
Published: February 2007

A pink-pigmented, facultatively methylotrophic bacterium, strain CBMB20T, isolated from stem tissues of rice, was analysed by a polyphasic approach. Strain CBMB20Tutilized 1-aminocyclopropane 1-carboxylate (ACC) as a nitrogen source and produced ACC deaminase. It was related phylogenetically to members of the genusMethylobacterium. 16S rRNA gene sequence analysis indicated that strain CBMB20Twas most closely related toMethylobacterium fujisawaense,Methylobacterium radiotoleransandMethylobacterium mesophilicum; however, DNA–DNA hybridization values were less than 70 % with the type strains of these species. The DNA G+C content of strain CBMB20Twas 70.6 mol%. The study presents a detailed phenotypic characterization of strain CBMB20Tthat allows its differentiation from otherMethylobacteriumspecies. In addition, strain CBMB20Tis the only known member of the genusMethylobacteriumto be described from the phyllosphere of rice. Based on the data presented, strain CBMB20Trepresents a novel species in the genusMethylobacterium, for which the nameMethylobacterium oryzaesp. nov. is proposed, with strain CBMB20T(=DSM 18207T=LMG 23582T=KACC 11585T) as the type strain.
Bacillus lehensis sp. nov., an alkalitolerant bacterium isolated from soil
Authors: Ghosh A. , Bhardwaj M. , Satyanarayana T. , Khurana M. , Mayilraj S. , Jain R. K.
Published: February 2007

A Gram-positive, endospore-forming, alkalitolerant bacterial strain, designated MLB2T, was isolated from soil from Leh, India, and was subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genusBacillus. Growth was observed at pH 7.0–11.0, but not at pH 6.0. The DNA G+C content was 41.4 mol%. The highest level of 16S rRNA gene sequence similarity was withBacillus oshimensisJCM 12663T(98.8 %). However, DNA–DNA hybridization experiments indicated low levels of genomic relatedness with the type strains ofB. oshimensis(62 %),Bacillus patagoniensis(55 %),Bacillus clausii(51 %) andBacillus gibsonii(34 %), the species with which strain MLB2Tformed a coherent cluster (based on the results of the phylogenetic analysis). On the basis of the phenotypic characteristics and genotypic distinctiveness of strain MLB2T, it should be classified within a novel species ofBacillus, for which the nameBacillus lehensissp. nov. is proposed. The type strain is MLB2T(=MTCC 7633T=JCM 13820T).
Exiguobacterium profundum sp. nov., a moderately thermophilic, lactic acid-producing bacterium isolated from a deep-sea hydrothermal vent
Authors: Crapart Sylvaine , Fardeau Marie-Laure , Cayol Jean-Luc , Thomas Pierre , Sery Christian , Ollivier Bernard , Combet-Blanc Yannick
Published: February 2007

A facultatively anaerobic, halotolerant, moderately thermophilic and non-sporulating bacterium, designated strain 10CT, was isolated from deep-sea hydrothermal vent samples collected on the 13° N East Pacific Rise at a depth of approximately 2600 m. Cells of strain 10CTwere Gram-positive, motile rods, and grew optimally at 45 °C (range 12–49 °C), pH 7.0 (range pH 5.5–9.5) and 0–2 % NaCl (range 0–11 %). (+)-l-Lactate was the main organic acid detected from carbohydrate fermentation with traces of formate, acetate and ethanol. Strain 10CTwas catalase-positive, oxidase-negative and reduced nitrate to nitrite under anaerobic conditions. The DNA G+C content was 50.4 mol%. Its closest phylogenetic relatives wereExiguobacterium aestuariiTF-16TandExiguobacterium marinumTF-80T(16S rRNA gene sequence similarity >99 %). However, strain 10CTdiffered genotypically from these twoExiguobacteriumspecies as indicated by DNA–DNA relatedness data. Therefore, on the basis of phenotypic, genotypic and phylogenetic characteristics, strain 10CTis considered to represent a novel species of the genusExiguobacterium, for which the nameExiguobacterium profundumsp. nov. is proposed. The type strain is 10CT(=CCUG 50949T=DSM 17289T).
Salegentibacter catena sp. nov., isolated from sediment of the South China Sea, and emended description of the genus Salegentibacter
Authors: Ying Jiao-Yan , Liu Zhi-Pei , Wang Bao-Jun , Dai Xin , Yang Su-Sheng , Liu Shuang-Jiang
Published: February 2007

