The finite number of global motion patterns available to symmetric protein complexes

In PDB, more than half of the entries are structure complexes and of these complexes, most are symmetric, composed of identical subunits. Complex formation is the way through which larger structures and even molecular machines are assembled and built in nature. In this work, we apply group theory and carry out a comprehensive study of the global motion patterns of protein complexes of various symmetries. The work presents for the first time a comprehensive list of all the symmetric, aesthetically pleasing, global motion patterns available to complexes of cyclic, dihedral, tetrahedral, or octahedral symmetry. Our results clearly demonstrate that complexes with the same symmetry will have the same global motion patterns and thus may function in a similar way, and that there are only a finite number of global motion patterns available to symmetric complexes as the number of protein symmetry groups is effectively finite. The work complements our current understanding of the principle of complex formation that has been mostly structure‐based by providing novel dynamics‐based insights. Furthermore, as dynamics is closely tied to function, these motion patterns can provide global insights into the general functional mechanisms of protein complexes.     

Are kea prosocial?

Prosocial behaviour is widespread in humans, but evidence for its occurrence in other species is mixed. We presented a parrot species, the kea (Nestor notabilis) with a series of experiments to test whether they exhibit prosocial tendencies. Across the first round of testing, in our first condition, two of the four kea acted prosocially, as they preferred to choose a prosocial token which rewarded both themselves and a partner, rather than a token that rewarded only themselves. Three of the four kea then showed a preference for the prosocial token in a second condition where they alternated taking turns with a partner. However, no kea showed a decrease in the third yoked control condition in which the experimenter replicated the token choice made by the partner in the previous alternating trials. This yoked condition was used to dissociate truly reciprocal behaviour, whereby the actor made choices based on their partner's choices, from a response to the amount of rewards conferred to the partner. Finally, three of the four kea continued to choose the prosocial token in the fourth asocial control condition where no partner was present. However, in round two of testing, one kea changed its token choices to a similar pattern to that expected if kea are prosocial, in that it preferred the prosocial token in the initial condition, showed a trend for the prosocial token when turns were alternated, but chose at chance in the yoked and asocial conditions. This study therefore found no evidence of spontaneous reciprocity in kea but further testing is required before we can conclude that kea are not capable of prosocial behaviour at all.     

Effects of Nocturnal Shiftwork on Mood States of Student Nurses

Daily mood changes were monitored over successive 24-h periods using the Profile of Mood States (POMS) (3) to assess the effect of nocturnal shiftwork on mood. Twenty-three student nurses, age range 19-24 years, were studied throughout their first experience of nocturnal shiftwork. The POMS was administered over four complete solar days during a 12-week period that included an 8-week block of night work. Five POMS dimensions displayed circadian rhythmicity. vigor-activity; fatigue-inertia; confusion-bewilderment; friendliness; and total-mood-disturbance. These five dimensions were sensitive to changes in living patterns, showing phase shifts in their circadian rhythms when subjects alternated between diurnal and nocturnal living patterns. The dimensions were also observed to be sensitive to adjustment to two different nocturnal shiftwork schedules. The subjects who worked “four on, three off showed similar phase shifts to the subjects who worked “eight on, seven off,” suggesting that mood adjustment takes place by the fourth night of a rotation of nights. The “commitment” of the students to the nocturnal living pattern was thought to have a bearing on the adaptation of the students to the nocturnal shifts, as regards mood.     

The effect of in-season, high-intensity interval training in soccer players

The effects of in-season, high-intensity interval training on professional male soccer players' running performances were investigated. Twenty-two subjects participated in 2 consecutive training periods of 10 weeks. The first period was considered a control period and was compared with a period where 2 high-intensity interval training exercises were included in the usual training program. Intermittent runs consisted of 12-15 runs lasting 15 seconds at 120% of maximal aerobic speed alternated with 15 seconds of rest. Sprint repetitions consisted of 12-15 all-out 40-m runs alternated with 30 seconds of rest. Results from the high-intensity interval training have shown that maximal aerobic speed was improved (+8.1 +/- 3.1%; p < 0.001) and that the time of the 40-m sprint was decreased (-3.5 +/- 1.5%; p < 0.001), whereas no change in either parameters were observed during the control period. This study shows that improvements in physical qualities can be made during the in-season period.     

