Opponent and nonopponent contributions to the zebrafish electroretinogram using heterochromatic flicker photometry

While some lower vertebrates, such as zebrafish, do not appear to possess anatomically separate pathways of processing visual information (such as M-pathways and P-pathways), it is believed that separate processing of the visual stimulus (such as luminance and chromatic processing) is a basic requirement of vertebrate vision. In this study, spectral sensitivity functions were obtained from electroretinogram responses to heterochromatic flicker photometry stimuli at several flicker rates, including a low flicker rate (2 Hz), in an attempt to predominantly stimulate chromatic processes and a high flicker rate (16 Hz), in an attempt to predominantly stimulate luminance processes. In addition, chromatic adaptation was used to isolate and examine the temporal properties of the different cone-type contributions to the electroretinogram response. Spectral sensitivity functions based on responses to heterochromatic stimuli of a low flicker rate appeared to receive both opponent and nonopponent contributions; however, when the stimulus flicker rate was high, spectral sensitivity appeared to be a function of only nonopponent mechanisms. Also, the differences in cone contributions to the spectral sensitivity functions across the different flicker rates appear to be related to the temporal properties of the cone contributions to the electroretinogram response.     

Perception of heterochromatic flicker by honeybees: a behavioural study

Freely flying honeybees were trained to discriminate a stimulus consisting of two alternating chromatic lights (heterochromatic flicker) from a steady mixture of the same two lights, using 3 different pairs of lights: blue-UV, UV-green, and green-UV. With each light pair, training to the heterochromatic flicker was conducted at several flicker frequencies, using experimentally naive bees in each training. In subsequent tests, the trained bees were given a choice between the two lights that constituted the flicker, presented steady, as well as between either of them and the steady mixture. We find that bees trained to particular frequencies of heterochromatic flicker prefer one of the component lights over the other as well as over the steady mixture, suggesting that the colour they perceive in the heterochromatic flicker to which they have been trained is shifted in the direction of one of the lights contained in the flicker. The colour shift occurs at flicker frequencies that depend on the pair of lights used. We propose that the shift is generated by an effect similar to the Brücke-Bartley phenomenon known from human vision. This effect is based on the enhancement of the photoreceptors' response upon onset of stimulation, causing an intermittent light to appear brighter than a steady light of identical physical intensity. We propose that the degree of enhancement might differ among the 3 spectral classes of photoreceptor, causing the colour perceived in a heterochromatic flicker to differ from that perceived in a steady mixture of its two light components.     

Ecological and morphological shifts in Lake Michigan fishes: glimpses of the ghost of competition past

Synopsis Both historical patterns and recent evidence of resource partitioning and complementarity within the Lake Michigan fish community provide circumstantial evidence for interspecific competition. But competition is difficult to document in the field without controlled experimentation. In Lake Michigan, controlled experiments on competition within the fish community are nearly impossible, but we still need to understand the interactions among the dominant fishes. For this purpose, I have relied upon hypothesis-based field observation, natural experiments in the field and designed laboratory experiments to evaluate competitive interactions. Resource use patterns and trophic morphology of the bloater, Coregonus hoyi, a native cisco, from samples taken before alewife, Alosa pseudoharengus, became abundant (1960) were compared to more recent data (1979–80). After the alewife density increase, bloaters had significantly fewer and shorter gill rakers. This suggests a morphological shift toward greater benthic foraging efficiency in response to high abundances of an efficient pelagic planktivore, alewife. Resource use comparisons suggested that bloaters now shift from pelagic zooplanktivory to benthic habitats and diets at least two years earlier in their life history than they did before alewife became abundant. This evidence, albeit not experimental, provides strong support for the importance of competition in the structure of the current Lake Michigan fish community.In Lake Michigan, seasonal thermal habitat compression can pack fish into a narrow thermal zone across the lake bottom, leading to increased habitat overlap, reduced prey availability and fish diets containing fewer and smaller prey. Thermal habitat compression, which can occur intermittently through the season, may create competitive bottlenecks which help maintain the observed resource partitioning among these fishes.     

The human erythrocyte ghost: A new experimental model for studying adenosine transport

