bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Staphylococcal GGDEF Domain Protein Regulates Biofilm Formation Independently of Cyclic Dimeric GMP
Authors: Holland Linda M. , O'Donnell Sinéad T. , Ryjenkov Dmitri A. , Gomelsky Larissa , Slater Shawn R. , Fey Paul D. , Gomelsky Mark , O'Gara James P. 
Published: May 2008

ABSTRACTCyclic dimeric GMP (c-di-GMP) is an important biofilm regulator that allosterically activates enzymes of exopolysaccharide biosynthesis. Proteobacterial genomes usually encode multiple GGDEF domain-containing diguanylate cyclases responsible for c-di-GMP synthesis. In contrast, only one conserved GGDEF domain protein, GdpS (forGGDEFdomainprotein fromStaphylococcus), and a second protein with a highly modified GGDEF domain, GdpP, are present in the sequenced staphylococcal genomes. Here, we investigated the role of GdpS in biofilm formation inStaphylococcus epidermidis. Inactivation ofgdpSimpaired biofilm formation in medium supplemented with NaCl under static and flow-cell conditions, whereasgdpSoverexpression complemented the mutation and enhanced wild-type biofilm development. GdpS increased production of theicaADBC-encoded exopolysaccharide, poly-N-acetyl-glucosamine, by elevatingicaADBCmRNA levels. Unexpectedly, c-di-GMP synthesis was found to be irrelevant for the ability of GdpS to elevateicaADBCexpression. Mutagenesis of the GGEEF motif essential for diguanylate cyclase activity did not impair GdpS, and the N-terminal fragment of GdpS lacking the GGDEF domain partially complemented thegdpSmutation. Furthermore, heterologous diguanylate cyclases expressed intransfailed to complement thegdpSmutation, and the purified GGDEF domain from GdpS possessed no diguanylate cyclase activity in vitro. ThegdpSgene fromStaphylococcus aureusexhibited similar characteristics to itsS. epidermidisortholog, suggesting that the GdpS-mediated signal transduction is conserved in staphylococci. Therefore, GdpS affects biofilm formation through a novel c-di-GMP-independent mechanism involving increasedicaADBCmRNA levels and exopolysaccharide biosynthesis. Our data raise the possibility that staphylococci cannot synthesize c-di-GMP and have only remnants of a c-di-GMP signaling pathway.
A Specialized Citric Acid Cycle Requiring Succinyl-Coenzyme A (CoA):Acetate CoA-Transferase (AarC) Confers Acetic Acid Resistance on the Acidophile
Acetobacter aceti
Authors: Mullins Elwood A. , Francois Julie A. , Kappock T. Joseph 
Published: May 2008

ABSTRACT

Microbes tailor macromolecules and metabolism to overcome specific environmental challenges. Acetic acid bacteria perform the aerobic oxidation of ethanol to acetic acid and are generally resistant to high levels of these two membrane-permeable poisons. The citric acid cycle (CAC) is linked to acetic acid resistance in
Acetobacter aceti
by several observations, among them the oxidation of acetate to CO
2
by highly resistant acetic acid bacteria and the previously unexplained role of
A. aceti
citrate synthase (AarA) in
a
cetic
a
cid
r
esistance at a low pH. Here we assign specific biochemical roles to the other components of the
A. aceti
strain 1023
aarABC
region. AarC is succinyl-coenzyme A (CoA):acetate CoA-transferase, which replaces succinyl-CoA synthetase in a variant CAC. This new bypass appears to reduce metabolic demand for free CoA, reliance upon nucleotide pools, and the likely effect of variable cytoplasmic pH upon CAC flux. The putative
aarB
gene is reassigned to SixA, a known activator of CAC flux. Carbon overflow pathways are triggered in many bacteria during metabolic limitation, which typically leads to the production and diffusive loss of acetate. Since acetate overflow is not feasible for
A. aceti
, a CO
2
loss strategy that allows acetic acid removal without substrate-level (de)phosphorylation may instead be employed. All three
aar
genes, therefore, support flux through a complete but unorthodox CAC that is needed to lower cytoplasmic acetate levels.
Lysine Represses Transcription of the
Escherichia coli dapB
Gene by Preventing Its Activation by the ArgP Activator
Authors: Bouvier Jean , Stragier Patrick , Morales Violette , Rémy Elisabeth , Gutierrez Claude 
Published: May 2008

