bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential Transcriptional Analysis of the Cyanobacterium
Cyanothece
sp. Strain ATCC 51142 during Light-Dark and Continuous-Light Growth
Authors: Toepel Jörg , Welsh Eric , Summerfield Tina C. , Pakrasi Himadri B. , Sherman Louis A.
Published: April 2008

We analyzed the metabolic rhythms and differential gene expression in the unicellular, diazotrophic cyanobacterium
Cyanothece
sp. strain ATCC 51142 under N
2
-fixing conditions after a shift from normal 12-h light-12-h dark cycles to continuous light. We found that the mRNA levels of ∼10% of the genes in the genome demonstrated circadian behavior during growth in free-running (continuous light) conditions. The genes for N
2
fixation displayed a strong circadian behavior, whereas photosynthesis and respiration genes were not as tightly regulated. One of our main objectives was to determine the strategies used by these cells to perform N
2
fixation under normal day-night conditions, as well as under the greater stress caused by continuous light. We determined that N
2
fixation cycled in continuous light but with a lower N
2
fixation activity. Glycogen degradation, respiration, and photosynthesis were also lower; nonetheless, O
2
evolution was about 50% of the normal peak. We also demonstrated that
nifH
(encoding the nitrogenase Fe protein),
nifB
, and
nifX
were strongly induced in continuous light; this is consistent with the role of these proteins during the assembly of the enzyme complex and suggested that the decreased N
2
fixation activity was due to protein-level regulation or inhibition. Many soluble electron carriers (e.g., ferredoxins), as well as redox carriers (e.g., thioredoxin and glutathione), were strongly induced during N
2
fixation in continuous light. We suggest that these carriers are required to enhance cyclic electron transport and phosphorylation for energy production and to maintain appropriate redox levels in the presence of elevated O
2
, respectively.
Growth ofEscherichia coli: Significance of Peptidoglycan Degradation during Elongation and Septation
Authors: Uehara Tsuyoshi , Park James T.
Published: April 2008

We have found a striking difference between the modes of action of amdinocillin (mecillinam) and compound A22, both of which inhibit cell elongation. This was made possible by employment of a new method using anEscherichia colipeptidoglycan (PG)-recycling mutant, lackingampD, to analyze PG degradation during cell elongation and septation. Using this method, we have found that A22, which is known to prevent MreB function, strongly inhibited PG synthesis during elongation. In contrast, treatment of elongating cells with amdinocillin, which inhibits penicillin-binding protein 2 (PBP2), allowed PG glycan synthesis to proceed at a nearly normal rate with concomitant rapid degradation of the new glycan strands. By treating cells with A22 to inhibit sidewall synthesis, the method could also be applied to study septum synthesis. To our surprise, over 30% of newly synthesized septal PG was degraded during septation. Thus, excess PG sufficient to form at least one additional pole was being synthesized and rapidly degraded during septation. We propose that during cell division, rapid removal of the excess PG serves to separate the new poles of the daughter cells. We have also employed this new method to demonstrate that PBP2 and RodA are required for the synthesis of glycan strands during elongation and that the periplasmic amidases that aid in cell separation are minor players, cleaving only one-sixth of the PG that is turned over by the lytic transglycosylases.
Insertion Hot Spot for Horizontally Acquired DNA within a Bidirectional Small-RNA Locus inSalmonella enterica
Authors: Balbontín Roberto , Figueroa-Bossi Nara , Casadesús Josep , Bossi Lionello
Published: April 2008

InEscherichia coliandSalmonella enterica, RyeA and RyeB RNAs are encoded on opposite DNA strands at the same locus. We present evidence indicating that the last 23 bp of theryeBgene, corresponding to an internal portion of theryeAgene, served repeatedly as the integration site for exogenous DNA duringSalmonellaevolution and still act as an attachment site for present-day bacteriophages. Interestingly,ryeAsequence and expression are modified upon lysogenization.
The
Methanothermobacter thermautotrophicus
Cdc6-2 Protein, the Putative Helicase Loader, Dissociates the Minichromosome Maintenance Helicase
Authors: Shin Jae-Ho , Heo Gun Young , Kelman Zvi
Published: April 2008

The Cdc6-1 and -2 proteins from the archaeon
Methanothermobacter thermautotrophicus
were previously shown to bind the minichromosome maintenance (MCM) helicase. It is shown here that Cdc6-2 protein dissociates the MCM complex. This observation supports the hypothesis that the Cdc6-2 protein functions as a helicase loader.
EspA, an Orphan Hybrid Histidine Protein Kinase, Regulates the Timing of Expression of Key Developmental Proteins of
Myxococcus xanthus
Authors: Higgs Penelope I. , Jagadeesan Sakthimala , Mann Petra , Zusman David R.
Published: April 2008

