bluuebunny/crossref_metadata_2025_split huggingface dataset:
Four VirB6 Paralogs and VirB9 Are Expressed and Interact inEhrlichia chaffeensis-Containing Vacuoles
Authors: Bao Weichao , Kumagai Yumi , Niu Hua , Yamaguchi Mamoru , Miura Koshiro , Rikihisa Yasuko 
Published: October 2008

ABSTRACTThe type IV secretion system is an important virulence factor in several host cell-associated pathogens, as it delivers various bacterial macromolecules to target eukaryotic cells. Genes homologous to severalvirBgenes andvirD4ofAgrobacterium tumefaciensare found in an intravacuolar pathogenEhrlichia chaffeensis, the tick-borne causative agent of human monocytic ehrlichiosis. In particular, despite its small genome size,E. chaffeensishas four tandemvirB6paralogs (virB6-1, -2, -3, and -4) that are 3- to 10-fold larger thanA. tumefaciens virB6. The present study for the first time illustrates the relevance of the larger quadruple VirB6 paralogs by demonstrating the protein expression and interaction inE. chaffeensis. All fourvirB6paralogs were cotranscribed in THP-1 human leukemia and ISE6 tick cell cultures. The four VirB6 proteins and VirB9 were expressed byE. chaffeensisin THP-1 cells, and amounts of these five proteins were similar in isolatedE. chaffeensis-containing vacuoles and vacuole-freeE. chaffeensis. In addition, an 80-kDa fragment of VirB6-2 was detected, which was strikingly more prevalent inE. chaffeensis-containing vacuoles than in vacuole-freeE. chaffeensis. Coimmunoprecipitation analysis revealed VirB9 interaction with VirB6-1 and VirB6-2; VirB6-4 interaction with VirB6-1, VirB6-2, and VirB6-3; and VirB6-2 80-kDa fragment interaction with VirB6-3 and VirB6-4. The interaction of VirB9 and VirB6-2 was confirmed by far-Western blotting. The results suggest thatE. chaffeensisVirB9, the quadruple VirB6 proteins, and the VirB6-2 80-kDa fragment form a unique molecular subassembly to cooperate in type IV secretion.
The GAF-Like-Domain-Containing Transcriptional Regulator DfdR Is a Sensor Protein for Dibenzofuran and Several Hydrophobic Aromatic Compounds
Authors: Iida Toshiya , Waki Taro , Nakamura Kaoru , Mukouzaka Yuki , Kudo Toshiaki 
Published: October 2008

ABSTRACT

Dibenzofuran (DF) is one of the dioxin carbon skeletal compounds used as a model to study the microbial degradation of dioxins. This study analyzed the transcriptional regulation of the DF dioxygenase genes
dfdA1
to
dfdA4
in the DF-utilizing actinomycetes
Rhodococcus
sp. strain YK2 and
Terrabacter
sp. strain YK3. An open reading frame designated
dfdR
was detected downstream of the
dfdC
genes. The C-terminal part of the DfdR amino acid sequence has high levels of similarity to several LuxR-type DNA binding helix-turn-helix domains, and a GAF domain sequence in the central part was detected by a domain search analysis. A derivative of YK2 with
dfdR
disrupted was not able to utilize DF and did not exhibit DF-dependent
dfdA1
transcriptional induction ability, and these dysfunctions were compensated for by introduction of
dfdR
. Promoter analysis of
dfdA1
in
Rhodococcus
strains indicated that activation of the
dfdA1
promoter (P

dfdA1

) was dependent on
dfdR
and DF and not on a metabolite of the DF pathway. The cell extract of a
Rhodococcus
strain that heterologously expressed DfdR showed electrophoretic mobility shift (EMS) activity for the P

dfdA1

DNA fragment in a DF-dependent manner. In addition, P

dfdA1

activation and EMS activity were observed with hydrophobic aromatic compounds comprising two or more aromatic rings, suggesting that DfdR has broad effector molecule specificity for several hydrophobic aromatic compounds.
Geobacter sulfurreducens
Contains Separate C- and A-Adding tRNA Nucleotidyltransferases and a Poly(A) Polymerase
Authors: Bralley Patricia , Cozad Madeline , Jones George H. 
Published: October 2008

