A new archaeobotanical database program

The available quantity of archaeobotanical data derived from the identification of macroremains has expanded considerably over the last few decades. In order to obtain a supraregional or even regional overview for a particular period of time, or of the distribution of a single species, a database is needed. At the Archaeobotanical Department of the Institute of the "Kommission für Arch?ologische Landesforschung in Hessen e.V." (KAL) such a database has been developed in the last few years. It is suitable for the handling of large quantities of archaeobotanical results, including a whole range of background information comprising archaeological, ecological and other related data, and offers various possibilities for the evaluation of these data. Received January 8, 2001 / Accepted April 9, 2002     

PeptideDepot: Flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information

Recently, dramatic progress has been achieved in expanding the sensitivity, resolution, mass accuracy, and scan rate of mass spectrometers able to fragment and identify peptides through MS/MS. Unfortunately, this enhanced ability to acquire proteomic data has not been accompanied by a concomitant increase in the availability of flexible tools allowing users to rapidly assimilate, explore, and analyze this data and adapt to various experimental workflows with minimal user intervention. Here we fill this critical gap by providing a flexible relational database called PeptideDepot for organization of expansive proteomic data sets, collation of proteomic data with available protein information resources, and visual comparison of multiple quantitative proteomic experiments. Our software design, built upon the synergistic combination of a MySQL database for safe warehousing of proteomic data with a FileMaker‐driven graphical user interface for flexible adaptation to diverse workflows, enables proteomic end‐users to directly tailor the presentation of proteomic data to the unique analysis requirements of the individual proteomics lab. PeptideDepot may be deployed as an independent software tool or integrated directly with our high throughput autonomous proteomic pipeline used in the automated acquisition and post‐acquisition analysis of proteomic data.     

Characterization of SCAR markers of Eimeria spp. of domestic fowl and construction of a public relational database (The Eimeria SCARdb)

This study reports the development and characterization of 151 sequence characterized amplified region (SCAR) markers for the seven Eimeria species that infect the domestic fowl. From this set, 84 markers are species-specific and 67 present partial specificity. The complete nucleotide sequence was derived for all markers, revealing the presence of micro- and minisatellite repetitive units in 22 SCARs, with up to five distinct repeat units being observed per marker. Only 15 markers showed significant hits in similarity searches against public sequence databases, thus confirming their anonymous and non-coding character. Finally, a relational database of the markers (the Eimeria SCARdb) was developed and made available on the Internet, providing a valuable resource of SCAR markers that can be useful for molecular diagnosis, and also for epizootiological, genetic variability and genome mapping studies.     

Antibody screening database for protein kinetic modeling

Knowledge-based proteomic studies rely on the availability of quality antibodies. The increasing number of commercially available antibodies covers a wide range of protein networks; however, performance of each antibody can vary, depending on what type of cells, treatments, and time points are studied. Here, we describe an antibody database in which we screened 279 antibodies against multiple cell lysates after various treatments and from different time points. We applied these quality-confirmed antibodies on protein arrays, showing their utility for protein kinetic modeling.     

MIPDB: a relational database dedicated to MIP family proteins

BACKGROUND INFORMATION: The MIPs (major intrinsic proteins) constitute a large family of membrane proteins that facilitate the passive transport of water and small neutral solutes across cell membranes. Since water is the most abundant molecule in all living organisms, the discovery of selective water-transporting channels called AQPs (aquaporins) has led to new knowledge on both the physiological and molecular mechanisms of membrane permeability. The MIPs are identified in Archaea, Bacteria and Eukaryota, and the rapid accumulation of new sequences in the database provides an opportunity for large-scale analysis, to identify functional and/or structural signatures or to infer evolutionary relationships. To help perform such an analysis, we have developed MIPDB (database for MIP proteins), a relational database dedicated to members of the MIP family. RESULTS: MIPDB is a motif-oriented database that integrates data on 785 MIP proteins from more than 200 organisms and contains 230 distinct sequence motifs. MIPDB proposes the classification of MIP proteins into three functional subgroups: AQPs, glycerol-uptake facilitators and aquaglyceroporins. Plant MIPs are classified into three specific subgroups according to their subcellular distribution in the plasma membrane, tonoplast or the symbiosome membrane. Some motifs of the database are highly selective and can be used to predict the transport function or subcellular localization of unknown MIP proteins. CONCLUSIONS: MIPDB offers a user-friendly and intuitive interface for a rapid and easy access to MIP resources and to sequence analysis tools. MIPDB is a web application, publicly accessible at http://idefix.univ-rennes1.fr:8080/Prot/index.html.     

