bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paternity determination of interspecific rhododendron hybrids by genomic in situ hybridization (GISH)
Authors: Czernicka Małgorzata , Mścichowska Anna , Klein Maria , Muras Piotr , Grzebelus Ewa 
Published: May 2010

Genomic in situ hybridization (GISH) has been proved to be the most effective and accurate technique for confirmation of hybrid character. The objective of our study was to adapt and optimize a GISH protocol for identification of donor chromatin in hybrids obtained by interspecific crosses between five Rhododendron taxa ( R. aureum , R. brachycarpum , R. catawbiense ‘Catharine van Tol’, R. catawbiense ‘Nova Zembla’, and R. yakushimanum ‘Koichiro Wada’). Positive results were obtained only when we used mitotic chromosome spreads prepared from anthers. The best differentiation of maternal and paternal chromosomes in hybrid genomes was obtained when 50 ng of probe was applied together with blocking DNA at a concentration of 3.0 µg/µL. The results demonstrate that GISH is a practical tool for detection of alien genomes and analysis of the constitution of the chromosomes in rhododendron hybrids.
Microsatellite-based genetic relationships in the genusCamellia: potential for improving cultivars
Authors: Caser Matteo , Torello Marinoni Daniela , Scariot Valentina 
Published: May 2010

There is a lack of published microsatellite data that characterizes Camellia spp. To address this, an initial study of sequence tagged microsatellite site (STMS) variation was undertaken with 132 accessions of Camellia spp., which included 24 accessions representing 22 different species or varieties as well as 63 cultivars of C. japonica , 33 cultivars of C. sasanqua , 7 cultivars of C. ×vernalis, 3 cultivars of C. ×hiemalis, and 2 cultivars of C. hybrida . The four primer sets used (MSCJAF37, MSCJAH46, MSCJAF25, and MSCJAH38) successfully amplified polymorphic alleles in all the species analysed, showing cross-transferability. Overall, 96 alleles were scored. MSCJAH38 primers produced the highest number of bands (30), while MSCJAH46 primers yielded the lowest number (15). The genetic distance between pairs of accessions was estimated on the basis of the Nei coefficient and a principal coordinate analysis was performed. The plot revealed a main differentiation between the C. japonica cultivars and the winter camellias. The distribution of the genetic variation, attributed by AMOVA, particularly highlighted genetic overlap among C. sasanqua cultivars and the cultivars belonging to C. ×vernalis, C. ×hiemalis, and C. hybrida. In conclusion, this study demonstrated that STMS markers offer a suitable method for detection of genetic variability and molecular study of camellia genotypes.
Impact of microwave radiation on nitrogen removal and quantity of nitrifiers in biofilmA paper submitted to the Journal of Environmental Engineering and Science.
Authors: Zieliński Marcin , Zielińska Magdalena 
Published: May 2010

The aim of this study was to determine the impact of microwave radiation on the efficiency of nitrification and on the percentage of ammonia-oxidizing bacteria in biofilm and to study the possibility of the occurrence of nonthermal effects caused by the interaction of microwaves and biofilm. Eight trickling filters with a biofilm were used in the experiment: four were exposed to microwave radiation, and four were heated with warm air as a control group. Microwave radiation at a frequency of 2.45 GHz was applied at an intensity of 18 W (0.01 W·cm–3of the reactor packing), which increased the biofilm temperature by 6 °C compared with the ambient temperature. The hydraulic loading averaged 0.30 m3·m–2·h–1, and the organic loading equalled 1.93 g chemical oxygen demand (COD)·m–2·d–1. Microwave radiation had an effect on the concentration of nitrogen compounds in the biofilm, and microwave heating triggered alterations within the biofilm that increased the efficiency of both nitrification and denitrification and the percentage of ammonia-oxidizing bacteria.
Hydraulic jump in sloping channels: roller length and energy loss
Authors: Beirami M. K. , Chamani M. R. 
Published: May 2010

