| 1. |
- Dornelas, M., et al.
(författare)
-
BioTIME: A database of biodiversity time series for the Anthropocene
- 2018
-
Ingår i: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 27:7, s. 760-786
-
Tidskriftsartikel (refereegranskat)abstract
- Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. Main types of variables included: The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. Spatial location and grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km(2) (158 cm(2)) to 100 km(2) (1,000,000,000,000 cm(2)). Time period and grainBio: TIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. Major taxa and level of measurement: BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.
|
|
| 2. |
- Kouki, Annika, et al.
(författare)
-
Identification of a Novel Streptococcal Adhesin P (SadP) Protein Recognizing Galactosyl-alpha 1-4-galactose-containing Glycoconjugates CONVERGENT EVOLUTION OF BACTERIAL PATHOGENS TO BINDING OF THE SAME HOST RECEPTOR
- 2011
-
Ingår i: Journal of Biological Chemistry. - 1083-351X. ; 286:45, s. 38854-38864
-
Tidskriftsartikel (refereegranskat)abstract
- Bacterial adhesion is often a prerequisite for infection, and host cell surface carbohydrates play a major role as adhesion receptors. Streptococci are a leading cause of infectious diseases. However, only few carbohydrate-specific streptococcal adhesins are known. Streptococcus suis is an important pig pathogen and a zoonotic agent causing meningitis in pigs and humans. In this study, we have identified an adhesin that mediates the binding of S. suis to galactosyl-alpha 1-4-galactose (Gal alpha 1-4Gal)-containing host receptors. A functionally unknown S. suis cell wall protein (SSU0253), designated here as SadP (streptococcal adhesin P), was identified using a Gal alpha 1-4Gal-containing affinity matrix and LC-ESI mass spectrometry. Although the function of the protein was not previously known, it was recently identified as an immunogenic cell wall protein in a proteomic study. Insertional inactivation of the sadP gene abolished S. suis Gal alpha 1-4Gal-dependent binding. The adhesin gene sadP was cloned and expressed in Escherichia coli. Characterization of its binding specificity showed that SadP recognizes Gal alpha 1-4Gal-oligosaccharides and binds its natural glycolipid receptor, GbO(3) (CD77). The N terminus of SadP was shown to contain a Gal alpha 1-Gal-binding site and not to have apparent sequence similarity to other bacterial adhesins, including the E. coli P fimbrial adhesins, or to E. coli verotoxin or Pseudomonas aeruginosa lectin I also recognizing the same Gal alpha 1-4Gal disaccharide. The SadP and E. coli P adhesins represent a unique example of convergent evolution toward binding to the same host receptor structure.
|
|
| 3. |
- Lappalainen, H. K., et al.
(författare)
-
Overview: Recent advances in the understanding of the northern Eurasian environments and of the urban air quality in China - a Pan-Eurasian Experiment (PEEX) programme perspective
- 2022
-
Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 22:7, s. 4413-4469
-
Tidskriftsartikel (refereegranskat)abstract
- The Pan-Eurasian Experiment (PEEX) Science Plan, released in 2015, addressed a need for a holistic system understanding and outlined the most urgent research needs for the rapidly changing Arctic-boreal region. Air quality in China, together with the long-range transport of atmospheric pollutants, was also indicated as one of the most crucial topics of the research agenda. These two geographical regions, the northern Eurasian Arctic-boreal region and China, especially the megacities in China, were identified as a "PEEX region". It is also important to recognize that the PEEX geographical region is an area where science-based policy actions would have significant impacts on the global climate. This paper summarizes results obtained during the last 5 years in the northern Eurasian region, together with recent observations of the air quality in the urban environments in China, in the context of the PEEX programme. The main regions of interest are the Russian Arctic, northern Eurasian boreal forests (Siberia) and peatlands, and the megacities in China. We frame our analysis against research themes introduced in the PEEX Science Plan in 2015. We summarize recent progress towards an enhanced holistic understanding of the land-atmosphere-ocean systems feedbacks. We conclude that although the scientific knowledge in these regions has increased, the new results are in many cases insufficient, and there are still gaps in our understanding of large-scale climate-Earth surface interactions and feedbacks. This arises from limitations in research infrastructures, especially the lack of coordinated, continuous and comprehensive in situ observations of the study region as well as integrative data analyses, hindering a comprehensive system analysis. The fast-changing environment and ecosystem changes driven by climate change, socio-economic activities like the China Silk Road Initiative, and the global trends like urbanization further complicate such analyses. We recognize new topics with an increasing importance in the near future, especially "the enhancing biological sequestration capacity of greenhouse gases into forests and soils to mitigate climate change" and the "socio-economic development to tackle air quality issues".
|
|
| 4. |
- Loimaranta, Vuokko, et al.
