MacStylet, software to analyse electrical penetration graph data on the Macintosh

Conclusion Since the EPG method is increasingly utilized in the investigation of plant-Homoptera interactions, this software has been developed to enable fast processing of abundant data. The objective seems to have been achieved and, with a little practice, a 2-hour experiment may be analysed in about 10–15 minutes. Mac-Stylet is stand-alone shareware, freely distributed to all persons interested (request to G. Febvay, email: febvay@jouy.inra.fr).     

Advances in Tools to Determine the Glycan-Binding Specificities of Lectins and Antibodies

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Highlights

• •Lectins and glycan-binding antibodies are valuable as probe of glycans.
• •Advanced bioinformatics tools enable the mining of glycan-array data.
• •New insights into protein-glycan interactions have value in biological research.

     

Algae on the internet

Increasingly electronic communication and a variety of electronic resources are accessible to a larger group of people within the scientific community. This paper outlines the range of resources that are available, and comments on their current and future value to the phycological community. Resources discussed include mailing lists and newsgroups. These are useful tools for rapid, informal, targeted communication, although the technology employed places limitations on the type and format of information which may be distributed. The World Wide Web (WWW) has the potential to overcome these limitations, the quality, complexity and value to the phycological community of the sites on the WWW are extremely variable, with some material being of dubious quality. However, it is possible to access high quality resources including culture collection catalogues, high quality images and microbial and molecular databases. As well as some of the current resources, this paper discusses some possible directions for the future of phycology on the internet.http://wiua.nwi.ac.uk/     

A spectral correlation function for efficient sequential NMR assignments of uniformly 15N-labeled proteins

Summary A new computer-based approach is described for efficient sequence-specific assignment of uniformly ¹⁵N-labeled proteins. For this purpose three-dimensional ¹⁵N-correlated [¹H, ¹H]-NOESY spectra are divided up into two-dimensional ¹H-¹H strips which extend over the entire spectral width along one dimension and have a width of ca. 100 Hz, centered about the amide proton chemical shifts along the other dimension. A spectral correlation function enables sorting of these strips according to proximity of the corresponding residues in the amino acid sequence. Thereby, starting from a given strip in the spectrum, the probability of its corresponding to the C-terminal neighboring residue is calculated for all other strips from the similarity of their peak patterns with a pattern predicted for the sequentially adjoining residue, as manifested in the scalar product of the vectors representing the predicted and measured peak patterns. Tests with five different proteins containing both -helices and -sheets, and ranging in size from 58 to 165 amino acid residues show that the discrimination achieved between the sequentially neighboring residue and all other residues compares well with that obtained with an unguided interactive search of pairs of sequentially neighboring strips, with important savings in the time needed for complete analysis of 3D ¹⁵N-correlated [¹H, ¹H]-NOESY spectra. The integration of this routine into the program package XEASY ensures that remaining ambiguities can be resolved by visual inspection of the strips, combined with reference to the amino acid sequence and information on spin-system types obtained from additional NMR spectra.Abbreviations 1D, 2D, 3D, 4D one-, two-, three-, four-dimensional - NOE nuclear Overhauser enhancement - NOESY nuclear Overhauser enhancement spectroscopy - COSY correlation spectroscopy - TOCSY total correlation spectroscopy     

