bluuebunny/crossref_metadata_2025 huggingface dataset:
The Reputation of Political Science Journals: Pluralist and Consensus Views
Authors: Norris Pippa , Crewe Ivor
Published: December 2006

Individual scholars and their departments are increasingly judged according to the alleged ‘quality’ of the academic journals in which they publish. This article is the first systematic attempt to measure the reputation of political science journals and is designed for comparison with American academics' evaluations. It explores academics' criteria for judging journals, the consensus of judgement on any one journal across different criteria, and the range of evaluations between different journals. A relatively strong consensus is found among academic political scientists about the relative quality of political science journals. Nevertheless the order of the ranking depends, in part, on the measure adopted. Ranking by impact scores supports the consensus theory, while the rankings by quality lend some weight to the pluralist argument that specialist journals can be highly rated by small groups of experts while having little impact in the profession as a whole. Striking contrasts between the British and American political science communities are revealed.
Human Rights and Power
Authors: Stammers Neil
Published: December 2006

This paper is an initial attempt to link the concepts of human rights and power from a social constructionist perspective. It looks at aspects of the social history of natural and human rights and the relationship of this history to extant power relations. It suggests that conceptions of human rights have both challenged and sustained particular forms of power, thus playing a highly ambivalent role. The paper also examines and criticises the philosophical underpinnings of liberal and marxist approaches to the concept of human rights. In a concluding section it considers the possibility of constructing a power analysis which might provide a way of anchoring the concept of human rights in social practices.
The Scotland—England Divide: Politics and Locality in Britain
Authors: McCrone David , Bechhofer Frank
Published: December 2006

Growing territorial cleavages within Britain have attracted considerable interest from social scientists in recent years. New spatial models of voting, accounting for the declining homogeneity of electoral behaviour,1 have drawn attention to localised patterns of political support, as well as the emergence of regional cleavages across Britain as a whole.2 Talk of a North–South split has become the common currency of political commentators to account for regional disparities between Conservative and Labour support.3 Alongside these local and regional divisions in voting patterns, there is a new interest in broader aspects of the political differences between the nations of the UK, notably between England on the one hand, and Scotland and Wales on the other.4
Theoretical Paradigms of Islamic Movements
Authors: Choueiri Y. M.
Published: December 2006

The discourse of contemporary Islamic radicalism derives its inspiration from the writings of three Muslim thinkers and activists: Abu al-A‘la al-Mawdudi (died 1979), Sayyid Qutb (died 1966), and Ayatollah Khumayni (died 1989). This article is devoted to an initial exposition of the main themes of their texts as the unique founders of this particular ‘discursivity’.1
Between Kantianism and Consequentialism in T. H. Green's Moral Philosophy
Authors: Weinstein David
Published: December 2006

This essay explores the good-maximizing role of freedom and stringent moral rights in Green's theory and his assessment of utilitarianism, notably Mill's improved utilitarianism. Though critical of Benthamite utilitarianism, Green was favourably disposed to Mill's version of utilitarianism. Mill sometimes understood the good to be maximized appropriately (especially where Mill embraced the virtue of ‘self-development’). The ‘practical’ strategies recommended by Mill for maximizing good mirrored the very ‘practical’ strategies that Green's own theory recommended. Green was a ‘dispositional’ consequentialist: Green's moral theory was a consequentialism of moral self-realization or good will. Sidgwick's assessment of Green's moral theory and Green's selective debt to Kant are adduced in support. Green emerges as an example of ‘Kantian consequentialism.’
Through a Missile Tube Darkly: ‘New Thinking’ about Nuclear Strategy
Authors: Gray Colin S.
Published: December 2006

Just as the ideas of arms control comprise a picnic basket for sunny international weather, so much of the allegedly ‘new thinking‘ on strategy and security claims to have ‘matched us with His hour’.1 The challenge, purportedly is between realist and ‘transformationist‘ approaches to security,2 between national security and common (or global) security,3 and – of course – between old and new thinking. We are told that ‘[t]here is scope to change the strategic culture of world politics’.4 Some of us old thinkers are a little puzzled by the content of a quotation such as that, since the same authors have written breezily and optimistically, albeit contingently, to be fair, that ‘[t]he “nature” of the [international] system would be changed because of the changed conceptions – strategic cultures – of the units‘.5 The relationship between strategic culture and cultures would stand some careful discussion, while the merit in the claim that there is scope to change ‘the strategic culture of world politics’, whatever that very big idea may mean, remains to be seen.6
Gender and Local Political Interest: Some International Comparisons
Authors: Hayes Bernadette C. , Bean Clive S.
Published: December 2006

Since the 1970s, political science research suggests no significant gender differences in overall levels of participation. For example, an examination of current rates of conventional political participation and voter turnout indicates little difference between men and women in either the United States, Great Britain, West Germany, Italy or other western industrial nations.1 Despite this disappearance of gender differences in political participation, however, both national and international research suggests an enduring gender gap in political interest. Regardless of country of origin, women remain less politically interested than men.2
Ideology after the Collapse of Communism
Authors: Minogue Kenneth
Published: December 2006

