Alternative states in the phytoplankton of Lake Kinneret, Israel (Sea of Galilee)

1. Through analyses of a 34‐year record of phytoplankton, zooplankton and physicochemical parameters from Lake Kinneret, Israel, we show that distinct and persistent phytoplankton assemblage states occurred from winter to summer. 2. The most obvious characteristic of these states was the presence or absence of a spring bloom of the dinoflagellate, Peridinium gatunense. 3. Analyses of the data within the framework of the alternative states model revealed a possible complex triggering mechanism, and system hysteresis. 4. A change in zooplankton biomass and body size coincident with changes in predation pressure associated with the collapse of the Kinneret Bleak, Acanthobrama terraesanctae, fishery appeared to be the ‘slow changing’ variable in the context of the alternative states model. Alternative phytoplankton states were only possible after this variable crossed a threshold in 1993–94, following the collapse of the fishery. 5. When alternative states were possible, some physicochemical parameters and the structure of the zooplankton assemblage appeared to control which phytoplankton state emerged in a given year. In years without a P. gatunense bloom, important physicochemical parameters in winter included low NO₃ loading, high water temperature, high water level, a deeper thermocline, low transparency, high concentrations of NO₃ and Cl in the epilimnion, and low concentration of epilimnetic total phosphorus. In addition, the cladoceran Chydorus sphaericus and adults of the copepod Mesocyclops ogunnus were observed in winter in years without a bloom. 6. Zooplankton biomass and body size of some taxa have recovered since the 1993–94 collapse of the fishery, yet incidence of both phytoplankton states in Lake Kinneret was still possible. Within the framework of the alternative states model, this suggests that the slow changing variable threshold where alternative states became possible is different from the threshold where alternative states will no longer be possible. In other words, the system is characterised by a hysteresis.     

Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme

Methods developed originally to analyze domain motions from simulation [Proteins 27:425–437, 1997] are adapted and extended for the analysis of X-ray conformers and for proteins with more than two domains. The method can be applied as an automatic procedure to any case where more than one conformation is available. The basis of the methodology is that domains can be recognized from the difference in the parameters governing their quasi-rigid body motion, and in particular their rotation vectors. A clustering algorithm is used to determine clusters of rotation vectors corresponding to main-chain segments that form possible dynamic domains. Domains are accepted for further analysis on the basis of a ratio of interdomain to intradomain fluctuation, and Chasles' theorem is used to determine interdomain screw axes. Finally residues involved in the interdomain motion are identified. The methodology is tested on citrate synthase and the M6I mutant of T4 lysozyme. In both cases new aspects to their conformational change are revealed, as are individual residues intimately involved in their dynamics. For citrate synthase the beta sheet is identified to be part of the hinging mechanism. In the case of T4 lysozyme, one of the four transitions in the pathway from the closed to the open conformation, furnished four dynamic domains rather than the expected two. This result indicates that the number of dynamic domains a protein possesses may not be a constant of the motion. Proteins 30:144–154, 1998. © 1998 Wiley-Liss, Inc.     

Multiplex single‐cell quantification of rare RNA transcripts from protoplasts in a model plant system

Here we demonstrate multiplex and simultaneous detection of four different rare RNA species from plant, Arabidopsis thaliana, using surface‐enhanced Raman spectroscopy (SERS) and gold nanoprobes at single‐cell resolution. We show the applicability of nanoparticle‐based Raman spectroscopic sensor to study intracellular RNA copies. First, we demonstrate that gold‐nanoparticles decorated with Raman probes and carrying specific nucleic acid probe sequences can be uptaken by the protoplasts. We confirm the internalization of gold nanoprobes by transmission electron microscopy, inductively‐coupled plasma‐mass spectrometry and fluorescence imaging. Second, we show the utility of a SERS platform to monitor individual alternatively spliced (AS) variants and miRNA copies within single cells. Finally, the distinctive spectral features of Raman‐active dyes were exploited for multiplex analysis of AtPTB2, AtDCL2, miR156a and miR172a. Furthermore, single‐cell studies were validated by in vitro quantification and evaluation of nanotoxicity of gold probes. Raman tag functionalized gold nanosensors yielded an approach for the tracking of rare RNAs within the protoplasts. The SERS‐based approach for quantification of RNAs has the capability to be a highly sensitive, accurate and discerning method for single‐cell studies including AS variants quantification and rare miRNA detection in specific plant species.     