Previous work on adenosine transport has always had problems with the interference of adenosine metabolism, due to its high metabolic rate and because the enzymes involved are consistently present in most tissues. A new experimental model for studying adenosine transport in human erythrocyte ghosts is presented in this work: Human erythrocyte ghosts were sealed in the presence of erythro-3(2-hydroxynonyl)adenine and P1-P5-di(adenosine)5′-pentaphosphate, inhibitors of adenosine deaminase and adenosine kinase, respectively. These ghosts proved to lack adenosine metabolism when incubated in [U-¹⁴C]adenosine at 10 μm concentration at 37 °C for 60 min. Ghosts were 99.4% sealed in the correct orientation and had constant intracellular water volume. With these characteristics, the erythrocyte ghost preparation has many advantages for studying adenosine transport without adenosine metabolism interference. Adenosine transport was studied following the technique of 24., 25. Experiments to study Zero-trans influx and efflux, equilibrium exchange, and infinite-trans influx and efflux are presented. Adenosine transport did not behave linearly in any of these experimental procedures. Adenosine basic kinetic constants, calculated according to the procedure of Lieb and Stein, were R_1→-2 = 4.1 × 10⁻⁴, R_2→-1 = 3.97 × 10⁻⁴, R_ee = 1.94 × 10⁻⁴, R_oo = 6.08 × 10⁻⁴, K_1→-2 = 125.67 μm, andK_2→-1 = 84.36 μm. Lieb and Stein rejection criteria were used to distinguish a simple pore from a simple carrier. The data accumulated indicate that adenosine transport is carried out by a system that satisfies the criteria used for the simple carrier model. Asymmetric behavior was observed indicating lower affinity of the carrier for adenosine influx, although V_max values for influx and efflux were similar.     

Phase shifts and the square-wave illusion.

When observers view a vertical triangle-wave luminance profile, they often report a square-wave illusion with a depth component, resembling a corrugated surface. Alternate bars seem to be in front of or behind adjacent bars and the surface appears to be illuminated from the right or left. These perspectives alternate with continuous viewing. One explanation for this illusion stems from the notion of instability among phase-selective mechanisms. Two experiments (1 and 3) were designed to determine whether systematic phase shifts introduced between the fundamental and the odd harmonics of the waveform would lead to a systematic bias of the illusion. The results indicated that a significant bias occurred when a phase shift as small as 9 deg was introduced, and that the bias from the phase shifts was more powerful than previous reports of drift-induced bias. There was a highly significant effect of direction of phase shift and the corresponding perceived direction of illumination. Another experiment (2) was designed to determine if illusional cues within the phase-shifted profiles aided phase discrimination. The results indicated that experienced subjects, presumably using cues within the profiles, discriminated between the stimuli significantly better than did naive subjects. These data support the role of phase in the square-wave illusion, but they also raise questions about the role of contrast changes in local regions of the stimulus.     

Predicting climate-induced range shifts: model differences and model reliability

Predicted changes in the global climate are likely to cause large shifts in the geographic ranges of many plant and animal species. To date, predictions of future range shifts have relied on a variety of modeling approaches with different levels of model accuracy. Using a common data set, we investigated the potential implications of alternative modeling approaches for conclusions about future range shifts and extinctions. Our common data set entailed the current ranges of 100 randomly selected mammal species found in the western hemisphere. Using these range maps, we compared six methods for modeling predicted future ranges. Predicted future distributions differed markedly across the alternative modeling approaches, which in turn resulted in estimates of extinction rates that ranged between 0% and 7%, depending on which model was used. Random forest predictors, a model‐averaging approach, consistently outperformed the other techniques (correctly predicting >99% of current absences and 86% of current presences). We conclude that the types of models used in a study can have dramatic effects on predicted range shifts and extinction rates; and that model‐averaging approaches appear to have the greatest potential for predicting range shifts in the face of climate change.     

Phase shifts in coral reef communities and their ecological significance

Many coral reefs around the world have degraded to a degree that their present intrinsic value and utility are greatly reduced: (mass coral mortality followed by algal invasions; local depletions of reef fisheries; deficit of reef accretion compared to physical and biological erosion). Though we can sometimes identify proximal causes (outbreaks of coral predators and eroders; over-fishing; habitat destruction), we do not have a good understanding of how population, community and ecosystem structure and function differ in degraded from un-degraded reefs. The deficiencies in our understanding limit our ability to interpret the long-term significance of reef degradation, and therefore to develop scientifically based plans for conservation and management of reefs.A particular course of action, or lack of action, based on uncritical acceptance of any of the various views of temporal variability can lead to further deterioration of specific reefs. None of these views — that reefs are either inherently robust, inherently fragile, or inherently resilient — is true over all time-space scales. This presentation reviews various models and case studies which suggest that reefs can be knocked precipitously or move slowly from one phase (coral-dominated) to another (coral-depleted and/or algal dominated). Transitions in the other direction (recovery) involve changes (e.g. succession) in populations and communities (of all reef-associated biota, not just sessile benthos), and in reef function (e.g. community metabolism, trophodynamics) which are of great intrinsic interest but only poorly understood.     

A new model for chemical shifts of amide hydrogens in proteins

We propose a new computational model to predict amide proton chemical shifts in proteins. In addition to the ring-current, susceptibility and electrostatic effects of earlier models, we add a hydrogen-bonding term based on density functional calculations of model peptide–peptide and peptide–water systems. Both distance and angular terms are included, and the results are rationalized in terms of natural bond orbital analysis of the interactions. Comparison to observed shifts for 15 proteins shows a significant improvement over existing structure-shift correlations. These additions are incorporated in a new version of the SHIFTS program.     

