HOMED: a homologous sequence editor

The alignment of homologous sequences with each other and theirdisplay has proved a–difficult task, despite a frequentrequirement for this process. HOMED enables related sequencesto be edited and listed in parallel with each other. The editorfunction uses a full screen editor which emulates the text editorsKED and EDT (on PDP–11 and VAX–11 respectively)and which can be adapted to emulate other text editors. Thisemulation has been adopted to simplify user learning of editingfunctions. HOMED provides functions for listing the sequencesin a variety of formats and for generating a consensus sequenceas well as providing a series of tools for maintenance of thesequence database. HOMED has been implemented in Pascal in amodular fashion to enhance portability. Received on November 27, 1986; accepted on January 8, 1987     

A mutation spectra database for bacterial and mammalian genes: 1998.

This database consists of over 24 000 mutations in 18 viral, bacterial, yeast or mammalian genes. The data are grouped as sets of DNA base sequence changes or spectra caused by a particular mutagen under defined conditions. The spectra are available on the World Wide Web at http://info.med.yale.edu/mutbase/ in two formats; in text format that can be browsed on-line or downloaded for use with a text editor and in dBASEIII format for use, after downloading, by relational database programs or by spreadsheets. Researchers are encouraged to submit DNA sequence changes to a suitable mutation database such as ours. A data entry program, MUTSIN, can be retrieved from this site. MUTSIN diagrams each mutation on the computer screen and alerts the user to any discrepancies.     

ALMA, an editor for large sequence alignments

A dedicated sequence editor, ALMA, was developed for aligning many sequences of proteins or RNA molecules or longer DNA fragments. Like previously published editors, ALMA is menu directed, screen oriented, and offers similarity and consensus display. ALMA has the additional features of collective movement of sequences, acceptance of input from many sources including structure files and databases, secondary structure display, and easy merging of alignments. In order to maintain sequence integrity and save disk space, gaps and sequences are stored separately. Automatic recovery of a session is possible. Finally, the program allows interaction between manual and automatic alignment.     

New coarse-grained DNA model

A new coarse-grained model of the DNA molecule has been proposed, which was elaborated on the basis of its all-atomic model analysis. The model has been shown to rather well reproduce the DNA structure under low and room temperatures. The Young’s and torsion moduli calculated using the coarse-grained model are in close agreement with experimental data and the theoretical results of other authors. The model can be used for DNA fragments of several hundreds base pairs for rather long time scales (of the order of μs) and for simulating their interactions with other structures.     

Novel Strategies to Construct Complex Synthetic Vectors to Produce DNA Molecular Weight Standards

DNA molecular weight standards (DNA markers, nucleic acid ladders) are commonly used in molecular biology laboratories as references to estimate the size of various DNA samples in electrophoresis process. One method of DNA marker production is digestion of synthetic vectors harboring multiple DNA fragments of known sizes by restriction enzymes. In this article, we described three novel strategies—sequential DNA fragment ligation, screening of ligation products by polymerase chain reaction (PCR) with end primers, and “small fragment accumulation”—for constructing complex synthetic vectors and minimizing the mass differences between DNA fragments produced from restrictive digestion of synthetic vectors. The strategy could be applied to construct various complex synthetic vectors to produce any type of low-range DNA markers, usually available commercially. In addition, the strategy is useful for single-step ligation of multiple DNA fragments for construction of complex synthetic vectors and other applications in molecular biology field. Zhe Chen and Jianbing Wu contributed to this work equally.     

碱基编辑系统研究最新进展及应用

CRISPR系统能够在基因组DNA中完成精准编辑,但依赖于细胞内的同源重组(Homology directed recombination,HDR)修复途径,且效率极低.基于CRISPR/Cas9系统开发的碱基编辑技术(Base editing)通过将失去切割活性的核酸酶与不同碱基脱氨基酶融合,构建了两套碱基编辑系统(...     

Emotions under Discussion: Gender,Status and Communication in Online Collaboration

Background

Despite the undisputed role of emotions in teamwork, not much is known about the make-up of emotions in online collaboration. Publicly available repositories of collaboration data, such as Wikipedia editor discussions, now enable the large-scale study of affect and dialogue in peer production.