Submerged macrophytes, zooplankton and the predominance of low- over high-chlorophyll states in western boreal, shallow-water wetlands

1. Shallow‐water (<2 m deep) wetlands in northern Alberta's western boreal forest tend to have either extremely high‐chlorophyll, pea‐green water or water that is low in chlorophyll and clear. The relative importance of top‐down processes (e.g. zooplankton grazing) compared with bottom‐up processes (e.g. nutrient limitation) for regulating the existence of these alternate states has yet to be explicitly investigated in these poorly studied waterbodies. 2. To assess the relationship between chemical and biological factors and the predominance of low‐chlorophyll over high‐chlorophyll states, a survey of 24 shallow‐water wetlands in northern Alberta was conducted over the summers of 2001 and 2002. 3. In wetlands without fish, statistical analysis indicated that high‐ and low‐chlorophyll sites could be differentiated with 82% accuracy based solely on whether submerged aquatic vegetation (SAV) coverage was greater or less than 25%. Further, high‐SAV lakes with zooplankton communities dominated by large cladocerans were clear 96% of the time. 4. In the few wetlands that supported stickleback populations, large cladocerans were absent. However, the development of zooplankton communities dominated by small cladocera (Bosmina) with calanoid copepods in fish‐containing wetlands corresponded with a shift from high‐ to low‐chlorophyll states. 5. Results suggest that in fishless wetlands high‐SAV coverage and grazing by large, SAV‐associated cladocerans promotes low‐chlorophyll states. Results also suggest that suppression of macroinvertebrate predators by sticklebacks allowing Bosmina to flourish may also promote low‐chlorophyll, clear‐water conditions.     

Prolylproline unit in model peptides and in fragments from databases

The prolylproline sequence unit is found in several naturally occurring linear and cyclic peptides with immunosuppressive and toxic activity. Furthermore, Pro-Pro units are abundant in collagen, in ligand motifs binding to SH3 or WW domains, as well as in vital enzymes such as DNA glycosylase and thrombin. In all these sequence units a special role is dedicated to conformation in order to successfully fulfill the appropriate biological function. Therefore, a detailed analysis of the basic conformational properties of Pro-Pro is expected to reveal the versatile structural role of this sequence. PCM (polarizable continuum model) calculations on the basis of ab initio and density functional theory investigations using the model peptide HCO-L-Pro-L-Pro-NH2 are presented. Cis-trans isomerism, backbone conformation and ring puckering are studied. A systematic comparison is made to experimental data gained on L-prolyl-L-proline sequence units retrieved from the Protein Data Bank as well as from the Cambridge Structural Database. PCM data are in good agreement with high-resolution X-ray crystallography. Population data derived from energy calculations and those gained directly from statistics predict that 87% of the Pro-Pro sequence units adopt elongated structures, while 13% form beta-turns. Both approaches prefer the same 6 out of the 36 ideally possible backbone folds. Polyproline II unit (t epsilonL t epsilonL), other elongated structures (c epsilonL t epsilonL, t epsilonL t alphaL and t epsilonL t gammaL), type VIa (t epsilonL c alphaL) and type I or III beta-turns (t alphaL t alphaL) altogether describe 96% of the prolylproline sequences. In disordered proteins or domains, Pro-Pro sequence units may sample the various conformers and contribute to the segmental motions.     

The (α-1,6) glycosidic bond of isomaltose: a tricky system for theoretical conformational studies

Stable conformations of β-isomaltose (α-d-glucopyranosyl-(1→6)-β-d-glucose) in gas-phase and aqueous solution are investigated in this study using quantum mechanical calculations. Conformational maps are calculated at HF/6-31G(d,p) level and lower energy structures are sampled in the most stable regions. Entropic and thermal corrections are considered and the Boltzmann population is obtained for conformers that are representative of the 18 most stable regions found on the potential energy surface. B3LYP/6-31+G(d,p) and B3LYP/6-311+G(2d,2p) calculations are used in conformational samplings. Solvation effects are considered through the polarizable continuum model approach. Hydroxymethyl group orientations are investigated for the most stable conformers. The influence of electronic correlation and solvation on the glycosidic linkage preference (TG, GT, and GG) and hydroxymethyl group orientation (tg, gt, and gg) are discussed. Heteronuclear spin coupling constants (³J_C,H) along the glycosidic linkage are calculated and comparison with other theoretical results and experiments is used to validate the obtained structures.     

