bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of Novel and Highly Diverse Acid-Tolerant Denitrifiers with N
2
O Fluxes of an Acidic Fen
Authors: Palmer Katharina , Drake Harold L. , Horn Marcus A.
Published: December 2009

Wetlands are sources of denitrification-derived nitrous oxide (N
2
O). Thus, the denitrifier community of an N
2
O-emitting fen (pH 4.7 to 5.2) was investigated. N
2
O was produced and consumed to subatmospheric concentrations in unsupplemented anoxic soil microcosms. Total cell counts and most probable numbers of denitrifiers approximated 10
11
cells·g
DW
−1
(where DW is dry weight) and 10
8
cells·g
DW
−1
, respectively, in both 0- to 10-cm and 30- to 40-cm depths. Despite this uniformity, depth-related maximum reaction rate (
v
max
) values for denitrification in anoxic microcosms ranged from 1 to 24 and −19 to −105 nmol N
2
O h
−1
· g
DW
−1
, with maximal values occurring in the upper soil layers. Denitrification was enhanced by substrates that might be formed via fermentation in anoxic microzones of soil. N
2
O approximated 40% of total nitrogenous gases produced at
in situ
pH, which was likewise the optimal pH for denitrification. Gene libraries of
narG
and
nosZ
(encoding nitrate reductase and nitrous oxide reductase, respectively) from fen soil DNA yielded 15 and 18 species-level operational taxonomic units, respectively, many of which displayed phylogenetic novelty and were not closely related to cultured organisms. Although statistical analyses of
narG
and
nosZ
sequences indicated that the upper 20 cm of soil contained the highest denitrifier diversity and species richness, terminal restriction fragment length polymorphism analyses of
narG
and
nosZ
revealed only minor differences in denitrifier community composition from a soil depth of 0 to 40 cm. The collective data indicate that the regional fen harbors novel, highly diverse, acid-tolerant denitrifier communities capable of complete denitrification and consumption of atmospheric N
2
O at
in situ
pH.
Functional Role of
Bradyrhizobium japonicum
Trehalose Biosynthesis and Metabolism Genes during Physiological Stress and Nodulation
Authors: Sugawara Masayuki , Cytryn Eddie J. , Sadowsky Michael J.
Published: December 2009

Trehalose, a disaccharide accumulated by many microorganisms, acts as a protectant during periods of physiological stress, such as salinity and desiccation. Previous studies reported that the trehalose biosynthetic genes (
otsA
,
treS
, and
treY
) in
Bradyrhizobium japonicum
were induced by salinity and desiccation stresses. Functional mutational analyses indicated that disruption of
otsA
decreased trehalose accumulation in cells and that an
otsA treY
double mutant accumulated an extremely low level of trehalose. In contrast, trehalose accumulated to a greater extent in a
treS
mutant, and maltose levels decreased relative to that seen with the wild-type strain. Mutant strains lacking the OtsA pathway, including the single, double, and triple Δ
otsA
, Δ
otsA
Δ
treS
and Δ
otsA
Δ
treY
, and Δ
otsA
Δ
treS
Δ
treY
mutants, were inhibited for growth on 60 mM NaCl. While mutants lacking functional OtsAB and TreYZ pathways failed to grow on complex medium containing 60 mM NaCl, there was no difference in the viability of the double mutant strain when cells were grown under conditions of desiccation stress. In contrast, mutants lacking a functional TreS pathway were less tolerant of desiccation stress than the wild-type strain. Soybean plants inoculated with mutants lacking the OtsAB and TreYZ pathways produced fewer mature nodules and a greater number of immature nodules relative to those produced by the wild-type strain. Taken together, results of these studies indicate that stress-induced trehalose biosynthesis in
B. japonicum
is due mainly to the OtsAB pathway and that the TreS pathway is likely involved in the degradation of trehalose to maltose. Trehalose accumulation in
B. japonicum
enhances survival under conditions of salinity stress and plays a role in the development of symbiotic nitrogen-fixing root nodules on soybean plants.
Thermococcus kodakarensis
Genetics: TK1827-Encoded β-Glycosidase, New Positive-Selection Protocol, and Targeted and Repetitive Deletion Technology
Authors: Santangelo Thomas J. , Čuboňová L'ubomíra , Reeve John N.
Published: December 2009

Inactivation of TK1761, the reporter gene established for
Thermococcus kodakarensis
, revealed the presence of a second β-glycosidase that we have identified as the product of TK1827. This enzyme (pTK1827) has been purified and shown to hydrolyze glucopyranoside but not mannopyranoside, have optimal activity at 95°C and from pH 8 to 9.5, and have a functional half-life of ∼7 min at 100°C. To generate a strain with both TK1761 and TK1827 deleted, a new selection/counterselection protocol has been developed, and the levels of β-glycosidase activity in
T. kodakarensis
strains with TK1761 and/or TK1827 deleted and with these genes expressed from heterologous promoters are described. Genetic tools and strains have been developed that extend the use of this selection/counterselection procedure to delete any nonessential gene from the
T. kodakarensis
chromosome. Using this technology, TK0149 was deleted to obtain an agmatine auxotroph that grows on nutrient-rich medium only when agmatine is added. Transformants can therefore be selected rapidly, and replicating plasmids can be maintained in this strain growing in rich medium by complementation of the TK0149 deletion.
Candida albicans
PEP12
Is Required for Biofilm Integrity and
In Vivo
Virulence
Authors: Palanisamy Suresh K. A. , Ramirez Melissa A. , Lorenz Michael , Lee Samuel A.
Published: December 2009

