The importance of the last strand at the C-terminus in βB2-crystallin stability and assembly

Congenital cataract is the leading cause of childhood blindness worldwide. Investigations of the effects of inherited mutations on protein structure and function not only help us to understand the molecular mechanisms underlying congenital hereditary cataract, but also facilitate the study of complicated cataract and non-lens abnormities caused by lens-specific genes. In this research, we studied the effects of the V187M, V187E and R188H mutations on βB2-crystallin structure and stability using a combination of biophysical, cellular and molecular dynamic simulation analysis. Both V187 and R188 are located at the last strand of βB2-crystallin Greek-key motif 4. All of the three mutations promoted βB2-crystallin aggregation in vitro and at the cellular level. These three mutations affected βB2-crystallin quite differentially: V187M influenced the hydrophobic core of the C-terminal domain, V187E was a Greek-key motif breaker with the disruption of the backbone H-bonding network, while R188H perturbed the dynamic oligomeric equilibrium by dissociating the dimer and stabilizing the tetramer. Our results highlighted the importance of the last strand in the structural integrity, folding, assembly and stability of β-crystallins. More importantly, we proposed that the perturbation of the dynamic equilibrium between β-crystallin oligomers was an important mechanism of congenital hereditary cataract. The selective stabilization of one specific high-order oligomer by mutations might also be deleterious to the stability and folding of the β-crystalllin homomers and heteromers. The long-term structural stability and functional maintenance of β-crystallins are achieved by the precisely regulated oligomeric equilibrium.     

Evaluation of species composition and seasonal dynamics of mosquito larvae in the Košice Basin during 2010 and 2011

In six sites in the Ko?ice Basin we collected 17,520 larvae of 15 mosquito species during the seasons (April–August) of 2010 and 2011. They were: Aedes vexans (Meigen, 1830), Ae. cinereus (Meigen, 1818) [or Ae. rossicus (Dolbeskin, Gorickaja & Mitrofanova, 1930], Ochlerotatus geniculatus (Olivier, 1791), Oc. refiki (Medschid, 1928), Oc. rusticus (Rossi, 1790), Oc. sticticus (Meigen, 1838), Oc. punctor (Kirby, 1837), Oc. cataphylla (Dyar, 1916), Oc. cantans (Meigen, 1818)[or Oc. annulipes (Meigen, 1830)], Oc. communis (De Geer, 1776), Oc. flavescens (Müller, 1764), Oc. leucomelas (Meigen, 1804), Culiseta annulata (Schrank, 1776), Culex pipiens (L., 1758) [or Cx. torrentium (Martini, 1925)] and Anopheles maculipennis s.l. The objective of the present research was to identify the mosquito larvae species diversity and compare their distribution and density in urban and suburban localities of the monitored territory.     

Foraging facilitation among predators and its impact on the stability of predator–prey dynamics

Predator foraging facilitation may strongly influence the dynamics of a predator–prey system. This behavioral pattern is well-observed in real life interactions, but less is known about its possible impacts on the predator–prey dynamics. In this paper we analyze a modified Rosenzweig–MacArthur model, where a predator-dependent family of functions describing predator foraging facilitation is introduced into the Holling type II functional response. As the general assumption of foraging facilitation is that higher predator densities give rise to an increased foraging efficiency, we model predator facilitation with an increasing encounter rate function. Using the tools of bifurcation analysis we describe all the nonlinear phenomena that occur in the system provoked by foraging facilitation, these include the fold, Hopf, transcritial, homoclinic and Bogdanov–Takens bifurcation. We show that foraging facilitation can stabilize the coexistence in the predator–prey system for specific rates, but in most of the cases it can have fatal consequences for the predators themselves.     

Cooperative pastoral production — the importance of kinship

While there is a general assumption that labour has a positive effect on pastoral production, studies that have quantified this relationship have been characterized by ambiguous results. This is most likely related to the fact that possible cooperative pastoral production has been little explored in the literature, although it is well documented that nomadic pastoralist households share and exchange labour in so-called cooperative herding groups. Consequently, this study aims at investigating possible cooperative labour-related effects on production among Saami reindeer herders in Norway by using kinship relations as a proxy for cooperation. This study found that cooperative labour investment is important for Saami reindeer herders, but that the effect of kinship and labour needs to be understood in relation to each other. When assessing the effect of labour and kinship simultaneously, both labour and genealogical relationship had positive effects on herd size. We also found a positive interaction between kinship and labour suggesting that high levels of relatedness coupled with a large potential labour pool had an increasingly positive effect on herd size.     

