| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Jarvis, Erich D., et al.
(författare)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Tidskriftsartikel (refereegranskat)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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| 3. |
- Ma, Tao, et al.
(författare)
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Genomic insights into salt adaptation in a desert poplar
- 2013
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2797-
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Tidskriftsartikel (refereegranskat)abstract
- Despite the high economic and ecological importance of forests, our knowledge of the genomic evolution of trees under salt stress remains very limited. Here we report the genome sequence of the desert poplar, Populus euphratica, which exhibits high tolerance to salt stress. Its genome is very similar and collinear to that of the closely related mesophytic congener, P. trichocarpa. However, we find that several gene families likely to be involved in tolerance to salt stress contain significantly more gene copies within the P. euphratica lineage. Furthermore, genes showing evidence of positive selection are significantly enriched in functional categories related to salt stress. Some of these genes, and others within the same categories, are significantly upregulated under salt stress relative to their expression in another salt-sensitive poplar. Our results provide an important background for understanding tree adaptation to salt stress and facilitating the genetic improvement of cultivated poplars for saline soils.
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| 4. |
- Hyde, Kevin D., et al.
(författare)
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One stop shop: backbones trees for important phytopathogenic genera: I (2014)
- 2014
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Ingår i: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 21-125
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Tidskriftsartikel (refereegranskat)abstract
- Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineage-specific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae, Botryosphaeria, Botrytis, Choanephora, Colletotrichum, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, Ustilago and Verticillium are dealt with in this paper.
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| 5. |
- Li, Cai, et al.
(författare)
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Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment
- 2014
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Ingår i: GigaScience. - 2047-217X. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Background: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adelie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. Results: Phylogenetic dating suggests that early penguins arose similar to 60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from similar to 1 million years ago to similar to 100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. Conclusions: Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
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| 6. |
- Ma, Wei-Juan, et al.
(författare)
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Proteomic changes in articular cartilage of human endemic osteoarthritis in China.
- 2011
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Ingår i: Proteomics. - : Wiley-VCH Verlagsgesellschaft. - 1615-9853 .- 1615-9861. ; 11:14, s. 2881-90
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Tidskriftsartikel (refereegranskat)abstract
- Kashin-Beck disease (KBD) is a chronic endemic osteochondropathy with unclear pathogenesis. It is a degenerative disease similar to osteoarthritis, but with different manifestations of cartilage damage. The aim of this investigation was to show the protein changes in KBD cartilage and to identify the candidate proteins in order to understand the pathogenesis of the disease. Proteins were extracted from the media of primary cell cultures of KBD and normal chondrocytes, and separated by two-dimensional fluorescence difference gel electrophoresis (2-D DIGE). MALDI-TOF/TOF analysis revealed statistically significant differences in 27 proteins from KBD chondrocyte cultures, which consisted of 17 up-regulated and ten down-regulated proteins. The results were further validated by Western blot analysis. The proteins identified are mainly involved in cellular redox homeostasis and stress response (MnSOD, Hsp27, Peroxiredoxin-1, and Cofilin-1), glycolysis (PGK-1, PGM-1, α-enolase), and cell motility and cytoskeletal organization (Actin, Calponin-2, and Keratin). These KBD-associated proteins indicate that cytoskeletal remodeling, glycometabolism, and oxidative stress are abnormal in KBD articular cartilage.
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| 7. |
- Magnusson, Cecilia, et al.
(författare)
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Regulation of cysteinyl leukotriene receptor 2 expression-a potential anti-tumor mechanism.
- 2011
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:12
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Tidskriftsartikel (refereegranskat)abstract
- The cysteinyl leukotrienes receptors (CysLTRs) are implicated in many different pathological conditions, such as inflammation and cancer. We have previously shown that colon cancer patients with high CysLT(1)R and low CysLT(2)R expression demonstrate poor prognosis. Therefore, we wanted to investigate ways for the transcriptional regulation of CysLT(2)R, which still remains to be poorly understood.
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| 8. |
- Okada, Yukinori, et al.
(författare)
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Genetics of rheumatoid arthritis contributes to biology and drug discovery
- 2014
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 506:7488, s. 376-381
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Tidskriftsartikel (refereegranskat)abstract
- A major challenge in human genetics is to devise a systematic strategy to integrate disease-associated variants with diverse genomic and biological data sets to provide insight into disease pathogenesis and guide drug discovery for complex traits such as rheumatoid arthritis (RA)(1). Here we performed a genome-wide association study meta-analysis in a total of >100,000 subjects of European and Asian ancestries (29,880 RA cases and 73,758 controls), by evaluating similar to 10 million single-nucleotide polymorphisms. We discovered 42 novel RA risk loci at a genome-wide level of significance, bringing the total to 101 (refs 2-4). We devised an in silico pipeline using established bioinformatics methods based on functional annotation(5), cis-acting expression quantitative trait loci(6) and pathway analyses(7-9)-as well as novel methods based on genetic overlap with human primary immunodeficiency, haematological cancer somatic mutations and knockout mouse phenotypes-to identify 98 biological candidate genes at these 101 risk loci. We demonstrate that these genes are the targets of approved therapies for RA, and further suggest that drugs approved for other indications may be repurposed for the treatment of RA. Together, this comprehensive genetic study sheds light on fundamental genes, pathways and cell types that contribute to RA pathogenesis, and provides empirical evidence that the genetics of RA can provide important information for drug discovery.
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| 9. |
- Wang, Zhaoming, et al.
(författare)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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| 10. |
- Xie, Gongnan, et al.
(författare)
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Comparative Study of Thermal Performance of Longitudinal and Transversal-Wavy Microchannel Heat Sinks for Electronic Cooling
- 2013
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Ingår i: Journal of Electronic Packaging. - : ASME International. - 1043-7398 .- 1528-9044. ; 135:2
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Tidskriftsartikel (refereegranskat)abstract
- Liquid cooling incorporating microchannels are used to cool electronic chips in order to remove more heat load. However, such microchannels are often designed to be straight with rectangular cross section. In this paper, on the basis of straight microchannels having rectangular cross section (SRC), longitudinal-wavy microchannel (LWC), and transversal microchannel (TWC) were designed, respectively, and then the corresponding laminar flow and heat transfer were investigated numerically. Among them, the channel wall of LWC undulates along the flow direction according to a sinusoidal function while the TWC undulates along the transversal direction. The numerical results show that for removing an identical heat load, the overall thermal resistance of the LWC is decreased with increasing inlet Reynolds number while the pressure drop is increased greatly, so that the overall thermal performance of LWC is inferior to that of SRC under the considered geometries. On the contrary, TWC has a great potential to reduce the pressure drop compared to SRC, especially for higher wave amplitudes at the same Reynolds number. Thus the overall thermal performance of TWC is superior to that of SRC. It is suggested that the TWC can be used to cool chips effectively with much smaller pressure drop penalty. In addition to the overall thermal resistance, other criteria of evaluation of the overall thermal performance, e. g., (Nu/Nu(0))/(f/f(0)) and (Nu/Nu(0))/(f/f(0))(1/3), are applied and some controversial results are obtained.
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| 11. |
- Zhang, Guojie, et al.
(författare)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Tidskriftsartikel (refereegranskat)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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| 12. |
- Zhang, Wei, et al.