A novel marine bacterial strain, HY1T, was isolated from sediment of the South China Sea. The strain was aerobic and heterotrophic and formed saffron yellow-pigmented colonies on marine agar 2216. Cells were non-motile, Gram-negative rods, frequently occurring in chains. blastn searches revealed that the 16S rRNA gene sequence of strain HY1T showed high similarity with those of members of the genera Gillisia (91.7–93.8 %) and Salegentibacter (92.6–93.5 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain clustered with members of both Salegentibacter and Gillisia and phylogenetic trees constructed using three different methods (neighbour-joining, maximum-parsimony and minimum-evolution) indicated that strain HY1T clustered more frequently with members of the genus Salegentibacter. The DNA G+C content of strain HY1T was 44.4 mol% and its major cellular fatty acids (⩾5 % of the total fatty acids) were iso-15 : 1 (5.0 %), iso-15 : 0 (6.8 %), anteiso-15 : 0 (6.4 %), 15 : 0 (10.4 %), iso-16 : 0 (13.5 %), summed feature 3 (comprising iso-15 : 0 2-OH and/or 16 : 1ω7c; 6.3 %), iso-17 : 0 3-OH (5.2 %) and 17 : 0 2-OH (5.0 %). Cells contained menaquinone 6. Based on the phylogenetic and phenotypic analyses, strain HY1T should be classified as representing a novel species within the genus Salegentibacter, for which the name Salegentibacter catena sp. nov. is proposed. The type strain is HY1T (=CGMCC 1.6101T=JCM 14015T). Based on this study and on previously described Salegentibacter species, an emended description of the genus Salegentibacter is given.
Haloferax prahovense sp. nov., an extremely halophilic archaeon isolated from a Romanian salt lake
Authors: Enache Madalin , Itoh Takashi , Kamekura Masahiro , Teodosiu Gabriela , Dumitru Lucia
Published: February 2007

A novel halophilic archaeon, strain TL6T, was isolated from Telega Lake, a hypersaline environment in Prahova county, Romania. Strain TL6Twas able to grow in media with a salt concentration of between 2.5 and 5.2 M, with optimum growth at a concentration of 3.5 M. The novel strain was able to grow at concentrations of 1 M MgCl2or less, with an optimum of 0.4 M Mg2+. Growth of the novel strain occurred between pH 6.0 and 8.5, with an optimum of pH 7.0–7.5. The G+C content of the total DNA was 63.7 mol%. The 16S rRNA gene sequence of the novel strain was most closely related to species of the genusHaloferax(97.3–99.3 % sequence similarity). The lipid profile of the novel strain corresponded to that of other species belonging to the genusHaloferax. A comparative analysis of the phenotypic properties and DNA–DNA hybridization between the novel strain and other species of the genusHaloferaxstrongly supported the conclusion that strain TL6Trepresents a novel species within this genus, for which the nameHaloferax prahovensesp. nov., is proposed. The type strain is TL6T(=JCM 13924T=DSM 18310T).
Haloquadratum walsbyi gen. nov., sp. nov., the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain
Authors: Burns David G. , Janssen Peter H. , Itoh Takashi , Kamekura Masahiro , Li Zhuo , Jensen Grant , Rodríguez-Valera Francisco , Bolhuis Henk , Dyall-Smith Mike L.
Published: February 2007

