bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and Characterization of a Novel Adhesin Unique to Oral Fusobacteria
Authors: Han Yiping W. , Ikegami Akihiko , Rajanna Chythanya , Kawsar Hameem I. , Zhou Yun , Li Mei , Sojar Hakimuddin T. , Genco Robert J. , Kuramitsu Howard K. , Deng Cheri X. 
Published: July 2005

ABSTRACT

Fusobacterium nucleatum
is a gram-negative anaerobe that is prevalent in periodontal disease and infections of different parts of the body. The organism has remarkable adherence properties, binding to partners ranging from eukaryotic and prokaryotic cells to extracellular macromolecules. Understanding its adherence is important for understanding the pathogenesis of
F. nucleatum
. In this study, a novel adhesin, FadA (
Fusobacterium ad
hesin
A
), was demonstrated to bind to the surface proteins of the oral mucosal KB cells. FadA is composed of 129 amino acid (aa) residues, including an 18-aa signal peptide, with calculated molecular masses of 13.6 kDa for the intact form and 12.6 kDa for the secreted form. It is highly conserved among
F. nucleatum
,
Fusobacterium periodonticum
, and
Fusobacterium simiae
, the three most closely related oral species, but is absent in the nonoral species, including
Fusobacterium gonidiaformans
,
Fusobacterium mortiferum
,
Fusobacterium naviforme
,
Fusobacterium russii
, and
Fusobacterium ulcerans
. In addition to FadA,
F. nucleatum
ATCC 25586 and ATCC 49256 also encode two paralogues, FN1529 and FNV2159, each sharing 31% identity with FadA. A double-crossover
fadA
deletion mutant,
F. nucleatum
12230-US1, was constructed by utilizing a novel sonoporation procedure. The mutant had a slightly slower growth rate, yet its binding to KB and Chinese hamster ovarian cells was reduced by 70 to 80% compared to that of the wild type, indicating that FadA plays an important role in fusobacterial colonization in the host. Furthermore, due to its uniqueness to oral
Fusobacterium
species,
fadA
may be used as a marker to detect orally related fusobacteria.
F. nucleatum
isolated from other parts of the body may originate from the oral cavity.
Induction of the MexXY Efflux Pump in
Pseudomonas aeruginosa
Is Dependent on Drug-Ribosome Interaction
Authors: Jeannot Katy , Sobel Mara L. , El Garch Farid , Poole Keith , Plésiat Patrick 
Published: July 2005

ABSTRACT

MexXY is an inducible efflux system that contributes to the natural resistance of
Pseudomonas aeruginosa
to antibiotics. Experiments involving real-time PCR after reverse transcription in reference strain PAO1 showed concentration-dependent induction of gene
mexY
by various ribosome inhibitors (e.g., chloramphenicol, tetracycline, macrolides, and aminoglycosides) but not by antibiotics acting on other cellular targets (e.g., β-lactams, fluoroquinolones). Confirming a functional link between the efflux system and the translational machinery, ribosome protection by plasmid-encoded proteins TetO and ErmBP increased the resistance of a Δ
mexAB-oprM
mutant of PAO1 to tetracycline and erythromycin, respectively, as well as the concentrations of both drugs required to induce
mexY
. Furthermore, spontaneous mutations resulting in specific resistance to dihydrostreptomycin or spectinomycin also raised the minimal drug concentration for
mexXY
induction in strain PAO1. While strongly upregulated in a PAO1 mutant defective in gene
mexZ
(which codes for a putative repressor of operon
mexXY
), gene
mexY
remained inducible by agents such as tetracycline, chloramphenicol, and spectinomycin, suggesting additional regulatory loci for
mexXY
. Altogether, these data demonstrate physiological interplays between MexXY and the ribosome and are suggestive of an alternative function for MexXY beyond antibiotic efflux.
Mutation of the
priA
Gene of
Neisseria gonorrhoeae
Affects DNA Transformation and DNA Repair
Authors: Kline Kimberly A. , Seifert H. Steven 
Published: July 2005