ABSTRACT

The genome of
Geobacter sulfurreducens
contains three genes whose sequences are quite similar to sequences encoding known members of an RNA nucleotidyltransferase superfamily that includes tRNA nucleotidyltransferases and poly(A) polymerases. Reverse transcription-PCR using
G. sulfurreducens
total RNA demonstrated that the genes encoding these three proteins are transcribed. These genes, encoding proteins designated NTSFI, NTSFII, and NTSFIII, were cloned and overexpressed in
Escherichia coli
. The corresponding enzymes were purified and assayed biochemically, resulting in identification of NTSFI as a poly(A) polymerase, NTSFII as a C-adding tRNA nucleotidyltransferase, and NTSFIII as an A-adding tRNA nucleotidyltransferase. Analysis of
G. sulfurreducens
rRNAs and mRNAs revealed the presence of heteropolymeric RNA 3′ tails. This is the first characterization of a bacterial system that expresses separate C- and A-adding tRNA nucleotidyltransferases and a poly(A) polymerase.
Cellodextrin and Laminaribiose ABC Transporters in
Clostridium thermocellum
Authors: Nataf Yakir , Yaron Sima , Stahl Frank , Lamed Raphael , Bayer Edward A. , Scheper Thomas-Helmut , Sonenshein Abraham L. , Shoham Yuval 
Published: October 2008

ABSTRACT

Clostridium thermocellum
is an anaerobic thermophilic bacterium that grows efficiently on cellulosic biomass. This bacterium produces and secretes a highly active multienzyme complex, the cellulosome, that mediates the cell attachment to and hydrolysis of the crystalline cellulosic substrate.
C. thermocellum
can efficiently utilize only β-1,3 and β-1,4 glucans and prefers long cellodextrins. Since the bacterium can also produce ethanol, it is considered an attractive candidate for a consolidated fermentation process in which cellulose hydrolysis and ethanol fermentation occur in a single process. In this study, we have identified and characterized five sugar ABC transporter systems in
C. thermocellum
. The putative transporters were identified by sequence homology of the putative solute-binding lipoprotein to known sugar-binding proteins. Each of these systems is transcribed from a gene cluster, which includes an extracellular solute-binding protein, one or two integral membrane proteins, and, in most cases, an ATP-binding protein. The genes of the five solute-binding proteins were cloned, fused to His tags, overexpressed, and purified, and their abilities to interact with different sugars was examined by isothermal titration calorimetry. Three of the sugar-binding lipoproteins (CbpB to -D) interacted with different lengths of cellodextrins (G
2
to G
5
), with disassociation constants in the micromolar range. One protein, CbpA, binds only cellotriose (G
3
), while another protein, Lbp (laminaribiose-binding protein) interacts with laminaribiose. The sugar specificity of the different binding lipoproteins is consistent with the observed substrate preference of
C. thermocellum
, in which cellodextrins (G
3
to G
5
) are assimilated faster than cellobiose.
Pleiotropic Roles of Polyglycerolphosphate Synthase of Lipoteichoic Acid in Growth of
Staphylococcus aureus
Cells
Authors: Oku Yusuke , Kurokawa Kenji , Matsuo Miki , Yamada Sakuo , Lee Bok-Luel , Sekimizu Kazuhisa 
Published: October 2008