(författare)
-
Leucine-rich repeats of bacterial surface proteins serve as common pattern recognition motifs of human scavenger receptor gp340.
- 2009
-
Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 284:28, s. 18614-23
-
Tidskriftsartikel (refereegranskat)abstract
- Scavenger receptors are innate immune molecules recognizing and inducing the clearance of non-host as well as modified host molecules. To recognize a wide pattern of invading microbes, many scavenger receptors bind to common pathogen-associated molecular patterns, such as lipopolysaccharides and lipoteichoic acids. Similarly, the gp340/DMBT1 protein, a member of the human scavenger receptor cysteine-rich protein family, displays a wide ligand repertoire. The peptide motif VEVLXXXXW derived from its scavenger receptor cysteine-rich domains is involved in some of these interactions, but most of the recognition mechanisms are unknown. In this study, we used mass spectrometry sequencing, gene inactivation, and recombinant proteins to identify Streptococcus pyogenes protein Spy0843 as a recognition receptor of gp340. Antibodies against Spy0843 are shown to protect against S. pyogenes infection, but no function or host receptor have been identified for the protein. Spy0843 belongs to the leucine-rich repeat (Lrr) family of eukaryotic and prokaryotic proteins. Experiments with truncated forms of the recombinant proteins confirmed that the Lrr region is needed in the binding of Spy0843 to gp340. The same motif of two other Lrr proteins, LrrG from the Gram-positive S. agalactiae and BspA from the Gram-negative Tannerella forsythia, also mediated binding to gp340. Moreover, inhibition of Spy0843 binding occurred with peptides containing the VEVLXXXXW motif, but also peptides devoid of the XXXXW motif inhibited binding of Lrr proteins. These results thus suggest that the conserved Lrr motif in bacterial proteins serves as a novel pattern recognition motif for unique core peptides of human scavenger receptor gp340.
|
|
| 5. |
- Pulliainen, Jouni, et al.
(författare)
-
Early snowmelt significantly enhances boreal springtime carbon uptake
- 2017
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 114:42, s. 11081-11086
-
Tidskriftsartikel (refereegranskat)abstract
- We determine the annual timing of spring recovery from spaceborne microwave radiometer observations across northern hemisphere boreal evergreen forests for 1979–2014. We find a trend of advanced spring recovery of carbon uptake for this period, with a total average shift of 8.1 d (2.3 d/decade). We use this trend to estimate the corresponding changes in gross primary production (GPP) by applying in situ carbon flux observations. Micrometeoro-logical CO2 measurements at four sites in northern Europe and North America indicate that such an advance in spring recovery would have increased the January–June GPP sum by 29 g·C·m−2 [8.4 g·C·m−2 (3.7%)/decade]. We find this sensitivity of the measured springtime GPP to the spring recovery to be in accordance with the corresponding sensitivity derived from simulations with a land ecosystem model coupled to a global circulation model. The model-predicted increase in springtime cumulative GPP was 0.035 Pg/decade [15.5 g·C·m−2 (6.8%)/decade] for Eurasian forests and 0.017 Pg/decade for forests in North America [9.8 g·C·m−2 (4.4%)/decade]. This change in the springtime sum of GPP related to the timing of spring snowmelt is quantified here for boreal evergreen forests.
|
|
| 6. |
- Pulliainen, Outi, et al.
(författare)
-
Poly-L-D-lactic acid scaffold in the repair of porcine knee cartilage lesions.