Myxococcus xanthus
undergoes a complex starvation-induced developmental program that results in cells forming multicellular fruiting bodies by aggregating into mounds and then differentiating into spores. This developmental program requires at least 72 h and is mediated by a temporal cascade of gene regulators in response to intra- and extracellular signals.
espA
mutants, encoding an orphan hybrid histidine kinase, alter the timing of this developmental program, greatly accelerating developmental progression. Here, we characterized EspA and demonstrated that it autophosphorylates in vitro on the conserved histidine residue and then transfers the phosphoryl group to the conserved aspartate residue in the associated receiver domain. The conserved histidine and aspartate residues were both required for EspA function in vivo. Analysis of developmental gene expression and protein accumulation in
espA
mutants indicated that the expression of the A-signal-dependent
spi
gene was not affected but that the MrpC transcriptional regulator accumulated earlier, resulting in earlier expression of its target, the FruA transcriptional regulator. Early expression of FruA correlated with acceleration of both the aggregation and sporulation branches of the developmental program, as monitored by early methylation of the FrzCD chemosensory receptor and early expression of the sporulation-specific
dev
and Mxan_3227 (Ω7536) genes. These results show that EspA plays a key role in the timing of expression of genes necessary for progression of cells through the developmental program.
Mutations in
ampG
or
ampD
Affect Peptidoglycan Fragment Release from
Neisseria gonorrhoeae
Authors: Garcia Daniel L. , Dillard Joseph P.
Published: April 2008

Neisseria gonorrhoeae
releases peptidoglycan fragments during growth. The majority of the fragments released are peptidoglycan monomers, molecules known to increase pathogenesis through the induction of proinflammatory cytokines and responsible for the killing of ciliated epithelial cells. In other gram-negative bacteria such as
Escherichia coli
, these peptidoglycan fragments are efficiently degraded and recycled. Peptidoglycan fragments enter the cytoplasm from the periplasm via the AmpG permease. The amidase AmpD degrades peptidoglycan monomers by removing the disaccharide from the peptide. The disaccharide and the peptide are further degraded and are then used for new peptidoglycan synthesis or general metabolism. We examined the possibility that peptidoglycan fragment release by
N. gonorrhoeae
results from defects in peptidoglycan recycling. The deletion of
ampG
caused a large increase in peptidoglycan monomer release. Analysis of cytoplasmic material showed peptidoglycan fragments as recycling intermediates in the wild-type strain but absent from the
ampG
mutant. An
ampD
deletion reduced the release of all peptidoglycan fragments and nearly eliminated the release of free disaccharide. The
ampD
mutant also showed a large buildup of peptidoglycan monomers in the cytoplasm. The introduction of an
ampG
mutation in the
ampD
background restored peptidoglycan fragment release, indicating that events in the cytoplasm (metabolic or transcriptional regulation) affect peptidoglycan fragment release. The
ampD
mutant showed increased metabolism of exogenously added free disaccharide derived from peptidoglycan. These results demonstrate that
N. gonorrhoeae
has an active peptidoglycan recycling pathway and can regulate peptidoglycan fragment metabolism, dependent on the intracellular concentration of peptidoglycan fragments.
Glycine Betaine Uptake by the ProXVWZ ABC Transporter Contributes to the Ability ofMycobacterium tuberculosisTo Initiate Growth in Human Macrophages
Authors: Price Christopher T. D. , Bukka Archana , Cynamon Michael , Graham James E.
Published: April 2008

Mycobacterium tuberculosismaintains a large genetic capacity necessary for growth in different environments during infection and survival upon aerosol transmission to new hosts. Screening for bacterial RNAs produced in response to host interactions produced candidate lists where we notedproXVWZ, annotated as encoding a putative glycine betaine or proline transporter. As high surface-to-volume ratios make bacterial cells particularly vulnerable to changes in water availability, we investigated the contributions of this transporter to the ability ofM. tuberculosisto colonize macrophages. An H37RvproXVWZmutant was impaired for initial survival and intracellular growth and exhibited reduced growth at elevated medium osmolarity. This defect could be complemented by restoringproXVWZand was attributable to a failure to accumulate the compatible solute glycine betaine. We then demonstrated that ProXVWZ allowsM. tuberculosisto obtain betaine from host macrophages and thereby contributes to early steps in colonizing this niche.
Functional and Phylogenetic Characterization of Vaginolysin, the Human-Specific Cytolysin fromGardnerella vaginalis
Authors: Gelber Shari E. , Aguilar Jorge L. , Lewis Kanako L. T. , Ratner Adam J.
Published: April 2008

Pore-forming toxins are essential to the virulence of a wide variety of pathogenic bacteria.Gardnerella vaginalisis a bacterial species associated with bacterial vaginosis (BV) and its significant adverse sequelae, including preterm birth and acquisition of human immunodeficiency virus.G. vaginalismakes a protein toxin that generates host immune responses and has been hypothesized to be involved in the pathogenesis of BV. We demonstrate thatG. vaginalisproduces a toxin (vaginolysin [VLY]) that is a member of the cholesterol-dependent cytolysin (CDC) family, most closely related to intermedilysin fromStreptococcus intermedius. Consistent with this predicted relationship, VLY lyses target cells in a species-specific manner, dependent upon the complement regulatory molecule CD59. In addition to causing erythrocyte lysis, VLY activates the conserved epithelial p38 mitogen-activated protein kinase pathway and induces interleukin-8 production by human epithelial cells. Transfection of human CD59 into nonsusceptible cells renders them sensitive to VLY-mediated lysis. In addition, a single amino acid substitution in the VLY undecapeptide [VLY(P480W)] generates a toxoid that does not form pores, and introduction of the analogous proline residue into another CDC, pneumolysin, significantly decreases its cytolytic activity. Further investigation of the mechanism of action of VLY may improve understanding of the functions of the CDC family as well as diagnosis and therapy for BV.
Identification ofEscherichia coliYgaF as anl-2-Hydroxyglutarate Oxidase
Authors: Kalliri Efthalia , Mulrooney Scott B. , Hausinger Robert P.
Published: April 2008

