bluuebunny/crossref_metadata_2025_split huggingface dataset:
Burkholderia cenocepacia Phenotypic Clonal Variation during a 3.5-Year Colonization in the Lungs of a Cystic Fibrosis Patient
Authors: Coutinho Carla P. , de Carvalho Carla C. C. R. , Madeira Andreia , Pinto-de-Oliveira Ana , Sá-Correia Isabel 
Published: May 2011

ABSTRACT

Chronic lung infection is the major cause of morbidity and premature mortality in cystic fibrosis (CF) patients. Bacteria of the
Burkholderia cepacia
complex are the most threatening pathogens in CF, and a better understanding of how these bacteria adapt to the CF airway environment and resist the host defense mechanisms and therapeutically administered antibiotics is crucial. To provide clues to the adaptive strategies adopted by
Burkholderia cenocepacia
during long-term colonization, we carried out a phenotypic assessment of 11 clonal variants obtained at the major Portuguese CF Center in Lisbon from sputa of the same CF patient during 3.5 years of colonization of the lungs, until the patient's death with cepacia syndrome. Phenotypic characterization included susceptibility assays against different classes of antimicrobials and characterization of cell motility, cell hydrophobicity and zeta potential, colony and cell morphology, fatty acid composition, growth under iron limitation/load conditions, exopolysaccharide production, and size of the biofilms formed. The results suggest the occurrence of clonal expansion during long-term colonization. For a number of the characteristics tested, no isolation time-dependent consistent alteration pattern could be identified. However, the values for antimicrobial susceptibility and swarming motility for the first
B. cenocepacia
isolate, thought to have initiated the infection, were consistently above those for the clonal variants obtained during the course of infection, and the opposite was found for the zeta potential. The adaptive strategy for long-term colonization, described here for the first time, involved the alteration of membrane fatty acid composition, in particular a reduction of the degree of fatty acid saturation, in the
B. cenocepacia
variants retrieved, along with the deterioration of pulmonary function and severe oxygen limitation.
Tumor Necrosis Factor Alpha Production from CD8+T Cells Mediates Oviduct Pathological Sequelae following Primary Genital Chlamydia muridarum Infection
Authors: Murthy Ashlesh K. , Li Weidang , Chaganty Bharat K. R. , Kamalakaran Sangamithra , Guentzel M. Neal , Seshu J. , Forsthuber Thomas G. , Zhong Guangming , Arulanandam Bernard P. 
Published: May 2011

ABSTRACTThe immunopathogenesis ofChlamydia trachomatis-induced oviduct pathological sequelae is not well understood. Mice genetically deficient in perforin (perforin−/−mice) or tumor necrosis factor alpha (TNF-α) production (TNF-α−/−mice) displayed comparable vaginal chlamydial clearance rates but significantly reduced oviduct pathology (hydrosalpinx) compared to that of wild-type mice. Since both perforin and TNF-α are effector mechanisms of CD8+T cells, we evaluated the role of CD8+T cells during genitalChlamydia muridaruminfection and oviduct sequelae. Following vaginal chlamydial challenge, (i) mice deficient in TAP I (and therefore the major histocompatibility complex [MHC] I pathway and CD8+T cells), (ii) wild-type mice depleted of CD8+T cells, and (iii) mice genetically deficient in CD8 (CD8−/−mice) all displayed similar levels of vaginal chlamydial clearance but significantly reduced hydrosalpinx, compared to those of wild-type C57BL/6 mice, suggesting a role for CD8+T cells in chlamydial pathogenesis. Repletion of CD8−/−mice with wild-type or perforin−/−, but not TNF-α−/−, CD8+T cells at the time of challenge restored hydrosalpinx to levels observed in wild-type C57BL/6 mice, suggesting that TNF-α production from CD8+T cells is important for pathogenesis. Additionally, repletion of TNF-α−/−mice with TNF-α+/+CD8+T cells significantly enhanced the incidence of hydrosalpinx and oviduct dilatation compared to those of TNF-α−/−mice but not to the levels found in wild-type mice, suggesting that TNF-α production from CD8+T cells and non-CD8+cells cooperates to induce optimal oviduct pathology following genital chlamydial infection. These results provide compelling new evidence supporting the contribution of CD8+T cells and TNF-α production toChlamydia-induced reproductive tract sequelae.
The Anaerobe-Specific Orange Protein Complex of Desulfovibrio vulgaris Hildenborough Is Encoded by Two Divergent Operons Coregulated by σ
54
and a Cognate Transcriptional Regulator
Authors: Fiévet Anouchka , My Laetitia , Cascales Eric , Ansaldi Mireille , Pauleta Sofia R. , Moura Isabel , Dermoun Zorah , Bernard Christophe S. , Dolla Alain , Aubert Corinne 
Published: April 2011

