bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comparison of Different Culture Methods for the Recovery ofCampylobacterSpecies from Pets
Authors: Acke E. , McGill K. , Golden O. , Jones B. R. , Fanning S. , Whyte P. 
Published: February 2009

SummaryFive culture methods for the recovery ofCampylobacterspecies (spp.) were evaluated on 361 rectal swabs collected from cats and dogs in Ireland. Speciation using PCR methods was performed on all isolates to assess the sensitivity of each culture method for isolation ofCampylobacterspp., and to establish the prevalence ofCampylobacter jejuni,C. coli,C. upsaliensis,C. lariandC. helveticus. Overall 163 of 361 (45.2%) samples were confirmedCampylobacterspp. positive. Direct plating onto modified charcoal cefoperazone deoxycholate agar (mCCDA) with cefoperazone, amphotericin and teicoplanin (CAT) selective supplement yielded a significantly higher prevalence ofCampylobacterspp. (33.0%) than each of the other four methods (P ≤ 0.05). This method was also the most sensitive method for isolation ofC. upsaliensiscompared with any of the other four methods used in the current study (P ≤ 0.05). A direct plating method onto mCCDA agar with CCDA selective supplement and a filtration method onto blood agar after pre‐enrichment in CAT supplemented broth yielded lowerCampylobacterspp. prevalences of 19.7% and 17.5% respectively. A filtration method onto CAT agar and pre‐enrichment in Preston broth before plating onto mCCDA agar were less sensitive for the isolation ofCampylobacterspp. Speciation results ofCampylobacterisolates revealed the majority ofCampylobacterisolates wereC. upsaliensis(50.0%) andC. jejuni(41.9%). A small number of isolates wereC. coli(2.6%),C. lari(1.5%) andC. helveticus(1.1%). The overall detection ofCampylobacterspp. in the 361 pets sampled was significantly increased by using a combination of isolation methods (P ≤ 0.05), producing a more accurate determination of the prevalence ofCampylobacterspp. in pets in Ireland and of the actualCampylobacterspecies. As the majority ofCampylobacterspp. were recovered by direct plating onto mCCDA agar with CAT supplement, this method is the method of choice if only a single method is selected for isolation of the most commonCampylobacterspp. detected in pets and humans.
Periplasmic
c
Cytochromes and Chlorate Reduction in
Ideonella dechloratans
Authors: Bäcklund Anna Smedja , Bohlin Jan , Gustavsson Niklas , Nilsson Thomas 
Published: February 2009

ABSTRACT

The aim of this study was to clarify the pathway of electron transfer between the inner membrane components and the periplasmic chlorate reductase. Several soluble
c
-type cytochromes were found in the periplasm. The optical difference spectrum of dithionite-reduced periplasmic extract shows that at least one of these components is capable of acting as an electron donor to the enzyme chlorate reductase. The cytochromes were partially separated, and the fractions were analyzed by UV/visible spectroscopy to determine the ability of donating electrons to chlorate reductase. Our results show that one of the
c
cytochromes (6 kDa) is able to donate electrons, both to chlorate reductase and to the membrane-bound cytochrome
c
oxidase, whereas the roles of the remaining
c
cytochromes still remain to be elucidated. Peptide extracts of the
c
cytochromes were obtained by tryptic in-gel digestion for matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis. Peptide sequences obtained indicate that the 6-kDa cytochrome
c
protein is similar to
c
cytochromes from the chlorate-reducing bacterium
Dechloromonas aromatica
.
Analysis of Variance Components Reveals the Contribution of Sample Processing to Transcript Variation
Authors: van der Veen Douwe , Oliveira José Miguel , van den Berg Willy A. M. , de Graaff Leo H. 
Published: February 2009

