bluuebunny/crossref_metadata_2025_split huggingface dataset:
An efficient method for the extraction of chloroplast proteins compatible for 2‐DE and MS analysis
Authors: Fan Pengxiang , Wang Xuchu , Kuang Tingyun , Li Yinxin 
Published: August 2009

AbstractComparative proteomic analysis of chloroplast by 2‐DE has received significant attention in recent years. However, the complication of membrane systems in chloroplast made it challenging to elucidate entire chloroplast proteome by 2‐DE. Here, we developed an efficient method for extracting chloroplast proteins, and produced excellent 2‐DE profiles from both Arabidopsis thaliana and Salicornia europaea. Comparison of this method with another two protocols for the extraction of A. thaliana chloroplast proteins showed that our method obtained higher protein yields and produced more protein spots on both pH 3–10 and 4–7 2‐DE gels. Moreover, this method recovered more proteins in the basic and high Mr regions, thereby offering the best extraction of chloroplast proteins. Identification of 15 specific chloroplast‐targeted proteins on our gels by MALDI‐TOF MS revealed that this method was compatible with MS, and recovered more chloroplast membrane proteins than the commonly used methods. This protocol is expected to have a wide application in future chloroplast proteomic analysis.
Proteomic analysis of date palm (Phoenix dactylifera L.) responses to endophytic colonization by entomopathogenic fungi
Authors: Gómez‐Vidal Sonia , Salinas Jesús , Tena Manuel , Lopez‐Llorca Luis Vicente 
Published: August 2009

AbstractThe entomopathogenic fungi Beauveria bassiana, Lecanicillium dimorphum and L. cf. psalliotae can survive and colonize living palm tissue as endophytes. The molecular interaction between these biocontrol agent fungi and the date palm Phoenix dactylifera L. was investigated using proteomic techniques. Field date palms inoculated with these fungi were analyzed 15 and 30 days after inoculation in two independent bioassays. In vitro date palms were also inoculated with B. bassiana or L. cf. psalliotae. Qualitative and quantitative differences in protein accumulation between controls (not inoculated) and inoculated palms were found using 2‐DE analysis, and some of these responsive proteins could be identified using MALDI/TOF‐TOF. Proteins involved in plant defence or stress response were induced in P. dactylifera leaves as a response to endophytic colonization by entomopathogenic fungi in field date palms. Proteins related with photosynthesis and energy metabolism were also affected by entomopathogenic fungi colonization. A myosin heavy chain‐like protein was accumulated in in vitro palms inoculated with these fungi. This suggests that endophytic colonization by these entomopathogenic fungi modulates plant defence responses and energy metabolism in field date palms and possibly modulates the expression of cell division‐related proteins in in vitro palms at proteomic level.
Establishing the mitochondrial DNA D‐loop structure of Columba livia
Authors: Tsai Li‐Chin , Lee James Chun‐I , Liao Shu‐Ping , Weng Lin‐Hsiang , Linacre Adrian , Hsieh Hsing‐Mei 
Published: August 2009

AbstractThe complete mitochondrial DNA D‐loop structure of pigeon (Columba livia) was established in this study. A strategy of amplifying three partial fragments of the D‐loop and then combing the three fragments to cover the full length of the D‐loop was adopted. Ten samples from pigeons were collected and were successfully amplified and sequenced. Repetitive sequences of a VNTR and an STR were both observed at the 3′‐end of D‐loop region. DNA sequence data revealed polymorphic sequences including indels, SNP, VNTR and STR within the D‐loop. The size of the D‐loop ranged from 1310 to 1327 bp from the initiation site of D‐loop to the site immediately upstream of the repeat sequences depending upon the number of insertions or deletions. Each sample could be distinguished based on four genotyping procedures; being indels, SNPs, VNTRs and STRs. The polymorphic nature of the D‐loop can be a valuable method for maternal identification and genetic linkage of pigeon in particular forensic science investigations.
Determination of DNA methylation by COBRA: A comparative study of CGE with LIF detection and conventional gel electrophoresis
Authors: Goedecke Simon , Schlosser Sabrina , Mühlisch Jörg , Hempel Georg , Frühwald Michael C. , Wünsch Bernhard 
Published: August 2009

