Stimulus analysis of BetP activation under in vivo conditions

The secondary active, Na⁺ coupled glycine betaine carrier BetP from Corynebacterium glutamicum BetP was shown to harbor two different functions, transport catalysis (betaine uptake) and stimulus sensing, as well as activity regulation in response to hyperosmotic stress. By analysis in a reconstituted system, the rise in the cytoplasmic K⁺ concentration was identified as a primary stimulus for BetP activation. We have now studied regulation of BetP in vivo by independent variation of both the cytoplasmic K⁺ concentration and the transmembrane osmotic gradient. The rise in internal K⁺ was found to be necessary but not sufficient for BetP activation in cells. In addition hyperosmotic stress is required for full transport activity in cells, but not in proteoliposomes. This second stimulus of BetP could be mimicked in cells by the addition of the amphiphile tetracaine which hints to a relationship of this type of stimulus to a change in membrane properties. Determination of the molecular activity of BetP in both cells and proteoliposomes provided experimental evidence that in proteoliposomes BetP exists in a pre-stimulated condition and reaches full activity already in response to the K⁺ stimulus.     

Stress protein synthesis by crayfish CNS tissue in vitro

Some crustacean axons remain functional for months after injury. This unusual property may require stress proteins synthesized by those neurons or provided to them by glial cells. To begin to explore this hypothesis, we examined the conditions that stimulated stress protein synthesis by crayfish CNS tissue in vitro. Incubation for 1–15 h with arsenite or at temperatures about 15°C higher than the acclimation temperature of 20°C induced transient expression of several stress proteins. The heat stress response was blocked by Actinomycin D, suggesting that synthesis of new mRNA was required. In addition, the major crayfish 66 kD stress protein and its mRNA had sequence identities with the 70 kD stress proteins of mammals. Since the crayfish stress response has much in common with that of other organisms, the unique advantages of the crayfish nervous system can be used to study the impact of stress proteins on glial and neuronal function.     

Appetitive odor learning does not change olfactory coding in a subpopulation of honeybee antennal lobe neurons

Odors elicit spatio-temporal patterns of activity in the olfactory bulb of vertebrates and the antennal lobe of insects. There have been several reports of changes in these patterns following olfactory learning. These studies pose a conundrum: how can an animal learn to efficiently respond to a particular odor with an adequate response, if its primary representation already changes during this process? In this study, we offer a possible solution for this problem. We measured odor-evoked calcium responses in a subpopulation of uniglomerular AL output neurons in honeybees. We show that their responses to odors are remarkably resistant to plasticity following a variety of appetitive olfactory learning paradigms. There was no significant difference in the changes of odor-evoked activity between single and multiple trial forward or backward conditioning, differential conditioning, or unrewarded successive odor stimulation. In a behavioral learning experiment we show that these neurons are necessary for conditioned odor responses. We conclude that these uniglomerular projection neurons are necessary for reliable odor coding and are not modified by learning in this paradigm. The role that other projection neurons play in olfactory learning remains to be investigated.     

In vivo stimulation of ovarian development in the red swamp crayfish,Procambarus clarkii (Girard), by 5-hydroxytryptamine

Summary

The possibility that biogenic amines affect ovarian development in the red swamp crayfish, Procambarus clarkii, was investigated. Females were administered 15 μg/g body weight (bw) of norepinephrine, dopamine, 5-hydroxytryptamine (5-HT) or octopamine on days 1, 5 and 10 and were sacrificed on day 15. Crayfish given 5-HT showed significant increases in ovarian index (30.5%) and oocyte size (34.0%) over the concurrent controls, while norepinephrine, dopamine and octopamine did not significantly affect either the ovarian index or oocyte size. Significantly more labeling by ¹⁴C-leucine of ovarian proteins was found in ovaries of crayfish that were injected with 5-HT in vivo, but when ovarian lobes from crayfish that had not been injected with 5-HT were incubated in vitro with 5-HT added to the incubation medium, no significant change in the level of incorporation of ¹⁴C-leucine into ovarian proteins occurred.

