bluuebunny/crossref_metadata_2025_split huggingface dataset:
Death Don't Have No Mercy and Neither Does Calcium: Arabidopsis CYCLIC NUCLEOTIDE GATED CHANNEL2 and Innate Immunity
Authors: Ali Rashid , Ma Wei , Lemtiri-Chlieh Fouad , Tsaltas Dimitrios , Leng Qiang , von Bodman Susannne , Berkowitz Gerald A. 
Published: March 2007

Abstract
Plant innate immune response to pathogen infection includes an elegant signaling pathway leading to reactive oxygen species generation and resulting hypersensitive response (HR); localized programmed cell death in tissue surrounding the initial infection site limits pathogen spread. A veritable symphony of cytosolic signaling molecules (including Ca2+, nitric oxide [NO], cyclic nucleotides, and calmodulin) have been suggested as early components of HR signaling. However, specific interactions among these cytosolic secondary messengers and their roles in the signal cascade are still unclear. Here, we report some aspects of how plants translate perception of a pathogen into a signal cascade leading to an innate immune response. We show that Arabidopsis thaliana CYCLIC NUCLEOTIDE GATED CHANNEL2 (CNGC2/DND1) conducts Ca2+ into cells and provide a model linking this Ca2+ current to downstream NO production. NO is a critical signaling molecule invoking plant innate immune response to pathogens. Plants without functional CNGC2 lack this cell membrane Ca2+ current and do not display HR; providing the mutant with NO complements this phenotype. The bacterial pathogen–associated molecular pattern elicitor lipopolysaccharide activates a CNGC Ca2+ current, which may be linked to NO generation due to buildup of cytosolic Ca2+/calmodulin.
Improperly Terminated, Unpolyadenylated mRNA of Sense Transgenes Is Targeted by RDR6-Mediated RNA Silencing in Arabidopsis
Authors: Luo Zhenghua , Chen Zhixiang 
Published: March 2007

Abstract
RNA silencing can be induced by highly transcribed transgenes through a pathway dependent on RNA-DEPENDENT RNA POLYMERASE6 (RDR6) and may function as a genome protection mechanism against excessively expressed genes. Whether all transcripts or just aberrant transcripts activate this protection mechanism is unclear. Consistent RNA silencing induced by a transgene with three direct repeats of the β-glucuronidase (GUS) open reading frame (ORF) is associated with high levels of truncated, unpolyadenylated transcripts, probably from abortive transcription elongation. Truncated, unpolyadenylated transcripts from triple GUS ORF repeats were degraded in the wild type but accumulated in an rdr6 mutant, suggesting targeting for degradation by RDR6-mediated RNA silencing. A GUS transgene without a 3′ transcription terminator produced unpolyadenylated readthrough mRNA and consistent RDR6-dependent RNA silencing. Both GUS triple repeats and terminator-less GUS transgenes silenced an expressed GUS transgene in trans in the wild type but not in the rdr6 mutant. Placing two 3′ terminators in the GUS transgene 3′ reduced mRNA 3′ readthrough, decreased GUS-specific small interfering RNA accumulation, and enhanced GUS gene expression. Moreover, RDR6 was localized in the nucleus. We propose that improperly terminated, unpolyadenylated mRNA from transgene transcription is subject to RDR6-mediated RNA silencing, probably by acting as templates for the RNA polymerase, in Arabidopsis thaliana.
Seed Germination of GA-Insensitivesleepy1Mutants Does Not Require RGL2 Protein Disappearance inArabidopsis
Authors: Ariizumi Tohru , Steber Camille M. 
Published: March 2007