A polymorphism for heterochromatic supernumerary segments in Chorthippus parallelus

Supernumerary heterochromatic segments have been found in the S₈ bivalent of two populations of Chorthippus parallelus. These segments occur both in the heterozygous and the homozygous states. In both populations the frequencies of basic homozygotes, structural heterozygotes and structural homozygotes conform to a Hardy-Weinberg distribution. In the structurally heterozygous and homozygous states there is a significant increase in the chiasma frequency of the bivalents other than the S₈ itself. It is suggested that the adaptive role of these supernumerary segments can be explained in terms of this interchromosomal effect.To Professor J. Seiler in commemoration both of his 80th birthday and his many distinguished years of cytological service.     

A simple model for determining affinity from irreversible thermal shifts

Thermal denaturation (Tm) data are easy to obtain; it is a technique that is used by both small labs and large‐scale industrial organizations. The link between ligand affinity (K _D) and ΔTm is understood for reversible denaturation; however, there is a gap in our understanding of how to quantitatively interpret ΔTm for the many proteins that irreversibly denature. To better understand the origin, and extent of applicability, of a K _D to ΔTm correlate, we define equations relating K _D and ΔTm for irreversible protein unfolding, which we test with computational models and experimental data. These results suggest a general relationship exists between K _D and ΔTm for irreversible denaturation.     

The ghost of unbalanced species distribution data in geographical model predictions

Unbalanced samples are considered a drawback in predictive modelling of species' potential habitats, and a prevalence of 0.5 has been extensively recommended. We argue that unbalanced species distribution data are not such a problem from a statistical point of view, and that good models can be obtained provided that the right predictors and cut-off to convert probabilities into presence/absence are chosen. The effects of unbalanced prevalence should not be confused with those of low-quality data affected by false absences, low sample size, or unrepresentativeness of the environmental and spatial gradient. Finally, we point out the necessity of greater research effort aimed at improving both the quality of training data sets, and the processes of validating and testing of models.     

Translocations between Eu- and heterochromatic chromosomes,and spermatocytes lacking a heterochromatic set in male mealy bugs

In male mealy bugs the chromosomes of paternal origin become heterochromatic (H) early in embryogeny while those of maternal origin remain euchromatic (E). First instarPseudococcus obscurus Essig males which were irradiated with 3000 r of X-rays carried translocations between E and H chromosomes [T(E;H)'s] in their spermatocytes. In the T(E;H)'s the border between the E and H segments was usually quite sharp, but occasionally short E segments may have become either partially or completely heterochromatic. During the second meiotic division the E and H sets normally segregate to opposite poles. The T(E;H)'s often formed bridges in AII and TII, but in most of the cells they did succeed in reaching one of the poles. The segregation of the T(E;H)'s depended on the relative size of their E and H segments. When the E and H segments were of the same size, the T(E;H)'s segregated more often with the E chromosomes, even though the latter have been observed to be attached to their pole with fewer spindle fibers. Thirty-five of the 173 males analyzed had sectors in their testes which lacked an H set. The number of cysts per sector suggested that each sector was derived from a single irradiated cell. The karyotypes observed in some of the sectors indicated that the lack of an H set was the result of reversal of heterochromatization and not due to the loss of the H set and the endoduplication of the E set. Most of the cells lacking an H set divided normally during the first meiotic division. The second division, however, was abortive and resulted in the production of diploid sperm. Two possibilities for the origin of spermatocytes lacking an H set are considered: (i) that these spermatocytes resulted from X-ray induced reversal of heterochromatization in spermatogonia, and (ii) that these spermatocytes originated from presumptive cyst wall cells whose H set had undergone reversal prior to the irradiation.Supported by grant GB 6745 from the National Science Foundation, Washington, D. C.     

Spectrin: the ghost in the machine

It has long been speculated that spectrin, the actin crosslinking and molecular scaffold protein, is involved in the development of apicobasal polarity in epithelia. While spectrins can undoubtedly influence the protein content of specific membrane domains, recent genetic evidence indicates that this activity is not necessary for the establishment or maintenance of this axis. Instead, these studies point to critical roles in tissue stability and morphogenesis. A possible role in cellular contractility is highlighted in this review.     