The 5-HT receptor blocker LY53857 (25 μg/g bw) retarded ovarian development. The 5-HT releaser fenfluramine and the 5-HT potentiator fluoxetine (both 15 μg/g bw) were also used. Crayfish given fenfluramine, fluoxetine, fenfluramine plus 5-HT or fluoxetine plus 5-HT showed significant increases of ovarian index (24.0–102.8%), oocyte size (20.0–87.4%) and in vitro ¹⁴C-leucine labeling of ovarian proteins (30.6–123.6%) over the concurrent controls. The ovaries of crayfish that received the 5-hydroxytryptaminergic neurotoxin 5,6-dihydroxytryptamme (10 μg/g bw) did not show any significant change as compared with the initial control. These findings are consistent with the hypothesis that 5-HT, which is present in the central nervous system of Procambarus clarkii, exerts its stimulatory effect on the ovary of this crayfish indirectly by triggering release of the ovary-stimulating hormone.     

Linear habitats and the nested clade analysis: an empirical evaluation of geographic versus river distances using an Ozark crayfish (Decapoda: Cambaridae)

Abstract .The nested clade analysis can be extremely useful in testing for an association between genetic variation and geography and in explaining these observed patterns in terms of historical or contemporary population processes. The strength of this method lies in its ability to test a variety of processes simultaneously under a rigorous statistical framework. Indeed, many recent studies have used the nested analysis in a wide range of terrestrial and aquatic taxa. However, it has been suggested that riverine, riparian, or coastal species may be better examined using river (or coastal) distances rather than the standard geographic (great circle) distances among populations. It is thought that the standard geographic distances may not adequately describe the actual distances involved between populations of species inhabiting these one-dimensional (riverine) habitats. Therefore, we analyzed population data from an Ozark crayfish, Orconectes luteus , to examine the effects on the results of a nested clade analysis using river distances. In most cases, the haplotypes detected in this crayfish were unique to a particular drainage or a group of neighboring drainages, indicating very little movement of individuals among drainages. Five major population groups were detected, corresponding to many of the major river drainages sampled in this study. The two types of distance analyses obtain similar results for higher-level (older) clades, but differ in many of the inferences made for lower-level (younger) clades. However, we suggest that the comparison of both types of analyses for riverine species may enhance the process of elucidating historical and contemporary population processes, especially in cases where the transfer of individuals among different drainages are involved.     

Mutual mate choice in crayfish: large body size is selected by both sexes, virginity by males only

Mate choice is often assumed to be a prerogative of females because of their putatively larger reproductive investment than males. However, recent evidence suggests that spermatogenesis is far from being limitless and that males show a high selectivity towards their mates, thus maximizing their reproductive success. We investigated mutual mate choice in the crayfish Procambarus clarkii through two experiments. The first experiment explored the effects of body size, chelar size and chelar symmetry and social status of a potential partner. In the second experiment, we asked whether this species can discriminate between partners of the same body size but with different mating status. We used a binary choice test paradigm, in which two 'targets' with opposing characteristics were simultaneously presented to a test animal, the 'chooser'. The results showed that P. clarkii males are more selective than expected. Similar to the other sex, they were significantly attracted by targets with large body sizes, but not by individuals with larger and symmetric chelae or with a dominant status. An inter-sexual difference was found in the second experiment, in which only males seemed to select virgin potential mates. The several adaptive explanations for these preferences, still under debate, are finally discussed.     

Synchronization by light of the circadian rhythm of motor activity in the crayfish

Abstract

We have studied the pattern for resetting the circadian rhythm in the spontaneous motor activity of the crayfish. Spontaneous motor activity was recorded continously at a constant temperature and under free running conditions in complete darkness. The effect of single light pulses applied at different circadian times, on the circadian rhythm of motor activity was measured in both transient stage and steady state. The results led us to construct a phase‐transition curve and phase‐response curve which were analyzed to obtain information about the oscillators which underlie the circadian rhythm of motor activity.     

