PubstractHelper: A Web-based Text-Mining Tool for Marking Sentences in Abstracts from PubMed Using Multiple User-Defined Keywords

While a huge amount of information about biological literature can be obtained by searching the PubMed database, reading through all the titles and abstracts resulting from such a search for useful information is inefficient. Text mining makes it possible to increase this efficiency. Some websites use text mining to gather information from the PubMed database; however, they are database-oriented, using pre-defined search keywords while lacking a query interface for user-defined search inputs. We present the PubMed Abstract Reading Helper (PubstractHelper) website which combines text mining and reading assistance for an efficient PubMed search. PubstractHelper can accept a maximum of ten groups of keywords, within each group containing up to ten keywords. The principle behind the text-mining function of PubstractHelper is that keywords contained in the same sentence are likely to be related. PubstractHelper highlights sentences with co-occurring keywords in different colors. The user can download the PMID and the abstracts with color markings to be reviewed later. The PubstractHelper website can help users to identify relevant publications based on the presence of related keywords, which should be a handy tool for their research.

Availability

http://bio.yungyun.com.tw/ATM/PubstractHelper.aspx and http://holab.med.ncku.edu.tw/ATM/PubstractHelper.aspx     

Integration of Metabolic Reactions and Gene Regulation

Metabolic reactions and gene regulation are two primary processes of cells. In response to environmental changes cells often adjust the regulatory programs and shift the metabolic states. An integrative investigation and modeling of these two processes would improve our understanding about the cellular systems and may generate substantial impacts in medicine, agriculture, environmental protection, and energy production. We review the studies of the various aspects of the crosstalk between metabolic reactions and gene regulation, including models, empirical evidence, and available databases.     

A Novel Method for Extracting Protoplasts from Large Brown Algae

Protoplasts have been isolated without the application of walldegrading enzymes from three large brown algal species: Macrocystisangustifolia, Ecklonia radiata and Durvillaea potatorum. Thecentral feature of this new protocol is the removal of wall-boundcalcium by substitution with sodium from the isolation medium.The new protocol is specific for cortex and inner meristodermcell walls with highest yields obtained from meristematic oryoung tissue. Protoplasts, extracted with this method, are approximately5–10 µm in diameter with viability estimates rangingfrom 73–86%. Consistent yields of 10⁷ protoplasts g^–1fresh weight have been obtained within 2–3 for all threespecies and this compares favourably with yields achieved usinga conventional enzyme-based system. Key words: Brown algae, protoplasts, alginate, calcium, enzymes     

以豆腐柴叶为原料提取果胶工艺研究

本文开发了一条从豆腐柴叶中提取果胶的新工艺。该工艺中,树脂吸附纯化、超滤浓缩和喷雾干燥是三个重要的单元操作。为了确定最佳提取条件和考察树脂吸附纯化和超滤浓缩两个单元操作的商业应用可行性,进行了三种不同规模的试验。结果表明,所开发的工艺在能耗和果胶质量方面明显优于传统的醇沉淀法。     

一种从鱼类肌肉组织中提取基因组DNA的简易方法

以泰山螭霖鱼、黄河鲤鱼、东平湖鲫鱼为材料,采用改进的酚-氯仿抽提法和蛋白酶K消化法提取基因组DNA,并对其进行紫外分光光度、琼脂糖凝胶电泳、聚丙烯酰胺凝胶电泳、微卫星PCR扩增等方法的鉴定。结果表明,本方法提取的鱼类基因组DNA浓度为0．9-3．25μg／μL,D260nm/D280nm值为1．79-1．87,电泳条带整齐明亮,适合微卫星PCR扩增。因此,本方法能够从鱼类肌肉组织中获得较为纯净的基因组DNA,适于进一步的分子生物学研究之用。     

A Simple Procedure for Extracting Methacrylic Acid from Water-Miscible Methacrylates

A simple procedure for removing methacrylic acid from water-miscible methacrylates is described. One volume of monomer is diluted with 9 volumes of diethyl ether. Three consecutive extractions are carried out with 5% aqueous NaHCO₃ at 4 C. Residual water is removed by shaking with anhydrous sodium sulfate. The ether is removed by flash evaporation on a Biichi Rotavapor. Weak alkali extraction produces good quality semithin sections which are free of background staining. This method may be a useful alternative to existing methods for removal of methacrylic acid.     

