bluuebunny/crossref_metadata_2025 huggingface dataset:
An insect symbiosis is influenced by bacterium-specific polymorphisms in outer-membrane protein A
Authors: Weiss Brian L. , Wu Yineng , Schwank Jonathon J. , Tolwinski Nicholas S. , Aksoy Serap
Published: September 2008

Beneficial bacterial symbioses are ubiquitous in nature. However, the functional and molecular basis of host tolerance to resident symbiotic microbes, in contrast to resistance to closely related bacteria that are recognized as foreign, remain largely unknown. We used the tsetse fly (
Glossina morsitans
), which depends on symbiotic flora for fecundity and has limited exposure to foreign microbes, to investigate the tolerance phenomenon exhibited during symbiosis. We examined the potential role of bacterium-specific polymorphisms present in the major bacterial surface protein, outer-membrane protein A (OmpA), on host infection outcomes. Tsetse were successfully superinfected with their mutualistic facultative symbiont,
Sodalis glossinidius
, whereas infections with
Escherichia coli
K12 were lethal. In contrast, tsetse were resistant to an
E. coli
OmpA mutant strain, whereas recombinant
Sodalis
expressing
E. coli
OmpA became pathogenic. Profiling of tsetse immunity-related gene expression incriminated
peptidoglycan recognition protein (pgrp)-lb
as a determinant of the infection outcomes we observed. RNAi-induced knockdown of tsetse
pgrp-lb
significantly reduced host mortality after infection with otherwise lethal
E. coli
K12. Our results show that polymorphisms in the exposed loop domains of OmpA represent a microbial adaptation that mediates host tolerance of endogenous symbiotic bacteria.
Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts
Authors: Tamas Ivica , Wernegreen Jennifer J. , Nystedt Björn , Kauppinen Seth N. , Darby Alistair C. , Gomez-Valero Laura , Lundin Daniel , Poole Anthony M. , Andersson Siv G. E.
Published: September 2008

Among host-dependent bacteria that have evolved by extreme reductive genome evolution, long-term bacterial endosymbionts of insects have the smallest (160–790 kb) and most A + T-rich (>70%) bacterial genomes known to date. These genomes are riddled with poly(A) tracts, and 5–50% of genes contain tracts of 10 As or more. Here, we demonstrate transcriptional slippage at poly(A) tracts within genes of
Buchnera aphidicola
associated with aphids and
Blochmannia pennsylvanicus
associated with ants. Several tracts contain single frameshift deletions; these apparent pseudogenes showed patterns of constraint consistent with purifying selection on the encoded proteins. Transcriptional slippage yielded a heterogeneous population of transcripts with variable numbers of As in the tract. Across several frameshifted genes, including
B. aphidicola
cell wall biosynthesis genes and a
B. pennsylvanicus
histidine biosynthesis gene, 12–50% of transcripts contained corrected reading frames that could potentially yield full-length proteins.
In situ
immunostaining confirmed the production of the cell wall biosynthetic enzyme UDP-N-acetylmuramyl pentapeptide synthase encoded by the frameshifted
murF
gene. Simulation studies indicated an overrepresentation of poly(A) tracts in endosymbiont genomes relative to other A + T-rich bacterial genomes. Polymerase infidelity at poly(A) tracts rescues the functionality of genes with frameshift mutations and, conversely, reduces the efficiency of expression for in-frame genes carrying poly(A) regions. These features of homopolymeric tracts could be exploited to manipulate gene expression in small synthetic genomes.
Salmonella
pathogenesis reveals that BMP signaling regulates blood cell homeostasis and immune responses in
Drosophila
Authors: Frandsen Joel L. , Gunn Bronwyn , Muratoglu Selen , Fossett Nancy , Newfeld Stuart J.
Published: September 2008

Intercellular signaling by bone morphogenetic proteins (BMPs) regulates developmental decisions in virtually all animals. Here, we report that Decapentaplegic (Dpp; a
Drosophila
BMP family member) plays a role in blood cell homeostasis and immune responses by regulating a transcription factor cascade. The cascade begins with Dpp repression of Zfh1, continues with Zfh1 activation of Serpent (Srp; a GATA factor), and terminates with Srp activation of U-shaped (Ush) in hematopoietic cells. Hyperactivation of Zfh1, Srp, and Ush in
dpp
mutants leads to hyperplasia of plasmatocytes.
Salmonella
challenge revealed that in
dpp
mutants the misregulation of this cascade also prevents the generation of lamellocytes. These findings support the hypothesis that Ush participates in a switch between plasmatocyte and lamellocyte fate in a common precursor and further suggests a mechanism for how all blood cell types can arise from a single progenitor. These results also demonstrate that combining
Drosophila
and
Salmonella
genetics can provide novel opportunities for advancing our knowledge of hematopoiesis and innate immunity.
Controlling for Severity of Illness in Outcome Studies Involving Infectious Diseases: Impact of Measurement at Different Time Points
Authors: Thom Kerri A. , Shardell Michelle D. , Osih Regina B. , Schweizer Marin L. , Furuno Jon P. , Perencevich Eli N. , McGregor Jessina C. , Harris Anthony D.
Published: September 2008

Background.

Severity of illness is an important confounder in outcome studies involving infectious diseases. However, it is unclear whether the time at which severity of illness is measured is important.

Methods.

