Modeling interactions of submersed plant biomass and environmental factors in a stream using structural equation modeling

This study investigated the interactions of submersed plants with environmental factors using structural equation modeling (SEM) and evaluated the effect strength of respective factors in an aquatic ecosystem using a data set collected at a fourth order stream in Japan. A model that simultaneously examines the relative importance of factors of the system has developed. The investigated factors included plant biomass (Biomass) of submersed macrophytes (Potamogeton malaianus and Potamogeton oxyphyllus) and other environmental factors, i.e. water velocity and water depth (Hydraulic), pore water nitrogen (TNL), pore water phosphorus (TPL), sediment organic matter (Organic) and sediment particle size (Texture). The estimated model showed that the Biomass was negatively correlated with Hydraulic but positively correlated with Organic whilst TNL and TPL affected the Biomass with almost equal strength. The effects caused by Hydraulic to Texture were greater than the ones caused by Biomass. At the narrow ranges of water velocity (0–7 cm s⁻¹) and shallow depth (0–35 cm), the effect of wash-away of Organic by Hydraulic were smaller than the retention effect of Organic by Biomass. These results provide more insights into interactions of the submersed macrophytes with environmental factors. Handling editor: K. Martens     

Toward better understanding of protein secondary structure: extracting prediction rules

Although numerous computational techniques have been applied to predict protein secondary structure (PSS), only limited studies have dealt with discovery of logic rules underlying the prediction itself. Such rules offer interesting links between the prediction model and the underlying biology. In addition, they enhance interpretability of PSS prediction by providing a degree of transparency to the predicting model usually regarded as a black box. In this paper, we explore the generation and use of C4.5 decision trees to extract relevant rules from PSS predictions modeled with two-stage support vector machines (TS-SVM). The proposed rules were derived on the RS126 data set of 126 nonhomologous globular proteins and on the PSIPRED data set of 1,923 protein sequences. Our approach has produced sets of comprehensible, and often interpretable, rules underlying the PSS predictions. Moreover, many of the rules seem to be strongly supported by biological evidence. Further, our approach resulted in good prediction accuracy, few and usually compact rules, and rules that are generally of higher confidence levels than those generated by other rule extraction techniques.     

Membrane Curvature Protein Exhibits Interdomain Flexibility and Binds a Small GTPase

The APPL1 and APPL2 proteins (APPL (adaptor protein, phosphotyrosine interaction, pleckstrin homology (PH) domain, and leucine zipper-containing protein)) are localized to their own endosomal subcompartment and interact with a wide range of proteins and small molecules at the cell surface and in the nucleus. They play important roles in signal transduction through their ability to act as Rab effectors. (Rabs are a family of Ras GTPases involved in membrane trafficking.) Both APPL1 and APPL2 comprise an N-terminal membrane-curving BAR (Bin-amphiphysin-Rvs) domain linked to a PH domain and a C-terminal phosphotyrosine-binding domain. The structure and interactions of APPL1 are well characterized, but little is known about APPL2. Here, we report the crystal structure and low resolution solution structure of the BARPH domains of APPL2. We identify a previously undetected hinge site for rotation between the two domains and speculate that this motion may regulate APPL2 functions. We also identified Rab binding partners of APPL2 and show that these differ from those of APPL1, suggesting that APPL-Rab interaction partners have co-evolved over time. Isothermal titration calorimetry data reveal the interaction between APPL2 and Rab31 has a K_d of 140 nm. Together with other biophysical data, we conclude the stoichiometry of the complex is 2:2.     

Conjugation site modulates the in vivo stability and therapeutic activity of antibody-drug conjugates

The reactive thiol in cysteine is used for coupling maleimide linkers in the generation of antibody conjugates. To assess the impact of the conjugation site, we engineered cysteines into a therapeutic HER2/neu antibody at three sites differing in solvent accessibility and local charge. The highly solvent-accessible site rapidly lost conjugated thiol-reactive linkers in plasma owing to maleimide exchange with reactive thiols in albumin, free cysteine or glutathione. In contrast, a partially accessible site with a positively charged environment promoted hydrolysis of the succinimide ring in the linker, thereby preventing this exchange reaction. The site with partial solvent-accessibility and neutral charge displayed both properties. In a mouse mammary tumor model, the stability and therapeutic activity of the antibody conjugate were affected positively by succinimide ring hydrolysis and negatively by maleimide exchange with thiol-reactive constituents in plasma. Thus, the chemical and structural dynamics of the conjugation site can influence antibody conjugate performance by modulating the stability of the antibody-linker interface.     