To investigate the role of the prevacuolar secretion pathway in biofilm formation and virulence in
Candida albicans
, we cloned and analyzed the
C. albicans
homolog of the
Saccharomyces cerevisiae
prevacuolar trafficking gene
PEP12
.
C. albicans
PEP12
encodes a deduced t-SNARE that is 28% identical to
S. cerevisiae
Pep12p, and plasmids bearing
C. albicans
PEP12
complemented the abnormal vacuolar morphology and temperature-sensitive growth of an
S. cerevisiae
pep12
null mutant. The
C. albicans
pep12
Δ null mutant was defective in endocytosis and vacuolar acidification and accumulated 40- to 60-nm cytoplasmic vesicles near the plasma membrane. Secretory defects included increased extracellular proteolytic activity and absent lipolytic activity. The
pep12
Δ null mutant was more sensitive to cell wall stresses and antifungal agents than the isogenic complemented strain or the control strain DAY185. Notably, the biofilm formed by the
pep12
Δ mutant was reduced in overall mass and fragmented completely upon the slightest disturbance. The
pep12
Δ mutant was markedly reduced in virulence in an
in vitro
macrophage infection model and an
in vivo
mouse model of disseminated candidiasis. These results suggest that
C. albicans
PEP12
plays a key role in biofilm integrity and
in vivo
virulence.
Glycine Betaine Biosynthesized from Glycine Provides an Osmolyte for Cell Growth and Spore Germination during Osmotic Stress in
Myxococcus xanthus
Authors: Kimura Yoshio , Kawasaki Shinji , Yoshimoto Hinae , Takegawa Kaoru
Published: December 2009

Glycine sarcosine methyltransferase (Gsm) and sarcosine dimethylglycine methyltransferase (Sdm) catalyze glycine betaine synthesis from glycine. Disruption of the
M. xanthus gsmA
(MXAN 7068) or
sdmA
(MXAN 3190) gene, encoding Gsm or Sdm homologue proteins, respectively, generated mutants that exhibited a longer lag period of growth and delayed spore germination under osmostress.
Evidence for Rare Capsular Switching in
Streptococcus agalactiae
Authors: Martins Elisabete Raquel , Melo-Cristino José , Ramirez Mário
Published: December 2009

The polysaccharide capsule is a major antigenic factor in
Streptococcus agalactiae
(Lancefield group B streptococcus [GBS]). Previous observations suggest that exchange of capsular loci is likely to occur rather frequently in GBS, even though GBS is not known to be naturally transformable. We sought to identify and characterize putative capsular switching events, by means of a combination of phenotypic and genotypic methods, including pulsed-field gel electrophoretic profiling, multilocus sequence typing, and surface protein and pilus gene profiling. We show that capsular switching by horizontal gene transfer is not as frequent as previously suggested. Serotyping errors may be the main reason behind the overestimation of capsule switching, since phenotypic techniques are prone to errors of interpretation. The identified putative capsular transformants involved the acquisition of the entire capsular locus and were not restricted to the serotype-specific central genes, the previously suggested main mechanism underlying capsular switching. Our data, while questioning the frequency of capsular switching, provide clear evidence for
in vivo
capsular transformation in
S. agalactiae
, which may be of critical importance in planning future vaccination strategies against this pathogen.
Characterization of a Gene Family of Outer Membrane Proteins (
ropB
) in
Rhizobium leguminosarum
bv.
viciae
VF39SM and the Role of the Sensor Kinase ChvG in Their Regulation
Authors: Foreman Dallas L. , Vanderlinde Elizabeth M. , Bay Denise C. , Yost Christopher K.
Published: December 2009

The outer membrane of Gram-negative bacteria represents the interface between the bacterium and its external environment. It has a critical role as a protective barrier against harmful substances and is also important in host-bacteria interactions representing the initial physical point of contact between the host cell and bacterial cell. RopB is a previously identified outer membrane protein from
Rhizobium leguminosarum
bv.
viciae
that is present in free-living cells but absent in bacteroids (H. P. Roest, I. H. Mulders, C. A. Wijffelman, and B. J. Lugtenberg, Mol. Plant Microbe Interact. 8:576-583, 1995). The functions of RopB and the molecular mechanisms of
ropB
gene regulation have remained unknown. We identified and cloned
ropB
and two homologs (
ropB2
and
ropB3
) from the
R. leguminosarum
VF39SM genome. Reporter gene fusions indicated that the expression of
ropB
was 8-fold higher when cells were grown in complex media than when they were grown in minimal media, while
ropB3
expression was constitutively expressed at low levels in both complex and minimal media. Expression of
ropB2
was negligible under all conditions tested. The use of minimal media supplemented with various sources of peptides resulted in a 5-fold increase in
ropB
expression. An increase in
ropB
expression in the presence of peptides was not observed in a
chvG
mutant background, indicating a role for the sensor kinase in regulating
ropB
expression. Each member of the
ropB
gene family was mutated using insertional mutagenesis, and the mutants were assayed for susceptibility to antimicrobial agents and symbiotic phenotypes. All mutants formed effective nodules on pea plants, and gene expression for each
rop
gene in bacteroids was negligible. The functions of
ropB2
and
ropB3
remain cryptic, while the
ropB
mutant had an increased sensitivity to detergents, hydrophobic antibiotics, and weak organic acids, suggesting a role for RopB in outer membrane stability.
The El Tor Biotype of
Vibrio cholerae
Exhibits a Growth Advantage in the Stationary Phase in Mixed Cultures with the Classical Biotype
Authors: Pradhan Subhra , Baidya Amit K. , Ghosh Amalendu , Paul Kalidas , Chowdhury Rukhsana
Published: December 2009