ABSTRACT

In
Escherichia coli
, PriA is central to the restart of chromosomal replication when replication fork progression is disrupted and is also involved in homologous recombination and DNA repair. To investigate the role of PriA in recombination and repair in
Neisseria gonorrhoeae
, we identified, cloned, and insertionally inactivated the gonococcal
priA
homologue. The
priA
mutant showed a growth deficiency and decreased DNA repair capability and was completely for deficient in DNA transformation compared to the isogenic parental strain. The
priA
mutant was also more sensitive to the oxidative damaging agents H
2
O
2
and cumene hydroperoxide compared to the parental strain. These phenotypes were complemented by supplying a functional copy of
priA
elsewhere in the chromosome. The
N. gonorrhoeae priA
mutant showed no alteration in the frequency of pilin antigenic variation. We conclude that PriA participates in DNA repair and DNA transformation processes but not in pilin antigenic variation.
Cationic Antimicrobial Peptide Resistance in
Neisseria meningitidis
Authors: Tzeng Yih-Ling , Ambrose Karita D. , Zughaier Susu , Zhou Xiaoliu , Miller Yoon K. , Shafer William M. , Stephens David S. 
Published: July 2005

ABSTRACT

Cationic antimicrobial peptides (CAMPs) are important components of the innate host defense system against microbial infections and microbial products. However, the human pathogen
Neisseria meningitidis
is intrinsically highly resistant to CAMPs, such as polymyxin B (PxB) (MIC ≥ 512 μg/ml). To ascertain the mechanisms by which meningococci resist PxB, mutants that displayed increased sensitivity (≥4-fold) to PxB were identified from a library of mariner transposon mutants generated in a meningococcal strain, NMB. Surprisingly, more than half of the initial PxB-sensitive mutants had insertions within the
mtrCDE
operon, which encodes proteins forming a multidrug efflux pump. Additional PxB-sensitive mariner mutants were identified from a second round of transposon mutagenesis performed in an
mtr
efflux pump-deficient background. Further, a mutation in
lptA
, the phosphoethanolamine (PEA) transferase responsible for modification of the lipid A head groups, was identified to cause the highest sensitivity to PxB. Mutations within the
mtrD
or
lptA
genes also increased meningococcal susceptibility to two structurally unrelated CAMPs, human LL-37 and protegrin-1. Consistently, PxB neutralized inflammatory responses elicited by the
lptA
mutant lipooligosaccharide more efficiently than those induced by wild-type lipooligosaccharide.
mariner
mutants with increased resistance to PxB were also identified in NMB background and found to contain insertions within the
pilMNOPQ
operon involved in pilin biogenesis. Taken together, these data indicated that meningococci utilize multiple mechanisms including the action of the MtrC-MtrD-MtrE efflux pump and lipid A modification as well as the type IV pilin secretion system to modulate levels of CAMP resistance. The modification of meningococcal lipid A head groups with PEA also prevents neutralization of the biological effects of endotoxin by CAMP.
Mosaic Nature of theWolbachiaSurface Protein
Authors: Baldo Laura , Lo Nathan , Werren John H. 
Published: July 2005

ABSTRACTLateral gene transfer and recombination play important roles in the evolution of many parasitic bacteria. Here we investigate intragenic recombination inWolbachiabacteria, considered among the most abundant intracellular bacteria on earth. We conduct a detailed analysis of the patterns of variation and recombination within theWolbachiasurface protein, utilizing an extensive set of published and new sequences from five main supergroups ofWolbachia. Analysis of nucleotide and amino acid sequence variations confirms four hypervariable regions (HVRs), separated by regions under strong conservation. Comparison of shared polymorphisms reveals a complex mosaic structure of the gene, characterized by a clear intragenic recombining of segments among several distinct strains, whose major recombination effect is shuffling of a relatively conserved set of amino acid motifs within each of the four HVRs. Exchanges occurred both within and between the arthropod supergroups. Analyses based on phylogenetic methods and a specific recombination detection program (MAXCHI) significantly support this complex partitioning of the gene, indicating a chimeric origin ofwsp. Althoughwsphas been widely used to define macro- and microtaxonomy amongWolbachiastrains, these results clearly show that it is not suitable for this purpose. The role ofwspin bacterium-host interactions is currently unknown, but results presented here indicate that exchanges of HVR motifs are favored by natural selection. Identifying host proteins that interact withwspvariants should help reveal how these widespread bacterial parasites affect and evolve in response to the cellular environments of their invertebrate hosts.
Unusual Group II Introns in Bacteria of theBacillus cereusGroup
Authors: Tourasse Nicolas J. , Stabell Fredrik B. , Reiter Lillian , Kolstø Anne-Brit 
Published: July 2005

