bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biosynthesis of a Rare Di-N-Acetylated Sugar in the Lipopolysaccharides of both
Pseudomonas aeruginosa
and
Bordetella pertussis
Occurs via an Identical Scheme despite Different Gene Clusters
Authors: Westman Erin L. , Preston Andrew , Field Robert A. , Lam Joseph S. 
Published: July 2008

ABSTRACT

Pseudomonas aeruginosa
and
Bordetella pertussis
produce lipopolysaccharide (LPS) that contains 2,3-diacetamido-2,3-dideoxy-
d
-mannuronic acid (
d
-ManNAc3NAcA). A five-enzyme biosynthetic pathway that requires WbpA, WbpB, WbpE, WbpD, and WbpI has been proposed for the production of this sugar in
P. aeruginosa
, based on analysis of genes present in the B-band LPS biosynthesis cluster. In the analogous
B. pertussis
cluster, homologs of
wbpB
to
wbpI
were present, but a putative dehydrogenase gene was missing; therefore, the biosynthetic mechanism for UDP-
d
-ManNAc3NAcA was unclear. Nonpolar knockout mutants of each
P. aeruginosa
gene were constructed. Complementation analysis of the mutants demonstrated that B-band LPS production was restored to
P. aeruginosa
knockout mutants when the relevant
B. pertussis
genes were supplied in
trans
. Thus, the genes that encode the putative oxidase, transaminase,
N
-acetyltransferase, and epimerase enzymes in
B. pertussis
are functional homologs of those in
P. aeruginosa
. Two candidate dehydrogenase genes were located by searching the
B. pertussis
genome; these have 80% identity to
P. aeruginosa wbpO
(serotype O6) and 32% identity to
wbpA
(serotype O5). These genes,
wbpO
1629
and
wbpO
3150
, were shown to complement a
wbpA
knockout of
P. aeruginosa
. Capillary electrophoresis was used to characterize the enzymatic activities of purified WbpO
1629
and WbpO
3150
, and mass spectrometry analysis confirmed that the two enzymes are dehydrogenases capable of converting UDP-
d
-GlcNAc, UDP-
d
-GalNAc, to a lesser extent, and UDP-
d
-Glc, to a much lesser extent. Together, these results suggest that
B. pertussis
produces UDP-
d
-ManNAc3NAcA through the same pathway proposed for
P. aeruginosa
, despite differences in the genomic context of the genes involved.
Different Pathways of Choline Metabolism in Two Choline-Independent Strains ofStreptococcus pneumoniaeand Their Impact on Virulence
Authors: Kharat Arun S. , Denapaite Dalia , Gehre Florian , Brückner Reinhold , Vollmer Waldemar , Hakenbeck Regine , Tomasz Alexander 
Published: July 2008

ABSTRACTThe two recently characterizedStreptococcus pneumoniaestrains—R6Chi and R6Cho−—that have lost the unique auxotrophic requirement of this bacterial species for choline differ in their mechanisms of choline independence. In strain R6Chi the mechanism is caused by a point mutation intacF, a gene that is part of the pneumococcallic2operon, which is essential for growth and survival of the bacteria. Cultures oflic2mutants of the encapsulated strain D39Chi growing in choline-containing medium formed long chains, did not autolyze, had no choline in their cell wall, and were completely avirulent in the mouse intraperitoneal model. In contrast, while the Cho−strain carried a complete pneumococcallic2operon and had no mutations in thetacFgene, deletion of the entirelic2operon had no effect on the growth or phenotype of strain Cho−. These observations suggest that the biochemical functions normally dependent on determinants of the pneumococcallic2operon may also be carried out in strain Cho−by a second set of genetic elements imported fromStreptococcus oralis, the choline-independent streptococcal strain that served as the DNA donor in the heterologous transformation event that produced strain R6Cho−. The identification in R6Cho−of a large (20-kb)S. oralisDNA insert carrying bothtacFandlicDgenes confirms this prediction and suggests that these heterologous elements may represent a “backup” system capable of catalyzing P-choline incorporation and export of teichoic acid chains under conditions in which the nativelic2operon is not functional.
Protein Aggregates: an Aging Factor Involved in Cell Death
Authors: Maisonneuve Etienne , Ezraty Benjamin , Dukan Sam 
Published: July 2008