Vibrio cholerae
strains of the O1 serogroup that typically cause epidemic cholera can be classified into two biotypes, classical and El Tor. The El Tor biotype emerged in 1961 and subsequently displaced the classical biotype as a cause of cholera throughout the world. In this study we demonstrate that when strains of the El Tor and classical biotypes were cocultured in standard LB medium, the El Tor strains clearly had a competitive growth advantage over the classical biotype starting from the late stationary phase and could eventually take over the population. The classical biotype produces extracellular protease(s) in the stationary phase, and the amounts of amino acids and small peptides in the late stationary and death phase culture filtrates of the classical biotype were higher than those in the corresponding culture filtrates of the El Tor biotype. The El Tor biotype cells could utilize the amino acids more efficiently than the classical biotype under the alkaline pH of the stationary phase cultures but not in medium buffered to neutral pH. The growth advantage of the El Tor biotype was also observed
in vivo
using the ligated rabbit ileal loop and infant mouse animal models.
Discovery and Characterization of Cadherin Domains in
Saccharophagus degradans
2-40
Authors: Fraiberg Milana , Borovok Ilya , Weiner Ronald M. , Lamed Raphael
Published: December 2009

Saccharophagus degradans
strain 2-40 is a prominent member of newly discovered group of marine and estuarine bacteria that recycle complex polysaccharides. The
S. degradans
2-40 genome codes for 15 extraordinary long polypeptides, ranging from 274 to 1,600 kDa. Five of these contain at least 52 cadherin (CA) and cadherin-like (CADG) domains, the types of which were reported to bind calcium ions and mediate protein/protein interactions in metazoan systems. In order to evaluate adhesive features of these domains, recombinant CA doublet domains (two neighboring domains) from CabC (Sde_3323) and recombinant CADG doublet domains from CabD (Sde_0798) were examined qualitatively and quantitatively for homophilic and heterophilic interactions. In addition, CA and CADG doublet domains were tested for adhesion to the surface of
S. degradans
2-40. Results showed obvious homophilic and heterophilic, calcium ion-dependent interactions between CA and CADG doublet domains. Likewise, CA and CADG doublet domains adhered to the
S. degradans
2-40 surface of cells that were grown on xylan from birch wood or pectin, respectively, as a sole carbon source. This research shows for the first time that bacterial cadherin homophilic and heterophilic interactions may be similar in their nature to cadherin domains from metazoan lineages. We hypothesize that
S. degradans
2-40 cadherin and cadherin-like multiple domains contribute to protein-protein interactions that may mediate cell-cell contact in the marine environment.
The Nonphosphorylative Entner-Doudoroff Pathway in the Thermoacidophilic Euryarchaeon
Picrophilus torridus
Involves a Novel 2-Keto-3-Deoxygluconate- Specific Aldolase
Authors: Reher Matthias , Fuhrer Tobias , Bott Michael , Schönheit Peter
Published: December 2009

The pathway of glucose degradation in the thermoacidophilic euryarchaeon
Picrophilus torridus
has been studied by
in vivo
labeling experiments and enzyme analyses. After growth of
P. torridus
in the presence of [1-
13
C]- and [3-
13
C]glucose, the label was found only in the C-1 and C-3 positions, respectively, of the proteinogenic amino acid alanine, indicating the exclusive operation of an Entner-Doudoroff (ED)-type pathway
in vivo
. Cell extracts of
P. torridus
contained all enzyme activities of a nonphosphorylative ED pathway, which were not induced by glucose. Two key enzymes, gluconate dehydratase (GAD) and a novel 2-keto-3-deoxygluconate (KDG)-specific aldolase (KDGA), were characterized. GAD is a homooctamer of 44-kDa subunits, encoded by Pto0485. KDG aldolase, KDGA, is a homotetramer of 32-kDa subunits. This enzyme was highly specific for KDG with up to 2,000-fold-higher catalytic efficiency compared to 2-keto-3-deoxy-6-phosphogluconate (KDPG) and thus differs from the bifunctional KDG/KDPG aldolase, KD(P)GA of crenarchaea catalyzing the conversion of both KDG and KDPG with a preference for KDPG. The KDGA-encoding gene,
kdgA
, was identified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) as Pto1279, and the correct translation start codon, an ATG 24 bp upstream of the annotated start codon of Pto1279, was determined by N-terminal amino acid analysis. The
kdgA
gene was functionally overexpressed in
Escherichia coli
. Phylogenetic analysis revealed that KDGA is only distantly related to KD(P)GA, both enzymes forming separate families within the dihydrodipicolinate synthase superfamily. From the data we conclude that
P. torridus
degrades glucose via a strictly nonphosphorylative ED pathway with a novel KDG-specific aldolase, thus excluding the operation of the branched ED pathway involving a bifunctional KD(P)GA as a key enzyme.
Escherichia coliRNase R Has Dual Activities, Helicase and RNase
Authors: Awano Naoki , Rajagopal Vaishnavi , Arbing Mark , Patel Smita , Hunt John , Inouye Masayori , Phadtare Sangita
Published: December 2009

