bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple
Authors: Zhang Qiong , Ma Baiquan , Li Hui , Chang Yuansheng , Han Yuanyuan , Li Jing , Wei Guochao , Zhao Shuang , Khan Muhammad Awais , Zhou Ying , Gu Chao , Zhang Xingzhong , Han Zhenhai , Korban Schuyler S , Li Shaohua , Han Yuepeng 
Published: October 2012

Abstract

Background
Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of perfect microsatellites in assembled contig sequences of the apple genome.

Results
A total of 28,538 SSRs have been identified in the apple genome, with an overall density of 40.8 SSRs per Mb. Di-nucleotide repeats are the most frequent microsatellites in the apple genome, accounting for 71.9% of all microsatellites. AT/TA repeats are the most frequent in genomic regions, accounting for 38.3% of all the G-SSRs, while AG/GA dimers prevail in transcribed sequences, and account for 59.4% of all EST-SSRs. A total set of 310 SSRs is selected to amplify eight apple genotypes. Of these, 245 (79.0%) are found to be polymorphic among cultivars and wild species tested. AG/GA motifs in genomic regions have detected more alleles and higher PIC values than AT/TA or AC/CA motifs. Moreover, AG/GA repeats are more variable than any other dimers in apple, and should be preferentially selected for studies, such as genetic diversity and linkage map construction. A total of 54 newly developed apple SSRs have been genetically mapped. Interestingly, clustering of markers with distorted segregation is observed on linkage groups 1, 2, 10, 15, and 16. A QTL responsible for malic acid content of apple fruits is detected on linkage group 8, and accounts for ~13.5% of the observed phenotypic variation.

Conclusions
This study demonstrates that di-nucleotide repeats are prevalent in the apple genome and that AT/TA and AG/GA repeats are the most frequent in genomic and transcribed sequences of apple, respectively. All SSR motifs identified in this study as well as those newly mapped SSRs will serve as valuable resources for pursuing apple genetic studies, aiding the apple breeding community in marker-assisted breeding, and for performing comparative genomic studies in Rosaceae.
A one-step cloning method for the construction of somatic cell gene targeting vectors: application to production of human knockout cell lines
Authors: Liu Yi , Li Shangze , Zhang Huihui , Wan Zurong , Zhang Xiaodong , Du Runlei 
Published: October 2012

Abstract

Background
Gene targeting is a powerful method that can be used for examining the functions of genes. Traditionally, the construction of knockout (KO) vectors requires an amplification step to obtain two homologous, large fragments of genomic DNA. Restriction enzymes that cut at unique recognitions sites and numerous cloning steps are then carried out; this is often a time-consuming and frustrating process.

Results
We have developed a one-step cloning method for the insertion of two arms into a KO vector using exonuclease III. We modified an adeno-associated virus KO shuttle vector (pTK-LoxP-NEO-AAV) to yield pAAV-LIC, which contained two cassettes at the two multiple-cloning sites. The vector was digested with EcoRV to give two fragments. The two homologous arms, which had an overlap of 16 bases with the ends of the vector fragments, were amplified by polymerase chain reaction. After purification, the four fragments were mixed and treated with exonuclease III, then transformed into Escherichia coli to obtain the desired clones. Using this method, we constructed SirT1 and HDAC2 KO vectors, which were used to establish SirT1 KO cells from the colorectal cancer cell line (HCT116) and HDAC2 KO cells from the colorectal cancer cell line (DLD1).

Conclusions
Our method is a fast, simple, and efficient technique for cloning, and has great potential for high-throughput construction of KO vectors.
Antioxidant and anti-inflammatory activities of selected Chinese medicinal plants and their relation with antioxidant content
Authors: Ravipati Anjaneya S , Zhang Lin , Koyyalamudi Sundar Rao , Jeong Sang Chul , Reddy Narsimha , Bartlett John , Smith Paul T , Shanmugam Kirubakaran , Münch Gerald , Wu Ming Jie , Satyanarayanan Manavalan , Vysetti Balaram 
Published: October 2012

Abstract

Background
The main aim of this study is to evaluate the antioxidant and anti-inflammatory properties of forty four traditional Chinese medicinal herbal extracts and to examine these activities in relation to their antioxidant content.

