bluuebunny/crossref_metadata_2025_split huggingface dataset:
HLA class II genetic diversity in southern Tunisia and the Mediterranean area
Authors: Abdennaji Guenounou B. , Loueslati B. Yacoubi , Buhler S. , Hmida S. , Ennafaa H. , Khodjet‐Elkhil H. , Moojat N. , Dridi A. , Boukef K. , Ben Ammar Elgaaied A. , Sanchez‐Mazas A. 
Published: March 2006

SummaryNorth Africa is populated by many Arab‐ and Berber‐speaking populations whose genetic history is still poorly understood. In this study, we analyse the HLA‐DRB1 and DQB1 molecular diversity in three populations from the south of Tunisia — Berbers from Jerba, Berbers from Matmata and Arabs from Gabes — and we compare them to a large set of populations from the whole Mediterranean region. Among the three populations studied, the Berbers from Jerba are the most peculiar, as they diverge significantly from other North Africans while being genetically highly diversified and close to populations from the Near East. Thus, Jerba may have been a crossing point, in historical times, where colonization from the eastern Mediterranean area left significant genetic traces. By contrast, the populations from Matmata and Gabes are genetically similar to other Arab and Berber‐speaking populations from different areas of the Maghrib, despite some peculiar allele and haplotype frequencies. At a larger scale, northwest Africa and southwest Europe are closely related according to these polymorphisms, while the populations from the eastern Mediterranean area are much more differentiated. The close genetic relatedness found for HLA among populations of the western Mediterranean region challenges previous results based on Y chromosome analyses, where the Gibraltar Strait appeared to constitute a main genetic barrier.
Auxiliary Bearing Life Prediction Using Hertzian Contact Bearing
Model
Authors: Sun Guangyoung 
Published: March 2006

Abstract
A rotating machine with active magnetic bearings (AMBs) requires conventional bearings as a backup support system in the case of AMB failure. This paper presents an estimated auxiliary/catcher bearing (CB) L10 fatigue life based on the Hertzian contact dynamic loads between bearing ball and races during the touchdown. The thermal growths of bearing components are predicted using a one-dimensional thermal model, and the resulting expansions contribute to the calculation for the Hertzian contact loads. Numerical simulations for an energy-storage flywheel module reveal that a high-speed backward whirl significantly reduces the CB life and that an optimal damping lowers the CB temperature and increases the CB life.
Nonlinear Modeling of Flexible Manipulators Using Nondimensional Variables
Authors: Shaker M. Chandra , Ghosal Ashitava 
Published: March 2006

Abstract
This paper deals with nonlinear modeling of planar one- and two-link, flexible manipulators with rotary joints using finite element method (FEM) based approaches. The equations of motion are derived taking into account the nonlinear strain-displacement relationship and two characteristic velocities, Ua and Ug, representing material and geometric properties (also axial and flexural stiffness) respectively, are used to nondimensionalize the equations of motion. The effect of variation of Ua and Ug on the dynamics of a planar flexible manipulator is brought out using numerical simulations. It is shown that above a certain Ug value (approximately ⩾45m∕s), a linear model (using a linear strain-displacement relationship) and the nonlinear model give approximately the same tip deflection. Likewise, it was found that the effect of Ua is prominent only if Ug is small. The natural frequencies are seen to be varying in a nonlinear manner with Ua and in a linear manner with Ug.
Chaos and Quasi-Periodic Motions on the Homoclinic Surface of Nonlinear Hamiltonian Systems With Two Degrees of Freedom
Authors: Luo Albert C. J. 
Published: March 2006

Abstract
The numerical prediction of chaos and quasi-periodic motion on the homoclinic surface of a two-degree-of-freedom (2-DOF) nonlinear Hamiltonian system is presented through the energy spectrum method. For weak interactions, the analytical conditions for chaotic motion in such a Hamiltonian system are presented through the incremental energy approach. The Poincaré mapping surfaces of chaotic motions for this specific nonlinear Hamiltonian system are illustrated. The chaotic and quasi-periodic motions on the phase planes, displacement subspace (or potential domains), and the velocity subspace (or kinetic energy domains) are illustrated for a better understanding of motion behaviors on the homoclinic surface. Through this investigation, it is observed that the chaotic and quasi-periodic motions almost fill on the homoclinic surface of the 2-DOF nonlinear Hamiltonian system. The resonant-periodic motions for such a system are theoretically countable but numerically inaccessible. Such conclusions are similar to the ones in the KAM theorem even though the KAM theorem is based on the small perturbation.
New Model of a CVT Rocker-Pin Chain With Exact Joint Kinematics
Authors: Neumann Lutz , Ulbrich Heinz , Pfeiffer Friedrich 
Published: March 2006