InEscherichia coli, the cold shock response occurs when there is a temperature downshift from 37°C to 15°C, and this response is characterized by induction of several cold shock proteins, including the DEAD-box helicase CsdA, during the acclimation phase. CsdA is involved in a variety of cellular processes. Our previous studies showed that the helicase activity of CsdA is critical for its function in cold shock acclimation of cells and that the only proteins that were able to complement its function were another helicase, RhlE, an RNA chaperone, CspA, and a cold-inducible exoribonuclease, RNase R. Interestingly, other major 3′-to-5′ processing exoribonucleases ofE. coli, such as polynucleotide phosphorylase and RNase II, cannot complement the cold shock function of CsdA. Here we carried out a domain analysis of RNase R and showed that this protein has two distinct activities, RNase and helicase, which are independent of each other and are due to different domains. Mutant RNase R proteins that lack the RNase activity but exhibit the helicase activity were able to complement the cold shock function of CsdA, suggesting that only the helicase activity of RNase R is essential for complementation of the cold shock function of CsdA. We also observed thatin vivodeletion of the two cold shock domains resulted in a loss of the ability of RNase R to complement the cold shock function of CsdA. We further demonstrated that RNase R exhibits helicase activityin vitroindependent of its RNase activity. Our results shed light on the unique properties of RNase R and how it is distinct from other exoribonucleases inE. coli.
Genome Diversity ofPseudomonas aeruginosaPAO1 Laboratory Strains
Authors: Klockgether Jens , Munder Antje , Neugebauer Jens , Davenport Colin F. , Stanke Frauke , Larbig Karen D. , Heeb Stephan , Schöck Ulrike , Pohl Thomas M. , Wiehlmann Lutz , Tümmler Burkhard
Published: December 2009

Pseudomonas aeruginosaPAO1 is the most commonly used strain for research on this ubiquitous and metabolically versatile opportunistic pathogen. Strain PAO1, a derivative of the original Australian PAO isolate, has been distributed worldwide to laboratories and strain collections. Over decades discordant phenotypes of PAO1 sublines have emerged. Taking the existing PAO1-UW genome sequence (named after the University of Washington, which led the sequencing project) as a blueprint, the genome sequences of reference strains MPAO1 and PAO1-DSM (stored at the German Collection for Microorganisms and Cell Cultures [DSMZ]) were resolved by physical mapping and deep short read sequencing-by-synthesis. MPAO1 has been the source of near-saturation libraries of transposon insertion mutants, and PAO1-DSM is identical in its SpeI-DpnI restriction map with the original isolate. The major genomic differences of MPAO1 and PAO1-DSM in comparison to PAO1-UW are the lack of a large inversion, a duplication of a mobile 12-kb prophage region carrying a distinct integrase and protein phosphatases or kinases, deletions of 3 to 1,006 bp in size, and at least 39 single-nucleotide substitutions, 17 of which affect protein sequences. The PAO1 sublines differed in their ability to cope with nutrient limitation and their virulence in an acute murine airway infection model. Subline PAO1-DSM outnumbered the two other sublines in late stationary growth phase. In conclusion,P. aeruginosaPAO1 shows an ongoing microevolution of genotype and phenotype that jeopardizes the reproducibility of research. High-throughput genome resequencing will resolve more cases and could become a proper quality control for strain collections.
Mechanisms underlying hypothermia-induced cardiac contractile dysfunction
Authors: Han Young-Soo , Tveita Torkjel , Prakash Y. S. , Sieck Gary C.
Published: December 2009

Rewarming patients after profound hypothermia may result in acute heart failure and high mortality (50–80%). However, the underlying pathophysiological mechanisms are largely unknown. We characterized cardiac contractile function in the temperature range of 15–30°C by measuring the intracellular Ca2+concentration ([Ca2+]i) and twitch force in intact left ventricular rat papillary muscles. Muscle preparations were loaded with fura-2 AM and electrically stimulated during cooling at 15°C for 1.5 h before being rewarmed to the baseline temperature of 30°C. After hypothermia/rewarming, peak twitch force decreased by 30–40%, but [Ca2+]iwas not significantly altered. In addition, we assessed the maximal Ca2+-activated force (Fmax) and Ca2+sensitivity of force in skinned papillary muscle fibers. Fmaxwas decreased by ∼30%, whereas the pCa required for 50% of Fmaxwas reduced by ∼0.14. In rewarmed papillary muscle, both total cardiac troponin I (cTnI) phosphorylation and PKA-mediated cTnI phosphorylation at Ser23/24 were significantly increased compared with controls. We conclude that after hypothermia/rewarming, myocardial contractility is significantly reduced, as evidenced by reduced twitch force and Fmax. The reduced myocardial contractility is attributed to decreased Ca2+sensitivity of force rather than [Ca2+]iitself, resulting from increased cTnI phosphorylation.
Calmodulin kinase II is required for angiotensin II-mediated vascular smooth muscle hypertrophy
Authors: Li Hui , Li Weiwei , Gupta Arun K. , Mohler Peter J. , Anderson Mark E. , Grumbach Isabella M.
Published: December 2009

