The effect of progressive hypoxia on school structure and dynamics in Atlantic herring Clupea harengus

The effect of progressive hypoxia on the structure and dynamics of herring (Clupea harengus) schools in laboratory conditions was investigated. The length, width and depth of schools of about 20 individuals were measured from video recordings to test the hypothesis that during hypoxia fish schools change their shape and volume. School shape (calculated as the ratios of length/depth, width/depth and length/width) did not change significantly during hypoxia. School length, width, depth, area and volume were all significantly increased at 20% oxygen saturation. Volume, area and width were more sensitive to hypoxia; volume and width were also increased at 25% and area at 30% oxygen saturation. The degree of position changing (shuffling) of individuals within the school was also analysed. Shuffling in normoxia was observed to occur largely through 'O-turn' manoeuvres, a 360( degrees )turn executed laterally to the school that allowed fishes in the front to move to the back. O-turn frequency during normoxia was 0.69 O-turns fish(-1) min(-1) but significantly decreased with hypoxia to 0.37 O-turns fish(-1) min(-1) at 30% oxygen saturation. Shuffling was also investigated by measuring the persistence time of individual herring in leading positions (i.e. the first half of the school). No significant changes occurred during hypoxia, indicating that the decrease in O-turn frequency does not affect shuffling rate during hypoxia, and that position shuffling in hypoxic conditions is mainly due to overtaking or falling back by individual fishes. School integrity and positional dynamics are the outcome of trade-offs among a number of biotic factors, such as food, predator defence, mating behaviour and various physical factors that may impose certain limits. Among these, our results indicate that oxygen level modulates schooling behaviour. Oxygen alters whole-school parameters at oxygen saturation values that can be encountered by herring in the field, indicating that oxygen availability is an important factor in the trade-offs that determine school volume. An increase in school volume in the wild may increase the oxygen available to each individual. However, shuffling rate is not affected by hypoxia, indicating that the internal dynamics of positioning is the result of the balance of other factors, for example related to the nutritional state of each individual fish as suggested by previous studies.     

The three-dimensional structure of schools in the minnow, Phoxinus phoxinus (L.)

A photographic technique is described for determining the three-dimensional position of fish schooling in front of a mirror in a flow tank. School structure is discussed in terms of the distance, horizontal bearing, and elevation of nearest neighbours. Nearest neighbour distances were measured snout-to-snout. A technique of analysis is described which considers the probability distribution of nearest neighbours in space. At speeds of flow 0 to 0·125 metres per second it was possible to show that Phoxinus, a facultative schooler, tended to maintain a school structure as previously reported for obligate schooling species. The structure was present only in a dynamic statistical sense and not in the sense of a rigid crystal lattice. Minnows maintained themselves at approximately 0·9 of their body length from each other under normal conditions and the bearings of neighbour fish suggested an attempt to maintain an optimum packing at this distance. At high speeds of flow the school structure tended to break up as fish sought areas of refuge from the current. All minnow schools were ellipsoidal in shape. The strategic and tactical methods by which schooling fish derive anti-predator advantage are discussed in relation to the school structure.     

Conflict and co-operation in White Cloud Mountain minnow schools

Schooling fish do not always behave co-operatively, and conflict is particularly evident when individuals compete for limited resources. In White Cloud Mountain minnows, Tanichrhys albonubes , aggression is associated with the defence of potential spawning sites. Agonistic encounters between males are more prevalent when available habitat is reduced and when the number of spawning sites (patches of weed) is restricted. Conversely, competition diminishes when the fish are in a potentially threatening situation, e.g. when they are exploring a new environment.     

Seasonal dynamics of the component community structure of parasites of the minnow Phoxinus phoxinus (L.)