AbstractDNA methylation as an epigenetic modification of the human genome is under emphatic investigation. Several studies have demonstrated a role of DNA methylation in oncogenesis. In conjunction with histone modifications, DNA methylation may cause the formation of heterochromatin and thus mediate the inactivation of gene transcription. It is important to develop methods that allow for an accurate quantification of the amount of DNA methylation in particular DNA regions, to gain information concerning the threshold of methylation levels necessary for gene inactivation. In this article, a CGE method with on‐column LIF detection using SYBR Green is compared with a conventional slab‐gel electrophoresis. We thus investigate the validity to analyze DNA methylation in the samples of a combined bisulfite restriction analysis. It is demonstrated that CGE is superior to gel electrophoresis in means of linearity, precision, accuracy, automatization (high throughput), and sample consumption. However, gel electrophoresis is easier to perform (simple devices, no PC usage), and the running costs are comparatively low. A further advantage of CGE is the sparse use of toxic compounds (MeOH and SYBR Green), whereas gel electrophoresis is performed in polyacrylamide gels with ethidium bromide staining.
Estimation and assessment of shipping emissions in the region of Ambarlı Port, Turkey
Authors: Deniz Cengiz , Kilic Alper 
Published: August 2009

AbstractShips are significant air pollution sources as their high powered main engines often use heavy fuels. The major atmospheric components emitted are nitrogen oxides, particulate matter, sulfur oxides, carbon oxide, and toxic air pollutants. Shipping emissions cause serious effects on health and environment. These effects of emissions are seen especially in territorial waters, inland seas, canals, straits, bays, and port regions.In this article, exhaust gas emissions from ships in Ambarlı Port, which is one of the main ports in Marmara Sea, are calculated by utilizing data acquired in 2005. Total emissions from ships in the port is estimated as 845 t y−1 for nitrogen oxides (NOx), 242 t y−1 for sulfur dioxide (SO2), 2127 t y−1 for carbon monoxide (CO), 78590 t y−1 for carbon dioxide (CO2), 504 t y−1 for volatile organic compound (VOC), and 36 t y−1 for particulate matter (PM). To simulate dispersions of emissions, a model program with the real topographic and meteorological conditions of the port region is used. Ships in Ambarlı Port contributed 100 μg m−3 NOx and 55 μg m−3 SO2 to ambient air concentrations in 2 km range from the port. It is estimated that 60,000 people live within this range and these people might be affected from the high level of NOx and SO2 due to combination of shipping emissions and other sources (traffic, industry, residential, etc). © 2009 American Institute of Chemical Engineers Environ Prog, 2010
Pilot‐scale combustion of fast‐pyrolysis bio‐oil: Ash deposition and gaseous emissions
Authors: Khodier Ala , Kilgallon Paul , Legrave Nigel , Simms Nigel , Oakey John , Bridgwater Tony 
Published: August 2009

AbstractFast pyrolysis is a promising method to transform solid biomass into a liquid product called “bio‐oil” with an energy density of four to five times greater than the feedstock. The process involves rapidly heating biomass to 450–600°C in the absence of air and condensing the vapor produced to give bio‐oil. Typically, 50–75% (weight) of the feedstock is converted into bio‐oil that has a number of uses, for example energy production or bio‐refinery feedstock. This study investigated the gaseous emissions and ash deposition characteristics resulting from bio‐oil combustion in a pilot scale combustion test rig at Cranfield University. A feeding system with heated lines and heated/stirred reservoir was used to feed a spray nozzle in the combustion chamber.Ash deposit samples were collected from the resulting flue gas using three air‐cooled probes that simulate heat exchanger tubes with surface temperatures of 500, 600, and 700°C. The deposits formed were analyzed using SEM/EDX and XRD techniques to assess the corrosion potential of the deposits. The results are compared to measured ash deposit compositions formed from biomass combustion. Thermodynamic modeling software was used to make predictions for the partitioning of a range of elements for bio‐oil combustion and the results compared to the measured data. © 2009 American Institute of Chemical Engineers Environ Prog, 2009
Robust glass‐ceramics catalysts for biomass gasification
Authors: Felix Larry G. , Choi Chun W. , Rue David M. , Weast Logan E. , Seward Thomas P. 
Published: August 2009