Robust discriminant analysis and its application to identify protein coding regions of rice genes

Identification of protein coding regions is fundamentally a statistical pattern recognition problem. Discriminant analysis is a statistical technique for classifying a set of observations into predefined classes and it is useful to solve such problems. It is well known that outliers are present in virtually every data set in any application domain, and classical discriminant analysis methods (including linear discriminant analysis (LDA) and quadratic discriminant analysis (QDA)) do not work well if the data set has outliers. In order to overcome the difficulty, the robust statistical method is used in this paper. We choose four different coding characters as discriminant variables and an approving result is presented by the method of robust discriminant analysis.     

Properties of single voltage-gated proton channels in human eosinophils estimated by noise analysis and by direct measurement

Voltage-gated proton channels were studied under voltage clamp in excised, inside-out patches of human eosinophils, at various pHi with pHo 7.5 or 6.5 pipette solutions. H+ current fluctuations were observed consistently when the membrane was depolarized to voltages that activated H+ current. At pHi < or = 5.5 the variance increased nonmonotonically with depolarization to a maximum near the midpoint of the H+ conductance-voltage relationship, gH-V, and then decreased, supporting the idea that the noise is generated by H+ channel gating. Power spectral analysis indicated Lorentzian and 1/f components, both related to H+ currents. Unitary H+ current amplitude was estimated from stationary or quasi-stationary variance, sigmaH2. We analyze sigmaH2 data obtained at various voltages on a linearized plot that provides estimates of both unitary conductance and the number of channels in the patch, without requiring knowledge of open probability. The unitary conductance averaged 38 fS at pHi 6.5, and increased nearly fourfold to 140 fS at pHi 5.5, but was independent of pHo. In contrast, the macroscopic gH was only 1.8-fold larger at pHi 5.5 than at pHi 6.5. The maximum H+ channel open probability during large depolarizations was 0.75 at pHi 6.5 and 0.95 at pHi 5.5. Because the unitary conductance increases at lower pHi more than the macroscopic gH, the number of functional channels must decrease. Single H+ channel currents were too small to record directly at physiological pH, but at pHi < or = 5.5 near Vthreshold (the voltage at which gH turns on), single channel-like current events were observed with amplitudes 7-16 fA.     

Quantitative analysis of antennal mosaic generation in Drosophila melanogaster by the MARCM system

Mosaics have been used in Drosophila to study development and to generate mutant structures when a mutant allele is homozygous lethal. New approaches of directed somatic recombination based on FRT/FLP methods, have increased mosaicism rates but likewise multiple clones in the same individual appeared more frequently. Production of single clones could be essential for developmental studies; however, for cell-autonomous gene function studies only the presence of homozygous cells for the target recessive allele is relevant. Herein, we report the number and extension of antennal mosaics generated by the MARCM system at different ages. This information is directed to obtain the appropriated mosaic type for the intended application. By applying heat shock at 10 different developmental stages from 0-12 h to 6-7 days after egg laying, more than 50% of mosaics were obtained from 5,028 adults. Single recombinant clones appeared mainly at early stages while massive recombinant areas were observed with late treatments.     

Investigation of hatching and early post‐embryonic life of freshwater crayfish by in vitro culture,behavioral analysis,and light and electron microscopy

The late embryonic and early post‐embryonic life period of freshwater crayfish, which is the main time period of organogenesis, is poorly investigated because of the protective brooding behavior of crayfish mothers. A combination of in vitro culture, behavioral observations, and microscopic investigations of organs involved in hatching, attachment, exploration of the environment, and searching and processing of food yielded deeper insights in this important period of life. Experiments were performed with the robust parthenogenetic marbled crayfish. The following results were obtained: (1) Marbled crayfish can be raised in simple in vitro systems from 80% embryonic development to juvenile Stage 4 with up to 100% survival; (2) Hatching is prepared by chemical weakening of the egg shell and completed by levering actions of the hatchling's appendages; (3) The telson thread, a safety line that keeps the hatchling secured to the mother, is formed by secretions from the telson and the detaching inner layer of the egg case; (4) Molting Stage‐1 juveniles are secured by an anal thread that results from delayed molting of the hindgut; (5) Active attachment of the hatchlings to the maternal pleopods with their 1st pereiopods is achieved by an innate fixed action pattern; (6) In vitro, juveniles are motile from Stage 2 despite incomplete development of their balance controlling statocysts. Movement pattern and social behavior vary greatly among individuals; and (7) Feeding starts in Stage 3, when the mouthparts and the gastric mill are fully developed. Onset of feeding is innate and does not require maternal contributions. In vitro culture of the isogenic marbled crayfish is recommended for broader use in research because it enables not only time and stage‐specific sampling but also precisely timed experimental manipulations. J. Morphol., 2008. © 2008 Wiley‐Liss, Inc.     

