Pollination and dispersal trait spectra recover faster than the growth form spectrum during spontaneous succession in sandy old‐fields

Question: Spontaneous succession is the most natural and cost‐effective solution for grassland restoration. However, little is known about the time required for the recovery of grassland functionality, i.e., for the recovery of reproductive and vegetative processes typical of pristine grasslands. Since these processes operate at different scales, we addressed the question: do reproductive and vegetative processes require different recovery times during spontaneous succession? Location: Kiskunság sand region (Central Hungary). Methods: As combinations of plant traits can be used to highlight general patterns in ecological processes, we compared reproductive (pollination‐ and dispersal‐related) and vegetative (growth form) traits between recovered grasslands of different age (<10 years old; 10–20 years old; 20–40 years old) and pristine grasslands. Results: During spontaneous succession, the reproductive trait spectra became similar to those of pristine grasslands earlier than the vegetative ones. In arable land abandoned for 10 years, pollination‐ and dispersal‐related trait spectra did not show significant difference to those of pristine grasslands; anemophily and anemochory were the prevailing strategies. Contrarily, significant differences in the growth form spectrum could be observed even after 40 years of abandonment; in recovered grasslands erect leafy species prevailed, while the fraction of dwarf shrubs and tussock‐forming species was significantly lower than in pristine grasslands. Conclusions: The recovery of the ecological processes of pristine grasslands might require different amounts of time, depending on the spatial scale at which they operate. The reproductive trait spectra recovered earlier than the vegetative one, since reproductive attributes first determine plant species sorting at the regional level towards their respective habitats. The recovery of the vegetative trait spectrum needs more time as vegetative‐based interactions operate on a smaller spatial scale. Thus, vegetative traits might be more effective in the long‐term assessment of restoration success than the reproductive ones

Learning biophysically-motivated parameters for alpha helix prediction

<p>Abstract</p> <p>Background</p> <p>Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.</p> <p>Results</p> <p>Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Q_{<it>α </it>}value of 77.6% and an SOV_{<it>α </it>}value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters.</p> <p>Conclusion</p> <p>The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.</p

Response of phytoplankton communities to nitrogen input reduction in mesocosm experiments

The effects of a reduction in inorganic nitrogen input on phytoplankton communities (species composition, biomass and production) were studied in mesocosms. Experiments were conducted in 6 land-based mesocosms consisting of 3 m(3) black polyethylene tanks. Light climate, temperature, mixing regime, and P and Si input were regulated to reproduce conditions comparable to those in Dutch coastal waters. Three levels of nitrogen availability were applied to the mesocosms used as replicates in 2 experiments, of 4 wk, in May-June and June-July 1994. In Expt 1, after 10 d in all treatments, diatoms (mainly Nitzschia delicatissima) became Si-Limited and flagellates dominated phytoplankton. Within the group of flagellates, Phaeocystis sp, dominated numerically in the last week of the experiment when N was Limiting and irradiance had increased. Phaeocystis sp, concentrations were higher in the mesocosms with the highest nitrogen load. In Expt 2, after the collapse of the initial diatom bloom due to Si-Limitation (Thalassiosira sp.), an N-Limited Phaeocystis sp. bloom developed and dominated the flagellate community. The decline of the Phaeocystis sp, bloom occurred together with the development of a second diatom bloom (Leptocylindrus danicus) under N- limitation. Phytoplankton biomass and production in these experiments reached levels measured in MERL mesocosm experiment for similar N-additions. The response of primary production to N-additions was tuned by the availability of Light and other macronutrients. A saturation model could be fitted to observations with a set of parameters corresponding to representative ecophysiological characteristics. Phytoplankton species composition was related to season and resembled field communities observed in similar periods of the year. N-Limited Phaeocystis colonial blooms were observed in mesocosms where 50% of the N-pool consisted of NH4+. [KEYWORDS: nitrogen; mesocosm; primary production; nutrient limitation competition; diatoms; Phaeocystis sp.Phaeocystis-pouchetii haptophyceae; dutch coastal waters; north-sea; spring bloom; eutrophication; nutrients; dynamics; productivity; irradiance; patterns

Response of phytoplankton communities to nitrogen input reduction in mesocosm experiments

The effects of a reduction in inorganic nitrogen input on phytoplankton communities (species composition, biomass and production) were studied in mesocosms. Experiments were conducted in 6 land-based mesocosms consisting of 3 m(3) black polyethylene tanks. Light climate, temperature, mixing regime, and P and Si input were regulated to reproduce conditions comparable to those in Dutch coastal waters. Three levels of nitrogen availability were applied to the mesocosms used as replicates in 2 experiments, of 4 wk, in May-June and June-July 1994. In Expt 1, after 10 d in all treatments, diatoms (mainly Nitzschia delicatissima) became Si-Limited and flagellates dominated phytoplankton. Within the group of flagellates, Phaeocystis sp, dominated numerically in the last week of the experiment when N was Limiting and irradiance had increased. Phaeocystis sp, concentrations were higher in the mesocosms with the highest nitrogen load. In Expt 2, after the collapse of the initial diatom bloom due to Si-Limitation (Thalassiosira sp.), an N-Limited Phaeocystis sp. bloom developed and dominated the flagellate community. The decline of the Phaeocystis sp, bloom occurred together with the development of a second diatom bloom (Leptocylindrus danicus) under N- limitation. Phytoplankton biomass and production in these experiments reached levels measured in MERL mesocosm experiment for similar N-additions. The response of primary production to N-additions was tuned by the availability of Light and other macronutrients. A saturation model could be fitted to observations with a set of parameters corresponding to representative ecophysiological characteristics. Phytoplankton species composition was related to season and resembled field communities observed in similar periods of the year. N-Limited Phaeocystis colonial blooms were observed in mesocosms where 50% of the N-pool consisted of NH4+. [KEYWORDS: nitrogen; mesocosm; primary production; nutrient limitation competition; diatoms; Phaeocystis sp.Phaeocystis-pouchetii haptophyceae; dutch coastal waters; north-sea; spring bloom; eutrophication; nutrients; dynamics; productivity; irradiance; patterns]