bluuebunny/crossref_metadata_2025_split huggingface dataset:
TheStreptococcuspneumoniaeCapsule Inhibits Complement Activity and Neutrophil Phagocytosis by Multiple Mechanisms
Authors: Hyams Catherine , Camberlein Emilie , Cohen Jonathan M. , Bax Katie , Brown Jeremy S. 
Published: December 2009

ABSTRACTTheStreptococcuspneumoniaecapsule is vital for virulence and may inhibit complement activity and phagocytosis. However, there are only limited data on the mechanisms by which the capsule affects complement and the consequences forS. pneumoniaeinteractions with phagocytes. Using unencapsulated serotype 2 and 4S. pneumoniaemutants, we have confirmed that the capsule has several effects on complement activity. The capsule impaired bacterial opsonization with C3b/iC3b by both the alternative and classical complement pathways and also inhibited conversion of C3b bound to the bacterial surface to iC3b. There was increased binding of the classical pathway mediators immunoglobulin G (IgG) and C-reactive protein (CRP) to unencapsulatedS. pneumoniae, indicating that the capsule could inhibit classical pathway complement activity by masking antibody recognition of subcapsular antigens, as well as by inhibiting CRP binding. Cleavage of serum IgG by the enzyme IdeS reduced C3b/iC3b deposition on all of the strains, but there were still marked increases in C3b/iC3b deposition on unencapsulated TIGR4 and D39 strains compared to encapsulated strains, suggesting that the capsule inhibits both IgG-mediated and IgG-independent complement activity againstS. pneumoniae. Unencapsulated strains were more susceptible to neutrophil phagocytosis after incubation in normal serum, normal serum treated with IdeS, complement-deficient serum, and complement-deficient serum treated with IdeS or in buffer alone, suggesting that the capsule inhibits phagocytosis mediated by Fcγ receptors, complement receptors, and nonopsonic receptors. Overall, these data show that theS. pneumoniaecapsule affects multiple aspects of complement- and neutrophil-mediated immunity, resulting in a profound inhibition of opsonophagocytosis.
Streptococcus pneumoniae
Resistance to Complement-Mediated Immunity Is Dependent on the Capsular Serotype
Authors: Hyams Catherine , Yuste Jose , Bax Katie , Camberlein Emilie , Weiser Jeffrey N. , Brown Jeremy S. 
Published: December 2009

ABSTRACT

Streptococcus pneumoniae
strains vary considerably in the ability to cause invasive disease in humans, and this is partially associated with the capsular serotype. The
S. pneumoniae
capsule inhibits complement- and phagocyte-mediated immunity, and differences between serotypes in these effects on host immunity may cause some of the variation in virulence between strains. However, the considerable genetic differences between
S. pneumoniae
strains independent of the capsular serotype prevent an unambiguous assessment of the effects of the capsular serotype on immunity using clinical isolates. We have therefore used capsular serotype-switched TIGR4 mutant strains to investigate the effects of the capsular serotype on
S. pneumoniae
interactions with complement. Flow cytometry assays demonstrated large differences in C3b/iC3b deposition on opaque-phase variants of TIGR4(−)+4, +6A, +7F, and +23F strains even though the thicknesses of the capsule layers were similar. There was increased C3b/iC3b deposition on TIGR4(−)+6A and +23F strains compared to +7F and +4 strains, and these differences persisted even in serum depleted of immunoglobulin G. Neutrophil phagocytosis of the TIGR4(−)+6A and +23F strains was also increased, but only in the presence of complement, showing that the effects of the capsular serotype on C3b/iC3b deposition are functionally significant. In addition, the virulence of the TIGR4(−)+6A and +23F strains was reduced in a mouse model of sepsis. These data demonstrate that resistance to complement-mediated immunity can vary with the capsular serotype independently of antibody and of other genetic differences between strains. This might be one mechanism by which the capsular serotype can affect the relative invasiveness of different
S. pneumoniae
strains.
Red Light Activates the σB-Mediated General Stress Response ofBacillus subtilisvia the Energy Branch of the Upstream Signaling Cascade
Authors: Ávila-Pérez Marcela , van der Steen Jeroen B. , Kort Remco , Hellingwerf Klaas J. 
Published: December 2009