ABSTRACTThe proper design of DNA microarray experiments requires knowledge of biological and technical variation of the studied biological model. For the filamentous fungusAspergillus niger, a fast, quantitative real-time PCR (qPCR)-based hierarchical experimental design was used to determine this variation. Analysis of variance components determined the contribution of each processing step to total variation: 68% is due to differences in day-to-day handling and processing, while the fermentor vessel, cDNA synthesis, and qPCR measurement each contributed equally to the remainder of variation. The global transcriptional response tod-xylose was analyzed using Affymetrix microarrays. Twenty-four statistically differentially expressed genes were identified. These encode enzymes required to degrade and metabolized-xylose-containing polysaccharides, as well as complementary enzymes required to metabolize complex polymers likely present in the vicinity ofd-xylose-containing substrates. These results confirm previous findings that thed-xylose signal is interpreted by the fungus as the availability of a multitude of complex polysaccharides. Measurement of a limited number of transcripts in a defined experimental setup followed by analysis of variance components is a fast and reliable method to determine biological and technical variation present in qPCR and microarray studies. This approach provides important parameters for the experimental design of batch-grown filamentous cultures and facilitates the evaluation and interpretation of microarray data.
Culture-Independent Characterization of Bacterial Communities Associated with the Cold-Water Coral
Lophelia pertusa
in the Northeastern Gulf of Mexico
Authors: Kellogg Christina A. , Lisle John T. , Galkiewicz Julia P. 
Published: February 2009

ABSTRACT

Bacteria are recognized as an important part of the total biology of shallow-water corals. Studies of shallow-water corals suggest that associated bacteria may benefit the corals by cycling carbon, fixing nitrogen, chelating iron, and producing antibiotics that protect the coral from other microbes. Cold-water or deep-sea corals have a fundamentally different ecology due to their adaptation to cold, dark, high-pressure environments and as such have novel microbiota. The goal of this study was to characterize the microbial associates of
Lophelia pertusa
in the northeastern Gulf of Mexico. This is the first study to collect the coral samples in individual insulated containers and to preserve coral samples at depth in an effort to minimize thermal shock and evaluate the effects of environmental gradients on the microbial diversity of samples. Molecular analysis of bacterial diversity showed a marked difference between the two study sites, Viosca Knoll 906/862 (VK906/862) and Viosca Knoll 826 (VK826). The bacterial communities from VK826 were dominated by a variety of unknown mycoplasmal members of the
Tenericutes
and
Bacteroidetes
, whereas the libraries from VK906/862 were dominated by members of the
Proteobacteria
. In addition to novel sequences, the 16S rRNA gene clone libraries revealed many bacterial sequences in common between Gulf of Mexico
Lophelia
corals and Norwegian fjord
Lophelia
corals, as well as shallow-water corals. Two
Lophelia
-specific bacterial groups were identified: a cluster of gammaproteobacteria related to sulfide-oxidizing gill symbionts of seep clams and a group of
Mycoplasma
spp. The presence of these groups in both Gulf and Norwegian
Lophelia
corals indicates that in spite of the geographic heterogeneity observed in
Lophelia
-associated bacterial communities, there are
Lophelia
-specific microbes.
Structural Insights into the Extracytoplasmic Thiamine-Binding Lipoprotein p37 of
Mycoplasma hyorhinis
Authors: Sippel Katherine H. , Robbins Arthur H. , Reutzel Robbie , Boehlein Susan K. , Namiki Kazunori , Goodison Steve , Agbandje-McKenna Mavis , Rosser Charles J. , McKenna Robert 
Published: February 2009

ABSTRACT

The
Mycoplasma hyorhinis
protein p37 has been implicated in tumorigenic transformation for more than 20 years. Though there are many speculations as to its function, based solely on sequence homology, the issue has remained unresolved. Presented here is the 1.6-Å-resolution refined crystal structure of
M. hyorhinis
p37, renamed the extracytoplasmic thiamine-binding lipoprotein (Cypl). The structure shows thiamine pyrophosphate (TPP) and two calcium ions are bound to Cypl and give the first insights into possible functions of the Cypl-like family of proteins. Sequence alignments of Cypl-like proteins between several different species of mycoplasma show that the thiamine-binding site is likely conserved and structural alignments reveal the similarity of Cypl to various binding proteins. While the experimentally determined function of Cypl remains unknown, the structure shows that the protein is a TPP-binding protein, opening up many avenues for future mechanistic studies and making Cypl a possible target for combating mycoplasma infections and tumorigenic transformation.
Health consequences of sustained smoking cessation
Authors: Bjartveit K , Tverdal A 
Published: February 2009