A Mathematical Model of the Human Metabolic System and Metabolic Flexibility

In healthy subjects some tissues in the human body display metabolic flexibility, by this we mean the ability for the tissue to switch its fuel source between predominantly carbohydrates in the postprandial state and predominantly fats in the fasted state. Many of the pathways involved with human metabolism are controlled by insulin and insulin-resistant states such as obesity and type-2 diabetes are characterised by a loss or impairment of metabolic flexibility. In this paper we derive a system of 12 first-order coupled differential equations that describe the transport between and storage in different tissues of the human body. We find steady state solutions to these equations and use these results to nondimensionalise the model. We then solve the model numerically to simulate a healthy balanced meal and a high fat meal and we discuss and compare these results. Our numerical results show good agreement with experimental data where we have data available to us and the results show behaviour that agrees with intuition where we currently have no data with which to compare.     

Chelex-100快速提取放线菌DNA作为PCR扩增模板

旨在建立有效扩增16S rRNA基因序列的放线菌DNA快速提取的方法。采用Chelex-100法提取放线菌DNA,使用PCR扩增16S rRNA基因序列评价提取核酸的质量。结果显示,Chelex-100法能够在10 min之内从放线菌中快速提取DNA,所提取的DNA可以直接用于PCR扩增反应,PCR扩增产物电泳条带清晰,符合理论预期结果。因此,Chelex-100法提取放线菌DNA可以作为16S rRNA基因序列PCR扩增的模板,该方法具有经济、简便、快速的特点,适合于放线菌菌株大规模地筛选和分类鉴定。     

SDS-CTAB结合法提取棉花总DNA

根据以往提取棉花总DNA的经验 ,并参考了几种相关的植物总DNA提取方法 ,得到一种更适合棉花 (GossypiumL .)总DNA提取的方法。该提取方法综合了SDS法与CTAB法的优点 ,使获得的棉花总DNA纯度高 ,得率大 ,完整性较好 ,可用于PCR检测 ,Southern杂交 ,RAPD ,染色体步移等分子生物学操作。     

PSAMM: A Portable System for the Analysis of Metabolic Models

The genome-scale models of metabolic networks have been broadly applied in phenotype prediction, evolutionary reconstruction, community functional analysis, and metabolic engineering. Despite the development of tools that support individual steps along the modeling procedure, it is still difficult to associate mathematical simulation results with the annotation and biological interpretation of metabolic models. In order to solve this problem, here we developed a Portable System for the Analysis of Metabolic Models (PSAMM), a new open-source software package that supports the integration of heterogeneous metadata in model annotations and provides a user-friendly interface for the analysis of metabolic models. PSAMM is independent of paid software environments like MATLAB, and all its dependencies are freely available for academic users. Compared to existing tools, PSAMM significantly reduced the running time of constraint-based analysis and enabled flexible settings of simulation parameters using simple one-line commands. The integration of heterogeneous, model-specific annotation information in PSAMM is achieved with a novel format of YAML-based model representation, which has several advantages, such as providing a modular organization of model components and simulation settings, enabling model version tracking, and permitting the integration of multiple simulation problems. PSAMM also includes a number of quality checking procedures to examine stoichiometric balance and to identify blocked reactions. Applying PSAMM to 57 models collected from current literature, we demonstrated how the software can be used for managing and simulating metabolic models. We identified a number of common inconsistencies in existing models and constructed an updated model repository to document the resolution of these inconsistencies.     

一种提取粉防己碱的新方法

本文报道了一种新的提取粉防己生物碱的方法.粉防己根粉用0.6%稀硫酸渗滤,提取液通过D72树脂柱,然后用氨水乙醇溶液洗脱,丙酮、甲苯结晶纯化得到粉防己碱纯品.该方法在提取过程中避免了使用毒性大的溶剂,提高了防己生物碱的提取率,简化了操作,是一种环保型提取工艺,适用于其他中药叔胺和季胺型生物碱的提取.     

