Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data

Upon the completion of the Saccharomyces cerevisiae genomic sequence in 1996 [Goffeau,A. et al. (1997) Nature, 387, 5], several creative and ambitious projects have been initiated to explore the functions of gene products or gene expression on a genome-wide scale. To help researchers take advantage of these projects, the Saccharomyces Genome Database (SGD) has created two new tools, Function Junction and Expression Connection. Together, the tools form a central resource for querying multiple large-scale analysis projects for data about individual genes. Function Junction provides information from diverse projects that shed light on the role a gene product plays in the cell, while Expression Connection delivers information produced by the ever-increasing number of microarray projects. WWW access to SGD is available at genome-www.stanford.edu/Saccharomyces/.

A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm

The database reported here is derived using the Combinatorial Extension (CE) algorithm which compares pairs of protein polypeptide chains and provides a list of structurally similar proteins along with their structure alignments. Using CE, structure–structure alignments can provide insights into biological function. When a protein of known function is shown to be structurally similar to a protein of unknown function, a relationship might be inferred; a relationship not necessarily detectable from sequence comparison alone. Establishing structure–structure relationships in this way is of great importance as we enter an era of structural genomics where there is a likelihood of an increasing number of structures with unknown functions being determined. Thus the CE database is an example of a useful tool in the annotation of protein structures of unknown function. Comparisons can be performed on the complete PDB or on a structurally representative subset of proteins. The source protein(s) can be from the PDB (updated monthly) or uploaded by the user. CE provides sequence alignments resulting from structural alignments and Cartesian coordinates for the aligned structures, which may be analyzed using the supplied Compare3D Java applet, or downloaded for further local analysis. Searches can be run from the CE web site, http://cl.sdsc.edu/ce.html, or the database and software downloaded from the site for local use.

PlasmoDB: An integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data

The Plasmodium falciparum Genome Database (http://PlasmoDB.org) integrates sequence information, automated analyses and annotation data emerging from the P.falciparum genome sequencing consortium. To date, raw sequence coverage is available for >90% of the genome, and two chromosomes have been finished and annotated. Data in PlasmoDB are organized by chromosome (1–14), and can be accessed using a variety of tools for graphical and text-based browsing or downloaded in various file formats. The GUS (Genomics Unified Schema) implementation of PlasmoDB provides a multi-species genomic relational database, incorporating data from human and mouse, as well as P.falciparum. The relational schema uses a highly structured format to accommodate diverse data sets related to genomic sequence and gene expression. Tools have been designed to facilitate complex biological queries, including many that are specific to Plasmodium parasites and malaria as a disease. Additional projects seek to integrate genomic information with the rich data sets now becoming available for RNA transcription, protein expression, metabolic pathways, genetic and physical mapping, antigenic and population diversity, and phylogenetic relationships with other apicomplexan parasites. The overall goal of PlasmoDB is to facilitate Internet- and CD-ROM-based access to both finished and unfinished sequence information by the global malaria research community.

Creating local bibliographic databases: new tools for evidence-based health care*

The Internet has created new opportunities for librarians to present literature search results to clinicians. In order to take full advantage of these opportunities, libraries need to create locally maintained bibliographic databases. A simple method of creating a local bibliographic database and publishing it on the Web is described. The method uses off-the-shelf software and requires minimal programming. A hedge search strategy for outcome studies of clinical process interventions is created, and Ovid is used to search MEDLINE. The search results are saved and imported into EndNote libraries. The citations are modified, exported to a Microsoft Access database, and published on the Web. Clinicians can use a Web browser to search the database. The bibliographic database contains 13,803 MEDLINE citations of outcome studies. Most searches take between four and ten seconds and retrieve between ten and 100 citations. The entire cost of the software is under $900. Locally maintained bibliographic databases can be created easily and inexpensively. They significantly extend the evidence-based health care services that libraries can offer to clinicians.

Transposon tools for recombinant DNA manipulation: characterization of transcriptional regulators from yeast, Xenopus, and mouse.

Transposon Tn1000 has been adapted to deliver novel DNA sequences for manipulating recombinant DNA. The transposition procedure for these "tagged" Tn1000s is simple and applicable to most plasmids in current use. For yeast molecular biology, tagged Tn1000s introduce a variety of yeast selective markers and replication origins into plasmids and cosmids. In addition, the beta-globin minimal promoter and lacZ gene of Tn(beta)lac serve as a mobile reporter of eukaryotic enhancer activity. In this paper, Tn(beta)lac was used to localize a mouse HoxB-complex enhancer in transgenic mice. Other tagged transposons create Gal4 DNA-binding-domain fusions, in either Escherichia coli or yeast plasmids, for use in one- and two-hybrid tests of transcriptional activation and protein-protein interaction, respectively. With such fusions, the Saccharomyces cerevisiae Swi6 G1/S-phase transcription factor and the Xenopus laevis Pintallavis developmental regulator are shown to activate transcription. Furthermore, the same transposon insertions also facilitated mapping of the Swi6 and Pintallavis domains responsible for transcriptional activation. Thus, as well as introducing novel sequences, tagged transposons share the numerous other applications of transposition such as producing insertional mutations, creating deletion series, or serving as mobile primer sites for DNA sequencing.