ABSTRACT

Analysis of sequenced bacterial genomes revealed that the genomes encode more than 30% hypothetical and conserved hypothetical proteins of unknown function. Among proteins of unknown function that are conserved in anaerobes, some might be determinants of the anaerobic way of life. This study focuses on two divergent clusters specifically found in anaerobic microorganisms and mainly composed of genes encoding conserved hypothetical proteins. We show that the two gene clusters
DVU2103-DVU2104-DVU2105
(
orp2
) and
DVU2107-DVU2108-DVU2109
(
orp1
) form two divergent operons transcribed by the σ
54
-RNA polymerase. We further demonstrate that the σ
54
-dependent transcriptional regulator DVU2106, located between
orp1
and
orp2
, collaborates with σ
54
-RNA polymerase to orchestrate the simultaneous expression of the divergent
orp
operons. DVU2106, whose structural gene is transcribed by the σ
70
-RNA polymerase, negatively retrocontrols its own expression. By using an endogenous pulldown strategy, we identify a physiological complex composed of DVU2103, DVU2104, DVU2105, DVU2108, and DVU2109. Interestingly, inactivation of DVU2106, which is required for
orp
operon transcription, induces morphological defects that are likely linked to the absence of the ORP complex. A putative role of the ORP proteins in positioning the septum during cell division is discussed.
Asp2 and Asp3 Interact Directly with GspB, the Export Substrate of the Streptococcus gordonii Accessory Sec System
Authors: Yen Yihfen T. , Seepersaud Ravin , Bensing Barbara A. , Sullam Paul M. 
Published: April 2011

ABSTRACT

GspB is a serine-rich glycoprotein adhesin of
Streptococcus gordonii
that is exported to the bacterial surface by the accessory Sec system. This dedicated export pathway is comprised of seven components (SecA2, SecY2, and five accessory Sec proteins [Asp1 to Asp5]). The latter proteins have no known homologs beyond the Asps of other species. Asp1 to Asp3 are absolutely required for export of the substrate GspB, but their roles in this process are unknown. Using copurification analysis and far-Western blotting, we found that Asp2 and Asp3 could individually bind the serine-rich repeat (SRR) domains of GspB. Deletion of both SRR regions of GspB led to a decrease in its export, suggesting that binding of the Asps to the SRR regions is important for GspB transport by the accessory Sec system. The Asps also bound a heterologous substrate for the accessory Sec system containing a slow-folding MalE variant, but they did not bind wild-type MalE. The combined results indicate that the Asps may recognize the export substrate through preferential interactions with its unstructured or unfolded regions. Glycosylation of the SRR domains on GspB prevented Asp binding, suggesting that binding of the Asps to the preprotein occurs prior to its full glycosylation. Together, these findings suggest that Asp2 and Asp3 are likely to function in part as chaperones in the early phase of GspB transport.
The Nudix Hydrolase CDP-Chase, a CDP-Choline Pyrophosphatase, Is an Asymmetric Dimer with Two Distinct Enzymatic Activities
Authors: Duong-Ly Krisna C. , Gabelli Sandra B. , Xu WenLian , Dunn Christopher A. , Schoeffield Andrew J. , Bessman Maurice J. , Amzel L. Mario 
Published: April 2011

ABSTRACT

A Nudix enzyme from
Bacillus cereus
(NCBI RefSeq accession no.
NP_831800
) catalyzes the hydrolysis of CDP-choline to produce CMP and phosphocholine. Here, we show that in addition, the enzyme has a 3′→5′ RNA exonuclease activity. The structure of the free enzyme, determined to a 1.8-Å resolution, shows that the enzyme is an asymmetric dimer. Each monomer consists of two domains, an N-terminal helical domain and a C-terminal Nudix domain. The N-terminal domain is placed relative to the C-terminal domain such as to result in an overall asymmetric arrangement with two distinct catalytic sites: one with an “enclosed” Nudix pyrophosphatase site and the other with a more open, less-defined cavity. Residues that may be important for determining the asymmetry are conserved among a group of uncharacterized Nudix enzymes from Gram-positive bacteria. Our data support a model where CDP-choline hydrolysis is catalyzed by the enclosed Nudix site and RNA exonuclease activity is catalyzed by the open site. CDP-Chase is the first identified member of a novel Nudix family in which structural asymmetry has a profound effect on the recognition of substrates.
Dual Function of a Tip Fimbrillin of Actinomyces in Fimbrial Assembly and Receptor Binding
Authors: Wu Chenggang , Mishra Arunima , Yang Jinghua , Cisar John O. , Das Asis , Ton-That Hung 
Published: April 2011