This paper deals with the roller length and energy loss of a large variety of hydraulic jumps in horizontal and sloping channels. The supercritical upstream flow originated from a standard ogee weir. A stilling basin with bottom slopes of 0.0, −0.025, −0.050, −0.075, and −0.100 was used to generate the jumps. Based on the energy principle, a semi-empirical method to predict the roller length is presented. Predictions based on the proposed method agree well with the results reported by the authors and other researchers. It is shown that the energy loss in the classical jump is greater than that in any jump forming on negative or positive slopes.
Geometry of developing and equilibrium scour holes at bridge piers in gravel
Authors: Diab Reda , Link Oscar , Zanke Ulrich 
Published: May 2010

Experimental results on scour at circular and square cylinders in uniform gravel under the clear-water scour condition are presented. Nonintrusive, high-resolution topographic measurements of developing and equilibrium scour holes were performed during running experiments with an experimental installation using a laser distance sensor (LDS) and precision step motors. Measurements were taken by the LDS in different azimuthal half-planes with θ = 0°, 15°, 30°, 45°, 60°, 75°, 90°, 105°, 135°, 150°, 165°, and 180° to study the spatio-temporal variation of geometric properties of scour holes. Experiments were conducted over 40 h until equilibrium, with bed shear stress equal to 95% of the critical bed shear stress for the initiation of sediment motion at the undisturbed plane gravel bed having a d50of 3.25 mm. Results show that scour in gravel progresses more slowly around the square cylinder, where steeper slopes than at the circular cylinder are observed. During experiments the scour slopes do not exceed the observed repose angle of the sediment particles. Maximum scour depth in different azimuthal half-planes and scoured volume are well correlated with the maximum scour depth at azimuthal half-plane with θ = 0°.
Fuzzy complexes of myelin basic protein: NMR spectroscopic investigations of a polymorphic organizational linker of the central nervous systemThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.
Authors: Libich David S. , Ahmed Mumdooh A.M. , Zhong Ligang , Bamm Vladimir V. , Ladizhansky Vladimir , Harauz George 
Published: May 2010

The classic 18.5 kDa isoform of myelin basic protein (MBP) is central to maintaining the structural homeostasis of the myelin sheath of the central nervous system. It is an intrinsically disordered, promiscuous, multifunctional, peripheral membrane protein, whose conformation adapts to its particular environment. Its study requires the selective and complementary application of diverse approaches, of which solution and solid-state NMR spectroscopy are the most powerful to elucidate site-specific features. We review here several recent solution and solid-state NMR spectroscopic studies of 18.5 kDa MBP, and the induced partial disorder-to-order transitions that it has been demonstrated to undergo when complexed with calmodulin, actin, and phospholipid membranes.
Partial unfolding and oligomerization of stromal interaction molecules as an initiation mechanism of store operated calcium entryThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.
Authors: Stathopulos Peter B. , Ikura Mitsuhiko 
Published: May 2010

Spatiotemporally discrete cytoplasmic Ca2+ fluctuations are fundamental eukaryotic signals in myriad physiological and pathophysiological functions. Store-operated Ca2+ entry is the process whereby a decrease in endoplasmic reticulum (ER) luminal Ca2+ levels activates Ca2+ release activated calcium (CRAC) channels on the plasma membrane (PM), providing a sustained Ca2+ elevation to the cytoplasm and ultimately replenishing the ER lumen Ca2+ supply. Stromal interaction molecules (STIMs) are the Ca2+ sensors of the ER lumen, which macromolecularly couple depleted ER Ca2+ to the assembly and opening of PM CRAC channels. The considerable stability difference caused by Ca2+ loading and depletion within the luminal portion of STIMs modulates intramolecular cytoplasmic domain interactions essential to the assembly of PM CRAC channels. Thus, the action of the entire complex is tightly regulated through the Ca2+ sensitivity of luminal STIM domains. Recent structural and biochemical studies suggest that partial unfolding – coupled oligomerization of STIMs is a crucial step in CRAC channel activation. Based on these and other published data, this minireview discusses what is currently known about the molecular mechanism of ER Ca2+ sensing by STIMs.
Mutational investigation of protein folding transition states by Φ-value analysis and beyond: lessons from SH3 domain foldingThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.
Authors: Zarrine-Afsar Arash , Lin Sung Lun , Neudecker Philipp 
Published: May 2010

