bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Characterization and Virulence Role of the RALP3/LSA Locus Upstream of the Streptolysin S Operon in Invasive M1T1 Group AStreptococcus
Authors: Kwinn Laura A. , Khosravi Arya , Aziz Ramy K. , Timmer Anjuli M. , Doran Kelly S. , Kotb Malak , Nizet Victor 
Published: November 2006

ABSTRACTGroup AStreptococcus(GAS) is a leading human pathogen associated with a wide spectrum of mucosal and invasive infections. GAS expresses a large number of virulence determinants whose expression is under the control of several transcriptional regulatory networks. Here we performed the first mutational analysis of a genetic locus immediately upstream of the streptolysin S biosynthetic operon in several GAS genome sequences, including that of the M1T1 serotype, the leading isolates associated with serious invasive disease. The locus consists of a predicted RofA-like stand-alone transcriptional regulator (RALP3) and the largest open reading frame in the GAS genome, encoding a predicted LPXSG motif cell wall-anchored protein we have named LSA (for “large surface-anchored” protein). Comparative reverse transcription-PCR analysis of wild-type M1T1 GAS and an isogenic RALP3-deficient mutant identifies RALP3 as a global transcriptional regulator affecting expression of numerous virulence factor genes, including those for strong repression of the hyaluronic acid capsule and cysteine protease production. RALP3 contributed to GAS epithelial cell invasion and bloodstream survival. LSA was found to be under negative regulation by RALP3 and to influence GAS-epithelial cell interactions and GAS antimicrobial peptide sensitivity. Isogenic M1T1 GAS mutants lacking either RALP3 or LSA were attenuated in a murine model of systemic infection, indicating that this locus plays a role in the virulence potential of the organism.
Bacillus subtilis
Genome Diversity
Authors: Earl Ashlee M. , Losick Richard , Kolter Roberto 
Published: November 2006

ABSTRACT

Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species
Bacillus subtilis
. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.
Translation Control of
trpG
from Transcripts Originating from the Folate Operon Promoter of
Bacillus subtilis
Is Influenced by Translation-Mediated Displacement of Bound TRAP, While Translation Control of Transcripts Originating from a Newly Identified
trpG
Promoter Is Not
Authors: Yakhnin Helen , Yakhnin Alexander V. , Babitzke Paul 
Published: November 2006

ABSTRACT

Bacillus subtilis trpG
encodes a glutamine amidotransferase subunit that participates in the biosynthesis of both tryptophan and folic acid. TRAP inhibits translation of
trpG
in response to tryptophan by binding to a site that overlaps the
trpG
Shine-Dalgarno sequence, thereby blocking ribosome binding. Similar mechanisms regulate
trpP
and
ycbK
translation. The equilibrium binding constants of tryptophan-activated TRAP for the
trpG
,
ycbK
, and
trpP
transcripts were determined to be 8, 3, and 50 nM, respectively. Despite TRAP having a higher affinity for the
trpG
transcript, TRAP exhibited the least control of
trpG
expression. The
trpG
Shine-Dalgarno sequence overlaps the stop codon of the upstream
pabB
gene, while six of nine triplet repeats within the TRAP binding site are located upstream of the
pabB
stop codon. Thus, ribosomes translating the upstream
pabB
cistron could be capable of reducing TRAP-dependent control of TrpG synthesis by displacing bound TRAP. Expression studies using
pabB-trpG
′
-
′
lacZ
fusions in the presence or absence of an engineered stop codon within
pabB
suggest that translation-mediated displacement of bound TRAP reduces TRAP-dependent inhibition of TrpG synthesis from transcripts originating from the folate operon promoter (

P
pabB

). A new
trpG
promoter (

P
trpG

) was identified in the
pabB
coding sequence that makes a larger contribution to
trpG
expression than does

P
pabB

. We found that TRAP-dependent regulation of
trpG
expression is more extensive for a transcript originating from

P
trpG

and that transcripts originating from

P
trpG

are not subject to translation-mediated displacement of bound TRAP.
Functional Reconstitution of SdcS, a Na
+
-Coupled Dicarboxylate Carrier Protein from
Staphylococcus aureus
Authors: Hall Jason A. , Pajor Ana M. 
Published: November 2006

