bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into Nuclear Organization in Plants as Revealed by the Dynamic Distribution ofArabidopsisSR Splicing Factors
Authors: Tillemans Vinciane , Leponce Isabelle , Rausin Glwadys , Dispa Laurence , Motte Patrick 
Published: November 2006

AbstractSerine/arginine-rich (SR) proteins are splicing regulators that share a modular structure consisting of one or two N-terminal RNA recognition motif domains and a C-terminal RS-rich domain. We investigated the dynamic localization of the Arabidopsis thaliana SR protein RSZp22, which, as we showed previously, distributes in predominant speckle-like structures and in the nucleolus. To determine the role of RSZp22 diverse domains in its nucleolar distribution, we investigated the subnuclear localization of domain-deleted mutant proteins. Our results suggest that the nucleolar localization of RSZp22 does not depend on a single targeting signal but likely involves different domains/motifs. Photobleaching experiments demonstrated the unrestricted dynamics of RSZp22 between nuclear compartments. Selective inhibitor experiments of ongoing cellular phosphorylation influenced the rates of exchange of RSZp22 between the different nuclear territories, indicating that SR protein mobility is dependent on the phosphorylation state of the cell. Furthermore, based on a leptomycin B– and fluorescence loss in photobleaching–based sensitive assay, we suggest that RSZp22 is a nucleocytoplasmic shuttling protein. Finally, with electron microscopy, we confirmed that RSp31, a plant-specific SR protein, is dynamically distributed in nucleolar cap-like structures upon phosphorylation inhibition. Our findings emphasize the high mobility of Arabidopsis SR splicing factors and provide insights into the dynamic relationships between the different nuclear compartments.
SND1, a NAC Domain Transcription Factor, Is a Key Regulator of Secondary Wall Synthesis in Fibers ofArabidopsis
Authors: Zhong Ruiqin , Demura Taku , Ye Zheng-Hua 
Published: November 2006

AbstractSecondary walls in fibers and tracheary elements constitute the most abundant biomass produced by plants. Although a number of genes involved in the biosynthesis of secondary wall components have been characterized, little is known about the molecular mechanisms underlying the coordinated expression of these genes. Here, we demonstrate that the Arabidopsis thaliana NAC (for NAM, ATAF1/2, and CUC2) domain transcription factor, SND1 (for secondary wall–associated NAC domain protein), is a key transcriptional switch regulating secondary wall synthesis in fibers. We show that SND1 is expressed specifically in interfascicular fibers and xylary fibers in stems and that dominant repression of SND1 causes a drastic reduction in the secondary wall thickening of fibers. Ectopic overexpression of SND1 results in activation of the expression of secondary wall biosynthetic genes, leading to massive deposition of secondary walls in cells that are normally nonsclerenchymatous. In addition, we have found that SND1 upregulates the expression of several transcription factors that are highly expressed in fibers during secondary wall synthesis. Together, our results reveal that SND1 is a key transcriptional activator involved in secondary wall biosynthesis in fibers.
Radiotherapy for metastatic melanoma presenting in pregnancy
Authors: Daly TA , Burmeister BH , Smithers BM , Doody J , Kane A 
Published: November 2006

SummaryWe describe the study of a patient with metastatic melanoma to axillary nodes presenting during pregnancy. The factors considered in her management are discussed, including issues related to staging, the decision not to terminate the pregnancy and the relative efficacy and fetal toxicity of the available treatment options. An overview of the known effects of radiotherapy on the fetus is presented and the technical alterations that were used to decrease the toxicity of radiotherapy are discussed.
Platelet function in paediatric patients undergoing surgery for cyanotic congenital heart defects
Authors: Rivo J. , Gozal Y. , Raushenbach M. , Varon D. , Katz J. 
Published: November 2006

