| 1. |
- Tinker, N. A., et al.
(författare)
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New DArT markers for oat provide enhanced map coverage and global germplasm characterization
- 2009
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 10:39
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Tidskriftsartikel (refereegranskat)abstract
- Background: Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT). Results: Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' x 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure. Conclusion: These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity.
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| 2. |
- Sikora, P., et al.
(författare)
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Mutagenesis as a Tool in Plant Genetics, Functional Genomics, and Breeding
- 2011
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Ingår i: International Journal of Plant Genomics. - : Hindawi Limited. - 1687-5389 .- 1687-5370. ; 2011
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Tidskriftsartikel (refereegranskat)abstract
- Plant mutagenesis is rapidly coming of age in the aftermath of recent developments in high-resolution molecular and biochemical techniques. By combining the high variation of mutagenised populations with novel screening methods, traits that are almost impossible to identify by conventional breeding are now being developed and characterised at the molecular level. This paper provides a comprehensive overview of the various techniques and workflows available to researchers today in the field of molecular breeding, and how these tools complement the ones already used in traditional breeding. Both genetic (Targeting Induced Local Lesions in Genomes; TILLING) and phenotypic screens are evaluated. Finally, different ways of bridging the gap between genotype and phenotype are discussed.
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| 3. |
- Carpenter, Stephen R., et al.
(författare)
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Program on ecosystem change and society : an international research strategy for integrated social-ecological systems
- 2012
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Ingår i: Current Opinion in Environmental Sustainability. - : Elsevier BV. - 1877-3435 .- 1877-3443. ; 4:1, s. 134-138
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Tidskriftsartikel (refereegranskat)abstract
- The Program on Ecosystem Change and Society (PECS), a new initiative within the ICSU global change programs, aims to integrate research on the stewardship of social-ecological systems, the services they generate, and the relationships among natural capital, human wellbeing, livelihoods, inequality and poverty. The vision of PECS is a world where human actions have transformed to achieve sustainable stewardship of social-ecological systems. The goal of PECS is to generate the scientific and policy-relevant knowledge of social-ecological dynamics needed to enable such a shift, including mitigation of poverty. PECS is a coordinating body for diverse independently funded research projects, not a funder of research. PECS research employs a range of transdisciplinary approaches and methods, with comparative, place-based research that is international in scope at the core.
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| 4. |
- Chapman, Elizabeth A., et al.
(författare)
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Perennials as Future Grain Crops : Opportunities and Challenges
- 2022
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Perennial grain crops could make a valuable addition to sustainable agriculture, potentially even as an alternative to their annual counterparts. The ability of perennials to grow year after year significantly reduces the number of agricultural inputs required, in terms of both planting and weed control, while reduced tillage improves soil health and on-farm biodiversity. Presently, perennial grain crops are not grown at large scale, mainly due to their early stages of domestication and current low yields. Narrowing the yield gap between perennial and annual grain crops will depend on characterizing differences in their life cycles, resource allocation, and reproductive strategies and understanding the trade-offs between annualism, perennialism, and yield. The genetic and biochemical pathways controlling plant growth, physiology, and senescence should be analyzed in perennial crop plants. This information could then be used to facilitate tailored genetic improvement of selected perennial grain crops to improve agronomic traits and enhance yield, while maintaining the benefits associated with perennialism.
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| 5. |
- Käll, Per-Olov, et al.
(författare)
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Preparation and Crystal Structure of of U-Phase Ln3(Si3-xAl3+x)O12+xN2-x (x≈0.5, Ln=La,Nd)
- 1991
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Ingår i: Journal of Materials Chemistry. - 0959-9428 .- 1364-5501. ; 1:2, s. 239-244
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Tidskriftsartikel (refereegranskat)abstract
- U-phase Ln3(Si3 –xAl3 +x)O12 +xN2 –x(Ln = La, Nd) occurs as a crystalline phase in rare-earth sialon ceramics formed by devitrification of grain-boundary glasses at 1000–1400 °C. The crystal structure of Nd U-phase has been determined from Cu-Kα X-ray powder diffractometer data and refined by the Rietveld full-profile technique to RF= 0.028. The space group is P321 and the cell dimensions are a= 7.974(1)Å, c= 4.873(1)Å and V= 268.29 Å3. The structure is isomorphic with the La3Ga5GeO14 structure, and exhibits corner-shared layers of (Si,Al)(O,N)4 tetrahedra interconnected by AlO6 octahedra. The rare-earth cations occupy sites between the tetrahedral layers. Transmission electron microscopy and lattice imaging studies support the X-ray structural findings. The structural relationship of the U-phase to other nitrogen-containing ceramic phases is discussed.
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| 6. |
- Olof Olsson, P., et al.