Utility and features of a customized PC Windows-based relational database for managing microbial strain data

In addition to storing microbes, culture collections in industry, government or universities manage a vast and continuously expanding library of information on strain history and properties. An efficient and cost-effective computer database system is required for entering, analyzing and searching these data. This report describes the utility and features of a comprehensive database which consists of a commercially available relational database system combined with customized screens for data entry, viewing and report generation. The application was developed using Microsoft Access and Visual Basic to operate in the Windows environment on a local area network. Received 18 June 1997/ Accepted in revised form 21 November 1997     

The Early Neolithic site at Hoge Vaart, Almere, the Netherlands, with particular reference to non-diffusion of crop plants, and the significance of site function and sample location

The construction of a new motorway necessitated the excavation of an Early Neolithic site in the Dutch Flevopolder near the Hoge Vaart canal. In 1994-1996, an area of ca. 1700 m² was excavated in 0.5x0.5-m squares. The excavation revealed 150 surface hearths and more than a hundred deep hearth pits. The finds, mainly flint and pottery, as well as¹⁴C dates from charcoal demonstrated that the area had been used mainly during the Early Neolithic (ca. 4900–4500 cal. B.C.). The investigation of the Early Neolithic remains included detailed botanical analyses of 182 samples and hand-sorting by the excavation team, which included archaeobotanists, of tens of thousands of samples sieved over 2-mm-mesh sieves. No remains of cultivated plants were recognised among the 87 taxa (40 identified to species level) that were preserved, mainly in carbonised form. These results are compared with other Early Neolithic sites studied in the Netherlands, such as Swifterbant S3 and Schokland P14. The possible significance of site function and sample location as important factors influencing presence/absence of cultivated plant remains at a particular site is discussed.     

BASECO: a floristic and ecological database of Mediterranean French flora

The French Mediterranean zone is one of the richest of the country, with 3200 species and many endemics. Because of its interest as a synthetic tool to store and manage data, an ecological Mediterranean flora database was created. Built around five tables, BASECO allows several queries about the botanical and ecological characteristics of about 1800 plants. The database was implemented in Access, which is a relational database management system. Each species is identified by a code and is characterised by several qualitative traits relating to morphology, reproduction, life forms and biogeographical distribution, including several modalities. Each trait is informed from one or two pre-defined reference botanical handbooks as much as possible. There are many different possible uses of this database, even at a huge scale, allowing to reveal patterns hard to detect with the taxonomic approach alone.     

An 11th century a.d. burnt granary at La Gravette, south-western France: preliminary archaeobotanical results

A thick layer of carbonised seeds was encountered in an 11th century a.d. room situated in the seigneurial part of the village of La Gravette. This paper presents the first results of charcoal and seed analyses which give information on the food products stored in the granary and on their arrangement there. Triticum aestivum/durum/turgidum was by far the most important stored crop, while Avena sp., then Hordeum vulgare, Secale cereale, Triticum monococcum and Vitis vinifera were secondary. Weeds were poorly represented. Charcoals were dominated by deciduous Quercus sp., and 11 additional wood taxa were recorded, including especially Fagus sylvatica, Fraxinus sp., Rosaceae, Corylus avellana, Acer campestre and Ulmus sp. According to the charcoal distribution, Quercus and Fagus were probably building materials while most of other taxa would have been used for basketry, wattling or joinery work. In the western part of the granary, naked wheat was stored in bulk. In the eastern part, various crops (at least naked wheat, barley, rye, oat and grape) were stored in small amounts, most of which were probably separated by light wooden structures. The cereal crops had largely been processed and cleaned. The stored products probably represent taxes paid to the lord who owned the granary.     

The translational signal database, TransTerm, is now a relational database.

TransTerm-97 contains more than 97 500 non-redundant coding-sequence initiation and termination contexts compiled from GenBank, release 101 (15-June-1997). In addition, several coding sequence parameters are available: coding sequence length, Nc, GC3, and, when it is computable, codon adaptation index (CAI). Codon usage tables and summaries of start and stop codon contexts are also included. The information covers more than 325 species and organelles, including seven complete bacterial genomes and one complete eukaryotic genome. To promote research in translational control of protein synthesis, TransTerm has been converted into a relational database to ease the process of making queries. The relational database manager, Postgresql, gives access to the database using SQL (Structured Query Language). A World Wide Web interface using forms is being completed to allow the casual user access to the database. Extensions are planned to include the full 5'-UTR, full coding sequence and 3'-UTR. TransTerm-97 is available on the World Wide Web at:http://biochem. otago.ac.nz:800/Transterm/homepage.html     