ABSTRACT

In a previous study, we demonstrated the presence of protein aggregates in an exponentially grown
Escherichia coli
culture. In light of these observations, protein aggregates could be considered damage to cells that is able to pass from one generation to the next. Based on the assumption that the amount of aggregate protein could represent an aging factor, we monitored this amount in a bacterial culture during senescence. In doing so, we observed (i) a significant increase in the amount of aggregate protein over time, (ii) a proportional relationship between the amount of aggregate protein and the level of dead cells, (iii) a larger amount in dead cells than in culturable cells, (iv) a heterogeneous distribution of different amounts within a homogenous population of culturable cells entering stasis, and (v) that the initial amount of aggregate protein within a culturable population conditioned the death rate of the culture. Together, the results presented in this study suggest that protein aggregates indeed represent one aging factor leading to bacterial cell death.
Characterization of an Inducible, Antibiotic-Resistant Aminoacyl-tRNA Synthetase Gene in
Streptomyces coelicolor
Authors: Vecchione James J. , Sello Jason K. 
Published: July 2008

ABSTRACT

Streptomyces coelicolor
has two genes encoding tryptophanyl-tRNA synthetases, one of which (
trpRS1
) is resistant to and transcriptionally activated by indolmycin. We found that this gene also confers resistance to chuangxinmycin (another antibiotic that inhibits bacterial tryptophanyl-tRNA synthetases) and that its transcription is not absolutely dependent on either antibiotic.
Identification of a σ
B
-Dependent Small Noncoding RNA in
Listeria monocytogenes
Authors: Nielsen Jesper Sejrup , Olsen Anders Steno , Bonde Mette , Valentin-Hansen Poul , Kallipolitis Birgitte H. 
Published: July 2008

ABSTRACT

In
Listeria monocytogenes
, the alternative sigma factor σ
B
plays important roles in stress tolerance and virulence. Here, we present the identification of SbrA, a novel small noncoding RNA that is produced in a σ
B
-dependent manner. This finding adds the σ
B
regulon to the growing list of stress-induced regulatory circuits that include small noncoding RNAs.
Mutational Analysis of the Connector Segment in the HAMP Domain of Tsr, theEscherichia coliSerine Chemoreceptor
Authors: Ames Peter , Zhou Qin , Parkinson John S. 
Published: July 2008

ABSTRACTHAMP domains are ∼50-residue motifs, found in many bacterial signaling proteins, that consist of two amphiphilic helices joined by a nonhelical connector segment. The HAMP domain of Tsr, the serine chemoreceptor ofEscherichia coli, receives transmembrane input signals from the periplasmic serine binding domain and in turn modulates output signals from the Tsr kinase control domain to elicit chemotactic responses. We created random amino acid replacements at each of the 14 connector residues of Tsr-HAMP to identify those that are critical for Tsr function. In all, we surveyed 179 connector missense mutants and identified three critical residues (G235, L237, and I241) at which most replacements destroyed Tsr function and another important residue (G245) at which most replacements impaired Tsr function. The region surrounding G245 tolerated 1-residue deletions and insertions of up to 10 glycines, suggesting a role as a relatively nonspecific, flexible linker. The critical connector residues are consistent with a structural model of the Tsr-HAMP domain based on the solution structure of an isolated thermophile HAMP domain (M. Hulko, F. Berndt, M. Gruber, J. U. Linder, V. Truffault, A. Schultz, J. Martin, J. E. Schultz, A. N. Lupas, and M. Coles, Cell 126:929-940, 2006) in which G235 defines a critical turn at the C terminus of the first helix and L237 and I241 pack against the helices, perhaps to stabilize alternative HAMP signaling conformations. Most I241 lesions locked Tsr signal output in the kinase-on mode, implying that this residue is responsible mainly for stabilizing the kinase-off signaling state. In contrast, lesions at L237 resulted in a variety of aberrant output patterns, suggesting a role in toggling output between signaling states.
Salmonella entericaSerovar Typhimurium BipA Exhibits Two Distinct Ribosome Binding Modes
Authors: deLivron Megan A. , Robinson Victoria L. 
Published: July 2008