Introduction:  Coagulation abnormalities accompany cardiac surgery in children with cyanotic congenital heart defects (CHD). However the state of primary haemostasis in such patients remains insufficiently investigated.Methods:  This study conforms to the principles of the Declaration of Helsinki. Nineteen pediatric patients aged 7 days–10 years with cyanotic CHD undergoing correction surgery were enrolled in the study. Citrated venous blood was taken at three points – prior to operation, after termination of cardiopulmonary bypass and neutralization of heparin by protamine and on postoperative day two. Optical platelet aggregometry with adenosine diphosphate, epinephrine, collagen and ristocetin as platelets agonists was used. The results were calculated statistically using Student's t‐test.Results:  Our results demonstrate that ADP‐induced platelet aggregation was markedly reduced after operation (73.2 ± 19 vs 43.2 ± 24.9; P < 0.005). Similar results were obtained for epinephrine (56.7 ± 28.9 vs 31 ± 29.4; P < 0.05) and ristocetin‐induced platelet aggregation (90.3 ± 25.6 vs 59 ± 21.4; P < 0.001), whereas the effect of collagen had a trend to decrease remaining however statistically insignificant (53.6 ± 40.4 vs 31.2 ± 34.3; P < 0.2). Both haemoglobin and haematocrit levels remained unchanged, whereas platelet count dramatically decreased (from 339.4 ± 159.4 to 138.9 ± 80.3; P < 0.001) that can potentially be explained by platelet destruction during cardiopulmonary bypass. On the second postoperative day, the amount of platelets remained unchanged (180.8 ± 102.0; P > 0.5) whereas platelet aggregation returned to the initial values (77.1 ± 14.2, 73.6 ± 17.1 and 81.0 ± 12.8 for ADP, epinephrine and ristocetin‐induced aggregation, respectively; in all cases P > 0.1 compared with the level before operation). Haemoglobin and haematorcrit levels were similar after operation and on the second day.Discussion:  As stated in the results section, platelet aggregation recovers on the second postoperative day whereas platelet count remains relatively low. Consequently, changes in platelet aggregation observed immediately after operation cannot be explained only by the decrease in platelet count.Conclusions:  (i) Platelet aggregation induced by different agonists, as well as platelet count, decrease in children with cyanotic CHD immediately after operation; and (ii) platelet aggregation but not platelet count recovers on the second postoperative day.
Carbohydrate characterization of quail primordial germ cells during migration and gonadal differentiation
Authors: Armengol Clara , Carretero Ana , Nacher Víctor , Ruberte Jesús , Navarro Marc 
Published: November 2006

AbstractA selection of lectins were used to study changes in the distribution of sugar residues in primordial germ cells (PGCs) during gonadal colonization and differentiation. Although the cytochemical characteristics of PGCs have been described in the chick, little is known about such characteristics in other avian species of interest to experimental biology. Therefore, we studied embryos of Japanese quail (Coturnix coturnix japonica) by light and laser confocal scanning microscopy, using the QH1 antibody as a tool to identify PGCs in both sexes and at all stages. LEA, WGA and RCA‐I bound to PGCs in a similar way to QH1. LEA was the best marker for all stages. The presence of acid phosphatase and the intense reaction of LEA, WGA, RCA‐I and WFA at the cell surface were shown to be a useful tool in the study of the migratory PGCs of the quail. Quails were sexed histologically in younger embryos than in chick; results were confirmed by PCR. The lectin‐binding pattern changed drastically in differentiated gonads. Cell surface reactivity was almost entirely lost. Quail differentiating oogonia showed a characteristic binding pattern to QH1 and to the lectins WGA, RCA‐I and WFA. Binding was observed in intense spots in the Golgi complex, and there was a specific PNA reaction. These results suggest that some selective sugar binding sites on the PGCs play a significant role in their migration, colonization and maturation.
Comprehensive Review of Campylobacter and Poultry Processing
Authors: Keener K.M. , Bashor M.P. , Curtis P.A. , Sheldon B.W. , Kathariou S. 
Published: November 2006

ABSTRACT Campylobacter has been recognized as a leading bacterial cause of human gastroenteritis in the United States, with 40000 documented cases annually. Epidemiological data suggest that contaminated products of animal origin, especially poultry, contribute significantly to campylobacteriosis. Thus, reduction of contamination of raw poultry would have a large impact in reducing incidence of illness. Contamination occurs both on the farm and in poultry slaughter plants. Routine procedures on the farm such as feed withdrawal, poultry handling, and transportation practices have a documented effect on Campylobacter levels at the processing plant. At the plant, defeathering, evisceration, and carcass chillers have been documented to cross‐contaminate poultry carcasses. Carcass washings and the application of processing aids have been shown to reduce populations of Campylobacter in the carcasses by log10 0.5 log10 1.5; however, populations of Campylobacter have been shown to enter a poultry processing plant at levels between log10 5 colony‐forming units (CFU)/mL and log10 8 CFU/mL of carcass rinse. The purpose of this article is to review Campylobacter, the infection that it causes, its association with poultry, contamination sources during processing, and intervention methods.
Nonlinear Strain Hardening Model for Predicting Clamp Load Loss in Bolted Joints
Authors: Nassar Sayed A. , Matin Payam H. 
Published: November 2006