AbstractGlass‐ceramics offer high melting points (1200–1500°C), excellent attrition‐resistance, and very low coefficients of thermal expansion. We have found that these materials can be employed to create active supported catalysts, bulk catalysts, or a combination of the two. Supported catalysts are created by the process of thermal impregnation in which thermal energy is employed to graft oxides of catalytically active metals directly into the surfaces of glass‐ceramic and mineral‐based supports. Bulk catalysts are prepared by heat‐treating specially formulated Li and Mg‐aluminosilicate glasses containing up to 40 wt % NiO to create a fine‐grained (0.5–5 μm) multiphase, crystalline ceramic. When any of these materials are reduced with hydrogen, exposed surfaces reveal a metallic state. Laboratory testing with simulated syngas mixtures containing surrogate tars (naphthalene and toluene) shows that these new materials can exhibit strong catalytic activity for tar and methane decomposition as well as methanation at lower temperatures. This work is supported by US‐DOE Cooperative Agreement DE‐FG36‐04GO14314 and GTI internal research funding. © 2009 American Institute of Chemical Engineers Environ Prog, 2009
Tar content and composition in producer gas of fluidized bed gasification of wood—Influence of temperature and pressure
Authors: Wolfesberger Ute , Aigner Isabella , Hofbauer Hermann 
Published: August 2009

AbstractIn thermochemical biomass conversion processes, especially gasification, the tar content, and composition is a major subject. Because of the various processes examined at VUT, this work picks up the opportunity to compare the different tar amounts and its composition at different temperatures and process parameters. Gasification of biomass was carried out at the 100‐kW steam‐blown dual fluidized bed gasifier pilot plant III (800–870°C) and the 70‐kW air‐blown pressurized research unit (800–900°C; 1–5 bar) at VUT. Olivine is a catalyst for tar conversion; hence it was used as bed material in steam gasification and also in pressurized air gasification. For better understanding of tar formation during thermochemical conversion of biomass, the tar content and composition in the producer gas were analyzed with a gas chromatograph coupled with a mass spectrometer.Basic differences between the two thermochemical conversion processes occurred especially at higher temperatures or higher pressures. The tar composition was shifted to higher molecular tars such as polyaromatic hydrocarbons. Decreasing tar amounts were found at higher temperatures or higher pressures. Therefore, in future, an optimization of gasification processes should be easier to accomplish, which means lower tar content in the producer gas, which results in a better utilization of the biomass. © 2009 American Institute of Chemical Engineers Environ Prog, 2009
Catalytic hydrotreatment of fast pyrolysis oil: Model studies on reaction pathways for the carbohydrate fraction
Authors: Wildschut J. , Arentz J. , Rasrendra C.B. , Venderbosch R.H. , Heeres H.J. 
Published: August 2009

AbstractFast pyrolysis oil can be upgraded by a catalytic hydrotreatment (250–400°C, 100–200 bar) using heterogeneous catalysts such as Ru/C to hydrocarbon‐like products that can serve as liquid transportation fuels. Insight into the complex reaction pathways of the various component fractions during hydrotreatment is desirable to reduce the formation of by‐products such as char and gaseous components. This paper deals with the catalytic hydrotreatment of representative model components for the carbohydrate fraction (viz., D‐glucose and D‐cellobiose) present in concentrations of 20–40% in fast pyrolysis oils. The hydrotreatment was conducted at a temperature of 250°C and 100 bar hydrogen using Ru and Pd on carbon catalysts in water. Two parallel reaction pathways are then observed, a thermal noncatalyzed pathway leading to insoluble humins (char) and a hydrogenation pathway leading to smaller polyols and gaseous hydrocarbons such as methane and ethane. The implications of these findings for the catalytic hydrotreatment of fast pyrolysis oil are discussed. © 2009 American Institute of Chemical Engineers Environ Prog, 2009
Detection of parent‐of‐origin effects using general pedigree data
Authors: Zhou Ji‐Yuan , Ding Jie , Fung Wing K. , Lin Shili 
Published: August 2009

AbstractGenomic imprinting is an important epigenetic factor in complex traits study, which has generally been examined by testing for parent‐of‐origin effects of alleles. For a diallelic marker locus, the parental‐asymmetry test (PAT) based on case‐parents trios and its extensions to incomplete nuclear families (1‐PAT and C‐PAT) are simple and powerful for detecting parent‐of‐origin effects. However, these methods are suitable only for nuclear families and thus are not amenable to general pedigree data. Use of data from extended pedigrees, if available, may lead to more powerful methods than randomly selecting one two‐generation nuclear family from each pedigree. In this study, we extend PAT to accommodate general pedigree data by proposing the pedigree PAT (PPAT) statistic, which uses all informative family trios from pedigrees. To fully utilize pedigrees with some missing genotypes, we further develop the Monte Carlo (MC) PPAT (MCPPAT) statistic based on MC sampling and estimation. Extensive simulations were carried out to evaluate the performance of the proposed methods. Under the assumption that the pedigrees and their associated affection patterns are randomly drawn from a population of pedigrees with at least one affected offspring, we demonstrated that MCPPAT is a valid test for parent‐of‐origin effects in the presence of association. Further, MCPPAT is much more powerful compared to PAT for trios or even PPAT for all informative family trios from the same pedigrees if there is missing data. Application of the proposed methods to a rheumatoid arthritis dataset further demonstrates the advantage of MCPPAT. Genet. Epidemiol. 34: 151–158, 2010. © 2009 Wiley‐Liss, Inc.
Assessing trade in health services in countries of the Eastern Mediterranean from a public health perspective
Authors: Siddiqi Sameen , Shennawy Azza , Mirza Zafer , Drager Nick , Sabri Belgacem 
Published: August 2009