ABSTRACT

Lipoteichoic acid (LTA) is one of two anionic polymers on the surface of the gram-positive bacterium
Staphylococcus aureus
. LTA is critical for the bacterium-host cell interaction and has recently been shown to be required for cell growth and division. To determine additional biological roles of LTA, we found it necessary to identify permissive conditions for the growth of an LTA-deficient mutant. We found that an LTA-deficient
S. aureus
Δ
ltaS
mutant could grow at 30°C but not at 37°C. Even at the permissive temperature, Δ
ltaS
mutant cells had aberrant cell division and separation, decreased autolysis, and reduced levels of peptidoglycan hydrolases. Upshift of Δ
ltaS
mutant cells to a nonpermissive temperature caused an inability to exclude Sytox green dye. A high-osmolarity growth medium remarkably rescued the colony-forming ability of the Δ
ltaS
mutant at 37°C, indicating that LTA synthesis is required for growth under low-osmolarity conditions. In addition, the Δ
ltaS
mutation was found to be synthetically lethal with the Δ
tagO
mutation, which disrupts the synthesis of the other anionic polymer, wall teichoic acid (WTA), at 30°C, suggesting that LTA and WTA compensate for one another in an essential function.
Transcriptome Divergence and the Loss of Plasticity in
Bacillus subtilis
after 6,000 Generations of Evolution under Relaxed Selection for Sporulation
Authors: Maughan Heather , Birky C. William , Nicholson Wayne L. 
Published: October 2008

ABSTRACT

We used microarrays to identify the causes of sporulation deficiencies in
Bacillus subtilis
after 6,000 generations of evolution. We found that sporulation loss did not result from large-scale deletions; therefore, it must have resulted from smaller indels and/or substitutions. Transcription patterns of one strain versus its ancestor showed that sporulation was not initiated and suggested that sporulation loss may be part of an overall decline in plasticity.
Complete Genome Sequence and Comparative Genome Analysis of Enteropathogenic
Escherichia coli
O127:H6 Strain E2348/69
Authors: Iguchi Atsushi , Thomson Nicholas R. , Ogura Yoshitoshi , Saunders David , Ooka Tadasuke , Henderson Ian R. , Harris David , Asadulghani M. , Kurokawa Ken , Dean Paul , Kenny Brendan , Quail Michael A. , Thurston Scott , Dougan Gordon , Hayashi Tetsuya , Parkhill Julian , Frankel Gad 
Published: October 2008

ABSTRACT

Enteropathogenic
Escherichia coli
(EPEC) was the first pathovar of
E. coli
to be implicated in human disease; however, no EPEC strain has been fully sequenced until now. Strain E2348/69 (serotype O127:H6 belonging to
E. coli
phylogroup B2) has been used worldwide as a prototype strain to study EPEC biology, genetics, and virulence. Studies of E2348/69 led to the discovery of the locus of enterocyte effacement-encoded type III secretion system (T3SS) and its cognate effectors, which play a vital role in attaching and effacing lesion formation on gut epithelial cells. In this study, we determined the complete genomic sequence of E2348/69 and performed genomic comparisons with other important
E. coli
strains. We identified 424 E2348/69-specific genes, most of which are carried on mobile genetic elements, and a number of genetic traits specifically conserved in phylogroup B2 strains irrespective of their pathotypes, including the absence of the ETT2-related T3SS, which is present in
E. coli
strains belonging to all other phylogroups. The genome analysis revealed the entire gene repertoire related to E2348/69 virulence. Interestingly, E2348/69 contains only 21 intact T3SS effector genes, all of which are carried on prophages and integrative elements, compared to over 50 effector genes in enterohemorrhagic
E. coli
O157. As E2348/69 is the most-studied pathogenic
E. coli
strain, this study provides a genomic context for the vast amount of existing experimental data. The unexpected simplicity of the E2348/69 T3SS provides the first opportunity to fully dissect the entire virulence strategy of attaching and effacing pathogens in the genomic context.
Genomic Characterization of
Ralstonia solanacearum
Phage φRSB1, a T7-Like Wide-Host-Range Phage
Authors: Kawasaki Takeru , Shimizu Mio , Satsuma Hideki , Fujiwara Akiko , Fujie Makoto , Usami Shoji , Yamada Takashi 
Published: October 2008