We performed a retrospective study of 328 episodes of gram-negative bacteremia in adult patients to assess the impact of the time of measurement of severity of illness on the association between empirical antimicrobial therapy received and in-hospital mortality. Using a modified Acute Physiology Score (APS), severity of illness was measured at 2 time points: (1) hospital admission and (2) 24 hours before the first culture-positive blood sample was collected. Multivariate logistic regression was used to estimate the impact of adjusting for the APS on the relationship between empirical therapy received (ie, the exposure) and in-hospital mortality (ie, the outcome).

Results.

The mean APS ( ± standard deviation) of patients with bacteremia increased during their hospital stay (from 19.2 ± 11.6 at admission to 24.2 ± 13.6 at the second time point; P < .01). When examining the association between empirical antimicrobial therapy received and in-hospital mortality, and controlling for the APS, there was a trend toward a decreased impact of appropriate therapy received on in-hospital mortality. The unadjusted odds ratio (OR) for the association between appropriate therapy received and in-hospital mortality was 0.83 (95% confidence interval [CI], 0.51-1.34). After controlling for the APS at admission, this association was attenuated (OR, 0.94 [95% CI, 0.57-1.55]), and when a change in the APS was also included in the multivariate logistic regression model, the association was further attenuated (OR, 0.99 [95% CI, 0.58-1.69]).

Conclusions.

The magnitude of the association between appropriate antimicrobial therapy received and in-hospital mortality among patients with gram-negative bacteremia was sensitive to the timing of adjustment for severity of illness.
Oxidative Folding and Assembly with Transthyretin Are Sequential Events in the Biogenesis of Retinol Binding Protein in the Endoplasmic Reticulum
Authors: Selvaraj Sundar Rajan , Bhatia Vaibhav , Tatu Utpal
Published: September 2008

Retinol-binding protein (RBP) is secreted out of the cell in its ligand-bound holo-form. The apo-form of RBP is selectively retained within the endoplasmic reticulum (ER) by a mechanism that remains unknown. Using isolated microsomal system, we have recapitulated the biogenesis of RBP involving its oxidative folding and assembly with transthyretin in the ER. In addition to dissecting its pathway of disulfide oxidation, we have analyzed association of its early folding intermediates with ER-chaperones. Our results show that of the three intramolecular disulfides present in RBP (4–160, 70–174, and 120–129) the smallest loop (120–129) was most critical for RBP to fold. Its absence caused RBP to aggregate into an intermolecular disulfide-linked structure. After acquisition of the small loop, formation of one of the two big disulfides (4–160 or 70–174) was sufficient for RBP to acquire a folded state. Using cross-linking in intact microsomes and sedimentation on sucrose gradients, we show that newly synthesized RBP is associated with a complex of chaperones consisting of Grp94, BiP, PDI, and calnexin. The complex was constitutively present in the ER, independent of the presence of folding substrates. RBP dissociated from this complex coincident with the formation of one of the two big disulfide loops, whereas RBP mutant lacking both the large disulfides showed persistent association. While highlighting the matrix-like characteristics of ER in isolated microsomal system our results provide insight into RBP folding and assembly mechanisms that will aid our understanding of its complex secretion properties.
Posttranslational Regulation of NF-YA Modulates NF-Y Transcriptional Activity
Authors: Manni Isabella , Caretti Giuseppina , Artuso Simona , Gurtner Aymone , Emiliozzi Velia , Sacchi Ada , Mantovani Roberto , Piaggio Giulia
Published: September 2008

NF-Y binds to CCAAT motifs in the promoter region of a variety of genes involved in cell cycle progression. The NF-Y complex comprises three subunits, NF-YA, -YB, and -YC, all required for DNA binding. Expression of NF-YA fluctuates during the cell cycle and is down-regulated in postmitotic cells, indicating its role as the regulatory subunit of the complex. Control of NF-YA accumulation is posttranscriptional, NF-YA mRNA being relatively constant. Here we show that the levels of NF-YA protein are regulated posttranslationally by ubiquitylation and acetylation. A NF-YA protein carrying four mutated lysines in the C-terminal domain is more stable than the wild-type form, indicating that these lysines are ubiquitylated Two of the lysines are acetylated in vitro by p300, suggesting a competition between ubiquitylation and acetylation of overlapping residues. Interestingly, overexpression of a degradation-resistant NF-YA protein leads to sustained expression of mitotic cyclin complexes and increased cell proliferation, indicating that a tight regulation of NF-YA levels contributes to regulate NF-Y activity.
Smoothened Signaling in Vertebrates Is Facilitated by a G Protein-coupled Receptor Kinase
Authors: Philipp Melanie , Fralish Gregory B. , Meloni Alison R. , Chen Wei , MacInnes Alyson W. , Barak Lawrence S. , Caron Marc G.
Published: September 2008

Smoothened, a heptahelical membrane protein, functions as the transducer of Hedgehog signaling. The kinases that modulate Smoothened have been thoroughly analyzed in flies. However, little is known about how phosphorylation affects Smoothened in vertebrates, mainly, because the residues, where Smoothened is phosphorylated are not conserved from Drosophila to vertebrates. Given its molecular architecture, Smoothened signaling is likely to be regulated in a manner analogous to G protein–coupled receptors (GPCRs). Previously, it has been shown, that arrestins and GPCR kinases, (GRKs) not only desensitize G protein–dependent receptor signaling but also function as triggers for GPCR trafficking and formation of signaling complexes. Here we describe that a GRK contributes to Smoothened-mediated signaling in vertebrates. Knockdown of the zebrafish homolog of mammalian GRK2/3 results in lowered Hedgehog transcriptional responses, impaired muscle development, and neural patterning. Results obtained in zebrafish are corroborated both in cell culture, where zGRK2/3 phosphorylates Smoothened and promotes Smoothened signal transduction and in mice where deletion of GRK2 interferes with neural tube patterning. Together, these data suggest that a GRK functions as a vertebrate kinase for Smoothened, promoting Hedgehog signal transduction during early development.
Filamin B Serves as a Molecular Scaffold for Type I Interferon-induced c-Jun NH2-terminal Kinase Signaling Pathway
Authors: Jeon Young Joo , Choi Joon Seok , Lee Jung Yun , Yu Kyung Ryun , Ka Seung Hyeun , Cho Yongcheol , Choi Eui-Ju , Baek Sung Hee , Seol Jae Hong , Park Dongeun , Bang Ok Sun , Chung Chin Ha
Published: September 2008