ABSTRACTA combination of sequence and structure analysis and reverse transcriptase PCR experiments was used to characterize the group II introns in the complete genomes of two strains of the pathogenBacillus cereus. WhileB. cereusATCC 14579 harbors a single intron element in the chromosome,B. cereusATCC 10987 contains three introns in the chromosome and four in its 208-kb pBc10987 plasmid. The most striking finding is the presence inB. cereusATCC 10987 of an intron [B.c.I2(a)] located on the reverse strand of a gene encoding a putative cell surface protein which appears to be correlated to strains of clinical origin. Because of the opposite orientation ofB.c.I2(a), the gene is disrupted. Even more striking is thatB.c.I2(a) splices out of an RNA transcript corresponding to the opposite DNA strand. All other intragenic introns studied here are inserted in the same orientation as their host genes and splice out of the mRNA in vivo, setting the flanking exons in frame. Noticeably,B.c.I3 inB. cereusATCC 10987 represents the first example of a group II intron entirely included within a conserved replication gene, namely, the α subunit of DNA polymerase III. Another striking finding is that the observed 3′ splice site ofB.c.I4 occurs 56 bp after the predicted end of the intron. This apparently unusual splicing mechanism may be related to structural irregularities in the 3′ terminus. Finally, we also show that the intergenic introns ofB. cereusATCC 10987 are transcribed with their upstream genes and do splice in vivo.
De Novo Alanine Synthesis by Bacteroids ofMesorhizobium lotiIs Not Required for Nitrogen Transfer in the Determinate Nodules ofLotus corniculatus
Authors: Kumar Shalini , Bourdès Alexandre , Poole Philip 
Published: July 2005

ABSTRACTDeletion of both alanine dehydrogenase genes (aldA) inMesorhizobium lotiresulted in the loss of AldA enzyme activity from cultured bacteria and bacteroids but had no effect on the symbiotic performance ofLotus corniculatusplants. Thus, neither indeterminate pea nodules nor determinateL. corniculatusnodules export alanine as the sole nitrogen secretion product.
Characterization of the
Vibrio cholerae vceCAB
Multiple-Drug Resistance Efflux Operon in
Escherichia coli
Authors: Woolley Robin C. , Vediyappan Govindsamy , Anderson Matthew , Lackey Melinda , Ramasubramanian Bhagavathi , Jiangping Bai , Borisova Tatyana , Colmer Jane A. , Hamood Abdul N. , McVay Catherine S. , Fralick Joe A. 
Published: July 2005

ABSTRACT

Herein, we identify
vceC
as a component of a
vceCAB
operon, which codes for the
Vibrio cholerae
VceAB multiple-drug resistance (MDR) efflux pump, and
vceR
, which codes for a transcriptional autoregulatory protein that negatively regulates the expression of the
vceCAB
operon and is modulated by some of the substrates of this MDR efflux pump.
ION BEAM LITHOGRAPHY AND NANOFABRICATION: A REVIEW
Authors: WATT F. , BETTIOL A. A. , VAN KAN J. A. , TEO E. J. , BREESE M. B. H. 
Published: July 2005