Di-codon usage for classification of genes

Genes are often classified into biologically related groups so that inferences on their functions can be made. This paper demonstrates that the di-codon usage is a useful feature for gene classification and gives better classification accuracy than the codon usage. Our experiments with different classifiers show that support vector machines performs better than other classifiers in classifying genes by using di-codon usage as features. The method is illustrated on 1841 HLA sequences which are classified into two major classes, HLA-I and HLA-II, and further classified into the subclasses of major classes. By using both codon and di-codon features, we show near perfect accuracies in the classification of HLA molecules into major classes and their sub-classes.     

Effects of self-thinning of shoots on the nutrient budgets of Zizania latifolia

This experimental study focused on the seasonal changes and mobilization of nutrients between plant parts to understand the implications of self-thinning in the ecology of Zizania latifolia (Griseb.) Turcz. ex Stapf. The observations of shoot density, above- and belowground biomass, and total nitrogen and total phosphorus concentrations were conducted from February 2002 to August 2003. The biomass of shoots that died during the period and daily uptake of nutrients were determined. The shoot density sharply increased until mid-April and thereafter decreased significantly due to self-thinning of shoots. Total nitrogen and phosphorus concentrations of rhizomes decreased initially due to translocation to new shoots; however, the nutrients of rhizomes were slightly replenished from dead shoots during self-thinning. In contrast to other species, self-thinning of Z. latifolia shoots reallocates some of the minerals contained in the dead shoots back to the rhizomes, which can be regarded as a strategy to replenish the reduced resources of the rhizomes. The initial intensive growth of shoots can be regarded as a strategy to maintain resource competition.     

Tolerance for Prolonged Darkness of Three Phytoplankton Species, Microcystis aeruginosa (Cyanophyceae), Scenedesmus quadricauda (Chlorophyceae), and Melosira ambigua (Bacillariophyceae)

Phytoplankton community dynamics are affected not only by atural events such as overwintering but also by artificial events such as artificial circulation and related darkness conditions. In order to clarify the effect of tolerance for prolonged darkness on community succession, laboratory cultures of three phytoplankton taxa, Microcystis aeruginosa(Cyanophyceae), Scenedesmus quadricauda(Chlorophyceae), and Melosira ambigua(Bacillariophyceae) were carried out in darkness. The period of darkness was varied: 5, 10, 15, 20 days, and the control. Thereafter, all samples were reilluminated. After more than 10 days of darkness, M. aeruginosa decreased markedly with the length of the darkness period and was reduced to only 1% of the initial cell number after 20 days darkness. In contrast, S. quadricauda and M. ambigua retained their biomass even after 20 days of darkness. After restarting the light–dark cycle, however, all three species similarly increased exponentially and reached their maximum biomass levels. These results suggest that differences in tolerance for prolonged darkness may cause the succession of the phytoplankton under certain conditions.     

Foraging behaviour of planktivorous fish in artificial vegetation: the effects on swimming and feeding

In the littoral zones of lakes, aquatic macrophytes produce considerable structural variation that can provide protection to prey communities by hindering predator foraging activity. The swimming and feeding behaviour of a planktivore, Pseudorasbora parva(Cyprinidae) on its prey (Daphnia pulex) was studied in a series of laboratory experiments with varying densities (0, 350, 700, 1400, 2100 and 2800 stems m^–2) of simulated submerged vegetation. Prey availability was varied from 0.5, 1.0, 2.0, 5.0, 10.0 and 25.0 prey l^–1. As the stem density increased, the predator's swimming speed and the number of prey captured decreased relative to feeding in open water. A good relation existed between the number of successful prey captures and swimming speed with the average stem distance to fish body length ratio (D). An abrupt reduction in feeding and swimming was recorded when D was reduced to values less than one.