Methods

We investigate the established Wikipedia community and focus on how emotion and dialogue differ depending on the status, gender, and the communication network of the editors who have written at least 100 comments on the English Wikipedia''s article talk pages. Emotions are quantified using a word-based approach comparing the results of two predefined lexicon-based methods: LIWC and SentiStrength.

Principal Findings

We find that administrators maintain a rather neutral, impersonal tone, while regular editors are more emotional and relationship-oriented, that is, they use language to form and maintain connections to other editors. A persistent gender difference is that female contributors communicate in a manner that promotes social affiliation and emotional connection more than male editors, irrespective of their status in the community. Female regular editors are the most relationship-oriented, whereas male administrators are the least relationship-focused. Finally, emotional and linguistic homophily is prevalent: editors tend to interact with other editors having similar emotional styles (e.g., editors expressing more anger connect more with one another).

Conclusions/Significance

Emotional expression and linguistic style in online collaboration differ substantially depending on the contributors'' gender and status, and on the communication network. This should be taken into account when analyzing collaborative success, and may prove insightful to communities facing gender gap and stagnation in contributor acquisition and participation levels.     

RALEE--RNA ALignment editor in Emacs

SUMMARY: Production of high quality multiple sequence alignments of structured RNAs relies on an iterative combination of manual editing and structure prediction. An essential feature of an RNA alignment editor is the facility to mark-up the alignment based on how it matches a given secondary structure prediction, but few available alignment editors offer such a feature. The RALEE (RNA ALignment Editor in Emacs) tool provides a simple environment for RNA multiple sequence alignment editing, including structure-specific colour schemes, utilizing helper applications for structure prediction and many more conventional editing functions. This is accomplished by extending the commonly used text editor, Emacs, which is available for Linux, most UNIX systems, Windows and Mac OS. AVAILABILITY: The ELISP source code for RALEE is freely available from http://www.sanger.ac.uk/Users/sgj/ralee/ along with documentation and examples. CONTACT: sgj@sanger.ac.uk     

SEQGEL: a versatile and comfortable DNA editor which supports a special keyboard and a speech synthesizer

A DNA editor for an Apple II is described which contains manyadditional functions apart from just editing sequences. Thedata files are normal ASCII text or binary files and can thusbe used easily by other programs. The program supports a specialkeyboard which greatly facilitates typing of DNA sequences.Furthermore a speech synthesizer is supported by the editor.The speech feedback, together with the special keyboard, reducestyping errors to a minimum. ; accepted on March 10, 1986     

Computer-aided construction of nucleic acid restriction maps using defined vectors

A new algorithm is described that will rapidly produce restrictionmaps of cloned DNA fragments. Information concerning the vectoris stored as a data file and used in constructing probable maps.As the program is based upon a permutation analysis it has twoprimary uses. First, preliminary restriction maps can be createdfrom fragment length data as a starting point for further analysis.Second, existing maps can be confirmed as being highly probable,and other probable maps examined to ensure certain combinationshave not been overlooked. Although primarily designed for linearvectors, the program can be used to calculate circular maps. Received on June 5, 1985; accepted on September 27, 1985     

基因编辑之“新宠”—单碱基基因组编辑系统

近年发展起来的人工核酸酶可通过引起特定位点的DNA双链断裂实现对目的片段的有效编辑。为进一步提高碱基修改的效率和精确度,2016年研究者们利用CRISPR/Cas9识别特定DNA序列的功能,结合胞嘧啶脱氨酶的生化活性发明了将胞嘧啶高效转换为胸腺嘧啶(C>T)的嘧啶单碱基编辑系统(base editor)。这一系统虽然能精准实现嘧啶直接转换,大大提高精确基因编辑效率,但美中不足的是无法对嘌呤进行修改。近期,Nature报道了将细菌中的tRNA腺嘌呤脱氨酶定向进化形成具有催化DNA腺嘌呤底物的脱氨酶,将其与Cas9系统融合发明了具有高效催化腺嘌呤转换为鸟嘌呤的新工具—腺嘌呤单碱基编辑系统(ABEs, adenine base editors)。本文总结了单碱基编辑工具的发展历程和最新研究进展,着重介绍ABEs的研发过程,并对单碱基编辑工具今后的应用方向和研发方向进行展望。     