ABSTRACT

The
Escherichia coli dapB
gene encodes one of the enzymes of the biosynthetic pathway leading to lysine and its immediate precursor, diaminopimelate. Expression of
dapB
is repressed by lysine, but no
trans
-acting regulator has been identified so far. Our analysis of the
dapB
regulatory region shows that sequences located in the −81/−118 interval upstream of the transcription start site are essential for full expression of
dapB
, as well as for lysine repression. Screening a genomic library for a gene that could alleviate lysine repression when present in multicopy led to the recovery of
argP
, a gene encoding an activating protein of the LysR-type family, known to use lysine as an effector. An
argP
null mutation strongly decreases
dapB
transcription that becomes insensitive to lysine. Purified His
6
-tagged ArgP protein binds with an apparent
K

d

of 35 nM to the
dapB
promoter in a gel retardation assay, provided that sequences up to −103 are present. In the presence of
l
-lysine and
l
-arginine, the binding of ArgP to
dapB
is partly relieved. These results fit with a model in which ArgP contributes to enhanced transcription of
dapB
when lysine becomes limiting.
Elucidation of the 4-Hydroxyacetophenone Catabolic Pathway in
Pseudomonas fluorescens
ACB
Authors: Moonen Mariëlle J. H. , Kamerbeek Nanne M. , Westphal Adrie H. , Boeren Sjef A. , Janssen Dick B. , Fraaije Marco W. , van Berkel Willem J. H. 
Published: May 2008

ABSTRACT

The catabolism of 4-hydroxyacetophenone in
Pseudomonas fluorescens
ACB is known to proceed through the intermediate formation of hydroquinone. Here, we provide evidence that hydroquinone is further degraded through 4-hydroxymuconic semialdehyde and maleylacetate to β-ketoadipate. The
P. fluorescens
ACB genes involved in 4-hydroxyacetophenone utilization were cloned and characterized. Sequence analysis of a 15-kb DNA fragment showed the presence of 14 open reading frames containing a gene cluster (
hapCDEFGHIBA
) of which at least four encoded enzymes are involved in 4-hydroxyacetophenone degradation: 4-hydroxyacetophenone monooxygenase (
hapA
), 4-hydroxyphenyl acetate hydrolase (
hapB
), 4-hydroxymuconic semialdehyde dehydrogenase (
hapE
), and maleylacetate reductase (
hapF
). In between
hapF
and
hapB
, three genes encoding a putative intradiol dioxygenase (
hapG
), a protein of the Yci1 family (
hapH
), and a [2Fe-2S] ferredoxin (
hapI
) were found. Downstream of the
hap
genes, five open reading frames are situated encoding three putative regulatory proteins (
orf10, orf12
, and
orf13
) and two proteins possibly involved in a membrane efflux pump (
orf11
and
orf14
). Upstream of
hapE
, two genes (
hapC
and
hapD
) were present that showed weak similarity with several iron(II)-dependent extradiol dioxygenases. Based on these findings and additional biochemical evidence, it is proposed that the
hapC
and
hapD
gene products are involved in the ring cleavage of hydroquinone.
Sir Charles Edward Saunders, Dominion Cerealist
Authors: Morrison Malcolm J. 
Published: May 2008