(författare)
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Knockdown of MMP-7 inhibits cell proliferation and enhances sensitivity to 5-fluorouracil and X-ray irradiation in colon cancer cells
- 2014
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Ingår i: Clinical and Experimental Medicine (Testo stampato). - : Springer Verlag (Germany). - 1591-8890 .- 1591-9528. ; 14:1, s. 99-106
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Tidskriftsartikel (refereegranskat)abstract
- The role of matrix metalloproteinase-7 (MMP-7) in the pathogenesis of colon cancer is not understood thoroughly. Previous studies from our group have shown that the expression levels of MMP-7 were highly elevated in colorectal cancer patient specimens and were correlated with Dukes Staging, histological differentiation grade and CEA level. The goal of this study was to investigate the cellular impact of MMP-7 in colon cancer. In this study, we used the SW480 colon cancer cell lines of MMP-7 knockdown by lentivirus-mediated RNA interference as a model system to investigate the impact of MMP-7 on cell proliferation and sensitivity to 5-Fluorouracil (5-FU) and X-ray irradiation (IR). Cell proliferation and sensitivity to 5-FU and IR were measured by MTT assay and colony formation assay. Cell cycle was evaluated by flow cytometry. We showed that the down regulation of MMP-7 inhibits colon cancer cell proliferation and sensitizes tumour cells to 5-FU and IR (P less than 0.05). Decreased MMP-7 expression in SW480 cells by RNA interference triggered cell cycle arrest at G1 phase (P less than 0.05). Down regulation of MMP-7 may inhibit the cell proliferation of colon cancer cells and increase tumour cells sensitivity to radiotherapy and chemotherapy. RNAi-mediated silencing of MMP-7 may represent a powerful therapeutic approach for controlling human colorectal cancer growth.
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| 13. |
- Adhikari, Deepak, et al.
(författare)
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Tsc/mTORC1 signaling in oocytes governs the quiescence and activation of primordial follicles
- 2010
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 19:3, s. 397-410
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Tidskriftsartikel (refereegranskat)abstract
- To maintain the female reproductive lifespan, the majority of ovarian primordial follicles are preserved in a quiescent state in order to provide ova for later reproductive life. However, the molecular mechanism that maintains the long quiescence of primordial follicles is poorly understood. Here we provide genetic evidence to show that the tumor suppressor tuberous sclerosis complex 1 (Tsc1), which negatively regulates mammalian target of rapamycin complex 1 (mTORC1), functions in oocytes to maintain the quiescence of primordial follicles. In mutant mice lacking the Tsc1 gene in oocytes, the entire pool of primordial follicles is activated prematurely due to elevated mTORC1 activity in the oocyte, ending up with follicular depletion in early adulthood and causing premature ovarian failure (POF). We further show that maintenance of the quiescence of primordial follicles requires synergistic, collaborative functioning of both Tsc and PTEN (phosphatase and tensin homolog deleted on chromosome 10) and that these two molecules suppress follicular activation through distinct ways. Our results suggest that Tsc/mTORC1 signaling and PTEN/PI3K (phosphatidylinositol 3 kinase) signaling synergistically regulate the dormancy and activation of primordial follicles, and together ensure the proper length of female reproductive life. Deregulation of these signaling pathways in oocytes results in pathological conditions of the ovary, including POF and infertility.
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| 14. |
- An, Junghwa, et al.
(författare)
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Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:2, s. 404-408
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Tidskriftsartikel (refereegranskat)abstract
- This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.
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| 15. |
- Aronsson, Helena, et al.
(författare)
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Effects of pig and dairy slurry application on N and P leaching from crop rotations with spring cereals and forage leys
- 2014
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Ingår i: Nutrient cycling in agroecosystems. - : Springer Science and Business Media LLC. - 1385-1314 .- 1573-0867. ; 98, s. 281-293
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Tidskriftsartikel (refereegranskat)abstract
- Two crop rotations dominated by spring cereals and grass/clover leys on a clay soil were studied over 2 years with respect to nitrogen (N) and phosphorus (P) leaching associated with pig or dairy slurry application in April, June and October. Leaching losses of total N (TN), total P (TP), nitrate-N and dissolved reactive P (DRP) were determined in separately tile-drained field plots (four replicates). Mean annual DRP leaching after October application of dairy slurry (17 kg P ha(-1)) to growing grass/clover was 0.37 kg ha(-1). It was significantly higher than after October application of pig slurry (13 kg ha(-1)) following spring cereals (0.16 kg ha(-1)) and than in the unfertilised control (0.07 kg P ha(-1)). The proportion of DRP in TP in drainage water from the grass/clover crop rotation (35 %) was higher than from the spring cereal rotation (25 %) and the control (14 %). The grass/clover rotation proved to be very robust with respect to N leaching, with mean TN leaching of 10.5 kg ha(-1) year(-1) compared with 19.2 kg ha(-1) year(-1) from the cereal crop rotation. Pig slurry application after cereals in October resulted in TN leaching of 25.7 kg ha(-1) compared with 7.0 kg ha(-1) year(-1) after application to grass/clover in October and 19.1 kg ha(-1) year(-1) after application to spring cereals in April. In conclusion, these results show that crop rotations dominated by forage leys need special attention with respect to DRP leaching and that slurry application should be avoided during wet conditions or combined with methods to increase adsorption of P to soil particles.
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| 16. |
- Aronsson, Helena, et al.
(författare)
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N and P losses from two crop rotations on a clay soil with applications of liquid manure
- 2011
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Ingår i: NJF Report. - 1653-2015. ; 7, s. 102-105
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- In Sweden, nitrogen (N) and phosphorus (P) leaching losses and mitigation strategies for cropping systems using liquid manure have been studied on sandy soils, e.g. at Mellby experimental field in southern Sweden (Halmstad, 7.2 oC and 803 mm) (Torstensson & Aronsson, 2000). In 2008, a corresponding experiment was established on a clay soil in a neighbouring field (Lilla Böslid; 30% clay) in order to enable estimations of leaching and recommendations relating to the use of pig and cattle slurry for clay soils in this region. The field consists of 36 separately tile-drained plots with flow-proportional water sampling for estimations of nutrient leaching. Two crop rotations, representing pig and dairy production, are being studied, including control plots (Table 1). The main objectives of the studies, which started in 2010, are to: 1) quantify P leaching from this soil, 2) determine how N and P leaching is affected by time of slurry application to different crops (with and without incorporation) and 3) identify possibilities for improving N and P use efficiency on farms with intensive livestock production. Transport of dissolved dinitrous oxide in drainage water is also being measured in a connected project together with Halmstad University. The study is being funded by the Swedish Farmers' Foundation for Agricultural Research.
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| 17. |
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| 18. |
- Berndt, Sonja I., et al.
(författare)
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Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:5, s. 501-U69
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Tidskriftsartikel (refereegranskat)abstract
- Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
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| 19. |
- Cho, Yoon Shin, et al.
(författare)
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Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians.
- 2012
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 44:1
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Tidskriftsartikel (refereegranskat)abstract
- We conducted a three-stage genetic study to identify susceptibility loci for type 2 diabetes (T2D) in east Asian populations. We followed our stage 1 meta-analysis of eight T2D genome-wide association studies (6,952 cases with T2D and 11,865 controls) with a stage 2 in silico replication analysis (5,843 cases and 4,574 controls) and a stage 3 de novo replication analysis (12,284 cases and 13,172 controls). The combined analysis identified eight new T2D loci reaching genome-wide significance, which mapped in or near GLIS3, PEPD, FITM2-R3HDML-HNF4A, KCNK16, MAEA, GCC1-PAX4, PSMD6 and ZFAND3. GLIS3, which is involved in pancreatic beta cell development and insulin gene expression, is known for its association with fasting glucose levels. The evidence of an association with T2D for PEPD and HNF4A has been shown in previous studies. KCNK16 may regulate glucose-dependent insulin secretion in the pancreas. These findings, derived from an east Asian population, provide new perspectives on the etiology of T2D.