YgaF, a protein of previously unknown function inEscherichia coli, was shown to possess noncovalently bound flavin adenine dinucleotide and to exhibitl-2-hydroxyglutarate oxidase activity. The inability of anaerobic, reduced enzyme to reverse the reaction by reducing the product α-ketoglutaric acid is explained by the very high reduction potential (+19 mV) of the bound cofactor. The likely role of this enzyme in the cell is to recover α-ketoglutarate mistakenly reduced by other enzymes or formed during growth on propionate. On the basis of the identified function, we propose that this gene be renamedlhgO.
Opr86 Is Essential for Viability and Is a Potential Candidate for a Protective Antigen against Biofilm Formation byPseudomonas aeruginosa
Authors: Tashiro Yosuke , Nomura Nobuhiko , Nakao Ryoma , Senpuku Hidenobu , Kariyama Reiko , Kumon Hiromi , Kosono Saori , Watanabe Haruo , Nakajima Toshiaki , Uchiyama Hiroo
Published: April 2008

Pseudomonas aeruginosais an opportunistic bacterial pathogen that is one of the most refractory to therapy when it forms biofilms in the airways of cystic fibrosis patients. To date, studies regarding the production of an immunogenic and protective antigen to inhibit biofilm formation byP. aeruginosahave been superficial. The previously uncharacterized outer membrane protein (OMP) Opr86 (PA3648) ofP. aeruginosais a member of the Omp85 family, of which homologs have been found in all gram-negative bacteria. Here we verify the availability of Opr86 as a protective antigen to inhibit biofilm formation byP. aeruginosaPAO1 and several other isolates. A mutant was constructed in which Opr86 expression could be switched on or off through atacpromoter-controlledopr86gene. The result, consistent with previous Omp85 studies, showed that Opr86 is essential for viability and plays a role in OMP assembly. Depletion of Opr86 resulted in streptococci-like morphological changes and liberation of excess membrane vesicles. A polyclonal antibody against Opr86 which showed reactivity to PAO1 cells was obtained. The antibody inhibited biofilm formation by PAO1 and the other clinical strains tested. Closer examination of early attachment revealed that cells treated with the antibody were unable to attach to the surface. Our data suggest that Opr86 is a critical OMP and a potential candidate as a protective antigen against biofilm formation byP. aeruginosa.
The risk for a cruciate ligament injury of the knee in adolescents and young adults: a population-based cohort study of 46 500 people with a 9 year follow-up
Authors: Parkkari J , Pasanen K , Mattila V M , Kannus P , Rimpelä A
Published: April 2008

Objectives:

The knee joint is the most common site for injury among younger people, the injury often resulting in expensive (surgical) treatment, long-term rehabilitation and permanent functional impairment and disability.

Methods:

We investigated the incidence and risk factors for a major knee-ligament injury in an adolescent Finnish population. A population-based cohort of 46 472 adolescents was followed for an average of 9 years. All patients hospitalised with the diagnosis of anterior or posterior cruciate ligament injury (ACL or PCL injury) were included in the analysis.

Results:

265 (0.6%) people (194 male and 71 female subjects) from the total cohort of 46 472 were treated for a cruciate ligament injury of the knee during the follow-up period, giving an injury incidence of 60.9 (95% CI 53.6 to 68.2) per 100 000 person-years. When the socioeconomic, health and lifestyle background variables were taken into account, the adjusted hazard ratio for a cruciate ligament injury of the knee was 8.5 (95% CI 4.3 to 16.4) for female and 4.0 (95% CI 2.7 to 6.1) for male subjects who participated in organised sports ⩾4 times/week.

Conclusions:

The general risk for a cruciate ligament injury of the knee is relatively low among adolescents and young adults, but participation in organised sports increases the risk significantly. The risk is especially high in active young women. Preventive measures should be adopted to decrease the short-term and long-term burden of these severe injuries.
Peer Review/Fair Review. How did A.V. Hill understand the VO2max and the "plateau phenomenon"? Still no clarity?
Authors: Noakes Timothy David
Published: April 2008

Introduction/Purpose:A recent editorial in Medicine and Science in Sports and Exercise concludes that the study of Hawkins and colleagues confirms “beyond any doubt the proposition of Hill and Lupton”. It is not clear which of Hill and Lupton’s propositions have been proved “beyond any doubt”.

Methods:A review of all the relevant publications of A.V. Hill and his colleagues.

Results:Hill and Lupton believed (i) that myocardial ischemia limits maximal exercise performance by inducing circulatory failure; ((ii) that a “governor” protects the ischemic heart by causing a “slowing of the circulation” during maximal exercise; ((iii) that the oxygen cost of running increases exponentially at speeds above 16km per hour; and ((iv) that humans reach their highest measurable oxygen consumption of about 4 litres per minute at that running speed. Hill and Lupton neither invented the concept of the “plateau phenomenon” not did they utilized this concept to establish that a “true” maximum oxygen consumption (VO2max) had been achieved. Nor did they measure cardiac output during exercise.