Understanding how proteins adopt their unique native structures requires a complete structural characterization of the rate-limiting transition state(s) along the folding pathway. By definition, transition states are not significantly populated and are only accessible via folding kinetics studies. In this respect, interpreting the kinetic effects of amino acid substitutions (especially to Ala) via Φ-value analysis is the most common method to probe the structure of these transient, yet important states. A critical review of the key assumptions required for rigorous interpretation of Φ values reveals that a multiple substitution strategy in which a position of interest is mutated to a variety of amino acids, and not exclusively to Ala, provides the best means to characterize folding transition states. This approach has proven useful in revealing non-native interactions and (or) conformations in folding transition states. Moreover, by simultaneously examining the folding kinetics of multiple substitutions made at a single surface-exposed position using the Brønsted analysis the backbone conformation in a folding transition state can be investigated. For folding equilibria with exchange rates on the order of milliseconds, the kinetic parameters for Φ-value analysis can be obtained from NMR relaxation dispersion experiments, under fully native conditions, along with a wealth of high-resolution structural information about the states in exchange (native, denatured, and intermediate states that populate the pathway). This additional structural information, which is not readily obtained through stopped-flow based methods, can significantly facilitate the interpretation of Φ values because it often reports on the validity of the assumptions required for a rigorous interpretation of Φ values.
The utility and application of real-time PCR and FISH in the detection of single-copy gene targets inEscherichia coliO157:H7 andSalmonellaTyphimurium
Authors: Haffar Merriam , Gilbride Kimberley A. 
Published: May 2010

The ultimate specificity in molecular-based assays for pathogen detection relies on the design of the primers and probes. Their ability to hybridize to DNA sequences found only in pathogens can be realized by designing primers and probes that are complementary to pathogen-specific virulence genes. This study evaluates the detection and enumeration strengths of real-time PCR (qPCR) and fluorescent in situ hybridization (FISH) for selected waterborne pathogens and their ultimate applicability within a monitoring framework. Detection limits calculated in the qPCR assay were 150 tir (intimin protein receptor) gene copies for Escherichia coli O157:H7 and 2 × 103invA (inner membrane invasive protein) gene copies for Salmonella enterica serovar Typhimurium. Detection limits were, however, at least 100-fold less sensitive in wastewater extracts, partly because of the inhibitory effect of the wastewater itself. Fluorescent signals from hybridized whole target cells were below the detection limit of the FISH assay. While this research demonstrates the potential detection strength of qPCR, it highlights the need for strong dependable primer and probe sets among PCR and FISH methodologies as well as the need for further signal amplification with DNA-targeted FISH for single-copy gene targets within environmental samples.
Effect of recombinant Panton–Valentine leukocidin in vitro on apoptosis and cytokine production of human alveolar macrophages
Authors: Wu Benquan , Zhang Wenxian , Huang Jing , Liu Hui , Zhang Tiantuo 
Published: May 2010

Panton–Valentine leukocidin (PVL) is associated with rare cases of necrotizing pneumonia that occur in otherwise healthy individuals. Human alveolar macrophages (HAMs) are major effector cells in host defense against infections. However, the impact of PVL on HAMs is uncertain. We evaluated the role of PVL in cytotoxicity and production of inflammatory cytokines secreted by HAMs. HAMs were purified from bronchoalveolar lavage fluid. Recombinant PVL (rPVL) was used in the study to interfere with HAM apoptosis and cytokine production in vitro. Hoechst 33342 fluorescence staining, transmission electron microscopy examination, and flow cytometry indicated that rPVL (10 nmol/L) treatment resulted in HAMs with markedly apoptotic characteristics, and HAMs treated with rPVL at 100 nmol/L showed clear indication of necrosis. A treatment of rPVL at 10 nmol/L elicited the secretion of IL-10 by HAMs relative to untreated control cells, but there was a slight decrease in the constitutive secretion of tumor necrosis factor (TNF)-α. Our results indicate that PVL-treated samples decreased HAM viability, leading to apoptosis at low concentrations and necrosis at high concentrations. In addition, PVL-treated cells released increased amounts of IL-10 and decreased amounts of TNF-α under apoptosis-inducing concentrations. Therefore, we speculated that PVL could play a negative role in HAM function at lower concentrations.
The characterization and diversity of bacterial endophytes of grapevine
Authors: West E. R. , Cother E. J. , Steel C. C. , Ash G. J. 
Published: May 2010

