bluuebunny/crossref_metadata_2025_split huggingface dataset:
APP independent and dependent effects on neurite outgrowth are modulated by the receptor associated protein (RAP)
Authors: Billnitzer Andrew J. , Barskaya Irina , Yin Cailing , Perez Ruth G. 
Published: October 2012

AbstractAmyloid precursor protein (APP) and its secreted form, sAPP, contribute to the development of neurons in hippocampus, a brain region critical for learning and memory. Full‐length APP binds the low‐density lipoprotein receptor‐related protein (LRP), which stimulates APP endocytosis. LRP also contributes to neurite growth. Furthermore, the receptor associated protein (RAP) binds LRP in a manner that blocks APP–LRP interactions. To elucidate APP contributions to neurite growth for full‐length APP and sAPP, we cultured wild type (WT) and APP knockout (KO) neurons in sAPPα and/or RAP and measured neurite outgrowth at 1 day in vitro. Our data reveal that WT neurons had less axonal outgrowth including less axon branching. RAP treatment potentiated the inhibitory effects of APP. KO neurons had significantly more outgrowth and branching, especially in response to RAP, effects which were also associated with ERK2 activation. Our results affirm a major inhibitory role by full‐length APP on all aspects of axonal and dendritic outgrowth, and show that RAP–LRP binding stimulated axon growth independently of APP. These findings support a major role for APP as an inhibitor of neurite growth and reveal novel signaling functions for LRP that may be disrupted by Alzheimer's pathology or therapies aimed at APP processing.
Improvement in patients with a TMD‐pain report. A 6‐month follow‐up study
Authors: Rollman A. , Visscher C. M. , Gorter R. C. , Naeije M. 
Published: October 2012

SummaryEven though chronic TMD pain tends to persist in most patients, some chronic patients show improvement. It is largely unknown which factors contribute to the improvement of chronic pain. The aim of this study is to investigate which factors, from a biopsychosocial perspective, help to predict improvement in patients with a report of TMD pain. Methods: Subjects with a report of TMD pain were recruited in seven TMD clinics. They received a baseline questionnaire which included a wide range of possible predictors for improvement. After 6 months they received a follow‐up questionnaire which included a measure to determine which participants were ‘improved’ or ‘not improved’. To study which predictive variables were associated with improvement, multiple regression models were built. Results: From the 129 patients who responded to the baseline questionnaire, 100 patients also filled in the follow‐up questionnaire (85% women, mean age (years) ± s.d. = 46·0 ± 13·8). Fifty percentage of these subjects had improved at the 6‐month follow‐up. Pain duration was the strongest (negative) predictor for 6‐month improvement (P = 0·009). Also the number of care providers (P = 0·017) and the degree of hindrance on function (P = 0·045) helped to predict improvement. Conclusions: The duration of the TMD‐pain complaint, the number of care practitioners attended and the degree of hindrance on function (negatively) helped to predict 6‐month improvement. No evidence is found to support the role of psychological or social factors on the improvement in patients with a report of TMD pain.
Identification and Molecular Characterization of Nocardia sp. as a New Causal Agent of Tobacco False Broomrape
Authors: Morán Yunior , Chacón Osmani , Córdoba‐Sellés Maria del Carmen , Domínguez‐Larrinaga Rosario , Herrera Lidcay , Borrás‐Hidalgo Orlando 
Published: October 2012

AbstractTobacco false broomrape disease is a serious problem in tropical countries. To identify its cause, experiments were conducted in tobacco fields. Six actinomycete strains were isolated from white succulent outgrowths of tobacco roots and their pathogenicity was confirmed by biological testing. Based on phenotypic and 16S rRNA gene sequence BLAST analysis, the strains were identified as members of the genus Nocardia. This association was also confirmed by secA1 gene phylogenetic analysis. This is the first report of Nocardia sp. as the cause of tobacco false broomrape.
One‐step Multiplex RT‐PCR for Simultaneous Detection of Four Viruses in Tobacco
Authors: Zhang Junqi , Wang Ran , Song Jizhen , Luo Zhaopeng , Yang Jun , Lin Fucheng 
Published: October 2012