Abstract
The improvement of continuously variable transmissions (CVTs) is a challenging task. Detailed dynamic models of the system are needed for the optimization process. This paper introduces a new model of a rocker-pin chain, which is the central part of a chain CVT. During the derivation of the equations of motion, special attention is turned on the exact description of the joint kinematics. An interesting method to speed up the numerical simulation of the chain drive is introduced, which takes into account the special structure of the mass matrix. Simulation results show the strong influence of the geometry of the rocker-pin joints on the dynamics of the whole gear. Further reasonable gear efficiencies can be estimated for arbitrary joint geometries. This model is an excellent basis for further work on optimization of the CVT chain.
Suppression of Planet Mode Response in Planetary Gear Dynamics Through Mesh Phasing
Authors: Ambarisha Vijaya Kumar , Parker Robert G. 
Published: March 2006

Abstract
This work analytically derives design rules to suppress certain harmonics of planet mode response in planetary gear dynamics through mesh phasing. Planet modes are one of three categories of planetary gear vibration modes. In these modes, only the plantes deflect while the carrier, ring, and sun gears have no motion (Lin, J., and Parker, R. G., 1999, ASME J. Vib. Acoust., 121, pp. 316–321;J. Sound Vib, 233(5), pp. 921–928). The dynamic mesh forces are not explicitly modeled for this study; instead, the symmetry of planetary gear systems and gear tooth mesh periodicity are sufficient to establish rules to suppress planet modes. Thus, the conclusions are independent of the mesh modeling details. Planetary gear systems with equally spaced planets and with diametrically opposed planet pairs are examined. Suppression of degenerate mode response in purely rotational degree-of-freedom models achieved in the limit of infinite bearing stiffness is also investigated. The mesh phasing conclusions are verified by dynamic simulations of various planetary gears using a lumped-parameter analytical model and by comparisons to others’ research.
Porin-Mediated Antibiotic Resistance in
Neisseria gonorrhoeae
: Ion, Solute, and Antibiotic Permeation through PIB Proteins with
penB
Mutations
Authors: Olesky Melanie , Zhao Shuqing , Rosenberg Robert L. , Nicholas Robert A. 
Published: March 2006

ABSTRACT

Neisseria gonorrhoeae
has two porins, PIA and PIB, whose genes (
porA
and
porB
, respectively) are alleles of a single
por
locus. We recently demonstrated that
penB
mutations at positions 120 and 121 in PIB, which are presumed to reside in loop 3 that forms the pore constriction zone, confer intermediate-level resistance to penicillin and tetracycline (M. Olesky, M. Hobbs, and R. A. Nicholas, Antimicrob. Agents Chemother.
46:
2811-2820, 2002). In the present study, we investigated the electrophysiological properties as well as solute and antibiotic permeation rates of recombinant PIB proteins containing
penB
mutations (G120K, G120D/A121D, G120P/A121P, and G120R/A121H). In planar lipid bilayers, the predominant conducting state of each porin variant was 30 to 40% of the wild type, even though the anion selectivity and maximum channel conductance of each PIB variant was similar to that of the wild type. Liposome-swelling experiments revealed no significant differences in the permeation of sugars or β-lactam antibiotics through the wild type or PIB variants. Although these results are seemingly contradictory with the ability of these variants to increase antibiotic resistance, they are consistent with MIC data showing that these porin mutations confer resistance only in strains containing an
mtrR
mutation, which increases expression of the MtrC-MtrD-MtrE efflux pump. Moreover, both the
mtrR
and
penB
mutations were required to decrease in vivo permeation rates below those observed in the parental strain containing either
mtrR
or porin mutations alone. Thus, these data demonstrate a novel mechanism of porin-mediated resistance in which mutations in PIB have no affect on antibiotic permeation alone but instead act synergistically with the MtrC-MtrD-MtrE efflux pump in the development of antibiotic resistance in gonococci.
Phenotypic Characterization ofStreptococcus pneumoniaeBiofilm Development
Authors: Allegrucci Magee , Hu F. Z. , Shen K. , Hayes J. , Ehrlich Garth D. , Post J. Christopher , Sauer Karin 
Published: March 2006