ABSTRACT

In
Staphylococcus aureus
, the transport of dicarboxylates is mediated in part by the Na
+
-linked carrier protein SdcS. This transporter is a member of the divalent-anion/Na
+
symporter (DASS) family, a group that includes the mammalian Na
+
/dicarboxylate cotransporters NaDC1 and NaDC3. In earlier work, we cloned and expressed SdcS in
Escherichia coli
and found it to have transport properties similar to those of its eukaryotic counterparts (J. A. Hall and A. M. Pajor, J. Bacteriol.
187:
5189-5194, 2005). Here, we report the partial purification and subsequent reconstitution of functional SdcS into liposomes. These proteoliposomes exhibited succinate counterflow activity, as well as Na
+
electrochemical-gradient-driven transport. Examination of substrate specificity indicated that the minimal requirement necessary for transport was a four-carbon terminal dicarboxylate backbone and that productive substrate-transporter interaction was sensitive to substitutions at the substrate C-2 and C-3 positions. Further analysis established that SdcS facilitates an electroneutral symport reaction having a 2:1 cation/dicarboxylate ratio. This study represents the first characterization of a reconstituted Na
+
-coupled DASS family member, thus providing an effective method to evaluate functional, as well as structural, aspects of DASS transporters in a system free of the complexities and constraints associated with native membrane environments.
Identification of Diverse Archaeal Proteins with Class III Signal Peptides Cleaved by Distinct Archaeal Prepilin Peptidases
Authors: Szabó Zalán , Stahl Adriana Oliveira , Albers Sonja-V. , Kissinger Jessica C. , Driessen Arnold J. M. , Pohlschröder Mechthild 
Published: November 2006

ABSTRACT

Most secreted archaeal proteins are targeted to the membrane via a tripartite signal composed of a charged N terminus and a hydrophobic domain, followed by a signal peptidase-processing site. Signal peptides of archaeal flagellins, similar to class III signal peptides of bacterial type IV pilins, are distinct in that their processing sites precede the hydrophobic domain, which is crucial for assembly of these extracytoplasmic structures. To identify the complement of archaeal proteins with class III signal sequences, a PERL program (FlaFind) was written. A diverse set of proteins was identified, and many of these FlaFind positives were encoded by genes that were cotranscribed with homologs of pilus assembly genes. Moreover, structural conservation of primary sequences between many FlaFind positives and subunits of bacterial pilus-like structures, which have been shown to be critical for pilin assembly, have been observed. A subset of pilin-like FlaFind positives contained a conserved
d
omain of
u
nknown
f
unction (DUF361) within the signal peptide. Many of the genes encoding these proteins were in operons that contained a gene encoding a novel
e
uryarchaeal
p
repilin-
p
eptidase, EppA, homolog. Heterologous analysis revealed that
Methanococcus maripaludis
DUF361-containing proteins were specifically processed by the EppA homolog of this archaeon. Conversely,
M. maripaludis
preflagellins were cleaved only by the archaeal preflagellin peptidase FlaK. Together, the results reveal a diverse set of archaeal proteins with class III signal peptides that might be subunits of as-yet-undescribed cell surface structures, such as archaeal pili.
I2 Imaging: Cancer Biology and the Tumor Microenvironment
Authors: Sloane Bonnie F. , Gillies Robert J. , Mohla Suresh , Sogn John A. , Menkens Anne E. , Sullivan Daniel C. 
Published: November 2006

Abstract
The use of imaging techniques to understand the role of the tumor microenvironment in cancer progression was the topic of a National Cancer Institute (NCI)–sponsored think tank entitled “I2 Imaging: Cancer Biology and the Tumor Microenvironment,” held in Alexandria, Virginia on June 8 to 10, 2006. Participants discussed both recent progress in the use of imaging to dissect cellular and molecular interactions within the tumor microenvironment and the challenges that remain. Recommendations made to the NCI included (a) holding an annual meeting at which biologists, clinicians, and imaging scientists could exchange data, facilitating new collaborations within this multidisciplinary field; (b) funding both research and training specifically designed to foster a cross-disciplinary focus; (c) creating and making available a variety of resources to interested investigators, such as a repository of stromal cells and extracellular matrix molecules; and (d) taking steps to encourage translation of the basic research findings into the clinic. (Cancer Res 2006; 66(23): 11097-9)
Patristic Biblical Quotations and Method: Four Changes to Lightfoot's Edition of Second Clement
Authors: Petersen William 
Published: November 2006