The diversity of culturable and nonculturable bacterial endophytes of grapevine ( Vitis vinifera L.) was examined using a combination of cultivation and molecular methods. Entire grapevines were sampled to characterize bacterial diversity from different locations throughout the vine. Gas chromatography of fatty acid methyl esters (FAMEs) was used to identify culturable isolates prior to subsequent further microbiological characterization, whilst denaturing gradient gel electrophoresis (DGGE) was used to profile the ribosomal DNA of the bacterial endophyte community extracted from grapevines. Gas chromatography of FAMEs identified 75% of culturable bacterial endophytes to genus level (similarity index >0.3). Many isolates were identified as Bacillus spp., Pseudomonas spp., and Curtobacterium spp. Additionally, actinomycetes are reported for the first time as endophytes of grapevines, with a number of isolates identified as Streptomyces spp. DGGE was successfully used to identify major bands present in samples and indicated a degree of homogeneity of bacterial endophyte community profiles within the grapevines sampled. The major bacterial bands were sequenced and used in identification. Comparison with bacterial markers produced from cultured bacterial endophytes suggested that bacteria in the DGGE profiles were not the species most commonly cultured. Additional research demonstrated similarities between epiphytic and endophytic populations and examined potential entry vectors. Endophyte entry was demonstrated in both field-grown and potted grapevines (‘Chardonnay’) using a rifampicin-resistant Bacillus cereus mutant. The possibility of grapevine epiphytes becoming endophytes, if the opportunity arises, was supported by comparison of gas chromatography of FAMEs from epiphytic and endophytic populations. This research adds grapevine bacterial endophyte communities to those that have been characterized by a multifaceted approach.
Characterization of arsenic-resistant bacteria from the rhizosphere of arsenic hyperaccumulatorPteris vittata
Authors: Huang Anhui , Teplitski Max , Rathinasabapathi Bala , Ma Lena 
Published: May 2010

Arsenic hyperaccumulator fern Pteris vittata L. produces large amounts of root exudates that are hypothesized to solubilize arsenic and maintain a unique rhizosphere microbial community. Total heterotrophic counts on rich or defined media supplemented with up to 400 mmol/L of arsenate showed a diverse arsenate-resistant microbial community from the rhizosphere of P. vittata growing in arsenic-contaminated sites. Twelve bacterial isolates tolerating 400 mmol/L of arsenate in liquid culture were identified. Selected bacterial isolates belonging to different genera were tested for their resistance to osmotic and oxidative stresses. Results showed that growth was generally better under osmotic stress generated by arsenic than under that generated by NaCl or PEG 6000, demonstrating that arsenic detoxification metabolism also cross-protected bacterial isolates from arsenic-induced osmotic stress. After 32 h of growth, all arsenate at 1 mmol/L was reduced to arsenite by strains Naxibacter sp. AH4, Mesorhizobium sp. AH5, and Pseudomonas sp. AH21, but arsenite at 1 mmol/L remained unchanged. Sensitivity to hydrogen peroxide was similar to that in broad-host pathogen Salmonella enterica sv. Typhimurium wild type, except strain AH4. The results suggested that these arsenic-resistant bacteria are metabolically adapted to arsenic-induced osmotic or oxidative stresses in addition to the specific bacterial system to exclude cellular arsenic. Both these adaptations contribute to the high arsenic resistance in the bacterial isolates.
Differentially expressed genes after hyper- and hypo-salt stress in the halophilic archaeonMethanohalophilus portucalensis
Authors: Shih Chao-Jen , Lai Mei-Chin 
Published: May 2010