Objectives:To estimate the risk of dying from all causes and from specified smoking-related diseases in people who were ex-smokers at two consecutive examinations, compared with never smokers and with people who were ex-smokers at the first examination but who had resumed smoking at the following examination.Design:A prospective cohort study.Setting:Three counties in Norway.Participants:A total of 23 560 men and 25 122 women, aged 20–49, screened for cardiovascular disease risk factors in the mid 1970s, rescreened after 3–13 years and followed throughout 2005 participated in this study.Outcomes:Absolute mortality and relative risks adjusted for confounding variables, of dying from all causes, cardiovascular disease, ischaemic heart disease, stroke, lung cancer and other smoking-related cancer.Results:With sustained never smokers as reference, the sustained ex-smokers had adjusted relative risk (95% CI), of dying from any cause, for men 0.97 (0.80 to 1.18), for women 0.98 (0.65 to 1.48). Corresponding risk for ex-smokers who resumed smoking was for men 1.59 (1.32 to 1.91), for women 1.40 (1.08 to 1.81). For the specified smoking-related diseases, the risk in sustained ex-smokers was not significantly different from the risk in sustained never-smokers, except for lung cancer in men. For ex-smokers who resumed smoking, the corresponding risk was on the whole significantly higher.Conclusions:A more valid and favourable picture of ex-smokers’ risk will be obtained if exposure is being based upon people with two consecutive examinations, years apart. The study confirms clearly the large health benefit of quitting smoking for good.
Genetic diversity analysis in blackgram (Vigna mungo (L.) Hepper) using AFLP and transferable microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi)
Authors: Gupta S. K. , Gopalakrishna T. 
Published: February 2009

Genetic diversity in 20 elite blackgram ( Vigna mungo (L.) Hepper) genotypes was studied using microsatellite and AFLP markers. Thirty-six microsatellite markers from azuki bean ( Vigna angularis (Willd.) Ohwi & Ohashi) were successfully amplified across the 20 blackgram genotypes and 33 microsatellite markers showed polymorphism. A total of 137 microsatellite alleles were generated with an average of 4.1 alleles per locus. The number of alleles ranged from two to nine and the polymorphic information content value for the microsatellite markers varied from 0.10 to 0.87 with an average of 0.49. Microsatellite markers were highly informative and a combination of only three microsatellite markers (CEDG264, CEDG173, and CEDG044) was sufficient to discriminate all 20 blackgram genotypes. In the case of AFLP, 11 primer pairs generated 324 polymorphic marker fragments. The polymorphic information content values for AFLP primer combinations ranged from 0.21 to 0.34 with an average of 0.29. Similarity measures and clustering analyses were made using microsatellite and AFLP data separately. The resulting dendrograms distributed the 20 blackgram genotypes into five main clusters. The dendrograms were comparable with each other with the Mantel test between the cophenetic matrices of microsatellite data and AFLP data showing moderate correlation (r = 0.64). The results of the principal components analysis were well congruent with the dendrograms. In the dendrograms as well as in the principal components analyses, genotype Trombay wild (Vigna mungo var. silvestris) was placed separately from rest of the genotypes. This study demonstrated that the azuki bean microsatellite markers are highly polymorphic and informative and can be successfully used for genome analysis in blackgram. Results indicate that sufficient variability is present in the blackgram genotypes and would be helpful in the selection of suitable parents for breeding purposes and gene mapping studies.
The heat shock 70 genes of the olive pest Bactrocera oleae: genomic organization and molecular characterization of a transcription unit and its proximal promoter region
Authors: Drosopoulou Elena , Chrysopoulou Anastasia , Nikita Venetia , Mavragani-Tsipidou Penelope 
Published: February 2009