Methods
The antioxidant activities were investigated using DPPH radical scavenging method and yeast model. The anti-inflammatory properties of the herbal extracts were evaluated by measuring their ability to inhibit the production of nitric oxide and TNF-α in RAW 264.7 macrophages activated by LPS and IFN- γ, respectively. The cytotoxic effects of the herbal extracts were determined by Alomar Blue assay by measuring cell viability. In order to understand the variation of antioxidant activities of herbal extracts with their antioxidant contents, the total phenolics, total flavonoids and trace metal (Mg, Mn, Cu, Zn, Se and Mo) quantities were estimated and a correlation analysis was carried out.

Results
Results of this study show that significant levels of phenolics, flavonoids and trace metal contents were found in Ligustrum lucidum, Paeonia suffuticosa, Salvia miltiorrhiza, Sanguisorba officinalis, Spatholobus suberectus, Tussilago farfara and Uncaria rhyncophylla, which correlated well with their antioxidant and anti-inflammatory activities. Some of the plants displayed high antioxidant and anti-inflammatory activities but contained low levels of phenolics and flavonoids. Interestingly, these plants contained significant levels of trace metals (such as Zn, Mg and Se) which are likely to be responsible for their activities.

Conclusions
The results indicate that the phenolics, flavonoids and trace metals play an important role in the antioxidant activities of medicinal plants. Many of the plants studied here have been identified as potential sources of new antioxidant compounds.
Methanolic extracts of Withania somnifera leaves, fruits and roots possess antioxidant properties and antibacterial activities
Authors: Alam Nadia , Hossain Monzur , Mottalib Md Abdul , Sulaiman Siti Amrah , Gan Siew Hua , Khalil Md Ibrahim 
Published: October 2012

Abstract

Background

Withania somnifera, also known as ashwagandha, is an important herb in ayurvedic and indigenous medical systems. The present study was designed to evaluate the antioxidant and antibacterial activities of an 80% aqueous methanolic extract of W. somnifera roots (WSREt), fruits (WSFEt) and leaves (WSLEt).

Methods
Several assays were performed to determine the antioxidant properties of this herb including 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) scavenging activity, ferric reducing antioxidant power (FRAP), ferrous chelation and inhibition of β-carotene bleaching.

Results
The values for DPPH, FRAP, ferrous chelation and inhibition of β carotene bleaching for the three types of extracts ranged from 101.73-801.93 μg/ml, 2.26-3.29 mM Fe/kg, 0.22-0.65 mg/ml and 69.87-79.67%, respectively, indicating that W. somnifera, particularly the leaves, possesses significant antioxidant properties. The mean ascorbic acid content was 20.60-62.60 mg/100 g, and the mean anthocyanin content was 2.86-12.50 mg/100 g. Antibacterial activities were measured using the agar well diffusion method and five pathogenic Gram-negative bacteria: Escherichia coli, Salmonella typhi, Citrobacter freundii, Pseudomonas aeruginosa and Klebsiella pneumoniae. The leaf extracts displayed the highest activity against S. typhi (32.00 ± 0.75 mm zone of inhibition), whereas the lowest activity was against K. pneumoniae (19.00 ± 1.48 mm zone of inhibition). The lowest minimum inhibitory concentration value was 6.25 mg/ml, which was against S. typhi, followed by 12.5 mg/ml against E. coli.

Conclusion
In addition to its antioxidant properties, W. somnifer a exhibited significant antibacterial activities against Gram-negative bacteria, particularly S. typhi.
High expression of CXCR4, CXCR7 and SDF-1 predicts poor survival in renal cell carcinoma
Authors: Wang Linhui , Chen Wei , Gao Li , Yang Qing , Liu Bing , Wu Zhenjie , Wang Yang , Sun Yinghao 
Published: October 2012

Abstract

Background
Chemokines and their receptors are known to play important roles in the tumorigenesis of many malignancies. The aim of this study was to evaluate the prognostic impact of the expression of the chemokine SDF-1 and its receptors CXCR4 and CXCR7 in patients with renal cell carcinoma.

Methods
The expression of CXCR4, CXCR7 and SDF-1 in specimens from 97 renal cell carcinoma patients was evaluated by immunohistochemistry on a tissue microarray. These results were correlated with the clinicopathological parameters and survival of the patients.