To overcome the diffraction constraints of traditional optical lithography, the next generation lithographies (NGLs) will utilize any one or more of EUV (extreme ultraviolet), X-ray, electron or ion beam technologies to produce sub-100 nm features. Perhaps the most under-developed and under-rated is the utilization of ions for lithographic purposes. All three ion beam techniques, FIB (Focused Ion Beam), Proton Beam Writing (p-beam writing) and Ion Projection Lithography (IPL) have now breached the technologically difficult 100 nm barrier, and are now capable of fabricating structures at the nanoscale. FIB, p-beam writing and IPL have the flexibility and potential to become leading contenders as NGLs. The three ion beam techniques have widely different attributes, and as such have their own strengths, niche areas and application areas. The physical principles underlying ion beam interactions with materials are described, together with a comparison with other lithographic techniques (electron beam writing and EUV/X-ray lithography). IPL follows the traditional lines of lithography, utilizing large area masks through which a pattern is replicated in resist material which can be used to modify the near-surface properties. In IPL, the complete absence of diffraction effects coupled with ability to tailor the depth of ion penetration to suit the resist thickness or the depth of modification are prime characteristics of this technique, as is the ability to pattern a large area in a single brief irradiation exposure without any wet processing steps. p-beam writing and FIB are direct write (maskless) processes, which for a long time have been considered too slow for mass production. However, these two techniques may have some distinct advantages when used in combination with nanoimprinting and pattern transfer. FIB can produce master stamps in any material, and p-beam writing is ideal for producing three-dimensional high-aspect ratio metallic stamps of precise geometry. The transfer of large scale patterns using nanoimprinting represents a technique of high potential for the mass production of a new generation of high area, high density, low dimensional structures. Finally a cross section of applications are chosen to demonstrate the potential of these new generation ion beam nanolithographies.
PROFILE-BASED STRING KERNELS FOR REMOTE HOMOLOGY DETECTION AND MOTIF EXTRACTION
Authors: KUANG RUI , IE EUGENE , WANG KE , WANG KAI , SIDDIQI MAHIRA , FREUND YOAV , LESLIE CHRISTINA 
Published: July 2005

We introduce novel profile-based string kernels for use with support vector machines (SVMs) for the problems of protein classification and remote homology detection. These kernels use probabilistic profiles, such as those produced by the PSI-BLAST algorithm, to define position-dependent mutation neighborhoods along protein sequences for inexact matching of k-length subsequences ("k-mers") in the data. By use of an efficient data structure, the kernels are fast to compute once the profiles have been obtained. For example, the time needed to run PSI-BLAST in order to build the profiles is significantly longer than both the kernel computation time and the SVM training time. We present remote homology detection experiments based on the SCOP database where we show that profile-based string kernels used with SVM classifiers strongly outperform all recently presented supervised SVM methods. We further examine how to incorporate predicted secondary structure information into the profile kernel to obtain a small but significant performance improvement. We also show how we can use the learned SVM classifier to extract "discriminative sequence motifs" — short regions of the original profile that contribute almost all the weight of the SVM classification score — and show that these discriminative motifs correspond to meaningful structural features in the protein data. The use of PSI-BLAST profiles can be seen as a semi-supervised learning technique, since PSI-BLAST leverages unlabeled data from a large sequence database to build more informative profiles. Recently presented "cluster kernels" give general semi-supervised methods for improving SVM protein classification performance. We show that our profile kernel results also outperform cluster kernels while providing much better scalability to large datasets.Supplementary website:.
Dispersion of gold in stream sediments in the Sungai Kuli region, Sabah, Malaysia
Authors: Fletcher W.K. , Muda J. 
Published: July 2005

The distribution of Au in a Au-rich tributary of the Sungai Kuamut, Sabah, Malaysia, was studied initially by the authors in 1999 prior to disturbance of the tropical rain forest by logging. That study found: (i) a strong but extremely erratic Au anomaly with median values of 230 to 690 ppb in the fine and medium sand sized fractions from both cobble and gravel sites; and (ii) Au values typically <15 ppb in the −53 μm fraction. It was suggested that increased input of fine sediment into the stream after logging might substantially dilute and modify the Au anomaly. Logging of the drainage basin in 2000–2001 provided an opportunity to test this possibility.
Results from sampling at gravel sites in 2001 show no dilution of Au values after logging. This is attributed to the occurrence of rainfall and flood events that counteracted dilution of the anomaly by releasing deeply buried Au and/or flushing excess fine sediment from the stream channel. It is concluded that the strength of Au anomalies in stream sediments is likely to fluctuate as a result of the interactions of rainfall events, stream discharge, and the effects of land disturbance on erosion.
Controls of element dispersion in aeolian sand and calcrete-dominated regolith associated with gold mineralization in the Kraaipan greenstone belt, South Africa
Authors: Okujeni C.D. , Ackon P. , Baugaard W. , Langa N. 
Published: July 2005

This paper focuses on the geochemical controls and associated patterns of element dispersion in aeolian sand/calcrete regolith overlying the Goldridge Au mineralization in the Kraaipan greenstone belt, South Africa, and discusses possible sampling strategies.