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| 20. |
- Du, Fang K., et al.
(författare)
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Direction and extent of organelle DNA introgression between two spruce species in the Qinghai-Tibetan Plateau
- 2011
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 192:4, s. 1024-1033
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Tidskriftsartikel (refereegranskat)abstract
- A recent model has shown that, during range expansion of one species in a territory already occupied by a related species, introgression should take place preferentially from the resident species towards the invading species and genome components experiencing low rates of gene flow should introgress more readily than those experiencing high rates of gene flow. Here, we use molecular markers from two organelle genomes with contrasted rates of gene flow to test these predictions by examining genetic exchanges between two morphologically distinct spruce Picea species growing in the Qinghai-Tibetan Plateau. The haplotypes from both mitochondrial (mt) DNA and chloroplast (cp) DNA cluster into two distinct lineages that differentiate allopatric populations of the two species. By contrast, in sympatry, the species share the same haplotypes, suggesting interspecific genetic exchanges. As predicted by the neutral model, all sympatric populations of the expanding species had received their maternally inherited mtDNA from the resident species, whereas for paternally inherited cpDNA introgression is more limited and not strictly unidirectional. Our results underscore cryptic introgressions of organelle DNAs in plants and the importance of considering rates of gene flow and range shifts to predict direction and extent of interspecific genetic exchanges.
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| 21. |
- Gu, Jian, et al.
(författare)
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TGF-beta-Induced CD4(+) Foxp3(+) T Cells Attenuate Acute Graft-versus-Host Disease by Suppressing Expansion and Killing of Effector CD8(+) Cells
- 2014
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Ingår i: Journal of Immunology. - : The American Association of Immunologists. - 0022-1767 .- 1550-6606. ; 193:7, s. 3388-3397
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Tidskriftsartikel (refereegranskat)abstract
- The use of TGF-beta-induced CD4(+) Foxp3(+) T cells (induced regulatory T cells [iTregs]) is an important prevention and treatment strategy in autoimmune diseases and other disorders. However, the potential use of iTregs as a treatment modality for acute graft-versus-host disease (aGVHD) has not been realized because they may be unstable and less suppressive in this disease. We restudied the ability of iTregs to prevent and treat aGVHD in two mouse models. Our results showed that, as long as an appropriate iTreg-generation protocol is used, these iTregs consistently displayed a potent ability to control aGVHD development and reduce mortality in the aGVHD animal models. iTreg infusion markedly suppressed the engraftment of donor CD8(+) cells and CD4(+) cells, the expression of granzyme A and B, the cytotoxic effect of donor CD8(+) cells, and the production of T cell cytokines in aGVHD. Therefore, we conclude that as long as the correct methods for generating iTregs are used, they can prevent and even treat aGVHD.
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| 22. |
- Jacobs, Kevin B, et al.
(författare)
-
Detectable clonal mosaicism and its relationship to aging and cancer.
- 2012
-
Ingår i: Nature Genetics. - New York : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 44:6, s. 651-658
-
Tidskriftsartikel (refereegranskat)abstract
- In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases.
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| 23. |
- Kang, Jian, et al.
(författare)
-
Understanding in the morphology and tensile behavior of isotactic polypropylene cast films with different stereo-defect distribution
- 2014
-
Ingår i: Journal of polymer research. - : Springer Science and Business Media LLC. - 1022-9760 .- 1572-8935. ; 21:6, s. 485-
-
Tidskriftsartikel (refereegranskat)abstract
- In this study, two iPP resins with similar molecular weight and average isotacticity but different uniformities of stereo-defect distribution were used in the production of cast films. The crystalline morphology and orientation, and tensile behavior during room temperature stretching of the cast films were investigated by scanning electronic microscopy (SEM), 2D-wide angle X-ray diffraction (2D-WAXD) and 2D-small-angle X-ray scattering (2D-SAXS). It was found that under fixed processing condition, iPP with more uniform stereo-defect distribution (PP2) favors the formation of row nucleated lamellar structure during cast film production, and therefore exhibiting hard-elastic deformation behavior during stretching; meanwhile, the sample with less uniform stereo-defect distribution (PP1) shows un-oriented spherulitical morphology in the cast film, and typical plastic deformation behavior during stretching. The crystallization and rheological analysis on the iPP raw materials revealed that, the uniformity of stereo-defect distribution determines the ability of nucleation and crystallization, and further influences the response of the crystalline morphology to the elongation effect of cast film production process, which is of great importance in the structure-property design in the production of iPP membranes.
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| 24. |
- Karlsson, Andréas, et al.
(författare)
-
ePUMA : A unique memory access based parallel DSP processor for SDR and CR
- 2013
-
Ingår i: Global Conference on Signal and Information Processing (GlobalSIP), 2013 IEEE. - : IEEE. - 9781479902484 ; , s. 1234-1237
-
Konferensbidrag (refereegranskat)abstract
- This paper presents ePUMA, a master-slave heterogeneous DSP processor for communications and multimedia. We introduce the ePUMA VPE, a vector processing slave-core designed for heavy DSP workloads and demonstrate how its features can used to implement DSP kernels that efficiently overlap computing, data access and control to achieve maximum datapath utilization. The efficiency is evaluated by implementing a basic set of kernels commonly used in SDR. The experiments show that all kernels asymptotically reach above 90% effective datapath utilization. while many approach 100%, thus the design effectively overlaps computing, data access and control. Compared to popular VLIW solutions, the need for a large register file with many ports is eliminated, thus saving power and chip area. When compared to a commercial VLIW solution, our solution also achieves code size reductions of up to 30 times and a significantly simplified kernel implementation.
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| 25. |
- Lango Allen, Hana, et al.
(författare)
-
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
- 2010
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 467:7317, s. 832-8
-
Tidskriftsartikel (refereegranskat)abstract
- Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P<0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.
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| 26. |
- Liao, Rong-Zhen, 1983-, et al.
(författare)
-
Dipeptide hydrolysis by the dinuclear zinc enzyme human renal dipeptidase: Mechanistic insights from DFT calculations
- 2010
-
Ingår i: Journal of Inorganic Biochemistry. - : Elsevier BV. - 0162-0134 .- 1873-3344. ; 104:1, s. 37-46
-
Tidskriftsartikel (refereegranskat)abstract
- The reaction mechanism of the dinuclear zinc enzyme human renal dipeptidase is investigated using hybrid density functional theory. This enzyme catalyzes the hydrolysis of dipeptides and beta-lactam antibiotics. Two different protonation states in which the important active site residue Asp288 is either neutral or ionized were considered. In both cases, the bridging hydroxide is shown to be capable of performing the nucleophilic attack on the substrate carbonyl carbon from its bridging position, resulting in the formation of a tetrahedral intermediate. This step is followed by protonation of the dipeptide nitrogen, coupled with C-N bond cleavage. The calculations establish that both cases have quite feasible energy barriers. When the Asp288 is neutral, the hydrolytic reaction occurs with a large exothermicity. However, the reaction becomes very close to thermoneutral with an ionized Asp288. The two zinc ions are shown to play different roles in the reaction. Zn1 binds the amino group of the substrate, and Zn2 interacts with the carboxylate group of the substrate, helping in orienting it for the nucleophilic attack. In addition, Zn2 stabilizes the oxyanion of the tetrahedral intermediate, thereby facilitating the nucleophilic attack
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| 27. |
- Lin, Zhaowei, et al.