Abstract
Closed form solution for the amount of clamp load loss due to an externally applied separating force is determined for a bolted assembly in which the fastener is initially tightened beyond its proportional limit. The joint may or may not have been yielded at initial assembly, however. After the initial tightening of the fastener, the joint is subsequently subjected to a tensile separating force, which further increases the fastener tensile stress into the nonlinear range. Such a separating force will simultaneously reduce the clamping force in the bolted joint. Upon the removal of the separating service load, the bolted joint system reaches a new equilibrium point between the fastener tension and the joint clamping force. At the new equilibrium point, the fastener tension is reduced from its value at initial assembly, due to the plastic elongation of the fastener. The reduction in fastener tension translates into a partial—yet permanent—loss of the clamping load, which may lead to joint leakage, loosening, or fatigue failure. A nonlinear strain hardening model is implemented in order to describe the fastener behavior past the proportional limit of its material, and to determine the clamp load loss due to the permanent set in the fastener after the separating force has been removed. In order to study the effect of strain hardening, various rates of strain hardening are used for modeling the behavior of the fastener material. The effect of three nondimensional variables on the amount of clamp load loss is investigated. This includes the joint-to-fastener stiffness ratio, the ratio of initial fastener tension to its elastic limit, and the ratio of the separating force to its maximum value that would cause joint separation to start. Analytical results are presented for a range of stiffness ratios that simulates both soft and hard joint applications.
Genes That Enhance the Ecological Fitness of
Shewanella oneidensis
MR-1 in Sediments Reveal the Value of Antibiotic Resistance
Authors: Groh Jennifer L. , Luo Qingwei , Ballard Jimmy D. , Krumholz Lee R. 
Published: November 2006

ABSTRACT

Environmental bacteria persist in various habitats, yet little is known about the genes that contribute to growth and survival in their respective ecological niches. Signature-tagged mutagenesis (STM) of
Shewanella oneidensis
MR-1 coupled with a screen involving incubations of mutant strains in anoxic aquifer sediments allowed us to identify 47 genes that enhance fitness in sediments. Gene functions inferred from annotations provide us with insight into physiological and ecological processes that environmental bacteria use while growing in sediment ecosystems. Identification of the
mexF
gene and other potential membrane efflux components by STM demonstrated that homologues of multidrug resistance genes present in pathogens are required for sediment fitness of nonpathogenic bacteria. Further studies with a
mexF
deletion mutant demonstrated that the multidrug resistance pump encoded by
mexF
is required for resistance to antibiotics, including chloramphenicol and tetracycline. Chloramphenicol-adapted cultures exhibited mutations in the gene encoding a TetR family regulatory protein, indicating a role for this protein in regulating expression of the
mexEF
operon. The relative importance of
mexF
for sediment fitness suggests that antibiotic efflux may be a required process for bacteria living in sediment systems.
Novel Role for
Aeromonas jandaei
as a Digestive Tract Symbiont of the North American Medicinal Leech
Authors: Siddall Mark E. , Worthen Paul L. , Johnson Matthew , Graf Joerg 
Published: November 2006

ABSTRACT

The gut bacteria of the North American medicinal leech,
Macrobdella decora
, were characterized. Biochemical tests and DNA sequences indicated that
Aeromonas jandaei
is the dominant culturable symbiont in leeches from a broad geographic area. In this work we identified a new habitat for
A. jandaei
, and here we suggest that there is unexpected specificity between leeches and
Aeromonas
species.
Degradation and Mineralization of Nanomolar Concentrations of the Herbicide Dichlobenil and Its Persistent Metabolite 2,6-Dichlorobenzamide by
Aminobacter
spp. Isolated from Dichlobenil-Treated Soils
Authors: Sørensen Sebastian R. , Holtze Maria S. , Simonsen Allan , Aamand Jens 
Published: November 2006