Host plant quality,spatial heterogeneity,and the stability of mite predator–prey dynamics

Population dynamics models suggest that both the over-all level of resource productivity and spatial variability in productivity can play important roles in community dynamics. Higher productivity environments are predicted to destabilize consumer–resource dynamics. Conversely, greater heterogeneity in resource productivity is expected to contribute to stability. Yet the importance of these two factors for the dynamics of arthropod communities has been largely overlooked. I manipulated nutrient availability for strawberry plants in a multi-patch experiment, and measured effects of overall plant quality and heterogeneity in plant quality on the stability of interactions between the phytophagous mite Tetranychus urticae and its predator Phytoseiulus persimilis. Plant size, leaf N content and T. urticae population growth increased monotonically with increasing soil nitrogen availability. This gradient in plant quality affected two correlates of mite population stability, population variability over time (i.e., coefficient of variation) and population persistence (i.e., proportion of plant patches colonized). However, the highest level of plant quality did not produce the least stable dynamics, which is inconsistent with the “paradox of enrichment”. Heterogeneity in plant productivity had modest effects on stability, with the only significant difference being less variable T. urticae densities in the heterogeneous compared to the corresponding homogeneous treatment. These results are generally congruent with metapopulation theory and other models for spatially segregated populations, which predict that stability should be governed largely by relative movement rates of predators and prey—rather than patch quality.     

Roles of dispersal, stochasticity, and nonlinear dynamics in the spatial structuring of seasonal natural enemy–victim populations

Natural enemy–victim systems may exhibit a range of dynamic space–time patterns. We used a theoretical framework to study spatiotemporal structuring in a transient natural enemy–victim system subject to differential rates of dispersal, stochastic forcing, and nonlinear dynamics. Highly mobile natural enemies that attacked less mobile victims were locally spatially segregated from each other when governed by approximate linear dynamics. In contrast, in nonlinear dynamical systems, such as cyclic populations, interacting species achieved local aggregation with each other regardless of dispersal rates, and aggregation was enhanced specifically when highly mobile enemies attacked less mobile victims. These patterns of spatial aggregation held under varying levels of stochastic forcing. This work thus shows a range of dynamic spatial patterns in interacting-species models, and how spatial aggregation between natural enemies and victims can be achieved in locally unstable populations that are linked through dispersal.     

Integrin activation—the importance of a positive feedback

Integrins mediate cell adhesion and are essential receptors for the development and functioning of multicellular organisms. Integrin activation is known to require both ligand and talin binding and to correlate with cluster formation but the activation mechanism and precise roles of these processes are not yet resolved. Here mathematical modeling, with known experimental parameters, is used to show that the binding of a stabilizing factor, such as talin, is alone insufficient to enable ligand-dependent integrin activation for all observed conditions; an additional positive feedback is required.     

Refuge evolution and the population dynamics of coupled host—parasitoid associations

Summary We have investigated the theoretical consequences of character evolution for the population dynamics of a host—parasitoid interaction, assuming a monophagous parasitoid. In the purely ecological model it is assumed that hosts can escape parasitism by being in absolute refuges. A striking property of this model is a threshold effect in control of the host by the parasitoid, when host density dependence is weak. The approximate criteria for the parasitoid to regulate the host to low densities are (1) that the parasitoid's maximum population growth rate should exceed the host's and (2) that the maximum growth rate of the host in the refuge should be less than unity. We then use this ecological framework as a basis for a model which considers evolutionary changes in quantitative characters influencing the size of the absolute refuge. For each species, an increase in its refuge-determining character comes at a cost to maximum population growth rate. We show that refuge evolution can substantially alter the population dynamics of the purely ecological model, resulting in a number of emergent and sometimes counter-intuitive properties. In general, when the host has a high carrying capacity, systems are polarized either with low or minor refuge and top-down control of the host by the parasitoid or with a refuge and bottom-up control of the host by a combination of its own density dependence and the parasitoid. A particularly tantalizing result is that co-evolutionary dynamics can modify ecologically unstable systems into ones which are either stable or quasi-stable (with bouts of unstable dynamics, punctuating long-term periods of quasi-stable behaviour). We present five quantitative criteria which must all be met for the parasitoid to be the agent responsible for control of the host at a co-evolutionary equilibrium. The apparent stringency of this full set of requirements supports the empirically-based suggestion that monophagous parasitoid-driven systems should be less common in nature than those driven by multiple forms of density dependence. Further, we apply our theory to the question of whether exploiters may harvest their victims at maximum sustainable yields and to the evolutionary stability of biological control. Finally, we present a series of testable predictions of our theory and methods useful for testing them.     

