| 1. |
- Conley, Daniel, et al.
(författare)
-
Past, present and future state of the biogeochemical Si cycle in the Baltic Sea
- 2008
-
Ingår i: Journal of Marine Systems. - : Elsevier BV. - 0924-7963 .- 1879-1573. ; 73:3-4, s. 338-346
-
Tidskriftsartikel (refereegranskat)abstract
- The Baltic Sea is one of many aquatic ecosystems that show long-term declines in dissolved silicate (DSi) concentrations due to anthropogenic alteration of the biogeochemical Si cycle. Reductions in DSi in aquatic ecosystems have been coupled to hydrological regulation reducing inputs, but also with eutrophication, although the relative significance of both processes remains unknown for the observed reductions in DSi concentrations. Here we combine present and historical data on water column DSi concentrations, together with estimates of present river DSi loads to the Baltic, the load prior to damming together with estimates of the long-term accumulation of BSi in sediments. In addition, a model has been used to evaluate the past, present and future state of the biogeochemical Si cycle in the Baltic Sea. The present day DSi load to the Baltic Sea is 855 ktons y(-1). Hydrological regulation and eutrophication of inland waters can account for a reduction of 420 ktons y(-1) less riverine DSi entering the Baltic Sea today. Using published data on basin-wide accumulation rates we estimate that 1074 ktons y(-1) of biogenic silica (BSi) is accumulating in the sediments, which is 36% higher than earlier estimates from the literature (791 ktons y(-1)). The difference is largely due to the high reported sedimentation rates in the Bothnian Sea and the Bothnian Bay. Using river DSi loads and estimated BSi accumulation, our model was not able to estimate water column DSi concentrations as burial estimates exceeded DSi inputs. The model was then used to estimate the BSi burial from measured DSi concentrations and DSj load. The model estimate for the total burial of BSi in all three basins was 620 ktons y(-1), 74% less than estimated from sedimentation rates and sediment BSi concentrations. The model predicted 20% less BSi accumulation in the Baltic Proper and 10% less in the Bothnian Bay than estimated, but with significantly less BSi accumulation in the Bothnian Sea by a factor of 3. The model suggests there is an overestimation of basin-wide sedimentation rates in the Bothnian Bay and the Bothnian Sea. In the Baltic Proper, modelling shows that historical DSi concentrations were 2.6 times higher at the turn of the last century (ca. 1900) than at present. Although the DSi decrease has leveled out and at present there are only restricted areas of the Baltic Sea with limiting DSi concentrations, further declines in DSi concentrations will lead to widespread DSi limitation of diatoms with severe implications for the food web.
|
|
| 2. |
- Lensink, Marc F., et al.
(författare)
-
Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
-
Ingår i: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
-
Tidskriftsartikel (refereegranskat)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
|
|
| 3. |
- Olli, Kalle, et al.
(författare)
-
Diatom stratigraphy and long-term dissolved silica concentrations in the Baltic Sea
- 2008
-
Ingår i: JOURNAL OF MARINE SYSTEMS. - : Elsevier BV. - 0924-7963. ; 73:3-4, s. 284-299
-
Tidskriftsartikel (refereegranskat)abstract
- In many parts of the world coastal waters with anthropogenic eutrophication have experienced a gradual depletion of dissolved silica (DSi) stocks. This could put pressure on spring bloom diatom populations, e.g. by limiting the intensity of blooms or by,causing shifts in species composition. In addition, eutrophication driven enhanced diatom growth is responsible for the redistribution of DSi from the water phase to the sediments, and changes in the growth conditions may be reflected in the sediment diatom stratigraphy. To test for changes in diatom communities we have analyzed four sediment cores from the Baltic Sea covering approximately the last 100 years. The sediment cores originate from the western Gulf of Finland, the Kattegat, the Baltic Proper and the Gulf of Riga. Three out of the four cores reveal only minor changes in composition of diatom assemblages, while the Gulf of Riga core contains major changes, occurring after the second World War. This area is set apart from the other Baltic Sea basins by a high frequency of low after spring bloom DSi concentrations (<2 mu mol L-1) during a relatively well defined time period from 1991-1998. In 1991 to 1993 a rapid decline of DSi spring concentrations and winter stocks (down to 5 mu mol L-1) in the Gulf was preceded by exceptionally intense diatom spring blooms dominated by the heavily silicified species Thalassiosira baltica (1991-1992; up to 5.5 mg ww L-1). T baltica has been the principal spring bloom diatom in the Gulf of Riga since records began in 1975. DSi consumption and biomass yield experiments with cultured T baltica suggest that intense blooms can potentially exhaust the DSi stock of the water column and exceed the annual Si dissolution in the Gulf of Riga. The phytoplankton time series reveals another exceptional T baltica bloom period in 1981-1983 (up to 8 mg L-1), which, however, took place before the regular DSi measurements. These periods may be reflected in the conspicuous accumulation of T baltica frustules in the sediment core corresponding to ca. 1975-1995.
|
|