(författare)
-
Effects of BMP2 and VEGF165 on the osteogenic differentiation of rat bone marrow-derived mesenchymal stem cells.
- 2014
-
Ingår i: Experimental and Therapeutic Medicine. - : Spandidos Publications. - 1792-1015 .- 1792-0981. ; 7:3, s. 625-629
-
Tidskriftsartikel (refereegranskat)abstract
- Bone marrow-derived mesenchymal stem cells (MSCs) are dominant seed cell sources for bone regeneration. Bone morphogenetic proteins (BMPs) initiate cartilage and bone formation in a sequential cascade. Vascular endothelial growth factor (VEGF) is an essential coordinator of extracellular matrix remodeling, angiogenesis and bone formation. In the present study, the effects of the vascular endothelial growth factor 165 (VEGF165) and bone morphogenetic protein 2 (BMP2) genes on bone regeneration were investigated by the lentivirus-mediated cotransfection of the two genes into rat bone marrow-derived MSCs. The successful co-expression of the two genes in the MSCs was confirmed using quantitative polymerase chain reaction (qPCR) and western blot analysis. The results of alizarin red and alkaline phosphatase (ALP) staining at 14 days subsequent to transfection showed that the area of staining in cells transfected with BMP2 alone was higher than that in cells transfected with BMP2 and VEGF165 or untransfected control cells, while the BMP2 + VEGF165 group showed significantly more staining than the untransfected control. This indicated that BMP2 alone exhibited a stronger effect in bone regeneration than BMP2 in combination with VEGF165. Similarly, in inducing culture medium, the ALP activity of the BMP2 + VEGF165 group was notably suppressed compared with that of the BMP2 group. The overexpression of VEGF165 inhibited BMP2-induced MSC differentiation and osteogenesis in vitro. Whether or not local VEGF gene therapy is likely to affect bone regeneration in vivo requires further investigation.
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| 28. |
- Liu, Dake, et al.
(författare)
-
ePUMA embedded parallel DSP processor with Unique Memory Access
- 2011
-
Ingår i: Information, Communications and Signal Processing (ICICS), 2011. - : IEEE. - 9781457700293 ; , s. 1-5
-
Konferensbidrag (refereegranskat)abstract
- Computing unto 100GOPS without cooling is essential for high-end embedded systems and much required by markets. A novel master-slave multi-SIMD architecture and its kernel (template) based parallel programming flow is thus introduced as a parallel signal processing platform, ePUMA, embedded Parallel DSP processor with Unique Memory Access. It is an on chip multi-DSP-processor (CMP) targeting to predictable signal processing for communications and multimedia. The essential technologies are to separate the processing of control stream from parallel computing, and to separate parallel data access from parallel arithmetic computing kernels. By separations, the computation and data access can be orthogonal both in hardware and in programs. Orthogonal operations can therefore be executed in parallel and the run time cost of data access can be minimized. Benchmark shows that the computing performance therefore reaches about 80% of the hardware limit. Less than 40% of the hardware limit can be reached by normal processors. The unique SIMD memory subsystem architecture offers programmable conflict free parallel data accesses. Programming flow and tools are also developed to support coding on the unique hardware architecture. A prototype on FPGA shows especially high performance over silicon cost.
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| 29. |
- Liu, Dake, et al.
(författare)
-
Parallel Programming and its architectures Based on data access separated algorithm Kernels
- 2010
-
Ingår i: International Journal of Embedded and Real-Time Communication Systems. - : IGI Global. - 1947-3176 .- 1947-3184. ; 1:1, s. 65-85
-
Tidskriftsartikel (refereegranskat)abstract
- A novel master-multi-SIMD architecture and its kernel (template) based parallel programming flow is introduced as a parallel signal processing platform. The name of the platform is ePUMA (embedded Parallel DSP processor architecture with Unique Memory Access). The essential technology is to separate data accessing kernels from arithmetic computing kernels so that the run-time cost of data access can be minimized by running it in parallel with algorithm computing. The SIMD memory subsystem architecture based on the proposed flow dramatically improves the total computing performance. The hardware system and programming flow introduced in this article will primarily aim at low-power high-performance embedded parallel computing with low silicon cost for communications and similar real-time signal processing. Copyright © 2010, IGI Global.
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| 30. |
- Liu, Jian, et al.
(författare)
-
Assessment of phosphorus (P) leaching losses from a long-term manured sandy soil
- 2012
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Long-term repeated applications of animal manure at high rates contribute to build-up of soil phosphorus (P) status, which poses a risk of P losses by leaching. However, soil characteristics such as P sorption capacity and degree of P saturation can greatly affect P leaching in certain circumstances. Phosphorus leaching was studied in a long-term experimental field with a sandy soil in southwest Sweden. Field measurements, model simulations, and laboratory lysimeters, were used to assess the risk of P leaching associated with pig slurry applications. The field plots received different P applications resulting in average annual P surpluses of 11-24 kg ha-1 during 1983-2009. Mean annual total-P leaching and total-P concentration measured at a drain depth of 90 cm were in general low, ranging respectively from 0.14 kg ha-1 and 0.06 mg L-1 at the high rate of slurry application to 0.20 kg ha-1 and 0.08 mg L-1 in the mineral P treatment. The simulations with the ICECREAM model confirmed that the abundant P sorption capacity due to considerable Fe, Al, and Ca present in the soil overshadowed the effects of soil P status and fertilization. Laboratory lysimeter studies showed high potential of P leaching from the top-soil due to long-term pig slurry applications even long before the field experiment started. The conclusion is that P sorption capacity of the sub-soil should also be considered, besides soil P status and fertilization, when identifying hotspots and designing P mitigation strategies.
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| 31. |
- Liu, Jian, et al.
(författare)
-
Catch crops for phosphorus
- 2010
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Catch crops have successfully been used to mitigate losses of nitrogen (N) from agricultural land, but their impacts on phosphorus (P) losses are uncertain. Cultivating catch crops of appropriate species and varieties may effectively reduce P losses through surface runoff and erosion by increasing water infiltration and improving soil structure. In addition, catch crops may act as a sink of plant-available P after the main crop has been harvested. Opposite, they may act as a source, since P may leach from the very plant cells e.g. when destroyed by frost. This is of great concern for Nordic countries with cold winter climate and many freezing-thawing cycles of the soil. As a part of the understanding of the role of plant, including those on buffer strips, for P retention, the leaching from some selected plants are studied after freezing and thawing the whole plants including the soil. In laboratory P leaching from various potential catch crops after a problematic winter climate is simulated through seven repeated freezing-thawing cycles. Lysimeters with five plants representing two different clay soils from two climatic regions in Sweden are used. The plants presently tested are: English ryegrass (Lolium perenne L.), cocksfoot (Dactylis glomerata L.), oil radish (Raphanus sativus L.), phacelia (Phacelia tanacetifolia L.) and chicory (Cichorium intybus L.). In each cycle, the plants and soils are frozen 12 hours at -18oC and thawed another 12 hours at +18oC. The soil columns (20 cm in diameter × 25 cm in height) are repeatedly irrigated with a total of 70 mm water, with the intensity of10 mm∙h-1, before and after freezing-thawing cycles. Basic soil physical and chemical properties, P content in plant, and dissolved reactive P (DRP), particulate bound P (PP) and total P (TP) in the water leachate are analyzed as well.