Despite our understanding that medial smooth muscle hypertrophy is a central feature of vascular remodeling, the molecular pathways underlying this pathology are still not well understood. Work over the past decade has illustrated a potential role for the multifunctional calmodulin-dependent kinase CaMKII in smooth muscle cell contraction, growth, and migration. Here we demonstrate that CaMKII is enriched in vascular smooth muscle (VSM) and that CaMKII inhibition blocks ANG II-dependent VSM cell hypertrophy in vitro and in vivo. Specifically, systemic CaMKII inhibition with KN-93 prevented ANG II-mediated hypertension and medial hypertrophy in vivo. Adenoviral transduction with the CaMKII peptide inhibitor CaMKIIN abrogated ANG II-induced VSM hypertrophy in vitro, which was augmented by overexpression of CaMKII-δ2. Finally, we identify the downstream signaling components critical for ANG II- and CaMKII-mediated VSM hypertrophy. Specifically, we demonstrate that CaMKII induces VSM hypertrophy by regulating histone deacetylase 4 (HDAC4) activity, thereby stimulating activity of the hypertrophic transcription factor MEF2. MEF2 transcription is activated by ANG II in vivo and abrogated by the CaMKII inhibitor KN-93. Together, our studies identify a complete pathway for ANG II-triggered arterial VSM hypertrophy and identify new potential therapeutic targets for chronic human hypertension.
Gene expression profile in flow-associated pulmonary arterial hypertension with neointimal lesions
Authors: van Albada Mirjam E. , Bartelds Beatrijs , Wijnberg Hans , Mohaupt Saffloer , Dickinson Michael G. , Schoemaker Regien G. , Kooi Krista , Gerbens Frans , Berger Rolf M. F.
Published: December 2009

Pulmonary arterial hypertension (PAH) is a pulmonary angioproliferative disease with high morbidity and mortality, characterized by a typical pattern of pulmonary vascular remodeling including neointimal lesions. In congenital heart disease, increased pulmonary blood flow has appeared to be a key mediator in the development of these characteristic lesions, but the molecular mechanisms underlying the pulmonary vascular lesions are largely unknown. We employed a rat model of flow-associated PAH, which induced specific pulmonary neointimal lesions. We identified gene expression profiles in rats specifically related to the addition of increased pulmonary blood flow to monocrotaline and the associated occurrence of neointimal lesions. Increased pulmonary blood flow induced the expression of the transcription factors activating transcription factor-3 (ATF3) and early growth response factor-1 (EGR-1), for which presence was confirmed in neointimal lesions. Monocrotaline alone induced increased numbers of activated mast cells and their products. We further identified molecular pathways that may be involved in treatment with the prostacyclin analog iloprost, a vasoactive compound with clinically beneficial effects in patients with PAH, which were similar to pathways described in samples from patient studies. These pathways, associated with the development of angioproliferative lesions as well as with the response to therapy in PAH, may provide new therapeutic targets.
Functional importance of the NH2-terminal insertion sequence of lung surfactant protein B
Authors: Frey Shelli L. , Pocivavsek Luka , Waring Alan J. , Walther Frans J. , Hernandez-Juviel Jose M. , Ruchala Piotr , Lee Ka Yee C.
Published: December 2009

Lung surfactant protein B (SP-B) is required for proper surface activity of pulmonary surfactant. In model lung surfactant lipid systems composed of saturated and unsaturated lipids, the unsaturated lipids are removed from the film at high compression. It is thought that SP-B helps anchor these lipids closely to the monolayer in three-dimensional cylindrical structures termed “nanosilos” seen by atomic force microscopy imaging of deposited monolayers at high surface pressures. Here we explore the role of the SP-B NH2terminus in the formation and stability of these cylindrical structures, specifically the distribution of lipid stack height, width, and density with four SP-B truncation peptides: SP-B 1–25, SP-B 9–25, SP-B 11–25, and SP-B 1–25Nflex (prolines 2 and 4 substituted with alanine). The first nine amino acids, termed the insertion sequence and the interface seeking tryptophan residue 9, are shown to stabilize the formation of nanosilos while an increase in the insertion sequence flexibility (SP-B 1–25Nflex) may improve peptide functionality. This provides a functional understanding of the insertion sequence beyond anchoring the protein to the two-dimensional membrane lining the lung, as it also stabilizes formation of nanosilos, creating reversible repositories for fluid lipids at high compression. In lavaged, surfactant-deficient rats, instillation of a mixture of SP-B 1–25 (as a monomer or dimer) and synthetic lung lavage lipids quickly improved oxygenation and dynamic compliance, whereas SP-B 11–25 surfactants showed oxygenation and dynamic compliance values similar to that of lipids alone, demonstrating a positive correlation between formation of stable, but reversible, nanosilos and in vivo efficacy.
HFE-Related Hemochromatosis: The Haptoglobin 2-2 Type Has a Significant but Limited Influence on Phenotypic Expression of the Predominant p.C282Y Homozygous Genotype
Authors: Le Gac Gérald , Ka Chandran , Gourlaouen Isabelle , Bryckaert Laurence , Mercier Anne-Yvonne , Chanu Brigitte , Scotet Virginie , Férec Claude
Published: December 2009

