FlyBase 102—advanced approaches to interrogating FlyBase

FlyBase (http://flybase.org) is the leading website and database of Drosophila genes and genomes. Whether you are using the fruit fly Drosophila melanogaster as an experimental system or wish to understand Drosophila biological knowledge in relation to human disease or to other model systems, FlyBase can help you successfully find the information you are looking for. Here, we demonstrate some of our more advanced searching systems and highlight some of our new tools for searching the wealth of data on FlyBase. The first section explores gene function in FlyBase, using our TermLink tool to search with Controlled Vocabulary terms and our new RNA-Seq Search tool to search gene expression. The second section of this article describes a few ways to search genomic data in FlyBase, using our BLAST server and the new implementation of GBrowse 2, as well as our new FeatureMapper tool. Finally, we move on to discuss our most powerful search tool, QueryBuilder, before describing pre-computed cuts of the data and how to query the database programmatically

EEG-aktivitás jellemzése különböző mértékű és jellegű figyelmet igénylő feladatok végzésekor = EEG activity during tasks requiring different levels of attention

A neuropedagógia kialakulásával megjelent a pedagógiának egy olyan irányzata, amely az oktatási folyamatok ter vezésénél biológiai mérésekre, többek között az elektroenkefalográfiára (EEG) támaszkodik. Kísérletünkben 14 csatornás, vezeték nélküli EEG-készüléket használtunk, és összehasonlítottuk a különböző kognitív igénybevételt jelentő feladatok alatti alfa-aktivitást. A vizsgálatban részt vevő 15 egyetemista EEG-jét zenehallgatás (nyitott és csukott szemmel), illet ve szövegolvasás közben rögzítettük. Összehasonlít va az egyes aktivitások alatti EEG-spektrogramokat megállapíthattuk, hogy a szem becsukása szignifikánsan növelte az alfa-aktivitás mértékét a nyitott szemű feladatokhoz képest, de a nyitott szemű feladatok nem különböztek egymástól. Bár behunyt szemmel mindenkinél nőtt az alfa-aktivitás, 4 esetben a spektrogramon nem jelent meg világosan elkülöníthető alfa csúcs. Nyitott szemű zene- hallgatás alatti alfa-aktivitás nem függött attól, hogy mennyire érezte a kísérleti alany nyugtató hatásúnak a zenét. Az olvasás alatti alfa-aktivitás mértéke nem korrelált a szöveghez kapcsolódó kérdésekre adott válaszok helyességével, az olvasás hosszával vagy azzal, hogy a kísérleti alany érdekesnek találta-e a szöveget. Méréseink alapján az Emotiv Epoc készülékkel regisztrált EEG-ben populáció szinten a csukott szemű alfa-aktivitás növekedés elkülöníthető, de a nagymértékű egyéni különbségek elfedik a koncentráció változását jelző ingadozásokat. ----- Educational neuroscience, an emerging scientific field, is aimed to investigate the mechanism of learning, by using the data of different physiological measurement s. In our experiment we studied the changes in alpha ac ti vi t y during di fferent cognitive tasks. We recorded the EEG activit y by a portable 14 channel EEG while subjects listened to music with eyes open or closed and when they read a text. Comparing the spectrograms of the recorded EEG activit y we found that closing the eyes significantly increased EEG alpha activit y. In that stage a clear alpha peak appeared in the FFT spectrum, in the majorit y of the subjects except 4 of them. Alpha power during listening to music varied and it was independent from the belief of subjects how relaxed they were. EEG alpha power during reading did not differ from the alpha power recorded during the listening to music, and did not correlate with concentration (expressed as the number of the correct answers about the contents of the text), the length of the reading, or engagement (whether subjects found the text interesting or boring). Our experiment demonstrated that the increase in alpha power when the eyes closed can be identified in population level but the differences in alpha activit y among subjects make impossible to detect the smaller changes occurring with the level of attention or engagement

Bryophyte Collection of Eszterházy Károly University (EGR): the digital database of peat moss (Sphagnum) species