ABSTRACTInteraction ofActinomyces oriswith salivary proline-rich proteins (PRPs), which serve as fimbrial receptors, involves type 1 fimbriae. Encoded by the gene locusfimQ-fimP-srtC1, the type 1 fimbria is comprised of the fimbrial shaft FimP and the tip fimbrillin FimQ. Fimbrial polymerization requires the fimbria-specific sortase SrtC1, which catalyzes covalent linkage of fimbrial subunits. Using genetics, biochemical methods, and electron microscopy, we provide evidence that the tip fimbrillin, FimQ, is involved in fimbrial assembly and interaction with PRPs. Specifically, while deletion offimPcompletely abolished the type 1 fimbrial structures, surface display of monomeric FimQ was not affected by this mutation. Surprisingly, deletion offimQsignificantly reduced surface assembly of the type 1 fimbriae. This defect was rescued by recombinant FimQ ectopically expressed from a plasmid. In agreement with the role of type 1 fimbriae in binding to PRPs, aggregation ofA. oriswith PRP-coated beads was abrogated in cells lackingsrtC1orfimP. This aggregation defect of the ΔfimPmutant was mainly due to significant reduction of FimQ on the bacterial surface, as the aggregation was not observed in a strain lackingfimQ. Increasing expression of FimQ in the ΔfimPmutant enhanced aggregation, while overexpression of FimP in the ΔfimQmutant did not. Furthermore, recombinant FimQ, not FimP, bound surface-associated PRPs in a dose-dependent manner. Thus, not only does FimQ function as the major adhesin of the type 1 fimbriae, it also plays an important role in fimbrial assembly.
Binding and Spreading of ParB on DNA Determine Its Biological Function in Pseudomonas aeruginosa
Authors: Kusiak Magdalena , Gapczyńska Anna , Płochocka Danuta , Thomas Christopher M. , Jagura-Burdzy Grażyna 
Published: April 2011

ABSTRACT

ParB protein of
Pseudomonas aeruginosa
belongs to a widely represented ParB family of chromosomally and plasmid-encoded partitioning type IA proteins. Ten putative
parS
sites are dispersed in the
P. aeruginosa
chromosome, with eight of them localizing in the
oriC
domain. After binding to
parS
, ParB spreads on the DNA, causing transcriptional silencing of nearby genes (A. A. Bartosik et al., J. Bacteriol. 186:6983–6998, 2004). We have studied ParB derivatives impaired in spreading either due to loss of DNA-binding ability or oligomerization. We defined specific determinants outside of the helix-turn-helix motif responsible for DNA binding. Analysis confirmed the localization of the main dimerization domain in the C terminus of ParB but also mapped another self-interactive domain in the N-terminal domain. Reverse genetics were used to introduce five
parB
alleles impaired in spreading into the
P. aeruginosa
chromosome. The single amino acid substitutions in ParB causing a defect in oligomerization but not in DNA binding caused a chromosome segregation defect, slowed the growth rate, and impaired motilities, similarly to the pleiotropic phenotype of
parB
-null mutants, indicating that the ability to spread is vital for ParB function in the cell. The toxicity of ParB overproduction in
Pseudomonas
spp. is not due to the spreading since several ParB derivatives defective in oligomerization were still toxic for
P. aeruginosa
when provided in excess.
CheY3 of Borrelia burgdorferi Is the Key Response Regulator Essential for Chemotaxis and Forms a Long-Lived Phosphorylated Intermediate
Authors: Motaleb M. A. , Sultan Syed Z. , Miller Michael R. , Li Chunhao , Charon Nyles W. 
Published: April 2011