Promoter trapping identifies real genes in C. elegans

Promoter trapping involved screening uncharacterized fragments of C. elegans genomic DNA for C. elegans promoter activity. By sequencing the ends of these DNA fragments and locating their genomic origin using the available genome sequence data, promoter trapping has now been shown to identify real promoters of real genes, exactly as anticipated. Developmental expression patterns have thereby been linked to gene sequence, allowing further inferences on gene function to be drawn. Some expression patterns generated by promoter trapping include subcellular details. Localization to the surface of particular cells or even particular aspects of the cell surface was found to be consistent with the genes, now associated with these patterns, encoding membrane-spanning proteins. Data on gene expression patterns are easier to generate and characterize than mutant phenotypes and may provide the best means of interpreting the large quantity of sequence data currently being generated in genome projects. Received: 12 June 1998 / Accepted: 21 August 1998     

GENEUS, a computer system for DNA and protein sequence analysis containing an information retrieval system for the EMBL data library.

We describe a comprehensive computer system, GENEUS, for extensive DNA, RNA and protein sequence analysis. The analysis system is developed for the DEC VAX/VMS computer and uses the EMBL Nucleic Acid Sequence Data Library. Help information is available on-line on terminal screen. To speed up system handling, a qualifier oriented user communication is employed. All results are stored on files making them accessible to the computer editor. An information retrieval system for the EMBL Nucleotide Sequence Data Library is also described. A defined data-base interface allows connection to other analysis programs.+     

Evolution of genome size: A phylogenetic test of the DNA loss hypothesis

It has been recently suggested that the C-value paradox, the lack of an obvious association between organismal complexity and genome size, can result simply from biases in insertion and deletion rates—the DNA loss hypothesis. This hypothesis has been heavily criticized, particularly because its evidence, a negative relationship between genome size and DNA loss rate, is based on a highly selective use of the available data. In this study it is shown that the even the most favorable interpretation of the data favoring the DNA loss hypothesis is largely an artifact of phylogenetic nonindependence, supporting the assertion made by other authors that the mechanisms underlying genome size evolution might be more complex than envisioned by the DNA loss hypothesis. The text was submitted by the author in English.     

'DNA Strider': a 'C' program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers

DNA Strider is a new integrated DNA and Protein sequence analysis program written with the C language for the Macintosh Plus, SE and II computers. It has been designed as an easy to learn and use program as well as a fast and efficient tool for the day-to-day sequence analysis work. The program consists of a multi-window sequence editor and of various DNA and Protein analysis functions. The editor may use 4 different types of sequences (DNA, degenerate DNA, RNA and one-letter coded protein) and can handle simultaneously 6 sequences of any type up to 32.5 kB each. Negative numbering of the bases is allowed for DNA sequences. All classical restriction and translation analysis functions are present and can be performed in any order on any open sequence or part of a sequence. The main feature of the program is that the same analysis function can be repeated several times on different sequences, thus generating multiple windows on the screen. Many graphic capabilities have been incorporated such as graphic restriction map, hydrophobicity profile and the CAI plot- codon adaptation index according to Sharp and Li. The restriction sites search uses a newly designed fast hexamer look-ahead algorithm. Typical runtime for the search of all sites with a library of 130 restriction endonucleases is 1 second per 10,000 bases. The circular graphic restriction map of the pBR322 plasmid can be therefore computed from its sequence and displayed on the Macintosh Plus screen within 2 seconds and its multiline restriction map obtained in a scrolling window within 5 seconds.     