AbstractThis study examines the putative New Testament parallels in Second Clement, especially as found in the enormously influential edition of J. B. Lightfoot. Such putative parallels are important not just for the Patristic text itself, but also for the establishment of the text of the New Testament. Additionally, they shed light on the probable date and provenance of the document. Close textual examination suggests there are four places where the text of Lightfoot's edition should be changed (three of these instances apply to all later editions, as well). Investigating how Lightfoot (and later editors) came to their textual decisions exposes serious flaws in their commonly-employed methodology, which we label "normative." The "normative" method is based on the anachronistic use of texts, flawed logic, and special pleading. An alternative to this "normative" method will be presented; it avoids these pitfalls, and produces more reliable results. We label this alternative method "non-normative." The implications for the editing of Patristic and apocryphal texts, as well as for producing critical editions of the New Testament, are significant.
Mechanisms of Anterior Cruciate Ligament Injury in Basketball
Authors: Krosshaug Tron , Nakamae Atsuo , Boden Barry P. , Engebretsen Lars , Smith Gerald , Slauterbeck James R. , Hewett Timothy E. , Bahr Roald 
Published: November 2006

Background The mechanisms of anterior cruciate ligament injury in basketball are not well defined. Purpose To describe the mechanisms of anterior cruciate ligament injury in basketball based on videos of injury situations. Study Design Case series; Level of evidence, 4. Methods Six international experts performed visual inspection analyses of 39 videos (17 male and 22 female players) of anterior cruciate ligament injury situations from high school, college, and professional basketball games. Two predefined time points were analyzed: initial ground contact and 50 milliseconds later. The analysts were asked to assess the playing situation, player behavior, and joint kinematics. Results There was contact at the assumed time of injury in 11 of the 39 cases (5 male and 6 female players). Four of these cases were direct blows to the knee, all in men. Eleven of the 22 female cases were collisions, or the player was pushed by an opponent before the time of injury. The estimated time of injury, based on the group median, ranged from 17 to 50 milliseconds after initial ground contact. The mean knee flexion angle was higher in female than in male players, both at initial contact (15° vs 9°, P = .034) and at 50 milliseconds later (27° vs 19°, P = .042). Valgus knee collapse occurred more frequently in female players than in male players (relative risk, 5.3; P = .002). Conclusion Female players landed with significantly more knee and hip flexion and had a 5.3 times higher relative risk of sustaining a valgus collapse than did male players. Movement patterns were frequently perturbed by opponents. Clinical Relevance Preventive programs to enhance knee control should focus on avoiding valgus motion and include distractions resembling those seen in match situations.
Epidemiology of 1.6 Million Pediatric Soccer-Related Injuries Presenting to US Emergency Departments from 1990 to 2003
Authors: Leininger Robert E. , Knox Christy L. , Comstock R. Dawn 
Published: November 2006