ABSTRACT

Spirochetes have a unique cell structure: These bacteria have internal periplasmic flagella subterminally attached at each cell end. How spirochetes coordinate the rotation of the periplasmic flagella for chemotaxis is poorly understood. In other bacteria, modulation of flagellar rotation is essential for chemotaxis, and phosphorylation-dephosphorylation of the response regulator CheY plays a key role in regulating this rotary motion. The genome of the Lyme disease spirochete
Borrelia burgdorferi
contains multiple homologues of chemotaxis genes, including three copies of
cheY
, referred to as
cheY1
,
cheY2
, and
cheY3
. To investigate the function of these genes, we targeted them separately or in combination by allelic exchange mutagenesis. Whereas wild-type cells ran, paused (flexed), and reversed, cells of all single, double, and triple mutants that contained an inactivated
cheY3
gene constantly ran. Capillary tube chemotaxis assays indicated that only those strains with a mutation in
cheY3
were deficient in chemotaxis, and
cheY3
complementation restored chemotactic ability.
In vitro
phosphorylation assays indicated that CheY3 was more efficiently phosphorylated by CheA2 than by CheA1, and the CheY3-P intermediate generated was considerably more stable than the CheY-P proteins found in most other bacteria. The results point toward CheY3 being the key response regulator essential for chemotaxis in
B. burgdorferi
. In addition, the stability of CheY3-P may be critical for coordination of the rotation of the periplasmic flagella.
Distribution of 10-year and lifetime predicted risk for cardiovascular disease in the Indian Sentinel Surveillance Study population (cross-sectional survey results)
Authors: Jeemon Panniyammakal , Prabhakaran Dorairaj , Huffman Mark D , Ramakrishnan Lakshmy , Goenka Shifalika , Thankappan K R , Mohan V , Joshi Prashant P , Mohan B V M , Ahmed F , Ramanathan Meera , Ahuja R , Chaturvedi Vivek , Lloyd-Jones Donald M , Reddy K Srinath 
Published: April 2011

IntroductionCardiovascular disease (CVD) prevention guidelines recommend lifetime risk stratification for primary prevention of CVD, but no such risk stratification has been performed in India to date.MethodsThe authors estimated short-term and lifetime predicted CVD risk among 10 054 disease-free, adult Indians in the 20–69-year age group who participated in a nationwide risk factor surveillance study. The study population was then stratified into high short-term (≥10% 10-year risk or diabetes), low short-term (<10%)/high lifetime and low short-term/low lifetime CVD risk groups.ResultsThe mean age (SD) of the study population (men=63%) was 40.8±10.9 years. High short-term risk for coronary heart disease was prevalent in more than one-fifth of the population (23.5%, 95% CI 22.7 to 24.4). Nearly half of individuals with low short-term predicted risk (48.2%, 95% CI 47.1 to 49.3) had a high predicted lifetime risk for CVD. While the proportion of individuals with all optimal risk factors was 15.3% (95% CI 14.6% to 16.0%), it was 20.6% (95% CI 18.7% to 22.6%) and 8.8% (95% CI 7.7% to 10.5%) in the highest and lowest educational groups, respectively.ConclusionApproximately one in two men and three in four women in India had low short-term predicted risks for CVD in this national study, based on aggregate risk factor burden. However, two in three men and one in two women had high lifetime predicted risks for CVD, highlighting a key limitation of short-term risk stratification.
Wood quality in artificially inclined 1-year-old trees of Eucalyptus regnans — differences in tension wood and opposite wood properties
Authors: Chauhan Shakti S. , Walker John C.F. 
Published: May 2011

This paper presents a new approach to assess wood quality in 1-year-old Eucalyptus regnans F. Muell. Twenty-two seedlings were grown tilted to induce tension wood and acoustic velocity, basic density, longitudinal shrinkage, and volumetric shrinkage of both opposite wood and tension wood were assessed subsequently. Longitudinal growth strains were also estimated in the leaning stems by sawing along the length through the pith and measuring the bending of the two halves. The derived longitudinal growth strain, which varied from 708 to 2319 µε, was uncorrelated with stem and wood characteristics. Wood characteristics differed significantly between upper-side wood (predominantly tension wood) and lower-side wood (opposite wood). Tension wood was characterized by a higher acoustic velocity (high stiffness), basic density, and volumetric shrinkage compared with opposite wood. Tension wood also exhibited significant collapse and dimensional distortion such as twisting. Longitudinal shrinkage exhibited a significant negative relationship with acoustic velocity in opposite wood and a positive relationship with the basic density in tension wood. This new approach has potential in early selection of breeding material with superior normal wood properties from 1-year-old material by isolating the influence of tension wood. This approach can also be useful in understanding the variability in propensity of tension wood production in breeding populations.
Comparing selection system and diameter-limit cutting in uneven-aged northern hardwoods using computer simulation
Authors: Bohn Kimberly K. , Nyland Ralph D. , Yanai Ruth D. 
Published: May 2011