Directionality of antennal sweeps elicited by water jet stimulation of the tailfan in the crayfish Procambarus clarkii

Summary Directionality and intensity dependence of antennal sweeps elicited by water jet stimulation of the tailfan in tethered, reversibly blinded adult and juvenile crayfish (Procambarus clarkii) were analyzed.Resting crayfish keep their antennae at about 50° symmetrically to the longitudinal body axis (Figs. 2 bottom, and 3).In adults, tailfan stimulation elicits synchronous backward sweeps of both antennae, which increase for more caudal stimulus directions (Figs. 2–4 and 5A). Directions differing by 30°–60° are significantly distinguished (Fig. 4). The mean sweep of the ipsilateral antenna significantly overrides that of the contralateral antenna for rostrolateral stimulation at 40–200 mm/s stimulus velocity and lateral to caudolateral stimulation at 40 mm/s and thus lateralization of the stimulus is revealed (Figs. 2 top, 4 and 5A). Mean antennal sweeps at a given stimulus direction and distance increase with increasing stimulus velocity (40–250 mm/s, Fig. 5A).In juveniles, the directional dependence of antennal sweeps is reduced compared to that of adults, while a similar intensity dependence is found (Fig. 5B).The pronounced directionality of the antennal response in adult crayfish vanishes and response latencies increase after reversibly covering the tailfan with a small bag or the telson with waterproof paste (Figs. 6 and 7). Thus, tailfan and especially telson mechanoreceptors play an important role in the localization of water movements elicited by predators or prey behind the crayfish.     

White noise analysis of graded response in a wind-sensitive,nonspiking interneuron of the cockroach

1. A novel approach using a Gaussian white noise as stimulus is described which allowed quantitative analysis of neuronal responses in the cercal system of the cockroach, Periplaneta americana. Cerci were stimulated by air displacement which was modulated by a sinusoidal and a white noise signal. During the stimulation, intracellular recordings were made from a uniquely identifiable, nonspiking, local interneuron which locates within the terminal abdominal ganglion. The white noise stimulation was cross-correlated with the evoked response to compute first- and second-order kernels that could define the cell's response dynamics. 2. The interneuron, cell 101, has an exceptionally large transverse neurite that connects two asymmetrical dendritic arborizations located on both sides of the ganglion. 3. The first-order Wiener kernels in cell 101 were biphasic (differentiating). The waveforms of the kernels produced by the ipsilateral and contralateral stimulations were roughly mirror images of each other: the kernels produced by wind stimuli on the side ipsilateral to the cell body of the interneuron are initially depolarized and then hyperpolarized, whereas those on the other side are initially hyperpolarized. The polarity reversal occurred along the midline of the animal's body, and no well-defined kernel was produced by a stimulus directed head on or from the tail. 4. Mean square error (MSE) between the actual response and the model prediction suggests that the linear component in cell 101 comprises half of the cell's total response (MSEs for the linear models were about 50% at preferred directions), whereas the second-order, non-linear component is insignificant. The linear component of the wind-evoked response was bandpass with the preferred frequency of 70-90 Hz. 5. Accounting for a noise, we reasonably assumed that at high frequencies the graded response in cell 101 is linearly related to a modulation of the air displacement and sensitive to the rate of change of the signal (i.e., wind velocity) and the direction of its source. It is suggested that the dynamics of the first-order kernel simply reflect the dynamics of sensory receptors that respond linearly to wind stimulation.     