Methanohalophilus portucalensis FDF1 can grow over a range of external NaCl concentrations, from 1.2 to 2.9 mol/L. Differential gene expression in response to long-term hyper-salt stress (3.1 mol/L of NaCl) and hypo-salt stress (0.9 mol/L of NaCl) were compared by differential display RT-PCR. Fourteen differentially expressed genes responding to long-term hyper- or hypo-salt stress were detected, cloned, and sequenced. Several of the differentially expressed genes were related to the unique energy-acquiring methanogenesis pathway in this organism, including the transmembrane protein MttP, cobalamin biosynthesis protein, methenyl-H4MPT cyclohydrolase and monomethylamine methyltransferase. One signal transduction histidine kinase was identified from the hyper-salt stress cultures. Moreover, 3 known stress-response gene homologues — the DNA mismatch repair protein, MutS, the universal stress protein, UspA, and a member of the protein-disaggregating multichaperone system, ClpB — were also detected. The transcriptional analysis of these long-term salt stress response and adaptation-related genes for cells immediately after salt stress indicated that the expression of the energy metabolism genes was arrested during hyper-salt shock, while the chaperone clpB gene was stimulated by both hypo- and hyper-salt shock.
The effect of silver nanoparticles on phytopathogenic spores of Fusarium culmorum
Authors: Kasprowicz Marek Jan , Kozioł Magdalena , Gorczyca Anna 
Published: May 2010

The aim of the present experiment was to investigate the influence of silver nanoparticles on Fusarium culmorum (W.G. Smith) Sacc. (FC) spores. The silver nanoparticles were produced by the high-voltage arc discharge method. To test the effect of silver nanoparticles on FC spores, 3 parameters were tested. One of these parameters was the vegetative mycelial growth in 2 experiments. The first involved the growth of FC spores on potato dextrose agar (PDA) medium after contact with 0.12–10 ppm of silver nanoparticles, and the second the growth of spores after contact with 0.12–2.5 ppm solutions of silver, but with culturing on 3 types of media (PDA, nutrient-poor PDA, and agar) instead. The next parameter was the formation of spores after the mycelia were cultured. The last parameter was spore germination in a 2.5 ppm solution of silver nanoparticles. A significant reduction in mycelial growth was observed for spores incubated with silver nanoparticles. This relationship was dependent on the incubation time and type of growth medium, but did not depend significantly on the concentration of silver nanoparticles up to 2.5 ppm. The sporulation test showed that, relative to control samples, the number of spores formed by mycelia increased in the culture after contact with silver nanoparticles, especially on the nutrient-poor PDA medium. The 24 h incubation of FC spores with a 2.5 ppm solution of silver nanoparticles greatly reduced the number of germinating fragments and sprout length relative to the control.
Comparison of the automated Phoenix with the Vitek 2 for the identification of Streptococcus pneumoniaePortions of this study were presented at the 2007 American Society of Microbiology 107th General Meeting in Toronto, Ontario, Canada.
Authors: Mittman Scott A. , Huard Richard C. , Della-Latta Phyllis , Whittier Susan 
Published: May 2010

Rapid and accurate identification of Streptococcus pneumoniae is a critical component in the optimal management of infected patients. The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, Md.) was evaluated for identification of S. pneumoniae (n = 311) and was compared to the Vitek 2 (bioMérieux, Marcy l’Étoile, France). Strains with discordant identification between methods were resolved with 16S rRNA gene sequencing as the gold standard. The Phoenix and the Vitek 2 correctly identified 96.8% (n = 301) and 95.2% (n = 296) of S. pneumoniae strains, respectively. Overall, there was no statistically significant difference in the performance of the 2 automated systems for the identification of S. pneumoniae in this study. The Vitek 2 mean time-to-results for all streptococcal identification was 1.5 h faster than that for the Phoenix. We conclude that the automated Phoenix and the Vitek 2 systems are comparable in their ability to identify S. pneumoniae and are preferable to the use of routine biochemical assays, which have delayed time-to-results and are not dependably accurate.