ABSTRACTThe σB-dependent general stress response in the common soil bacteriumBacillus subtiliscan be elicited by a range of stress factors, such as starvation or an ethanol, salt, or heat shock, via a complex upstream signaling cascade. Additionally, σBcan be activated by blue light via the phototropin homologue YtvA, a component of the environmental branch of the signaling cascade. Here we use a reporter-gene fusion to show that σBcan also be activated by red light via the energy branch of its upstream signaling cascade. Deletion mutagenesis and homologous overproduction experiments indicate that the RsbP protein (composed of an N-terminal Per-ARNT-Sim [PAS] domain and a C-terminal PP2C-type phosphatase domain) is involved in the red light response. This second light input pathway functions complementarily to YtvA; it shows broader spectral sensitivity but requires higher light intensities. These results are confirmed by transcriptome analyses, which show that both light effects result in upregulation of the σBregulon, with minimal activation of other responses.
Control of Directionality in Bacteriophage mv4 Site-Specific Recombination: Functional Analysis of the Xis Factor
Authors: Coddeville Michèle , Ritzenthaler Paul 
Published: December 2009

ABSTRACTThe integrase of the temperate bacteriophage mv4 catalyzes site-specific recombination between the phageattPsite and the hostattBsite duringLactobacillus delbrueckiilysogenization. The mv4 prophage is excised during the induction of lytic growth. Excisive site-specific recombination between theattRandattLsites is also catalyzed by the phage-encoded recombinase, but the directionality of the recombination is determined by a second phage-encoded protein, the recombination directionality factor (RDF). We have identified and functionally characterized the RDF involved in site-specific excision of the prophage genome. The mv4 RDF,mv4Xis, is encoded by the second gene of the early lytic operon. It is a basic protein of 56 amino acids. Electrophoretic mobility shift assays demonstrated thatmv4Xis binds specifically to theattPandattRsites via two DNA-binding sites, introducing a bend into the DNA.In vitroexperiments andin vivorecombination assays with plasmids inEscherichiacoliandLactobacillusplantarumdemonstrated thatmv4Xis is absolutely required for inter- or intramolecular recombination between theattRandattLsites. In contrast to the well-known phage site-specific recombination systems, the integrative recombination between theattPandattBsites seems not to be inhibited by the presence ofmv4Xis.
A Comprehensive Proteomics and Transcriptomics Analysis ofBacillus subtilisSalt Stress Adaptation
Authors: Hahne Hannes , Mäder Ulrike , Otto Andreas , Bonn Florian , Steil Leif , Bremer Erhard , Hecker Michael , Becher Dörte 
Published: December 2009

ABSTRACTIn its natural habitats,Bacillus subtilisis exposed to changing osmolarity, necessitating adaptive stress responses. Transcriptomic and proteomic approaches can provide a picture of the dynamic changes occurring in salt-stressedB. subtiliscultures because these studies provide an unbiased view of cells coping with high salinity. We applied whole-genome microarray technology and metabolic labeling, combined with state-of-the-art proteomic techniques, to provide a global and time-resolved picture of the physiological response ofB. subtiliscells exposed to a severe and sudden osmotic upshift. This combined experimental approach provided quantitative data for 3,961 mRNA transcription profiles, 590 expression profiles of proteins detected in the cytosol, and 383 expression profiles of proteins detected in the membrane fraction. Our study uncovered a well-coordinated induction of gene expression subsequent to an osmotic upshift that involves large parts of the SigB, SigW, SigM, and SigX regulons. Additionally osmotic upregulation of a large number of genes that do not belong to these regulons was observed. In total, osmotic upregulation of about 500B. subtilisgenes was detected. Our data provide an unprecedented rich basis for further in-depth investigation of the physiological and genetic responses ofB. subtilisto hyperosmotic stress.
Identification of the
Salmonella enterica damX
Gene Product, an Inner Membrane Protein Involved in Bile Resistance
Authors: López-Garrido Javier , Cheng Nancy , García-Quintanilla Fátima , García-del Portillo Francisco , Casadesús Josep 
Published: December 2009