Conclusion:Accepting uncritically this modern interpretation of Hill and Luptons’ theory that the cardiac output limits maximal exercise performance whether or not the plateau phenomenon is present fails to answer the question first posed more than 20 years ago: What causes the termination of exercise when the “true” VO2max is achieved without the “plateau phenomenon”? According to the Hill and Lupton model, this cannot be because a limiting cardiac output has been reached. Since a majority of maximal exercise tests terminate in the absence of the “plateau phenomenon”, this is a seemingly an important question.
Comparison of aspects of smoking among the four histological types of lung cancer
Authors: Kenfield S A , Wei E K , Stampfer M J , Rosner B A , Colditz G A
Published: April 2008

Background:

The magnitude of the link between cigarette smoking and lung cancer may vary by histological type.

Methods:

We used polytomous logistic regression to evaluate whether aspects of smoking have different effects across four histological types in the Nurses’ Health Study.

Results:

From 1976 to 2002, we identified 1062 cases of lung cancer: squamous cell (n  201), small cell (n  236), adenocarcinoma (n  543) and large cell carcinoma (n  82), among 65 560 current or former smokers. Risk reduction after quitting ranged from an 8 reduction (relative risk (RR): 0.92, 95 CI 0.91 to 0.94) to a 17 reduction (RR: 0.83, 95 CI 0.80 to 0.86) per year for adenocarcinoma and small cell carcinoma, respectively, with a 9 reduction observed for large cell carcinoma and an 11 reduction observed for squamous cell carcinoma. The association of age at smoking initiation and former cigarette smoking was similar across types, while the association of smoking duration differed. The risk of adenocarcinoma increased by 6 per year of smoking, compared to 7 for large cell, 10 for squamous cell and 12 for small cell. The 6 difference between adenocarcinoma and small cell carcinoma is equivalent to a 3.2 to 9.7-fold increase in risk for 20 years of smoking.

Conclusions:

The effects of the number of cigarettes smoked per day and years since quitting smoking are different across the major types of lung cancer, which are fully appreciated at long durations of smoking and smoking cessation. Smoking prevention and cessation should continue to be the focus of public health efforts to reduce lung cancer incidence and mortality.
Zooplankton Community Structure in the North Sea and Northeast Atlantic: Development and Test of a Biological Model
Authors: Koslow J. Anthony
Published: April 2008

A simulation model was used to examine whether predatory interactions may regulate the size structure of marine zooplankton communities, as observed in many freshwater systems. Results of the model were consistent with the freshwater studies, such that large increases or decreases in planktivorous fish led to the dominance of small or large zooplankters, respectively. However, model predictions were not consistent with the recent decline in the northeastern Atlantic of most major elements of the pelagic zooplankton community along with North Sea herring and mackerel stocks. The overall decline of the pelagic community throughout this region indicates that zooplankton abundance may be regulated by physical forcing, and that these populations may be food- rather than predator-limited. Realistic ecological simulations of marine pelagic systems may require more complex two-layer models allowing for the effects of vertical migration, and with day–night differences in food availability and selectivity.
BURDEN OF FAMILY CARE-GIVERS AND THE RATIONING IN THE LONG-TERM CARE INSURANCE BENEFITS OF JAPAN
Authors: SUZUKI WATARU , OGURA SEIRITSU , IZUMIDA NOBUYUKI
Published: April 2008

Long-Term Care Insurance (LTCI), introduced in Japan in 2000, is rapidly turning into a system of rationed benefits due to financial difficulty. Based on our survey of 2,530 family care-givers and the Zarit Care-Giver Burden Index, we have examined how LTCI is affecting their subjective burden. We have found that, as Kishida and Tanigaki (2004) had shown, (i) insufficient provision of short-term stays, day services and home-helper services, as well as (ii) disruptive or antisocial behaviors of the elderly, increase the care-giver's burden. We then argue that (iii) these results establish the positive contribution of LTCI in the well-being of family care-givers, (iv) short-term stay is the most efficient service, followed by home-helper service, and day service is the least efficient, and we show that (v) J-ZBIC-8 works well enough for many practical purposes.
Group-based key predistribution for wireless sensor networks
Authors: Liu Donggang , Ning Peng , Du Wenliang
Published: April 2008

Many key predistribution techniques have been developed recently to establish pairwise keys between sensor nodes in wireless sensor networks. To further improve these schemes, researchers have also proposed to take advantage of the sensors' expected locations and discovered locations to help the predistribution of the keying materials. However, in many cases, it is very difficult to deploy sensor nodes at their expected locations or guarantee the correct location discovery at sensor nodes in hostile environments. In this article, a
group-based deployment model
is developed to improve key predistribution. In this model, sensor nodes are only required to be deployed in groups. The critical observation in the article is that
the sensor nodes in the same group are usually close to each other after deployment
. This deployment model is practical; it greatly simplifies the deployment of sensor nodes, while still providing an opportunity to improve key predistribution. Specifically, the article presents a novel framework for improving key predistribution using the group-based deployment knowledge. This framework does not require the knowledge of the sensors' expected or discovered locations and is thus suitable for applications where it is difficult to deploy the sensor nodes at their expected locations or correctly estimate the sensors' locations after deployment. To seek practical key predistribution schemes, the article presents two efficient instantiations of this framework, a
hash key-based scheme
and a
polynomial-based scheme
. The evaluation shows that these two schemes are efficient and effective for pairwise key establishment in sensor networks; they can achieve much better performance than the previous key predistribution schemes when the sensor nodes are deployed in groups.
First-order complete and computationally complete query languages for spatio-temporal databases
Authors: Geerts Floris , Haesevoets Sofie , Kuijpers Bart
Published: April 2008

We address a fundamental question concerning spatio-temporal database systems: “What are exactly spatio-temporal queries?” We define spatio-temporal queries to be computable mappings that are also
generic
, meaning that the result of a query may only depend to a limited extent on the actual internal representation of the spatio-temporal data. Genericity is defined as invariance under groups of geometric transformations that preserve certain characteristics of spatio-temporal data (e.g., collinearity, distance, velocity, acceleration, …). These groups depend on the notions that are relevant in particular spatio-temporal database applications. These transformations also have the distinctive property that they respect the monotone and unidirectional nature of time.