Type I interferons (IFNs) activate Janus tyrosine kinase-signal transducer and activator of transcription pathway for exerting pleiotropic biological effects, including antiviral, antiproliferative, and immunomodulatory responses. Here, we demonstrate that filamin B functions as a scaffold that links between activated Rac1 and a c-Jun NH2-terminal kinase (JNK) cascade module for mediating type I IFN signaling. Filamin B interacted with Rac1, mitogen-activated protein kinase kinase kinase 1, mitogen-activated protein kinase kinase 4, and JNK. Filamin B markedly enhanced IFNα-dependent Rac1 activation and the sequential activation of the JNK cascade members. Complementation assays using M2 melanoma cells revealed that filamin B, but not filamin A, is required for IFNα-dependent activation of JNK. Furthermore, filamin B promoted IFNα-induced apoptosis, whereas short hairpin RNA-mediated knockdown of filamin B prevented it. These results establish a novel function of filamin B as a molecular scaffold in the JNK signaling pathway for type I IFN-induced apoptosis, thus providing the biological basis for antitumor and antiviral functions of type I IFNs.
Use of probability-based sampling of water-quality indicators in supporting development of quality criteria
Authors: Nelson Walter G. , Brown Cheryl A.
Published: September 2008

Nelson, W. G., and Brown, C. A. 2008. Use of probability-based sampling of water-quality indicators in supporting development of quality criteria. – ICES Journal of Marine Science, 65: 1421–1427. Intensive, site-based data are typically used to establish protective water-quality criteria, but may only exist for few systems in a region. We examine whether or not water-quality indicator data collected from large-scale, probability-based assessments can support the development of regional quality criteria. Because such indicators may be subject to high natural variation over short time-scales, a key question is whether survey values will be sufficiently similar to site-based sampling to merit use in extrapolating quality criteria spatially. Median values for dissolved inorganic nitrogen, phosphorus, and Chl a for dry-season data collected within Yaquina Bay (OR, USA) over a 7-year period were compared with dry-season datasets collected from two studies comprising 6 and 14 Oregon estuaries, respectively. A second, reduced dataset (August–September only) was compared with data from 38 estuaries within the same ecoregion. All comparisons were made for marine and riverine salinity zones. Medians for Yaquina Bay were higher than those from the comparison surveys. Stochastic variation of coastal upwelling during sampling appears to cause the contrasts. Further work is required to define upwelling-based adjustments for regional, probability-based survey data before they can be used in regulatory applications. However, even without adjustment, these data may help in determining the appropriate regional context for quality criteria.
Salinity dependence of parasite infestation in the European eel Anguilla anguilla in northern Germany
Authors: Jakob Eva , Hanel Reinhold , Klimpel Sven , Zumholz Karsten
Published: September 2008

Jakob, E., Hanel, R., Klimpel, S., and Zumholz, K. 2009. Salinity dependence of parasite infestation in the European eel Anguilla anguilla in northern Germany. – ICES Journal of Marine Science, 66: 358–366. The aim of the study was to examine metazoan parasite communities of European eels (Anguilla anguilla) in fresh-water, brackish water and marine localities in northern Germany. In all, 29 parasite species/taxa were found in 170 eels: eight digeneans, one monogenean, five cestodes, ten nematodes, two acanthocephalans, and three crustaceans. Measures of diversity characteristics of the helminth communities included species richness, Shannon's diversity index and its evenness, and the Berger–Parker dominance index. The highest species diversity and lowest dominance values were calculated for the helminth communities of eels from the two Baltic Sea localities. Parasite communities of European eels clearly exhibit the habitat preferences of their hosts, salinity-dependent specificities, and a clustering into fresh-water, brackish, and marine groups. The highly pathogenic parasite species Anguillicola crassus and Pseudodactylogyrus spp. were found at all sampling sites in fresh water and brackish water, with high prevalence. Basic information is provided on the risks of restocking programmes solely focusing on fresh-water sites.
Powdery Mildew Resistance Conferred by Loss of the ENHANCED DISEASE RESISTANCE1 Protein Kinase Is Suppressed by a Missense Mutation in KEEP ON GOING, a Regulator of Abscisic Acid Signaling
Authors: Wawrzynska Anna , Christiansen Katy M. , Lan Yinan , Rodibaugh Natalie L. , Innes Roger W.
Published: September 2008