Charles Edward Saunders was born in London, Ontario, in 1867. His father, Sir William Saunders, was the first director of the Dominion Experimental Farms (1886–1911). Charles received his B.A. with honours in science from the University of Toronto in 1888 and his Ph.D. in chemistry from Johns Hopkins University in Baltimore, Maryland, in 1891. He attempted a career in music, his first love, from 1893 to 1902. With his father, Charles attended the 1902 International Conference on Plant Breeding and Hybridization in New York, where he learned of Mendel’s theories of inheritance and their applicability to plant breeding. When he began work in 1903 in the Division of Cereal Breeding and Experimentation at the Central Experimental Farm in Ottawa, he used the knowledge he had gained at that conference. It was Charles’s goal to achieve “fixity” in the varieties that had been bred and released using phenotypic mass selection, prior to his tenure as Cerealist. He selected four heads from the wheat variety Markham and in the winter of 1904 he performed a “chewing test” to select for gluten elasticity and colour. Seeds from two heads were chosen, and seeds from one went on to produce the variety Marquis after extensive yield trials on the Prairies. Marquis was 7 to 10 days earlier than Red Fife, the standard bread wheat of the Prairies. The earliness and tremendous yield of Marquis wheat resulted in the rapid and successful settlement of the Great Plains and countless billions of dollars in revenue to Canada. By 1923, 90% of the spring wheat in Canada and 70% in the USA was Marquis. Charles continued as Dominion Cerealist until his retirement in 1922. He was knighted in 1934, and died in 1937.
MEASUREMENT OF THIN OIL FILM THICKNESS USING ULTRASONIC TECHNIQUE
Authors: TAKEUCHI AKITOSHI , TERADA SEIICHI , TODA SO 
Published: May 2008

An application of ultrasonic technique is attempted for the purpose of measuring thin oil film thickness between two surfaces. The amplitude of the wave reflected from the boundary is vary depending on film thickness, because the ultrasonic wave emitted to the interface between two surfaces does multiple reflection and interference in oil film. Quantitative measurement of oil film thickness then can be possible. For instance, it is possible to measure the submicron film thickness which exists near the point contact formed by convex glass and plate with high frequency probe. And it is confirmed that the oil film thickness estimated from the echo height agrees with the film thickness decided by the curvature of the lens or obtained by the optical interference method, even if it is 100 nm. On the other hand, the thickness of oil film between cylinder and piston ring can be easily measured by setting the small ultrasonic probe on the back of piston ring. For example, the influence of the second ring and oil ring for the behavior of an oil film formed on a top ring is able to evaluate quantitatively. As mentioned above, it is cleared that quantitative evaluation of thin film thickness is possible with investigating the echo height obtained by ultrasonic wave pulse reflection method.
Civil Society and Peace Negotiations: Confronting Exclusion
Authors: Kew Darren , Wanis-St. John Anthony 
Published: May 2008

AbstractThe fact that civil society groups play important roles in post-conflict peacebuilding has entered the mainstream of international conflict resolution dogma. Rarely do local civil society groups get a seat at the negotiation table for peace accords. Although the exclusion of civil society from peace negotiations may streamline the process, the absence of civil society voices and interests at the negotiating table can negatively impact the sustainability of a peace agreement during peacebuilding. Surveying a wide variety of different peace processes, a strong correlation was found between active civil society participation in peace negotiations and the durability of peace during the peacebuilding phase. Cases in which civil society groups actively engaged in peace negotiations seemed to enjoy more sustained peace in the peacebuilding phase. This holds true also for cases in which civil society groups did not have a direct seat at the table, but did exercise significant influence with the negotiators because they were democratic actors. War resumed in many cases not characterized by direct or indirect civil society involvement in the peace negotiations. No claim of causality is made; the sustainability of peace surely rests on causes as complex and dynamic as the initiation of war does. However, these findings do call attention to the need for further research to understand the special impact that civil society inclusion at the peace table may have.
A Diagnostic Model of the Nordic Seas and Arctic Ocean Circulation: Quantifying the Effects of a Variable Bottom Density along a Sloping Topography
Authors: Aaboe Signe , Nøst Ole Anders 
Published: May 2008

Abstract
A linear diagnostic model, solving for the time-mean large-scale circulation in the Nordic seas and Arctic Ocean, is presented. Solutions on depth contours that close within the Nordic seas and Arctic Ocean are found from vorticity balances integrated over the areas enclosed by the contours. Climatological data for wind stress and hydrography are used as input to the model, and the bottom geostrophic flow is assumed to follow depth contours. Comparison against velocity observations shows that the simplified dynamics in the model capture many aspects of the large-scale circulation.
Special attention is given to the dynamical effects of an along-isobath varying bottom density, which leads to a transformation between barotropic and baroclinic transport. Along the continental slope, enclosing both the Nordic seas and Arctic Ocean, the along-slope barotropic transport has a maximum in the Nordic seas and a minimum in the Canadian Basin with a difference of 9 Sv (1 Sv ≡ 106 m3 s−1) between the two. This is caused by the relatively lower bottom densities in the Canadian Basin compared to the Nordic seas and suggests that most of the barotropic transport entering the Arctic Ocean through the Fram Strait is transformed to baroclinic transport. A conversion from barotropic to baroclinic flow may be highly important for the slope–basin exchange in the Nordic seas and Arctic Ocean.
The model has obvious shortcomings due to its simplicity. However, the simplified physics and the agreement with observations make this model an excellent framework for understanding the large-scale circulation in the Nordic seas and Arctic Ocean.
Optimal Surface Salinity Perturbations of the Meridional Overturning and Heat Transport in a Global Ocean General Circulation Model
Authors: Sévellec Florian , Huck Thierry , Ben Jelloul Mahdi , Grima Nicolas , Vialard Jérôme , Weaver Anthony 
Published: May 2008