We investigate different genericity classes with respect to the constraint database model for spatio-temporal databases and we identify sound and complete languages for the first-order and the computable queries in these genericity classes. We distinguish between genericity determined by time-invariant transformations, genericity notions concerning physical quantities and genericity determined by time-dependent transformations.
A logic of nonmonotone inductive definitions
Authors: Denecker Marc , Ternovska Eugenia
Published: April 2008

Well-known principles of induction include monotone induction and different sorts of nonmonotone induction such as inflationary induction, induction over well-founded sets and iterated induction. In this work, we define a logic formalizing induction over well-founded sets and monotone and iterated induction. Just as the principle of positive induction has been formalized in FO(LFP), and the principle of inflationary induction has been formalized in FO(IFP), this article formalizes the principle of iterated induction in a new logic for Nonmonotone Inductive Definitions (ID-logic). The semantics of the logic is strongly influenced by the well-founded semantics of logic programming.

This article discusses the formalisation of different forms of (non-)monotone induction by the well-founded semantics and illustrates the use of the logic for formalizing mathematical and common-sense knowledge. To model different types of induction found in mathematics, we define several subclasses of definitions, and show that they are correctly formalized by the well-founded semantics. We also present translations into classical first or second order logic. We develop modularity and totality results and demonstrate their use to analyze and simplify complex definitions. We illustrate the use of the logic for temporal reasoning. The logic formally extends Logic Programming, Abductive Logic Programming and Datalog, and thus formalizes the view on these formalisms as logics of (generalized) inductive definitions.
Experiences with open overlays
Authors: Grace Paul , Hughes Danny , Porter Barry , Blair Gordon S. , Coulson Geoff , Taiani Francois
Published: April 2008

In order to provide an increasing number of functionalities and benefit from sophisticated and application-tailored services from the network, distributed applications are led to integrate an ever-widening range of networking technologies. As these applications become more complex, this requirement for 'network heterogeneity' is becoming a crucial issue in their development. Although progress has been made in the networking community in addressing such needs through the development of network overlays, we claim in this paper that the middleware community has been slow to integrate these advances into middleware architectures, and, hence, to provide the foundational bedrock for heterogeneous distributed applications. In response, we propose our 'open overlays' framework. This framework, which is part of a wider middleware architecture, accommodates 'overlay plug-ins', allows physical nodes to support multiple overlays, supports the stacking of overlays to create composite protocols, and adopts a declarative approach to configurable deployment and dynamic reconfigurability. The framework has been in development for a number of years and supports an extensive range of overlay plug-ins including popular protocols such as Chord and Pastry. We report on our experiences with the open overlays framework, evaluate it in detail, and illustrate its application in a detailed case study of network heterogeneity.
Irreducible polynomials and barker sequences
Authors: Borwein Peter , Kaltofen Erich , Mossinghoff Michael J.
Published: April 2008

A
Barker sequence
is a finite sequence
a
o
, ...,
a

n
-1

, each term ±1, for which every sum Σ

i
a
i
a
i
+k

with 0 <
k
<
n
is either 0, 1, or -- 1. It is widely conjectured that no Barker sequences of length
n
> 13 exist, and this conjecture has been verified for the case when
n
is odd. We show that in this case the problem can in fact be reduced to a question of irreducibility for a certain family of univariate polynomials: No Barker sequence of length 2
m
+ 1 exists if a particular integer polynomial of degree 4
m
is irreducible over Q. A proof of irreducibility for this family would thus provide a short, alternative proof that long Barker sequences of odd length do not exist. However, we also prove that the polynomials in question are always reducible modulo
p
, for every prime
p
.
PGB
Authors: Nabeshima Katsusuke
Published: April 2008

We present a new software package in the computer algebra system Risa/Asir [NT92], named PGB, for computing parametric Gröbner bases in various domains and related objects. A parametric Gröbner basis is a Gröbner basis for a polynomial ideal with parametric coefficients. One can download the package PGB from the following website. http://www.risc.uni-linz.ac.at/research/compalg/software/
Mast cell stabilization improves cardiac contractile function following hemorrhagic shock and resuscitation
Authors: Santone David J. , Shahani Rohan , Rubin Barry B. , Romaschin Alex D. , Lindsay Thomas F.
Published: April 2008