Medieval plant depictions as a source for archaeobotanical research

This paper summarises the research methodology and most important results of a study which was carried out on flowering plant depictions (representations) in late medieval religious paintings from southern central Europe. This approach derives from the studies of material culture by historians of everyday life. Plant depictions may be used as a source for archaeobotanical research and studies into vegetation history after fully recognising their particularities. Firstly, the pictures show “the reality effect” and not reality itself, and an abundance of apparently realistically depicted objects; secondly, the research must be fully contextual, considering both the contemporary cultural background and participants involved. Thirdly, as pictures are great mosaics of different experience and knowledge, their language is symbolic and their relationship with geographical space uncertain. This, however, does not mean that reading and interpreting pictures is impossible. The major results of this study include the list of plant species not discovered from archaeobotanical research; the knowledge that the frequencies of occurrence of plant depictions might correspond to their occurrence in real cultural spaces that also may be indicated in pictures; and it highlights the importance of using several types of sources when pursuing research into the history, uses and perceptions of plants in the medieval period.     

Raccoon ecology database: A resource for population dynamics modelling and meta-analysis

The value of scientific studies increases and is extended when their data are stored in a manageable and accessible format. This is demonstrated through development of a raccoon ecology database (REDB) to store, manage and disseminate available peer-reviewed and unpublished data on raccoon (Procyon lotor) biology, ecology and raccoon rabies, including citations for data sources. Over 800 documents were identified and citations for them entered into the database as literature references. Approximately 1000 trait values were entered from almost 200 of these sources. These data included estimates of population density, survival rates, rabies incubation period, litter size, body weight, dispersal distance and home-range size, often by age or sex class. Each datum is linked to a citation for its source, and to information about location and land use in the study area, time of year the study was undertaken, sample size, and variance. The relational database design enables querying and easy updating and manipulation of data.

The relational data model is presented, as is its application in further developing an individual-based, spatially-explicit population model of raccoon rabies. Using information queried from the REDB benefits model development by: i) assessing the appropriateness of input parameter values, ii) providing sources for citing input values, iii) parameterising the model to different geographic regions, iv) enabling meta-analyses for evaluating model structure, as well as further contributing to parameterisation at specific locations, and v) providing biologically appropriate parameter input values for model sensitivity testing. The REDB is a useful research resource that will increase in value with ongoing inclusion of data from future raccoon and raccoon rabies studies and serves as a model for database design and research applications to other species. The database and an empty database for use with other species are available online (http://redb.nrdpfc.ca).     

IMIRS: a high-resolution 3D reconstruction package integrated with a relational image database

Recent advances in electron cryomicroscopy instrumentation and single particle reconstruction have created opportunities for high-throughput and high-resolution three-dimensional (3D) structure determination of macromolecular complexes. However, it has become impractical and inefficient to rely on conventional text file data management and command-line programs to organize and process the increasing numbers of image data required in high-resolution studies. Here, we present a distributed relational database for managing complex datasets and its integration into our high-resolution software package IMIRS (Image Management and Icosahedral Reconstruction System). IMIRS consists of a complete set of modular programs for icosahedral reconstruction organized under a graphical user interface and provides options for user-friendly, step-by-step data processing as well as automatic reconstruction. We show that the integration of data management with processing in IMIRS automates the tedious tasks of data management, enables data coherence, and facilitates information sharing in a distributed computer and user environment without significantly increasing the time of program execution. We demonstrate the applicability of IMIRS in icosahedral reconstruction toward high resolution by using it to obtain an 8-A 3D structure of an intermediate-sized dsRNA virus.     

The introduction of Old World crops (wheat, barley and peach) in Andean Argentina during the 16th century a.d.: archaeobotanical and ethnohistorical evidence

It was believed for a long time that the first Old World crops were introduced to the northwest of Argentina in a.d. 1550 during the foundation of Barco, and that the indigenous people incorporated them into their subsistence almost passively. However, since wheat, barley, and peach have been recovered from El Shincal, an Inka (Inca) administrative centre, new questions have arisen about who first brought these crops to the study region, as well as about where they were grown for the first time and which routes they followed after that. This paper will try to solve these questions during a period ranging from the 16th to the 18th century. This time span, although arbitrary, is consistent with the major damage to the original social structure caused by the Spaniards to the local indigenous populations. Our approach includes the comparison of ethnohistorical with archaeobotanical evidence. It is concluded that the first Old World crops were brought from Chile to Santiago del Estero by Spanish soldiers in a.d. 1556, and to Londres in a.d. 1558. These crops were taken up by local indigenous people during the period of the encomenderos and used to carry out a pachamanca ceremony at El Shincal during a Diaguita rebellion. Electronic Supplementary Material Supplementary material is available in the online version of this article at     