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| 32. |
- Liu, Jian, et al.
(författare)
-
Catch crops to mitigate phosphorus leaching under cold climate
- 2012
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Nutrient leaching from agricultural land contributes greatly to the eutrophication of recipient water bodies. Catch crops (cover crops) used for reducing nitrogen leaching are proposed to mitigate phosphorus (P) leaching too. However, in regions with winter frost, catch crops may act as a source of P losses after plant cell lysis. A field study on two clay soils in south Sweden in 2009-2012 examined eight potential P catch crops; chicory (Cichorium intybus L.), cocksfoot (Dactylis glomerata L.), perennial ryegrass (Lolium perenne L.), red clover (Trifolium pretense L.), phacelia (Phacelia tanacetifolia L.), white mustard (Sinapis alba L.), and radish (Raphanus sativus L.) with the latter represented by both R. oleiformis and R. longipinnatus. Soil columns with catch crops and controls were collected in late autumn and used in leaching experiments. The columns were undergone seven repeated freezing-thawing cycles (FTCs) in the laboratory and irrigated with 70 mm simulated rainfall both before and after FTCs. The P content in leachate was analyzed after each irrigation. Leaching of total-P increased after FTCs compared with before (p=0.045) and varied significantly with year (p<0.0001) and species (p=0.037). Chicory and white mustard had lower total-P leaching than the control, while radish (R. oleiformis) and red clover had highest total-P leaching of all species. Ryegrass and radish (R. oleiformis) were the most sensitive species to frost in terms of causing the largest increase in total-P concentrations compared with the control. Radish (R. longipinnatus), cocksfoot, and chicory were the least sensitive crops and caused no significant increase in P leaching after FTCs. It was concluded that the effect of catch crops on P leaching differs between years and that perennial ryegrass, commonly grown as a catch crop in the Nordic countries, tends to leach more P than other potential catch crops after exposure to severe frost.
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| 33. |
- Liu, Jian, et al.
(författare)
-
Freezing-thawing effects on phosphorus leaching from catch crops
- 2014
-
Ingår i: Nutrient cycling in agroecosystems. - : Springer Science and Business Media LLC. - 1385-1314 .- 1573-0867. ; 99, s. 17-30
-
Tidskriftsartikel (refereegranskat)abstract
- It is suggested that catch crops can be grown to reduce phosphorus (P) losses. However, after exposure to freezing-thawing cycles (FTCs), catch crop material can become a source of P losses to waters in moderately cold climates. This study screened potential P leaching from intact plant material of eight catch crop species: chicory (Chichorium intybus L.), cocksfoot (Dactylis glomerata L.), perennial ryegrass (Lolium perenne L.), red clover (Trifolium pratense L.), phacelia (Phacelia tanacetifolia L.), white mustard (Sinapis alba L.), oilseed radish (Raphanus sativus L. oleiformis), and white radish (R. longipinnatus). The catch crops were grown in six field experiments on clay soils, where soil lysimeters (0.25 m deep) with intact crops were extracted in autumn and after used for leaching experiments before and after seven FTCs in the laboratory. The eight catch crops did not reduce P leaching before FTCs. After FTCs, leachate total-P concentration from ryegrass, oilseed radish and red clover lysimeters were significantly (p=0.0022) higher than those from the other species and the control without a catch crop. FTCS significantly (p= 0.0064) altered total-P concentration and the proportions of different forms of P. There was a significant increase in total-P concentration in leachate from ryegrass (p=0.0008) and oilseed radish (p= 0.02). Thus, the potential risk of P leaching from ryegrass and oilseed radish material after FTCs must ne considered, since they are commonly grown as nitrogen catch crops in the Nordic countries. Morever, the roots of the tested catch crops contained 7-86 % total-P, which is important when ealuating O leaching risks.
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| 34. |
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| 35. |
- Liu, Jian, et al.
(författare)
-
Long-term measurements and model simulations of phosphorus leaching from a manured sandy soil
- 2012
-
Ingår i: Journal of Soil and Water Conservation. - 0022-4561. ; 67, s. 101-110
-
Tidskriftsartikel (refereegranskat)abstract
- Cropping systems with high phosphorus (P) inputs may constitute a risk of P leaching, which contributes to eutrophication. This study was to identify P leaching risks associated with three long-term fertilization regimes in separately tile-drained plots on a sandy soil in southwest Sweden. The three regimes resulted in different annual P surpluses of, on average: 16 kg P ha-1 (14 lb P ac-1) in mineral form, and 18 kg P ha-1 (16 lb P ac-1) and 37 kg P ha-1 (33 lb P ac-1) as pig slurry. The importance of different soil characteristics (soil P, iron, aluminum, and calcium content, and degree of P saturation (DPS)) and processes (water flow and P sorption/desorption) was examined using 15 years (1989 to 2003) of P leaching measurements and simulations with the ICECREAM model. Measurements of high soil P content and DPS values in the topsoil, in combination with high precipitation and rapid water flow, indicated a high potential for P losses, which was confirmed by the model simulations. However, the model considerably overestimated total-P leaching by a factor of 5 to 9, since measured P leaching was small for all treatments. Measured mean annual total-P leaching and total-P concentration ranged respectively from 0.14 kg ha-1 (0.12 lb ac-1) and 0.06 mg L-1 at a high rate of slurry application to 0.20 kg ha-1 (0.18 lb ac-1) and 0.08 mg L-1 in the mineral P treatment. The differences in concentration were statistically significant (p < 0.001). A main conclusion from this 15-year study was that annual pig slurry application rates of 37 to 58 kg P ha-1 (33 to 52 lb P ac-1) did not increase P leaching. High sorption capacity of the subsoil, caused by Fe, Al, and Ca, was obviously very important for controlling P losses. Thus, information on soil P content and fertilization must be supplemented with estimates of soil P sorption capacity when evaluating the risk of P leaching for different soils. This must also be considered in models used for assessment of P leaching from arable land. The current ICECREAM model does not include appropriate functions for describing P sorption/desorption processes in this type of soil and needs further development.
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| 36. |
- Liu, Jian
(författare)
-
Phosphorus leaching as influenced by animal manure and catch crops
- 2013
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Leaching of phosphorus (P) constitutes an important part of P losses from Swedish agricultural soils. Phosphorus leaching is complex and is influenced by many factors, from source and mobilisation to transport pathways, as well as agricultural management practices. In order to design appropriate mitigation strategies to reduce P leaching, it is urgent to understand how different factors influence P leaching and to understand the methods for assessing P leaching. This thesis investigated the influence of two management practices, application of animal manure and use of catch crops, on P leaching under Swedish conditions and devised corresponding mitigation strategies. In the case of manure application, lysimeters were used to study P leaching from topsoil as influenced by soil type, manure application method and long-term manure application. In addition, P leaching from a field associated with long-term manure application was simulated with the ICECREAM model to clarify the processes dominating P leaching. In the case of catch crops, uptake of P by potential species and leaching of P from them after freezing and thawing were examined in a greenhouse and in a topsoil lysimeter study. Conclusions are: (1) Recent manure application to clay soils with macropore flow pathways generates a high risk of P leaching and thus such application of P during wet periods must be followed by incorporation of manure into the soil or avoided; (2) application of moderate rates of pig slurry to sandy soils with sufficient P sorption capacity does not increase the risk of P leaching, and P can be applied at a rate in balance with crop removal; (3) given the same P rate, pig slurry does not constitute a larger risk of P leaching than mineral P fertilisers; (4) descriptions of P sorption/desorption processes dominated by Fe and Al oxides must be included in P models such as ICECREAM; and (5) catch crops can become a source of P losses after exposure to freezing-thawing, which should be considered when using a catch crop. In future, more research is needed to investigate mitigation strategies to minimise P leaching from clay soils, to select or modify catch crop species to be efficient for P, and to develop methods for accurately assessing risk of P leaching.