ABSTRACTStreptococcus pneumoniaeis among the most common pathogens associated with chronic otitis media with effusion, which has been hypothesized to be a biofilm disease.S. pneumoniaehas been shown to form biofilms, however, little is known about the developmental process, the architecture, and the changes that occur upon biofilm development. In the current study we made use of a continuous-culture biofilm system to characterize biofilm development of 14 differentS. pneumoniaestrains representing at least 10 unique serotypes. The biofilm development process was found to occur in three distinct stages, including initial attachment, cluster formation, and biofilm maturation. While all 14 pneumococcal strains displayed similar developmental stages, the mature biofilm architecture differed significantly among the serotypes tested. Overall, three biofilm architectural groups were detected based on biomass, biofilm thickness, and cluster size. The biofilm viable cell counts and total protein concentration increased steadily over the course of biofilm development, reaching ∼8 × 108cells and ∼15 mg of protein per biofilm after 9 days of biofilm growth. Proteomic analysis confirmed the presence of distinct biofilm developmental stages by the detection of multiple phenotypes over the course of biofilm development. The biofilm development process was found to correlate not only with differential production of proteins but also with a dramatic increase in the number of detectable proteins, indicating that biofilm formation byS. pneumoniaemay be a far more complex process than previously anticipated. Protein identification revealed that proteins involved in virulence, adhesion, and resistance were more abundant under biofilm growth conditions. A possible role of the identified proteins in biofilm formation is discussed.
Single-Strand-Specific Exonucleases Prevent Frameshift Mutagenesis by Suppressing SOS Induction and the Action of DinB/DNA Polymerase IV in Growing Cells
Authors: Hersh Megan N. , Morales Liza D. , Ross Kimberly J. , Rosenberg Susan M. 
Published: March 2006

ABSTRACT

Escherichia coli
strains carrying null alleles of genes encoding single-strand-specific exonucleases ExoI and ExoVII display elevated frameshift mutation rates but not base substitution mutation rates. We characterized increased spontaneous frameshift mutation in ExoI
−
ExoVII
−
cells and report that some of this effect requires RecA, an inducible SOS DNA damage response, and the low-fidelity, SOS-induced DNA polymerase DinB/PolIV, which makes frameshift mutations preferentially. We also find that SOS is induced in ExoI
−
ExoVII
−
cells. The data imply a role for the single-stranded exonucleases in guarding the genome against mutagenesis by removing excess single-stranded DNA that, if left, leads to SOS induction and PolIV-dependent mutagenesis. Previous results implicated PolIV in
E. coli
mutagenesis specifically during starvation or antibiotic stresses. Our data imply that PolIV can also promote mutation in growing cells under genome stress due to excess single-stranded DNA.
Oxygen-Dependent Regulation of the Central Pathway for the Anaerobic Catabolism of Aromatic Compounds inAzoarcussp. Strain CIB
Authors: Durante-Rodríguez Gonzalo , Zamarro María Teresa , García José Luis , Díaz Eduardo , Carmona Manuel 
Published: March 2006

ABSTRACTThe role of oxygen in the transcriptional regulation of thePNpromoter that controls thebzdoperon involved in the anaerobic catabolism of benzoate in the denitrifyingAzoarcussp. strain CIB has been investigated. In vivo experiments usingPN::lacZtranslational fusions, in bothAzoarcussp. strain CIB andEscherichia colicells, have shown an oxygen-dependent repression effect on the transcription of thebzdcatabolic genes.E. coliFnr was required for the anaerobic induction of thePNpromoter, and the oxygen-dependent repression of thebzdgenes could be bypassed by the expression of a constitutively active Fnr* protein. In vitro experiments revealed that Fnr binds to thePNpromoter at a consensus sequence centered at position −41.5 from the transcription start site overlapping the −35 box, suggesting thatPNbelongs to the class II Fnr-dependent promoters. Fnr interacts with RNA polymerase (RNAP) and is strictly required for transcription initiation after formation of the RNAP-PNcomplex. Anfnrortholog, theacpRgene, was identified in the genome ofAzoarcussp. strain CIB. TheAzoarcussp. strain CIBacpRmutant was unable to grow anaerobically on aromatic compounds and it did not drive the expression of thePN::lacZfusion, suggesting that AcpR is the cognate transcriptional activator of thePNpromoter. Since the lack of AcpR inAzoarcussp. strain CIB did not affect growth on nonaromatic carbon sources, AcpR can be considered a transcriptional regulator of the Fnr/Crp superfamily that has evolved to specifically control the central pathway for the anaerobic catabolism of aromatic compounds inAzoarcus.
Polyamines Are Essential for the Formation of Plague Biofilm
Authors: Patel Chandra N. , Wortham Brian W. , Lines J. Louise , Fetherston Jacqueline D. , Perry Robert D. , Oliveira Marcos A. 
Published: March 2006