一种适于微生物多样性分析的青贮饲料总DNA的提取方法

目的:提出一种适于微生物多样性分析的青贮饲料中微生物总DNA的提取方法,并评价其效果.方法:间接法抽提样本的总DNA,通过琼脂糖电泳、紫外吸收及PCR分析DNA质量,DGGE评价提取效果,用PCR扩增目的菌株的特定片段来检测提取方法的灵敏度.结果:两个样本DNA的A260/A280值分别为1.99和1.93,A260/,A230值分别为2.19和1.90,提取的DNA不需纯化便可直接用于16S rRNA基因的扩增,提取方法灵敏度为3cfu/g,DGGE结果表明提取方法可以涵盖样品中的所有微生物.结论:提取的DNA纯度较高,可直接用于下游分子操作,提取方法灵敏度较高,能全面反映样品中的微生物原貌,可用于免培养法研究青贮饲料中的微生物菌群组成.     

一种简单高效的食用真菌总RNA提取方法

以金针菇为材料,建立了一种适合于富含RNase、多酚、多糖和糖蛋白的食用真菌RNA的提取方法,此方法在高浓度变性剂存在的条件下2次用苯酚-氯仿-异戊醇进行抽提去除DNA、蛋白质,并用异丙醇和乙酸钠选择性沉淀RNA、去除多糖,得到完整、均一的RNA样品。 Abstract:With Flammulina velutipes material,an improved method was developed for extracting total RNA from domestic fungus that are rich in RNase,polyphenols,polymeric carbohydrates and proteoglycans..Phenol-chloroform-isoamyl alcohol were used twice to clear DNA and protein under higher concentration of denaturing solution and isopentanol,sodium acetate were used to precipitate RNA selectively.Pure and intact RNA can be effectively prepared by this method.     

Rapid Methods for Extracting Autolysins from Bacillus subtilis

Two procedures are described for the extraction of autolysins from whole cells. One method uses 5 M LiCl at 4 C. The amount of enzyme obtained by this method is six times more than that obtained by autolysis of cell walls and fourteen times more than that obtained by extracting cell walls with LiCl. With the other method, cells are extracted with 2% Triton X-100. This is less efficient than the LiCl method but yields about one-half the amount of enzyme obtained by cell wall autolysis and about the same amount as obtained by extracting cell walls with salt. Both procedures yield autolysin with multiple pH optima. Autolysins can be extracted from several bacterial species by either the LiCl or the detergent method. The data suggest that these techniques have sufficient sensitivity to detect small differences in autolytic activity among mutants and various organisms and are also suitable for large-scale isolation of autolysin for purification and characterization studies.     

硫酸烟碱提取新工艺

本文介绍了含烟碱植物源农药的优点，国内外提取硫酸烟碱现状，本工艺技术特色，并分析了本工艺经济效益。本文还预测了植物源农药市场前景。     

植原体DNA提取方法的改良

在总结多种植原体DNA提取方法的基础上 ,发展了一种提取植原体DNA新方法。用此方法提取的DNA经琼脂糖凝胶电泳检测到大于 15kb的DNA主带 ,基本无DNA碎带 ,不用RNase处理 ,也无RNA干扰 ,OD2 60 / 2 80 值显示产物纯度较高 ,无需任何处理 ,即可以作为模板扩增     

A Comprehensive Survey of Retracted Articles from the Scholarly Literature

Background

The number of retracted scholarly articles has risen precipitously in recent years. Past surveys of the retracted literature each limited their scope to articles in PubMed, though many retracted articles are not indexed in PubMed. To understand the scope and characteristics of retracted articles across the full spectrum of scholarly disciplines, we surveyed 42 of the largest bibliographic databases for major scholarly fields and publisher websites to identify retracted articles. This study examines various trends among them.

Results

We found, 4,449 scholarly publications retracted from 1928–2011. Unlike Math, Physics, Engineering and Social Sciences, the percentages of retractions in Medicine, Life Science and Chemistry exceeded their percentages among Web of Science (WoS) records. Retractions due to alleged publishing misconduct (47%) outnumbered those due to alleged research misconduct (20%) or questionable data/interpretations (42%). This total exceeds 100% since multiple justifications were listed in some retraction notices. Retraction/WoS record ratios vary among author affiliation countries. Though widespread, only miniscule percentages of publications for individual years, countries, journals, or disciplines have been retracted. Fifteen prolific individuals accounted for more than half of all retractions due to alleged research misconduct, and strongly influenced all retraction characteristics. The number of articles retracted per year increased by a factor of 19.06 from 2001 to 2010, though excluding repeat offenders and adjusting for growth of the published literature decreases it to a factor of 11.36.