The collapse of communism has not, as might be expected, led to the end of ideologies. Instead of the grand revolutionary projects of the past, however, we now have a set of overlapping fragments of revelation which cooperate with each other in social transformation. These fragments exhibit an ‘identity monism’ which can tell us something about the character of ideology in general. This form of monism is the necessary condition of turning a modern state into a managed enterprise for the satisfaction of human needs – a project which happens also to be adumbrated in much normative political philosophy. A managed civil state responds to opinion rather than interest, and the opinions on which the project rests commend themselves by some version of self-evidence.
Public Trust in the New Parliaments of Central and Eastern Europe
Authors: Hibbing John R. , Patterson Samuel C.
Published: December 2006

After the collapse of the Soviet empire, democratic parliamentary elections were conducted in the countries of Central and Eastern Europe, and new parliaments convened, in the early 1990s. How much confidence did citizens in these new democracies have in their new parliament? Under what conditions is citizens' trust in parliament meagre or ample? Public opinion surveys conduced in 1990–1 in nine countries – Bulgaria, Czechoslovakia, Estonia, Hungary, Lithuania, Poland, Romania, Slovenia, and Ukraine – provide data for analysing citizens', trusting or distrusting orientations. Parliamentary trust is significantly influenced by perceptions of economic conditions, and by confidence in politicians and government generally but, surprisingly, not much affected by political awareness or involvement levels, political efficacy, or social class differentials. These findings indicate that public confidence in these parliaments will grow with economic prosperity and the demonstrated effectiveness of the government to govern.
Political Participation in Postcommunist Russia: Voting, Activism, and the Potential for Mass Protest
Authors: McAllister Ian , White Stephen
Published: December 2006

The collapse of communism in Russia and the process of democratization raise questions about political participation in the postcommunist era. Using Russian survey data collected in early 1992, we analyse the nature of political participation and the potential for mass political action. The results show that while voting and activism are similar to the established democracies, abstention and withdrawal are associated with political disaffection from the regime. The potential for mass political action is based on economic dissatisfaction. The strong link between the likelihood of protest and economic dissatisfaction, coupled with the widespread popular sympathies that remain for the old Soviet regime, represent one of the greatest obstacles to the consolidation of a democratic political system in postcommunist Russia.
C. B. Macpherson's Critique of Liberal Democracy and Capitalism
Authors: Morrice David
Published: December 2006

C. B. Macpherson's project was to revise liberal-democratic theory in the light of Marxism, to rescue the valuable part of the liberal tradition from the dangers of capitalist market relations, and to democratize socialism. I identify Macpherson's concept of political theory, which informs his project; reconstruct his criticisms of liberal democratic theory and capitalist market relations; and note his prescriptions for a better political theory and practice. The project remains significant and valuable in a world in which political and economic liberalism is said to be triumphant and socialism dead or in retreat. It is not without its problems, however, which include an inadequate theory of human nature and a lack of detail on the nature of a democratic socialist society.
Are there Perennial Problems in Political Theory?
Authors: Bevir Mark
Published: December 2006

A justification is offered for approaching classic works of political theory as relevant to problems that concern us. Perennial problems are shown to exist in three increasingly controversial senses. First, past authors addressed a problem which we can ponder. Second, past authors addressed a problem which authors who wrote on these authors also addressed and which we can ponder. Third, numerous authors expressed beliefs relevant to a problem which we can ponder. The errors identified by opponents of perennial problems arise from empirical misjudgements concerning the ways that different authors addressed such problems, not from the assumption that such problems exist.
Global Security and Economic Well-being: A Strategic Perspective
Authors: Gray Colin
Published: December 2006

The end of the Cold War has wrought havoc among Western students of strategy as well as among and to the political institutions of the post-war period. Many erstwhile ‘strategists' have decided that it is more correct for the 1990s to become specialists in security, even global security. This paper examines critically, in strategic perspective, the purported connections between economic well-being and global security. The proposition that a strategic, more broadly a ‘realist’, perspective either neglects or discourages ethical considerations is also discussed. There is less than meets the eye to claims for a rising pre-eminence for economic issues vis à vis a global security, while the very concept of a global security is more attractive than it is useful.
Pluralist Justice and its Limits: The Case of Northern Ireland
Authors: O'Neill Shane
Published: December 2006

This article is a philosophical critique of certain communitarian conceptions of justice. It focuses on the work of Michael Walzer who argues that justice reflects the shared understandings of particular historical communities. In assessing the implications of this view for a divided society such as Northern Ireland I wish to set limits to this pluralist notion of justice. In the later part of the article I turn to Jürgen Habermas's proceduralist, universalist discourse ethics so as to transcend these limits and to argue that justice in Northern Ireland can only be achieved if the participants involved begin to adopt the critically-reflexive stance towards their identities that real discourse requires.
Policy Networks and State-Farmer Relations in Northern Ireland, 1921–72
Authors: Greer Alan
Published: December 2006

An extensive literature already applies a variety of theories of interest intermediation to case studies of British agricultural policy. This paper applies the concept of policy network to one particular territorial aspect of agricultural policy – the relationship between the state and the farmer in Northern Ireland during the period of devolution between 1921–72. The conclusion is that although theories of policy community and meso-corporatism have some explanatory value, La Palombara's notion of parentela is necessary to any understanding of the essential nature of the farmer-state relationship in Northern Ireland.
Studying Political Leadership: The Case of François Mitterrand
Authors: Cole Alistair
Published: December 2006