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| 37. |
- Liu, Jian, et al.
(författare)
-
Phosphorus leaching from a clay and sandy soil supplied with manure and mineral fertilizer
- 2012
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Phosphorus (P) leaching from agricultural fields contributes to eutrophication of adjacent water bodies. The complexity among factors controlling P leaching losses requires careful consideration in designing effective mitigation strategies. We studied P leaching (both total-P and dissolved reactive P) from lysimeters filled with clay or sandy topsoil before and after addition of 30 kg P ha-1 in the laboratory. The clay lysimeters were collected from a field with separately tile-drained plots and the results were compared with data from that field. The topsoils were treated with different sources of P (pig slurry or mineral P), which were either surface applied or incorporated into the soil. The initial total-P concentrations in lysimeter leachate were lower from the clay soil (0.13 mg L-1) than from the sandy soil (0.21 mg L-1), but in the clay soil they increased considerably after slurry application, to 1.39 mg L-1 for incorporated slurry and 2.76 mg L-1 for surface-applied slurry. The field study on the clay soil confirmed that surface-applied slurry increases P leaching under certain conditions. Critical events in the crop rotation were application in autumn on the soil surface, after cereals or on grass/clover, while spring application did not increase P leaching. Thus time of application and incorporation of slurry after application may be important for reducing P losses from clay soils.
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| 38. |
- Liu, Jian, et al.
(författare)
-
Phosphorus leaching from loamy sand and clay loam topsoils after application of pig slurry
- 2012
-
Ingår i: SpringerPlus. - : Springer Science and Business Media LLC. - 2193-1801. ; 1, s. 1-10
-
Tidskriftsartikel (refereegranskat)abstract
- Management of animal waste is essential for guaranteeing good water quality. A laboratory leaching study with intact soil columns was performed to investigate the risk of phosphorus (P) leaching from a clay loam and a loamy sand. The columns (0.2 m deep) were irrigated before and after application of pig slurry on the surface or after incorporation, or application of mineral P, each at a rate of 30 kg P ha-1. The two soils had different initial P contents (i.e. the ammonium lactate-extractable P was 65 and 142 mg kg-1 for the clay loam and loamy sand, respectively), but had similar P sorption characteristics (P sorption index 3.0) and degree of P saturation (17-21%). Concentrations of dissolved reactive P (DRP) and total P (TP) before P application were significantly higher in leachate from the loamy sand (TP 0.21 mg L-1) than from the clay loam (TP 0.13 mg L-1), but only increased significantly after P application to the clay loam. The highest concentrations were found when slurry was surface-applied (DRP 1.77 mg L-1), while incorporation decreased the DRP concentration by 64% in the clay loam. Thus moderate slurry application to a sandy soil with low P saturation did not pose a major risk of P leaching. However, application of P increased the risk of P leaching from the clay loam, irrespective of application method and despite low P saturation. The results show the importance of considering soil texture and structure in addition to soil chemical characteristics in risk assessments of P leaching. Structured soils such as the clay loam used in this study are high risk soils and application of P to bare soil during wet periods, e.g. in autumn or spring, should be followed by incorporation or avoided completely.
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| 39. |
- Liu, Jian, et al.
(författare)
-
Phosphorus leaching risk assessments and measured losses from a long-term manured sandy soil
- 2011
-
Ingår i: NJF Report. - 1653-2015. ; 7, s. 30-33
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Long-term repeated applications of animal manure at high rates contribute to buildup of soil P status, which poses a risk of P losses by leaching. However, contrary phenomenon may present in soils with abundant P sorption capacities, which brings difficulties in assessing the risk of P leaching. Phosphorus leaching was studied in a long-term experimental field with a sandy soil in southwest Sweden. Field measurements, model simulations, and laboratory lysimeter experiments, were used to assess the risk of P leaching associated with pig slurry applications. The plots in the field received different P applications, i.e. high rate of P (58 kg P ha-1 yr-1) with pig slurry, low rate of P (37 kg P ha-1 yr-1) with pig slurry, and mineral P (24 kg P ha-1 yr-1) without N applications, since the experiment started in 1983. These treatments resulted in average annual surpluses of P from 16 kg ha-1 to 37 kg ha-1. Mean annual total-P leaching and total-P concentration measured at a drain depth of 90 cm ranged respectively from 0.14 kg ha-1 and 0.06 mg L-1 at the high rate of slurry application to 0.20 kg ha-1 and 0.08 mg L-1 in the mineral P treatment. These observations were in general low in a Swedish context and pig slurry application did not elevate P concentrations in drainage water. One explanation was that the abundant P sorption capacity due to considerable Fe, Al, and Ca present in the soil overshadowed the effects of soil P status and fertilization. It was confirmed by the simulations with the ICECREAM model, where the role of the soil P pool for leaching was tested. The model produced 5 to 9 times higher P leaching than measured when no special attention was paid to the high sorption capacity. Laboratory lysimeter studies showed high potential of P leaching from the topsoils in this field, which was resulted from long-term pig slurry applications even long before the field experiment started. This was consistent with the results with model simulations with the low P sorption capacity. On one hand, although high amount of P leaching has not been observed, this field has a high risk of P leaching if pig slurry application continues to saturate the soil P sorption capacity; on the other hand, it indicated that the subsoil played a crucial role in sorbing P moving through the soil profile and reducing P concentrations in drainage. One main conclusion from the study was that soil P sorption capacity should also be considered, besides soil P status and fertilization, when identifying hotspots and designing P mitigation strategies.
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| 40. |
- Liu, Jian, et al.
(författare)
-
Potential of phosphorus (P) release from eight catch crops
- 2011
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Growing catch crops (cover crops) is an important option to mitigate nitrogen (N) leaching losses in the late autumn and in winter after harvest of the main crop. However, their efficiency in leaching losses of dissolved reactive phosphorus (DRP) and dissolved organic phosphorus (DOP) is uncertain and may vary between crop species and varieties. The crop and root may act as sources of P when the plant cells are burst by frost which is of special concern for countries with cold winter climate and many freezing-thawing cycles. A green house experiment was carried out to study the potential of P release from 8 catch crops: English ryegrass (Lolium perenne L.), cocks foot (Dactylis glomerata L.), chicory (Cichorium intybus L.), red clover (Trifolium pretense L.), white mustard (Sinapis alba L.), phacelia (Phacelia tanacetifolia L.), oilseed radish (Raphanus sativus L. var. Oleiformis), and a variety of the latter specie, structurator (Raphanus sativus L. var. Longipinnatus). The root and shoot parts of the catch crops were separated at harvest. The roots were scanned for the morphology parameters: total length, total surface area, and specific surface area. Dissolved reactive P (DRP) and total P (TP) were extracted with water from root and shoot samples which had undergone different freezing (-thawing) cycle modes. Extractions (including control) were made after 4 continuous freezing-thawing cycles, after each of the 4 continuous freezing-thawing cycles, and after 3 continuous freezing days and l thawing day. The results were evaluated together with a laboratory leaching experiment with topsoil lysimeters and natural grown catch crops.