The Bryophyte Herbarium of the University of Eger (EGR) is considered to be one of the most important collections of this kind in Central Europe. Bryophyte specimens held at EGR count around 200.000 specimens, of which approximately 2700 are the Sphagnum specimens. The first Sphagnum specimens arrived probably by exchange to M. Vrabélyi from prominent botanists, as K. G. Limpricht, A. W. Evans, V. Schiffner and J. E. Zetterstedt. Imortant are the duplicate specimens collected by Á. Boros and L. Vajda (their first specimens are stored in BP). Members of the Department of Botany has also increased this part of the collection during their field research, as by: T. Pócs, J. Suba, I. Bakalár, S. Dulai and A. Vojtkó. Our main aim was to digitalize and publish first information on the cryptogam herbarium in order to provide an easier access to the data. After photographing the pages of the collection, we read the information on the photos and recorded them in an MS Excel spreadsheet. During the record process the following information could be filled: species name (Latin), section where it belongs, place of occurrence (administrative area, geographical area, coordinates), habitat, date of collection (year/month/day), substrate, name of collector and of identifier. We choose to present here our Sphagnum (peat mosses) collection as the digitization process started in 2014, and based on stage from July 2017. There are 2700 Sphagnum samples of our bryophyte collection representing around 1.35 % of the whole bryophyte collection. Among others exsiccata specimens of Sphagnotheca Borealiamericana (Ed. R. E. Andrus and D.H. Vitt). Isotype of Sphagnum amoenum Warnst. (Bryotheca brasiliensis) and isotype of Sphagnum squarrosiforme Dixon and Sherrin (Bryophytorum typorum exsiccata) are also preserved in our Sphagna collection. The most active Hungarian collectors were: Á. Boros, L. Vajda, Á. Károlyi, T. Pócs and J. Suba. In addition to this, many specimens collected by foreigners can also be found: R. E. Andrus, A. M. Cleef, J. Duda, A. Stebel, etc. There are 554 specimens from today's Hungary, most of the Hungarian specimens are from the active years of Á. Boros. The oldest Sphagnum specimen was collected by J. E. Zetterstedt in June 23, 1860 from Sweden. The collection has been growing slowly but steadily during the XIXth century. We have specimens in the collections from more than forty countries. The peat moss collection has a great floristical significance as preserves important probative specimens of bogs from which the Sphagnum species have been extinct due to the decline of the wet habitats in these days. Increasing collection activity was continuous since 2010, with completion of new data enties. It is hoped that the unified inventory of cryptogam collection will be easily searcheable facilitating loans and research

EEG-aktivitás jellemzése különböző mértékű és jellegű figyelmet igénylő feladatok végzésekor

A neuropedagógia kialakulásával megjelent a pedagógiának egy olyan irányzata, amely az oktatási folyamatok ter vezésénél biológiai mérésekre, többek között az elektroenkefalográfiára (EEG) támaszkodik. Kísérletünkben 14 csatornás, vezeték nélküli EEG-készüléket használtunk, és összehasonlítottuk a különböző kognitív igénybevételt jelentő feladatok alatti alfa-aktivitást. A vizsgálatban részt vevő 15 egyetemista EEG-jét zenehallgatás (nyitott és csukott szemmel), illet ve szövegolvasás közben rögzítettük. Összehasonlít va az egyes aktivitások alatti EEG-spektrogramokat megállapíthattuk, hogy a szem becsukása szignifikánsan növelte az alfa-aktivitás mértékét a nyitott szemű feladatokhoz képest, de a nyitott szemű feladatok nem különböztek egymástól. Bár behunyt szemmel mindenkinél nőtt az alfa-aktivitás, 4 esetben a spektrogramon nem jelent meg világosan elkülöníthető alfa csúcs. Nyitott szemű zene- hallgatás alatti alfa-aktivitás nem függött attól, hogy mennyire érezte a kísérleti alany nyugtató hatásúnak a zenét. Az olvasás alatti alfa-aktivitás mértéke nem korrelált a szöveghez kapcsolódó kérdésekre adott válaszok helyességével, az olvasás hosszával vagy azzal, hogy a kísérleti alany érdekesnek találta-e a szöveget. Méréseink alapján az Emotiv Epoc készülékkel regisztrált EEG-ben populáció szinten a csukott szemű alfa-aktivitás növekedés elkülöníthető, de a nagymértékű egyéni különbségek elfedik a koncentráció változását jelző ingadozásokat. ----- Educational neuroscience, an emerging scientific field, is aimed to investigate the mechanism of learning, by using the data of different physiological measurement s. In our experiment we studied the changes in alpha ac ti vi t y during di fferent cognitive tasks. We recorded the EEG activit y by a portable 14 channel EEG while subjects listened to music with eyes open or closed and when they read a text. Comparing the spectrograms of the recorded EEG activit y we found that closing the eyes significantly increased EEG alpha activit y. In that stage a clear alpha peak appeared in the FFT spectrum, in the majorit y of the subjects except 4 of them. Alpha power during listening to music varied and it was independent from the belief of subjects how relaxed they were. EEG alpha power during reading did not differ from the alpha power recorded during the listening to music, and did not correlate with concentration (expressed as the number of the correct answers about the contents of the text), the length of the reading, or engagement (whether subjects found the text interesting or boring). Our experiment demonstrated that the increase in alpha power when the eyes closed can be identified in population level but the differences in alpha activit y among subjects make impossible to detect the smaller changes occurring with the level of attention or engagement