AbstractWe explore the roles of gibberellin (GA) signaling genes SLEEPY1 (SLY1) and RGA-LIKE2 (RGL2) in regulation of seed germination in Arabidopsis thaliana, a plant in which the hormone GA is required for seed germination. Seed germination failure in the GA biosynthesis mutant ga1-3 is rescued by GA and by mutations in the DELLA gene RGL2, suggesting that RGL2 represses seed germination. RGL2 protein disappears before wild-type seed germination, consistent with the model that GA stimulates germination by causing the SCFSLY1 E3 ubiquitin ligase complex to trigger ubiquitination and destruction of RGL2. Unlike ga1-3, the GA-insensitive sly1 mutants show variable seed dormancy. Seed lots with high seed dormancy after-ripened slowly, with stronger alleles requiring more time. We expected that if RGL2 negatively controls seed germination, sly1 mutant seeds that germinate well should accumulate lower RGL2 levels than those failing to germinate. Surprisingly, RGL2 accumulated at high levels even in after-ripened sly1 mutant seeds with 100% germination, suggesting that RGL2 disappearance is not a prerequisite for seed germination in the sly1 background. Without GA, several GA-induced genes show increased accumulation in sly1 seeds compared with ga1-3. It is possible that the RGL2 repressor of seed germination is inactivated by after-ripening of sly1 mutant seeds.
Spectrum of cytomorphology of tuberculous lymphadenitis and changes during anti‐tubercular treatment
Authors: Sharma M. , Agarwal S. , Wadhwa N. , Mishra K. , Gadre D. J. 
Published: March 2007

Objective:  To analyse the morphological changes in tuberculous lymph nodes and the clinical response during short course anti tubercular chemotherapy.Methods:  Thirty‐six patients with tuberculous lymphadenitis under treatment were followed up clinically and cytologically at 0, 2, 4 and 6 months.Results:  Twenty‐six (72.2%) patients had palpable lymph nodes at the end of chemotherapy. Of the 14 patients with residual lymph nodes exceeding 1 cm in size, 92.8% (13) still had evidence of continuation of the disease. Acid‐fast bacilli could be found in 38.8% patients at the end of 6 months. Intense lymphocytic infiltration of granulomata in the early phase of chemotherapy predicted a favourable outcome.Conclusions:  Following completion of anti‐tubercular treatment a significant percentage of patients have persistent lymphadenopathy and harbour the disease. Morphological follow up of these patients is essential as they may be at increased risk of relapse.
Does the Giant Wood Spider Nephila pilipes Respond to Prey Variation by Altering Web or Silk Properties?
Authors: Tso I‐Min , Chiang Shu‐Ya , Blackledge Todd A. 
Published: March 2007

AbstractRecent studies demonstrated that orb‐weaving spiders may alter web architectures, the amount of silk in webs, or the protein composition of silks in response to variation in amount or type of prey. In this study, we conducted food manipulations to examine three mechanisms by which orb‐weaving spiders may adjust the performance of webs to variation in prey by altering the architectures of webs, making structural changes to the diameters of silk threads, and manipulating the material properties or amino acid composition of silk fibers. We fed Nephila pilipes two different types of prey, crickets or flies, and then compared orb structure and the chemical and physical properties of major ampullate (MA) silk between groups. Prey type did not affect orb structures in N. pilipes, except for mesh size. However, MA silk diameter and the stiffness of orbs constructed by spiders fed crickets were significantly greater than for the fly group. MA fibers forcibly silked from N. pilipes fed crickets was significantly thicker, but less stiff, than silk from spiders fed flies. Spiders in the cricket treatment also produced MA silk with slightly, but statistically significantly, more serine than silk from spiders in the fly treatment. Percentages of other major amino acids (proline, glycine, and glutamine) did not differ between treatments. This study demonstrated that orb‐weaving spiders can simultaneously alter some structural and material properties of MA silk, as well as the physical characteristics of webs, in response to different types of prey.
RADICAL CYSTECTOMY FOR PRIMARY BLADDER MALIGNANCY: A 10 YEAR REVIEW
Authors: Louie‐Johnsun Mark W. , Braslis Karl G. , Murphy Donald L. , Neerhut Gregory J. , Grills Richard J. 
Published: March 2007