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| 41. |
- Liu, Jian, et al.
(författare)
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Potential phosphorus leaching from sandy topsoils with different fertilizer histories before and after application of pig slurry
- 2012
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Ingår i: Soil Use and Management. - : Wiley. - 0266-0032 .- 1475-2743. ; 28, s. 457-467
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Tidskriftsartikel (refereegranskat)abstract
- This study investigated the effects of historical long-term and recent single applications of pig slurry on P leaching from intact columns of two sandy topsoils (Mellby and Böslid). The soils had similar physical properties, but different soil P status (ammonium lactate-extractable P; P-AL) and degree of P saturation (DPS-AL). Mellby had P-AL of 220-280 mg kg-1 and DPS-AL of 32-42%, which was higher than for Böslid (P-AL 140 mg kg-1 and DPS 21%). The study investigated the effects since 1983 of four treatments with different fertilizer histories, in summary high (HighSlurryMellby) and low (LowSlurryMellby) rates of pig slurry and mineral P (MinMellby) applications at Mellby and mineral P application at Böslid (MinBöslid). The columns were irrigated in the laboratory five times before and five times after a single application of pig slurry (22 kg P ha-1). Concentrations of dissolved reactive P (DRP), dissolved organic P and total-P (TP) in leachate and loads were significantly higher (p <0.005) from the treatments at Mellby than those at Böslid. TP concentrations followed the trend: HighSlurryMellby (0.57-0.59 mg L-1) > MinMellby (0.41-0.49 mg L-1) > LowSlurryMellby (0.31-0.36 mg L-1) > MinBöslid (0.14-0.15 mg L-1), both before and after the single slurry application. DRP concentrations in leachate were positively correlated with DPS-AL values in the topsoil (R2=0.95, p<0.0001), and increased with greater DPS-AL values after the single slurry application (R2=0.79, p<0.0001). Thus, DPS-AL can be an appropriate indicator of P leaching risk from sandy soils. Moreover, the build-up of soil P due to long-term repeated manure applications seems to be more important for potential P losses than a single manure application.
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| 42. |
- Liu, Jian, et al.
(författare)
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Potential phosphorus release from catch crop shoots and roots after freezing-thawing
- 2013
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Ingår i: Plant and Soil. - : Springer Science and Business Media LLC. - 0032-079X .- 1573-5036. ; 371, s. 543-557
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Tidskriftsartikel (refereegranskat)abstract
- Background and Aims Catch crops used for mitigating nutrient losses to water can release phosphorus (P) when exposed to repeated freezing-thawing cycles (FTCs). This study sought to evaluate potential P losses from shoots and roots of eight catch crops. Methods Shoots and roots sampled from perennial ryegrass (Lolium perenne L.), cocksfoot (Dactylis glomerata L.), chicory (Cichorium intybus L.), phacelia (Phacelia tanacetifolia L.), red clover (Trifolium pratense L.), white mustard (Sinapis alba L.), oilseed radish (Raphanus sativus var. oleiformis L.) and white radish (R. sativus var. longipinnatus L.) were treated with no freezing, one single FTC, four continuous FTCs and four discontinuous FTCs. All samples were analysed for water-extractable P (WEP), and root samples also for characteristics such as specific root surface area (SSA). Results Freezing-thawing significantly increased potential P losses from both shoots and roots compared with no freezing. The two radish species and white mustard contained significantly higher concentrations of WEP than the other species, among which chicory and phacelia had the lowest WEP. On average, shoots had 43% higher WEP than roots. Cumulative P release from shoots and roots was strongly correlated with their total-P content (p=0.006 and p=0.002, respectively). Cumulative release of P from taproots was correlated with SSA (p=0.03). Conclusions Chicory, and possibly phacelia, appear to be promising catch crops for P.
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| 43. |
- Liu, Jian, et al.
(författare)
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Printable highly conductive conjugated polymer sensitized ZnO NCs as cathode interfacial layer for efficient polymer solar cells
- 2014
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Ingår i: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 6:11, s. 8237-8245
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Tidskriftsartikel (refereegranskat)abstract
- We report a facile way to produce printable highly conductive cathode interfacial layer (CIL) for efficient polymer solar cells (PSCs) by sensitizing ZnO nanocrystals (NCs) with a blue fluorescent conjugated polymer, poly(9, 9-bis-(6-diethoxylphosphorylhexyl) fluorene) (PFEP). Herein, PFEP plays dual distinctive roles in the composite. Firstly, PFEP chains can effectively block the aggregation of ZnO NCs, leading to uniform and smooth film during solution processing via assembly on ZnO NC surfaces through their pending phosphonate groups. Secondly, PFEP can greatly improve the conductivity of ZnO NCs by charge transfer doping, that is the charge transfer from the sensitizer driven by electron-chemical potential equilibrium, which could be even more pronounced under light illumination because of light excitation of PFEP sensitizer. The increased conductivity in ZnO-PFEP layer renders more efficient electron transport and extraction compared to pristine ZnO layer. This ZnO-PFEP CIL was successfully applied to PSCs based on three polymer donor systems with different band-gaps, and efficiency enhancements from 44 to 70% were observed compared to those PSCs with pristine ZnO CIL. The highest efficiency of 7.56% was achieved in P(IID-DTC):PC70BM-based PSCs by using ZnO-PFEP film as CIL. Moreover, the enhanced conductivity due to the charge-transfer doping effect allows thick ZnO-PFEP film to be used as CIL in high-performance PSCs. Both the high conductivity and good film-forming properties of ZnO-PFEP CIL are favorable for large-scale printable PSCs, which is also verified by high-efficiency PSCs with ZnO-PFEP CIL fabricated using doctor-blading, a large-scale processing technique. The work provides an efficient printable cathode interfacial material for efficient PSCs.
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| 44. |
- Liu, Ning, et al.
(författare)
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Transcriptional regulation mechanisms of hypoxia-induced neuroglobin gene expression.
- 2012
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Ingår i: The Biochemical journal. - 1470-8728 .- 0264-6021. ; 443:1, s. 153-164
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Tidskriftsartikel (refereegranskat)abstract
- Ngb (neuroglobin) has been identified as a novel endogenous neuroprotectant. However, little is known about the regulatory mechanisms of Ngb expression, especially under conditions of hypoxia. In the present study, we located the core proximal promoter of the mouse Ngb gene to a 554bp segment, which harbours putative conserved NF-κB (nuclear factor κB)- and Egr1 (early growth-response factor 1) -binding sites. Overexpression and knockdown of transcription factors p65, p50, Egr1 or Sp1 (specificity protein 1) increased and decreased Ngb expression respectively. Experimental assessments with transfections of mutational Ngb gene promoter constructs, as well as EMSA (electrophoretic mobility-shift assay) and ChIP (chromatin immunoprecipitation) assays, demonstrated that NF-κB family members (p65, p50 and cRel), Egr1 and Sp1 bound in vitro and in vivo to the proximal promoter region of the Ngb gene. Moreover, a κB3 site was found as a pivotal cis-element responsible for hypoxia-induced Ngb promoter activity. NF-κB (p65) and Sp1 were also responsible for hypoxia-induced up-regulation of Ngb expression. Although there are no conserved HREs (hypoxia-response elements) in the promoter of the mouse Ngb gene, the results of the present study suggest that HIF-1α (hypoxia-inducible factor-1α) is also involved in hypoxia-induced Ngb up-regulation. In conclusion, we have identified that NF-κB, Egr1 and Sp1 played important roles in the regulation of basal Ngb expression via specific interactions with the mouse Ngb promoter. NF-κB, Sp1 and HIF-1α contributed to the up-regulation of mouse Ngb gene expression under hypoxic conditions.