Strains C23T and HBSQ001 were isolated from solar salterns and are novel square-shaped, aerobic, extremely halophilic members of the domain Archaea and family Halobacteriaceae. Cells stained Gram-negative and grew optimally in media containing 18 % salts at around neutral pH. Mg2+ is not required. The DNA G+C content of both isolates was 46.9 mol% and DNA–DNA cross-hybridization showed a relatedness of 80 %. Their 16S rRNA gene sequences showed only 2 nucleotide differences (99.9 % identity) and phylogenetic tree reconstructions with other recognized members of the Halobacteriaceae indicated that they formed a distinct clade, with the closest relative being Halogeometricum borinquense PR 3T (91.2 % sequence identity). The major polar glycolipid of both isolates was the sulfated diglycosyl diether lipid S-DGD-1. Electron cryomicrosopy of whole cells revealed similar internal structures, such as gas vesicles and polyhydroxyalkanoate granules, but the cell wall of isolate HBSQ001 displayed a more complex S-layer compared with that of isolate C23T. The phenotypic characterization and phylogenetic data support the placement of isolates C23T and HBSQ001 in a novel species in a new genus within the Halobacteriaceae, for which we propose the name Haloquadratum walsbyi gen. nov., sp. nov. The type strain of Haloquadratum walsbyi is C23T (=JCM 12705T=DSM 16854T).
Learning-dependent potentiation in the vibrissal motor cortex is closely related to the acquisition of conditioned whisker responses in behaving mice
Authors: Troncoso Julieta , Múnera Alejandro , Delgado-García José María
Published: February 2007

The role of the primary motor cortex in the acquisition of new motor skills was evaluated during classical conditioning of vibrissal protraction responses in behaving mice, using a trace paradigm. Conditioned stimulus (CS) presentation elicited a characteristic field potential in the vibrissal motor cortex, which was dependent on the synchronized firing of layer V pyramidal cells. CS-evoked and other event-related potentials were particular cases of a motor cortex oscillatory state related to the increased firing of pyramidal neurons and to vibrissal activities. Along conditioning sessions, but not during pseudoconditioning, CS-evoked field potentials and unitary pyramidal cell responses grew with a time-course similar to the percentage of vibrissal conditioned responses (CRs), and correlated significantly with CR parameters. High-frequency stimulation of barrel cortex afferents to the vibrissal motor cortex mimicked CS-related potentials growth, suggesting that the latter process was due to a learning-dependent potentiation of cortico-cortical synaptic inputs. This potentiation seemed to enhance the efficiency of cortical commands to whisker-pad intrinsic muscles, enabling the generation of acquired motor responses.
Cortical barrel lesions impair whisker-CS trace eyeblink conditioning
Authors: Galvez Roberto , Weible Aldis P. , Disterhoft John F.
Published: February 2007

Whisker deflection is an effective conditioned stimulus (CS) for trace eyeblink conditioning that has been shown to induce a learning-specific expansion of whisker-related cortical barrels, suggesting that memory storage for an aspect of the trace association resides in barrel cortex. To examine the role of the barrel cortex in acquisition and retrieval of trace eyeblink associations, the barrel cortex was lesioned either prior to (acquisition group) or following (retention group) trace conditioning. The acquisition lesion group was unable to acquire the trace conditioned response, suggesting that the whisker barrel cortex is vital for learning trace eyeblink conditioning with whisker deflection as the CS. The retention lesion group exhibited a significant reduction in expression of the previously acquired conditioned response, suggesting that an aspect of the trace association may reside in barrel cortex. These results demonstrate that the barrel cortex is important for both acquisition and retention of whisker trace eyeblink conditioning. Furthermore, these results, along with prior anatomical whisker barrel analyses suggest that the barrel cortex is a site for long-term storage of whisker trace eyeblink associations.
On the role of hippocampal protein synthesis in the consolidation and reconsolidation of object recognition memory
Authors: Rossato Janine I. , Bevilaqua Lia R.M. , Myskiw Jociane C. , Medina Jorge H. , Izquierdo Iván , Cammarota Martín
Published: February 2007