- 2007
-
Ingår i: Tissue engineering. - : Mary Ann Liebert Inc. - 1076-3279 .- 1557-8690. ; 13:6, s. 1347-55
-
Tidskriftsartikel (refereegranskat)abstract
- Articular cartilage injuries cause a major clinical problem because of the negligible repair capacity of cartilage. Autologous chondrocyte transplantation is a surgical method developed to repair cartilage lesions. In the operation, cartilage defect is covered with a periosteal patch and the suspension of cultured autologous chondrocytes is injected into the lesion site. The method can form good repair tissue, but new techniques are needed to make the operation easier and to increase the postoperative biomechanical properties of the repair tissue. In this study, we investigated poly-L,D-lactic acid (PLDLA) scaffolds alone or seeded with autologous chondrocytes in the repair of circular 6-mm cartilage lesions in immature porcine knee joints. Spontaneous repair was used as a reference. Histologic evaluation of the repair tissue showed that spontaneous repair exhibited higher scores than either PLDLA scaffold group (with or without seeded chondrocytes). The scaffold material was most often seen embedded in the subchondral bone underneath the defect area, probably because of the hardness of the PLDLA material. However, some of the cell-seeded and nonseeded scaffolds contained cartilaginous tissue, suggesting that invasion of mesenchymal cells inside nonseeded scaffolds had occurred. Hyaluronan deposited in the scaffold had possibly acted as a chemoattractant for the cell recruitment. In conclusion, the PLDLA scaffold material used in this study was obviously mechanically too hard to be used for cartilage repair in immature animals.
|
|
| 7. |
- Tiitu, Virpi, et al.
(författare)
-
Bioreactor improves the growth and viability of chondrocytes in the knitted poly-L,D-lactide scaffold.
- 2008
-
Ingår i: Biorheology. - : IOS Press. - 0006-355X .- 1878-5034. ; 45:3-4, s. 539-546
-
Tidskriftsartikel (refereegranskat)abstract
- In the present study bovine chondrocytes were cultured in two different environments (static flasks and bioreactor) in knitted poly-L,D-lactide (PLDLA) scaffolds up to 4 weeks. Chondrocyte viability was assessed by employing cell viability fluorescence markers. The cells were visualized using confocal laser scanning microscopy and scanning electron microscopy. The mechanical properties and uronic acid contents of the scaffolds were tested. Our results showed that cultivation in a bioreactor improved the growth and viability of the chondrocytes in the PLDLA scaffolds. Cells were observed both on and in between the fibrils of scaffold. Furthermore, chondrocytes cultured in the bioreactor, regained their original round phenotypes, whereas those in the static flask culture were flattened in shape. Confocal microscopy revealed that chondrocytes from the bioreactor were attached on both sides of the scaffold and sustained viability better during the culture period. Uronic acid contents of the scaffolds, cultured in bioreactor, were significantly higher than in those cultured in static flasks for 4 weeks. In summary, our data suggests that the bioreactor is superior over the static flask culture when culturing chondrocytes in knitted PLDLA scaffold.
|
|
| 8. |
- Vasara, Anna I, et al.
(författare)
-
Immature porcine knee cartilage lesions show good healing with or without autologous chondrocyte transplantation.
- 2006
-
Ingår i: Osteoarthritis and cartilage / OARS, Osteoarthritis Research Society. - : Elsevier BV. - 1063-4584 .- 1522-9653. ; 14:10, s. 1066-74
-
Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: The purpose of this study was to find out how deep chondral lesions heal in growing animals spontaneously and after autologous chondrocyte transplantation. METHODS: A 6mm deep chondral lesion was created in the knee joints of 57 immature pigs and repaired with autologous chondrocyte transplantation covered with periosteum or muscle fascia, with periosteum only, or left untreated. After 3 and 12 months, the repair tissue was evaluated with International Cartilage Repair Society (ICRS) macroscopic grading, modified O'Driscoll histological scoring, and staining for collagen type II and hyaluronan, and with toluidine blue and safranin-O staining for glycosaminoglycans. The repair tissue structure was also examined with quantitative polarized light microscopy and indentation analysis of the cartilage stiffness. RESULTS: The ICRS grading indicated nearly normal repair tissue in 65% (10/17) after the autologous chondrocyte transplantation and 86% (7/8) after no repair at 3 months. At 1 year, the repair tissue was nearly normal in all cases in the spontaneous repair group and in 38% (3/8) in the chondrocyte transplantation group. In most cases, the cartilage repair tissue stained intensely for glycosaminoglycans and collagen type II indicating repair tissue with true constituents of articular cartilage. There was a statistical difference in the total histological scores at 3 months (P=0.028) with the best repair in the spontaneous repair group. A marked subchondral bone reaction, staining with toluidine blue and collagen type II, was seen in 65% of all animals. CONCLUSIONS: The spontaneous repair ability of full thickness cartilage defects of immature pigs is significant and periosteum or autologous chondrocytes do not bring any additional benefits to the repair.