Phenotypic expression of the common p.C282Y/p.C282YHFE-related hemochromatosis genotype is heterogeneous and depends on a complex interplay of genetic and non-genetic factors. Haptoglobin has a crucial role in free hemoglobin iron recovery, and exists as three major types: Hp1-1, Hp2-1 and Hp2-2. Hp2-2 favors endocytosis of hemoglobin iron in monocytes/macrophages, resulting in partial iron retention and increased intracellular ferritin levels. This situation is generally not expected to severely affect iron homeostasis, but was found to correlate with elevated serum iron indices in healthy men. Whether the Hp2-2 genotype acts as a modifier inHFE-related hemochromatosis is unclear. In this study we investigated influence of Hp2-2 and of potential confounders on the iron indices of 351 p.C282Y homozygous patients. We conclude that there is a cause-and-effect relationship between the Hp2-2 genotype and increased iron indices in p.C282Y homozygous patients. The Hp2-2 effect is, however, limited and only apparent in males.
Global Dynamics of an Epidemic Model with a Ratio‐Dependent Nonlinear Incidence Rate
Authors: Yuan Sanling , Li Bo
Published: December 2009

We study an epidemic model with a nonlinear incidence rate which
describes the psychological effect of certain serious diseases on the community when the ratio
of the number of infectives to that of the susceptibles is getting larger. The model has set up
a challenging issue regarding its dynamics near the origin since it is not well defined there.
By carrying out a global analysis of the model and studying the stabilities of the disease‐free equilibrium and the endemic equilibrium, it is shown that either the number of infective
individuals tends to zero as time evolves or the disease persists. Computer simulations are
presented to illustrate the results.
Permanence and Global Attractivity of a Discrete Two‐Prey One‐Predator Model with Infinite Delay
Authors: Yu Zhixiang , Li Zhong
Published: December 2009

A discrete two‐prey one‐predator model with infinite delay is proposed. A set of sufficient conditions which guarantee the permanence of the system is obtained. By constructing a suitable Lyapunov functional, we also obtain sufficient conditions ensuring the global attractivity of the system. An example together with its numerical simulation shows the feasibility of the main results.
Cooperative Bacterial Foraging Optimization
Authors: Chen Hanning , Zhu Yunlong , Hu Kunyuan
Published: December 2009

Bacterial Foraging Optimization (BFO) is a novel optimization algorithm based on the social foraging behavior ofE. colibacteria. This paper presents a variation on the original BFO algorithm, namely, the Cooperative Bacterial Foraging Optimization (CBFO), which significantly improve the original BFO in solving complex optimization problems. This significant improvement is achieved by applying two cooperative approaches to the original BFO, namely, the serial heterogeneous cooperation on the implicit space decomposition level and the serial heterogeneous cooperation on the hybrid space decomposition level. The experiments compare the performance of two CBFO variants with the original BFO, the standard PSO and a real‐coded GA on four widely used benchmark functions. The new method shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.
A Proposal for Automatic Testing of GUIs Based on Annotated Use Cases
Authors: Mateo Navarro Pedro Luis , Sevilla Ruiz Diego , Martínez Pérez Gregorio
Published: December 2009

This paper presents a new approach to automatically generate GUI test
cases and validation points from a set of annotated use cases. This technique helps to reduce the effort required in GUI modeling and test coverage analysis during the software testing process. The test case generation process described in this paper is initially guided by use cases describing the GUI behavior, recorded as a set of interactions with the GUI elements (e.g., widgets being clicked, data input, etc.). These use cases (modeled as a set of initial test cases) are annotated by the tester to indicate interesting variations in widget values (ranges, valid or invalid values) and validation rules with expected results. Once the use cases are annotated, this approach uses the new defined values and validation rules to automatically generate new test cases and validation points, easily expanding the test coverage. Also, the process allows narrowing the GUI model testing to precisely identify the set of GUI elements, interactions, and values the tester is interested in.
Causal Contraction
Authors: Buehner Marc J. , Humphreys Gruffydd R.
Published: December 2009

Causality is a higher-level mental construct derived from low-level percepts such as contiguity in space–time. We show that low-level spatial perception is distorted by the presence of a causal connection, such that two objects appear closer in space when they are causally linked than when they are not. This finding parallels recent demonstrations of temporal causal binding and suggests that causality is at the root of a general ambiguity-resolution process operating on the human perceptual system.
The Structure of Individual Differences in the Cognitive Abilities of Children and Chimpanzees
Authors: Herrmann Esther , Hernández-Lloreda Maria Victoria , Call Josep , Hare Brian , Tomasello Michael
Published: December 2009

Most studies of animal cognition focus on group performance and neglect individual differences and the correlational structure of cognitive abilities. Moreover, no previous studies have compared the correlational structure of cognitive abilities in nonhuman animals and humans. We compared the structure of individual differences of 106 chimpanzees and 105 two-year-old human children using 15 cognitive tasks that posed problems about the physical or social world. We found a similar factor of spatial cognition for the two species. But whereas the chimpanzees had only a single factor in addition to spatial cognition, the children had two distinct additional factors: one for physical cognition and one for social cognition. These findings, in combination with previous research, support the proposal that humans share many cognitive skills with nonhuman apes, especially for dealing with the physical world, but in addition have evolved some specialized skills of social cognition.
A Survey of Family Members’ Satisfaction With the Services Provided by Hospice Palliative Care Volunteers
Authors: Claxton-Oldfield Stephen , Gosselin Natasha , Schmidt-Chamberlain Kirsten , Claxton-Oldfield Jane
Published: December 2009