Regolith in the Goldridge area consists of
in-situ
weathered basement rocks, overlain by a colluvium and valley-filled sedimentary sequence comprising carbonate-impregnated pebbly to coarse/medium-grained sands at the base, followed by an upper reworked friable/laminated calcrete. These units are unconformably overlain by a fine- to medium-grained ferruginized aeolian sand. The thickest and most laterally extensive regolith sequence occurs along major drainages. Broad valleys and deep channels permitted widespread development and preservation of thick colluvial and alluvial sediments, which were subsequently overlain by aeolian sand.

Gold shows variable dispersion patterns in aeolian sand, often with peak Au concentrations occurring in the central portions of the profile, coinciding with the transition zone between deep red and reddish-brown sands, that is geochemically characterized by a
c
. two-fold increase in the Fe/Mn ratio. The underlying calcite-rich laminated carbonate facies are accompanied by enhanced contents of CaO, MgO, Fe
2
O
3
, LOI, H
2
O
−
and a decrease in SiO
2
contents. The laminated calcretes are associated with the highest accumulation of Au in the entire regolith, whereas the calcrete-impregnated basal pebbly to sandy zone shows generally low but sporadically high Au content.

Results of multivariate analysis of geochemical data suggest an association of Au with Fe–Mn oxides/ oxyhydroxides in the upper zones of aeolian sand. Increased influence of ferricrete nodules and underlying calcrete in the distribution pattern of Au and associated base metals occurs with depth. The use of stacked or additive element plots (e.g Cu+Ni+Co+Mn) show patterns that reflect various rock types or lithologies concealed beneath aeolian sand.
The laminated to hardpan carbonate horizon and the basal zone of the aeolian sand horizon should therefore be sampled in exploration. An understanding of the spatial distribution of these regolith components is essential to maintain a consistent sample.
Exploring the impact of Acute Pain Teams (APTs) on patient outcomes using routine data
Authors: McDonnell Ann , Nicholl Jon , Read Susan 
Published: July 2005

Acute Pain Teams (APTs) in every hospital performing surgery have been advocated to improve the management of post-operative pain. Poor postoperative analgesia is a perennial problem that may result in complications such as chest infection and pulmonary embolus which may have an impact on outcomes such as mortality and length of stay. This paper considers the feasibility of using routine data to explore the impact of APTs on patient outcomes, using as an illustrative example a study which investigated relationships between the introduction of APTs and post-operative length of stay and in-patient post-operative mortality.
A multinational study of pain management among Hispanics
Authors: Sherwood Gwen , McNeill Jeanette A. , Hernandez Lesbia , Penarrieta Isabel , Petersen Jeannie M. 
Published: July 2005

A multinational project involving pain research teams from three countries examined pain management outcomes in Hispanics. The limited research on pain management outcomes in Hispanics are primarily from the USA, lacking the distinct multinational cultural influences. This article compares the descriptive analysis of the post-operative pain experience of Hispanics in the USA, Puerto Rico and Mexico and tests the reliability of a new Spanish language instrument, the Cuestionario de Houston Sobre el Dolor (Houston Pain Outcome Instrument, HPOI). There were similarities in expectations related to pain relief, proportion of patients reporting worst pain, usual pain and pain-related interference with function. Significant differences were found on adequacy of pain management. Participants reported high use of non-pharmacologic approaches, particularly prayer and family support. The newly developed instrument indicated acceptable reliability in all settings, Chronbach’s Alpha > 0.75, with some variability by study site. Further cross-ethnic and multinational research are needed to provide culturally relevant evidence-based practice models to overcome barriers and reduce disparity.