Comparisons of selection system and diameter-limit cutting based on trials in specific settings have often yielded conflicting results. We used a simulation approach to evaluate sawtimber production over three cutting cycles on 10 sugar maple ( Acer saccharum Marsh.) dominated plots of varying initial forest structure. Treatments on each plot included light, moderate, and heavy intensities of selection system silviculture and diameter-limit cutting. Harvested sawtimber volumes were initially higher on all plots using diameter-limit cutting, but selection system outperformed diameter-limit cutting at later entries on 7 of the 10 plots. Volume differences between cutting types ranged among plots from 0.3 to 26 m3·ha–1, equating to a less than 1% to as much as a twofold difference. Average volumes from selection system at later entries were 20%–40% greater than diameter-limit cutting, due in part to consistent production in large sawtimber (≥46 cm). Yields from real stands could vary from these simulations where mortality losses (not modeled here) differ between treatments as a result of competition or logging damage. Findings suggest that cumulative sawtimber volumes from repeated selection system silviculture could eventually surpass that of diameter-limit cutting, but at a rate depending on initial stand conditions and harvesting intensity.
Pre-fire forest conditions and fire severity as determinants of the quality of burned forests for deadwood-dependent species: the case of the black-backed woodpecker
Authors: Nappi Antoine , Drapeau Pierre 
Published: May 2011

Burned forests represent high-quality habitats for many deadwood-dependent species. Yet, post-fire conditions may vary greatly within and among burns and thereby may affect habitat suitability for these species. We studied habitat selection of nesting black-backed woodpeckers ( Picoides arcticus Swainson) in recently burned spruce-dominated boreal forests. Our objectives were to (i) identify factors involved in snag selection for both nesting and foraging and (ii) examine selection of nest sites within the burned landscape. A total of 92 nests and 1612 foraging observations were used to investigate snag selection. Our results show that both pre-fire forest conditions and fire severity are important in determining the quality of burned forests for black-backed woodpeckers. This species selected large snags for both nesting (>20 cm DBH) and foraging (>15 cm DBH). Woodpeckers selected deciduous and degraded “pre-fire” snags for nesting whereas black spruce snags that had been created by fire and that were moderately burned were preferred for foraging. Nest sites were concentrated in burned mature stands and supported higher densities of large snags (e.g., >15 cm DBH). Our results suggest that burned forest patches of at least 20 ha and composed mainly of burned mature and old-growth forests should be maintained during post-fire harvesting. The decrease in the amount of late seral stands in managed forest landscapes raises concerns about the future availability of high-quality burned forests for this species.
Protective effect of neferine on endothelial cell nitric oxide production induced by lysophosphatidylcholine: the role of the DDAH–ADMA pathway
Authors: Peng Zhen-Yu , Zhang Sai-Dan , Liu Shao , He Bai-Mei 
Published: May 2011

Neferine, extracted from the seed embryo of Nelumbo nucifera Gaertn., has multiple cardiovascular pharmacological effects. The dimethylarginine dimethylaminohydrolase (DDAH) – asymmetric dimethylarginine (ADMA) system is a novel pathway for modulating nitric oxide (NO) production. The aim of this study was to investigate whether the protective effect of neferine on endothelial NO production was related to the DDAH–ADMA pathway. Human umbilical vein endothelial cells (HUVECs) were first exposed to neferine (0.1, 1.0, or 10.0 μmol/L) for 1 h, and then incubated with lysophosphatidylcholine (LPC; 10 μg/mL) in the presence of neferine for 24 h. The medium was collected for measuring the levels of NO, maleic dialdehyde (MDA), as well as ADMA. The endothelial cells were collected for measuring DDAH activity and the level of reactive oxygen species (ROS). LPC significantly decreased NO concentration and DDAH activity and increased the levels of ADMA, ROS, and MDA. Neferine could partially counteract the changes induced by LPC. These findings suggested that neferine could modulate the DDAH–ADMA pathway via its antioxidant properties, which was involved in its beneficial effect on endothelial NO production.