Soft and sticky development: some underlying reasons for microarchitectural pattern convergence

Surface sculpture of spores, pollen and other walled microscopic organisms commonly resembles patterns seen elsewhere in nature. These patterns are often species specific and of significant use in taxonomic study, particularly so in the fossil record where other data may be minimal. It can be argued that patterning, which must be governed to some extent by genotype, could simply reflect other natural patterns as a result of physical and chemical interaction during development. But does this diminish the view that patterning can often perform important biological functions? With examples drawn from fossil and living walled structures, we analyse the complex relationship between genetic constraints, construction mechanism and biological function, and we conclude that similar function may often result in similar pattern, perhaps further enhanced by similar aspects of development. The genetic complement, by way of selection, ‘learns’ to repeat the pattern, but each pattern creation mechanism retains a ‘personal signature’ reflecting its evolutionary history. With this new perspective in mind, we assess the potential implications in the study of Palaeozoic microfossils when many different groups are first developing surface patterning.     

LIFE HISTORIES OF BLIDINGIA MINIMA (CHLOROPHYCEAE), ESPECIALLY SEXUAL REPRODUCTION1

Blidingia minima (Näg. ex Kütz.) Kylin from Muroran, Hokkaido, Japan, has been shown to exhibit four patterns of life history in culture. Sexual reproduction, reported fully for the first time in the genus, occurs in two of them. I. An isomorphic-heteromorphic complex in which erect, tubular sporophytes alternate with dioecious gametophytes of the same forms, with the irregular production by both phases of discoid or pulvinate (pincushion-like) microthalli capable of both sexual and asexual reproduction. II. An alternation of heteromorphic phases in which an erect, tubular sporophyte alternated irregularly with a gametophytic microthallus. III. An asexual alternation of heteromorphic phases in which an erect, tubular frond alternates irregularly with a microthallus by means of quadriflagellate zoospores. IV. An asexual, monophasic life cycle in which erect, tubular fronds are perpetuated by quadriflagellate zoospores. The first pattern occurred in spring populations from one of three sites. The second occurred in populations from two sites. The third and fourth occurred in all populations tested. The life history of Blidingia minima from Muroran is similar to that of Kornmannia zostericola from Muroran.     

Rhythmic swimming activity in Anguilla anguilla glass eels: Synchronisation to water current reversal under laboratory conditions

Synchronisation of swimming activity to water current reversal every 6.2 h was tested in the European glass eel (Anguilla anguilla L.). When presented with a change in water current direction, glass eels exhibited rhythmic patterns of activity with a period close to the tidal one. Glass eels began to swim with the current and then alternated between positive and negative rheotaxis after each change in the water current direction. Results are discussed in relation to the flood tidal transport theory. Following synchronisation to current reversal, glass eels subjected to constant conditions displayed a weak rhythmic activity suggesting that locomotor behaviour might, in the wild, synchronise to several environmental cues related to the tide. Results obtained with different densities also suggest that social cues might improve the synchronisation.     

Light-driven periodic changes in urocanase activity of a heterotrophic bacterium

Summary Urocanase activity in Pseudomonas putida cells showed periodic changes corresponding to a light-dark cycle. Apparent interconversion of the active and inactive forms of urocanase was accomplished by photoactivation by nearultraviolet light and by dark thermal inactivation. The purified enzyme exhibited similar behavior. This system suggests a possible molecular basis for an hour-glass timer. Photoinactivation by light of 290 nm alternated with photoactivation at 340 nm also generated regular changes in urocanase activity.     

Design and folding of dimeric proteins

In a similar way in which the folding of single-domain proteins provides an important test in the study of self-organization, the folding of homodimers constitutes a basic challenge in the quest for the mechanisms that are the basis of biological recognition. Dimerization is studied by following the evolution of two identical 20-letter amino acid chains within the framework of a lattice model and using Monte Carlo simulations. It is found that when design (evolution pressure) selects few, strongly interacting (conserved) amino acids to control the process, a three-state folding scenario follows, where the monomers first fold forming the halves of the eventual dimeric interface independently of each other, and then dimerize ("lock and key" kind of association). On the other hand, if design distributes the control of the folding process on a large number of (conserved) amino acids, a two-state folding scenario ensues, where dimerization takes place at the beginning of the process, resulting in an "induced type" of association. Making use of conservation patterns of families of analogous dimers, it is possible to compare the model predictions with the behavior of real proteins. It is found that theory provides an overall account of the experimental findings.     