(författare)
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Inhibition of integrin αvβ6 changes fibril thickness of stromal collagen in experimental carcinomas
- 2018
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Ingår i: Cell Communication and Signaling. - : Springer Science and Business Media LLC. - 1478-811X. ; 16:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Chemotherapeutic efficacy can be improved by targeting the structure and function of the extracellular matrix (ECM) in the carcinomal stroma. This can be accomplished by e.g. inhibiting TGF-β1 and -β3 or treating with Imatinib, which results in scarcer collagen fibril structure in xenografted human KAT-4/HT29 (KAT-4) colon adenocarcinoma. Methods: The potential role of αVβ6 integrin-mediated activation of latent TGF-β was studied in cultured KAT-4 and Capan-2 human ductal pancreatic carcinoma cells as well as in xenograft carcinoma generated by these cells. The monoclonal αVβ6 integrin-specific monoclonal antibody 3G9 was used to inhibit the αVβ6 integrin activity. Results: Both KAT-4 and Capan-2 cells expressed the αVβ6 integrin but only KAT-4 cells could utilize this integrin to activate latent TGF-β in vitro. Only when Capan-2 cells were co-cultured with human F99 fibroblasts was the integrin activation mechanism triggered, suggesting a more complex, fibroblast-dependent, activation pathway. In nude mice, a 10-day treatment with 3G9 reduced collagen fibril thickness and interstitial fluid pressure in KAT-4 but not in the more desmoplastic Capan-2 tumors that, to achieve a similar effect, required a prolonged 3G9 treatment. In contrast, a 10-day direct inhibition of TGF-β1 and -β3 reduced collagen fibril thickness in both tumor models. Conclusion: Our data demonstrate that the αVβ6-directed activation of latent TGF-β plays a pivotal role in modulating the stromal collagen network in carcinoma, but that the sensitivity to αVβ6 inhibition depends on the simultaneous presence of alternative paths for latent TGF-β activation and the extent of desmoplasia.
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| 7. |
- Olsson, Björne, et al.
(författare)
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Physiological and proteomic responses in Mytilus edulis exposed to PCBs and PAHs extracted from Baltic Sea sediments
- 2004
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Ingår i: Hydrobiologia. - 0018-8158 .- 1573-5117. ; 514:1-3, s. 15-27
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Tidskriftsartikel (refereegranskat)abstract
- Stress responses in blue mussels (Mytilus edulis. L.) exposed to organic pollutants were measured using several physiological measures and as changes in protein expression. Blue mussels from the Baltic Sea were exposed for 6 days in a flow-through system to two fractions of extracted Baltic sediments (containing primarily PAHs or PCBs) from one industrially impacted site and one off-shore site. Exposure to Aroclor1248 (a commercial PCB mixture) was included as a reference treatment. Physiological response was measured as changes in respiration, excretion, clearance rates and scope for growth. Of the physiological responses, only clearance rate and scope for growth in the Aroclor and impacted site PCB treatments differed significantly (p < 0.05) from control organisms, perhaps due to a large variation among individuals. Seven proteins were observed, presumed to be from stress protein families (hsp60, hsp70 and hsp90) on one-dimensional electrophoresis gels. All protein levels, except three proteins, 62, 73 and 90 kDa, in response to PCB exposure from the industrial site, were significantly higher (p < 0.05) in treated than in control organisms, suggesting the use of stress-inducible proteins as diagnostics in risk assessment. A wider sample of proteins was observed using two-dimensional gel electrophoresis. The presence or absence of protein spots compared to control organisms was used as an indication of stress. Between 23 and 76 proteins or spots were present and 15 to 23 absent compared to controls, and the results supported the physiological and one-dimensional gel results, suggesting that the mussels were indeed suffering from stress. The methods used here represent stress monitoring at two different levels of biological organization; the cellular- and the level of individual organisms. In this experiment the protein response showed less variation among individuals compared to the physiological parameters. The protein response, however, still suffers from the lack of interpretation into commonly used monitoring terms, which emphasizes the need for more knowledge of whether the response is a momentary reflection of exposure or an early warning of higher order effects.
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| 8. |
- Olsson, P. Olof, et al.
(författare)
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Fibromodulin deficiency reduces collagen structural network but not glycosaminoglycan content in a syngeneic model of colon carcinoma.
- 2017
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12:8
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Tidskriftsartikel (refereegranskat)abstract
- Tumor barrier function in carcinoma represents a major challenge to treatment and is therefore an attractive target for increasing drug delivery. Variables related to tumor barrier include aberrant blood vessels, high interstitial fluid pressure, and the composition and structure of the extracellular matrix. One of the proteins associated with dense extracellular matrices is fibromodulin, a collagen fibrillogenesis modulator expressed in tumor stroma but scarce in normal loose connective tissues. Here, we investigated the effects of fibromodulin on stroma ECM in a syngeneic murine colon carcinoma model. We show that fibromodulin deficiency decreased collagen fibril thickness but glycosaminoglycan content and composition were unchanged. Furthermore, vascular density, pericyte coverage and macrophage amount were unaffected. Fibromodulin can therefore be a unique effector of dense collagen matrix assembly in tumor stroma and, without affecting other major matrix components or the cellular composition, can function as a main agent in tumor barrier function.