AbstractA one‐step multiplex RT‐PCR method has been developed for the simultaneous detection of four viruses frequently occurring in tobacco (Cucumber mosaic virus, Tobacco mosaic virus, Tobacco etch virus and Potato virus Y). Four sets of specific primers were designed to work with the same reaction reagents and cycling conditions, resulting in four distinguishable amplicons representative of the four viruses independently. This one‐step multiplex RT‐PCR is consistently specific using different combinations of virus RNA as templates, and no non‐specific band was observed. It has high sensitivity compared to single RT‐PCR. Moreover, field samples in China can be tested by this method for virus detection. Our results show that one‐step multiplex RT‐PCR is a high‐throughput, specific, sensitive method for tobacco virus detection.
Effect of concentration and addition method of glycerol on the quality of cryopreserved mithun (Bos frontalis) spermatozoa
Authors: Baruah K. K. , Dhali A. , Mech A. , Bora B. , Das J. , Bora R. , Mondal M. , Sarmah B. C. , Deka B. C. , Rajkhowa C. 
Published: October 2012

SummaryThe effect of concentration and addition method of glycerol on the quality of cryopreserved mithun (Bos frontalis) spermatozoa was investigated. Semen samples were collected from five healthy mithun bulls through rectal massage method and cryopreserved in liquid nitrogen. The samples were diluted in Tris–egg yolk–glycerol extender, equilibrated for 4 h at 4 °C and loaded into 0.50‐ml straws. The straws were then frozen in liquid nitrogen vapour for 10 min and finally plunged into liquid nitrogen for storage. The required amount of glycerol was added into the diluted samples either in a single dose (3%, 4%, 5%, 6% or 7%; added at 37 °C immediately before equilibration) or in split doses (5%, 6% or 7%; the total amount was divided into four equal parts, and a part was added at 37 °C immediately before equilibration, and the remaining parts were added subsequently at 1, 2 and 3 h of equilibration at 4 °C). In the single‐dose addition method, following freeze‐thawing, greater (p < 0.05) motility (%) and proportion of live spermatozoa with intact acrosome (LSIA, %) in 5% glycerol (40.6 ± 1.7 and 43.4 ± 1.8 respectively) and lesser (p < 0.05) total morphological abnormalities (%) in 5% (14.1 ± 0.8) and 6% (13.7 ± 1.0) glycerol were observed compared to the other glycerol concentrations. In the split‐dose addition method, following freeze‐thawing, greater (p < 0.05) motility (%) and LSIA proportion (%) were found in 5% (50.2 ± 1.9 and 53.3 ± 1.8 respectively) compared to 6% or 7% glycerol, but the total morphological abnormalities were not different among the glycerol concentrations. In addition, in all the glycerol concentrations, better (p < 0.05) post‐freeze‐thaw motility and LSIA proportions were observed when glycerol was added in split doses compared to a single dose. In conclusion, Tris–egg yolk extender with 5% glycerol added in split doses was found most suitable for cryopreserving mithun sperm.
Impact of matrix metalloproteinases on inhibition of mineralization by fetuin
Authors: Schure R. , Costa K. D. , Rezaei R. , Lee W. , Laschinger C. , Tenenbaum H. C. , McCulloch C. A. 
Published: October 2012

Background and ObjectiveHuman subjects affected by inflammatory diseases, such as periodontitis, may be at increased risk for the development of cardiovascular diseases and calcification of atheromas; however, the potential mechanisms have not been defined. Alpha‐2‐Heremans Schmid glycoprotein (fetuin A) is an abundant serum glycoprotein of ~49 kDa that inhibits ectopic arterial calcification. We examined whether matrix metalloproteinases (MMPs), which are increased in inflammatory diseases, including periodontitis, bind and degrade fetuin and alter its ability to inhibit calcification in vitro.Material and MethodsBinding and cleavage of fetuin by MMPs were assessed by sodium dodecyl sulfate–polyacrylamide gel electrophoresis, in‐silico analyses and mass spectrometry. The effects of intact and MMP‐degraded human fetuin on mineralization were measured in a cell‐free assay.ResultsFrom in‐silico analyses and literature review, we found that only MMP‐3 (stromelysin) and MMP‐7 (matrilysin) were predicted to cleave human fetuin at levels that were physiologically relevant. In‐vitro assays showed that MMP‐7, and, to a lesser extent, MMP‐3, degraded human fetuin in a time‐ and dose‐dependent manner. Fetuin peptides generated by MMP‐7 cleavage were identified and sequenced by mass spectrometry; novel cleavage sites were found. Hydroxyapatite mineralization in vitro was strongly inhibited by fetuin (> 1 μm), as was MMP‐3‐cleaved fetuin, while MMP‐7‐cleaved fetuin was threefold less effective in blocking mineralization.ConclusionMMP‐7 and, to a lesser extent, MMP‐3, affect the ability of fetuin to inhibit the formation of hydroxyapatite in vitro. These data suggest that the MMPs increased in inflammatory diseases, such as periodontitis, could affect regulation of mineralization and potentially enhance the risk of calcified atheroma formation.
Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick‐lippedMidas cichlid fishes fromNicaragua
Authors: Manousaki Tereza , Hull Pincelli M. , Kusche Henrik , Machado‐Schiaffino Gonzalo , Franchini Paolo , Harrod Chris , Elmer Kathryn R. , Meyer Axel 
Published: October 2012