AbstractAssessing trade in health services (TiHS) in developing countries is challenging since the sources of information are diverse, information is not accessible and professionals lack grasp of issues. A multi‐country study was conducted in the Eastern Mediterranean Region (EMR) – Egypt, Jordan, Lebanon, Morocco, Oman, Pakistan, Sudan, Syrian Arab Republic, Tunisia, and Yemen. The objective was to estimate the direction, volume, and value of TiHS; analyze country commitments; and assess the challenges and opportunities for health services.Trade liberalization favored an open trade regime and encouraged foreign direct investment. Consumption abroad and movement of natural persons were the two prevalent modes. Yemen and Sudan are net importers, while Jordan promotes health tourism. In 2002, Yemenis spent US$ 80 million out of pocket for treatment abroad, while Jordan generated US$ 620 million. Egypt, Pakistan, Sudan and Tunisia export health workers, while Oman relies on import and 40% of its workforce is non‐Omani. There is a general lack of coherence between Ministries of Trade and Health in formulating policies on TiHS.This is the first organized attempt to look at TiHS in the EMR. The systematic approach has helped create greater awareness, and a move towards better policy coherence in the area of trade in health services. Copyright © 2009 John Wiley & Sons, Ltd.
Sensitization of ovarian carcinoma cells to the atypical retinoid ST1926 by the histone deacetylase inhibitor, RC307: enhanced DNA damage response
Authors: Zuco Valentina , Benedetti Valentina , De Cesare Michelandrea , Zunino Franco 
Published: August 2009

AbstractThe synthetic atypical retinoids containing an adamantyl group exhibit antiproliferative or proapoptotic activities. Apoptosis induction is a dose‐dependent effect independent of retinoid receptors. We have reported that induction of apoptosis by the atypical retinoid, ST1926, is associated with early manifestations of genotoxic stress. Indeed, in this study performed in ovarian carcinoma cells, we show that exposure to ST1926 resulted in an increase of early markers of DNA damage, including ATM and H2AX phosphorylation. In addition, we found that a novel histone deacetylase (HDAC) inhibitor (RC307) was able to enhance sensitivity of ovarian carcinoma cells to ST1926. Under conditions where single‐agent treatment caused only antiproliferative effects, the combination of the atypical retinoid and HDAC inhibitor resulted in marked apoptotic cell death with a more rapid onset in wild‐type p53 ovarian carcinoma cells. The sensitization to ST1926‐induced apoptosis was associated with an enhanced DNA damage response, because a prolonged expression of DNA damage markers (e.g., H2AX, p53 and RPA‐2 phosphorylation) and a marked activation of DNA damage checkpoint kinases (in particular, phosphorylation of Chk1) were observed indicating an accumulation of DNA damage by the ST1926/HDAC inhibitor combination. The study provides additional support to the role of DNA damage as a primary event leading to the activation of apoptosis in ovarian carcinoma cells by adamantyl retinoids and documents the potential therapeutic efficacy of the combination of ST1926 and HDAC inhibitors of the novel series.
Targeted knockdown of Bcl2 in tumor cells using a synthetic TRAIL 3′‐UTR microRNA
Authors: Zhang Jianjun , Huang Shenglin , Zhang He , Wang Haibo , Guo Haiyan , Qian Guanxiang , Fan Xianqun , Lu Jian , Hoffman Andrew R. , Hu Ji‐Fan , Ge Shengfang 
Published: August 2009