ABSTRACTBipA is a highly conserved prokaryotic GTPase that functions to influence numerous cellular processes in bacteria. InEscherichia coliandSalmonella entericaserovar Typhimurium, BipA has been implicated in controlling bacterial motility, modulating attachment and effacement processes, and upregulating the expression of virulence genes and is also responsible for avoidance of host defense mechanisms. In addition, BipA is thought to be involved in bacterial stress responses, such as those associated with virulence, temperature, and symbiosis. Thus, BipA is necessary for securing bacterial survival and successful invasion of the host. Steady-state kinetic analysis and pelleting assays were used to assess the GTPase and ribosome-binding properties ofS. entericaBipA. Under normal bacterial growth, BipA associates with the ribosome in the GTP-bound state. However, using sucrose density gradients, we demonstrate that the association of BipA and the ribosome is altered under stress conditions in bacteria similar to those experienced during virulence. The data show that this differential binding is brought about by the presence of ppGpp, an alarmone that signals the onset of stress-related events in bacteria.
Determination of Antibiotic Hypersensitivity among 4,000 Single-Gene-Knockout Mutants of
Escherichia coli
Authors: Tamae Cindy , Liu Anne , Kim Katherine , Sitz Daniel , Hong Jeeyoon , Becket Elinne , Bui Ann , Solaimani Parrisa , Tran Katherine P. , Yang Hanjing , Miller Jeffrey H. 
Published: July 2008

ABSTRACT

We have tested the entire Keio collection of close to 4,000 single-gene knockouts in
Escherichia coli
for increased susceptibility to one of seven different antibiotics (ciprofloxacin, rifampin, vancomycin, ampicillin, sulfamethoxazole, gentamicin, or metronidazole). We used high-throughput screening of several subinhibitory concentrations of each antibiotic and reduced more than 65,000 data points to a set of 140 strains that display significantly increased sensitivities to at least one of the antibiotics, determining the MIC in each case. These data provide targets for the design of “codrugs” that can potentiate existing antibiotics. We have made a number of double mutants with greatly increased sensitivity to ciprofloxacin, and these overcome the resistance generated by certain
gyrA
mutations. Many of the gene knockouts in
E. coli
are hypersensitive to more than one antibiotic. Together, all of these data allow us to outline the cell's “intrinsic resistome,” which provides innate resistance to antibiotics.
The Poetic Treatment of atque from Catullus to Juvenal
Authors: Butterfield  
Published: July 2008

Abstract
The remarkable avoidance of unelided, i.e. preconsonantal, atque in Latin poetry has long been observed, although scholars have either offered no reason for it or but a single, and thereby necessarily inadequate, explanation. My purpose in this paper is twofold: (i) to establish accurate figures, based upon close textual scrutiny and emendation, for the poetic treatment of atque from Catullus to Juvenal; (ii) to draw together multiple interconnected reasons for why the handling of atque was so distinct. After a chronological account of the poetic treatment of the conjunction, both linguistic and stylistic reasons are found to be of great importance, whereas metrical reasons are seen to be of far lesser relevance.
Erysichthon der Jäger: SSH 970.22 und Call. Cer. 81-2
Authors: Skempis Marios 
Published: July 2008

Abstract
This paper proposes a solution to the longstanding controversy over the identity of the obscure hunter named Aithon in SSH 970.22 by identifying him with the Callimachean Erysichthon. The fact that Erysichthon's alternative name Aithon has already been established in the Hellenistic period constitutes the primary indication for this identification. Callimachus' Hymn to Demeter includes a key-reference to Erysichthon as a hunter (ll. 81 f.) which can be suggestive of the hero's participation in the Calydonian Hunt. It is the premise of my argument that the association of the two Hellenistic texts is possible by assuming a variant list of Calydonian hunters, featuring Erysichthon among others. This list could have been the source of both the anonymous elegist and Callimachus. Further intertextual affinities and structural similarities between the two narratives are put forward to support this view.
Polos euergetês: Rhetoric and Poetry in the Gorgias
Authors: Robertson G.I.C. 
Published: July 2008