ABSTRACT

φRSΒ1 is a wide-host-range, T7-like bacteriophage that infects and efficiently lyses the phytopathogenic bacterium
Ralstonia solanacearum
. The φRSB1 genome comprises 43,079 bp of double-stranded DNA (61.7% G+C) with 325-bp terminal repeats and contains 47 open reading frames. Strong activity of tandem early promoters and wide specificity of phage promoters of φRSB1 were demonstrated.
The Type 4 Pili of EnterohemorrhagicEscherichia coliO157:H7 Are Multipurpose Structures with Pathogenic Attributes
Authors: Xicohtencatl-Cortes Juan , Monteiro-Neto Valério , Saldaña Zeus , Ledesma Maria A. , Puente Jose Luís , Girón Jorge A. 
Published: October 2008

ABSTRACTEnterohemorrhagicEscherichia coli(EHEC) O157:H7 produces long bundles of polar type 4 pili (T4P) called HCP (forhemorrhagiccolipili) that form physical bridges between bacteria associating with human and animal epithelial cells. Here, we sought to further investigate whether HCP possessed other pathogenicity attributes associated with T4P production. Comparative studies performed with wild-type EHEC EDL933 and an isogenichcpAmutant revealed that HCP play different roles in the biology of this organism. We found that in addition to promoting bacterial attachment to host cells, HCP mediate (i) invasion of epithelial cells, (ii) hemagglutination of rabbit erythrocytes, (iii) interbacterial connections conducive to biofilm formation, (iv) specific binding to host extracellular matrix proteins laminin and fibronectin but not collagen, and (v) twitching motility. Nonadherent laboratoryE. colistrain HB101 complemented withhcpABCgenes on plasmid pJX22, which specifies for HCP overproduction in EDL933, became hyperadherent and invasive and produced a thick biofilm, suggesting that the presence of HCP confers HB101(pJX22) new attributes otherwise not exhibited by HB101. Analogous to other bacteria in which T4P are involved in the pathogenesis of several infectious diseases, our data strongly suggest that HCP display multiple functions that may contribute to EHEC colonization of different hosts and to virulence, survival, and transmission of this food-borne pathogen.
Distinct Sensory Pathways in
Vibrio cholerae
El Tor and Classical Biotypes Modulate Cyclic Dimeric GMP Levels To Control Biofilm Formation
Authors: Hammer Brian K. , Bassler Bonnie L. 
Published: October 2008

ABSTRACT

Quorum sensing (QS), or cell-cell communication in bacteria, is achieved through the production and subsequent response to the accumulation of extracellular signal molecules called autoinducers (AIs). To identify AI-regulated target genes in
Vibrio cholerae
El Tor (
V. cholerae
El
), the strain responsible for the current cholera pandemic, luciferase expression was assayed in an AI
−
strain carrying a random
lux
transcriptional reporter library in the presence and absence of exogenously added AIs. Twenty-three genes were identified and shown to require the QS transcription factor, HapR, for their regulation. Several of the QS-dependent target genes, annotated as encoding hypothetical proteins, in fact encode HD-GYP proteins, phosphodiesterases that degrade the intracellular second messenger cyclic dimeric GMP (c-di-GMP), which is important for controlling biofilm formation. Indeed, overexpression of a representative QS-activated HD-GYP protein in
V. cholerae
El
reduced the intracellular concentration of c-di-GMP, which in turn decreased exopolysaccharide production and biofilm formation. The
V. cholerae
classical biotype (
V. cholerae
Cl
), which caused previous cholera pandemics and is HapR
−
, controls c-di-GMP levels and biofilm formation by the VieA signaling pathway. We show that the VieA pathway is dispensable for biofilm formation in
V. cholerae
El
but that restoring HapR in
V. cholerae
Cl
reestablishes QS-dependent repression of exopolysaccharide production. Thus, different pandemic strains of
V. cholerae
modulate c-di-GMP levels and control biofilm formation in response to distinct sensory pathways.
The Complete Genome Sequence of
Bacillus anthracis
Ames “Ancestor”
Authors: Ravel Jacques , Jiang Lingxia , Stanley Scott T. , Wilson Mark R. , Decker R. Scott , Read Timothy D. , Worsham Patricia , Keim Paul S. , Salzberg Steven L. , Fraser-Liggett Claire M. , Rasko David A. 
Published: October 2008