Abstract
Recent observations and modeling studies have stressed the influence of surface salinity perturbations on the North Atlantic circulation over the past few decades. As a step toward the estimation of the sensitivity of the thermohaline circulation to salinity anomalies, optimal initial surface salinity perturbations are computed and described for a realistic mean state of a global ocean general circulation model [Océan Parallélisé (OPA)]; optimality is defined successively with respect to the meridional overturning circulation intensity and the meridional heat transport maximum. Although the system is asymptotically stable, the nonnormality of the dynamics is able to produce a transient growth through an initial stimulation. Optimal perturbations are calculated subject to three constraints: the perturbation applies to surface salinity; the perturbation conserves the global salt content; and the perturbation is normalized, to remove the degeneracy in the linear maximization problem. Maximization using Lagrangian multipliers leads to explicit solutions (rather than eigenvalue problems), involving the integration of the model adjoint for each value to maximize.
The most efficient transient growth for the intensity of the meridional overturning circulation appears for a delay of 10.5 yr after the perturbation by the optimal surface salinity anomaly. This optimal growth is induced by an initial anomaly located north of 50°N. In the same way, the most efficient transient growth for the intensity of the meridional heat transport appears for a shorter delay of 2.2 yr after the perturbation by the optimal surface salinity anomaly. This initial optimal perturbation corresponds to a zonal salinity gradient around 24°N. The optimal surface salinity perturbations studied herein yield upper bounds on the intensity of the response in meridional overturning circulation and meridional heat transport. Using typical amplitudes of the Great Salinity Anomalies, the upper bounds for the associated variability are 0.8 Sv (1 Sv ≡ 106 m3 s−1) (11% of the mean circulation) and 0.03 PW (5% of the mean circulation), respectively.
The Variability of Adjoint Sensitivity with Respect to Model Physics and Basic-State Trajectory
Authors: Ancell Brian C. , Mass Clifford F. 
Published: May 2008

Abstract
Adjoint sensitivity fields have generally been viewed deterministically in the atmospheric science literature. However, uncertainty exists in the components of the adjoint model, such as the physics and the basic-state trajectories used to calculate the sensitivity fields. In this paper, the variability of adjoint sensitivity fields is examined for two collections of trajectories, each valid over a single time window: one supplied by three global operational models, and the other from a regional, operational ensemble Kalman filter system. Adjoint sensitivities are also compared using a dry adjoint and dry basic state, a moist adjoint and moist basic state, and a moist basic state and dry adjoint. The goal of these latter experiments is to explore the differences in mesoscale sensitivity fields with and without moisture, and to examine how sensitivities degrade when adjoint models utilize simplified physics. In all cases, 24-h sensitivities are produced with a low-level pressure response function over the coastal lowlands of the Pacific Northwest. Furthermore, this study examines these adjoint sensitivities at higher resolution than in previous studies. It is found that adjoint sensitivity can vary significantly in structure, magnitude, and location when different, but equally likely, basic-state trajectories are considered. Since the predicted response function shows large variance when using different basic-state trajectories, adjoint sensitivity should be viewed probabilistically. It is also found that the inclusion of moisture in both the forward and adjoint model produces significantly different sensitivity fields from the fully dry run. Furthermore, a large degradation occurs when removing moisture from the adjoint model but retaining moisture in the basic state, causing sensitivity fields to resemble that of a fully dry adjoint integration. This suggests that simplified physics relative to the forward nonlinear physics may produce significant differences from the desired “true” sensitivity field. The implications of these results for modern applications of adjoint models are discussed.
Childhood Giftedness and Adulthood Genius
Authors: Simonton Dean Keith 
Published: May 2008