Results
CXCR4 and CXCR7 were expressed in all patients, whereas SDF-1 was expressed in 61 patients (62.9%). No association was observed between the expression of CXCR4, CXCR7 or SDF-1 and the clinical or pathological data except between SDF-1 expression and Fuhrman’s grade (P = 0.015). Patients with high expression of CXCR4, CXCR7 and SDF-1 had shorter overall survival and recurrence-free survival than those with low expression. In a multivariate analysis, the high expression of CXCR4, CXCR7 and SDF-1 correlated with poor overall survival and recurrence-free survival independent of gender, age, AJCC stage, lymph node status, metastasis, histologic variant and Fuhrman’s grade.

Conclusions
High levels of CXCR4, CXCR7 and SDF-1 were associated with poor overall survival and recurrence-free survival in renal cell carcinoma patients. CXCR4, CXCR7 and SDF-1 may serve as useful prognostic markers and therapeutic targets for renal cell carcinoma.
Thermal conductivity in porous silicon nanowire arrays
Authors: Weisse Jeffrey M , Marconnet Amy M , Kim Dong Rip , Rao Pratap M , Panzer Matthew A , Goodson Kenneth E , Zheng Xiaolin 
Published: October 2012

Abstract
The nanoscale features in silicon nanowires (SiNWs) can suppress phonon propagation and strongly reduce their thermal conductivities compared to the bulk value. This work measures the thermal conductivity along the axial direction of SiNW arrays with varying nanowire diameters, doping concentrations, surface roughness, and internal porosities using nanosecond transient thermoreflectance. For SiNWs with diameters larger than the phonon mean free path, porosity substantially reduces the thermal conductivity, yielding thermal conductivities as low as 1 W/m/K in highly porous SiNWs. However, when the SiNW diameter is below the phonon mean free path, both the internal porosity and the diameter significantly contribute to phonon scattering and lead to reduced thermal conductivity of the SiNWs.
Pain in experimental autoimmune encephalitis: a comparative study between different mouse models
Authors: Lu Jianning , Kurejova Martina , Wirotanseng Laura N , Linker Ralf A , Kuner Rohini , Tappe-Theodor Anke 
Published: October 2012

Abstract

Background
Pain can be one of the most severe symptoms associated with multiple sclerosis (MS) and develops with varying levels and time courses. MS-related pain is difficult to treat, since very little is known about the mechanisms underlying its development. Animal models of experimental autoimmune encephalomyelitis (EAE) mimic many aspects of MS and are well-suited to study underlying pathophysiological mechanisms. Yet, to date very little is known about the sensory abnormalities in different EAE models. We therefore aimed to thoroughly characterize pain behavior of the hindpaw in SJL and C57BL/6 mice immunized with PLP139-151 peptide or MOG35-55 peptide respectively. Moreover, we studied the activity of pain-related molecules and plasticity-related genes in the spinal cord and investigated functional changes in the peripheral nerves using electrophysiology.

Methods
We analyzed thermal and mechanical sensitivity of the hindpaw in both EAE models during the whole disease course. Qualitative and quantitative immunohistochemical analysis of pain-related molecules and plasticity-related genes was performed on spinal cord sections at different timepoints during the disease course. Moreover, we investigated functional changes in the peripheral nerves using electrophysiology.

Results
Mice in both EAE models developed thermal hyperalgesia during the chronic phase of the disease. However, whereas SJL mice developed marked mechanical allodynia over the chronic phase of the disease, C57BL/6 mice developed only minor mechanical allodynia over the onset and peak phase of the disease. Interestingly, the magnitude of glial changes in the spinal cord was stronger in SJL mice than in C57BL/6 mice and their time course matched the temporal profile of mechanical hypersensitivity.

Conclusions
Diverse EAE models bearing genetic, clinical and histopathological heterogeneity, show different profiles of sensory and pathological changes and thereby enable studying the mechanistic basis and the diversity of changes in pain perception that are associated with distinct types of MS.
Survey of B-spline functions to approximate the solution of mathematical problems
Authors: Rashidinia Jalil , Sharifi Sh 
Published: October 2012

Abstract

Purpose
In the present paper, we describe a survey of B-spline techniques which have been used for numerical solutions of mathematical problems recently.

Methods
Here, we discussed the definition of B-splines of various degrees by two different approaches to generate the recurrence relation to drive the formulation of B-splines.

Results
Cubic B-spline applied on two test equations and absolute errors in interpolation are compared with cubic and quintic splines. Some remarks have been included.