Frequency-dependent membrane impedance inChara corallina estimated by Fourier analysis

Summary The white noise method of measuring membrane impedance has been applied to internodal cells ofChara corallina. Fourier analysis of a white noise transmembrane current signal and the voltage response has been used to obtain the frequency-dependent impedance of the in-series combination of the plasmalemma and tonoplast membranes. The results are similar to those of other workers who have measured membrane impedances by different techniques. At very low frequencies the equivalent capacitance of the membrane treated as an RC-circuit becomes negative, indicating a pseudoinductive effect.Membrane impedance has been measured over a range of pH values from pH 5.2 to pH 11; impedance magnitude reaches a maximum at pH 7. At interesting effect of fusicoccin at pH 11 has been observed, in which a decrease in membrane conductance occurs simultaneously with a small hyperpolarization of membrane PD.     

Sperm dispersal distances estimated by parentage analysis in a brooding scleractinian coral

Within populations of brooding sessile corals, sperm dispersal constitutes the mechanism by which gametes interact and mating occurs, and forms the first link in the network of processes that determine specieswide connectivity patterns. However, almost nothing is known about sperm dispersal for any internally fertilizing coral. In this study, we conducted a parentage analysis on coral larvae collected from an area of mapped colonies, to measure the distance sperm disperses for the first time in a reef‐building coral and estimated the mating system characteristics of a recently identified putative cryptic species within the Seriatopora hystrix complex (ShA; Warner et al. 2015). We defined consensus criteria among several replicated methods (colony 2.0, cervus 3.0, mltr v3.2) to maximize accuracy in paternity assignments. Thirteen progeny arrays indicated that this putative species produces exclusively sexually derived, primarily outcrossed larvae (mean t_m = 0.999) in multiple paternity broods (mean r_p = 0.119). Self‐fertilization was directly detected at low frequency for all broods combined (2.8%), but comprised 23% of matings in one brood. Although over 82% of mating occurred between colonies within 10 m of each other (mean sperm dispersal = 5.5 m ± 4.37 SD), we found no evidence of inbreeding in the established population. Restricted dispersal of sperm compared to slightly greater larval dispersal appears to limit inbreeding among close relatives in this cryptic species. Our findings establish a good basis for further work on sperm dispersal in brooding corals and provide the first information about the mating system of a newly identified and abundant cryptic species.     

Time series analysis of climate‐related factors and their impact on a red‐listed noble crayfish population in northern Sweden

1. Global climate change is predicted to raise water temperatures and alter flow regimes in northern river systems. Climate‐related factors might have profound impacts on survival, reproduction and distribution of freshwater species such as red‐listed noble crayfish (Astacus astacus) in its northern limit of distribution. 2. In this study, noble crayfish capture data over 27 years from the River Ljungan, Sweden, were examined. Time series of catch per unit effort (CPUE) were analysed in relation to the North Atlantic Oscillation (NAO) index, regional weather factors and water flow. CPUE was assumed to reflect differences in population size. Two models were constructed to explore the relative impact of different climate factors and density dependence on variability of catch sizes. 3. The most parsimonious model for CPUE time series, explaining 72% of the variance in CPUE, included density‐dependent population dynamics of the crayfish and climate or weather factors. The specific effect from density dependence in the model was 37%, while climate/weather factors contributed with 35% of the variation. The most important climate/weather factors are variations in NAO index and water flow. Temperature did not improve the model fit to capture data. 4. The best model was evaluated using independent data sets that gave correlations between model predictions and data ranging from 0.44 to 0.53. The density dependence shows a time lag of 1 year, while climate variables show time lags from 2 to 6 years in relation to CPUE, indicating effects on different cohorts of the crayfish population. 5. Both density dependence and climatic factors play a significant role in population fluctuations of noble crayfish. A 6‐year time lag for NAO index is puzzling but indicates that some as yet unidentified factors related to NAO might act on the juvenile stages of the population. Water flow shows a 2‐year lag to the CPUE, and high flow in the river may affect adult survival. The reasons for fluctuation of crayfish catches in response to climate need to be identified, and fishing quotas should consider the different cohort sizes because of variation in environment. Reintroduction programmes for crayfish need to consider effects of climate change when designing management strategies.     