The study of political leadership, in France and elsewhere, must be appreciated in terms of the interaction between leadership resources (personal and positional) on the one hand, and environmental constraints and opportunities on the other. This article proposes a general framework for appraising comparative liberal democratic political leaderships. It illustrates the possibilities of the framework by evaluating the political leadership of the French President François Mitterrand.
Citizenship and Pluralism
Authors: Miller David
Published: December 2006

The idea of citizenship has played a prominent role in recent political debate. But how is common citizenship possible in societies that seem increasingly prone to cultural fragmentation along ethnic and other lines? The paper distinguishes three conceptions of citizenship – liberal, libertarian and republican – and asks how far each is able to respond to cultural pluralism. The liberal conception, exemplified by Rawls, interprets citizenship in terms of a set of principles that everyone has reason to accept; but Rawls fails to show why everyone should give political priority to the citizen perspective as he defines it. The libertarian conception views the citizen as a rational consumer who through contract and choice can gain access to a range of public goods. This caters to pluralism, but at the cost of eroding the idea of citizenship as a common status enjoyed by all members of society. The republican conception sees the citizen as someone who plays an active role in shaping his or her society through public discussion. Contrary to the claims of critics such as I. M. Young, this does not require the imposition of norms of impartiality and publicity which exclude certain cultural groups. This conception offers the best prospect of developing a political consensus to which all groups can subscribe.
Internationalization and Unionist Isolation: A Response to Feargal Cochrane
Authors: Dixon Paul
Published: December 2006

‘… Northern Ireland is a miserable place, with bigots at one end of the spectrum and murderers at the other, while all sorts in the middle make what terms and partial terms they can with the dominant brutes of their own tribe. … Ulster is a valley cut off, but alas not lost, at some stage in the seventeenth century. … I doubt if the British would grieve too deeply if one bunch of offshore primitives decided to massacre the other; we haven't minded in ex-colonial Africa. … Candidly, we want these people at arm's length, governed by rules fairer than their own brutal instincts. They are not part of us, but we have a sort of duty to them.’2
The New Political Economy
Authors: Gamble Andrew
Published: December 2006

Political economy has been an extremely diverse field of study, embracing a large number of different approaches and methodologies. The fading of old ideological and methodological disputes and the development of new intellectual agendas in response to far-reaching changes in the economic and political structures of the world system have created the possibility of a new political economy which promises a reconstruction of the field and the overcoming of the methodological division between economics and political science. Recent critiques of established literatures in international political economy, state theory, comparative government-industry relations, and public choice are contributing to a new paradigm. Drawing on recent developments in economics such as New Keynesianism it combines the historical and institutionalist analysis of structure with rational choice analysis of agency.
Game Theory and the Politics of Global Warming: The State of Play and beyond
Authors: Ward Hugh
Published: December 2006

Global climate change is characterized as a collective-action game played by nations through time. The conditions under which conditional cooperation can occur are explored. The model clarifies the bargaining tactics used by nations in the negotiation of the Framework Convention on Climate Change and the reasons why there may be collective action failure. The model also illuminates issues of regime design.
Insuring Security
Authors: Bellany Ian
Published: December 2006

Alliances for collective defence are likened to mutual insurance arrangements. External attack is seen as a risk in much the same way that illness is a risk to a bread-winner, who will often want to insure against it by combining with other persons in similar circumstances to pool the risks involved (usually mediated by an insurance company). Here, alliance members' defence budgets become insurance premiums entitling them to group protection against attack. In such alliances size is strongly beneficial since there are always economies of scale in risk-sharing. Indefinite geographical expansion of such arrangements is checked by the comparatively slow speed with which alliance forces may be brought to bear on behalf of an endangered member and the difficulties of harmonizing within the same arrangement members who belong to different statistical categories of risk.
Sovereignty and Subsidiarity in EU Environmental Policy
Authors: Golub Jonathan
Published: December 2006

This article explores the connection between the subsidiarity principle and national sovereignty in the context of EU environmental policy. In addition to providing an historical account of this connection, the article suggests that subsidiarity represents a Janus-faced concept capable of either supporting or undermining the legitimacy of EU environmental policy. By developing explicit criteria by which to apply subsidiarity, a number of areas are identified in which existing EU authority could be replaced by exclusively national action or laws which granted states significantly more discretion over environmental decision making. Examples are then presented where this shift of power back to the member states has already been proposed and in some cases already occurred, recasting the balance between national sovereignty and supranational environmental constraints. Throughout the analysis, particular attention is paid to the efforts of Britain, a primary antagonist in the debate, to preserve its sovereignty over environmental policy.
Women and Citizenship: Some Lessons from Israel
Authors: Bryson Valerie
Published: December 2006

Many of the conditions which British feminists have identified as necessary for the full citizenship of women seem to have been met in Israel. Even Jewish women, however, remain disadvantaged in many ways. This paper analyses the causes of their disadvantage, showing that some are shared with other nations while others are specific to Israel.
A Misconceived Discourse on Political Obligation
Authors: Parekh Bhikhu
Published: December 2006

In much of the post-Hobbesian discourse on political obligation, the question is defined as an inquiry into the reasons why a citizen should obey the law, but this depoliticizes political obligation and fails to appreciate its specific nature. Legal, civil and political obligation are distinguished and it is argued that political obligation properly so-called is concerned with such things as the citizen's obligation to take an active interest in political life, to promote the well-being of his community and to help redress its injustices. The paper then goes to explore why political obligation was confused with civil obligation and with what consequences.
Reviews
Authors: Bookbinder G. E. , Miller Jane , Treadwell Alan
Published: December 2006

Foster, John, L. (Editor). (1977). Reluctant to Read?