Part–whole relations between food webs and the validity of local food-web descriptions

This work analyzes the relationship between large food webs describing potential feeding relations between species and smaller sub-webs thereof describing relations actually realized in local communities of various sizes. Special attention is given to the relationships between patterns of phylogenetic correlations encountered in large webs and sub-webs. Based on the current theory of food-web topology as implemented in the matching model, it is shown that food webs are scale invariant in the following sense: given a large web described by the model, a smaller, randomly sampled sub-web thereof is described by the model as well. A stochastic analysis of model steady states reveals that such a change in scale goes along with a re-normalization of model parameters. Explicit formulae for the re-normalized parameters are derived. Thus, the topology of food webs at all scales follows the same patterns, and these can be revealed by data and models referring to the local scale alone. As a by-product of the theory, a fast algorithm is derived which yields sample food webs from the exact steady state of the matching model for a high-dimensional trophic niche space in finite time.     

Influence of the SNPs on the structural stability of CBS protein： Insight from molecular dynamics simulations

Cystathionine β-synthase is an essential enzyme of the trans-suifuration pathway that condenses serine with homocysteine to form cystathionine. Missense mutations in CBS are the major cause of inherited homocystinuria, and the detailed effect of disease associated amino acid substitutions on the structure and stability of human CBS is yet unknown. Here, we apply a unique approach in combining in silico tools and molecular dynamics simulation to provide structural and functional insight into the effect of SNP on the stability and activity of mutant CBS. In addition, principal component analysis and free energy landscape were used to predict the collective motions, thermodynamic stabilities and essential subspace relevant to CBS function. The obtained results indicate that C109R, E176K and D376N mutations have the diverse effect on dynamic behavior of CBS protein. We found that highly conserved D376N mutation, which is present in the active pocket, affects the protein folding mechanism. Our strategy may provide a way in near future to understand and study effects of functional nsSNPs and their role in causing homocystinuria.     

Biomanipulation: the next phase — making it stable

Review of the literature on biomanipulation shows that fish manipulations have occurred through the following methods: piscivore addition; piscivore catch restriction; habitat enhancement; piscivore removal; planktivore exclusion; planktivore removal by selective catch, lake emptying, fish poisons, fish diseases, winterkill, summerkill; habitat expansion or contraction; planktivore addition; and natural events. The methods can be classified as deliberate, inadvertent, or natural, all of which have successful and unsuccessful examples. However, the problem of perpetuation of successful results remains unsolved. It is proposed that this may be resolved through use of a refuge or refuges from among the following: low light intensity refuge; low temperature refuge; low dissolved oxygen refuge; physical concealment refuge; visual clutter refuge; behavior modification refuge; and predator inefficiency refuge. Perhaps through use of such mechanisms large herbivorous zooplankters can continue to exist in lakes. Examples are given. Contribution no. 383 from the Limnological Research center.     

Adaptive movement and food-chain dynamics: towards food-web theory without birth–death processes

Population density can be affected by its prey [resource] and predator [consumer] abundances through two different mechanisms: the alternation of birth [or somatic growth] or death rate and inter-habitat movement. While the food-web theory has traditionally been built on the former mechanism, the latter mechanism has formed the basis of a successful theory explaining the spatial distribution of organisms in the context of behavioral and evolutionary ecology. Yet, few studies have compared these two mechanisms, leaving the question of how similar (or different) predictions derived from birth–death-based and movement-based food-web theories unanswered. Here, theoretical models of the tri-trophic (resource–consumer-top predator) food chain were used to compare food-web patterns arising from these two mechanisms. Specifically, we evaluated the response of the food-chain structure to inter-patch differences in productivity for movement-based models and birth–death-based models. Model analysis reveals that adaptive movements give rise to positively correlated responses of all trophic levels to increased productivity; however, this pattern was not observed in the corresponding birth–death-based model. The movement-based model predicts that the food chain response to productivity is determined by the sensitivity of animal movement to the environmental conditions. More specifically, increasing sensitivity of a consumer or top predator leads to smaller inter-patch variance of the resource or consumer density, while increasing inter-patch variance in the consumer or resource density. In conclusion, adaptive movement provides an alternative mechanism correlating the food-web structure to environmental conditions.     