ABSTRACT

The
damX
gene product of
Salmonella enterica
serovar Typhimurium is a protein located in the inner membrane. DamX migrates as a 70-kDa protein in SDS-PAGE even though the predicted protein size is 46 kDa. Synthesis of DamX protein occurs in both exponential- and stationary-phase cultures. Disruption of
damX
causes severe sensitivity to bile. Lack of the outer membrane protein AsmA suppresses bile sensitivity in
Salmonella damX
mutants.
Genome Sequence of the Fleming Strain of
Micrococcus luteus
, a Simple Free-Living Actinobacterium
Authors: Young Michael , Artsatbanov Vladislav , Beller Harry R. , Chandra Govind , Chater Keith F. , Dover Lynn G. , Goh Ee-Been , Kahan Tamar , Kaprelyants Arseny S. , Kyrpides Nikos , Lapidus Alla , Lowry Stephen R. , Lykidis Athanasios , Mahillon Jacques , Markowitz Victor , Mavromatis Konstantinos , Mukamolova Galina V. , Oren Aharon , Rokem J. Stefan , Smith Margaret C. M. , Young Danielle I. , Greenblatt Charles L. 
Published: December 2009

ABSTRACT

Micrococcus luteus
(NCTC2665, “Fleming strain”) has one of the smallest genomes of free-living actinobacteria sequenced to date, comprising a single circular chromosome of 2,501,097 bp (G+C content, 73%) predicted to encode 2,403 proteins. The genome shows extensive synteny with that of the closely related organism,
Kocuria rhizophila
, from which it was taxonomically separated relatively recently. Despite its small size, the genome harbors 73 insertion sequence (IS) elements, almost all of which are closely related to elements found in other actinobacteria. An IS element is inserted into the
rrs
gene of one of only two
rrn
operons found in
M. luteus
. The genome encodes only four sigma factors and 14 response regulators, a finding indicative of adaptation to a rather strict ecological niche (mammalian skin). The high sensitivity of
M. luteus
to β-lactam antibiotics may result from the presence of a reduced set of penicillin-binding proteins and the absence of a
wblC
gene, which plays an important role in the antibiotic resistance in other actinobacteria. Consistent with the restricted range of compounds it can use as a sole source of carbon for energy and growth,
M. luteus
has a minimal complement of genes concerned with carbohydrate transport and metabolism and its inability to utilize glucose as a sole carbon source may be due to the apparent absence of a gene encoding glucokinase. Uniquely among characterized bacteria,
M. luteus
appears to be able to metabolize glycogen only via trehalose and to make trehalose only via glycogen. It has very few genes associated with secondary metabolism. In contrast to most other actinobacteria,
M. luteus
encodes only one resuscitation-promoting factor (Rpf) required for emergence from dormancy, and its complement of other dormancy-related proteins is also much reduced.
M. luteus
is capable of long-chain alkene biosynthesis, which is of interest for advanced biofuel production; a three-gene cluster essential for this metabolism has been identified in the genome.
A novel Dance Dance Revolution (DDR) system for in-home training of stepping ability: basic parameters of system use by older adults
Authors: Smith S T , Sherrington C , Studenski S , Schoene D , Lord S R 
Published: December 2009

ObjectiveThis series of studies was conducted to develop and establish characteristics of exercise videogame play in older adults. The videogame was a modified version of the popular Dance Dance Revolution (DDR; Konomi).MethodsParticipants aged ≥70 were asked to make simple step movements in response to vertically drifting arrows presented on a video screen. Step responses were detected by a modified USB DDR mat, and characteristics of stepping performance such as step timing, percentage of missed target steps and percentage of correct steps were recorded by purpose-built software. Drift speed and step rate of visual stimuli were modified to increase task difficulty.ResultsSignificant linear relationships between stepping performance and stimulus characteristics were observed. Performance of older adults decreased as stimulus speed and step rate were increased. Optimal step performance occurred for a stimulus speed of 17° of visual angle per second and a step rate of one step every 2 s. At fast drift speeds (up to 35°/s), participants were more than 200 ms too slow in coordinating their steps with the visual stimulus. Younger adults were better able to perform the stepping task across a wider range of drift speeds than older adults.ConclusionThe findings suggest that older adults are able to interact with video games based upon DDR but that stepping performance is determined by characteristics of game play such as arrow drift speed and step rate. These novel “exergames” suggest a low-cost method by which older adults can be engaged in exercises that challenge balance and which can be conducted in their own homes.
Impact of WASID and Wingspan on the frequency of intracranial angioplasty and stenting at a high volume tertiary care hospital
Authors: Moskowitz S I , Kelly M E , Obuchowski N , Fiorella D 
Published: December 2009