Phase shifts and the role of herbivory in the resilience of coral reefs

Cousin Island marine reserve (Seychelles) has been an effectively protected no-take marine protected area (MPA) since 1968 and was shown in 1994 to support a healthy herbivorous fish assemblage. In 1998 Cousin Island reefs suffered extensive coral mortality following a coral bleaching event, and a phase shift from coral to algal dominance ensued. By 2005 mean coral cover was <1%, structural complexity had fallen and there had been a substantial increase in macroalgal cover, up to 40% in some areas. No clear trends were apparent in the overall numerical abundance and biomass of herbivorous fishes between 1994 and 2005, although smaller individuals became relatively scarce, most likely due to the loss of reef structure. Analysis of the feeding habits of six abundant and representative herbivorous fish species around Cousin Island in 2006 demonstrated that epilithic algae were the preferred food resource of all species and that macroalgae were avoided. Given the current dominance of macroalgae and the apparent absence of macroalgal consumers, it is suggested that the increasing abundance of macroalgae is reducing the probability of the system reverting to a coral dominated state.     

A probabilistic model for secondary structure prediction from protein chemical shifts

Protein chemical shifts encode detailed structural information that is difficult and computationally costly to describe at a fundamental level. Statistical and machine learning approaches have been used to infer correlations between chemical shifts and secondary structure from experimental chemical shifts. These methods range from simple statistics such as the chemical shift index to complex methods using neural networks. Notwithstanding their higher accuracy, more complex approaches tend to obscure the relationship between secondary structure and chemical shift and often involve many parameters that need to be trained. We present hidden Markov models (HMMs) with Gaussian emission probabilities to model the dependence between protein chemical shifts and secondary structure. The continuous emission probabilities are modeled as conditional probabilities for a given amino acid and secondary structure type. Using these distributions as outputs of first‐ and second‐order HMMs, we achieve a prediction accuracy of 82.3%, which is competitive with existing methods for predicting secondary structure from protein chemical shifts. Incorporation of sequence‐based secondary structure prediction into our HMM improves the prediction accuracy to 84.0%. Our findings suggest that an HMM with correlated Gaussian distributions conditioned on the secondary structure provides an adequate generative model of chemical shifts. Proteins 2013; © 2012 Wiley Periodicals, Inc.     

Noise-triggered regime shifts in a simple aquatic model

We examined the effects of random fluctuations and diffusion on regime shifts in bistable aquatic ecosystems, using a simple two-component reaction–diffusion model with nutrients and phytoplankton. The corresponding mean-field model generates two stable attractors: one is a nutrient-dominated (ND) state or a clear-water state, and the other is a phytoplankton-dominated (PD) state or a turbid-water state. According to our simulations of the reaction–diffusion model without fluctuations, either of two stable states can be dominant corresponding to the given parameters and the configuration of two states, meaning that the long-term coexistence of these two states is difficult. The dominant state expands gradually eliminating the other non-dominant one, which results in the homogeneous distribution of the dominant state in the whole lake. Further simulations including the effects of temporally changing fluctuations show that the regime shifts driven by external noise proceed even within a bistable region, which complicates the detection of hysteresis in real aquatic ecosystems.     

Intermediate heterochromatic zones in Triturus (Amphibia: Caudata)

Employment of the C-banding procedure disclosed the presence of slightly stained bands in some chromosome regions of several Triturus species. These regions have been previously described in other organisms as 'grey C-bands'. Possible explanations for the presence of these bands in Triturus karyotypes are discussed.     

Phase shifts and the stability of macroalgal communities on Caribbean coral reefs

Caribbean coral reefs are widely thought to exhibit two alternate stable states with one being dominated by coral and the other by macroalgae. However, the observation of linear empirical relationships among grazing, algal cover and coral recruitment has led the existence of alternate stable states to be questioned; are reefs simply exhibiting a continuous phase shift in response to grazing or are the alternate states robust to certain changes in grazing? Here, a model of a Caribbean forereef is used to reconcile the existence of two stable community states with common empirical observations. Coral-depauperate and coral-dominated reef states are predicted to be stable on equilibrial time scales of decades to centuries and their emergence depends on the presence or absence of a bottleneck in coral recruitment, which is determined by threshold levels of grazing intensity and other process variables. Under certain physical and biological conditions, corals can be persistently depleted even while increases in grazing reduce macroalgal cover and enhance coral recruitment; only once levels of recruitment becomes sufficient to overwhelm the population bottleneck will the coral-dominated state begin to emerge. Therefore, modest increases in grazing will not necessarily allow coral populations to recover, whereas large increases, such as those associated with recovery of the urchin Diadema antillarum, are likely to exceed threshold levels of grazing intensity and set a trajectory of coral recovery. The postulated existence of alternate stable states is consistent with field observations of linear relationships between grazing, algal cover and coral recruitment when coral cover is low and algal exclusion when coral cover is high. The term ‘macroalgal dominated’ is potentially misleading because the coral-depauperate state can be associated with various levels of macroalgal cover. The term ‘coral depauperate’ is preferable to ‘macroalgal dominated’ when describing alternate states of Caribbean reefs.