Edinburgh Reading Tests ‐ Stages 1 and 4 ‐ Godfrey Thomson Unit.

Dubin, F. and Olshtain, E. (1977). Facilitating Language Learning.

Skitt, Frank. (1978). Themes for Language Learning.
Shorter Notices
Authors: Green Nancy
Published: December 2006

Mackay, David and Simon, Joseph, (1976) Help Your Child to Read and Write and More.

Chamberlin, Anthony, and Stenberg, Kurt. (1976). Play and Practice.
Shorter Notice
Authors: Green Nancy
Published: December 2006

Ames, Ted, (1978) Teach Yourself to Diagnose Reading Problm.
Shorter Notices
Authors: Green Nancy
Published: December 2006

Jarman, Christopher, (1979) The Development of Handwriting Skills, A Book of Resources for Teachers

Youth Libraries Group (1979) Practical Guides: Storytelling.
Reviews
Authors: Litherland Barry , Hudson Jean , Seex Christine
Published: December 2006

Taverner, D. T. (1980) Developing a Reading Programme.

Downing, John (1979) Reading and Reasoning

Pollock, Joy, (1980) Signposts of Spelling
Improving Students’Essay‐writing
Authors: Hunter‐Carsch C. Morag
Published: December 2006

This paper concerns University Tutors’and students’perceptions of essay‐writing difficulties in examinations and on coursework, and how to improve essay‐writing in the case of those with problems. It is assumed that an awareness of both Tutors’and students’expectations and attitudes to essays is necessary in order to understand what are considered to be‘faults’or problems and how best to improve the situation.

On the basis of experience with students, teachers and workshop discussions with University colleagues, a framework for analysing types of problems and providing support, is offered. The framework differentiates between those problems mainly associated with form of writing and those associated with content. Within this broad classification the perceived‘faults’are related to apparent difficulties and these in turn regarded as suggesting areas of need or possibly underlying issues. The‘needs’are not necessarily 'special educational needs’but issues for both student and Tutor to tackle sensibly and positively, using relevant learning/ teaching strategies, some of which are listed and outlined.
Evolutionary Dynamics of
Ralstonia solanacearum
Authors: Castillo José A. , Greenberg Jean T.
Published: December 2006

We investigated the genetic diversity, extent of recombination, natural selection, and population divergence of
Ralstonia solanacearum
samples obtained from sources worldwide. This plant pathogen causes bacterial wilt in many crops and constitutes a serious threat to agricultural production due to its very wide host range and aggressiveness. Five housekeeping genes, dispersed around the chromosome, and three virulence-related genes, located on the megaplasmid, were sequenced from 58 strains belonging to the four major phylogenetic clusters (phylotypes). Whereas genetic variation is high and consistent for all housekeeping loci studied, virulence-related gene sequences are more diverse. Phylogenetic and statistical analyses suggest that this organism is a highly diverse bacterial species containing four major, deeply separated evolutionary lineages (phylotypes I to IV) and a weaker subdivision of phylotype II into two subgroups. Analysis of molecular variations showed that the geographic isolation and spatial distance have been the significant determinants of genetic variation between phylotypes.
R. solanacearum
displays high clonality for housekeeping genes in all phylotypes (except phylotype III) and significant levels of recombination for the virulence-related
egl
and
hrpB
genes, which are limited mainly to phylotype strains III and IV. Finally, genes essential for species survival are under purifying selection, and those directly involved in pathogenesis might be under diversifying selection.
Characterization of Strong Promoters from an Environmental
Flavobacterium hibernum
Strain by Using a Green Fluorescent Protein-Based Reporter System
Authors: Chen S. , Bagdasarian M. , Kaufman M. G. , Walker E. D.
Published: December 2006

We developed techniques for the genetic manipulation of
Flavobacterium
species and used it to characterize several promoters found in these bacteria. Our studies utilized
Flavobacterium hibernum
strain W22, an environmental strain we isolated from tree hole habitats of mosquito larvae. Plasmids from
F. hibernum
strain W22 were more efficiently (∼1,250-fold) transferred by electroporation into
F. hibernum
strain W22 than those isolated from
Escherichia coli
, thus indicating that an efficient restriction barrier exists between these species. The strong promoter,
tac
, functional in proteobacteria, did not function in
Flavobacterium
strains. Therefore, a promoter-trap plasmid, pSCH03, containing a promoterless
gfpmut3
gene was constructed. A library of 9,000 clones containing chromosomal fragments of
F. hibernum
strain W22 in pSCH03 was screened for their ability to drive expression of the promoterless
gfpmut3
gene. Twenty strong promoters were used for further study. The transcription start points were determined from seven promoter clones by the 5′ rapid amplification of cDNA ends technique. Promoter consensus sequences from
Flavobacterium
were identified as TAnnTTTG and TTG, where
n
is any nucleotide, centered approximately 7 and 33 bp upstream of the transcription start site, respectively. A putative novel ribosome binding site consensus sequence is proposed as TAAAA by aligning the 20-bp regions upstream of the translational start site in 25 genes. Our primary results demonstrate that at least some promoter and ribosome binding site motifs of
Flavobacterium
strains are unusual within the bacterial domain and suggest an early evolutionary divergence of this bacterial group. The techniques presented here allow for more detailed genetics-based studies and analyses of
Flavobacterium
species in the environment.
Mechanism of Resistance to
Bacillus thuringiensis
Toxin Cry1Ac in a Greenhouse Population of the Cabbage Looper,
Trichoplusia ni
Authors: Wang Ping , Zhao Jian-Zhou , Rodrigo-Simón Ana , Kain Wendy , Janmaat Alida F. , Shelton Anthony M. , Ferré Juan , Myers Judith
Published: December 2006

