| 1. |
- Aronsson, Mora, et al.
(författare)
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Nya Artportalen
- 2013
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Ingår i: Fauna och flora. - 0014-8903. ; 108, s. 2-11
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Tidskriftsartikel (populärvet., debatt m.m.)
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| 2. |
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| 3. |
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| 4. |
- Buckland, Philip I., et al.
(författare)
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BugsCEP : Coleopteran Ecology Package (software)
- 2006
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Annan publikation (populärvet., debatt m.m.)abstract
- BugsCEP is a research and teaching aid for palaeoentomology, entomology and ecology. As well as habitat and distribution data, it includes tools for climate and environmental reconstruction, and facilities for storing site based abundance/collection data. A variety of searching and reporting functions greatly augment the efficiency of beetle based research. Bugs is built around a comprehensive database of beetle ecology and European fossil records which has been accumulated over the past 20 years.
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| 5. |
- Hubendick, Bengt, 1916-2012
(författare)
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Människa - miljö - överlevnad
- 1990
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Ingår i: Kulturmiljövård. - Stockholm : Riksantikvarieämbetet. - 1100-4800. ; [15]:2, s. 19-25
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Tidskriftsartikel (populärvet., debatt m.m.)
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| 6. |
- Kierczak, Marcin, 1981-, et al.
(författare)
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A Monte Carlo approach to modeling post-translational modification sites using local physicochemical properties.
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Annan publikation (populärvet., debatt m.m.)abstract
- Many proteins undergo various chemical modifications during or shortly after translation. Post-translational modifications (PTM) greatly contribute to the diversity of protein functions and play crucial role in many cellular processes. Therefore understanding where and why certain protein is modified is an important issue in biomedical research. Mechanisms underlying some types of PTMs have been elucidated but many still remain unknown and a number of tools for predicting PTMs from short sequence fragments exists. While usually accurate at predicting modification sites, these tools are not designed to increase the understanding of modification mechanisms. Here we attempted at building easy-to-interpret models of PTMs and at identifying the physicochemical properties significant for determining modification status. To this end we applied our Monte Carlo feature selection and interdependency discovery (MCFS-ID) method. Considering 9 aa-long sequence fragments that were represented in terms of their physicochem- ical properties we analyzed 76 types of PTMs and for each type we identified the properties that played significant (p ≤ 0.05) role in the classification process. For 17 types of modifications no significant prop- erty was found. For the remaining 59 types, we used the significant properties to construct random forest-based high quality predictive models. We also showed an example of how to interpret the models by analyzing interdependency networks of significant properties and how to complement the networks with decision rules inferred using rough set theory. The obtained results showed the necessity of applying feature selection prior to constructing a model that considers short sequence fragments. Interestingly, for some types of modifications we saw that models based on insignificant features can yield accurate results. This observation deserves further investigation. Among the examined PTMs we observed groups that share similar patterns of significant properties. We also showed how to complement our models with decision rules that can guide life scientists in their research and to shed light on the actual molecular mechanisms determining modification status.
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| 7. |
- Martinez Barrio, Alvaro, 1977-, et al.
(författare)
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Data mining of the dog genome reveals novel Canine Endogenous Retroviruses(CfERVs)
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Annan publikation (populärvet., debatt m.m.)abstract
- Mining the dog genome for canine endogenous retroviruses (CfERV) using the program RetroTector© identified 407 CfERVs (0.15% of the total genome size). Phylogenetic analysis showed that the majority of these CfERVs belong to the gammaretroviridae (n=313) genus. In this group, we found 33 integrated CfERVs with similarity to the human HERV-Fc1. Eighteen of them had conserved open reading frames open and seven of the 18 were recent integrations (≤ 5% LTR divergence). Some of these CfERVs may have potential for active retrotransposition and could actively contribute to the plasticity of canine genomes. Similar to other vertebrates, betaretroviruses (n=28) was the second most common group. In addition, four spuma-like and four gypsy-like CfERVs were identified, the latter group being rare in vertebrate genomes. Moreover, we identified 55 CfERVs that could not be classified unambiguously to any known retroviral genera. The integration landscape shows that all dog chromosomes have CfERV integrations with non-uniform distribution both along and across chromosomes. Some regions were essentially devoid of CfERVs whereas other regions had large numbers. Notably, in a comparison between dog and human genomes, CfERV were approximately one fifth of the amount of HERVs found. Species-specific mechanisms for purging and protection against retroviral infections are suggested to act in the dog genome. The CfERV integration pattern showed that a substantial fraction of annotated genes were found within 100 kb distance from annotated proviruses. The majority of such integrations were placed in antisense orientation relative to the transcriptional direction of the neighboring chromosomal genes. In conclusion, our results from Canis familiaris genome analysis support the notion that different mammals may interact distinctively with endogenous retroviruses.
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| 8. |
- Martinez Barrio, Alvaro, 1977-, et al.
(författare)
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GeneFinder: "in silico" positional cloning of trait genes
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Annan publikation (populärvet., debatt m.m.)abstract
- Motivation: Positional cloning of trait genes is extremely laborious and the amount of information available on gene function in different organisms is increasing so rapidly that it is hard for a research group to collect all the relevant information from a number of data sources without performing a large number of manual and time consuming searches. Results: A web service application named GeneFinder was designed and implemented. It collects selected available information related to trait loci within a given chromosomal region that control a specific phenotype. The information contains details on gene function, disease conditions, tissue expression as well as predicted gene homologies in several other species. The information gathered is further ordered by a special-purpose ranking algorithm. A web interface to the GeneFinder web service was also developed where the results are presented in a ranked list easing its interpretation. We explain the design of the architecture, show how our web interface works, and finally test a candidate region. Availability: GeneFinder is publicly available and free to use. The web interface is available at http://www.genefinder.org/.
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