ABSTRACT

2,6-Dichlorobenzamide (BAM), a persistent metabolite from the herbicide 2,6-dichlorobenzonitrile (dichlobenil), is the pesticide residue most frequently detected in Danish groundwater. A BAM-mineralizing bacterial community was enriched from dichlobenil-treated soil sampled from the courtyard of a former plant nursery. A BAM-mineralizing bacterium (designated strain MSH1) was cultivated and identified by 16S rRNA gene sequencing and fatty acid analysis as being closely related to members of the genus
Aminobacter
, including the only cultured BAM degrader,
Aminobacter
sp. strain ASI1. Strain MSH1 mineralized 15 to 64% of the added [
ring
-U-
14
C]BAM to
14
CO
2
with BAM at initial concentrations in the range of 7.9 nM to 263.1 μM provided as the sole carbon, nitrogen, and energy source. A quantitative enzyme-linked immunoassay analysis with antibodies against BAM revealed residue concentrations of 0.35 to 18.05 nM BAM following incubation for 10 days, corresponding to a BAM depletion of 95.6 to 99.9%. In contrast to the
Aminobacter
sp. strain ASI1, strain MSH1 also mineralized the herbicide itself along with several metabolites, including
ortho
-chlorobenzonitrile,
ortho
-chlorobenzoic acid, and benzonitrile, making it the first known dichlobenil-mineralizing bacterium.
Aminobacter
type strains not previously exposed to dichlobenil or BAM were capable of degrading nonchlorinated structural analogs. Combined, these results suggest that closely related
Aminobacter
strains may have a selective advantage in BAM-contaminated environments, since they are able to use this metabolite or structurally related compounds as a carbon and nitrogen source.
Biotransformation of Patulin by
Gluconobacter oxydans
Authors: Ricelli A. , Baruzzi F. , Solfrizzo M. , Morea M. , Fanizzi F. P. 
Published: November 2006

ABSTRACT

A bacterium isolated from patulin-contaminated apples was capable of degrading patulin to a less-toxic compound, ascladiol. The bacterium was identified as
Gluconobacter oxydans
by 16S rRNA gene sequencing, whereas ascladiol was identified by liquid chromatography-tandem mass spectrometry and proton and carbon nuclear magnetic resonance. Degradation of up to 96% of patulin was observed in apple juices containing up to 800 μg/ml of patulin and incubated with
G. oxydans
.
Use of
Tetrahymena thermophila
To Study the Role of Protozoa in Inactivation of Viruses in Water
Authors: Pinheiro Marcel D. O. , Power Mary E. , Butler Barbara J. , Dayeh Vivian R. , Slawson Robin , Lee Lucy E. J. , Lynn Denis H. , Bols Niels C. 
Published: November 2006

ABSTRACT

The ability of a ciliate to inactivate bacteriophage was studied because these viruses are known to influence the size and diversity of bacterial populations, which affect nutrient cycling in natural waters and effluent quality in sewage treatment, and because ciliates are ubiquitous in aquatic environments, including sewage treatment plants.
Tetrahymena thermophila
was used as a representative ciliate; T4 was used as a model bacteriophage. The T4 titer was monitored on
Escherichia coli
B in a double-agar overlay assay. T4 and the ciliate were incubated together under different conditions and for various times, after which the mixture was centrifuged through a step gradient, producing a top layer free of ciliates. The T4 titer in this layer decreased as coincubation time increased, but no decrease was seen if phage were incubated with formalin-fixed
Tetrahymena
. The T4 titer associated with the pellet of living ciliates was very low, suggesting that removal of the phage by
Tetrahymena
inactivated T4. When
Tetrahymena
cells were incubated with SYBR gold-labeled phage, fluorescence was localized in structures that had the shape and position of food vacuoles. Incubation of the phage and ciliate with cytochalasin B or at 4°C impaired T4 inactivation. These results suggest the active removal of T4 bacteriophage from fluid by macropinocytosis, followed by digestion in food vacuoles. Such ciliate virophagy may be a mechanism occurring in natural waters and sewage treatment, and the methods described here could be used to study the factors influencing inactivation and possibly water quality.
Morphogenesis of the
Bacillus anthracis
Spore
Authors: Giorno Rebecca , Bozue Joel , Cote Christopher , Wenzel Theresa , Moody Krishna-Sulayman , Mallozzi Michael , Ryan Matthew , Wang Rong , Zielke Ryszard , Maddock Janine R. , Friedlander Arthur , Welkos Susan , Driks Adam 
Published: November 2006