A total of 22 family members, whose deceased loved ones had used the services of a hospice palliative care volunteer, responded to a brief survey designed to assess the importance of the different kinds of support offered to them (family members) by the volunteer, their impressions of the volunteers’ personal qualities/characteristics, their general experiences with the volunteer, and their overall satisfaction with the volunteer services. The kind of support that received the highest importance rating from family members was the opportunity to take a much-needed break from the demands of caring for their loved one, closely followed by emotional support, the volunteer spending time with them, and the volunteer providing them with information. Family members rated volunteers highly on a list of qualities/characteristics that exemplify individuals who are effective in this role. In all, 85% of the family members felt that their volunteer was well trained and 95% did not feel that their or their loved one’s privacy had been invaded by having a volunteer. Overall, family members were very satisfied with the volunteer support they received. Some limitations of the study are discussed.
An Ability Traitor at Work: A Treasonous Call to Subvert Writing From Within
Authors: Holbrook Teri
Published: December 2009

In questioning conventional qualitative research methods, St. Pierre asked, “What else might writing do except mean?” The author answers, it oppresses. Co-opting the race traitor figurative, she calls on qualitative researchers to become “ability traitors” who interrogate how a valuable coinage of their trade—the written word—is used to rank and categorize individuals with troubling effects. In this article, she commits three betrayals: (a) multigenre writing that undermines the authoritative text; (b) assemblage as a method of analysis that deprivileges the written word; and(c) a gesture toward a dis/ comfort text intended to take up Lather’s example of challenging the “usual ways of making sense”. In committing these betrayals, the author articulates her “traitorous agenda” designed to interrogate assumptions about inquiry, power, equity, and writing as practice-as-usual.
The Liminal Experience: Loss of Extended Self After the Fire
Authors: Lollar Karen
Published: December 2009

This article explores the traumatic loss of home through an autoethnographic account of the period of disorientation after a residential fire described by Turner as the “betwixt and between” stage of grief. The author explores her experience of a loss of extended self and illustrates in this personal account how technologies in the form of possessions extend the human self. The reflection is guided by McLuhan’s understanding of the extension of the body, Belk’s description of how the self is extended through possessions, and Bachelard’s understanding of the significance of the house. The narrative demonstrates the usefulness of autoethnography in understanding traumatic loss.
The Truth About the Truth: A Meta-Analytic Review of the Truth Effect
Authors: Dechêne Alice , Stahl Christoph , Hansen Jochim , Wänke Michaela
Published: December 2009

Repetition has been shown to increase subjective truth ratings of trivia statements. This truth effect can be measured in two ways: (a) as the increase in subjective truth from the first to the second encounter ( within-items criterion) and (b) as the difference in truth ratings between repeated and other new statements ( between-items criterion). Qualitative differences are assumed between the processes underlying both criteria. A meta-analysis of the truth effect was conducted that compared the two criteria. In all, 51 studies of the repetition-induced truth effect were included in the analysis. Results indicate that the between-items effect is larger than the within-items effect. Moderator analyses reveal that several moderators affect both effects differentially. This lends support to the notion that different psychological comparison processes may underlie the two effects. The results are discussed within the processing fluency account of the truth effect.
Use of Foot Orthoses and Calf Stretching for Individuals With Medial Tibial Stress Syndrome
Authors: Loudon Janice K. , Dolphino Martin R.
Published: December 2009

Use of orthotics and calf stretching may alleviate symptoms in runners with medial tibial stress syndrome (MTSS). The objective of this study was to determine which patients with MTSS have a positive response to off-the-shelf foot orthoses and calf stretching based on selected clinical tests to establish a clinical prediction rule. This prospective cohort/predictive validity study enrolled 23 women and men aged 22 to 44 years with symptoms of MTSS. Interventions included off-the-shelf basic foot orthotics and calf stretching. Fifteen of the 23 runners had a 50% reduction of pain in 3 weeks of intervention. Duration was a significant factor that differentiated groups. Although an initial treatment for runners with MTSS may include off-the-shelf orthotics and calf stretching, this regimen should be only one component of an individualized rehabilitation program.
αB-crystallin regulation of angiogenesis by modulation of VEGF
Authors: Kase Satoru , He Shikun , Sonoda Shozo , Kitamura Mizuki , Spee Christine , Wawrousek Eric , Ryan Stephen J. , Kannan Ram , Hinton David R.
Published: December 2009

αB-crystallin is a chaperone belonging to the small heat shock protein family. Herein we show attenuation of intraocular angiogenesis in αB-crystallin knockout (αB-crystallin−/−) mice in 2 models of intraocular disease: oxygen-induced retinopathy and laser-induced choroidal neovascularization. Vascular endothelial growth factor A (VEGF-A) mRNA and hypoxia inducible factor-1α protein expression were induced during retinal angiogenesis, but VEGF-A protein expression remained low in αB-crystallin−/− retina versus wild-type mice, whereas VEGF-R2 expression was not affected. Both αB-crystallin and its phosphorylated serine59 formwere expressed, and immunoprecipitation revealed αB-crystallin binding to VEGF-A but not transforming growth factor-β in cultured retinal pigment epithelial (RPE) cells. αB-crystallin and VEGF-A are colocalized in the endoplasmic reticulum in RPE cells under chemical hypoxia. αB-crystallin−/− RPE showed low VEGF-A secretion under serum-starved conditions compared with wild-type cells. VEGF-A is polyubiquitinated in control and αB-crystallin siRNA treated RPE; however, mono-tetra ubiquitinated VEGF-A increases with αB-crystallin knockdown. Endothelial cell apoptosis in newly formed vessels was greater in αB-crystallin−/− than wild-type mice. Proteasomal inhibition in αB-crystallin−/− mice partially restores VEGF-A secretion and angiogenic phenotype in choroidal neovascularization. Our studies indicate an important role for αB-crystallin as a chaperone for VEGF-A in angiogenesis and its potential as a therapeutic target.
Identification of ATP binding residues of a protein from its primary sequence
Authors: Chauhan Jagat S , Mishra Nitish K , Raghava Gajendra PS
Published: December 2009

Background

One of the major challenges in post-genomic era is to provide functional annotations for large number of proteins arising from genome sequencing projects. The function of many proteins depends on their interaction with small molecules or ligands. ATP is one such important ligand that plays critical role as a coenzyme in the functionality of many proteins. There is a need to develop method for identifying ATP interacting residues in a ATP binding proteins (ABPs), in order to understand mechanism of protein-ligands interaction.