Background and PurposeThe impact of the Warfarin and Aspirin for Symptomatic Intracranial Disease (WASID) data is described in combination with the commercial release of the Wingspan stenting system on the frequency of neurointervention for the treatment of symptomatic intracranial atherosclerotic disease (ICAD) in a tertiary care center.MethodsEndovascular case logs were reviewed from April 2004 to July 2007. The total number of intracranial neurointerventions and the number of neurointerventions (percutaneous transluminal angioplasty alone (PTA) or with stenting (PTAS)) performed for symptomatic ICAD were calculated. The time period evaluated was divided into two equal 19.5-month epochs representing the time periods before and after the availability of the Wingspan system.ResultsThe frequency of neurointerventions for ICAD increased by 763%, from seven of 354 total cases (2%) to 56 of 367 total cases (15.3%) (p<0.001) after the Wingspan system became available. The increase in intracranial PTAS volume occurred immediately and was stable throughout the “Wingspan era”.ConclusionsThe publication of the WASID trial results combined with the availability of the Wingspan stent system led to a marked increase in the frequency of neurointervention for symptomatic ICAD at our institution. The adoption of this technology occurred without direct evidence that PTAS with Wingspan is superior to traditional medical therapy. These findings underscore the need for a randomized trial of stenting and medical therapy for the treatment of this disease process.
Remarkable high-yielding chemical modification of gold nanoparticles using uncatalyzed click-type 1,3-dipolar cycloaddition chemistry and hyperbaric conditions
Authors: Ismaili Hossein , Alizadeh Abdolhamid , Snell Kristen E. , Workentin Mark S. 
Published: December 2009

Azide-terminated alkyl thiolate monolayer-protected gold nanoparticles (1-C12MPN) with a core size of 1.8 ± 0.2 nm were prepared. 1-C12MPN was modified in high yields via an uncatalyzed 1,3-dipolar cycloaddition (click-type reaction) with a variety of terminal acyl–alkynes under hyperbaric conditions at 11 000 atm. The resulting 1,2,3-triazole modified MPNs (2-C12MPN) were characterized using 1H NMR spectroscopy and were verified by comparison of the spectra to those obtained for the products of the model reactions of 1-azidododecane with the same alkynes. TEM analysis showed that the high-pressure conditions did not affect the size of the gold core, suggesting that the only effect is to facilitate the chemical reaction on the particles.
A spectral displacement study of cyclodextrin/naphthenic acids inclusion complexes
Authors: Mohamed Mohamed H. , Wilson Lee D. , Headley John V. , Peru Kerry M. 
Published: December 2009

The spectral displacement technique has been used to obtain 1:1 β-cyclodextrin (β-CD)/carboxylate anion equilibrium binding constants (K2) for some complex mixtures of naphthenic acids (NAs) and some examples of single-component NAs in aqueous solution. Three specific examples of single-component NAs were chosen with variable Z values as follows: 2-hexyldecanoic acid (Z = 0; S1), trans-4-pentylcyclohexanecarboxylic acid (Z = –2; S2), and dicyclohexylacetic acid (Z = –4; S3). The estimated K2 values for S1, S2, and S3 are as follows: 1.42 × 103 M–1, 52.2 × 104 M–1, and 13.1 × 104 M–1, respectively. The corresponding K2 values are 2.34 × 104 M–1 and 1.27 × 104 M–1 for commercial (Fluka) and industrial (Syncrude) sourced NAs, respectively. The magnitude of K2 for 1:1 complexes formed between β-CD and S1, S2, or S3 did not correlate with the degree of hydrogen deficiency (Z-series) but there was a correlation with the size of the guest molecules (n) examined in this study. The correlation between complex stability and the relative size of the lipophilic fragments of the guest molecule are related to the importance of the hydrophobic effect for inclusion of such carboxylic acid guest molecules within β-CD.
Diagnosing Learners’ Problem-Solving Strategies Using Learning Environments with Algorithmic Problems in Secondary Education
Authors: Kiesmüller Ulrich 
Published: December 2009