Conclusions
Numerical results are tabulated in tables; these tables show that the results obtained by cubic B-spline are considerable and accurate with respect to the cubic spline and more or less similar to the quintic spline.
Correlation of C-reactive protein haplotypes with serum C-reactive protein level and response to anti-tumor necrosis factor therapy in UK rheumatoid arthritis patients: results from the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate cohort
Authors: Plant Darren , Ibrahim Ibrahim , Lunt Mark , Eyre Stephen , Flynn Edward , Hyrich Kimme L , Morgan Ann W , Wilson Anthony G , Isaacs John D ,   BRAGGGSS, Barton Anne 
Published: October 2012

Abstract

Introduction

In many European countries, restrictions exist around the prescription of anti-tumor necrosis factor (anti-TNF) treatments for rheumatoid arthritis (RA). Eligibility and response to treatment is assessed by using the disease activity score 28 (DAS28) algorithm, which incorporates one of two inflammatory markers, erythrocyte sedimentation rate (ESR) or C-reactive protein (CRP). Although DAS28-CRP provides a more reliable measure of disease activity, functional variants exist within the CRP gene that affect basal CRP production.
Therefore, we aimed to determine the relation between functional genetic variants at the CRP gene locus and levels of serum CRP in RA patients, and whether these variants, alone or in combination, are correlated with DAS28-CRP and change in DAS28-CRP after anti-TNF treatment.

Methods

DNA samples from the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate (BRAGGSS) were genotyped for rs1205, rs1800947, and rs3091244 by using either TaqMan or the Sequenom MassARRAY iPLEX system.
Estimated haplotypes were constructed for each sample by using the expectation maximization algorithm implemented in the haplo.stats package within the R statistical program.
CRP values were log transformed, and the association between single nucleotide polymorphisms (SNPs), haplotypes of SNPs and baseline CRP, baseline DAS28-CRP, and change in DAS28-CRP were evaluated by using linear regression in STATA v.10.

Results

Baseline CRP measurements were available for 599 samples with 442 also having data 6 months after treatment with an anti-TNF. For these 442 samples, the study had > 80% power to detect a clinically meaningful difference of 0.6 DAS28 Units for an allele frequency of 5%. Estimated haplotype frequencies corresponded with previous frequencies reported in the literature. Overall, no significant association was observed between any of the markers investigated and baseline CRP levels. Further, CRP haplotypes did not correlate with baseline CRP (P = 0.593), baseline DAS28-CRP (P = 0.540), or change in DAS28-CRP after treatment with an anti-TNF over a 6-month period (P = 0.302).

Conclusions

Although CRP genotype may influence baseline CRP levels, in patients with very active disease, no such association was found. This suggests that genetic variation at the CRP locus does not influence DAS28-CRP, which may continue to be used in determining eligibility for and response to anti-TNF treatment, without adjusting for CRP genotype.
Sequential phosphorylation of GRASP65 during mitotic Golgi disassembly
Authors: Tang Danming , Yuan Hebao , Vielemeyer Ole , Perez Franck , Wang Yanzhuang 
Published: October 2012

Summary
GRASP65 phosphorylation during mitosis and dephosphorylation after mitosis are required for Golgi disassembly and reassembly during the cell cycle. At least eight phosphorylation sites on GRASP65 have been identified, but whether they are modified in a coordinated fashion during mitosis is so far unknown. In this study, we raised phospho-specific antibodies that recognize phosphorylated T220/T224, S277 and S376 residues of GRASP65, respectively. Biochemical analysis showed that cdc2 phosphorylates all three sites, while plk1 enhances the phosphorylation. Microscopic studies using these antibodies for double and triple labeling demonstrate sequential phosphorylation and dephosphorylation during the cell cycle. S277 and S376 are phosphorylated from late G2 phase through metaphase until telophase when the new Golgi is reassembled. T220/224 is not modified until prophase, but is highly modified from prometaphase to anaphase. In metaphase, phospho-T220/224 signal localizes on both Golgi haze and mitotic Golgi clusters that represent dispersed Golgi vesicles and Golgi remnants, respectively, while phospho-S277 and S376 labeling is more concentrated on mitotic Golgi clusters. Expression of a phosphorylation-resistant GRASP65 mutant T220A/T224A inhibited mitotic Golgi fragmentation to a much larger extent than the expression of the S277A and S376A mutants. In cytokinesis, T220/224 dephosphorylation occurs prior to that of S277, but after S376. This study provides evidence that GRASP65 is sequentially phosphorylated and dephosphorylated during mitosis at different sites to orchestrate Golgi disassembly and reassembly during cell division, with phosphorylation of the T220/224 site being most critical in the process.
The bacterial and cellular determinants controlling the recruitment of mTOR to the Salmonella-containing vacuole
Authors: Tattoli Ivan , Philpott Dana J. , Girardin Stephen E. 
Published: October 2012