The cabbage looper,
Trichoplusia ni
, is one of only two insect species that have evolved resistance to
Bacillus thuringiensis
in agricultural situations. The trait of resistance to
B. thuringiensis
toxin Cry1Ac from a greenhouse-evolved resistant population of
T. ni
was introgressed into a highly inbred susceptible laboratory strain. The resulting introgression strain, GLEN-Cry1Ac-BCS, and its nearly isogenic susceptible strain were subjected to comparative genetic and biochemical studies to determine the mechanism of resistance. Results showed that midgut proteases, hemolymph melanization activity, and midgut esterase were not altered in the GLEN-Cry1Ac-BCS strain. The pattern of cross-resistance of the GLEN-Cry1Ac-BCS strain to 11
B. thuringiensis
Cry toxins showed a correlation of the resistance with the Cry1Ab/Cry1Ac binding site in
T. ni
. This cross-resistance pattern is different from that found in a previously reported laboratory-selected Cry1Ab-resistant
T. ni
strain, evidently indicating that the greenhouse-evolved resistance involves a mechanism different from the laboratory-selected resistance. Determination of specific binding of
B. thuringiensis
toxins Cry1Ab and Cry1Ac to the midgut brush border membranes confirmed the loss of midgut binding to Cry1Ab and Cry1Ac in the resistant larvae. The loss of midgut binding to Cry1Ab/Cry1Ac is inherited as a recessive trait, which is consistent with the recessive inheritance of Cry1Ab/Cry1Ac resistance in this greenhouse-derived
T. ni
population. Therefore, it is concluded that the mechanism for the greenhouse-evolved Cry1Ac resistance in
T. ni
is an alteration affecting the binding of Cry1Ab and Cry1Ac to the Cry1Ab/Cry1Ac binding site in the midgut.
Escherichia coli
O157:H7 Colonization at the Rectoanal Junction of Long-Duration Culture-Positive Cattle
Authors: Lim Ji Youn , Li Jie , Sheng Haiqing , Besser Thomas E. , Potter Kathleen , Hovde Carolyn J.
Published: December 2006

Long-duration consistently
Escherichia coli
O157:H7 culture-positive cattle were euthanized and necropsied. Tissue and digesta from along the gastrointestinal tract (GIT) were cultured for the bacteria and examined histologically for lymphoid character.
E. coli
O157:H7 was detected only at the rectoanal junction mucosa and not at any other GIT location.
Retention of Virulence in a Viable but Nonculturable
Edwardsiella tarda
Isolate
Authors: Du Meng , Chen Jixiang , Zhang Xiaohua , Li Aijuan , Li Yun , Wang Yingeng
Published: December 2006

Edwardsiella tarda
is pathogen of fish and other animals. The aim of this study was to investigate the viable but nonculturable (VBNC) state and virulence retention of this bacterium.
Edwardsiella tarda
CW7 was cultured in sterilized aged seawater at 4°C. Total cell counts remained constant throughout the 28-day period by acridine orange direct counting, while plate counts declined to undetectable levels (<0.1 CFU/ml) within 28 days by plate counting. The direct viable counts, on the other hand, declined to ca. 10
9
CFU/ml active cells and remained fairly constant at this level by direct viable counting. These results indicated that a large population of cells existed in a viable but nonculturable state. VBNC
E. tarda
CW7 could resuscitate in experimental chick embryos and in the presence of nutrition with a temperature upshift. The resuscitative times were 6 days and 8 days, respectively. The morphological changes of VBNC, normal, and resuscitative
E. tarda
CW7 cells were studied with a scanning electron microscope. The results showed that when the cells entered into the VBNC state, they gradually changed in shape from short rods to coccoid and decreased in size, but the resuscitative cells did not show any obvious differences from the normal cells. The VBNC and the resuscitative
E. tarda
CW7 cells were intraperitoneally inoculated into turbot separately, and the fish inoculated with the resuscitative cells died within 7 days, which suggested that VBNC
E. tarda
CW7 might retain pathogenicity.
A Novel High-Throughput Screen Reveals Yeast Genes That Increase Secretion of Heterologous Proteins
Authors: Wentz Alane E. , Shusta Eric V.
Published: December 2006