Upon retrieval, consolidated memories are again rendered vulnerable to the action of metabolic blockers, notably protein synthesis inhibitors. This has led to the hypothesis that memories are reconsolidated at the time of retrieval, and that this depends on protein synthesis. Ample evidence indicates that the hippocampus plays a key role both in the consolidation and reconsolidation of different memories. Despite this fact, at present there are no studies about the consequences of hippocampal protein synthesis inhibition in the storage and post-retrieval persistence of object recognition memory. Here we report that infusion of the protein synthesis inhibitor anisomycin in the dorsal CA1 region immediately or 180 min but not 360 min after training impairs consolidation of long-term object recognition memory without affecting short-term memory, exploratory behavior, anxiety state, or hippocampal functionality. When given into CA1 after memory reactivation in the presence of familiar objects, ANI did not affect further retention. However, when administered into CA1 immediately after exposing animals to a novel and a familiar object, ANI impaired memory of both of them. The amnesic effect of ANI was long-lasting, did not happen after exposure to two novel objects, following exploration of the context alone, or in the absence of specific stimuli, suggesting that it was not reversible but was contingent on the reactivation of the consolidated trace in the presence of a salient, behaviorally relevant novel cue. Our results indicate that hippocampal protein synthesis is required during a limited post-training time window for consolidation of object recognition memory and show that the hippocampus is engaged during reconsolidation of this type of memory, maybe accruing new information into the original trace.
Mutation at the TrkB PLCγ-docking site affects hippocampal LTP and associative learning in conscious mice
Authors: Gruart Agnès , Sciarretta Carla , Valenzuela-Harrington Mauricio , Delgado-García José M. , Minichiello Liliana
Published: February 2007

Previous in vitro studies have characterized the electrophysiological properties and molecular events associated with long-term potentiation (LTP), but as yet there are no in vivo data from molecular-level dissection that directly identify LTP as the biological substrate for learning and memory. Understanding whether the molecular pathways required for learning are also those generating LTP when measured directly on the relevant circuit of a learning animal is clearly important, although so far has proved technically difficult. Here, for the first time, we combine highly defined genetic mouse models with behavior and in vivo recordings. We recorded the activity-dependent changes taking place at the CA3–CA1 synapses during the acquisition and extinction of a simple form of an associative learning task in mice carrying point mutations on specific docking sites of TrkB receptors (trkBSHC, trkBPLC). The learning task consisted of a classical eyeblink conditioning using a trace paradigm. The conditioned stimulus (CS) consisted of a tone and was followed by a periorbital electrical shock as an unconditioned stimulus (US). The US started 500 msec after the end of the CS. We show that a single pulse presented to the Schaffer collateral-commissural pathway during the CS-US interval evoked a monosynaptic field excitatory postsynaptic potential (fEPSP) at the CA1 pyramidal cells, with a slope linearly related to learning evolution in controls and trkBSHC mutants, but the relationship was impaired in trkBPLC mice. These data support a link between the PLCγ-docking site downstream of TrkB and the activity-dependent synaptic changes evoked at the CA3–CA1 synapses during associative learning in conscious mice, and indicate that TrkB PLCγ-site-activated molecular pathway(s) underlie both associative learning and LTP triggered at the CA3–CA1 synapse.
Reduction and S-Carboxymethylation of Proteins: Microscale Method
Authors: Simpson Richard J.
Published: February 2007

INTRODUCTION

Reduction and alkylation of microscale amounts of protein (10-50 μg) require special attention. Classical methods for desalting and dialysis should be avoided due to large sample losses. Adding a small quantity of detergent to the protein solution during all manipulations can also reduce protein loss. This protocol describes a procedure for reduction and S-carboxymethylation of low-microgram amounts of protein. Samples are reduced and alkylated in small volumes (<200 μl) in the presence of detergent and desalted (and concentrated) by RP-HPLC in yields of >90%.