The material represented by 75 specimens of minnow of the age 2-2(+) was collected according to the standard technique in the Chovju River (tributary of the Vychegda River, a region of the settlement Nizniy Chov, district of Syktyvkar town) during the period June-September 2000. The quantitative estimation of the structure of the component parasite communities was performed by calculating errors of the equation of regression for each species group separately, with subsequent summarizing of means of errors by all parasite groups comprising the community (Dorovskikh, 2001 6; 2002 B). In order to have a possibility to get data complementing each other, the calculation of variety indexes and other indexes have been made for metazoan parasites only and for the whole community, including the protozoan parasites. In both cases, i.e. considering only metazoan parasites and the whole composition of parasite species, three states of the component parasite community have been recognised: the formed community (June), the community in destroying (July and August), the community in the process of formation (September). In the course of working on the total species composition we recorded the beginning of community destroying on 30th of June, and the beginning of community formation in August. Considering only the metazoan parasites, the community is defined (after: Pugachev, 1999) as the mature (balanced) one in June, while in July, August and September, it was unmature (off-balance) by its characteristics. Regarding the protozoan parasites, the community in June, August and September was characterized as the mature one based on indices of parasite biomass, and as unripe one based on the number of parasite individuals; however in July, both groups of indices allowed to refer it to the unripe state. However, these unripe states are essentially different. In July, it is the result of dieing out the parasites of the past generation; in August and September, it is the result of the appearances of new generations. Therefore we recognise three states of parasite community named above. Considering the whole species composition of parasites we noted the greater difference of index values based on the parasite specimen numbers and their conventional biomass, that was in the case of the metazoan parasites only. It is particularly noticeable in the middle of the June, in the period of the formed community. This fact, together with high errors of the equations of regression and the presence of the high number of Apiosoma, points to the disturbance in the structure of component parasite community in the minnow from the Chovju River. This is easily explicable, because the Chovju River is the polluted reservoir, and pollution comes from agricultural fields, Verhny-Chov settlement, pigsties and cow-sheds. The pollution is a seasonal factor here. The most powerful pollution was noted at May-June, and then it decreased along the beginning of rains in the end of August; in September it increased again. It is important to point out that the monitoring of the metazoan parasites only allows to reveal the general dynamics of the community during the period of observation, but does not allow to catch the beginning of its destroying and developing and to notice possible disturbances in the community structure caused by pollution of reservoirs, particularly, if this pollution is a seasonal factor as in the Chovju River. Three named states of the component community of the fish parasites take place in other periods of year than this observed in the intestional parasite communities of fish helminths of the temperate climate zone. The developing of parasite communities of the intestinal helminths of the Anguilla anguilla in England (Kennedy, 1997) and of Leuciscus idus from the Rybinsk reservoir (Zhohov, 2003) starts in the beginning of summer. In May, their species diversity is minimal and in August is maximal. In conditions of the middle stream of the Vychegda River, the species diversity of parasite community associated with the minnow is maximal in June and minimal in August, when it only begins developing.     

The effect of acidification in enclosures on the biomass and population size structure of Bosmina longirostris

An in situ enclosure experiment was performed from June to September, 1982, in Lake O'Woods, West Virginia (pH7.0), to examine the effects of acidification on the Bosmina longirostris population. Treatments were two control enclosures and two enclosures acidified from an initial pH of 7.2 to pH 4.2 over a 44 day period, using H₂SO₄. B. longirostris was not adversely affected by the acidification. In fact, its abundance, biomass, and mean body size increased in the acid treatment, as compared withe control. This positive response was probably not a direct consequence of the altered water chemistry, but instead may have occured due to reduced competition for food, and also reduced predation pressure. Acidification resulted in a decreased abundance of other herbivores, and elimination of the dominant carnivore, Mesocyclops edax.     

The genetic structure and microdistribution of shoals of Phoxinus phoxinus, the European minnow

Efficient foraging and a reduction in predation risk have been proposed as reasons for shoal formation. Some behaviours in cyprinid shoals are at first sight altruistic (e.g. predator inspection behaviour, reactions to alarm substance), such that kin selection may have been involved in their evolution. If shoaling behaviour does evolve through kin selection, then genetic differentiation is expected to be greater between shoals than within shoals. Such a hypothesis was tested here by examining shoal integrity and the relatedness of individuals within and between shoals in the European minnow, Phoxinus phoxinus , using nuclear and mitochondrial DNA markers. The breeding structure of 13 minnow shoals collected from Dorset and North Wales, U.K., was examined using allozymes. Genetic affinity within and between shoals was tested using mitochondrial DNA and multi-locus DNA fingerprinting. Shoals consisted of a random assortment of allozyme genotypes, shoal members did not share the same maternal mtDNA lineages and DNA fingerprint profiles were as varied within shoals as between them. The data indicate that it is unlikely that kin selection occurs in P. phoxinus and there is no apparent relationship between shoaling behaviour and genotype distribution in this species.     