AbstractThe study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips inMidas cichlid fishes (theAmphilophus citrinellusspecies complex)—from two Great Lakes and two crater lakes inNicaragua—to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next‐generation sequencing technology, we characterize transcriptome‐wide differential gene expression in the lips of wild‐caught sympatric thick‐ and thin‐lipped cichlids from all four instances of repeated thick‐lip evolution. Six genes (apolipoproteinD, myelin‐associated glycoprotein precursor, four‐and‐a‐halfLIMdomain protein 2, calpain‐9, GTPaseIMAPfamily member 8‐like and one hypothetical protein) are significantly underexpressed in the thick‐lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake‐specific pattern, including the magnitude of differentially expressed genes (97‐510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the olderGreatLakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in theGreatLakeNicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick‐ and thin‐lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution.
Modelling the global distribution of fungal species: new insights into microbial cosmopolitanism
Authors: Sato Hirotoshi , Tsujino Riyou , Kurita Kazuki , Yokoyama Kazumasa , Agata Kiyokazu 
Published: October 2012

AbstractMicrobes are usually believed to have cosmopolitan distributions. However, for estimating the global distributions of microorganisms, discriminating among cryptic species and eliminating undersampling biases are important challenges. We used a novel approach to address these problems and infer the global distribution of a given fungal ecological guild. We collected mushroom‐forming fungi from Yakushima, Japan. We sequenced the internal transcribed spacer 2 (ITS2) from these samples and queried their sequences against GenBank. After identifying similar sequences, we tracked down the geographical origins of samples that yielded those sequences. We used Bayesian zero‐inflated models to allow for species whose DNA sequences have not yet been deposited in GenBank. Results indicated that the geographical distribution of ectomycorrhizal (ECM) fungi was strongly constrained by host specificity, resulting in the occurrence of these fungi intensively in the neighbouring regions. On the other hand, saprotrophic (SAP) fungi were less constrained by climatic conditions, resulting in a much broader distribution range. We inferred that differences in constraints during colonization between ECM and SAP fungi were responsible for the different geographical distribution ranges. We hypothesize that the degree of host/habitat specificity and the degree of isolation of potentially suitable habitats determine microbial biogeographic patterns.
Natural selection maintains a single‐locus leaf shape cline in Ivyleaf morning glory, Ipomoea hederacea
Authors: Campitelli Brandon E. , Stinchcombe John R. 
Published: October 2012

AbstractClines in phenotypic traits with an underlying genetic basis potentially implicate natural selection. However, neutral evolutionary processes such as random colonization, spatially restricted gene flow, and genetic drift could also result in similar spatial patterns, especially for single‐locus traits because of their susceptibility to stochastic events. One way to distinguish between adaptive and neutral mechanisms is to compare the focal trait to neutral genetic loci to determine whether neutral loci demonstrate clinal variation (consistent with a neutral cline), or not. Ivyleaf morning glory, Ipomoea hederacea, exhibits a latitudinal cline for a Mendelian leaf shape polymorphism in eastern North America, such that lobed genotypes dominate northern populations and heart‐shaped genotypes are restricted to southern populations. Here, we evaluate potential evolutionary mechanisms for this cline by first determining the allele frequencies at the leaf shape locus for 77 populations distributed throughout I. hederacea's range and then comparing the geographical pattern at this locus to neutral amplified fragment length polymorphism (AFLP) loci. We detected both significant clinal variation and high genetic differentiation at the leaf shape locus across all populations. In contrast, 99% of the putatively neutral loci do not display clinal variation, and I. hederacea populations show very little overall genetic differentiation, suggesting that there is a moderate level of gene flow. In addition, the leaf shape locus was identified as a major FST outlier experiencing divergent selection, relative to all the AFLP loci. Together, these data strongly suggest that the cline in leaf shape is being maintained by spatially varying natural selection.
Role of ATP binding and hydrolysis in assembly of MacAB–TolC macrolide transporter
Authors: Lu Shuo , Zgurskaya Helen I. 
Published: October 2012