ABSTRACT

Bacillus
spp. and
Clostridium
spp. form a specialized cell type, called a spore, during a multistep differentiation process that is initiated in response to starvation. Spores are protected by a morphologically complex protein coat. The
Bacillus anthracis
coat is of particular interest because the spore is the infective particle of anthrax. We determined the roles of several
B. anthracis
orthologues of
Bacillus subtilis
coat protein genes in spore assembly and virulence. One of these,
cotE
, has a striking function in
B. anthracis
: it guides the assembly of the exosporium, an outer structure encasing
B. anthracis
but not
B. subtilis
spores. However, CotE has only a modest role in coat protein assembly, in contrast to the
B. subtilis
orthologue.
cotE
mutant spores are fully virulent in animal models, indicating that the exosporium is dispensable for infection, at least in the context of a
cotE
mutation. This has implications for both the pathophysiology of the disease and next-generation therapeutics. CotH, which directs the assembly of an important subset of coat proteins in
B. subtilis
, also directs coat protein deposition in
B. anthracis
. Additionally, however, in
B. anthracis
, CotH effects germination; in its absence, more spores germinate than in the wild type. We also found that SpoIVA has a critical role in directing the assembly of the coat and exosporium to an area around the forespore. This function is very similar to that of the
B. subtilis
orthologue, which directs the assembly of the coat to the forespore. These results show that while
B. anthracis
and
B. subtilis
rely on a core of conserved morphogenetic proteins to guide coat formation, these proteins may also be important for species-specific differences in coat morphology. We further hypothesize that variations in conserved morphogenetic coat proteins may play roles in taxonomic variation among species.
Anaerobic Central Metabolic Pathways in
Shewanella oneidensis
MR-1 Reinterpreted in the Light of Isotopic Metabolite Labeling
Authors: Tang Yinjie J. , Meadows Adam L. , Kirby James , Keasling Jay D. 
Published: November 2006

ABSTRACT

It has been proposed that during growth under anaerobic or oxygen-limited conditions,
Shewanella oneidensis
MR-1 uses the serine-isocitrate lyase pathway common to many methylotrophic anaerobes, in which formaldehyde produced from pyruvate is condensed with glycine to form serine. The serine is then transformed through hydroxypyruvate and glycerate to enter central metabolism at phosphoglycerate. To examine its use of the serine-isocitrate lyase pathway under anaerobic conditions, we grew
S. oneidensis
MR-1 on [1-
13
C]lactate as the sole carbon source, with either trimethylamine
N
-oxide (TMAO) or fumarate as an electron acceptor. Analysis of cellular metabolites indicated that a large percentage (>70%) of lactate was partially oxidized to either acetate or pyruvate. The
13
C isotope distributions in amino acids and other key metabolites indicate that under anaerobic conditions, although glyoxylate synthesized from the isocitrate lyase reaction can be converted to glycine, a complete serine-isocitrate pathway is not present and serine/glycine is, in fact, oxidized via a highly reversible degradation pathway. The labeling data also suggest significant activity in the anapleurotic (malic enzyme and phosphoenolpyruvate carboxylase) reactions. Although the tricarboxylic acid (TCA) cycle is often observed to be incomplete in many other anaerobes (absence of 2-oxoglutarate dehydrogenase activity), isotopic labeling supports the existence of a complete TCA cycle in
S. oneidensis
MR-1 under certain anaerobic conditions, e.g., TMAO-reducing conditions.
RamB, the Transcriptional Regulator of Acetate Metabolism in
Corynebacterium glutamicum
, Is Subject to Regulation by RamA and RamB
Authors: Cramer Annette , Auchter Marc , Frunzke Julia , Bott Michael , Eikmanns Bernhard J. 
Published: November 2006

ABSTRACT

In
Corynebacterium glutamicum
, the transcriptional regulator RamB negatively controls the expression of genes involved in acetate metabolism. Here we show that RamB represses its own expression by direct interaction with a 13-bp motif in the
ramB
promoter region. Additionally,
ramB
expression is subject to carbon source-dependent positive control by RamA.
Derepression of Excision of Integrative and Potentially Conjugative Elements from
Streptococcus thermophilus
by DNA Damage Response: Implication of a cI-Related Repressor
Authors: Bellanger Xavier , Morel Catherine , Decaris Bernard , Guédon Gérard 
Published: November 2006

ABSTRACT

A DNA-damaging agent, mitomycin C, derepresses the site-specific excision of two integrative and potentially conjugative elements from
Streptococcus thermophilus
, ICE
St1
and ICE
St3
. The regulation pathway involves a repressor related to phage lambda cI repressor. It could also involve a putative regulator related to another type of phage repressors, the “cI-like” repressors.