1,051 research outputs found

    Avian Immunome DB: an example of a user-friendly interface for extracting genetic information

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    BackgroundGenomic and genetic studies often require a target list of genes before conducting any hypothesis testing or experimental verification. With the ever-growing number of sequenced genomes and a variety of different annotation strategies, comes the potential for ambiguous gene symbols, making it cumbersome to capture the “correct” set of genes. In this article, we present and describe the Avian Immunome DB (Avimm) for easy gene property extraction as exemplified by avian immune genes. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes. It is a vital trait to study particularly in birds considering that they are a significant driver in spreading zoonotic diseases. With the completion of phase II of the B10K (“Bird 10,000 Genomes”) consortium’s whole-genome sequencing effort, we have included 363 annotated bird genomes in addition to other publicly available bird genome data which serve as a valuable foundation for Avimm.Construction and contentA relational database with avian immune gene evidence from Gene Ontology, Ensembl, UniProt and the B10K consortium has been designed and set up. The foundation stone or the “seed” for the initial set of avian immune genes is based on the well-studied model organism chicken (Gallus gallus). Gene annotations, different transcript isoforms, nucleotide sequences and protein information, including amino acid sequences, are included. Ambiguous gene names (symbols) are resolved within the database and linked to their canonical gene symbol. Avimm is supplemented by a command-line interface and a web front-end to query the database.Utility and discussionThe internal mapping of unique gene symbol identifiers to canonical gene symbols allows for an ambiguous gene property search. The database is organised within core and feature tables, which makes it straightforward to extend for future purposes. The database design is ready to be applied to other taxa or biological processes. Currently, the database contains 1170 distinct avian immune genes with canonical gene symbols and 612 synonyms across 363 bird species. While the command-line interface readily integrates into bioinformatics pipelines, the intuitive web front-end with download functionality offers sophisticated search functionalities and tracks the origin for each record. Avimm is publicly accessible at https://avimm.ab.mpg.de.publishe

    Population-level consequences of complementary sex determination in a solitary parasitoid

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    BACKGROUND: Sex determination mechanisms are known to be evolutionarily labile but the factors driving transitions in sex determination mechanisms are poorly understood. All insects of the Hymenoptera are haplodiploid, with males normally developing from unfertilized haploid eggs. Under complementary sex determination (CSD), diploid males can be produced from fertilized eggs that are homozygous at the sex locus. Diploid males have near-zero fitness and thus represent a genetic load, which is especially severe under inbreeding. Here, we study mating structure and sex determination in the parasitoid Cotesia vestalis to investigate what may have driven the evolution of two complementary sex determination loci in this species.RESULTS: We genotyped Cotesia vestalis females collected from eight fields in four townships in Western Taiwan. 98 SNP markers were developed by aligning Illumina sequence reads of pooled DNA of eight different females against a de novo assembled genome of C. vestalis. This proved to be an efficient method for this non-model species and provides a resource for future use in related species. We found significant genetic differentiation within the sampled population but variation could not be attributed to sampling locations by AMOVA. Non-random mating was detected, with 8.1% of matings between siblings. Diploid males, detected by flow cytometry, were produced at a rate of 1.4% among diploids.CONCLUSIONS: We think that the low rate of diploid male production is best explained by a CSD system with two independent sex loci, supporting laboratory findings on the same species. Fitness costs of diploid males in C. vestalis are high because diploid males can mate with females and produce infertile triploid offspring. This severe fitness cost of diploid males combined with non-random mating may have resulted in evolution from single locus CSD to CSD with two independent loci.</p

    Detecting the Companions and Ellipsoidal Variations of RS CVn Primaries: I. sigma Geminorum