A Bactrocera oleae genomic library was constructed and several genomic clones bearing hsp70 sequences were isolated. All clones were in situ hybridized on the major heat shock puff locus of the salivary gland polytene chromosomes. Restriction mapping of the isolated clones and genomic Southern hybridization indicated the presence of several putative hsp70 genes organized in a single cluster. Sequence analysis of an hsp70 transcription unit revealed a single 1905 nt long open reading frame that exhibits characteristic features of the inducible members of the HSP70 family. The presence and organization of many typical binding sites for the Heat Shock and GAGA factors suggest that the promoter of this gene is highly heat-inducible and could be used for conditional expression in transformation systems.
HcrVfparalogs are present on linkage groups 1 and 6 ofMalus
Authors: Broggini Giovanni A.L. , Galli Paolo , Parravicini Gabriella , Gianfranceschi Luca , Gessler Cesare , Patocchi Andrea 
Published: February 2009

Molecular markers derived from resistance gene analogs of HcrVf2, the first apple resistance gene cloned, may pave the way to the cloning of additional apple scab resistance genes. The Malus ×domestica ‘Florina’ (Vf) bacterial artificial chromosome (BAC) genomic library was screened by hybridization using HcrVf2 as a probe. Positive BAC clones were assembled into contigs and microsatellite markers developed from each contig mapped. Only linkage groups 1 and 6 contained HcrVf2 paralogs. On linkage group 1, five loci in addition to the Vf locus were identified. A single locus was detected on linkage group 6. Representative BAC clones of these loci including the Vf locus were sequenced and the gene structure compiled. A total of 22 sequences, showing high sequence similarity to HcrVf2, were identified. Nine sequences were predicted to encode all seven protein domains described in HcrVf2, while three were truncated. Transcriptional analysis indicated that six genes with a complete HcrVf-like structure were constitutively expressed in young uninfected leaves of ‘Florina’. The map position of each HcrVf analog was compared with the location of the major apple scab resistance genes. None of the major genes conferring scab resistance co-localized with HcrVf paralogs, indicating that they are unlikely to belong to the leucine-rich repeat – transmembrane class, which includes the Vf gene.
Genetic analysis and historical perspective of cashew (Anacardium occidentaleL.) introduction into India
Authors: Archak S. , Gaikwad A. B. , Swamy K. R.M. , Karihaloo J. L. 
Published: February 2009

Cashew ( Anacardium occidentale L.), introduced into India about 400 years ago, is distributed widely in the coastal regions as spontaneous populations as well as in cultivation. Despite the plant’s commercial exploitation, little is known about its actual introduction and diversification. We attempted to construct these events by investigating the level of genetic variation and genetic structure of cashew populations collected from different geographical regions of India. A total of 91 individuals from four populations were analysed using AFLP markers and morphometric data. AFLP analysis based on 354 polymorphic loci revealed Indian cashew to have low but relatively substantial genetic diversity for an introduced species (HE = 0.262 and IS = 0.404). Twenty-seven qualitative and quantitative traits also revealed the existence of considerable morphometric variation (24% around the mean values). Bayesian cluster analysis based on AFLP data did not indicate the existence of definite population differentiation. Morphometric analysis allocated 12% variation among all four populations, whereas AFLP variation observed in cashew individuals was entirely within populations. The results, supporting the possibility of cashew having been introduced into India repeatedly over a period of time but at a single location (west coast), are discussed and their implications for germplasm management are described.
Physical activity, cardiorespiratory fitness, and metabolic syndrome in young Mexican and Mexican-American women
Authors: Vella Chantal A. , Zubia Raul Y. , Ontiveros Diana , Cruz Martha L. 
Published: February 2009