Tools for loading MEDLINE into a local relational database

Background  

Researchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of MEDLINE that they can manage locally. The National Library of Medicine (NLM) distributes MEDLINE in eXtensible Markup Language (XML)-formatted text files, but it is difficult to query MEDLINE in that format. We have developed software tools to parse the MEDLINE data files and load their contents into a relational database. Although the task is conceptually straightforward, the size and scope of MEDLINE make the task nontrivial. Given the increasing importance of text analysis in biology and medicine, we believe a local installation of MEDLINE will provide helpful computing infrastructure for researchers.     

SNObase,a database for S-nitrosation modification

S-Nitros(yl)ation is a ubiquitous redox-based posttranslational modification of protein cysteine thiols by nitric oxide or its derivatives, which transduces the bioactivity of nitric oxide (NO) by regulation of protein conformation, activity, stability, localization and protein- protein interactions. These years, more and more S-nitrosated proteins were identified in physiological and pathological processes and the number is still growing. Here we developed a database named SNObase (http://www.nitrosation.org), which collected S-nitrosation targets extracted from literatures up to June 1st, 2012. SNObase contained 2561 instances, and provided information about S-nitrosation targets, sites, biological model, related diseases, trends of S-nitrosation level and effects of S-nitrosation on protein function. With SNObase, we did functional analysis for all the SNO targets: In the gene ontology (GO) biological process category, some processes were discovered to be related to S-nitrosation (“response to drug”, “regulation of cell motion”) besides the previously reported related processes. In the GO cellular component category, cytosol and mitochondrion were both enriched. From the KEGG pathway enrichment results, we found SNO targets were enriched in different diseases, which suggests possible significant roles of S-nitrosation in the progress of these diseases. This SNObase means to be a database with precise, comprehensive and easily accessible information, an environment to help researchers integrate data with comparison and relevancy analysis between different groups or works, and also an SNO knowledgebase offering feasibility for systemic and global analysis of S-nitrosation in interdisciplinary studies.     

The ecology of The Netherlands wetlands: characteristics,threats, prospects and perspectives for ecological research

Wetlands are among the worlds' most important, but also most threatened, environmental resources. Wetland losses have been in progress particularly from the industrial revolution onwards, because wetland functions could not successfully compete for space with other land uses. Wetlands became recently foci of conservation efforts because of the increased awareness of their importance in water management and wildlife conservation, and because of the diversity of their habitats. The Netherlands are relatively rich in wetlands: 16% of its' territory is regarded as internationally important wetland and 7% has been registered as such. The major Dutch wetland types are: coastal ecosystems, large riverine systems, base-rich freshwater systems, and nutrient-poor freshwater systems. Most threats to the Dutch wetlands are of man-made origin. They comprise: (1) Changes in hydrology leading to changed discharges, currents and desiccation; (2) Acidification; (3) Eutrophication; and (4) Toxification. Long-term threats are largely climate-change related, and concern temperature rise and the UV-B increase in irradiation. General conservation goals also apply to wetlands but Ramsar-registered wetlands have a special status. Conservation of the Dutch wetlands is difficult, because of the high population density of the country and its inherent threats. However, ecological targets and standards are increasingly set in national Policy Plans and international agreements. Rehabilitation and creation of wetlands is presently widely advocated, and sometimes realised. For ecological research, the sustainability of wetlands should get top priority. Such a research programme would focus on understanding the underlying ecological processes in natural and man-dominated wetland systems to prescribe conservation, rehabilitation and management strategies that would enhance the sustainability of these systems. Within this framework special attention should be directed to studies (1) At the ecosystem level of ecosystem parameters, of which natural oscillations and trends in time, and on which the impact of disturbances are quantified. Particularly these studies, in which often simulation models are used as tools for interpretation, can provide the basis for extrapolations in space and time; (2) On adaptation capacity and mechanisms of (groups of) species to extreme environmental conditions; (3) On (mutual) relationships between plants, animals and microorganisms (e.g. competition, grazing and mineralization); (4) On dispersion between small wetlands. For the contemporary quantitative assessment of the long-term effects of climate changes, the effects of temperature rise and increase in UV-B irradiation on individual species, communities and ecosystems should also be studied.     

PACSY, a relational database management system for protein structure and chemical shift analysis

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.