Effects of a synchronizer phase-shift on circadian rhythms in response of mice to ethanol or ouabain

The percentage of mice dying from a toxic dose of ethanol or ouabain was determined at 4-hour intervals during the first 3 days after inversion of an LD(12:12) lighting regimen. In comparison to unshifted control animals at similar stages of the synchronizer schedule, spans of relative advantage alternated with spans of relative disadvantage due to a gradual phase-shift of the circadian susceptibility rhythm. Overall mortality, determined for an integral number of day, was not obviously affected by the regimen-shift.Supported by grants from the United States Public Health Service (5-K6-GM-13,981), NASA (NGR-24-005-006) and the U.S. Air Force (F29600-69-C-0011).     

Pattern discrimination by the honeybee (Apis mellifera): training on two pairs of patterns alternately

Pattern discrimination in the honeybee was studied by training alternately with two different pairs of patterns. Individually marked bees made a forced choice from a fixed distance in a standard Y-choice maze for a reward of sugar solution. Bees were trained, first on one pair of patterns for 10min then on a second pair, and so on, alternately between the two pairs. The pairs of patterns were selected to test the hypothesis that bees have a limited number of parallel mechanisms for the detection and discrimination of certain generalized global features. If this is so, it might be expected that each channel could process one pair of patterns simultaneously, but two pairs of patterns that are processed by the same channel would interfere with each other during the learning process. Features tested were: average orientation of edges, radial and tangential edges based on a symmetry of three or six, the position of a black spot, and the exchange of black and white. The bees fail to learn when the two alternated pairs of patterns offer the same feature, and they discriminate when the pairs offer two different features.     

The evolution of life-history traits in parasitic and free-living platyhelminthes: a new perspective

Parasite life histories have been assumed to be shaped by their particular mode of existence. To test this hypothesis, we investigate the relationships between life-history traits of free-living and parasitic platyhelminthes. Using phylogenetically independent contrasts we examine patterns of interspecific covariation in adult size, progeny volume, daily fecundity, total reproductive capacity, age at first reproduction and longevity. The correlations obtained indicate a similar causal chain of life history variations for free-living and parasitic platyhelminthes. These results suggest that increased longevity favours delayed reproduction. Furthermore, growth pattern determines adult body size and age at maturity. For platyhelminthes, whether free-living or parasitic, the total reproductive capacity is found to be directly determined by the size of the worm. Within this group the parasitic way of life does not seem to influence the basic patterns of life history evolution. Received: 20 September 1997 / Accepted: 1 March 1998     

Spatial patterns in the distribution of damselfishes on a fringing coral reef

Damselfishes are an important element of the fauna of coral reefs. This study describes spatial patterns in the distribution of 15 species of damselfishes at Lizard Island, northern Great Barrier Reef (GBR). The aim of the work was to identify the spatial scales at which major changes in the composition and abundance of the fauna occurred. These patterns were then compared with previous studies in an attempt to determine if distributions followed general patterns at a range of localities. The assemblage found at Lizard Island was similar to that of reefs in the central GBR. The most important changes in the composition of the fauna occurred among reef zones. Shallow zones (the reef flat and crest) were dominated by herbivorous species while planktivorous and omnivorous species were most abundant in deeper zones (the reef slope). Densities of herbivorous damselfishes in shallow reef zones at Lizard Island averaged 45.5 individuals per 80 m², a value comparable to densities found in similar zones on reefs in the central and southern GBR and at one locality in the Caribbean. Comparisons of relative distributions suggested that abundant species tend to be widely distributed among zones and habitats, while rare species have restricted distributions at Lizard Island. However, computer simulation of the sampling program suggested that the ability of our study to describe the distribution patterns of rare species was limited, despite intensive sampling. Correlations between breadth of distribution and abundance may have occurred simply because rare species were less likely to be recorded within a transect. Our results suggest that it will be difficult to compare the distribution patterns of species among studies. Furthermore, the interpretation of relative patterns of distribution at a single locality in terms of ecological specialization or partitioning may first require an assessment of the ability of the sampling program to accurately record spatial patterns.     