Interisland and interarchipelago transfer of stone tools in prehistoric Polynesia.

Tracing interisland and interarchipelago movements of people and artifacts in prehistoric Polynesia has posed a challenge to archaeologists due to the lack of pottery and obsidian, two materials most readily used in studies of prehistoric trade or exchange. Here we report the application of nondestructive energy-dispersive x-ray fluorescence (EDXRF) analysis to the sourcing of Polynesian artifacts made from basalt, one of the most ubiquitous materials in Polynesian archaeological sites. We have compared excavated and surface-collected basalt adzes and adze flakes from two sites in Samoa (site AS-13-1) and the Cook Islands (site MAN-44), with source basalts from known prehistoric quarries in these archipelagoes. In both cases, we are able to demonstrate the importing of basalt adzes from Tutuila Island, a distance of 100 km to Ofu Island, and of 1600 km to Mangaia Island. These findings are of considerable significance for Polynesian prehistory, as they demonstrate the movement of objects not only between islands in the same group (where communities were culturally and linguistically related) but also between distant island groups. Further applications of EDXRF analysis should greatly aid archaeologists in their efforts to reconstruct ancient trade and exchange networks, not only in Polynesia but also in other regions where basalt was a major material for artifact production.

Trees as Tools in Environmental Improvement; An Analysis of the Contribution of Vegetation to Energy and Water Conservation in the Front Range of Colorado

The Denver metropolitan area is facing rapid population growth that increases the stress on already limited resources. Research and advanced computer modeling show that trees, especially those in urban areas, have significant environmental benefits. These benefits include air quality improvements, energy savings, greenhouse gas reduction, and possible water conservation. This Capstone Project applies statistical methods to analyze a small data set of residential homes and their energy and water consumption, as a function of their individual landscape. Results indicate that tree shade can influence water conservation, and that irrigation methods can be an influential factor as well. The Capstone is a preliminary analysis for future study to be performed by the Institute for Environmental Solutions in 2007.

Evaluation of online tools as didactic resource in the university education

Recently, many efforts have been made in the academic world to adapt the new degrees to the new European Higher Education Area (EHEA). New technologies have been the most important factor to carry out this adaptation. In particular, the tools 2.0 have been spreading quickly, not just the Web 2.0, but even in all the educational levels. Nevertheless, it is now necessary to evaluate whether all these efforts and all the changes, carried out in order to obtain improved academic performance among students, have provided good results. Therefore, the aim of this paper is focused on studying the impact of the implementation of information and communication technologies (ICTs) in a subject belonging to a Master from the University of Alicante in the academic year (2010-2011). In special, it is an elective course called "Advanced Visual Ergonomics" from the Master of Clinical Optometry and Vision. The methodology used to teach this course differs from the traditional one in many respects. For example, one of the resources used for the development of this course is a blog developed specifically to coordinate a series of virtual works, whose purpose is that the student goes into specific aspects of the current topic. Next, the student participates in an active role by writing a personal assessment on the blog. However, in the course planning, there is an attendance to lessons, where the teacher presents certain issues in a more traditional way, that is, with a lecture supported with audiovisual materials, such as materials generated in powerpoint. To evaluate the quality of the results achieved with this methodology, in this work the personal assessment of the students, who have completed this course during this academic year, are collected. In particular, we want to know their opinion about the used resources, as well as the followed methodology. The tool used to collect this information was a questionnaire. This questionnaire evaluates different aspects of the course: a general opinion, quality of the received information, satisfaction about the followed methodology and the student´s critical awareness. The design of this questionnaire is very important to get conclusive information about the methodology followed in the course. The questionnaire has to have an adequate number of questions; whether it has many questions, it might be boring for the student who would pay no enough attention. The questions should be well-written, with a clear structure and message, to avoid confusion and an ambiguity. The questions should be objectives, without any suggestion for a desired answer. In addition, the questionnaire should be interesting to encourage the student´ s interest. In conclusion, this questionnaire developed for this subject provided good information to evaluate whether the methodology was a useful tool to teach "Advanced Visual Ergonomics". Furthermore, the student´s opinion collected by this questionnaire might be very helpful to improve this didactic resource.