The yeast
Saccharomyces cerevisiae
is an attractive host for the production of heterologous proteins. However, low-yield production of many proteins (from micrograms to milligrams/liter) leaves considerable room for optimization. By engineering the yeast cell via traceable genome-wide libraries, genes that can enhance protein expression level because of their roles in protein transcription, translation, folding, and trafficking processes can be readily identified. This report details a novel approach that combines yeast cDNA overexpression libraries with yeast surface display to allow the rapid flow cytometric screening of engineered yeast for gene products that improve the display of heterologous proteins. After optimization of the screening conditions, a genome-wide scan yielded five yeast gene products that promoted increased display levels of a single-chain T-cell receptor (scTCR). The display-enhancing genes included those coding for cell wall proteins (
CCW12
,
CWP2
, and
SED1
), a ribosomal subunit protein (
RPP0
), and an endoplasmic reticulum-resident protein (
ERO1
). Under the premise that yeast surface display levels could be used as a predictor of secretion efficiency, each display-enhancing gene product was tested for its ability to affect secretion levels of multiple scTCR and single-chain antibodies (scFv). All of the selected yeast gene products were shown to promote increased secretion of active protein (1.5-fold to 7.9-fold), with
CCW12
and
ERO1
being the most generalizable enhancers of scFv/scTCR secretion.
Synthesis and Selection of De Novo Proteins That Bind and Impede Cellular Functions of an Essential Mycobacterial Protein
Authors: Rao Alka , Ram Geeta , Saini Adesh Kumar , Vohra Reena , Kumar Krishan , Singh Yogendra , Ranganathan Anand
Published: December 2006

Recent advances in nonrational and part-rational approaches to de novo peptide/protein design have shown increasing potential for development of novel peptides and proteins of therapeutic use. We demonstrated earlier the usefulness of one such approach recently developed by us, called “codon shuffling,” in creating stand-alone de novo protein libraries from which bioactive proteins could be isolated. Here, we report the synthesis and selection of codon-shuffled de novo proteins that bind to a selected
Mycobacterium tuberculosis
protein target, the histone-like protein HupB, believed to be essential for mycobacterial growth. Using a versatile bacterial two-hybrid system that entailed utilization of HupB and various codon-shuffled protein libraries as bait and prey, respectively, we were able to identify proteins that bound strongly to HupB. The observed interaction was also confirmed using an in vitro assay. One of the protein binders was expressed in
Mycobacterium smegmatis
and was shown to appreciably affect growth in the exponential phase, a period wherein HupB is selectively expressed. Furthermore, the transcription profile of
hupB
gene showed a significant reduction in the transcript quantity in mycobacterial strains expressing the protein binder. Electron microscopy of the affected mycobacteria elaborated on the extent of cell damage and hinted towards a cell division malfunction. It is our belief that a closer inspection of the obtained de novo proteins may bring about the generation of small-molecule analogs, peptidomimetics, or indeed the proteins themselves as realistic leads for drug candidates. Furthermore, our strategy is adaptable for large-scale targeting of the essential protein pool of
Mycobacterium tuberculosis
and other pathogens.
BcSAK1, a Stress-Activated Mitogen-Activated Protein Kinase, Is Involved in Vegetative Differentiation and Pathogenicity in
Botrytis cinerea
Authors: Segmüller Nadja , Ellendorf Ursula , Tudzynski Bettina , Tudzynski Paul
Published: December 2006

The gene
bcsak1
, encoding a mitogen-activated protein kinase (MAPK) of
Botrytis cinerea
, was cloned and characterized. The protein has high homology to the yeast Hog1 and to corresponding MAPKs from filamentous fungi, but it shows unique functional features. The protein is phosphorylated under osmotic stress, specific fungicides, and oxidative stress mediated by H
2
O
2
and menadione. Northern blot analyses indicate that only a subset of typical oxidative stress response genes is regulated by BcSAK1. In contrast to most other fungal systems, Δbcsak1 mutants are significantly impaired in vegetative and pathogenic development: they are blocked in conidia formation, show increased sclerotial development, and are unable to penetrate unwounded plant tissue. These data indicate that in
B. cinerea
the stress-activated MAPK cascade is involved in essential differentiation programs.
Divergence of Protein Kinase A Catalytic Subunits in
Cryptococcus neoformans
and
Cryptococcus gattii
Illustrates Evolutionary Reconfiguration of a Signaling Cascade
Authors: Hicks Julie K. , Heitman Joseph
Published: December 2006

Gene duplication and divergence via both the loss and gain of gene activities are powerful evolutionary forces underlying the origin of new biological functions. Here a comparative genetics approach was applied to examine the roles of protein kinase A (PKA) catalytic subunits in three closely related varieties or sibling species of the pathogenic fungus genus
Cryptococcus
. Previous studies revealed that two PKA catalytic subunits, Pka1 and Pka2, control virulence factor production and mating. However, only one of the two plays the predominant physiological role, and this function has been exchanged between Pka1 and Pka2 in strains of the
Cryptococcus neoformans
var.
grubii
serotype A lineage compared to divergent
C. neoformans
var.
neoformans
serotype D isolates. To understand the basis for this functional plasticity, here the activities of Pka1 and Pka2 were defined in the two varieties and the related sibling species
Cryptococcus gattii
by gene disruption and characterization, heterologous complementation, and analysis of serotype AD hybrid mutant strains. The findings provide evidence for a shared ancestral role of PKA in governing mating and virulence factor production and indicate that the exchange of catalytic subunit roles is attributable to loss of function. Our studies illustrate the plasticity of signaling networks enabling rapid rewiring during speciation of a clade of common human fungal pathogens.
Novel
phacB
-Encoded Cytochrome P450 Monooxygenase from
Aspergillus nidulans
with 3-Hydroxyphenylacetate 6-Hydroxylase and 3,4-Dihydroxyphenylacetate 6-Hydroxylase Activities
Authors: Ferrer-Sevillano Francisco , Fernández-Cañón José M.
Published: December 2006