Loss-of-function mutations in the Arabidopsis (Arabidopsis thaliana) ENHANCED DISEASE RESISTANCE1 (EDR1) gene confer enhanced resistance to infection by powdery mildew (Golovinomyces cichoracearum). EDR1 encodes a protein kinase, but its substrates and the pathways regulated by EDR1 are unknown. To identify components of the EDR1 signal transduction pathway(s), we conducted a forward genetic screen for mutations that suppressed edr1-mediated disease resistance. Genetic mapping and cloning of one of these suppressor mutations revealed a recessive missense mutation in the KEEP ON GOING gene (KEG; At5g13530), which we designated keg-4. KEG encodes a multidomain protein that includes a RING E3 ligase domain, a kinase domain, ankyrin repeats, and HERC2-like repeats. The KEG protein has previously been shown to have ubiquitin ligase activity and to negatively regulate protein levels of the transcription factor ABCISIC ACID INSENSITIVE5. KEG mRNA levels were found to be 3-fold higher in edr1 mutant plants compared to wild type. Loss-of-function mutations in KEG are seedling lethal and are hypersensitive to glucose and abscisic acid (ABA). The keg-4 mutation, in contrast, conferred resistance to 6% glucose and suppressed edr1-mediated hypersensitivity to ABA, suggesting that the keg-4 mutation suppresses ABA signaling by altering KEG function. Several ABA-responsive genes were found to be further up-regulated in the edr1 mutant following ABA treatment, and this up-regulation was suppressed by the keg-4 mutation. We conclude that edr1-mediated resistance to powdery mildew is mediated, in part, by enhanced ABA signaling.
Further Evidence for the Mandatory Nature of Polysaccharide Debranching for the Aggregation of Semicrystalline Starch and for Overlapping Functions of Debranching Enzymes in Arabidopsis Leaves
Authors: Wattebled Fabrice , Planchot Véronique , Dong Ying , Szydlowski Nicolas , Pontoire Bruno , Devin Aline , Ball Steven , D'Hulst Christophe
Published: September 2008

Four isoforms of debranching enzymes are found in the genome of Arabidopsis (Arabidopsis thaliana): three isoamylases (ISA1, ISA2, and ISA3) and a pullulanase (PU1). Each isoform has a specific function in the starch pathway: synthesis and/or degradation. In this work we have determined the levels of functional redundancy existing between these isoforms by producing and analyzing different combinations of mutations: isa3-1 pu1-1, isa1-1 isa3-1, and isa1-1 isa3-1 pu1-1. While the starch content strongly increased in the isa3-1 pu1-1 double mutant, the latter decreased by over 98% in the isa1-1 isa3-1 genotype and almost vanished in triple mutant combination. In addition, whereas the isa3-1 pu1-1 double mutant synthesizes starch very similar to that of the wild type, the structure of the residual starch present either in isa1-1 isa3-1 or in isa1-1 isa3-1 pu1-1 combination is deeply affected. In the same way, water-soluble polysaccharides that accumulate in the isa1-1 isa3-1 and isa1-1 isa3-1 pu1-1 genotypes display strongly modified structure compared to those found in isa1-1. Taken together, these results show that in addition to its established function in polysaccharide degradation, the activity of ISA3 is partially redundant to that of ISA1 for starch synthesis. Our results also reveal the dual function of pullulanase since it is partially redundant to ISA3 for degradation and to ISA1 for synthesis. Finally, x-ray diffraction analyses suggest that the crystallinity and the presence of the 9- to 10-nm repetition pattern in starch precisely depend on the level of debranching enzyme activity.
Solution structure of the extraterminal domain of the bromodomain‐containing protein BRD4
Authors: Lin Yi‐Jan , Umehara Takashi , Inoue Makoto , Saito Kohei , Kigawa Takanori , Jang Moon‐Kyoo , Ozato Keiko , Yokoyama Shigeyuki , Padmanabhan Balasundaram , Güntert Peter
Published: September 2008

BRD4, which is a member of the BET (bromodomains and extraterminal) protein family, interacts preferentially with acetylated chromatin and possesses multiple cellular functions in meiosis, embryonic development, the cell cycle, and transcription. BRD4 and its family members contain two bromodomains known to bind acetylated lysine, and a conserved ET domain whose function is unclear. Here we show the solution structure of the ET domain of mouse BRD4, which provides the first three‐dimensional structure of an ET domain in the BET family. We determined the NMR structure of BRD4‐ET with a root‐mean‐square deviation of 0.41 Å for the backbone atoms in the structured region of residues 608–676 on the basis of 1793 upper distance limits derived from NOE intensities measured in three‐dimensional NOESY spectra. The structure of the BRD4‐ET domain comprises three α‐helices and a characteristic loop region of an irregular but well‐defined structure. A DALI search revealed no close structural homologs in the current Protein Data Bank. The BRD4‐ET structure has an acidic patch that forms a continuous ridge with a hydrophobic cleft, which may interact with other proteins and/or DNA.
Association of polymorphisms in CASP10 and CASP8 with FEV1/FVC and bronchial hyperresponsiveness in ethnically diverse asthmatics
Authors: Smith Alicia K. , Lange Leslie A. , Ampleford Elizabeth J. , Meyers Deborah A. , Bleecker Eugene R. , Howard Timothy D.
Published: September 2008

Background
Several chromosomal regions have been identified using family‐based linkage analysis to contain genes contributing to the development of asthma and allergic disorders. One of these regions, chromosome 2q32‐q33, contains a gene cluster containing CFLAR, CASP10 and CASP8. These genes regulate the extrinsic apoptosis pathway utilized by several types of immune and structural cells that have been implicated in the pathogenesis of asthma.

Objective
To assess the role of genetic variation in CFLAR, CASP10 and CASP8 in asthma and related phenotypes in individuals of diverse ethnic backgrounds.

Methods
We tested 26 single nucleotide polymorphisms (SNPs) in the CFLAR, CASP10 and CASP8 gene cluster for association with asthma and related phenotypes in African‐American, non‐Hispanic whites, and Hispanic case–control populations (cases, N=517, controls, N=644).