Nucleosomes structure and dynamics: effect of CHAPS

Dynamics of nucleosomes and spontaneous unwrapping of DNA are fundamental property of the chromatin enabling access to nucleosomal DNA for regulatory proteins. Probing of such dynamics of nucleosomes performed by single molecule techniques revealed a large scale dynamics of nucleosomes including their spontaneous unwrapping. Dissociation of nucleosomes at low concentrations is a complicating issue for studies with single molecule techniques. In this paper, we tested the ability of 3-[(3-Cholamidopropyl)dimethylammonio]-l-propanesulfonate (CHAPS) to prevent dissociation of nucleosomes. The study was performed with mononucleosome system assembled with human histones H2A, H2B, H3 and H4 on the DNA substrate containing sequence 601 that provides the sequencespecific assembly of nucleosomes. We used Atomic Force Microscopy (AFM) to directly identify nucleosomes and analyze their structure at the nanometer level. These studies showed that in the presence of CHAPS at millimolar concentrations, nucleosomes, even at sub-nanomolar concentrations, remain intact over days compared to a complete dissociation of the same nucleosome sample over 10 min in the absence of CHAPS. Importantly, CHAPS does not change the conformation of nucleosomes as confirmed by the AFM analysis. Moreover, 16 µM CHAPS stabilizes nucleosomes in over one hour incubation in the solution containing as low as 0.4 nM in nucleosomes. The stability of nucleosomes is slightly reduced at physiological conditions (150 mM NaCl), although the nucleosomes dissociate rapidly at 300 mM NaCl. The sequence specificity of the nucleosome in the presence of CHAPS decreased suggesting that the histone core translocates along the DNA substrate utilizing sliding mechanism.     

The effect of sample size in studies of soil microbial community structure

Replicate soil samples of 0.01, 0.1, 0.25, 1.0 and 10.0 g were taken from a single, large, homogenized sample from a field maintained as continuous meadow. The samples were processed for direct enumeration of bacterial cells and community structure assays by DGGE analysis of PCR-amplified 16S-rDNA fragments from whole community extracts. The goal was to determine the sample size or size range that produced the most consistent results (i.e., mean values) and the lowest variance. Enumeration data were analyzed by ANOVA, and the community composition fingerprints were analyzed by discriminant analysis (DA). Acceptable results were obtained for sample sizes from 0.1 to 1.0 g for both enumeration and community fingerprinting, but the size that yielded the best results for both measures was 0.25 g. The results suggest that for well homogenized silt loam soils with moderate organic matter concentrations, this sample size should produce high quality consistent results. For soils that differ in organic concentrations or clay content, a reconnaissance survey similar to the present examination is recommended.     

The effect of hydrological and morphometric parameters of temporary waterbodies on the structure and abundance dynamics of crustacean zooplankton

The effects of hydrological conditions and morphometry of the temporary waterbodies on the structure, abundance, and biomass of crustacean zooplankton are described. This study was performed in the southeast of the European part of Russia. The existence duration (hydrological regime) of the temporary waterbodies has the most profound effect on the zooplankton patterns. A significant effect was observed for the number of dominant species, the zooplankton biomass, the calanoid-cyclopoid ratio, and the Shannon index. The brackish lagoons were characterized by the highest biodiversity and abundance and the lowest values of these parameters were found in the steppe puddles and waterbodies of terraces above the flood-plain in the river valleys.     

The effect of the trp repressor from Escherichia coli on the structure and dynamics of dA20dT20

We have determined the effect of the tryptophan (trp) repressor from Escherichia coli on the structure and dynamics of dA20dT20. The structure was determined using time-dependent nuclear Overhauser effects and spin-lattice relaxation times. The deoxyribose conformation is near C3' endo for the thymine residues, and a mixture of about 30% C3' endo and 70% C2' endo for the adenine residues. The glycosidic torsion angles are -50 degrees for T and -60 degrees for A. The roll is 20 degrees and the propellor twist is about 29 degrees. The conformation is consistent with recent calculations (Rao, K. and Kollman, P.A. (1985) J. Am. Chem. Soc. 107, 1507-1511). The rate constant for exchange of the imino protons is similar to that usually found for AT base-pairs, with an activation energy of 20 +/- 2 kcal/mol, and an activation entropy of 17 +/- 7 cal/mol per K. The repressor greatly retards the exchange of imino protons, and the activation energy increases to 38 kcal/mol. There are small changes in the structure of the DNA on forming the complex, with the adenine and thymidine residues becoming more similar in conformation.     

Molecular dynamics calculations on peroxidases: the effect of calcium ions on protein structure

 Molecular dynamics (MD) calculations were performed on two peroxidases, lignin peroxidase (LiP) and horseradish peroxidase (HRP), in the presence of the two endogenous calcium ions. The resulting averaged structures were compared to the structures obtained in the absence of the calcium ions. The overall protein folding was not affected by the presence or the lack of the calcium ions, while the active site was perturbed. In particular, on the distal side, a sizeable rearrangement of the distal histidine was observed in the absence of the calcium ions. These structural rearrangements are critically discussed with respect to the enzymatic mechanism. Received: 15 November 1995 / Accepted: 1 March 1996     

The effect of cross linking density on the mechanical properties and structure of the epoxy polymers: molecular dynamics simulation

Recently, great attention has been focused on using epoxy polymers in different fields such as aerospace, automotive, biotechnology, and electronics, owing to their superior properties. In this study, the classical molecular dynamics (MD) was used to simulate the cross linking of diglycidyl ether of bisphenol-A (DGEBA) with diethylenetriamine (DETA) curing agent, and to study the behavior of resulted epoxy polymer with different conversion rates. The constant-strain (static) approach was then applied to calculate the mechanical properties (Bulk, shear and Young’s moduli, elastic stiffness constants, and Poisson’s ratio) of the uncured and cross-linked systems. Estimated material properties were found to be in good agreement with experimental observations. Moreover, the dependency of mechanical properties on the cross linking density was investigated and revealed improvements in the mechanical properties with increasing the cross linking density. The radial distribution function (RDF) was also used to study the evolution of local structures of the simulated systems as a function of cross linking density.     