At schools special learning and programming environments are often used in the field of algorithms. Particularly with regard to computer science lessons in secondary education, they are supposed to help novices to learn the basics of programming. In several parts of Germany (e.g., Bavaria) these fundamentals are taught as early as in the seventh grade, when pupils are 12 to 13 years old. Designed age-based learning and programming environments such as Karel the robot and Kara, the programmable ladybug, are used, but learners still underachieve. One possible approach to improving both the teaching and the learning process is to specify the knowledge concerning the learners’ individual problem solving strategies, their solutions, and their respective quality.
A goal of the research project described here is to design the learning environment so that it can identify and categorize several problem-solving strategies automatically. Based on this knowledge, learning and programming environments can be improved, which will optimize the computer science lessons in which they are applied. Therefore, the environments must be enhanced with special analytic and diagnostic modules, the results of which can be given to the learner in the form of individualized system feedback messages in the future.
In this text preliminary considerations are demonstrated. The research methodology as well as the design and the implementation of the research instruments are explained. We describe first studies, whose results are presented and discussed.
Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications
Authors: Wang Xiujuan , Huang Yong , Lavrov Dennis V , Gu Xun 
Published: December 2009

Abstract

Background
Gene and genome duplication is the principle creative force in evolution. Recently, protein subcellular relocalization, or neolocalization was proposed as one of the mechanisms responsible for the retention of duplicated genes. This hypothesis received support from the analysis of yeast genomes, but has not been tested thoroughly on animal genomes. In order to evaluate the importance of subcellular relocalizations for retention of duplicated genes in animal genomes, we systematically analyzed nuclear encoded mitochondrial proteins in the human genome by reconstructing phylogenies of mitochondrial multigene families.

Results
The 456 human mitochondrial proteins selected for this study were clustered into 305 gene families including 92 multigene families. Among the multigene families, 59 (64%) consisted of both mitochondrial and cytosolic (non-mitochondrial) proteins (mt-cy families) while the remaining 33 (36%) were composed of mitochondrial proteins (mt-mt families). Phylogenetic analyses of mt-cy families revealed three different scenarios of their neolocalization following gene duplication: 1) relocalization from mitochondria to cytosol, 2) from cytosol to mitochondria and 3) multiple subcellular relocalizations. The neolocalizations were most commonly enabled by the gain or loss of N-terminal mitochondrial targeting signals. The majority of detected subcellular relocalization events occurred early in animal evolution, preceding the evolution of tetrapods. Mt-mt protein families showed a somewhat different pattern, where gene duplication occurred more evenly in time. However, for both types of protein families, most duplication events appear to roughly coincide with two rounds of genome duplications early in vertebrate evolution. Finally, we evaluated the effects of inaccurate and incomplete annotation of mitochondrial proteins and found that our conclusion of the importance of subcellular relocalization after gene duplication on the genomic scale was robust to potential gene misannotation.

Conclusion
Our results suggest that protein subcellular relocalization is an important mechanism for the retention and gain of function of duplicated genes in animal genome evolution.
Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers
Authors: Cabrera Antonio , Kozik Alex , Howad Werner , Arus Pere , Iezzoni Amy F , Knaap Esther van der 
Published: December 2009

Abstract

Background
Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple), Fragaria (strawberry), and Prunus (peach, cherry, apricot and almond)]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies.

Results
We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS), 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae.

Conclusion
Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently ongoing in this family as well as for comparative QTL analyses.