Aspergillus nidulans
catabolizes phenylacetate (PhAc) and 3-hydroxy-, 4-hydroxy-, and 3,4-dihydroxyphenylacetate (3-OH-PhAc, 4-OH-PhAc, and 3,4-diOH-PhAc, respectively) through the 2,5-dihydroxyphenylacetate (homogentisic acid) catabolic pathway. Using cDNA subtraction techniques, we isolated a gene, denoted
phacB
, which is strongly induced by PhAc (and its hydroxyderivatives) and encodes a new cytochrome P450 (CYP450). A disrupted
phacB
strain (
ΔphacB
) does not grow on 3-hydroxy-, 4-hydroxy-, or 3,4-dihydroxy-PhAc. High-performance liquid chromatography and gas chromatography-mass spectrum analyses of in vitro reactions using microsomes from wild-type and several
A. nidulans
mutant strains confirmed that the
phacB
-encoded CYP450 catalyzes 3-hydroxyphenylacetate and 3,4-dihydroxyphenylacetate 6-hydroxylations to generate 2,5-dihydroxyphenylacetate and 2,4,5-trihydroxyphenylacetate, respectively. Both of these compounds are used as substrates by homogentisate dioxygenase. This cytochrome P450 protein also uses PhAc as a substrate to generate 2-OH-PhAc with a very low efficiency. The
phacB
gene is the first member of a new CYP450 subfamily (CYP504B).
The
pio
Operon Is Essential for Phototrophic Fe(II) Oxidation in
Rhodopseudomonas palustris
TIE-1
Authors: Jiao Yongqin , Newman Dianne K.
Published: December 2006

Phototrophic Fe(II)-oxidizing bacteria couple the oxidation of ferrous iron [Fe(II)] to reductive CO
2
fixation by using light energy, but until recently, little has been understood about the molecular basis for this process. Here we report the discovery, with
Rhodopseudomonas palustris
TIE-1 as a model organism, of a three-gene operon, designated the
pio
operon (for
p
hototrophic
i
ron
o
xidation), that is necessary for phototrophic Fe(II) oxidation. The first gene in the operon,
pioA
, encodes a
c
-type cytochrome that is upregulated under Fe(II)-grown conditions. PioA contains a signal sequence and shares homology with MtrA, a decaheme
c
-type cytochrome from
Shewanella oneidensis
MR-1. The second gene,
pioB
, encodes a putative outer membrane beta-barrel protein. PioB is a homologue of MtrB from
S. oneidensis
MR-1. The third gene,
pioC
, encodes a putative high potential iron sulfur protein (HiPIP) with a twin-arginine translocation (Tat) signal sequence and is similar to the putative Fe(II) oxidoreductase (Iro) from
Acidithiobacillus ferrooxidans
. Like PioA, PioB and PioC appear to be secreted proteins. Deletion of the
pio
operon results in loss of Fe(II) oxidation activity and growth on Fe(II). Complementation studies confirm that the phenotype of this mutant is due to loss of the
pio
genes. Deletion of
pioA
alone results in loss of almost all Fe(II) oxidation activity; however, deletion of either
pioB
or
pioC
alone results in only partial loss of Fe(II) oxidation activity. Together, these results suggest that proteins encoded by the
pio
operon are essential and specific for phototrophic Fe(II) oxidation in
R. palustris
TIE-1.
Glucosylglycerate Biosynthesis in the Deepest Lineage of theBacteria: Characterization of the Thermophilic Proteins GpgS and GpgP fromPersephonella marina
Authors: Costa Joana , Empadinhas Nuno , da Costa Milton S.
Published: December 2006

The pathway for the synthesis of glucosylglycerate (GG) in the thermophilic bacteriumPersephonella marinais proposed based on the activities of recombinant glucosyl-3-phosphoglycerate (GPG) synthase (GpgS) and glucosyl-3-phosphoglycerate phosphatase (GpgP). The sequences ofgpgSandgpgPfrom the cold-adapted bacteriumMethanococcoides burtoniiwere used to identify the homologues in the genome ofP. marina, which were separately cloned and overexpressed as His-tagged proteins inEscherichia coli. The recombinant GpgS protein ofP. marina, unlike the homologue fromM. burtonii, which was specific for GDP-glucose, catalyzed the synthesis of GPG from UDP-glucose, GDP-glucose, ADP-glucose, and TDP-glucose (in order of decreasing efficiency) and fromd-3-phosphoglycerate, with maximal activity at 90°C. The recombinant GpgP protein, like theM. burtoniihomologue, dephosphorylated GPG and mannosyl-3-phosphoglycerate (MPG) to GG and mannosylglycerate, respectively, yet at high temperatures the hydrolysis of GPG was more efficient than that of MPG. Gel filtration indicates that GpgS is a dimeric protein, while GpgP is monomeric. This is the first characterization of genes and enzymes for the synthesis of GG in a thermophile.
Borrelia burgdorferi
BBA74, a Periplasmic Protein Associated with the Outer Membrane, Lacks Porin-Like Properties
Authors: Mulay Vishwaroop , Caimano Melissa J. , Liveris Dionysios , Desrosiers Daniel C. , Radolf Justin D. , Schwartz Ira
Published: December 2006