ABSTRACT

The pathogenic bacterium
Bacillus anthracis
has become the subject of intense study as a result of its use in a bioterrorism attack in the United States in September and October 2001. Previous studies suggested that
B. anthracis
Ames Ancestor, the original Ames fully virulent plasmid-containing isolate, was the ideal reference. This study describes the complete genome sequence of that original isolate, derived from a sample kept in cold storage since 1981.
The Complete Genome Sequence ofHelicobacter pyloriStrain G27
Authors: Baltrus David A. , Amieva Manuel R. , Covacci Antonello , Lowe Todd M. , Merrell D. Scott , Ottemann Karen M. , Stein Markus , Salama Nina R. , Guillemin Karen 
Published: October 2008

ABSTRACTHelicobacter pyloriis a gram-negative pathogen that colonizes the stomachs of over half the world's population and causes a spectrum of gastric diseases including gastritis, ulcers, and gastric carcinoma. TheH. pylorispecies exhibits unusually high levels of genetic variation between strains. Here we announce the complete genome sequence ofH. pyloristrain G27, which has been used extensively inH. pyloriresearch.
Impact of reporting rules of biopsy Gleason score for prostate cancer
Authors: Kuroiwa K , Uchino H , Yokomizo A , Naito S 
Published: October 2008

Aims:To investigate how the biopsy Gleason score (GS) and the clinical risk classification have been changed by the reporting rules.Methods:565 prostate biopsy specimens were reassessed. Each Gleason pattern, 1 to 5, was interpreted according to the modified Gleason grading system proposed by the International Society of Urological Pathology. The GS for each case was assigned by the previous reporting rules in the institute (OLD rules), applying the overall-scoring, and ignoring a pattern occupying less than 5% and the tertiary pattern. The GS was also assigned according to the NEW rules, applying the highest-core scoring and reflecting a pattern occupying less than 5% and the tertiary pattern.Results:GS upgrading by the NEW rules was observed in 195 (35%) patients. Of these, 179 (92%) patients were upgraded only by applying the highest-core scoring. Of 198 patients with GS 6 by the OLD rules, 22 (11%) were upgraded to GS 3+4. Of 172 patients with GS 3+4 by the OLD rules, 59 (34%) and 28 (16%), respectively, were upgraded to GS 4+3 and ⩾8. Of 108 patients with GS 4+3 by the OLD rules, 63 (58%) were upgraded to GS ⩾8. As a result, the distribution of D’Amico’s clinical risk classification (low, intermediate and high risk) was changed from 26%, 43% and 31% to 23%, 35% and 41%, respectively.Conclusions:Clinicians should be aware that the reporting rules, especially the highest-core scoring, contribute to a significant upward shift of the biopsy GS and risk classification.
Was There Doctrinal Dissemination in Early Yahweh Religion?
Authors:   Noll
Published: October 2008

AbstractRecent research on scribal practice demonstrates that the scrolls of the Jewish canon were produced by a tiny elite class who did not attempt to disseminate the contents of the scrolls to the largely illiterate Hebrew-speaking peoples. However, the Bible contains a number of passages that describe or command dissemination of their contents (e.g., Deut. 31:10-13), as well as stories about individuals who try to influence common religious belief and practice (e.g., 1 Kigs 18:17-40). These biblical commandments and stories frequently persuade researchers that something like a "doctrinal dissemination" must have been common among pre-Hellenistic Yahwists. Recent research by anthropologists observing processes of religious dissemination is pertinent to this question, calls common assumptions about dissemination into question, and supports the recent conclusions about Hebrew scribal practice.
Mosaic Disability and Identity in Exodus 4:10; 6:12, 30
Authors: Junior Nyasha , Schipper Jeremy 
Published: October 2008