Intrapopulation variation in macro tooth wear patterns—a case study from Igloolik,Canada

The pattern of human tooth wear—the way it varies between teeth in the mouth—is crucial to our understanding of important questions in archeology and paleoanthropology, such as the contrasts in diet and behavior between Neanderthals and early modern humans in Europe and Asia, or with the adoption of agriculture in the Americas. Little is known, however, about the way in which wear patterns develop with increasing age or the way in which they differ between males and females. One explanation is that few living people show the high rates of tooth wear seen worldwide throughout the preindustrial archaeological record. The study described here investigates the macroscopic pattern of tooth wear in a unique group of known age and sex dental casts from living Canadian Inuit from Igloolik. The results show that the Igloolik people possessed a pattern of extremely heavy anterior tooth wear, relative to the first molar and the other posterior teeth, which is attributed to the use of the anterior teeth in cultural practices as well as the extreme and marginal environments in which they lived. Heavy anterior tooth wear was established at an early age and maintained throughout life; statistically significant differences were found between the wear patterns of males and females and are explained in terms of sexual division of labor within the community. This study highlights the need to understand both intra‐ and interpopulation variation in tooth wear patterns when interpreting patterns in past human groups. Am J Phys Anthropol, 2012. © 2012 Wiley Periodicals, Inc.     

Dynamics of populations with individual variation in dispersal on bounded domains

Most classical models for the movement of organisms assume that all individuals have the same patterns and rates of movement (for example, diffusion with a fixed diffusion coefficient) but there is empirical evidence that movement rates and patterns may vary among different individuals. A simple way to capture variation in dispersal that has been suggested in the ecological literature is to allow individuals to switch between two distinct dispersal modes. We study models for populations whose members can switch between two different nonzero rates of diffusion and whose local population dynamics are subject to density dependence of logistic type. The resulting models are reaction–diffusion systems that can be cooperative at some population densities and competitive at others. We assume that the focal population inhabits a bounded region and study how its overall dynamics depend on the parameters describing switching rates and local population dynamics. (Traveling waves and spread rates have been studied for similar models in the context of biological invasions.) The analytic methods include ideas and results from reaction–diffusion theory, semi-dynamical systems, and bifurcation/continuation theory.     

Explore the Functional Connectivity between Brain Regions during a Chemistry Working Memory Task

Previous studies have rarely examined how temporal dynamic patterns, event-related coherence, and phase-locking are related to each other. This study assessed reaction-time-sorted spectral perturbation and event-related spectral perturbation in order to examine the temporal dynamic patterns in the frontal midline (F), central parietal (CP), and occipital (O) regions during a chemistry working memory task at theta, alpha, and beta frequencies. Furthermore, the functional connectivity between F-CP, CP-O, and F-O were assessed by component event-related coherence (ERCoh) and component phase-locking (PL) at different frequency bands. In addition, this study examined whether the temporal dynamic patterns are consistent with the functional connectivity patterns across different frequencies and time courses. Component ERCoh/PL measured the interactions between different independent components decomposed from the scalp EEG, mixtures of time courses of activities arising from different brain, and artifactual sources. The results indicate that the O and CP regions’ temporal dynamic patterns are similar to each other. Furthermore, pronounced component ERCoh/PL patterns were found to exist between the O and CP regions across each stimulus and probe presentation, in both theta and alpha frequencies. The consistent theta component ERCoh/PL between the F and O regions was found at the first stimulus and after probe presentation. These findings demonstrate that temporal dynamic patterns at different regions are in accordance with the functional connectivity patterns. Such coordinated and robust EEG temporal dynamics and component ERCoh/PL patterns suggest that these brain regions’ neurons work together both to induce similar event-related spectral perturbation and to synchronize or desynchronize simultaneously in order to swiftly accomplish a particular goal. The possible mechanisms for such distinct component phase-locking and coherence patterns were also further discussed.     