Results
Five CASP10 SNPS were associated with forced expiratory volume in 1 s (FEV1)/forced expiration volume capacity (FVC) in the African‐American subjects with asthma (P=0.0009–0.047). Nine SNPs, seven in CASP10 and two in CASP8, were also associated with the degree of bronchial hyperresponsiveness (BHR) (as determined by PC20) in race‐specific analysis, predominately in the Non‐Hispanic white cases. Two SNPs, rs6750157 in CASP10 and rs1045485 in CASP8 were modestly associated with asthma in the African‐American (P=0.025) and Hispanic (P=0.033) populations, respectively.

Conclusion
These data suggest a role for CASP10 as a potential modifier of the asthma phenotype, specifically with measures of airway obstruction and BHR.
Allergens to wheat and related cereals
Authors: Tatham A. S. , Shewry P. R.
Published: September 2008

Wheat is one of the major crops grown, processed and consumed by humankind and is associated with both intolerances (notably coeliac disease) and allergies.

Two types of allergy are particularly well characterized. The first is bakers' asthma, which results from the inhalation of flour and dust during grain processing. Although a number of wheat proteins have been shown to bind IgE from patients with bakers' asthma, there is no doubt a well‐characterized group of inhibitors of α‐amylase (also called chloroform methanol soluble, or CM, proteins) are the major components responsible for this syndrome. The second well‐characterized form of allergy to wheat proteins is wheat‐dependent exercise‐induced anaphylaxis (WDEIA), with the ω5‐gliadins (part of the gluten protein fraction) being the major group of proteins which are responsible. Other forms of food allergy have also been reported, with the proteins responsible including gluten proteins, CM proteins and non‐specific lipid transfer proteins.

Processing of wheat and of related cereals (barley and rye, which may contain related allergens) may lead to decreased allergenicity while genetic engineering technology offers opportunities to eliminate allergens by suppressing gene expression.
Renin‐angiotensin system gene polymorphisms and diastolic heart failure
Authors: Wu C.‐K. , Tsai C.‐T. , Hwang J.‐J. , Luo J.‐L. , Juang J. J.‐M. , Hsu K.‐L. , Lai L.‐P. , Lin J.‐L. , Tseng C.‐D. , Chiang F.‐T.
Published: September 2008

Background  Diastolic heart failure (DHF) refers to an abnormality of diastolic distensibility, filling or relaxation of the left ventricle. The genetic study of DHF is scarce in the literature. The association of renin‐angiotensin system (RAS) and DHF are well known. We hypothesized that RAS genes might be the susceptible genes for DHF and conducted a case‐control study to prove the hypothesis.

Materials and methods  A total of 1452 consecutive patients were analysed and 148 patients with a diagnosis of DHF confirmed by echocardiography were recruited. We had two control populations. The first controls consisted of 286 normal subjects while the second were 148 matched controls selected on a 1‐to‐1 basis by age, sex, hypertension, diabetes and medication use. The angiotensin‐converting enzyme (ACE) gene insertion/deletion polymorphism; multilocus polymorphisms of the angiotensinogen gene; and the A1166C polymorphisms of the angiotensin II type I receptor (AT1R) gene were genotyped.

Results  In a single‐locus analysis, the odds ratios (ORs) for DHF were significant with the ACE DD genotype and the AT1R 1166 CC plus AC genotype. In addition, the concomitant presence of ACE DD and AT1R 1166 CC/AC genotypes synergistically increased the predisposition to DHF.

Conclusions  Genetic variants in the RAS genes may determine an individual's risk to develop DHF. There is also a synergistic gene‐gene interaction between the RAS genes in the development of DHF.
Effect of obesity and insulin sensitivity on adiponectin isoform distribution
Authors: Kaser S. , Tatarczyk T. , Stadlmayr A. , Ciardi C. , Ress C. , Tschoner A. , Sandhofer A. , Paulweber B. , Ebenbichler C. F. , Patsch J. R.
Published: September 2008

Background  Adiponectin is an insulin‐sensitizing, antiatherogenic and anti‐inflammatory adipocytokine that circulates in three isoforms: a trimer [low‐molecular weight (LMW)], a hexamer (trimer‐dimer) of medium molecular weight (MMW) and a multimeric high molecular weight (HMW) isoform. Evidence is accumulating that HMW adiponectin is the active isoform of the adipocytokine. We investigated the impact of adipose tissue and insulin sensitivity on adiponectin isoform distribution.

Materials and methods  One hundred and eighty‐seven normolipidaemic, non‐diabetic lean or obese subjects with or without insulin resistance participating in the Salzburg Atherosclerosis Prevention program in subjects at High Individual Risk (SAPHIR) were included in the study. Insulin sensitivity was determined by the short insulin tolerance test and the homeostasis model assessment (HOMA) index. Serum adiponectin isoform distribution was determined by an enzyme immunoassay.

Results  Total adiponectin as well as HMW/total adiponectin ratio was significantly increased in female subjects. Circulating total adiponectin levels were lowest in obese patients due to reduced concentrations of HMW adiponectin. As determined by stepwise regression analysis, besides age and high density lipoprotein (HDL) cholesterol, visceral fat area and waist‐to‐hip ratio predicted concentrations of HMW adiponectin, while insulin sensitivity had no influence on either total adiponectin or its isoforms.