Background:  Radical cystectomy is universally accepted as the definitive treatment for muscle invasive bladder cancer and preventing stage progression in high‐risk groups. There are few recent reviews outside of major international centres. We compared our institution’s results with published literature.Methods:  Records of 50 consecutive patients treated with radical cystectomy for biopsy‐proven bladder carcinoma between 1995 and 2005 were reviewed.Results:  The mean age was 70 years and 76% were male. Median follow up was 38 months (1–111 months). Twenty‐three patients (46%) had known history of superficial transitional cell carcinoma and 12 patients (24%) had undergone previously intravesical therapy. Transitional cell carcinomas accounted for 94% of cases and most (76%) were poorly differentiated. Twenty‐four (48%) had disease at pT3 stage or higher. Regional lymph nodes were involved in 35%. Twenty‐three patients (46%) developed recurrence and over half (12 patients) recurred within 12 months. Both lymph node involvement and recurrence were associated with higher pT stage (P < 0.001). All patients with recurrent disease were dead within a year (median 103 days). Median hospital stay was 19 days and there was one postoperative death (2%). Five‐year disease‐free and overall survival were 42 and 34% respectively.Conclusion:  Survival following curative resection for primary bladder malignancy is at best modest. Our overall proportion of higher stage disease contributed to earlier recurrence and lower survival rates. Our postoperative morbidity and mortality rates as well as length of stay are acceptable compared with major international units.
Biomass‐dependent susceptibility to drought in experimental grassland communities
Authors: Wang Yongfan , Yu Shixiao , Wang Jiang 
Published: March 2007

AbstractEarlier studies indicated that plant diversity influences community resistance in biomass when ecosystems are exposed to perturbations. This relationship remains controversial, however. Here we constructed grassland communities to test the relationships between species diversity and productivity under control and experimental drought conditions. Species richness was not correlated with biomass either under constant conditions or under drought conditions. However, communities with lower biomass production were more resistant to drought stress than those that were more productive. Our results also showed that ecosystem resistance to drought is a decreasing but nonlinear function of biomass. In contrast, species diversity had little and an equivocal effect on ecosystem resistance. From the results reported here, and the results of several previous studies, we suggest that high biomass systems exhibited a greater biomass reduction in response to drought than low biomass systems did, regardless of the relationship between plant diversity and community biomass production.
Growth‐mortality tradeoffs and ‘personality traits’ in animals
Authors: Stamps Judy A. 
Published: March 2007

AbstractConsistent individual differences in boldness, reactivity, aggressiveness, and other ‘personality traits’ in animals are stable within individuals but vary across individuals, for reasons which are currently obscure. Here, I suggest that consistent individual differences in growth rates encourage consistent individual differences in behavior patterns that contribute to growth‐mortality tradeoffs. This hypothesis predicts that behavior patterns that increase both growth and mortality rates (e.g. foraging under predation risk, aggressive defense of feeding territories) will be positively correlated with one another across individuals, that selection for high growth rates will increase mean levels of potentially risky behavior across populations, and that within populations, faster‐growing individuals will take more risks in foraging contexts than slower‐growing individuals. Tentative empirical support for these predictions suggests that a growth‐mortality perspective may help explain some of the consistent individual differences in behavioral traits that have been reported in fish, amphibians, reptiles, and other animals with indeterminate growth.
Caribbean mangroves adjust to rising sea level through biotic controls on change in soil elevation
Authors: McKee Karen L. , Cahoon Donald R. , Feller Ilka C. 
Published: March 2007

ABSTRACTAim  The long‐term stability of coastal ecosystems such as mangroves and salt marshes depends upon the maintenance of soil elevations within the intertidal habitat as sea level changes. We examined the rates and processes of peat formation by mangroves of the Caribbean Region to better understand biological controls on habitat stability.Location  Mangrove‐dominated islands on the Caribbean coasts of Belize, Honduras and Panama were selected as study sites.Methods  Biological processes controlling mangrove peat formation were manipulated (in Belize) by the addition of nutrients (nitrogen or phosphorus) to Rhizophora mangle (red mangrove), and the effects on the dynamics of soil elevation were determined over a 3‐year period using rod surface elevation tables (RSET) and marker horizons. Peat composition and geological accretion rates were determined at all sites using radiocarbon‐dated cores.Results  The addition of nutrients to mangroves caused significant changes in rates of mangrove root accumulation, which influenced both the rate and direction of change in elevation. Areas with low root input lost elevation and those with high rates gained elevation. These findings were consistent with peat analyses at multiple Caribbean sites showing that deposits (up to 10 m in depth) were composed primarily of mangrove root matter. Comparison of radiocarbon‐dated cores at the study sites with a sea‐level curve for the western Atlantic indicated a tight coupling between peat building in Caribbean mangroves and sea‐level rise over the Holocene.Main conclusions  Mangroves common to the Caribbean region have adjusted to changing sea level mainly through subsurface accumulation of refractory mangrove roots. Without root and other organic inputs, submergence of these tidal forests is inevitable due to peat decomposition, physical compaction and eustatic sea‐level rise. These findings have relevance for predicting the effects of sea‐level rise and biophysical processes on tropical mangrove ecosystems.
Government and the Reverse‐Holdup Problem
Authors: WICKELGREN ABRAHAM L. 
Published: March 2007