SummaryMacB is a founding member of the Macrolide Exporter family of transporters belonging to the ATP‐Binding Cassette superfamily. These proteins are broadly represented in genomes of both Gram‐positive and Gram‐negative bacteria and are implicated in virulence and protection against antibiotics and peptide toxins. MacB transporter functions together with MacA, a periplasmic membrane fusion protein, which stimulates MacB ATPase. In Gram‐negative bacteria, MacA is believed to couple ATP hydrolysis to transport of substrates across the outer membrane through a TolC‐like channel. In this study, we report a real‐time analysis of concurrent ATP hydrolysis and assembly of MacAB–TolC complex. MacB binds nucleotides with a low millimolar affinity and fast on‐ and off‐rates. In contrast, MacA–MacB complex is formed with a nanomolar affinity, which further increases in the presence of ATP. Our results strongly suggest that association between MacA and MacB is stimulated by ATP binding to MacB but remains unchanged during ATP hydrolysis cycle. We also found that the large periplasmic loop of MacB plays the major role in coupling reactions separated in two different membranes. This loop is required for MacA‐dependent stimulation of MacB ATPase and at the same time, contributes to recruitment of TolC into a trans‐envelope complex.
Comparative genotyping of Streptococcus mutans by repetitive extragenic palindromic polymerase chain reaction and multilocus sequence typing
Authors: Momeni S.S. , Whiddon J. , Moser S.A. , Cheon K. , Ruby J.D. , Childers N.K. 
Published: October 2012

SummaryThe genetic diversity of Streptococcus mutans has been extensively studied using a variety of genotyping methods. Repetitive extragenic palindromic‐polymerase chain reaction (rep‐PCR) is a genotyping approach used for screening large numbers of bacterial isolates. This two‐part study used multilocus sequence typing (MLST) analysis to evaluate genotypes previously identified as unique using rep‐PCR. In part one, an isolate was selected from each of the 22 S. mutans rep‐PCR genotype groups representing 8000 clinical isolates. For part two, four additional isolates were selected from the six most commonly occurring genotype groups (GG) for further analysis. Real‐time PCR was performed using eight housekeeping S. mutans gene loci and the amplicons were sequenced. Sequence data analysis was performed using CLC DNA Workbench and alleles were compared with the PubMLST database for Oral Streptococcus using the Nakano scheme. Concatenated sequences were evaluated with MEGA using a minimum evolution method with bootstrap. All 22 rep‐PCR genotypes were unique by MLST analysis. Within rep‐PCR GGs, MLST matched rep‐PCR in three groups demonstrating clonality; three groups exhibited more diversity with MLST. The discovery of three clonal groups is unique to this study and suggests that S. mutans genotypes are shared between unrelated subjects. Furthermore, MLST defined 19 new alleles and 26 new sequence types that have been confirmed and registered with PubMLST. Methods for processing were streamlined and a process for using MLST with rep‐PCR is suggested. In conclusion, MLST verified that rep‐PCR is a reliable and cost‐effective method for screening large numbers of S. mutans strains for epidemiological study.
Electrochemical detection of extracellular hydrogen peroxide in Arabidopsis thaliana: a real‐time marker of oxidative stress
Authors: GONZÁLEZ‐SÁNCHEZ M. I. , GONZÁLEZ‐MACIA L. , PÉREZ‐PRIOR M. T. , VALERO E. , HANCOCK J. , KILLARD A. J. 
Published: October 2012

