Zooplankton biomass dynamics in oligotrophic versus eutrophic conditions: a test of the PEG model

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The effect of hydration on the mobility of phospholipids in the gel state. A proton nuclear magnetic resonance spin echo study

Proton nuclear magnetic resonance (NMR) dipolar echo studies are presented for the gel state of dipalmitoylglycerophosphocholine (dipalmitoyl-GPC) — heavy water dispersions. The mobility and the mean order of the chains and the head group of dipalmitoyl-GPC were determined for different water concentrations and temperatures. For smaller than 5 mol D₂O per mol dipalmitoyl-GPC the molecule undergoes temperature- and hydration-dependent restricted rotational oscillations about the long axis of the molecule. For hydration numbers equal or larger than 5 mol D₂O per mol dipalmitoyl-GPC the molecules rotate effectively about their long axes and intermolecular dipolar interactions between proton groups of neighbour molecules are averaged. The onset of the lateral diffusion of dipalmitoyl-GPC is observed which averages out all intermolecular dipolar interactions. Deviations of the individual segments of the chains from the all-trans state have to be considered. The widely accepted model that the dipalmitoyl-GPC molecules rotate about their long axes with stiff all-trans chains should be modified. The polar head groups of dipalmitoyl-GPC effectively rotate about the bilayer-normal and restricted rotations about single bonds in the head group are allowed. An order parameter of about 0.6 for the head group was obtained for fully hydrated dipalmitoyl-GPC molecules at ambient temperature.     

The osmolyte trimethylamine‐N‐oxide stabilizes the Fyn SH3 domain without altering the structure of its folding transition state

Trimethylamine‐N‐oxide (TMAO) is a naturally occurring osmolyte that stabilizes proteins against denaturation. Although the impact of TMAO on the folding thermodynamics of many proteins has been well characterized, far fewer studies have investigated its effects on protein folding kinetics. In particular, no previous studies have used Φ‐value analysis to determine whether TMAO may alter the structure of the folding transition state. Here we have measured the effects on folding kinetics of 16 different amino acid substitutions distributed across the structure of the Fyn SH3 domain both in the presence and absence of TMAO. The folding and unfolding rates in TMAO, on average, improved to equivalent degrees, with a twofold increase in the protein folding rate accompanied by a twofold decrease in the unfolding rate. Importantly, TMAO caused little alteration to the Φ‐values of the mutants tested, implying that this compound minimally perturbs the folding transition state structure. Furthermore, the solvent accessibility of the transition state was not altered as reflected in an absence of a TMAO‐induced change in the denaturant β factors. Through TMAO‐induced folding studies, a β factor of 0.5 was calculated for this compound, suggesting that the protein backbone, which is the target of action of TMAO, is 50% exposed in the transition state as compared to the native state. This finding is consistent with the equivalent effects of TMAO on the folding and unfolding rates. Through thermodynamic analysis of mutants, we also discovered that the stabilizing effect of TMAO is lessened with increasing temperature.     

Effect of glutathione biosynthesis-related modulators on the thiol redox state enzymes and on sclerotial differentiation of filamentous phytopathogenic fungi

In this study, sclerotial differentiation in filamentous phytopathogenic fungi, representing the four main types of sclerotia, was studied in relation to thiol redox state (TRS)-related enzymes and their substrates/products. TRS was altered by the general TRS modulator Ν-acetylcysteine (AcCSH) and by the glutathione (GSH) biosynthesis modulators l-oxo-thiazolidine-4-carboxylate (OTC), and l-buthionine-S,R-sulfoximine (BSO). This study showed that the four studied types of sclerotial differentiation are directly related with the antioxidant –SH groups of GSH and/or CSH, since the decrease of sclerotial differentiation concurred with an increase of these thiols by the GSH biosynthesis modulators AcCSH, OTC, and BSO. Supportive to that conclusion is the fact that, in general, the activities of the TRS-related enzymes GR/GPDH and Ttase decrease in the end of the undifferentiated stage due to the substitution of their antioxidant function by the antioxidant potential of the –SH group providers AcCSH and OTC. Moreover, it was found that BSO expectedly suppressed GSH biosynthesis in the tested fungi, and unexpectedly decreased their sclerotial differentiation by a dose-dependent manner typical for antioxidants. The possible antioxidant role of BSO was supported by the decrease it caused in the antioxidant enzymes GR/GPDH and Ttase. The results of this study are in accordance with our hypothesis that sclerotial differentiation in phytopathogenic fungi is induced by oxidative stress.     