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| 45. |
- Liu, Yan Fang, et al.
(författare)
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Theoretical Study of the Oxidation of Phenolates by the [Cu2O2(N,N-di-tert-butylethylenediamine)2]2+Complex
- 2013
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Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 19:6, s. 1942-1954
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Tidskriftsartikel (refereegranskat)abstract
- Experiments have shown that the -2:2-peroxodicopper(II) complex [Cu2O2(N,N-di-tert-butylethylenediamine)2]2+ rapidly oxidizes 2,4-di-tert-butylphenolate into a mixture of catechol and quinone and that, at the extreme temperature of 120 degrees C, a bis--oxodicopper(III)phenolate intermediate, labeled complex A, can be observed. These experimental results suggest a new mechanism of action for the dinuclear copper-containing enzyme tyrosinase, involving an early OO bond-cleavage step. However, whether phenolate binding occurs before or after the cleavage of the OO bond has not been possible to answer. In this study, hybrid density functional theory is used to study the synthetic reaction and, based on the calculated free-energy profile, a mechanism is suggested for the entire phenolate-oxidation reaction that agrees with the experimental observations. Most importantly, the calculations show that the very first step in the reaction is the cleavage of the OO bond in the peroxo complex and that, subsequently, the phenolate substrate coordinates to one of the copper ions in the bis--oxodicopper(III) complex to yield the experimentally characterized phenolate intermediate (A). The oxidation of the phenolate substrate into a quinone then occurs in three steps: 1)CO bond formation, 2)coupled internal proton and electron transfer, and 3)electron transfer coupled to proton transfer from an external donor (acidic workup, experimentally). The first of these steps is rate limiting for the decay of complex A, with a calculated free-energy barrier of 10.7kcalmol1 and a deuterium kinetic isotope effect of 0.90, which are in good agreement with the experimental values of 11.2kcalmol1 and 0.83(+/- 0.09). The tert-butyl substituents on both the phenol substrate and the copper ligands need to be included in the calculations to give a correct description of the reaction mechanism.
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| 46. |
- Magnusson, Cecilia, et al.
(författare)
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Cysteinyl leukotriene receptor expression pattern affects migration of breast cancer cells and survival of breast cancer patients.
- 2011
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Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136. ; Okt, s. 9-22
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Tidskriftsartikel (refereegranskat)abstract
- The fact that breast cancer patients with local or distal dissemination exhibit decreased survival, promotes a search for novel mechanisms to suppress such tumor progression. Here we have determined the expression of pro-inflammatory cysteinyl leukotriene receptors (CysLTRs) in breast tumor tissue and their signaling effect on breast cancer cell functions related to tumor progression. Patients with breast tumors characterized by high CysLT(1)R and low CysLT(2)R expression levels exhibited increased risk of cancer-induced death in univariate analysis for both the total patient group (HR = 2.88, 95% CI 1.11-7.41), as well as patients with large (>20mm) tumors (HR = 5.08, 95% CI 1.39-18.5). Multivariate analysis revealed that patients with large tumors exhibiting high CysLT(1)R and low CysLT(2)R expression levels had a significantly reduced survival, also when adjusted for established prognostic parameters (HR = 7.51, 95% CI 1.83-30.8). In patients with large (>20mm) tumors, elevated CysLT(2)R expression predicted an improved five-year survival (log-rank test P = 0.04). Surprisingly, for longer time periods this prognostic value was lost. This disappearance coincided with the termination of hormonal treatment. Tamoxifen preserved and even induced transcription of CysLT(2)R, but not CysLT(1)R, in ER-positive MCF-7 breast cancer cells. This elevated CysLT(2)R expression decreased, even below the level of untreated cells, when tamoxifen was withdrawn. CysLT(2)R signaling reduced MCF-7 cell migration, but had no effect on either proliferation or apoptosis. Our data indicate that low CysLT(1)R together with high CysLT(2)R expression levels might be useful parameters in prognostication and treatment stratification of breast cancer patients.
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| 47. |
- Mingbo, Sun, et al.
(författare)
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A Modified Sub-Cell-Fix Method for Re-Initialization of Level-Set Distance Function and Its Dependence Tests on Grid Stretching
- 2010
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Ingår i: Modern Physics Letters B. - 0217-9849. ; 24:15, s. 1615-1629
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Tidskriftsartikel (refereegranskat)abstract
- The sub-cell-fix (SCF) method proposed by Russo and Smereka(3) computes the distance function of the cells adjacent to the zero level-set without disturbing the original zero level-set. A modified sub-cell-fix scheme independent of local curvature is developed in this paper, which makes use of a combination of the points adjacent to zero level-set surfaces and preserves the interface in a second-order accuracy. The new sub-cell-fix scheme is capable of handling large local curvature, and as a result it demonstrates satisfactory performance on several challenging test cases. The limitations of the modified scheme on stretched grids are tested and it is found that the highly stretched grid causes large numerical errors, and needs further assessment and modification.
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| 48. |
- Movérare-Skrtic, Sofia, et al.
(författare)
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Osteoblast-derived WNT16 represses osteoclastogenesis and prevents cortical bone fragility fractures.
- 2014
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Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 20:11, s. 1279-88
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Tidskriftsartikel (refereegranskat)abstract
- The WNT16 locus is a major determinant of cortical bone thickness and nonvertebral fracture risk in humans. The disability, mortality and costs caused by osteoporosis-induced nonvertebral fractures are enormous. We demonstrate here that Wnt16-deficient mice develop spontaneous fractures as a result of low cortical thickness and high cortical porosity. In contrast, trabecular bone volume is not altered in these mice. Mechanistic studies revealed that WNT16 is osteoblast derived and inhibits human and mouse osteoclastogenesis both directly by acting on osteoclast progenitors and indirectly by increasing expression of osteoprotegerin (Opg) in osteoblasts. The signaling pathway activated by WNT16 in osteoclast progenitors is noncanonical, whereas the pathway activated in osteoblasts is both canonical and noncanonical. Conditional Wnt16 inactivation revealed that osteoblast-lineage cells are the principal source of WNT16, and its targeted deletion in osteoblasts increases fracture susceptibility. Thus, osteoblast-derived WNT16 is a previously unreported key regulator of osteoclastogenesis and fracture susceptibility. These findings open new avenues for the specific prevention or treatment of nonvertebral fractures, a substantial unmet medical need.
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| 49. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Improving ITS sequence data for identification of plant pathogenic fungi
- 2014
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 11-19
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Tidskriftsartikel (refereegranskat)abstract
- Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.
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| 50. |
- Schoch, Conrad L., et al.
(författare)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Tidskriftsartikel (refereegranskat)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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