Multivariate analysis of noise in genetic regulatory networks

Stochasticity is an intrinsic property of genetic regulatory networks due to the low copy numbers of the major molecular species, such as, DNA, mRNA, and regulatory proteins. Therefore, investigation of the mechanisms that reduce the stochastic noise is essential in understanding the reproducible behaviors of real organisms and is also a key to design synthetic genetic regulatory networks that can reliably work. We use an analytical and systematic method, the linear noise approximation of the chemical master equation along with the decoupling of a stoichiometric matrix. In the analysis of fluctuations of multiple molecular species, the covariance is an important measure of noise. However, usually the representation of a covariance matrix in the natural coordinate system, i.e. the copy numbers of the molecular species, is intractably complicated because reactions change copy numbers of more than one molecular species simultaneously. Decoupling of a stoichiometric matrix, which is a transformation of variables, significantly simplifies the representation of a covariance matrix and elucidates the mechanisms behind the observed fluctuations in the copy numbers. We apply our method to three types of fundamental genetic regulatory networks, that is, a single-gene autoregulatory network, a two-gene autoregulatory network, and a mutually repressive network. We have found that there are multiple noise components differently originating. Each noise component produces fluctuation in the characteristic direction. The resulting fluctuations in the copy numbers of the molecular species are the sum of these fluctuations. In the examples, the limitation of the negative feedback in noise reduction and the trade-off of fluctuations in multiple molecular species are clearly explained. The analytical representations show the full parameter dependence. Additionally, the validity of our method is tested by stochastic simulations.     

Distinct error rates for reference and nonreference genotypes estimated by pedigree analysis

Errors in genotype calling can have perverse effects on genetic analyses, confounding association studies, and obscuring rare variants. Analyses now routinely incorporate error rates to control for spurious findings. However, reliable estimates of the error rate can be difficult to obtain because of their variance between studies. Most studies also report only a single estimate of the error rate even though genotypes can be miscalled in more than one way. Here, we report a method for estimating the rates at which different types of genotyping errors occur at biallelic loci using pedigree information. Our method identifies potential genotyping errors by exploiting instances where the haplotypic phase has not been faithfully transmitted. The expected frequency of inconsistent phase depends on the combination of genotypes in a pedigree and the probability of miscalling each genotype. We develop a model that uses the differences in these frequencies to estimate rates for different types of genotype error. Simulations show that our method accurately estimates these error rates in a variety of scenarios. We apply this method to a dataset from the whole-genome sequencing of owl monkeys (Aotus nancymaae) in three-generation pedigrees. We find significant differences between estimates for different types of genotyping error, with the most common being homozygous reference sites miscalled as heterozygous and vice versa. The approach we describe is applicable to any set of genotypes where haplotypic phase can reliably be called and should prove useful in helping to control for false discoveries.     

Microhabitat use by foraging white-clawed crayfish (<Emphasis Type="Italic">Austropotamobius pallipes</Emphasis>) in stream pools in the NE Iberian Peninsula

The white-clawed crayfish (Austropotamobius pallipes) is an endangered species across most of its distribution range, and information on its ecological requirements is needed to implement effective conservation measures. Its habitat use has been studied in different areas and at various spatial scales. However, being a nocturnal species, there is scarce information on its habitat selection during foraging periods. In this work we analyse nocturnal habitat use of white-clawed crayfish in pools of a small stream in the northeastern Iberian Peninsula at two different scales: (1) microhabitat selection and (2) pool characteristics. Large crayfish showed a clear positive selection for deeper microhabitats, a selection pattern that was weaker for medium-sized crayfish and absent for small ones. On the other hand, crayfish of all sizes avoided cobble and boulder microhabitats and positively selected fine substrate and more exposed microhabitats. Crayfish abundance in pools was positively influenced by pool area, pool depth and the availability of fine substrates, especially silt. While studies on white-clawed crayfish habitat use have often stressed the importance of rough substrates as crayfish refuge, our results show that fine substrates are positively selected by foraging crayfish of all size classes and promoted active crayfish abundance in pools. These apparently contradictory results may be due to the differences in microhabitat preferences exhibited by active and inactive crayfish. Thus, our results help to better complete the picture of white-clawed crayfish habitat requirements.