Immobilization of luciferase from the firefly Luciola mingrelica — Catalytic properties and stability of the immobilized enzyme

Firefly (Luciola mingrelica) luciferase [Photinus luciferin 4-monooxygenase (ATP-hydrolysing); Photinus luciferin: oxygen 4-oxidoreductase (decarboxylating, ATP-hydrolysing), EC 1.13.12.7] has been immobilized on albumin and polyacrylamide gel, on AH-, CH- and CNBr-Sepharose 4B as well as on Ultragel, Ultradex and cellophane film activated by cyanogen bromide. Only immobilization on cyanogen bromide-activated polysaccharide carriers resulted in highly active immobilized luciferase. Kinetic properties of immobilized luciferase hardly differed from those of the soluble enzyme. The inactivation rate constants of soluble and immobilized luciferase were measured at pH 5.5–9.0 and 25°C as well as at pH 7.8 and 20–40°C. The ΔH^≠ and ΔS^≠ values for inactivation of soluble and immobilized luciferases were obtained. A 1000-fold stabilization effect was noted for the luciferase immobilized on CNBr-Sepharose 4B at pH 7.5 and 25°C. A stabilization mechanism for the immobilized luciferase is discussed.     

Epilithon δ15N signatures indicate the origins of nitrogen loading and its seasonal dynamics in a volcanic Lake

The intensification of agricultural land use and urbanisation has increased nutrient loads in aquatic ecosystems. Nitrogen loads can alter ecosystem structure and functioning, resulting in increased algal productivity, algal blooms and eutrophication. The principal aim of the present paper is to extend the use of epilithic δ¹⁵N signatures to a lake ecosystem in order to evaluate the potential impact of anthropogenic nitrogen discharges (organic and inorganic) that can also reach coastal waters.Epilithic associations were collected from volcanic rocks in different seasons in shallow water along the entire perimeter of Lake Bracciano and analysed for their nitrogen stable isotope signatures. Furthermore, some stones were moved from an unpolluted site to a polluted one in order to verify the effect on the nitrogen signature of the epilithic association. The epilithon’s δ¹⁵N signatures provided strong evidence of the space-time variability of N inputs. The differing quality of nitrogen loads was reflected in high isotopic variation within the lake, especially at the beginning of summer (1.7‰ ≤ δ¹⁵N ≤ 13.3‰), while in winter, when anthropogenic pressure was lowest, the δ¹⁵N signature variation was less accentuated (3.1‰ ≤ δ¹⁵N ≤ 7.6‰). At all sampling times, spatial variability was found to be related to the various human activities along the lake shore (especially tourism and agriculture), while seasonal variation at all sampling sites was related to the intensity of anthropogenic pressures (higher in summer and lower in winter).Our results showed that epilithic algal associations and the physicochemical properties of the water did not influence the δ¹⁵N signature, which in contrast was strongly related to the site-specific effect of human activities around the lake. Thus, the distribution of δ¹⁵N across space and time can be used to direct nutrient reduction strategies in the region and can assist in monitoring the effectiveness of environmental protection measures.     

Transformation of cytoplasmic actin importance for the organization of the contractile gel reticulnm and the contraction — relaxation cycle of cytoplasmic actomyosin

(1) Within the low viscous flowing endoplasm of Physarum polycephalum a considerable amount of actin is in the non-filamentous state. This can be demonstrated by applying poly-L-lysin to surface spreads of native protoplasm. (2) It has been shown that in protoplasmic drops the endoplasm-ectoplasm transformation is accompanied by an actin polymerization from the non-filamentous state to F-actin. (3) The actual state of the labile G-F-actin equilibrium determines the varying consistency (viscosity) of the cytoplasm. (4) Increasing viscosity can be interpreted as being brought about by a) shifting of the G-F-actin equilibrium to the filamentous side, and (b) increased myosin-mediated binding sites between actin filaments. (5) Polymerization and depolymerization processes are involved in the rhythmically occurring contraction-relaxation cycle of cytoplasmic actomyosin in Physarum. (6) Cytoplasmic actin and myosin represent the architectural proteins of the contractile gel reticulum in eukaryotic cells. (7) The importance of the regulation of actin polymerization as a basic control mechanism of the eukaryotic cell is discussed.     