AbstractTargeting tumor‐related overexpression of anti‐apoptotic Bcl2 protein by RNAi has been suggested as a potential treatment for cancer. However, the stability of RNAi and its delivery are still major obstacles to the clinical testing of Bcl2 RNAi. Here, we explore a novel strategy of expressing a synthetic Bcl2 microRNA (smRNA) in the 3′ untranslated region (UTR) of the tumor necrosis factor‐related apoptosis‐inducing ligand (TRAIL), an apoptosis‐inducing protein without apparent toxic effects in normal cells. TRAIL was specifically expressed from the human telomerase reverse transcriptase promoter (pTRT) that is active in many human tumors. Using this approach, we demonstrated that pTRT drove the tumor‐specific expression of Bcl2 smRNA, which was processed by the host RNAi machinery and silenced endogenous Bcl2 expression in tumor cells. Bcl2 smRNA induced tumor cell apoptosis by activating caspase‐3 and led to significant sensitization of tumor cells to TRAIL‐induced apoptosis, while normal cells were spared. We also showed that the combined therapy of TRAIL‐induced apoptosis and Bcl2 downregulation was superior to the mono‐therapy of TRAIL or Bcl2 smRNA alone. This study proves a general paradigm for cancer therapy by using 3′ UTR microRNA technology.
Prognostic significance of integrin‐linked kinase1 overexpression in astrocytoma
Authors: Li Jun , Zhang Heng , Wu Jueheng , Guan Hongyu , Yuan Jie , Huang Zhengsong , Li Mengfeng 
Published: August 2009

AbstractIntegrin‐linked kinase 1 (ILK1), a member of the serine/threonine kinases, has been demonstrated to be associated with numerous biological and pathological processes. However, the clinical and functional significance of ILK1 expression has not been characterized previously in human astrocytoma. In this study, we found that ILK1 was overexpressed, at both mRNA and protein levels, in astrocytoma cell lines as compared with normal human astrocytes. The ILK1 mRNA and protein were significantly increased up to 5.6‐fold and 10.1‐fold, respectively, in primary astrocytoma in comparison with the paired adjacent noncancerous brain tissues obtained from the same patient. Furthermore, immunohistochemical analysis revealed that ILK1 protein was positive in 208 of 228 (91.2%) paraffin‐embedded archival astrocytoma specimens. Statistical analysis suggested that the upregulation of ILK1 was significantly correlated with the histological grading of astrocytoma (p = 0.000), and that patients with high ILK1 level exhibited shorter survival time (p < 0.001). Multivariate analysis revealed that ILK1 upregulation might be an independent prognostic indicator for the survival of patients with astrocytoma. Taken together, our results suggest that ILK1 might represent a novel and useful prognostic marker for astrocytoma and play a role during the development and progression of the disease.
Loss of STARD10 expression identifies a group of poor prognosis breast cancers independent of HER2/Neu and triple negative status
Authors: Murphy Niamh C. , Biankin Andrew V. , Millar Ewan K.A. , McNeil Catriona M. , O'Toole Sandra A. , Segara Davendra , Crea Paul , Olayioye Monilola A. , Lee C. Soon , Fox Stephen B. , Morey Adrienne L. , Christie Michael , Musgrove Elizabeth A. , Daly Roger J. , Lindeman Geoffrey J. , Henshall Susan M. , Visvader Jane E. , Sutherland Robert L. 
Published: August 2009

AbstractThe phospholipid transfer protein STARD10 cooperates with c‐erbB signaling and is overexpressed in Neu/ErbB2 breast cancers. We investigated if STARD10 expression provides additional prognostic information to HER2/neu status in primary breast cancer. A published gene expression dataset was used to determine relationships between STARD10 and HER2 mRNA levels and patient outcome. The central findings were independently validated by immunohistochemistry in a retrospective cohort of 222 patients with breast cancer with a median follow‐up of 64 months. Kaplan–Meier and Cox proportional hazards analyses were used for univariate and multivariate analyses. Patients with low STARD10 or high HER2 tumor mRNA levels formed discrete groups each associated with a poor disease‐specific survival (p = 0.0001 and p = 0.0058, respectively). In the immunohistochemical study low/absent STARD10 expression i.e. ≤10% positive cells was observed in 24 of 222 (11%) tumors. In a univariate model, low/absent STARD10 expression was significantly associated with decreased patient survival (p = 0.0008). In multivariate analyses incorporating tumor size, tumor grade, lymph node status, ER, PR and HER2 status, low STARD10 expression was an independent predictor of death from breast cancer (HR: 2.56 (95% CI: 1.27–5.18), p = 0.0086). Furthermore, low/absent STARD10 expression, HER2 amplification and triple negative status were independent prognostic variables. Loss of STARD10 expression may provide an additional marker of poor outcome in breast cancer identifying a subgroup of patients with a particularly adverse prognosis, which is independent of HER2 amplification and the triple negative phenotype.