Although the association between giftedness and genius has been the subject of several retrospective, longitudinal, and historiometric studies, this research concentrated on majority-culture samples. In the current study, Cox's (1926) findings regarding 301 geniuses were replicated on a sample of 291 eminent African Americans. Relative genius was measured by two archival eminence measures (majority White and minority Black culture) and by scores on the Creative Achievement Scale (Ludwig, 1992). Giftedness was assessed by raters blind to the identity of the individuals being evaluated. Control variables were defined for gender, year of birth, status as a living contemporary, and 18 domains of achievement. Multiple regression analyses indicated that adulthood eminence and creative achievement are positively correlated with early giftedness, with an effect size comparable to that found in the Cox study. Furthermore, this association was not moderated by gender, birth year, or most of the remaining variables. Putting Research to Use: The study provides support for a basic tenet of most gifted and talented programs, namely, that exceptional giftedness in childhood and adolescence is associated with adulthood achievements. Accordingly, education programs designed for these select populations can be legitimately viewed as an investment in the nation's future. The young talents of today are indeed likely to become the high achievers of tomorrow. Furthermore, this developmental continuity is found not just for youths who come from majority-culture backgrounds; the same forecast holds for those who come from minority-culture environments—African Americans in the case of the present study. Moreover, the degree to which childhood giftedness predicts adulthood success is the same for both majority and minority cultures. The longitudinal correspondence also stays the same for both males and females and for the diverse domains of achievement, whether creativity, leadership, entertainment, or sports. However, the long-term connection between early gifts and later achievements presumes a distinct manner of identifying and assessing giftedness. In particular, giftedness must not be evaluated according to a “one-size-fits-all” procedure. On the contrary, the magnitude of giftedness should be assessed according to the occurrence of precocious behaviors that are to a certain extent specific to a given culture and achievement domain. It is for this reason that the 291 African Americans in this study could attain distinction in a remarkable diversity of domains, including domains more characteristic of the minority culture—from gospel and soul musicians to civil rights activists and Black nationalists. This heterogeneity stands in stark contrast to what would have happened if giftedness had been defined in terms of performance on a standard intelligence test.
Impaired function of human T-lymphotropic virus type 1 (HTLV-1)–specific CD8+ T cells in HTLV-1–associated neurologic disease
Authors: Sabouri Amir H. , Usuku Koichiro , Hayashi Daisuke , Izumo Shuji , Ohara Yoshiro , Osame Mitsuhiro , Saito Mineki 
Published: May 2008

AbstractDespite abundant activated virus-specific cytotoxic T lymphocytes (CTLs), patients with human T-lymphotropic virus type 1 (HTLV-1)–associated myelopathy/tropical spastic paraparesis (HAM/TSP) showed a significantly higher frequency of infected T cells than did healthy virus carriers (HVCs). Here, we demonstrate that at a given proviral load, the frequency of CD8+ T cells that are negative for specific costimulatory molecules was significantly higher in HAM/TSP than in age-matched HVCs and uninfected healthy controls (HCs), whereas the frequency of intracellular perforin-positive CD8+ T cells was significantly lower in both HAM/TSP and HVCs than in HCs. An inverse correlation between HTLV-1 proviral load (PVL) and percent perforin-positive CD8+ T cells were observed only in disease-protective allele HLA-A*02–positive HVCs, but not in HAM/TSP patients, whether HLA-A*02 positive or negative, nor in HLA-A*02–negative HVCs. Significantly lower perforin expression was observed in HTLV-1–specific than in cytomegalovirus-specific CD8+ T cells. Majority of HTLV-1–specific CD8+ T cells in HVCs showed a CD28−CD27+ phenotype, whereas HAM/TSP showed a CD28−CD27− phenotype. HTLV-1–specific CD8+ T cells from HAM/TSP patients showed significantly lower degranulation than HVCs by CD107a mobilization assay. These findings suggest that an impaired function of HTLV-1–specific CTLs is associated with failing antiviral control and disease HAM/TSP.