金银花花形基因的发掘及生物信息学分析

金银花作为我国重要的中药材,具有消炎、抗菌、抗病毒、抗氧化、防癌等多种功效。随着金银花市场供需矛盾日益加剧,通过分子标记辅助选择育种方法来培育高产优质品种势在必行。通过NCBI的Blast工具扫描金银花蛋白组数据发掘花形候选基因,并执行候选基因的亲缘关系分析、结构域分析、表达模式分析、理化性质分析、蛋白质结构预测等一系列生物信息学分析。依据拟南芥调控花形的ABE类基因,通过NCBI-Blast工具扫描金银花氨基酸序列,筛选出包含MADS结构域的8个调控花形的金银花候选基因。经LjaFGD表达模式分析发现,金银花的花中GWHGAAZE016592和GWHGAAZE014905表达量显著高于其他部位,可能正向调控金银花花形。GWHGAAZE014905是一个包含MADS结构域的调控花器官发育的B类基因;GWHGAAZE016592是AP3同源基因。生物信息学分析发现,GWHGAAZE016592和GWHGAAZE014905均是稳定的亲水蛋白,属于非分泌蛋白,包括Motif1、Motif3、Motif4、Motif2、Motif6和Motif5,蛋白质三级结构模板为6byy.2.A和4ox0.2.C。GWHGAAZE014905被定位到细胞核上,而GWHGAAZE016592被定位到叶绿体上,且包含1个位于151~173 bp的跨膜螺旋区域,属于膜蛋白。研究结果为分子标记辅助选择方式培育道地高产优质金银花品种提供了基因资源和分子标记。     

snpR: User friendly population genomics for SNP data sets with categorical metadata

The analysis of genomic data can be an intimidating process, particularly for researchers who are not experienced programmers. Commonly used analyses are spread across many programs, each requiring their own specific input formats, and so data must often be repeatedly reorganized and transformed into new formats. Analyses often require splitting data according to metadata variables such as population or family, which can be challenging to manage in large data sets. Here, we introduce snpR, a user-friendly data analysis package in R for processing SNP genomic data. snpR is designed to automate data subsetting and analyses across categorical metadata while also streamlining repeated analyses by integrating approaches contained in many different packages in a single ecosystem. snpR facilitates iterative and efficient analyses centred on a single R object for an entire analysis pipeline.     

Epstein-Barr病毒基因组编码的BARF-1和EC-LF4蛋白质与免疫球蛋白结构同源

将EB病毒蛋白质BARF-1和EC-LF4与NBRF蛋白质库的序列进行局部同源性检索以及与已知的Ig V或C功能区相关分子进行对准比较,检查了同源性积分的统计学意义,并进行了二级结构预测和疏水性分析,确定了BARF-1的第13-124位和第126-221位残基片段分别与V和C样功能区类似,EC-LF4的第20-135位残基片段与V样功能区相似,BARF-1是非膜蛋白,EC-LF4是膜整合蛋白,其胞外部分近膜侧有一个类似于Ig绞链区的序列。因此,BARF-1与Ig轻链结构相似,EC-LF4与CD8抗原的第一条链相似。根据Ig超族分子的一般功能(即介导细胞粘附和细胞识别),推测EC-LF4可能作为一种粘附分子与淋巴细胞表面的Ig相关分子结合而促进EB病毒对淋巴细胞的感染。BARF-1因已知与病毒复制有关,与Ig超族的一般功能无关。EC-LF4和BARF-1的Ig样功能区可能来源于EB病毒对宿主细胞Ig基因的整合。     

hw‐quickcheck: an easy‐to‐use computer program for checking genotypes for agreement with Hardy–Weinberg expectations

Deviations from Hardy–Weinberg expectations are frequently a sign of genotyping error. hw‐quickcheck is an easy‐to‐use computer program for detecting departures from Hardy–Weinberg equilibrium. hw‐quickcheck uses exact tests for all of its calculations. These tests include a global test for heterozygote excess/deficiency and genotype‐specific tests.     

burnr: Fire history analysis and graphics in R

We developed a new software package, burnr, for fire history analysis and plotting in the R statistical programming environment. It was developed for tree-ring fire-scar analysis, but is broadly applicable to other event analyses (e.g., avalanches, frost rings, or culturally modified trees). Our new package can read, write, and manipulate standard tree-ring fire history FHX files, produce fire—demography charts, calculate fire frequency and seasonality statistics, and run superposed epoch analysis (SEA). A key benefit of burnr is that it enables automation of analyses and plotting, especially for large data sets. The package also facilitates creative plotting, mapping, and analyses when combined with the thousands of packages available in R. In this paper, we describe the basic functionality of burnr and introduce users to fire history analyses in R.