Conclusions  Our results underline that determination of adiponectin isoforms are more useful than measurement of total adiponectin in clinical settings. Our data suggest that adiponectin concentrations are strongly associated with visceral fat area but not with insulin sensitivity. Thus, we hypothesize that insulin resistance is a consequence rather than the cause of hypoadiponectinaemia in obese subjects.
Presence of hepatitis C Virus DNA sequences in the DNA of infected patients
Authors: Zemer R. , Cohen Y. Kitay , Naftaly T. , Klein A.
Published: September 2008

Background  Hepatitis C virus (HCV) consists of a single positive RNA molecule. In the present study we investigated the possibility that HCV may undergo integration into the genomic DNA of infected cells.

Materials and methods  HCV(+) patients (n = 51) and 21 HCV(–) controls were investigated for HCV integration. RNase treated DNA samples of mononuclear cells (MNC) and liver biopsies of the patients were screened by PCR and seminested PCR processes for detection of integration. Positive results were further investigated by means of Southern analysis of patient's DNA as well as sequencing of PCR products of patient's DNA.

Results  Positive PCR results were detected in 4/51 of the HCV(+) patients and in none of the control group. Southern analysis showed the presence of HCV sequence in a 23 kbp band of the patient which is much larger than the viral genome itself (9·646 kbp). Sequencing of cloned PCR products showed an identity of over 95·0% to HCV.

Conclusions  As much as we are aware this is the first demonstration of the possible integration of HCV sequences into the DNA of HCV(+) patients.
A curve fitting approach to estimate the extent of fermentation of indigestible carbohydrates
Authors: Wang H. , Weening D. , Jonkers E. , Boer T. , Stellaard F. , Small A. C. , Preston T. , Vonk R. J. , Priebe M. G.
Published: September 2008

Background  Information about the extent of carbohydrate digestion and fermentation is critical to our ability to explore the metabolic effects of carbohydrate fermentation in vivo. We used cooked 13C‐labelled barley kernels, which are rich in indigestible carbohydrates, to develop a method which makes it possible to distinguish between and to assess carbohydrate digestion and fermentation.

Materials and methods  Seventeen volunteers ingested 86 g (dry weight) of cooked naturally 13C enriched barley kernels after an overnight fast. 13CO2 and H2 in breath samples were measured every half hour for 12 h. The data of 13CO2 in breath before the start of the fermentation were used to fit the curve representing the digestion phase. The difference between the area under curve (AUC) of the fitted digestion curve and the AUC of the observed curve was regarded to represent the fermentation part. Different approaches were applied to determine the proportion of the 13C‐dose available for digestion and fermentation.

Results  Four hours after intake of barley, H2‐excretion in breath started to rise. Within 12 h, 24–48% of the 13C‐dose was recovered as 13CO2, of which 18–19% was derived from colonic fermentation and the rest from digestion. By extrapolating the curve to baseline, it was estimated that eventually 24–25% of the total available 13C in barley would be derived from colon fermentation.

Conclusion  Curve fitting, using 13CO2‐ and H2‐breath data, is a feasible and non‐invasive method to assess carbohydrate digestion and fermentation after consumption of 13C enriched starchy food.
Diversity and activity of aquatic fungi under low oxygen conditions
Authors: MEDEIROS A. O. , PASCOAL C. , GRAÇA M. A. S.
Published: September 2008

1. The objective was to test whether a decrease in oxygen concentration in streams affects the diversity and activity of aquatic hyphomycetes and consequently leaf litter decomposition.

2. Senescent leaves of Alnus glutinosa were immersed for 7 days in a reference stream, for fungal colonization, and then incubated for 18 days in microcosms at five oxygen concentrations (4%, 26%, 54%, 76% and 94% saturation). Leaf decomposition (as loss of leaf toughness), fungal diversity, reproduction (as spore production) and biomass (ergosterol content) were determined.

3. Leaf toughness decreased by 70% in leaves exposed to the highest O2 concentration, whereas the decrease was substantially less (from 25% to 45%) in treatments with lower O2. Fungal biomass decreased from 99 to 12 mg fungi g−1 ash‐free dry mass on exposure to 94% and 4% O2 respectively. Sporulation was strongly inhibited by reduction of dissolved O2 in water (3.1 × 104 versus 1.3 × 103 spores per microcosms) for 94% and 4% saturation respectively.

4. A total of 20 species of aquatic hyphomycetes were identified on leaves exposed to 94% O2, whereas only 12 species were found in the treatment with 4% O2 saturation. Multidimensional scaling revealed that fungal assemblages exposed to 4% O2 were separated from all the others. Articulospora tetracladia, Cylindrocarpon sp. and Flagellospora curta were the dominant species in microcosms with 4% O2, while Flagellospora curvula and Anguillospora filiformis were dominant at higher O2 concentrations.

5. Overall results suggest that the functional role of aquatic hyphomycetes as decomposers of leaf litter is limited when the concentration of dissolved oxygen in streams is low.
Plant diversity positively affects short‐term soil carbon storage in experimental grasslands
Authors: STEINBEISS SIBYLLE , BEßLER HOLGER , ENGELS CHRISTOF , TEMPERTON VICKY M. , BUCHMANN NINA , ROSCHER CHRISTIANE , KREUTZIGER YVONNE , BAADE JUSSI , HABEKOST MAIKE , GLEIXNER GERD
Published: September 2008