Abstract
Halfway through his conversation with Sokrates in the Gorgias, Polos claims that it would be easy to refute the philosopher's argument that it is better to act with justice than without it. Asking his interlocutor to proceed with the refutation, Sokrates urges him (470c): 'do not tire of doing favours (ευεργετων) for a friend'. In its metre and sense, this phrase is reminiscent of Pindaric lyric, and its vocabulary recalls that of Olympian 2.93-4 in particular; it will be argued here that a 'Pindaric' reading of Sokrates' injunction to Polos is appropriate. Sokrates' adoption of the language of a laudator of tyrants at this point in the conversation is relevant to the presentation in the Gorgias of related themes (flattery, tyranny, and euergesia) and to Sokrates' eironic posture in the dialogue; it also suits Platonic treatments of Pindar and poetry in general.
Personification Allegory in the Aeneid and Ovid's Metamorphoses
Authors: Lowe Dunstan 
Published: July 2008

Abstract
This article will show that Ovid's well-known innovations in the use of personification allegory combine closely with those of Virgil, to form a distinctive 'Augustan' phase in the development of allegory in classical literature. Both Ovid and Virgil make fictional abstractions concrete and ontologically ambiguous. Innovations common to both the Aeneid and Metamorphoses constitute an important stage in the emergence of 'compositional allegory', in the wake of the Roman adoption of Stoicising interpretative reading practices in the course of the first century BC. Both epics involve Furies as models for their major personified abstractions, both in narrative role and in concrete detail. Uniquely in and to Roman literature, Furies changed from supernatural beings into personified abstractions. This change, enabled by the semantic replacement of proper names such as Erinys or Eumenis with the word Furia ('frenzy'), produced new depth and complexity in the form and metaliterary function of personifications in Roman epic and later literary traditions.
Eighteenth (duodevicesimus) or Twenty-Second (duoetvicesimus)? Twenty-Second but duovicesimus (Gel. 5.4.1-5 and Non. s.v. duodevicesimo p. 100M)
Authors: Verbrugghe Gerald 
Published: July 2008

Abstract
Manuscripts of two relatively late authors of classical Latin, Aulus Gellius and Nonius Marcellus, have garbled the word duovicesimus, a word that fell out of use after the first century BC. Modern scholars have had difficulty in restoring the true form of the word to the ancient manuscripts and then in assessing the effect of that restoration on the histories written by three authors of the second and first centuries BC, who are cited as having used that word: Fabius Pictor, Cato the Elder, and Varro. Once the valid form of the word is restored and its meaning realized, the following conclusions are possible. Fabius Pictor had his own peculiar chronology of the period between the Gallic sack of Rome and the first plebeian consul. Cato the Elder marked the beginning of the siege of Sarguntum as the sixth violation of a treaty by the Carthaginians. It is highly likely that Varro had Ancus Marcius die in the twenty-second year of his reign.
What's In A Name? Scholarship and the Pathology of Conservative Protestantism
Authors: Smith Leslie 
Published: July 2008

AbstractConservative Protestants are often defined by their reactionary response to a changing world, and their social and theological embrace of a rigid, absolutist order. This essay considers what is at stake in this definition. The essay analyzes common modes of differentiation between liberal and conservative Protestants (e.g., theology, demographics, and political affiliations) to see whether the different ways of describing these two groups is methodologically warranted. Concluding that significant overlap exists between these communities, the essay turns to Judith Butler's model of pathological rhetoric to consider why such otherwise descriptively problematic labels such as “conservative Protestant,” “fundamentalist,” and “evangelical” continue to be used by scholars.
Challenges Facing the Neurological Study of Religious Behavior, Belief, and Experience
Authors: McNamara Patrick , Wildman Wesley 
Published: July 2008

AbstractThe neurological study of religious behavior, belief, and experience faces many challenges related to research conception, experimental design, and interpretation of results. Some of these problems are common to other types of neurological study of behavioral and cognitive phenomena. Others are distinctive to the specifically religious domain of behavior, belief, and experience. This paper discusses eight of these problems and three key strategic principles for mitigating them. It then proposes an eight-step framework for research into the neurology of religious behavior, belief, and experience that implements the three strategic principles and addresses all eight of the problems.
Authenticity, Invention, Articulation: Theorizing Contemporary Hawaiian Traditions from the Outside
Authors: Johnson Greg 
Published: July 2008