Summary
Bacterial invasion results in the rapid induction of an acute state of cytosolic amino acid (AA) starvation, provoked by host membrane damage. Bacteria-induced AA starvation, in turn, down-regulates mTOR signaling while triggering autophagy and the integrated stress response pathway dependent on GCN2, eIF2α and ATF3. In Salmonella-infected cells, we now demonstrate that the host AA starvation response program depended on the Salmonella pathogenicity island (SPI)-1, the activity of which was required to damage the Salmonella-containing vacuole (SCV) in the early stage of infection. At a later stage (3–4 hour post-infection), the progressive recruitment of mTOR to the surface of the SCV appeared to be independent of the activity of SPI-2 and of SCV positioning in the cell. Instead, mTOR localization to the SCV required the activity of host AA transporters SLC1A5, SLC3A2 and SLC7A5, resulting in bacterial escape from autophagy. These results expand our understanding of the mechanisms underlying the AA starvation response in Salmonella-infected cells.
Study of Liquid–Liquid Equilibria of Toluene + (Hexane, Heptane, or Cyclohexane) with 1-Ethyl-3-methylimidazolium Ethylsulfate at 308.15 K
Authors: Martínez-Reina Marlon , Amado-González Eliseo , Muñoz-Muñoz Yonny Mauricio 
Published: October 2012

Abstract
The extraction of toluene from hydrocarbons (hexane, heptane, and cyclohexane) was analyzed by liquid extraction with 1-ethyl-3-methylimidazolium ethylsulfate [EMim][EtSO4] ionic liquid, as a solvent. The experimental liquid + liquid equilibrium (LLE) data were determined at T = 308.15 K and atmospheric pressure. Selectivity and distribution coefficient, derived from the tie-lines, were used to determine the ability of [EMim][EtSO4] as solvent for the separation of toluene from its mixtures with alkanes and cycloalkane. The degree of consistency of the experimental LLE data was ascertained using the Othmer–Tobias equation. The experimental data for LLE of the ternary systems were correlated with the nonrandom two-liquid (NRTL) and universal quasi-chemical (UNIQUAC) thermodynamic models.
Self-Assembly, Chromic Properties, and Nanostructure Formation of Tetrathiafulvalene-Fused Dodecadehydro[18]annulenes
Authors: Enozawa Hideo , Takahashi Takeshi , Nishinaga Tohru , Kato Tadashi , Hasegawa Masashi , Iyoda Masahiko 
Published: October 2012

Abstract
Multifunctional dodecadehydrotris(tetrathiafulvaleno)[18]annulenes 1b–1d, which have six peripheral butylthio substituents or six ester substituents, were synthesized together with the corresponding [12]annulene 2c. The [18]annulenes 1b–1d easily formed stacked dimers and higher oligomers in solution via nanoscopic phase separation among the π-frame, ester or alkylthio substituents, and inner sphere to show solvatochromism and thermochromism. Furthermore, the strong self-aggregation of their oxidized radical cations in solution resulted in electrochromism depending on the formation of various types of mixed-valence states and π-dimers. Interestingly, self-aggregation of the [18]annulenes 1b–1d in amphiphilic media such as THF–H2O either produced fibrous structures in the case of the hexabutylthio derivative 1b and hexabutyl ester 1c or resulted in the temperature hysteresis of the color, UV–vis absorptions, and 1H NMR signals obtained in solution in the case of the hexaoctyl ester 1d which forms no fiber and precipitate under similar conditions. It is noted that fibers of the hexabutyl ester 1c can be aligned in a magnetic field using the large diamagnetic response of the [18]annulene frame for the driving force. A small difference in the substituents of 1b–1d causes a remarkable change in either their solvato- and electrochromism or nanostructure formation of 1b–1d based on the self-assembling nature both in solution and in the solid state.