Protozoan grazing of bacteria in soil—impact and importance

Interactions between bacteria and protozoa in soil were studied over 2-week periods in the field and in a pot experiment. Under natural conditions the total biological activity was temporarily synchronized by a large rainfall, and in the laboratory by the addition of water to dried-out soil, with or without plants. In the field, peaks in numbers and biomass of bacteria appeared after the rain, and a peak of naked amoebae quickly followed. Of the three investigated groups—flagellates, ciliates, and amoebae—only populations of the latter were large enough and fluctuated in a way that indicated a role as bacterial regulators. The bacterial increase was transient, and the amoebae alone were calculated to be able to cause 60% of the bacterial decrease. The same development of bacteria and protozoa was observed in the pot experiment: in the presence of roots, amoebic numbers increased 20 times and became 5 times higher than in the unplanted soil. In the planted pots, the amoebic increase was large enough to cause the whole bacterial decrease observed; but in the unplanted soil, consumption by the amoebae caused only one-third of the bacterial decrease.     

Effects of the binding of calcium ions on the structure and dynamics of the ΦX174 virus investigated using molecular dynamics

It is known that the presence of calcium ions (Ca^2 +) is necessary for the enterobacterial virus ΦX174 to inject its DNA into the host cell, and that some mutations in the major capsid proteins lead to better survivability at higher temperatures. Our goal in the current study is to determine the physical changes in both the wild-type and mutant virus due to the binding of Ca^2 +. Thus, we performed molecular dynamics simulations of the ΦX174 major capsid protein complex with and without Ca^2 + bound. Our results show that binding of Ca^2 + leads to energetic and dynamical changes in the virus proteins. In particular, the results suggest that binding of Ca^2 + is energetically favorable and that the mutation leads to increased fluctuations of the protein complex (especially with the calcium ions bound to the complex), which may increase the rate of genome packaging and ejection for ΦX174.     

The importance of genetic variation for the viability of small avian populations—the Seychelles Warbler and the African Marsh Warbler

Eising, C.M., Blaakmeer, K.B. & Komdeur, J. 2000. The importance of genetic variation for the viability of small avian populations—the Seychelles Warbler and the African Marsh Warbler. Ostrich 71 (1 & 2): 304–306.

Nowadays, many natural populations have to face up to problems such as genetic drift and ‘forced’ inbreeding as a result of reduced numbers and population isolation. This is thought to have a major effect on their survival. Research on the isolated Seychelles warbler showed that fitness parameters are not negatively affected by a high inbreeding frequency and a low level of heterozygosity. However, one has to be careful to translate these results to other isolated species. It is hypothesised that the effect of ‘genetic erosion’ on fitness may be less disastrous for island species, which are used to go through narrow population bottlenecks, as compared to continental species. Conservationists should be aware of these differences between species and of the fact that the long-term prospects can be reduced by lack of adaptive genetic potential.     

Molecular dynamics simulations to investigate the relationship between the structural stability and amyloidogenesis of the wild-type and N-terminal hexapeptide deletion ΔN6 β2-microglobulin

β2-Microglobulin (β2m) forms amyloid fibrils in patients undergoing long-term haemodialysis, leading to dialysis-related amyloidosis. Proteolysis of the N-terminal region of β2m results in a truncation of the six N-terminal residues (ΔN6 β2m) in ～30% of the β2m molecules extracted from ex vivo fibrils. The ΔN6 β2m has been shown to exhibit a higher tendency for self-association comparing to the wild-type (wt) β2m, particularly at neutral pH. In order to gain atomic insights into the early stages of amyloid formation of the wt and ΔN6 β2m, various molecular dynamics simulations were conducted to investigate the stability and dynamics of these two molecules at various temperatures and neutral pH in this study. Our results, in agreement with previous experimental results, indicate that the structural stability of the ΔN6 β2m is lower than that of the wt β2m. It can be attributed to fact that the removal of the N-terminal six residues results in the loss of the salt–bridge interaction between residues R3 and D59, leading to the increased solvent exposure of the K3 peptide. It further allows water molecules to destabilise the interior region of the K3 peptide, leading to the elongation between the B- and E-strands. It may further accelerate the conformational changes of the ΔN6 β2m, leading to the formation of amyloid fibrils more readily at neutral pH. Our results also suggest that the K3 peptide may be a potential initiation site of amyloid formation for the ΔN6 β2m due to its increased solvent exposure. We further suggest that fibril morphology of the ΔN6 β2m formed at neutral pH is similar to that of the wt β2m formed at low pH (1.5–3) since they adopt the similar conformation with the elongation between B- and E-strands for their partially unfolded amyloidogenic intermediates.