Hemorrhagic shock (HS) is associated with cardiac contractile dysfunction. Mast cell (MC) degranulation is hypothesized to mediate the cardiodepressant effect. Cardiac function was assessed after HS and resuscitation (HS/R) with the administration of the MC stabilizers to prevent MC degranulation. Anesthetized male Sprague-Dawley rats were randomized to sham-operated control or HS/R groups and underwent 60 min of HS followed by 2 h of resuscitated reperfusion. Animals in the HS/R groups were randomized to receive cromolyn (5 mg/kg), ketotifen (1 mg/kg), or saline 15 min before shock. Hearts were excised following HS or 2 h of reperfusion, and function was assessed on a Langendorff apparatus. A second group of randomized animals had serial blood samples taken to assess MC degranulation by quantifying levels of serum β-hexosaminidase. Hearts were excised at 0 min (before HS) and following 60 min of HS (before resuscitation) for a histological evaluation of MC density and degranulation. In vivo MC stabilization using ketotifen and cromolyn improved cardiac peak systolic pressure ( P < 0.05), contractility ( P < 0.05), and relaxation ( P < 0.05) compared with that of HS controls. Serum β-hexosaminidase increased during HS/R and was inhibited by MC stabilization ( P < 0.05). Degranulation was inhibited when assessed by histochemistry and immune fluorescence. The inhibition of MC degranulation can significantly improve cardiac function following HS/R.
Impaired capsaicin-induced relaxation of coronary arteries in a porcine model of the metabolic syndrome
Authors: Bratz Ian N. , Dick Gregory M. , Tune Johnathan D. , Edwards Jason M. , Neeb Zachary P. , Dincer U. Deniz , Sturek Michael
Published: April 2008

Recent studies implicate channels of the transient receptor potential vanilloid family (e.g., TRPV1) in regulating vascular tone; however, little is known about these channels in the coronary circulation. Furthermore, it is unclear whether metabolic syndrome alters the function and/or expression of TRPV1. We tested the hypothesis that TRPV1 mediates coronary vasodilation through endothelium-dependent mechanisms that are impaired by the metabolic syndrome. Studies were conducted on coronary arteries from lean and obese male Ossabaw miniature swine. In lean pigs, capsaicin, a TRPV1 agonist, relaxed arteries in a dose-dependent manner (EC50 = 116 ± 41 nM). Capsaicin-induced relaxation was blocked by the TRPV1 antagonist capsazepine, endothelial denudation, inhibition of nitric oxide synthase, and K+ channel antagonists. Capsaicin-induced relaxation was impaired in rings from pigs with metabolic syndrome (91 ± 4% vs. 51 ± 10% relaxation at 100 μM). TRPV1 immunoreactivity was prominent in coronary endothelial cells. TRPV1 protein expression was decreased 40 ± 11% in obese pigs. Capsaicin (100 μM) elicited divalent cation influx that was abolished in endothelial cells from obese pigs. These data indicate that TRPV1 channels are functionally expressed in the coronary circulation and mediate endothelium-dependent vasodilation through a mechanism involving nitric oxide and K+ channels. Impaired capsaicin-induced vasodilation in the metabolic syndrome is associated with decreased expression of TRPV1 and cation influx.
Angiotensin II type 1 receptor blocker preserves tolerance to ischemia-reperfusion injury in Dahl salt-sensitive rat heart
Authors: Matsuhisa Seiji , Otani Hajime , Okazaki Toru , Yamashita Koji , Akita Yuzo , Sato Daisuke , Moriguchi Akira , Imamura Hiroji , Iwasaka Toshiji
Published: April 2008

Oxidative stress is involved in the tolerance to ischemia-reperfusion (I/R) injury. Because angiotensin II type 1 receptor blockers (ARBs) inhibit oxidative stress, there is concern that ARBs abolish the tolerance to I/R injury. Dahl salt-sensitive (DS) hypertensive and salt-resistant (DR) normotensive rats received an antioxidant, 2-mercaptopropionylglycine (MPG), or an ARB, losartan, for 7 days. Losartan and MPG significantly inhibited oxidative stress as determined by tissue malondialdehyde + 4-hydroxynoneal and increased expression of inducible nitric oxide synthase (iNOS) in the DS rat heart. However, losartan but not MPG activated endothelial nitric oxide synthase (eNOS) as assessed by phosphorylation of eNOS on Ser1177. Infarct size after 30-min left coronary artery occlusion followed by 2-h reperfusion was comparable between DS and DR rat hearts. Although MPG and losartan had no effect on infarct size in the DR rat heart, MPG but not losartan significantly increased infarct size in the DS rat heart. A selective iNOS inhibitor, 1400W, increased infarct size in the DS rat heart, but it had no effect on infarct size in the losartan-treated DS rat heart. However, a nonselective NOS inhibitor, Nω-nitro-l-arginine methyl ester, increased infarct size in the losartan-treated DS rat heart. These results suggest that losartan preserves the tolerance to I/R injury by activating eNOS despite elimination of redox-sensitive upregulation of iNOS and iNOS-dependent cardioprotection in the DS rat heart.
PPARβ/δ agonist stimulates human lung carcinoma cell growth through inhibition of PTEN expression: the involvement of PI3K and NF-κB signals
Authors: Han ShouWei , Ritzenthaler Jeffrey D. , Zheng Ying , Roman Jesse
Published: April 2008