Results

We have compared the amino acid composition of ATP interacting and non-interacting regions of proteins and observed that certain residues are preferred for interaction with ATP. This study describes few models that have been developed for identifying ATP interacting residues in a protein. All these models were trained and tested on 168 non-redundant ABPs chains. First we have developed a Support Vector Machine (SVM) based model using primary sequence of proteins and obtained maximum MCC 0.33 with accuracy of 66.25%. Secondly, another SVM based model was developed using position specific scoring matrix (PSSM) generated by PSI-BLAST. The performance of this model was improved significantly (MCC 0.5) from the previous one, where only the primary sequence of the proteins were used.

Conclusion

This study demonstrates that it is possible to predict 'ATP interacting residues' in a protein with moderate accuracy using its sequence. The evolutionary information is important for the identification of 'ATP interacting residues', as it provides more information compared to the primary sequence. This method will be useful for researchers studying ATP-binding proteins. Based on this study, a web server has been developed for predicting 'ATP interacting residues' in a protein http://www.imtech.res.in/raghava/atpint/.
Endoplasmic Reticulum Stress-Induced Activation of Activating Transcription Factor 6 Decreases cAMP-Stimulated Hepatic Gluconeogenesis via Inhibition of CREB
Authors: Seo Hye-Young , Kim Mi-Kyung , Min Ae-Kyung , Kim Hye-Soon , Ryu Seong-Yeol , Kim Nam-Kyeong , Lee Kyeong Min , Kim Han-Jong , Choi Hueng-Sik , Lee Ki-Up , Park Keun-Gyu , Lee In-Kyu
Published: December 2009

The expression of genes encoding key hepatic gluconeogenic enzymes, including phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase), is regulated at the transcriptional level by a network of transcription factors and cofactors, including cAMP response element-binding protein (CREB). It has been suggested that increased endoplasmic reticulum (ER) stress in the liver impairs hepatic glucose metabolism. However, the direct effect of ER stress on hepatic gluconeogenesis is still not clear. Here, we investigated whether ER stress influences hepatic gluconeogenesis and whether this process is mediated by activating transcription factor 6 (ATF6) through the inhibition of cAMP-mediated activation of CREB. A cAMP stimulant, forskolin, and 8-bromoadenosine-cAMP increased PEPCK and G6Pase mRNA expression in H4IIE rat hepatoma cells, and ER stress induced by tunicamycin or thapsigargin decreased the expression of these genes in forskolin or 8-bromoadenosine-cAMP-treated cells. In a transient transfection study, ATF6 inhibited the PEPCK and G6Pase promoters. Also, adenovirus-mediated overexpression of ATF6 in H4IIE cells decreased forskolin-stimulated PEPCK and G6Pase gene expression. Moreover, the inhibition of endogenous ATF6 expression by small interfering RNAs restored the ER stress-induced suppression of PEPCK and G6Pase gene expression. Transient transfection of ATF6 inhibited transactivation by CREB on the PEPCK and G6Pase promoters, and a gel shift assay showed that Ad-ATF6 inhibits forskolin-stimulated CREB DNA-binding activity. Finally, we found that expression of ATF6 decreased fasting-induced PEPCK, G6Pase mRNA expression, and blood glucose levels in mice. Taken together, these data extend our understanding of ER stress and the regulation of liver gluconeogenesis by ATF6.
Functional Role of c-Jun-N-Terminal Kinase in Feeding Regulation
Authors: Unger Elizabeth K. , Piper Merisa L. , Olofsson Louise E. , Xu Allison W.
Published: December 2009

c-Jun-N-terminal kinase (JNK) is a signaling molecule that is activated by proinflammatory signals, endoplasmic reticulum (ER) stress, and other environmental stressors. Although JNK has diverse effects on immunological responses and insulin resistance in peripheral tissues, a functional role for JNK in feeding regulation has not been established. In this study, we show that central inhibition of JNK activity potentiates the stimulatory effects of glucocorticoids on food intake and that this effect is abolished in mice whose agouti-related peptide (AgRP) neurons are degenerated. JNK1-deficient mice feed more upon central administration of glucocorticoids, and glucocorticoid receptor nuclear immunoreactivity is enhanced in the AgRP neurons. JNK inhibition in hypothalamic explants stimulates Agrp expression, and JNK1-deficient mice exhibit increased Agrp expression, heightened hyperphagia, and weight gain during refeeding. Our study shows that JNK1 is a novel regulator of feeding by antagonizing glucocorticoid function in AgRP neurons. Paradoxically, JNK1 mutant mice feed less and lose more weight upon central administration of insulin, suggesting that JNK1 antagonizes insulin function in the brain. Thus, JNK may integrate diverse metabolic signals and differentially regulate feeding under distinct physiological conditions.