ABSTRACTWe provide the first evidence for a link between polyamines and biofilm levels inYersinia pestis, the causative agent of plague. Polyamine-deficient mutants ofY. pestiswere generated with a single deletion inspeAorspeCand a double deletion mutant. The genesspeAandspeCcode for the biosynthetic enzymes arginine decarboxylase and ornithine decarboxylase, respectively. The level of the polyamine putrescine compared to the parentalspeA+speC+strain (KIM6+) was depleted progressively, with the highest levels found in theY. pestisΔspeCmutant (55% reduction), followed by the ΔspeAmutant (95% reduction) and the ΔspeAΔspeCmutant (>99% reduction). Spermidine, on the other hand, remained constant in the single mutants but was undetected in the double mutant. The growth rates of mutants with single deletions were not altered, while the ΔspeAΔspeCmutant grew at 65% of the exponential growth rate of thespeA+speC+strain. Biofilm levels were assayed by three independent measures: Congo red binding, crystal violet staining, and confocal laser scanning microscopy. The level of biofilm correlated to the level of putrescine as measured by high-performance liquid chromatography-mass spectrometry and as observed in a chemical complementation curve. Complementation of the ΔspeAΔspeCmutant withspeAshowed nearly full recovery of biofilm to levels observed in thespeA+speC+strain. Chemical complementation of the double mutant and recovery of the biofilm defect were only observed with the polyamine putrescine.
Chromosome Evolution in theThermotogales: Large-Scale Inversions and Strain Diversification of CRISPR Sequences
Authors: DeBoy Robert T. , Mongodin Emmanuel F. , Emerson Joanne B. , Nelson Karen E. 
Published: March 2006

ABSTRACTIn the present study, the chromosomes of two members of theThermotogaleswere compared. A whole-genome alignment ofThermotoga maritimaMSB8 andThermotoga neapolitanaNS-E has revealed numerous large-scale DNA rearrangements, most of which are associated with CRISPR DNA repeats and/or tRNA genes. These DNA rearrangements do not include the putative origin of DNA replication but move within the same replichore, i.e., the same replicating half of the chromosome (delimited by the replication origin and terminus). Based on cumulative GC skew analysis, both theT. maritimaandT. neapolitanalineages contain one or two major inverted DNA segments. Also, based on PCR amplification and sequence analysis of the DNA joints that are associated with the major rearrangements, the overall chromosome architecture was found to be conserved at most DNA joints for other strains ofT. neapolitana. Taken together, the results from this analysis suggest that the observed chromosomal rearrangements in theThermotogaleslikely occurred by successive inversions after their divergence from a common ancestor and before strain diversification. Finally, sequence analysis shows that size polymorphisms in the DNA joints associated with CRISPRs can be explained by expansion and possibly contraction of the DNA repeat and spacer unit, providing a tool for discerning the relatedness of strains from different geographic locations.
Significant Gene Order and Expression Differences inBordetella pertussisDespite Limited Gene Content Variation
Authors: Brinig Mary M. , Cummings Craig A. , Sanden Gary N. , Stefanelli Paola , Lawrence Andrew , Relman David A. 
Published: March 2006

ABSTRACTBordetella pertussis, an obligate human pathogen and the agent of whooping cough, is a clonal species, despite the dynamic selection pressures imposed by host immunity and vaccine usage. Because the generation of variation is critical for species evolution, we employed a variety of approaches to examine features ofB. pertussisgenetic variation. We found a high level of conservation of gene content among 137B. pertussisstrains with different geographical, temporal, and epidemiological associations, using comparative genomic hybridization. The limited number of regions of difference were frequently located adjacent to copies of the insertion element IS481, which is present in high numbers in theB. pertussischromosome. This repeated sequence appears to provide targets for homologous recombination, resulting in deletion of intervening sequences. Using subtractive hybridization, we searched for previously undetected genes in diverse clinical isolates but did not detect any new genes, indicating that gene acquisition is rare inB. pertussis. In contrast, we found evidence of altered gene order in the several strains that were examined and again found an association of IS481with sites of rearrangement. Finally, we compared whole-genome expression profiles of different strains and found significant changes in transcript abundance, even in the same strain after as few as 12 laboratory passages. This combination of approaches provides a detailed picture of a pathogenic species with little gene loss or gain but with the capacity to generate variation by rearranging its chromosome and altering gene expression. These findings have broad implications for host adaptation by microbial pathogens.
Nucleotide-Dependent Dimerization of the C-Terminal Domain of the ABC Transporter CvaB in Colicin V Secretion
Authors: Guo Xiangxue , Harrison Robert W. , Tai Phang C. 
Published: March 2006