Recent studies suggest that activation of peroxisome proliferator-activated receptor β/δ (PPARβ/δ) promotes cancer cell survival. We previously demonstrated that a selective PPARβ/δ agonist, GW501516, stimulated human non-small cell lung carcinoma (NSCLC) cell growth. Here, we explore the mechanisms responsible for this effect. We show that GW501516 decreased phosphate and tensin homolog deleted on chromosome 10 (PTEN), a tumor suppressor known to decrease cell growth and induce apoptosis. Activation of PPARβ/δ and phosphatidylinositol 3-kinase (PI3K)/Akt signaling was associated with inhibition of PTEN. GW501516 increased NF-κB DNA binding activity and p65 protein expression through activation of PPARβ/δ and PI3K/Akt signals and enhanced the physical interactions between PPARβ/δ and p65 protein. Conversely, inhibition of PI3K and silencing of p65 by small RNA interference (siRNA) blocked the effect of GW501516 on PTEN expression and on NSCLC cell proliferation. GW501516 also inhibited IKBα protein expression. Silencing of IKBα enhanced the effect of GW501516 on PTEN protein expression and on cell proliferation. It also augmented the GW501516-induced complex formation of PPARβ/δ and p65 proteins. Overexpression of PTEN suppressed NSCLC cell growth and eliminated the effect of GW501516 on phosphorylation of Akt. Together, our observations suggest that GW501516 induces the proliferation of NSCLC cells by inhibiting the expression of PTEN through activation of PPARβ/δ, which stimulates PI3K/Akt and NF-κB signaling. Overexpression of PTEN overcomes this effect and unveils PPARβ/δ and PTEN as potential therapeutic targets in NSCLC.
The human zinc transporter SLC39A8 (Zip8) is critical in zinc-mediated cytoprotection in lung epithelia
Authors: Besecker Beth , Bao Shengying , Bohacova Barbara , Papp Audrey , Sadee Wolfgang , Knoell Daren L.
Published: April 2008

Zinc is an essential micronutrient and cytoprotectant involved in the host response to inflammatory stress. We tested whether zinc transporters, the critical regulators that maintain intracellular zinc concentrations, play a role in cell survival, particularly in lung epithelia, during inflammation. Initially, mRNA transcripts were quantitatively measured by RT-PCR for all known human zinc transporters, including 14 importers (SLC39A1–14) and 10 exporters (SLC30A1–10), in primary human lung epithelia obtained from multiple human donors and BEAS-2B cell cultures under baseline and TNF-α-stimulated conditions. While many zinc transporters were constitutively expressed, only SLC39A8 (Zip8) mRNA was strongly induced by TNF-α. Endogenous Zip8 protein was not routinely detected under baseline conditions. In sharp contrast, TNF-α induced the expression of a glycosylated protein that translocated to the plasma membrane and mitochondria. Increased Zip8 expression resulted in an increase in intracellular zinc content and coincided with cell survival in the presence of TNF-α. Inhibition of Zip8 expression using a short interfering RNA probe reduced cellular zinc content and impaired mitochondrial function in response to TNF-α, resulting in loss of cell viability. These data are the first to characterize human Zip8 and remarkably demonstrate that upregulation of Zip8 is sufficient to protect lung epithelia against TNF-α-induced cytotoxicity. We conclude that Zip8 is unique, relative to other Zip proteins, by functioning as an essential zinc importer at the onset of inflammation, thereby facilitating cytoprotection within the lung.
Pyrrolidine dithiocarbamate restores endothelial cell membrane integrity and attenuates monocrotaline-induced pulmonary artery hypertension
Authors: Huang Jing , Kaminski Pawel M. , Edwards John G. , Yeh Albert , Wolin Michael S. , Frishman William H. , Gewitz Michael H. , Mathew Rajamma
Published: April 2008

Monocrotaline (MCT)-induced pulmonary artery hypertension (PAH) in rats is preceded by an inflammatory response, progressive endothelial cell membrane disruption, reduction in the expression of caveolin-1, and reciprocal activation of STAT3 (PY-STAT3). Superoxide and NF-κB have been implicated in PAH. To evaluate the role of caveolin-1, PY-STAT3 activation, and superoxide in PAH, MCT-injected rats were treated daily with pyrrolidine dithiocarbamate (PDTC; starting on days 1, 3, and 14 × 2 wk), an inhibitor of inflammation and NF-κB activation. Hemodynamic data, the expression of inhibitory (I)-κBα, caveolin-1, and Tie2 (a membrane protein), activation of PY-STAT3 and NF-κB, and superoxide chemiluminescence were examined. Rats developed progressive PAH at 2 wk post-MCT. There was progressive reduction in the expression of caveolin-1, Tie2, and activation of PY-STAT3 in the lungs. Reduction in I-κBα expression was present at 2 and 4 wk post-MCT. Superoxide chemiluminescence and NF-κB activation were observed only at 2 wk post-MCT and both decreased by 4 wk post-MCT despite progressive PAH. PDTC (starting on days 1 and 3) rescued caveolin-1 and Tie2, reversed MCT-induced PY-STAT3 activation, and attenuated PAH. In addition, PDTC restored I-κBα expression and reduced superoxide chemiluminescence at 2 wk but did not inhibit NF-κB activation despite attenuation of PAH. PDTC had no effect on established PAH. Increased superoxide chemiluminescence and NF-κB activation appear to be a transient phenomenon in the MCT model. Thus the disruption of endothelial cell membrane integrity resulting in caveolin-1 loss and reciprocal activation of PY-STAT3 plays a key role in the MCT-induced PAH.
Impact of the FcγII-receptor on quartz uptake and inflammatory response by alveolar macrophages
Authors: Haberzettl Petra , Schins Roel P. F. , Höhr Doris , Wilhelmi Verena , Borm Paul J. A. , Albrecht Catrin
Published: April 2008