The Drosophila phenotype ontology

BACKGROUND: Phenotype ontologies are queryable classifications of phenotypes. They provide a widely-used means for annotating phenotypes in a form that is human-readable, programatically accessible and that can be used to group annotations in biologically meaningful ways. Accurate manual annotation requires clear textual definitions for terms. Accurate grouping and fruitful programatic usage require high-quality formal definitions that can be used to automate classification. The Drosophila phenotype ontology (DPO) has been used to annotate over 159,000 phenotypes in FlyBase to date, but until recently lacked textual or formal definitions. RESULTS: We have composed textual definitions for all DPO terms and formal definitions for 77% of them. Formal definitions reference terms from a range of widely-used ontologies including the Phenotype and Trait Ontology (PATO), the Gene Ontology (GO) and the Cell Ontology (CL). We also describe a generally applicable system, devised for the DPO, for recording and reasoning about the timing of death in populations. As a result of the new formalisations, 85% of classifications in the DPO are now inferred rather than asserted, with much of this classification leveraging the structure of the GO. This work has significantly improved the accuracy and completeness of classification and made further development of the DPO more sustainable. CONCLUSIONS: The DPO provides a set of well-defined terms for annotating Drosophila phenotypes and for grouping and querying the resulting annotation sets in biologically meaningful ways. Such queries have already resulted in successful function predictions from phenotype annotation. Moreover, such formalisations make extended queries possible, including cross-species queries via the external ontologies used in formal definitions. The DPO is openly available under an open source license in both OBO and OWL formats. There is good potential for it to be used more broadly by the Drosophila community, which may ultimately result in its extension to cover a broader range of phenotypes

Toward an interactive article: integrating journals and biological databases.

BACKGROUND: Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture. RESULTS: We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD) WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC) step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD) and FlyBase, and has been implemented in marking up a paper with links to multiple databases. CONCLUSIONS: Our semi-automated pipeline hyperlinks articles published in GENETICS to model organism databases such as WormBase. Our pipeline results in interactive articles that are data rich with high accuracy. The use of a manual quality control step sets this pipeline apart from other hyperlinking tools and results in benefits to authors, journals, readers and databases.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Galectin-1 as a marker for microglia activation in the aging brain

Microglia cells, the immune cells residing in the brain, express immune regulatory molecules that have a central role in the manifestation of age-related brain characteristics. Our hypothesis suggests that galectin-1, an anti-inflammatory member of the beta-galactoside-binding lectin family, regulates microglia and neuroinflammation in the aging brain. Through our in-silico analysis, we discovered a subcluster of microglia in the aged mouse brain that exhibited increased expression of galectin-1 mRNA. In our Western blotting experiments, we observed a decrease in galectin-1 protein content in our rat primary cortical cultures over time. Additionally, we found that the presence of lipopolysaccharide, an immune activator, significantly increased the expression of galectin-1 protein in microglial cells. Utilizing flow cytometry, we determined that a portion of the galectin-1 protein was localized on the surface of the microglial cells. As cultivation time increased, we observed a decrease in the expression of activation-coupled molecules in microglial cells, indicating cellular exhaustion. In our mixed rat primary cortical cell cultures, we noted a transition of amoeboid microglial cells labeled with OX42(CD11b/c) to a ramified, branched phenotype during extended cultivation, accompanied by a complete disappearance of galectin-1 expression. By analyzing the transcriptome of a distinct microglial subpopulation in an animal model of aging, we established a correlation between chronological aging and galectin-1 expression. Furthermore, our in vitro study demonstrated that galectin-1 expression is associated with the functional activation state of microglial cells exhibiting specific amoeboid morphological characteristics. Based on our findings, we identify galectin-1 as a marker for microglia activation in the context of aging

Mapping the Interacting Regions between Troponins T and C. Binding of TnT and TnI peptides to TnC and NMR mapping of the TnT-binding site on TnC

Muscular contraction is triggered by an increase in calcium concentration, which is transmitted to the contractile proteins by the troponin complex. The interactions among the components of the troponin complex (troponins T, C, and I) are essential to understanding the regulation of muscle contraction. While the structure of TnC is well known, and a model for the binary TnC·TnI complex has been recently published (Tung, C.-S., Wall, M. E., Gallagher, S. C., and Trewhella, J. (2000)Protein Sci. 9, 1312–1326), very little is known about TnT. Using non-denaturing gels and NMR spectroscopy, we have analyzed the interactions between TnC and five peptides from TnT as well as how three TnI peptides affect these interactions. Rabbit fast skeletal muscle peptide TnT-(160–193) binds to TnC with a dissociation constant of 30 ± 6 µm. This binding still occurs in the presence of TnI-(1–40) but is prevented by the presence of TnI-(56–115) or TnI-(96–139), both containing the primary inhibitory region of TnI. TnT-(228–260) also binds TnC. The binding site for TnT-(160–193) is located on the C-terminal domain of TnC and was mapped to the surface of TnC using NMR chemical shift mapping techniques. In the context of the model for the TnC·TnI complex, we discuss the interactions between TnT and the other troponin subunits