Background As soccer participation in the United States increases, so does the number of children at risk for injury. Purpose To examine pediatric soccer-related injuries presenting to US emergency departments from 1990 to 2003. Study Design Descriptive epidemiology study. Methods A descriptive analysis of nationally representative, pediatric, soccer-related injury data from the US Consumer Product Safety Commission's National Electronic Injury Surveillance System. Results Among those 2 to 18 years of age, a nationally estimated 1 597 528 soccer-related injuries presented to US emergency departments from 1990 to 2003. Mean age was 13.2 years (range, 2-18 years); 58.6% were male. From 1990 to 2003, there was an increase in the absolute number of injuries among girls (P < .0001). The wrist/finger/hand (20.3%), ankle (18.2%), and knee (11.4%) were the most commonly injured body parts. The most common diagnoses were sprain/strain (35.9%), contusion/abrasion (24.1%), and fracture (23.2%). Boys were more likely to have face and head/neck injuries (17.7%; relative risk, 1.40; 95% confidence interval, 1.32-1.49; P < .01) and lacerations/punctures (7.5%; relative risk, 3.31; 95% confidence interval, 2.93-3.74; P < .01) than were girls (12.7% and 2.3%, respectively). Girls were more likely to have ankle injuries (21.8%; relative risk, 1.38; 95% confidence interval, 1.33-1.45; P < .01) and knee injuries (12.9%; relative risk, 1.25; 95% confidence interval, 1.15-1.35; P < .01) than were boys (15.7% and 10.4%, respectively). Girls were more likely to have sprains or strains (42.4%) than were boys (31.3%; relative risk, 1.36; 95% confidence interval, 1.31-1.40; P < .01). Children 2 to 4 years old sustained a higher proportion of face and head/neck injuries (41.0%) than did older children (15.5%; relative risk, 2.65; 95% confidence interval, 2.09-3.36; P < .01). Conclusion When comparing these data to available national statistics that estimate participation in youth soccer, true injury rates may actually be decreasing for boys and girls. Young children should be closely supervised because of risk of head injuries and rate of hospitalization. The establishment of a national database of soccer participation and injury data is needed to better identify injury risks.
Significance of the Arthroscopic Meniscal Flounce Sign
Authors: Wright Rick W. , Boyer Dory S. 
Published: November 2006

Background The meniscal flounce sign is a fold in the free, nonanchored inner edge of the medial meniscus that can be noted during routine arthroscopy of the knee. Hypothesis The meniscal flounce sign can be a significant indicator of the presence or absence of medial meniscus injury. Study Design Cohort study (diagnosis); Level of evidence, 4. Methods One hundred sixty-eight patients were prospectively evaluated at the time of the arthroscopy for the presence or absence of the arthroscopic meniscal flounce sign. These results were then correlated with the presence of medial meniscus tears. Results The presence of the meniscal flounce sign has a positive predictive value of a normal meniscus of 0.97 (63/65). The absence of the meniscal flounce sign has a positive predictive value of an abnormal meniscus of 0.98 (101/103). Specificity is 98%, and sensitivity is 97%. Conclusion The absence of the arthroscopic meniscal flounce sign is a sensitive and specific predictor of the presence of medial meniscus tears that should alert the surgeon to probe carefully for an occult medial meniscus tear.
Organo-bentonites with quaternary alkylammonium ions
Authors: Favre H. , Lagaly G. 
Published: November 2006

AbstractThree bentonites, from Bavaria, Wyoming and Brazil, were separated into various fractions. The layer charge was determined by alkylammonium ion exchange and increases with particle size from 0·25 Eq/(Si, Al)4O10 (<0·06 µm) to 0·28 Eq/(Si, Al)4O10 (1–10 µm). The charge density corresponds to an interlayer cation density of 0·75–0·80 mEq/g silicate. Total amounts of 0·90–1·0 mEq of different surfactant cations (dimethyl dioctadecylammonium, trimethyl tetradecylammonium, alkylammonium ions) are bound per gram silicate. The difference between the total and the interlayer amount of surfactant ions decreases with increasing particle size. The amounts exceeding the interlayer CEC are bound at the edges. Tetramethylammonium (TM) ions restrict the interlayer adsorption of long-chain quaternary alkylammonium ions such as trimethyl tetradecylammonium (TMTD) ions, and only monolayers of flat-lying surfactants are formed. A ratio of TMTD and TM is attained which leads to densely packed monolayers of organic ions. The collapsing effect is smaller for tetraethylammonium ions so that considerable amounts of TMTD ions are adsorbed in bilayers. When bentonites are reacted with quaternary alkylammonium ions of technical quality some selectivity is observed according to particle size and layer charge. Smaller particles with lower charge density preferentially bind the longer chain compounds, whereas large particles with higher charge density select smaller sized surfactants.
Preparation of porous materials by chemical activation of the Llano vermiculite
Authors: Suquet H. , Chevalier S. , Marcilly C. , Barthomeuf D. 
Published: November 2006