A reassessment of traditional lexicographical tools in the light of new corpora: sports Anglicisms in Spanish

There is no question nowadays as to the international and powerful status of English at a global scale and, consequently, as to its presence in non-English speaking countries at different levels. Linguistically speaking, English is one of the languages which have mostly influenced Spanish throughout its history and especially from the late 1960s. In this study, the impact of English on Spanish is considered in the language of sports; particularly, sports Anglicisms and false Anglicisms are analysed. Due attention is paid to the different forms that an Anglicism may adopt and to which of those forms are more widely accepted or rejected by prescriptivists and speakers at large, in the light of a contrastive analysis of their appearance in the Nuevo diccionario de anglicismos, the Diccionario de la Real Academia Española and the Corpus de Referencia del Español Actual.

Amination of enzymes to improve biocatalyst performance: coupling genetic modification and physicochemical tools

Improvement of the features of an enzyme is in many instances a pre-requisite for the industrial implementation of these exceedingly interesting biocatalysts. To reach this goal, the researcher may utilize different tools. For example, amination of the enzyme surface produces an alteration of the isoelectric point of the protein along with its chemical reactivity (primary amino groups are the most widely used to obtain the reaction of the enzyme with surfaces, chemical modifiers, etc.) and even its “in vivo” behavior. This review will show some examples of chemical (mainly modifying the carboxylic groups using the carbodiimide route), physical (using polycationic polymers like polyethyleneimine) and genetic amination of the enzyme surface. Special emphasis will be put on cases where the amination is performed to improve subsequent protein modifications. Thus, amination has been used to increase the intensity of the enzyme/support multipoint covalent attachment, to improve the interaction with cation exchanger supports or polymers, or to promote the formation of crosslinkings (both intra-molecular and in the production of crosslinked enzyme aggregates). In other cases, amination has been used to directly modulate the enzyme properties (both in immobilized or free form). Amination of the enzyme surface may also pursue other goals not related to biocatalysis. For example, it has been used to improve the raising of antibodies against different compounds (both increasing the number of haptamers per enzyme and the immunogenicity of the composite) or the ability to penetrate cell membranes. Thus, amination may be a very powerful tool to improve the use of enzymes and proteins in many different areas and a great expansion of its usage may be expected in the near future.

Innovative education networking aimed at multimedia tools for geometrical optics learning

We present a purposeful initiative to open new grounds for teaching Geometrical Optics. It is based on the creation of an innovative education networking involving academic staff from three Spanish universities linked together around Optics. Nowadays, students demand online resources such as innovative multimedia tools for complementing the understanding of their studies. Geometrical Optics relies on basics of light phenomena like reflection and refraction and the use of simple optical elements such as mirrors, prisms, lenses, and fibers. The mathematical treatment is simple and the equations are not too complicated. But from our long time experience in teaching to undergraduate students, we realize that important concepts are missed by these students because they do not work ray tracing as they should do. Moreover, Geometrical Optics laboratory is crucial by providing many short Optics experiments and thus stimulating students interest in the study of such a topic. Multimedia applications help teachers to cover those student demands. In that sense, our educational networking shares and develops online materials based on 1) video-tutorials of laboratory experiences and of ray tracing exercises, 2) different online platforms for student self-examinations and 3) computer assisted geometrical optics exercises. That will result in interesting educational synergies and promote student autonomy for learning Optics.

Advances in camera trap data management tools: Towards collaborative development and integration with GIS

Camera traps have become a widely used technique for conducting biological inventories, generating a large number of database records of great interest. The main aim of this paper is to describe a new free and open source software (FOSS), developed to facilitate the management of camera-trapped data which originated from a protected Mediterranean area (SE Spain). In the last decade, some other useful alternatives have been proposed, but ours focuses especially on a collaborative undertaking and on the importance of spatial information underpinning common camera trap studies. This FOSS application, namely, “Camera Trap Manager” (CTM), has been designed to expedite the processing of pictures on the .NET platform. CTM has a very intuitive user interface, automatic extraction of some image metadata (date, time, moon phase, location, temperature, atmospheric pressure, among others), analytical (Geographical Information Systems, statistics, charts, among others), and reporting capabilities (ESRI Shapefiles, Microsoft Excel Spreadsheets, PDF reports, among others). Using this application, we have achieved a very simple management, fast analysis, and a significant reduction of costs. While we were able to classify an average of 55 pictures per hour manually, CTM has made it possible to process over 1000 photographs per hour, consequently retrieving a greater amount of data.