AbstractIn the book of Exodus, Moses describes himself as having a speech difficulty at three different points (4:10; 6:12, 30). These descriptions occur at points in the narrative in which his complex relationship to the Egyptians or Hebrews is at issue. Informed by the burgeoning field of disability studies, this article explores the construction of Moses' identity in the book of Exodus in order to show that his references to his disability provide more than simply an excuse to avoid his divine commission. While his disability may function as an excuse, Moses' emphasis on his disability allows him to circumvent questions about his group identity.
Modern Day Moabites: The Bible and the Debate About Same-Sex Marriage
Authors: Stahlberg Lesleigh Cushing 
Published: October 2008

AbstractWith the debate about same-sex marriage raging in the United States, this paper asks whether the canonical scriptures of Judaism and Christianity offer any justification for blessing same-sex unions. It looks to the ways that the Bible is used by proponents and opponents of same-sex marriage. It analyzes the hermeneutics of the religious left and the religious right, particularly as they grapple with the "clobber texts" of Lev. 18:22 and 20:13. It then turns to the biblical book of Ruth, which critic J. Hillis Miller describes as having "been alienated from itself, translated from itself" through new uses. The paper puts the book of Ruth to yet another new use/misprision, using it as a prooftext to support same-sex marriage. The book has already been upheld by lesbian readers of scripture because of the intimate relationship between the protagonists, Ruth and Naomi, but this paper "misreads" the text differently. Ruth describes how a marriage made between an Israelite and a Moabite brings about the line of King David, one of the most important figures in the Bible and the man from whose line the Messiah is expected to come. The biblical law, however, is unequivocal: Moabites are not permitted to enter into the community of Israel. Juxtaposing the levitical laws (ostensibly) prohibiting homosexuality with those banning Moabites from Israel, this paper argues that the religious left could hold up the book of Ruth as a biblical model for allowing marriage that seems explicitly forbidden by biblical law.
The Mappe and the Bible: Nation, Empire and the Collective Memory of Jonah
Authors: Staffell Simon 
Published: October 2008

AbstractThis article uses the work of the English cartographer John Speed as a way to explore the role of the collective memory of Jonah in social and political discourses during the sixteenth and seventeenth centuries. The paper engages with debates concerning nationalism during the early modern period. Collective memory theory is also used to consider how Jonah became a reified site of memory. By placing Speed's writing alongside the works of his forebears and examining the function of the Jonah text within three sermons, the evolving collective memory of the biblical text, and its imagined attachment to national identity, is traced. It is suggested that Speed's cartographic selectivity in depicting biblical narratives can be seen in relation to the nascent nationalist and imperialist worldviews and ideologies of sixteenth and seventeenth century England.
Zum periphrastischen Infinitiv in Genesis viii 5
Authors: Gzella Holger 
Published: October 2008

AbstractThe astonishing use of the double infinitive absolute with the verb, attested only in Gen. viii 5, has not yet been explained satisfactorily. The present paper argues that this construction is neither a variant form of the periphrastic participle, nor that serves as a pluperfect. Instead, the two infinitives provide an adverbial modification for the main verb by specifically marking durativity and/or iterativity. However, precisely the combination with appears to be special. The past tense indicator, itself being semantically void here, has been employed instead of a full verb, even though such a full verb would normally be expected with this expression, in order to retrieve a piece of information given in Gen. viii 3 and move it from the background to the foreground. It is thus the information structure which conditions the author's decision to explicitly mark the durative Aktionsart.