ABSTRACT

The cytoplasmic membrane proteins CvaB and CvaA and the outer membrane protein TolC constitute the bacteriocin colicin V secretion system in
Escherichia coli
. CvaB functions as an ATP-binding cassette transporter, and its C-terminal domain (CTD) contains typical motifs for the nucleotide-binding and Walker A and B sites and the ABC signature motif. To study the role of the CvaB CTD in the secretion of colicin V, a truncated construct of this domain was made and overexpressed. Different forms of the CvaB CTD were found during purification and identified as monomer, dimer, and oligomer forms by gel filtration and protein cross-linking. Nucleotide binding was shown to be critical for CvaB CTD dimerization. Oligomers could be converted to dimers by nucleotide triphosphate-Mg, and nucleotide release from dimers resulted in transient formation of monomers, followed by oligomerization and aggregation. Site-directed mutagenesis showed that the ABC signature motif was involved in the nucleotide-dependent dimerization. The spatial proximity of the Walker A site and the signature motif was shown by disulfide cross-linking a mixture of the A530C and L630C mutant proteins, while the A530C or L630C mutant protein did not dimerize on its own. Taken together, these results indicate that the CvaB CTD formed a nucleotide-dependent head-to-tail dimer.
Identification of a Novel α-Galactosidase from the Hyperthermophilic ArchaeonSulfolobus solfataricus
Authors: Brouns Stan J. J. , Smits Nicole , Wu Hao , Snijders Ambrosius P. L. , Wright Phillip C. , de Vos Willem M. , van der Oost John 
Published: March 2006

ABSTRACTSulfolobus solfataricusis an aerobic crenarchaeon that thrives in acidic volcanic pools. In this study, we have purified and characterized a thermostable α-galactosidase from cell extracts ofS. solfataricusP2 grown on the trisaccharide raffinose. The enzyme, designated GalS, is highly specific for α-linked galactosides, which are optimally hydrolyzed at pH 5 and 90°C. The protein consists of 74.7-kDa subunits and has been identified as the gene product of open reading frame Sso3127. Its primary sequence is most related to plant enzymes of glycoside hydrolase family 36, which are involved in the synthesis and degradation of raffinose and stachyose. Both thegalSgene fromS. solfataricusP2 and an orthologous gene fromSulfolobus tokodaiihave been cloned and functionally expressed inEscherichia coli, and their activity was confirmed. At present, theseSulfolobusenzymes not only constitute a distinct type of thermostable α-galactosidases within glycoside hydrolase clan D but also represent the first members from theArchaea.
Receptor-Binding Protein of
Lactococcus lactis
Phages: Identification and Characterization of the Saccharide Receptor-Binding Site
Authors: Tremblay Denise M. , Tegoni Mariella , Spinelli Silvia , Campanacci Valérie , Blangy Stéphanie , Huyghe Céline , Desmyter Aline , Labrie Steve , Moineau Sylvain , Cambillau Christian 
Published: March 2006

ABSTRACT

Phage p2, a member of the lactococcal 936 phage species, infects
Lactococcus lactis
strains by binding initially to specific carbohydrate receptors using its receptor-binding protein (RBP). The structures of p2 RBP, a homotrimeric protein composed of three domains, and of its complex with a neutralizing llama VH domain (VHH5) have been determined (S. Spinelli, A. Desmyter, C. T. Verrips, H. J. de Haard, S. Moineau, and C. Cambillau, Nat. Struct. Mol. Biol. 13:85-89, 2006). Here, we show that VHH5 was able to neutralize 12 of 50 lactococcal phages belonging to the 936 species. Moreover, escape phage mutants no longer neutralized by VHH5 were isolated from 11 of these phages. All of the mutations (but one) cluster in the RBP/VHH5 interaction surface that delineates the receptor-binding area. A glycerol molecule, observed in the 1.7-Å resolution structure of RBP, was found to bind tightly (

K
d

= 0.26 μM) in a crevice located in this area. Other saccharides bind RBP with comparable high affinity. These data prove the saccharidic nature of the bacterial receptor recognized by phage p2 and identify the position of its binding site in the RBP head domain.