Young adult women have had the greatest increase in prevalence of metabolic syndrome (MetS) over time, and prevalence is highest in Hispanic women, compared with women of other ethnicities. Factors contributing to the high prevalence of MetS in Hispanic women are unknown. This study was conducted to determine if physical activity or fitness were associated with individual features of MetS in young Mexican and Mexican-American women, and if the associations were independent of fat mass. Sixty young Mexican and Mexican-American women participated in the study. MetS was defined according to the Adult Treatment Panel III. A fasting blood sample was drawn for the measurement of glucose, insulin, high-density lipoprotein cholesterol (HDL-c), and triglycerides. Physical activity was assessed by questionnaire and accelerometer. Fitness was assessed by progressive treadmill test to exhaustion and ventilatory threshold. Body composition was assessed with Bod Pod. Multivariate regression was used to establish the independent contributions of physical activity and fitness to the individual features of MetS. After controlling for fat mass and fat-free mass, physical activity was found to be independently related to HDL-c and fitness was found to be independently related to triglycerides (p < 0.05). The independent associations between physical activity, fitness, and features of MetS were mediated by, rather than independent of, fat mass. Fat mass was independently related to triglycerides, systolic blood pressure, and diastolic blood pressure. Although physical activity and fitness were related to features of MetS, these associations were not independent of fat mass.
Replicating chromatin: a tale of histonesThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.
Authors: Groth Anja 
Published: February 2009

Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures reassembly on nascent DNA strands. The aim of this review is to discuss how histones — new and old — are handled at the replication fork, highlighting new mechanistic insights and revisiting old paradigms.
Stand-replacing windthrow in the boreal forests of eastern Quebec
Authors: Bouchard Mathieu , Pothier David , Ruel Jean-Claude 
Published: February 2009

The frequency of stand-replacing windthrow has rarely been evaluated over large spatio-temporal scales in boreal forests. This study examines stand-replacing windthrow that occurred within a forested area of 3 061 000 ha, both at the regional scale and at the scale of individual windthrow events. We specifically examined windthrow that covered at least 5 ha and for which mortality affected >75% of pre-windthrow canopy cover. At the regional scale, we found that windthrow affected, on average, 0.0255% of the area per year between 1971 and 2000. Logistic regressions indicate that stand age was the most important predictor variable at this scale, with severe windthrow less likely to occur in relatively young stands (<75 years). At the scale of individual windthrow events, slope direction was the most important predictor variable, with slopes facing the wind affected more. However, this factor was not significant at the regional scale probably because wind direction varied from one windthrow event to another. Overall, our results suggest that stand-replacing windthrow is difficult to predict and integrate into regional-scale forest management scenarios because it is primarily associated with the random occurrence of exceptional windstorms, while other biotic and abiotic variables play a relatively marginal role.
Role of oxidative stress in ischemia–reperfusion-induced alterations in myofibrillar ATPase activities and gene expression in the heartThis article is one of a selection of papers from the NATO Advanced Research Workshop on Translational Knowledge for Heart Health (published in part 1 of a 2-part Special Issue).
Authors: Maddika Srilekha , Elimban Vijayan , Chapman Donald , Dhalla Naranjan S. 
Published: February 2009

Ischemia–reperfusion (IR) in the heart has been shown to produce myofibrillar remodeling and depress Ca2+ sensitivity of myofilaments; however, the mechanisms for these alterations are not clearly understood. In view of the role of oxidative stress in cardiac dysfunction due to IR, isolated rat hearts were subjected to global ischemia for 30 min followed by a 30-minute period of reperfusion. IR was found to induce cardiac dysfunction, as reflected by depressed LVDP, +dP/dt, and –dP/dt, and elevated LVEDP, and to reduce myofibrillar Ca2+-stimulated ATPase activity. These changes were simulated by perfusing the hearts with a mixture of xanthine plus xanthine oxidase, which is known to generate oxyradicals. The alterations in cardiac function and myofibrillar Ca2+-stimulated ATPase in IR hearts were attenuated by pretreatment with antioxidants (superoxide dismutase plus catalase, and N-acetylcysteine) and leupeptin, an inhibitor of Ca2+-dependent protease. The levels of mRNA for myosin heavy chain isoforms (α-MHC and β-MHC) and myosin light chain (MLC1) were depressed in IR hearts. These changes in gene expression due to IR were prevented upon perfusing the hearts with superoxide plus catalase, with N-acetylcysteine, or with leupeptin. The results suggest that oxidative stress due to IR injury and associated proteolysis play an important role in inducing changes in myofibrillar Ca2+-stimulated ATPase activity and gene expression in the heart.