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| 9. |
- Olsson, P. Olof, et al.
(författare)
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Inhibition of integrin alpha(V)beta(6) changes fibril thickness of stromal collagen in experimental carcinomas
- 2018
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Ingår i: Cell Communication and Signaling. - : BMC. - 1478-811X. ; 16
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Chemotherapeutic efficacy can be improved by targeting the structure and function of the extracellular matrix (ECM) in the carcinomal stroma. This can be accomplished by e.g. inhibiting TGF beta 1 and -beta 3 or treating with Imatinib, which results in scarcer collagen fibril structure in xenografted human KAT-4/HT29 (KAT-4) colon adenocarcinoma.Methods: The potential role of a(v)beta(6) integrin-mediated activation of latent TGF-beta was studied in cultured KAT-4 and Capan-2 human ductal pancreatic carcinoma cells as well as in xenograft carcinoma generated by these cells. The monoclonal a(v)beta(6) integrin-speafic monoclonal antibody 3G9 was used to inhibit the a(v)beta(6) integrin activity.Results: Both KAT-4 and Capan-2 cells expressed the a(v)beta(6) integrin but only KAT-4 cells could utilize this integrin to activate latent TGF-beta in vitro. Only when Capan-2 cells were co-cultured with human F99 fibroblasts was the integrin activation mechanism triggered, suggesting a more complex, fibroblast-dependent, activation pathway. In nude mice, a 10-day treatment with 3G9 reduced collagen fibril thickness and interstitial fluid pressure in KAT-4 but not in the more desmoplastic Capan-2 tumors that, to achieve a similar effect, required a prolonged 3G9 treatment. In contrast, a 10-day direct inhibition of TGF-beta 1 and -beta 3 reduced collagen fibril thickness in both tumor models.Conclusion: Our data demonstrate that the a(v)beta(6)-directed activation of latent TGF-beta plays a pivotal role in modulating the stromal collagen network in carcinoma, but that the sensitivity to a(v)beta(6) inhibition depends on the simultaneous presence of alternative paths for latent TGF-beta activation and the extent of desmoplasia.
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| 10. |
- Patterson, Allison, et al.
(författare)
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Foraging range scales with colony size in high-latitude seabirds
- 2022
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 32:17, s. 3800-3807
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Tidskriftsartikel (refereegranskat)abstract
- Density-dependent prey depletion around breeding colonies has long been considered an important factor controlling the population dynamics of colonial animals.1, 2, 3, 4 Ashmole proposed that as seabird colony size increases, intraspecific competition leads to declines in reproductive success, as breeding adults must spend more time and energy to find prey farther from the colony.1 Seabird colony size often varies over several orders of magnitude within the same species and can include millions of individuals per colony.5,6 As such, colony size likely plays an important role in determining the individual behavior of its members and how the colony interacts with the surrounding environment.6 Using tracking data from murres (Uria spp.), the world’s most densely breeding seabirds, we show that the distribution of foraging-trip distances scales to colony size0.33 during the chick-rearing stage, consistent with Ashmole’s halo theory.1,2 This pattern occurred across colonies varying in size over three orders of magnitude and distributed throughout the North Atlantic region. The strong relationship between colony size and foraging range means that the foraging areas of some colonial species can be estimated from colony sizes, which is more practical to measure over a large geographic scale. Two-thirds of the North Atlantic murre population breed at the 16 largest colonies; by extrapolating the predicted foraging ranges to sites without tracking data, we show that only two of these large colonies have significant coverage as marine protected areas. Our results are an important example of how theoretical models, in this case, Ashmole’s version of central-place-foraging theory, can be applied to inform conservation and management in colonial breeding species.
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| 11. |
- Witt, Michael, et al.
(författare)
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Python Programming Exercise With Specimen Data for Two Snakes
- 2019
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Ingår i: Purdue University Research Repository.
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The Engineering in the World of Data Learning Community at Purdue University partnered with the Columbian Park Zoo on a co-curricular, educational program called Python With Pythons in January 2019. Zoo educators introduced two snakes to our 53 first-year engineering students: Pauli, a Ball Python, and Salazar, a Dumeril's Ground Boa Constrictor. Students were given data from the Species360 animal management system that includes feeding and weight measurements from both snakes over a period of years as well as a programming challenge with an introduction to the Python programming language. Dataset includes two Excel spreadsheets with each specimen dataset and a PDF with the programming challenge along with an answer key with a cleaned dataset and python script that builds an ascii chart that reports the schedule.
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| 12. |
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| 13. |
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