Effects of Hurricanes on Rare Plant Demography in Fire‐Controlled Ecosystems

Hurricanes have dramatic effects on forest vegetation, but their effects on shrublands have rarely been studied. We analyzed the effects of three 2004 hurricanes—among the strongest on record in Florida—on vital rates of 12 rare plant species of pyrogenic interior Florida scrub and sandhill. Tree damage varied by vegetation type (being highest in areas with Pinus clausa) and was associated with debris deposition. Most rare species were minimally impacted by hurricanes. The two most frequently damaged species were the shrubs Prunus geniculata (11% of individuals) and Asimina obovata (7%); both were resilient to damage. Prunus geniculata had little mortality during the hurricane year but damaged plants had a temporary (1‐yr) reduction in relative growth rate. Prunus geniculata flowering was unaffected by hurricane damage. Hurricane damage had no effects on vital rates of A. obovata, Eriogonum longifolium var. gnaphalifolium, or Chrysopsis highlandsensis. Other species suffered little or no observable hurricane damage. Of 12 species analyzed, nine had similar annual survival in hurricane and nonhurricane years. Relatively low survival in the hurricane year (compared with other years) was linked to prehurricane drought or prescribed fire in two of three species. Thus, the 2004 hurricanes did not have important effects on populations of interior Florida scrub and sandhill plants, especially herbaceous species. This is in marked contrast to dramatic demographic responses to fire in central Florida and strong effects of hurricanes in coastal Florida, highlighting that these different disturbances may have divergent effects on vegetation and populations over short distances.     

Characterization of the near native conformational states of the SAM domain of Ste11 protein by NMR spectroscopy

The sterile alpha motif or SAM domain is one of the most frequently present protein interaction modules with diverse functional attributions. SAM domain of the Ste11 protein of budding yeast plays important roles in mitogen‐activated protein kinase cascades. In the current study, urea‐induced, at subdenaturing concentrations, structural, and dynamical changes in the Ste11 SAM domain have been investigated by nuclear magnetic resonance spectroscopy. Our study revealed that a number of residues from Helix 1 and Helix 5 of the Ste11 SAM domain display plausible alternate conformational states and largest chemical shift perturbations at low urea concentrations. Amide proton (H/D) exchange experiments indicated that Helix 1, loop, and Helix 5 become more susceptible to solvent exchange with increased concentrations of urea. Notably, Helix 1 and Helix 5 are directly involved in binding interactions of the Ste11 SAM domain. Our data further demonstrate that the existence of alternate conformational states around the regions involved in dimeric interactions in native or near native conditions. Proteins 2014; 82:2957–2969. © 2014 Wiley Periodicals, Inc.     

Roving females and patient males: a new perspective on the mating strategies of chimpanzees

Mating strategies are sets of decisions aimed at maximizing reproductive success. For male animals, the fundamental problem that these strategies address is attaining mating access to females in a manner that maximizes their chances of achieving paternity. For chimpanzees (Pan troglodytes), despite substantial interest in mating strategies, very little attention has been paid to the most fundamental problem that mating strategies need to solve: finding mates. Only a single model, Dunbar's general model of male mating strategies, exists to explain mate‐searching behaviour in chimpanzees. Under this model, males in most populations are regarded as pursuing a ‘roving’ strategy: searching for and sequestering fertile females who are essentially passive with respect to mate searching. The roving mating strategy is an assumption deeply embedded in the way chimpanzee behaviour is considered; it is implicit in the conventional model for chimpanzee social structure, which posits that male ranging functions both to monitor female reproductive state and to ward these females from other groups of males through collective territoriality: essentially, ranging as mating effort. This perspective is, however, increasingly at odds with observations of chimpanzee behaviour. Herein, I review the logic and evidence for the roving‐male mating strategy and propose a novel alternative, a theoretical framework in which roving is a strategy pursued by female chimpanzees in order to engage successfully in promiscuous mating. Males, unable to thwart this female strategy, instead maximise the number of reproductive opportunities encountered by focusing their behaviour on countering threats to health, fertility and reproductive career. Their prolonged grooming bouts are seen, in consequence, as functioning to mitigate the negative impacts of socially induced physiological stress. In this new framework, the roving‐male strategy becomes, at best, a ‘best of a bad job’ alternative for low‐ranking males when faced with high levels of competition for mating access. Male chimpanzees do not search for mates, but for one another, for food, and, at times, for rivals in other communities. To the extent that female promiscuity functions to counter infanticide risk, mate searching by female chimpanzees—and any associated costs—can be seen as an unavoidable consequence of male sexual coercion. This novel framework is a better fit to the available data than is the conventional account. This review highlights the desperate need for additional work in an area of chimpanzee biology that has been somewhat neglected, perhaps in part because assumptions of roving males have remained unquestioned for too long. It also highlights the need, across taxa, to revisit and revise theory, and to test old assumptions, when faced with contrary data.