|
|
| 9. |
- Vepsäläinen, M., et al.
(författare)
-
Precipitation of dissolved sulphide in pulp and paper mill wastewater by electrocoagulation
- 2011
-
Ingår i: Environmental technology. - : Informa UK Limited. - 0959-3330 .- 1479-487X. ; 32:12, s. 1393-1400
-
Tidskriftsartikel (refereegranskat)abstract
- The precipitation of dissolved sulphide ions by electrocoagulation was studied at laboratory scale using pulp and paper mill wastewaters. Concentrations of dissolved organic carbon and phosphorus were analysed before and after the electrocoagulation process to examine the suitability of the process for treatment of sulphide odour from pulp and paper mill wastewater. The electrochemical cell used in this study was constructed from monopolar dissolving iron electrodes. The dissolved iron concentration was directly proportional to the applied electric charge (C/L) at the tested current densities. Electrochemically produced ferrous iron (Fe2+) precipitated dissolved sulphide ions efficiently. Electricity consumption of the treatment was 4-8 C/mg S2- while iron consumption was 1.1-2.2 mg/mg S2- during the initial phase of the sulphide precipitation when the applied electric charge was 10-60 C/L. When 60 C/L was applied, 88% of dissolved sulphides and 40% of phosphorus was precipitated. The reduction in DOC was low during the sulphide precipitation. According to these results, electrocoagulation can precipitate dissolved sulphides effectively and thereby reduce sulphide odours of pulp and paper mill wastewaters.
|
|
| 10. |
- Virtanen, Risto, et al.
(författare)
-
Where do the treeless tundra areas of northern highlands fit in the global biome system : toward an ecologically natural subdivision of the tundra biome
- 2016
-
Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 6:1, s. 143-158
-
Tidskriftsartikel (refereegranskat)abstract
- According to some treatises, arctic and alpine sub-biomes are ecologically similar, whereas others find them highly dissimilar. Most peculiarly, large areas of northern tundra highlands fall outside of the two recent subdivisions of the tundra biome. We seek an ecologically natural resolution to this long-standing and far-reaching problem. We studied broad-scale patterns in climate and vegetation along the gradient from Siberian tundra via northernmost Fennoscandia to the alpine habitats of European middle-latitude mountains, as well as explored those patterns within Fennoscandian tundra based on climate-vegetation patterns obtained from a fine-scale vegetation map. Our analyses reveal that ecologically meaningful January-February snow and thermal conditions differ between different types of tundra. High precipitation and mild winter temperatures prevail on middle-latitude mountains, low precipitation and usually cold winters prevail on high-latitude tundra, and Scandinavian mountains show intermediate conditions. Similarly, heath-like plant communities differ clearly between middle latitude mountains (alpine) and high-latitude tundra vegetation, including its altitudinal extension on Scandinavian mountains. Conversely, high abundance of snowbeds and large differences in the composition of dwarf shrub heaths distinguish the Scandinavian mountain tundra from its counterparts in Russia and the north Fennoscandian inland. The European tundra areas fall into three ecologically rather homogeneous categories: the arctic tundra, the oroarctic tundra of northern heights and mountains, and the genuinely alpine tundra of middlelatitude mountains. Attempts to divide the tundra into two sub-biomes have resulted in major discrepancies and confusions, as the oroarctic areas are included in the arctic tundra in some biogeographic maps and in the alpine tundra in others. Our analyses based on climate and vegetation criteria thus seem to resolve the long-standing biome delimitation problem, help in consistent characterization of research sites, and create a basis for further biogeographic and ecological research in global tundra environments.
|
|