The inflammatory response following particle inhalation is described as a key event in the development of lung diseases, e.g., fibrosis and cancer. The essential role of alveolar macrophages (AM) in the pathogenicity of particles through their functions in lung clearance and mediation of inflammation is well known. However, the molecular mechanisms and direct consequences of particle uptake are still unclear. Inhibition of different classic phagocytosis receptors by flow cytometry shows a reduction of the dose-dependent quartz particle (DQ12) uptake in the rat AM cell line NR8383. Thereby the strongest inhibitory effect was observed by blocking the FcγII-receptor (FcγII-R). Fluorescence immunocytochemistry, demonstrating FcγII-R clustering at particle binding sites as well as transmission electron microscopy, visualizing zippering mechanism-like morphological changes, confirmed the role of the FcγII-R in DQ12 phagocytosis. FcγII-R participation in DQ12 uptake was further strengthened by the quartz-induced activation of the Src-kinase Lyn, the phospho-tyrosine kinases Syk (spleen tyrosine kinase) and PI3K (phosphatidylinositol 3-kinase), as shown by Western blotting. Activation of the small GTPases Rac1 and Cdc42, shown by immunoprecipitation, as well as inhibition of tyrosine kinases, GTPases, or Rac1 provided further support for the role of the FcγII-R. Consistent with the uptake results, FcγII-R activation with its specific ligand caused a similar generation of reactive oxygen species and TNF-α release as observed after treatment with DQ12. In conclusion, our results indicate a major role of FcγII-R and its downstream signaling cascade in the phagocytosis of quartz particles in AM as well as in the associated generation and release of inflammatory mediators.
RAGE: developmental expression and positive feedback regulation by Egr-1 during cigarette smoke exposure in pulmonary epithelial cells
Authors: Reynolds Paul R. , Kasteler Stephen D. , Cosio Manuel G. , Sturrock Anne , Huecksteadt Tom , Hoidal John R.
Published: April 2008

The receptor for advanced glycation end-products (RAGE) is a member of the immunoglobin superfamily of multiligand receptors. Following ligand binding, mechanisms associated with host defense, tissue remodeling, and inflammation are activated. RAGE is highly expressed in pulmonary epithelium transitioning from alveolar type (AT) II to ATI cells and is upregulated in the presence of ligand; however, the regulation and function of RAGE during development are less clear. Herein, immunohistochemistry demonstrated a temporal-spatial pattern of RAGE expression in pulmonary epithelial cells from embryonic day 17.5 to postnatal day 10. Cotransfection experiments revealed that the mouse RAGE promoter was activated by early growth response gene 1 (Egr-1) and inhibited by thyroid transcription factor-1 (TTF-1) via interaction with specific regulatory elements. A rat ATI cell line (R3/1) with endogenous RAGE expression also differentially regulated RAGE when transfected with TTF-1 or Egr-1. Because Egr-1 is markedly induced in pulmonary epithelial cells exposed to cigarette smoke extract (CSE; Reynolds PR, Hoidal JR. Am J Respir Cell Mol Biol 35: 314–319, 2006.), we sought to investigate RAGE induction by CSE. Employing RT-PCR and Western blotting, RAGE and common ligands (amphoterin and S100A12) were upregulated in epithelial (R3/1 and A549) and macrophage (RAW) cell lines following exposure to CSE. Immunostaining for RAGE in cells similarly exposed and in lungs from mice exposed to cigarette smoke for 6 mo revealed elevated RAGE expression in pulmonary epithelium. After the addition of glyoxylated BSA, an advanced glycation end-product that binds RAGE, real-time RT-PCR detected a 200-fold increase in Egr-1. These results indicate that Egr-1 regulates RAGE expression during development and the likelihood of positive feedback involving Egr-1 and RAGE in cigarette smoke-related disease.
Endoplasmic reticulum stress in alveolar epithelial cells is prominent in IPF: association with altered surfactant protein processing and herpesvirus infection
Authors: Lawson William E. , Crossno Peter F. , Polosukhin Vasiliy V. , Roldan Juan , Cheng Dong-Sheng , Lane Kirk B. , Blackwell Thomas R. , Xu Carol , Markin Cheryl , Ware Lorraine B. , Miller Geraldine G. , Loyd James E. , Blackwell Timothy S.
Published: April 2008

Recent evidence suggests that dysfunctional type II alveolar epithelial cells (AECs) contribute to the pathogenesis of idiopathic pulmonary fibrosis (IPF). Based on the hypothesis that disease-causing mutations in surfactant protein C ( SFTPC) provide an important paradigm for studying IPF, we investigated a potential mechanism of AEC dysfunction suggested to result from mutant SFTPC expression: induction of endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). We evaluated biopsies from 23 IPF patients (including 3 family members with L188Q SFTPC mutations, 10 individuals with familial interstitial pneumonia without SFTPC mutations, and 10 individuals with sporadic IPF) and sections from 10 control lungs. After demonstrating UPR activation in cultured A549 cells expressing mutant SFTPC, we identified prominent expression of UPR markers in AECs in the lungs of patients with SFTPC mutation-associated fibrosis. In individuals with familial interstitial pneumonia without SFTPC mutations and patients with sporadic IPF, we also found UPR activation selectively in AECs lining areas of fibrotic remodeling. Because herpesviruses are found frequently in IPF lungs and can induce ER stress, we investigated expression of viral proteins in lung biopsies. Herpesvirus protein expression was found in AECs from 15/23 IPF patients and colocalized with UPR markers in AECs from these patients. ER stress and UPR activation are found in the alveolar epithelium in patients with IPF and could contribute to disease progression. Activation of these pathways may result from altered surfactant protein processing or chronic herpesvirus infection.