ON THE INDEPENDENCE OF SYSTEMATICS

Abstract— Before the publication of On the Origin of Species the standing patterns of natural history—common plan, homology, ontogenetic parallelism, and the hierarchy of groups — were taken as indications of a biological order that had not yet been understood. Darwin covered all of these in chapter 13 of the Origin , arguing that his theory was the first to provide a reasonable explanation for the existence of such patterns. Since Darwin took these relations to be established by previous biology, and used them as evidence for the explanatory power of his theory, he was clearly of the opinion that they were independent of that theory. Although several modern figures have argued to the contrary, it seems that Darwin was right. The patterns listed above are recoverable from observation without reference to evolutionary theory, which theory may then be applied to provide an account of the processes by which they may have come about. That aspect of systematics concerned with the identification of the empirical patterns evidently constitutes a study prior to and independent of theories of process.     

Optimization of oxygen tolerance extension in rats by intermittent exposure.

Optimization of oxygen tolerance extension by intermittent exposure was studied in groups of 20 rats exposed to systematically varied patterns of alternating oxygen and normoxic breathing periods at 4.0, 2.0, and 1.5 ATA. Oxygen periods of 20, 60, and 120 min were alternated with normoxic intervals that provided oxygen-to-normoxia ratios of 4:1, 2:1, 1:1, and 1:3. In general, median survival times had nearly linear relationships to increasing normoxic intervals with oxygen period held constant. Exceptions occurred at 4.0 and 2.0 ATA where a 5-min normoxic interval was too short for adequate recovery even with a 20-min oxygen period, and an oxygen period of 120 min was too long even with a normoxic interval of 30 min. These exceptions did not occur at 1.5 ATA. Survival time for many intermittent exposure patterns was equivalent to that for continuous exposure to an oxygen pressure definable as a time-weighted average of the alternating oxygen and normoxia periods. However, this predictive method underestimated the degree of protection achieved by several of the intermittent exposure patterns, especially those performed at 4.0 ATA. Results provided guidance for selection of intermittent exposure patterns for direct evaluation in humans breathing oxygen at 2.0 ATA. Definition of intermittent exposure patterns and conditions that produced prominent gains in oxygen tolerance can also facilitate the performance of future experiments designed to study potential mechanisms for oxygen tolerance extension by intermittent exposure. Heat shock and oxidation-specific stress proteins that are induced by exposure to oxidant injury are suggested for emphasis in such investigations.     

Synchronization of the circannual reproductive rhythm of the ewe by discrete photoperiodic signals

Although many species display endogenous circannual rhythms of biological activity that are synchronized by day length, the specific photoperiodic requirements for synchronizing such rhythms are not established for any species. We tested the hypothesis that the circannual reproductive rhythm of sheep can be synchronized by exposure to just one or two discrete blocks of photoperiodic information each year. Ewes were pinealectomized to prevent their ability to transduce photoperiodic information into altered reproductive neuroendocrine activity. During the 53/4 yr following pinealectomy, specific photoperiodic signals were restored for discrete periods of time via replacement of 24-h patterns of melatonin, the pineal hormone that transmits photic information to the reproductive neuroendocrine axis. The ewes were kept in a 12-mo photoycycle that alternated between short (8L:16D) and long (16L:8D) days every 6 mo and that was 6 mo out of phase with the geophysical year. Pineal-intact control ewes exhibited synchronous annual reproductive cycles. Noninfused pinealectomized control ewes did not exhibit synchronous cycles. Pinealectomized ewes infused with alternating 70-day blocks of short- and long-day patterns of melatonin every 6 mo for the first 21/2 yr of the experiment exhibited synchronous annual reproductive cycles that were 6 mo out of phase with those of ewes maintained outdoors. This synchrony persisted when the frequency of the melatonin treatment was reduced to just one 70-day block of a long-day pattern of melatonin each 365 days. Cycle period was 368 +/- 3 days; standard deviation of the date of onset of reproductive induction averaged only 3 days. Our study provides the first direct evidence that a single block of photoperiodic information a year can synchronize a circannual rhythm.