AbstractWhen the government bargains with a private firm, the firm cares about only its own profits, but the firm's profits may also enter into the government's utility function. As a result, the government will not bargain as aggressively for a low price. This can lead the government to “over pay” for quality. In contrast to the standard holdup problem, this reverse‐holdup problem can give the firm an incentive to overinvest in non‐contractible quality. The paper also discusses some examples where the reverse‐holdup problem may explain excessive quality in government procurement.
Collective Risk Control and Group Security: The Unexpected Consequences of Differential Risk Aversion
Authors: IHORI TOSHIHIRO , McGUIRE MARTIN C. 
Published: March 2007

AbstractWe provide an analysis of odds‐improving self‐protection for when it yields collective benefits to groups, such as alliances of nations, for whom risks of loss are public bads and prevention of loss is a public good. Our analysis of common risk reduction shows how diminishing returns in risk improvement can be folded into income effects. These income effects then imply that whether protection is inferior or normal depends on the risk aversion characteristics of underlying utility functions, and on the interaction between these, the level of risk, and marginal effectiveness of risk abatement. We demonstrate how public good inferiority is highly likely when the good is “group risk reduction.” In fact, we discover a natural or endogenous limit on the size of a group and of the amount of risk controlling outlay it will provide under Nash behavior. We call this limit an “Inferior Goods Barrier” to voluntary risk reduction. For the paradigm case of declining risk aversion, increases in group size(wealth) will cause provision of more safety to change from a normal to an inferior good thereby creating such a barrier.
P2Y2‐ and P2Y4purinergic receptors are over‐expressed in human colon cancer
Authors: Nylund G. , Hultman L. , Nordgren S. , Delbro D. S. 
Published: March 2007

Summary1A characteristic of cancer is altered signal transduction leading to uninhibited growth. Adenosine‐5′‐triphosphate (ATP), a natural ligand at P2X‐ and P2Y purinergic receptors may regulate cell growth in non‐neoplastic, as well as neoplastic tissues. In the human colon cancer cell line, HT‐29, we previously demonstrated the expression of purinergic receptors of the P2Y2‐ and P2Y4subclasses.2The aim of the current study was to investigate whether these two purinergic receptors are expressed also in human colon cancer, and, if so, how such expression is related to that in tumour‐free colonic tissue.3The immunohistochemical findings of both P2Y2‐ and P2Y4receptors in the tumours from three patients, prompted us to conduct an investigation of a consecutive series of patients utilizing Western blotting for protein detection and densitometry for quantitation.4Both P2Y2‐ and P2Y4purinergic receptors could be identified in tumour‐free tissue, and both were significantly over‐expressed in each of the 10 colon cancers.
Effect of Exogenous Reductant on Growth and Iron Mobilization from Ferrihydrite by the
Pseudomonas mendocina ymp
Strain
Authors: Dhungana Suraj , Anthony Charles R. , Hersman Larry E. 
Published: March 2007

ABSTRACT

Growth of the
Pseudomonas mendocina ymp
strain on insoluble ferrihydrite is enhanced by exogenous reductants with concurrent increase in soluble iron concentrations. This shows that exogenous reductants play a substantial role in the overall microbial iron bioavailability. The exogenous reductants may work together with the siderophores, Fe-scavenging agents, to facilitate ferrihydrite dissolution.
Tight Modulation of
Escherichia coli
Bacterial Biofilm Formation through Controlled Expression of Adhesion Factors
Authors: Da Re Sandra , Le Quéré Benjamin , Ghigo Jean-Marc , Beloin Christophe 
Published: March 2007