The outer membrane of
Borrelia burgdorferi
, the causative agent of Lyme disease, contains very few integral membrane proteins, in contrast to other gram-negative bacteria. BBA74, a
Borrelia burgdorferi
plasmid-encoded protein, was proposed to be an integral outer membrane protein with putative porin function and designated as a 28-kDa outer membrane-spanning porin (Oms28). In this study, the biophysical properties of BBA74 and its subcellular localization were investigated. BBA74 is posttranslationally modified by signal peptidase I cleavage to a mature 25-kDa protein. The secondary structure of BBA74 as determined by circular dichroism spectroscopy consists of at least 78% α-helix with little β-sheet structure. BBA74 in intact
B. burgdorferi
cells was insensitive to proteinase K digestion, and indirect immunofluorescence microscopy showed that BBA74 was not exposed on the cell surface. Triton X-114 extraction of outer membrane vesicle preparations indicated that BBA74 is not an integral membrane protein. Taken together, the data indicate that BBA74 is a periplasmic, outer membrane-associated protein that lacks properties typically associated with porins.
The Alternative Sigma Factor σHIs Required for Toxin Gene Expression byBacillus anthracis
Authors: Hadjifrangiskou Maria , Chen Yahua , Koehler Theresa M.
Published: December 2006

Expression of the structural genes for the anthrax toxin proteins is coordinately controlled by host-related signals, such as elevated CO2, and thetrans-acting positive regulator AtxA. In addition to these requirements, toxin gene expression is under growth phase regulation. The transition state regulator AbrB repressesatxAexpression to influence toxin synthesis. During the late exponential phase of growth, when AbrB levels begin to decrease, toxin synthesis increases. Here we report that toxin gene expression also requires the presence ofsigH, a gene encoding the RNA polymerase sigma factor associated with development inBacillus subtilis. In the well-studiedB. subtilissystem, σHis required for sporulation and other post-exponential-phase processes and is part of a feedback control pathway forabrBexpression. Our data indicate that aBacillus anthracis sigH-null mutant is asporogenous and toxin deficient. Yet the sigma factor is required for toxin gene expression in a manner that is independent of the pathway leading to post-exponential-phase gene expression. σHpositively controlsatxAin an AbrB-independent manner. These findings, combined with previous observations, suggest that the steady-state level ofatxAexpression is critical for optimal toxin gene transcription. We propose a model whereby, under toxin-inducing growth conditions, control of toxin gene expression is fine-tuned by the independent effects of σHand AbrB on the expression ofatxA.
Nitric Oxide in Chemostat-Cultured
Escherichia coli
Is Sensed by Fnr and Other Global Regulators: Unaltered Methionine Biosynthesis Indicates Lack of S Nitrosation
Authors: Pullan Steven T. , Gidley Mark D. , Jones Richard A. , Barrett Jason , Stevanin Tania M. , Read Robert C. , Green Jeffrey , Poole Robert K.
Published: December 2006

We previously elucidated the global transcriptional responses of
Escherichia coli
to the nitrosating agent
S
-nitrosoglutathione (GSNO) in both aerobic and anaerobic chemostats, demonstrated the expression of nitric oxide (NO)-protective mechanisms, and obtained evidence of critical thiol nitrosation. The present study was the first to examine the transcriptome of NO-exposed
E. coli
in a chemostat. Using identical conditions, we compared the GSNO stimulon with the stimulon of NO released from two NO donor compounds {3-[2-hydroxy-1-(1-methyl-ethyl)-2-nitrosohydrazino]-1-propanamine (NOC-5) and 3-(2-hydroxy-1-methyl-2-nitrosohydrazino)-
N
-methyl-1-propanamine (NOC-7)} simultaneously and demonstrated that there were marked differences in the transcriptional responses to these distinct nitrosative stresses. Exposure to NO did not induce
met
genes, suggesting that, unlike GSNO, NO does not elicit homocysteine S nitrosation and compensatory increases in methionine biosynthesis. After entry into cells, exogenous methionine provided protection from GSNO-mediated killing but not from NO-mediated killing. Anaerobic exposure to NO led to up-regulation of multiple Fnr-repressed genes and down-regulation of Fnr-activated genes, including
nrfA
, which encodes cytochrome
c
nitrite reductase, providing strong evidence that there is NO inactivation of Fnr. Other global regulators apparently affected by NO were IscR, Fur, SoxR, NsrR, and NorR. We tried to identify components of the NorR regulon by performing a microarray comparison of NO-exposed wild-type and
norR
mutant strains; only
norVW
, encoding the NO-detoxifying flavorubredoxin and its cognate reductase, were unambiguously identified. Mutation of
norV
or
norR
had no effect on
E. coli
survival in mouse macrophages. Thus, GSNO (a nitrosating agent) and NO have distinct cellular effects; NO more effectively interacts with global regulators that mediate adaptive responses to nitrosative stress but does not affect methionine requirements arising from homocysteine nitrosation.