The effect of visibility on territory size and shape

Although several authors have suggested that visibility affectsterritorial behavior, there have been few systematic studiesof this phenomenon. Here we review five ways that visibilitymight influence the use and defense of space in territorialanimals, and then we discuss a laboratory study on the effectof visibility on territory size and shape. Juvenile lizardswere allowed to establish territories in two habitats identicalexcept for a visual obstacle that bisected one of the two habitats.Lizards in the habitat with good visibility defended compactterritories of a size comparable to those in the field. In contrast,those in the low-visibility situation avoided territories thatincluded the visibility barrier and instead chose either verysmall or highly elongated territories. Territories with goodvisibility probably cost less to defend than those with poorvisibility; territory owners may also prefer high-visibilityterritories because they reduce predation risk or increase foragingsuccess.     

The effect of water on protein dynamics

Neutron diffraction and spectroscopy were applied to describe the hydration and dynamics of a soluble protein and a natural membrane from extreme halophilic Archaea. The quantitative dependence of protein motions on water activity was clearly illustrated, and it was established that a minimum hydration shell is required for the systems to access their functional resilience, i.e. a dynamics state that allows biological activity.     

The effect of podophyllotoxin on microtubule dynamics

We have investigated the effects of podophyllotoxin on the dynamic properties of microtubules assembled from pure tubulin dimer. Excess podophyllotoxin causes the complete disassembly of microtubules, through formation of a tubulin-GTP-podophyllotoxin ternary complex with a dissociation rate constant of 160 s-1 at 37 degrees C, similar to that found upon extensive isothermal dilution in this buffer system. Addition of substoichiometric concentrations of podophyllotoxin causes partial disassembly of microtubules through production of an equivalent amount of the ternary complex. Microtubule length measurements and incorporation of [3H]GTP-tubulin dimer show that podophyllotoxin can suppress the dynamic instability of tubulin dimer microtubules and that it acts substoichiometrically in so doing. We interpret the action of substoichiometric podophyllotoxin on microtubule ends in terms of effects on interconversion of growing and shrinking microtubules in a dynamic system in which tubulin-GTP-podophyllotoxin is kinetically analogous to tubulin-GTP in addition and to tubulin-GDP in dissociation. The ability to suppress dynamic instability may be one way in which drugs such as podophyllotoxin, acting at relatively low concentrations, are able to arrest cell growth and development in a selective way, without necessarily affecting the integrity of the major part of the cytoskeletal microtubule network.     

The influence of substrate quality and stream size on wood decomposition dynamics

Woody materials decayed more rapidly in a first order stream than in larger streams in eastern Quebec, Canada. The rate of annual mass loss (k) was highest (k=1.20) for alder wood chips in a first order stream and lowest (k=0.04) for black spruce wood chips in a ninth order stream. Decay rates for woody materials in a first order stream were inversely related to their initial lignin to nitrogen ratios. In larger streams, decay rates of woody materials were inversely related to their initial lignin concentrations. A number of quantifiable relationships were found to exist between the initial lignin and nitrogen contents of woody materials and the nitrogen dynamics of decaying wood.     

The influence of environmental factors on the dynamics of the size and spatial structure of the chamois (Rupicapra rupicapra caucasica) population on the Caucasian Reserve

The size and structure of the chamois (Rupicapra rupicapra caucasica) population as well as the influence of anthropogenic factors on it were studied on the Caucasian Reserve (Western Caucasus). The negative effect of the snow cover, the thickness of which differed from the usual level, is shown. The effect of winters with thick snow cover is confirmed by the relation between these factors and the proportion of yearlings in the population one year after the winter. An increased death rate of animals in winters with a deep snow cover is observed in the case when their density exceeds the optimal one. Wolf predation does not affect the chamois population on the reserve. The number of wolves increases with an increase in the chamois population density to 15–20 ind./1000 ha. The adverse impact of humans on the chamois population is manifested in the regions with motor roads. The chamois, as compared to the deer, suffers from poachers to a lesser degree because it inhabits inaccessible areas and its trophy value is low.