ABSTRACT

Despite the economic and sanitary problems caused by harmful biofilms, biofilms are nonetheless used empirically in industrial environmental and bioremediation processes and may be of potential use in medical settings for interfering with pathogen development.
Escherichia coli
is one of the bacteria with which biofilm formation has been studied in great detail, and it is especially appreciated for biotechnology applications because of its genetic amenability. Here we describe the development of two new genetic tools enabling the constitutive and inducible expression of any gene or operon of interest at its native locus. In addition to providing valuable tools for complementation and overexpression experiments, these two compact genetic cassettes were used to modulate the biofilm formation capacities of
E. coli
by taking control of two biofilm-promoting factors, autotransported antigen 43 adhesin and the
bscABZC
cellulose operon. The modulation of the biofilm formation capacities of
E. coli
or those of other bacteria capable of being genetically manipulated may be of use both for reducing and for improving the impact of biofilms in a number of industrial and medical applications.
Assessment and Interpretation of Bacterial Viability by Using the LIVE/DEAD BacLight Kit in Combination with Flow Cytometry
Authors: Berney Michael , Hammes Frederik , Bosshard Franziska , Weilenmann Hans-Ulrich , Egli Thomas 
Published: March 2007

ABSTRACT

The commercially available LIVE/DEAD BacLight kit is enjoying increased popularity among researchers in various fields of microbiology. Its use in combination with flow cytometry brought up new questions about how to interpret LIVE/DEAD staining results. Intermediate states, normally difficult to detect with epifluorescence microscopy, are a common phenomenon when the assay is used in flow cytometry and still lack rationale. It is shown here that the application of propidium iodide in combination with a green fluorescent total nucleic acid stain on UVA-irradiated cells of
Escherichia coli
,
Salmonella enterica
serovar Typhimurium,
Shigella flexneri
, and a community of freshwater bacteria resulted in a clear and distinctive flow cytometric staining pattern. In the gram-negative bacterium
E. coli
as well as in the two enteric pathogens, the pattern can be related to the presence of intermediate cellular states characterized by the degree of damage afflicted specifically on the bacterial outer membrane. This hypothesis is supported by the fact that EDTA-treated nonirradiated cells exhibit the same staining properties. On the contrary, this pattern was not observed in gram-positive
Enterococcus faecalis
, which lacks an outer membrane. Our observations add a new aspect to the LIVE/DEAD stain, which so far was believed to be dependent only on cytoplasmic membrane permeability.
Irradiation Sensitivity of Planktonic and Biofilm-Associated
Escherichia coli
O157:H7 Isolates Is Influenced by Culture Conditions
Authors: Niemira Brendan A. 
Published: March 2007

ABSTRACT

Ionizing radiation effectively inactivates
Escherichia coli
O157:H7, but the efficacy of the process against biofilm cells versus that against free-living planktonic cells is not well documented. The radiation sensitivity of planktonic or biofilm cells was determined for three isolates of
E. coli
O157:H7 (C9490, ATCC 35150, and ATCC 43894). Biofilms were formed on sterile glass slides incubated at 37°C for either 24 h, 48 h, or 72 h. The biofilm and planktonic cultures were gamma irradiated at doses ranging from 0.0 (control) to 1.5 kGy. The dose of radiation value required to reduce the population by 90% (D
10
) was calculated for each isolate, culture, and maturity based on viable populations at each radiation dose. For each of the times sampled, the D
10
values of isolate 43894 planktonic cells (0.454 to 0.479 kGy) were significantly (
P
< 0.05) higher than those observed for biofilm cells (0.381 to 0.385 kGy), indicating a significantly increased sensitivity to irradiation for cells in the biofilm habitat. At the 24-h sampling time, isolate C9490 showed a similar pattern, in which the D
10
values of planktonic cells (0.653 kGy) were significantly higher than those for biofilm cells (0.479 kGy), while isolate 35150 showed the reverse, with D
10
values of planktonic cells (0.396 kGy) significantly lower than those for biofilm cells (0.526 kGy). At the 48-h and 72-h sampling times, there were no differences in radiation sensitivities based on biofilm habitat for C9490 or 35150. Biofilm-associated cells, therefore, show a response to irradiation which can differ from that of planktonic counterparts, depending on the isolate and the culture maturity. Culture maturity had a more significant influence on the irradiation efficacy of planktonic cells but not on biofilm-associated cells of
E. coli
O157:H7.