Increasing atmospheric CO2concentration and related climate change have stimulated much interest in the potential of soils to sequester carbon. In ‘The Jena Experiment’, a managed grassland experiment on a former agricultural field, we investigated the link between plant diversity and soil carbon storage. The biodiversity gradient ranged from one to 60 species belonging to four functional groups. Stratified soil samples were taken to 30 cm depth from 86 plots in 2002, 2004 and 2006, and organic carbon contents were determined. Soil organic carbon stocks in 0–30 cm decreased from 7.3 kg C m−2in 2002 to 6.9 kg C m−2in 2004, but had recovered to 7.8 kg C m−2by 2006. During the first 2 years, carbon storage was limited to the top 5 cm of soil while below 10 cm depth, carbon was lost probably as short‐term effect of the land use change. After 4 years, carbon stocks significantly increased within the top 20 cm. More importantly, carbon storage significantly increased with sown species richness (log‐transformed) in all depth segments and even carbon losses were significantly smaller with higher species richness. Although increasing species diversity increased root biomass production, statistical analyses revealed that species diversityper sewas more important than biomass production for changes in soil carbon. Below 20 cm depth, the presence of one functional group, tall herbs, significantly reduced carbon losses in the beginning of the experiment. Our analysis indicates that plant species richness and certain plant functional traits accelerate the build‐up of new carbon pools within 4 years. Additionally, higher plant diversity mitigated soil carbon losses in deeper horizons. This suggests that higher biodiversity might lead to higher soil carbon sequestration in the long‐term and therefore the conservation of biodiversity might play a role in greenhouse gas mitigation.
Microarray analysis of acaricide‐inducible gene expression in the southern cattle tick, Rhipicephalus (Boophilus) microplus
Authors: Saldivar L. , Guerrero F. D. , Miller R. J. , Bendele K. G. , Gondro C. , Brayton K. A.
Published: September 2008

Acaricide‐inducible differential gene expression was studied in larvae of Rhipicephalus (Boophilus) microplus using a microarray‐based approach. The acaricides used were: coumaphos, permethrin, ivermectin, and amitraz. The microarrays contained over 13 000 probes, having been derived from a previously described R. microplus gene index (BmiGI Version 2; Wang et al., 2007). Relative quantitative reverse transcriptase‐PCR, real time PCR, and serial analysis of gene expression data was used to verify microarray data. Among the differentially expressed genes with informative annotation were legumain, glutathione S‐transferase, and a putative salivary gland‐associated protein.
Impact of outdoor winter sports on the abundance of a key indicator species of alpine ecosystems
Authors: Patthey Patrick , Wirthner Sven , Signorell Natalina , Arlettaz Raphaël
Published: September 2008

Tourism and leisure activities have increased continuously all over the world during the past decades, exerting a growing pressure upon naturally fragile ecosystems, such as mountainous habitats. Recent studies have established that disturbance by outdoor winter sports (e.g. skiing, snowboarding and snowshoeing) is a source of stress for wildlife. This may in turn affect its abundance, but we still lack quantitative evidence.

We tested the effect of outdoor winter sports (ski lifts and related recreational activities) on the abundance of the alpine black grouse Tetrao tetrix, a vulnerable indicator species of the timberline ecosystem, the favoured habitat for outdoor winter sports in the European Alps.

Generalized linear models and a model selection approach were used to rank environmental factors influencing black grouse abundance and to make predictions about population status in the theoretical absence of ski resorts. We modelled the number of displaying cocks along census transects in spring, as a function of habitat characteristics (vegetation structure and typology), ski lift density and hunting pressure at 15 natural sites (none or a very low level of anthropogenic disturbance) and 15 ski resorts in the south‐western Swiss Alps.

Ski lift density and habitat typology were the principal determinants of black grouse abundance, whereas hunting pressure had no discernable effect. Ski lifts and related winter sport activities had a strong negative effect on the number of displaying cocks, which may have led to a mean 36% reduction of local abundance in ski lift areas, as determined after controlling for the confounding effect of habitat type.

Synthesis and applications. Conservation action plans for black grouse should aim at reducing the multiple negative effects generated by outdoor winter sports (ski facilities and related winter sport activities). First, vegetation patchiness (i.e. a mosaic of grassy shrubland with scattered trees) should be maintained along ski runs. Secondly, wintering preserves where human access is banned or strictly limited should be promoted within ski resorts. Spatially explicit human–wildlife conflict maps can be constructed from the present model to allow delineation of those areas likely to become effective protection areas.
Phylogeography of red deer (Cervus elaphus) in Europe
Authors: Skog A. , Zachos F. E. , Rueness E. K. , Feulner P. G. D. , Mysterud A. , Langvatn R. , Lorenzini R. , Hmwe S. S. , Lehoczky I. , Hartl G. B. , Stenseth N. C. , Jakobsen K. S.
Published: September 2008

Aim  To investigate the phylogeographical patterns of red deer (Cervus elaphus) in Europe, and to disentangle the influence of ancient (e.g. Pleistocene ice ages) from more recent processes (e.g. human translocations).

Location  Europe.

Methods  In this study we provide by far the most extensive analysis of genetic structure in European red deer, based on analyses of variation at two mitochondrial markers (cyt b and D‐loop) in a large number of individuals from 39 locations. Relationships of mitochondrial DNA haplotypes were determined using minimum spanning networks and phylogenetic analyses. Population structure was examined by analyses of molecular variance. Historical processes shaping the present patterns were inferred from nested clade analysis and nucleotide diversity statistics.

Results  Within Europe, we detected three deeply divergent mitochondrial DNA lineages. The three lineages displayed a phylogeographical pattern dividing individuals into western European, eastern European and Mediterranean (Sardinia, Spain and Africa) groups, suggesting contraction into three separate refugia during the last glaciation. Few haplotypes were shared among these three groups, a finding also confirmed by FST values. Calculations of divergence times suggest that the groups probably split during the Pleistocene.