AbstractA mild acid attack of the Llano vermiculite produces porous materials suitable for use as cracking catalysts and/or catalysts supports. After HCl attack at 80°C (1 m), the number of acid sites measured by the Hammett indicator method is ∼0·50/nm2, and the specific surfaces are 245 m2/g after calcination at 550°C (4 h), and 55 m2/g after steaming at 750°C (4 h). The performance of leached (1 m HCl) vermiculite has been compared with another hydrocarbon cracking catalyst—γ-Al2O3. The leached vermiculite produces a definite higher conversion and higher C3, C4 and gasoline yields, but much lower coke production. By electron microscopy, infrared spectroscopy, X-ray powder diffraction and thermal analysis, it has been shown that the leached vermiculite samples are composed of more or less attacked layers retaining their original platy morphology, and non-crystalline hydrated silica. Chemical analyses indicate that octahedral cations are dissolved first.
Smectites in the montmorillonite-beidellite series
Authors: Yamada H. , Nakazawa H. , Yoshioka K. , Fujita T. 
Published: November 2006

AbstractSmectites in the montmorillonite-beidellite pseudo-binary system were synthesized from glass at the hydrothermal conditions 100 MPa and 250–500°C. Products were analysed by X-ray powder diffraction for randomly oriented and glycolated samples, and also according to the Greene-Kelly test. A new mixed-layer mineral consisting of regularly interstratified montmorillonite-beidellite was found below 400°C for M50B50 composition, where M and B denote the compositions of ideal Na-montmorillonite and Na-beidellite, respectively. Montmorillonite was obtained as a single phase below 375°C in the composition range from M100B0 to M78B22. Above 375°C, montmorillonite decomposed into an assemblage of beidellite, saponite and a silica mineral. Beidellite as a single phase was synthesized below 400°C for M0B100 composition. Above 450°C, Na-rectorite (regularly interstratified paragonite-beidellite), Mg-free dioctahedral smectite and/or Mg-rich trioctahedral smectite appeared together with silica minerals. These smectites showed the same swelling behaviour as that of montmorillonite. Phase relations in the montmorillonite-beidellite pseudo-binary system indicate no complete solid-solution series.
Diagenesis of the Central Basque-Cantabrian Basin (Iberian Peninsula) based on illite-smectite distribution
Authors: Aróstegui J. , Zuluaga M. C. , Velasco F. , Ortega-Huertas M. , Nieto F. 
Published: November 2006

AbstractX-ray diffraction was used to analyse the distribution of clay minerals in the <2 µm fraction of the lutitic and marly facies from the centre of the Basque-Cantabrian Basin (Basque Arc), where the sedimentary section is 2000 to 10,000 m thick. Most of the deposits were laid down during the Cretaceous and Paleogene and were related to the opening and closing of the Bay of Biscay. The most noteworthy variations are in kaolinite, smectite and mixed-layered (R = 0, R = 1 and R ≥ 3) illite-smectite, which can be ascribed both to provenance and to diagenesis. A general diminution in expandability is related to the gradual transformation of smectite to illite from south to north, and with depth. Temperature, residence time and chemical activity during diagenesis are the factors that had greatest influence on the changes in the original mineral assemblages inherited from the source area. On the basis of the clay minerals and the Kübler index, a general scheme is proposed for the diagenetic evolution of the area from the initial stages to anchimetamorphism.
Improved evaluation of layer charge of n-alkylammonium-treated fine soil clays by Lorentz- and polarization-correction and curve-fitting
Authors: Stanjek H. , Niederbudde E. A. , Häusler W. 
Published: November 2006

AbstractThe clay mineralogy of K-fixing soils from southern Germany was investigated using the alkylammonium method. Conventional X-ray diffraction chart recordings of glycerol-saturated <0·1 µm samples showed peaks at 18 Å that were initially interpreted as smectites. However, step-scanning combined with the Lorentz- and polarization-correction and curve-fitting, revealed the presence of low- and high-charge smectites and of low- and high-charge vermiculites. The severe overlap of the 001 basal reflections of the high-charge vermiculites with the broad and intensive peaks of smectites sensu stricto prevented visual evaluation at the alkylchains nc = 5–9, but this problem was overcome by curve-fitting. The 002 peaks of high-charge vermiculites (nc = 8 and nc = 10) in the fraction 0·1–0·2 µm could furthermore be clearly resolved from the 001 peaks of illite by curve-fitting. In one example, 003 (at nc = 17) could be resolved from 001 of illite.