2D finite element ecological model for the Curonian lagoon

The results of application of 2D finite element model SHYFEM to the Curonian lagoon (Baltic Sea) are considered. SHYFEM consist of a physical processes module and an eutrophication module EUTRO adapted for the SHYFEM code from well known modelling system WASP. The SHYFEM/EUTRO model calibration results were compared with the performance of various biogeochemical models analysed in other studies (153 studies published from 1990 to 2002). The performance of all corresponding state variables—dissolved oxygen, NO₃, NH₄, PO₄, phyto- and zooplankton—was slightly lower than median model performance which could be considered satisfactory given the initial state of model formulation and calibration. Model underestimates phytoplankton autumn blooms, especially for the southern part of the lagoon, where fine sediments dominate and water residence time is high. It can be concluded that, in order to increase model performance, the eutrophication module should be improved to account for the dominance of different phytoplankton groups as well as for the exchanges between the sediments and the water column. The amount and quality of the data available for the model setup and calibration are unsatisfactory and should be improved for the development of the next enhanced model version. Guest editors: A. Razinkovas, Z. R. Gasiūnaitė, J. M. Zaldivar & P. Viaroli European Lagoons and their Watersheds: Function and Biodiversity     

基于CRISPR/Cas系统的DNA碱基编辑技术及其在生物医学和农业中的应用

近年来,基于成簇的规律间隔短回文重复序列及其相关系统(Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein,CRISPR/Cas)的基因编辑技术飞速发展,该系统可以利用同源定向重组(Homology directed repair,HDR)来完成其介导的精准编辑,但效率极低,限制了其在农业和生物医学等领域上的推广应用。基于CRISPR/Cas系统的DNA碱基编辑技术作为一种新兴的基因组编辑技术,能在不产生双链断裂的情况下实现碱基的定向突变,相对于CRISPR/Cas介导的HDR编辑具有更高的编辑效率和特异性。目前,已开发出了可将C碱基突变为T碱基的胞嘧啶碱基编辑器(Cytidine base editors,CBE),将A碱基突变为G碱基的腺嘌呤碱基编辑器(Adenine base editors,ABE),以及可实现碱基任意变换和小片段精准插入和缺失的Prime编辑器(Prime editors,PE)。另外,能实现C到G颠换的糖基化酶碱基编辑器(Glycosylase base editors,GBE)以及能同时编辑A和C两种底物的双碱基编辑器也已被开发出来。文中主要综述了几种DNA碱基编辑器的开发历程、研究进展及各自优点和局限性;介绍了DNA碱基编辑技术在生物医学以及农业中的成功应用案例,以期为DNA碱基编辑器的进一步优化和选择应用提供借鉴。     

New coarse-grained DNA model

A new coarse-grained model of the DNA molecule has been proposed, which was elaborated on the basis of its all-atomic model analysis. The model has been shown to rather well reproduce the DNA structure under low and room temperatures. The Young's and torsion moduli calculated using the coarse-grained model are in close agreement with experimental data and the theoretical results of other authors. The model can be used for DNA fragments of several hundreds base pairs for rather long time scales (of the order of micros) and for simulating their interactions with other structures.     

Processing DNA molecules as text

Polymerase Chain Reaction (PCR) is the DNA-equivalent of Gutenberg’s movable type printing, both allowing large-scale replication of a piece of text. De novo DNA synthesis is the DNA-equivalent of mechanical typesetting, both ease the setting of text for replication. What is the DNA-equivalent of the word processor? Biology labs engage daily in DNA processing—the creation of variations and combinations of existing DNA—using a plethora of manual labor-intensive methods such as site-directed mutagenesis, error-prone PCR, assembly PCR, overlap extension PCR, cleavage and ligation, homologous recombination, and others. So far no universal method for DNA processing has been proposed and, consequently, no engineering discipline that could eliminate this manual labor has emerged. Here we present a novel operation on DNA molecules, called Y, which joins two DNA fragments into one, and show that it provides a foundation for DNA processing as it can implement all basic text processing operations on DNA molecules including insert, delete, replace, cut and paste and copy and paste. In addition, complicated DNA processing tasks such as the creation of libraries of DNA variants, chimeras and extensions can be accomplished with DNA processing plans consisting of multiple Y operations, which can be executed automatically under computer control. The resulting DNA processing system, which incorporates our earlier work on recursive DNA composition and error correction, is the first demonstration of a unified approach to DNA synthesis, editing, and library construction.

Electronic supplementary material

The online version of this article (doi:10.1007/s11693-010-9059-y) contains supplementary material, which is available to authorized users.