ABSTRACTAn electrochemical approach to directly measure the dynamic process of H2O2 release from cultures of Arabidopsis thaliana cells is reported. This approach is based on H2O2 oxidation on a Pt electrode in conjunction with continuous measurement of sample pH. For [H2O2] <1 mm, calibration plots were linear and the amperometric response of the electrode was maximum at pH 6. At higher concentrations ([H2O2] >1 mm), the amperometric response can be described by Michaelian‐type kinetics and a mathematical expression relating current intensity and pH was obtained to quantitatively determine H2O2 concentration. At pH 5.5, the detection limit of the sensor was 3.1 µm (S/N = 3), with a response sensitivity of 0.16 Am−1 cm−2 and reproducibility was within 6.1% in the range 1–5 × 10−3 m (n = 5). Cell suspensions under normal physiological conditions had a pH between 5.5–5.7 and H2O2 concentrations in the range 7.0–20.5 µm (n = 5). The addition of exogenous H2O2, as well as other potential stress stimuli, was made to the cells and the change in H2O2 concentration was monitored. This real‐time quantitative H2O2 analysis is a potential marker for the evaluation of oxidative stress in plant cell cultures.
Plant hydraulics and photosynthesis of 34 woody species from different successional stages of subtropical forests
Authors: ZHU SHI‐DAN , SONG JUAN‐JUAN , LI RONG‐HUA , YE QING 
Published: October 2012

ABSTRACTIt is important to understand the ecophysiological characters of plants when exploring mechanisms underlying species substitution in the process of plant succession. In the present study, we selected 34 woody species from different stages of secondary succession in subtropical forests of southern China, and measured their hydraulic conductivity, gas exchange rates, leaf nutrients and drought‐tolerance traits such as xylem resistance to cavitation, turgor loss point and carbon isotope ratio. Principal component analysis revealed that early‐, mid‐ and late‐successional species were significantly separated along axis 1, which was strongly associated with hydraulic‐photosynthetic coordination. In contrast to species distributed in late‐successional forest, early‐successional species had the highest hydraulic conductivity, net photosynthetic rates, photosynthetic nitrogen and phosphorus use efficiencies, but had the lowest photosynthetic water‐use efficiency. However, changes of the measured drought‐tolerance traits of the 34 species along the succession did not demonstrate a clear trend – no significant correlations between these traits and plant successional stages were found. Moreover, the trade‐off between hydraulic efficiency and safety was not identified. Taken together, our results suggested that hydraulic efficiency and photosynthetic function, rather than drought tolerance, play an important role in species distributions along plant succession in subtropical forests.
Comparison of Different Glycerol and Egg Yolk Concentrations Added toTris‐based Extender for the Collared Peccaries (Tayassu tajacu) Semen Freezing
Authors: Alves HM , Oliveira IRS , Castelo TS , Lima GL , Souza ALP , Moreira MAP , de Paula VV , Silva AR 
Published: October 2012

ContentsThis study aimed to evaluate various concentrations of egg yolk (5, 10, or 20%) in combination with different concentrations of glycerol (3% or 6%) added to aTris‐based extender on the post‐thaw characteristics of sperm obtained fromTayassu tajacu. For this purpose, semen from 10 sexually male mature collared peccaries was collected by electroejaculation and evaluated for sperm motility, vigour, viability, morphology and functional membrane integrity. The ejaculates were initially extended inTris‐fructose plus egg yolk (5%, 10% or 20%). After cooling, the semen was added toTris‐egg yolk plus glycerol (6% or 12%), resulting in a final concentration of 3% or 6% glycerol of the extender. Straws were frozen using liquid nitrogen and thawed in a water bath at 37°C for 30 s. The frozen–thawed semen was evaluated as reported for fresh semen. After thawing, a significant decrease was verified for sperm motility and vigour, for all the samples in comparison with fresh semen. However, no differences were evidenced among treatments for any sperm characteristics evaluated (p > 0.05), except for the combination between 10% egg yolk and 6% glycerol, which provided the worst preservation of functional membrane integrity (p < 0.05). The interactions between higher concentrations of egg yolk (20%) and glycerol (6%) and also between lower concentrations of the same substances (5% egg yolk and 3% glycerol) added to the Tris‐based extender negatively affected the preservation of the normal sperm morphology after thawing (p < 0.05). In conclusion, the use of Tris‐based extender added to 10% or 20% egg yolk plus 3% glycerol is recommended for effective sperm cryopreservation in collared peccaries.