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    To measure the properties of both components of the RS CVn binary sigma Geminorum (sigma Gem), we directly detect the faint companion, measure the orbit, obtain model-independent masses and evolutionary histories, detect ellipsoidal variations of the primary caused by the gravity of the companion, and measure gravity darkening. We detect the companion with interferometric observations obtained with the Michigan InfraRed Combiner (MIRC) at Georgia State University's Center for High Angular Resolution Astronomy (CHARA) Array with a primary-to-secondary H-band flux ratio of 270+/-70. A radial velocity curve of the companion was obtained with spectra from the Tillinghast Reflector Echelle Spectrograph (TRES) on the 1.5-m Tillinghast Reflector at Fred Lawrence Whipple Observatory (FLWO). We additionally use new observations from the Tennessee State University Automated Spectroscopic and Photometric Telescopes (AST and APT, respectively). From our orbit, we determine model-independent masses of the components (M_1 = 1.28 +/- 0.07 M_Sun, M_2 = 0.73 +/- 0.03 M_Sun), and estimate a system age of 5 -/+ 1 Gyr. An average of the 27-year APT light curve of sigma Gem folded over the orbital period (P = 19.6027 +/- 0.0005 days) reveals a quasi-sinusoidal signature, which has previously been attributed to active longitudes 180 deg apart on the surface of sigma Gem. With the component masses, diameters, and orbit, we find that the predicted light curve for ellipsoidal variations due to the primary star partially filling its Roche lobe potential matches well with the observed average light curve, offering a compelling alternative explanation to the active longitudes hypothesis. Measuring gravity darkening from the light curve gives beta < 0.1, a value slightly lower than that expected from recent theory.Comment: Accepted to ApJ, 11 pages, 6 figures, 8 table

    Microtesla MRI of the human brain combined with MEG

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    One of the challenges in functional brain imaging is integration of complementary imaging modalities, such as magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI). MEG, which uses highly sensitive superconducting quantum interference devices (SQUIDs) to directly measure magnetic fields of neuronal currents, cannot be combined with conventional high-field MRI in a single instrument. Indirect matching of MEG and MRI data leads to significant co-registration errors. A recently proposed imaging method - SQUID-based microtesla MRI - can be naturally combined with MEG in the same system to directly provide structural maps for MEG-localized sources. It enables easy and accurate integration of MEG and MRI/fMRI, because microtesla MR images can be precisely matched to structural images provided by high-field MRI and other techniques. Here we report the first images of the human brain by microtesla MRI, together with auditory MEG (functional) data, recorded using the same seven-channel SQUID system during the same imaging session. The images were acquired at 46 microtesla measurement field with pre-polarization at 30 mT. We also estimated transverse relaxation times for different tissues at microtesla fields. Our results demonstrate feasibility and potential of human brain imaging by microtesla MRI. They also show that two new types of imaging equipment - low-cost systems for anatomical MRI of the human brain at microtesla fields, and more advanced instruments for combined functional (MEG) and structural (microtesla MRI) brain imaging - are practical.Comment: 8 pages, 5 figures - accepted by JM

    Consortium of Otolaryngology Journal Editors: Collegiality and Contributions

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    There is a new tradition in the otolaryngology publishing community that is unique to our specialty, so far as we know. Editors-in-Chief of otolaryngology journals in the United States, and intermittently some of our international colleagues such as the Editor of the Journal of Laryngology and Otology (England), sit down together twice a year to discuss topics of mutual interest, maintain lines of communication and friendships, and share perspectives on the evolution of otolaryngology—head and neck surgery and needs that our journals might help address. To establish these collegial, uninhibited, informative, and productive meetings, Dr Robert Ruben proposed the idea of a Consortium of Otolaryngology Journal Editors. During the consortium’s formative years, the organization was solidified and supported by Jonas Johnson who was Editor-in-Chief of Laryngoscope from 2003 to 2008 and whose journal funded our meetings. The editors have discussed many topics including standardization of terminology, duplicate publication and plagiarism, increasing physician interest and involvement in peer-review, peer-review education, new publication models and their implications for our colleagues, support for resident presentations at scientific meetings, innovations at individual journals that might prove useful for other journals, increasing international involvement in our journals, predatory journals, and other topics

    The alpha-prime stretched horizon in the Heterotic string

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    The linear alpha-prime corrections and the field redefinition ambiguities are studied for half-BPS singular backgrounds representing a wrapped fundamental string. It is showed that there exist schemes in which the inclusion of all the linear alpha-prime corrections converts these singular solutions to black holes with a regular horizon for which the modified Hawking-Bekenstein entropy is in agreement with the statistical entropy.Comment: 22 pages JHEP; new discussions and more details added to section

    Economic development, human development, and the pursuit of happiness, April 1, 2, and 3, 2004

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    This repository item contains a single issue of the Pardee Conference Series, a publication series that began publishing in 2006 by the Boston University Frederick S. Pardee Center for the Study of the Longer-Range Future. This was the Center's spring conference, which took place during April 1, 2, and 3, 2004.The conference asks the questions, how can we make sure that the benefits of economic growth flow into health, education, welfare, and other aspects of human development; and what is the relationship between human development and economic development? Speakers and participants discuss the role that culture, legal and political institutions, the UN Developmental Goals, the level of decision-making, and ethics, play in development
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