Conclusions

Retracted articles occur across the full spectrum of scholarly disciplines. Most retracted articles do not contain flawed data; and the authors of most retracted articles have not been accused of research misconduct. Despite recent increases, the proportion of published scholarly literature affected by retraction remains very small. Articles and editorials discussing retractions, or their relation to research integrity, should always consider individual cases in these broad contexts. However, better mechanisms are still needed for raising researchers’ awareness of the retracted literature in their field.     

Lactose-Inducible System for Metabolic Engineering of Clostridium ljungdahlii

The development of tools for genetic manipulation of Clostridium ljungdahlii has increased its attractiveness as a chassis for autotrophic production of organic commodities and biofuels from syngas and microbial electrosynthesis and established it as a model organism for the study of the basic physiology of acetogenesis. In an attempt to expand the genetic toolbox for C. ljungdahlii, the possibility of adapting a lactose-inducible system for gene expression, previously reported for Clostridium perfringens, was investigated. The plasmid pAH2, originally developed for C. perfringens with a gusA reporter gene, functioned as an effective lactose-inducible system in C. ljungdahlii. Lactose induction of C. ljungdahlii containing pB1, in which the gene for the aldehyde/alcohol dehydrogenase AdhE1 was downstream of the lactose-inducible promoter, increased expression of adhE1 30-fold over the wild-type level, increasing ethanol production 1.5-fold, with a corresponding decrease in acetate production. Lactose-inducible expression of adhE1 in a strain in which adhE1 and the adhE1 homolog adhE2 had been deleted from the chromosome restored ethanol production to levels comparable to those in the wild-type strain. Inducing expression of adhE2 similarly failed to restore ethanol production, suggesting that adhE1 is the homolog responsible for ethanol production. Lactose-inducible expression of the four heterologous genes necessary to convert acetyl coenzyme A (acetyl-CoA) to acetone diverted ca. 60% of carbon flow to acetone production during growth on fructose, and 25% of carbon flow went to acetone when carbon monoxide was the electron donor. These studies demonstrate that the lactose-inducible system described here will be useful for redirecting carbon and electron flow for the biosynthesis of products more valuable than acetate. Furthermore, this tool should aid in optimizing microbial electrosynthesis and for basic studies on the physiology of acetogenesis.     

用于微生物多样性分析的棉田土壤总DNA的提取

目的：探讨适用于微生物多样性研究的棉田土壤微生物总DNA提取方法。方法：采用4种方法提取不同连作和轮作处理的棉田土壤微生物总DNA,比较其纯度、产率、片段大小,并应用ARDRA技术验证其质量。结果：其中3种方法均可获得23kb的DNA片段,但不同方法提取的DNA的产率和纯度上有明显差异。改良CTAB-SDS法提取的DNA完整性好,得率为24.20μg.g-1干土,纯化后A260/A280和A260/A230为分别为1.80和1.70,纯化回收率可达70.1%,完全适用于后续的PCR分析。结论：采用该法提取棉田土壤总DNA简便而高效。对该法提取获得的棉田土壤微生物总DNA进行ARDRA和DGGE分析,所得图谱能较全面地反映不同处理间微生物多样性及群落结构的差别,为不同栽培体系下棉田土壤微生物的分子生态学研究提供了基础。     

盾叶薯蓣中薯蓣皂甙元提取新工艺的研究

为研究新工艺提取盾叶薯蓣薯蓣中薯蓣皂甙元的最佳实验指标,以薯蓣皂甙元得率为评价参数,采用6因素5水平的正交实验,用分光光度法对25种提取方法所得到的薯蓣皂甙元进行比较分析。结果表明,硫酸浓度对薯蓣皂甙元提取的影响最大,在实验室条件下,可采用20g样品加甲醇回流提取4h,回流速度为10min／次,用2．5mol／L的硫酸水解6h,120号溶剂汽油回流提取2h,回流速度为15min／次,能清洁快速提取盾叶薯蓣中的薯蓣皂甙元。