AbstractThis article theorizes potential contributions of outsider analysis to the study of contemporary indigenous traditions, taking Native Hawaiian canoe voyaging and repatriation disputes as its primary examples. The argument proceeds by specifying analytical contributions of articulation theory in contrast to limitations of invention and authenticity discourses. A shared liability of the latter discourses is identified in their tendency to reify identity in ways that preclude engagement with the full range of cultural articulations constitutive of living tradition. Cultural struggle, in particular, is theorized as the aspect of identity articulation that is most explanatory of the character of tradition and least addressed by theories of invention and authenticity.
Inside Out and In Between: Comparing the Comparativists
Authors: McKeown Elizabeth 
Published: July 2008

AbstractThis review essay constructs a comparison among three scholars who think about religion and comparison: Jonathan Z. Smith, Francis X. Clooney and Robert A. Orsi. It employs Smith's rules for comparison in the study of religion by recalling his essays on Judaism and suggesting that we might also want to “Take Catholicism, For Example.” It is intended to express the author's deep gratitude to Smith for making the study of religion pretty interesting.
“Of And and Of : The Politics of Grammar and the Study of Religion”
Authors: Ellis Thomas 
Published: July 2008

AbstractGrammatical constructions in course titles and research agendas reflect particular theoretical orientations in the study of religion. Privileging one construction over the others amounts to a politics of grammar. Two constructions are examined here—the conjunction and the genitive: “Religion and. . .” and “. . .of Religion.” Whereas non-reductive methods such as theology/phenomenology and cultural anthropology endorse the conjunction, reductive methodologies such as biological anthropology invoke the genitive. With the evidence amassing in favor of natural, human universals (pace cultural anthropology) and against supernatural realities (pace theology/phenomenology), the essay argues that only the genitive construction has a place in the study of religion.
Justice and Peace? – The Role of Law in Resolving Colombia's Civil Conflict
Authors: Burbidge Peter 
Published: July 2008

AbstractThe Colombian Parliament's Justice and Peace law of 2005, introduced by the government of President Alvaro Uribe, allows members of armed groups involved in Colombia's 40-year old conflict to re-enter civilian life by paying an alternative penalty of 5-8 years' prison, even where their crimes concern mass-murder. The process is conditional on a full confession and the proper recompense for the victims. The Law however benefits primarily the pro-state paramilitaries, as the left-wing guerrilla groups have yet to make peace, and has thus been described as a transitional justice system without the transition. This article considers the provisions of the 2005 law against the background of the Constitutional Court's 2006 decision on its validity and the requirements of international criminal law and human rights law. It considers whether it satisfies the requirements of the International Criminal Court, which has jurisdiction over Colombia's conflict but with an opt-out till 2009 for war-crimes. Will the process resolve the problem of Colombia's "impunity" – the failure to prosecute paramilitary crimes - which has been condemned by the Inter-American Court of Human Rights? In conclusion it compares the process to other transitional justice systems in South Africa and Northern Ireland.
The Law of Interim Release in the Jurisprudence of the International Criminal Tribunals
Authors: Müller Clemens 
Published: July 2008

AbstractThe right of interim release during trial is an international recognized fundamental right of the accused which is deduced from the presumption of innocence. Although the ICTY has shifted to a more liberal practice, the other tribunals and the ICC are still applying the law of interim release in a restrictive manner. Decisions on interim release are not guided by clearly decisive factors to be applicable for every single accused in each case. Rather an examination of the particular facts of the case and the personality or character of the accused, surrounded by a framework of requirements set forth in the Rules of Procedure and Evidence, determine the practice on interim release. The way international criminal tribunals apply the law of interim release is, like international criminal proceedings as such, of a design sui generis. This article summarises the case-law concerning interim release at the international criminal tribunals. It gives an in-depth study on the requirements set forth in the Rules of Procedure and Evidence which the accused must fulfil to be provisional released.
The Special Court for Sierra Leone – Fair Trials and Justice for the Accused and Victims
Authors: Howarth Kathryn 
Published: July 2008

AbstractThis article examines the issues of a "fair trial" and "justice" at the Special Court for Sierra Leone. It considers these issues in a broad sense, from both the perspective of the accused and the victims, through the exploration of three specific topics: first, the idea of prosecuting "those bearing greatest responsibility" for crimes committed during the conflict in Sierra Leone, second, the first prosecution of the crime of recruiting child soldiers, and third, the first prosecution of forced marriage.