Predicting the onset of filamentous bulking in biological wastewater treatment systems by exploiting image analysis information

The performance of the activated sludge process is limited by the ability of the sedimentation tank (1) to separate the activated sludge from the treated effluent and (2) to concentrate it. Apart from bad operating strategies or poorly designed clarifiers, settling failures can mainly be attributed to filamentous bulking. Image analysis is a promising technique that can be used for early detection of filamentous bulking. The aim of this paper is therefore twofold. Foremost, correlations are sought between image analysis information (i.e., the total filament length per image, the mean form factor, the mean equivalent floc diameter, the mean floc roundness and the mean floc reduced radius of gyration) and classical measurements (i.e., the Sludge Volume Index (SVI)). Secondly, this information is both explored and exploited in order to identify dynamic ARX and state space-type models. Their performance is compared based on two criteria.     

Exploring subdomain cooperativity in T4 lysozyme I: structural and energetic studies of a circular permutant and protein fragment

Small proteins are generally observed to fold in an apparent two-state manner. Recently, however, more sensitive techniques have demonstrated that even seemingly single-domain proteins are actually made up of smaller subdomains. T4 lysozyme is one such protein. We explored the relative autonomy of its two individual subdomains and their contribution to the overall stability of T4 lysozyme by examining a circular permutation (CP13*) that relocates the N-terminal A-helix, creating subdomains that are contiguous in sequence. By determining the high-resolution structure of CP13* and characterizing its energy landscape using native state hydrogen exchange (NSHX), we show that connectivity between the subdomains is an important determinant of the energetic cooperativity but not structural integrity of the protein. The circular permutation results in a protein more easily able to populate a partially unfolded form in which the C-terminal subdomain is folded and the N-terminal subdomain is unfolded. We also created a fragment model of this intermediate and demonstrate using X-ray crystallography that its structure is identical to the corresponding residues in the full-length protein with the exception of a small network of hydrophobic interactions. In sum, we conclude that the C-terminal subdomain dominates the energetics of T4 lysozyme folding, and the A-helix serves an important role in coupling the two subdomains.     

Assessing spatial covariance among time series of abundance

For species of conservation concern, an essential part of the recovery planning process is identifying discrete population units and their location with respect to one another. A common feature among geographically proximate populations is that the number of organisms tends to covary through time as a consequence of similar responses to exogenous influences. In turn, high covariation among populations can threaten the persistence of the larger metapopulation. Historically, explorations of the covariance in population size of species with many (>10) time series have been computationally difficult. Here, we illustrate how dynamic factor analysis (DFA) can be used to characterize diversity among time series of population abundances and the degree to which all populations can be represented by a few common signals. Our application focuses on anadromous Chinook salmon (Oncorhynchus tshawytscha), a species listed under the US Endangered Species Act, that is impacted by a variety of natural and anthropogenic factors. Specifically, we fit DFA models to 24 time series of population abundance and used model selection to identify the minimum number of latent variables that explained the most temporal variation after accounting for the effects of environmental covariates. We found support for grouping the time series according to 5 common latent variables. The top model included two covariates: the Pacific Decadal Oscillation in spring and summer. The assignment of populations to the latent variables matched the currently established population structure at a broad spatial scale. At a finer scale, there was more population grouping complexity. Some relatively distant populations were grouped together, and some relatively close populations – considered to be more aligned with each other – were more associated with populations further away. These coarse‐ and fine‐grained examinations of spatial structure are important because they reveal different structural patterns not evident in other analyses.     

Basking Activity is Modulated by Health State but is Constrained by Conspicuousness to Predators in Male Spanish Terrapins

Aerial basking may have several benefits for freshwater turtles in addition to thermoregulation such as removing parasites from the skin, which would improve health state. However, basking outside of water may be risky because it may expose freshwater turtles to terrestrial predators. Here, we monitored the basking activity of male Spanish terrapins (Mauremys leprosa) in a wild population of the south‐western of the Iberian Peninsula. We also measured body size, health state parameters, parasite prevalence, and limb coloration of these individuals. We aimed to examine whether basking may improve health state of turtles. The results showed that male turtles with higher basking activity were those parasitized by Hepatozoon and that had lower total white blood cell (WBC). This might indicate that turtles in worse health condition increase their time spent basking to improve their immune system. In addition, because basking might be risky, we also expected that turtles with more conspicuous coloration should reduce their basking activity to avoid being detected by potential predators. We found that infected turtles, but not uninfected ones, that spent more time basking also had less bright coloration in limb stripes. Our study provides evidence that basking activity may improve health state of terrapins, but that color conspicuity may increase costs of basking, especially for parasitized individuals. Understanding the balance between the benefits and the costs of basking might be essential for the conservation of freshwater turtle populations.