Main conclusions  The observed pattern is interpreted to result from isolation in different refugia during the last glaciation. The western and eastern European lineages could be linked to an Iberian and Balkan refugium, respectively. The third lineage might originate from a Sardinian or African refugium. We link local phylogeographical patterns observed in Europe to the post‐glacial recolonization process, shaped by the geographical localization of refugia and barriers to gene flow. Regardless of the importance of red deer as a game species and the tradition of translocating red deer in Europe, we detected few individuals that did not match the trichotomous pattern, suggesting that translocations have occurred mainly at smaller spatial scales.
The application of Bayesian spectral analysis to optical sectioning using structured light imaging
Authors: Ó RUANAIDH J.J.K. , MCKAY R.R. , ZHANG Y. , BRIGGS M. , GEORGE J. , MASOUMI Z.
Published: September 2008

We describe significant improvements to a well‐established method of obtaining optical sectioning in a conventional wide‐field microscope. This method relies on the projection of a single‐frequency grid pattern onto an object followed by mathematical manipulation of three images taken with the grid in different phases. Here, we present the use of Bayesian Spectral Analysis to determine accurate estimates of the phase of the grid pattern, permitting rapid and precise calibration of grid location. In common with previous algorithms, multiple images are combined to produce both an optical section and a wide‐field image. We describe innovations such as the use of non‐uniform phase or least‐squares solutions involving more than three images, in conjunction with direct phase estimates obtained using Bayesian Spectral Analysis, to yield images substantially free of artefacts. Auxiliary results, such as a method for determining the tilt of the grid, are also presented.
The fractional Talbot effect in differential x‐ray phase‐contrast imaging for extended and polychromatic x‐ray sources
Authors: ENGELHARDT M. , KOTTLER C. , BUNK O. , DAVID C. , SCHROER C. , BAUMANN J. , SCHUSTER M. , PFEIFFER F.
Published: September 2008

The influence of different physical parameters, such as the source size and the energy spectrum, on the functional capability of a grating interferometer applied for phase‐contrast imaging is discussed using numerical simulations based on Fresnel diffraction theory. The presented simulation results explain why the interferometer could be well combined with polychromatic laboratory x‐ray sources in recent experiments. Furthermore, it is shown that the distance between the two gratings of the interferometer is not in general limited by the width of the photon energy spectrum. This implies that interferometers that give a further improved image quality for phase measurements can be designed, because the primary measurement signal for phase measurements can be increased by enlargement of this distance. Finally, the mathematical background and practical instructions for the quantitative evaluation of measurement data acquired with a polychromatic x‐ray source are given.
Differentiation of live‐viable versus dead bacterial endospores by calibrated hyperspectral reflectance microscopy
Authors: ANDERSON J. , REYNOLDS C. , RINGELBERG D. , EDWARDS J. , FOLEY K.
Published: September 2008

This paper describes the use of hyperspectral imaging microscopy (HIM) for the characterization and differentiation of live viable versus dead/non‐viable bacterial endospores for two species of Bacillus. To accomplish this, endospore‐forming Bacillus were cultured and differentiated into endospores. Non‐viable endospores were produced using sporicidal methods representing standard decontamination procedures incorporating chlorine and peroxide. Finally, endospore samples were lyophilized to prepare them for spectral analysis. Prior to HIM, baseline spectral reflectance characterizing the endospores was measured using an ASD (400–900 nm) reflectance spectrometer. These data were used to calibrate the resulting spectral image data. HIM data comprising 32 images ranging from 400 to 720 nm (visible to near infrared) were recorded using a C‐mounted VariSpec hyperspectral camera attached to an epifluorescent microscope. The images produced by the system record the reflectance and absorption features of endospores based on the structure of the outer coat. Analysis of the HIM data was performed using accepted image and spectral processing routines. Where peroxide was the sporicide, changes in the outer endospore coat contributed to structurally significant visible and near infrared signature differences between live‐viable versus dead, non‐viable endospores. A statistical test for divergence, a method for scoring spectral structural diversity, also showed the difference between viable and non‐viable peroxide killed endospores to be statistically significant. These findings may lead to an improved optical procedure to rapidly identify viable and non‐viable endospores in situations of decontamination.
Contribution of electron precession to the study of perovskites displaying small symmetry departures from the ideal cubic ABO3 perovskite: applications to the LaGaO3 and LSGM perovskites
Authors: MORNIROLI J.‐P. , AUCHTERLONIE G. J. , DRENNAN J. , ZOU J.
Published: September 2008

Electron microscopy and electron diffraction are well adapted to the study of the fine‐grained, faulted pure and doped LaGaO3 and LSGM perovskites in which the latter is useful for fuel cell components. Because these perovskites display small symmetry departures from an ideal cubic ABO3 perovskite, many conventional electron diffraction patterns look similar and cannot be indexed without ambiguity. Electron precession can easily overcome this difficulty mainly because the intensity of the diffracted beams on the precession patterns is integrated over a large deviation domain around the exact Bragg condition. This integrated intensity can be trusted and taken into account to identify the ‘ideal’ symmetry of the precession patterns (the symmetry which takes into account both the position and the intensity of the diffracted beams). In the present case of the LaGaO3 and LSGM perovskites, the determination of the ‘ideal’ symmetry of the precession patterns is based on the observation of weak ‘superlattice’ reflections typical of the symmetry departures. It allows an easy and sure identification of any zone axes as well as the correct attribution of hkl indices to each of the diffracted beams. Examples of applications of this analysis to the characterizations of twins and to the identification of the space groups are given. This contribution of electron precession can be easily extended to any other perovskites or to any crystals displaying small symmetry departures.