Evolution of Tandemly Repeated Sequences: What Happens at the End of an Array?

Tandemly repeated sequences are a major component of the eukaryotic genome. Although the general characteristics of tandem repeats have been well documented, the processes involved in their origin and maintenance remain unknown. In this study, a region on the paternal sex ratio (PSR) chromosome was analyzed to investigate the mechanisms of tandem repeat evolution. The region contains a junction between a tandem array of PSR2 repeats and a copy of the retrotransposon NATE, with other dispersed repeats (putative mobile elements) on the other side of the element. Little similarity was detected between the sequence of PSR2 and the region of NATE flanking the array, indicating that the PSR2 repeat did not originate from the underlying NATE sequence. However, a short region of sequence similarity (11/15 bp) and an inverted region of sequence identity (8 bp) are present on either side of the junction. These short sequences may have facilitated nonhomologous recombination between NATE and PSR2, resulting in the formation of the junction. Adjacent to the junction, the three most terminal repeats in the PSR2 array exhibited a higher sequence divergence relative to internal repeats, which is consistent with a theoretical prediction of the unequal exchange model for tandem repeat evolution. Other NATE insertion sites were characterized which show proximity to both tandem repeats and complex DNAs containing additional dispersed repeats. An ``accretion model' is proposed to account for this association by the accumulation of mobile elements at the ends of tandem arrays and into ``islands' within arrays. Mobile elements inserting into arrays will tend to migrate into islands and to array ends, due to the turnover in the number of intervening repeats. Received: 18 August 1997 / Accepted: 18 September 1998     

Modeling the Effect of Prey Refuge on a Ratio-Dependent Predator–Prey System with the Allee Effect

The extinction of species is a major threat to the biodiversity. The species exhibiting a strong Allee effect are vulnerable to extinction due to predation. The refuge used by species having a strong Allee effect may affect their predation and hence extinction risk. A mathematical study of such behavioral phenomenon may aid in management of many endangered species. However, a little attention has been paid in this direction. In this paper, we have studied the impact of a constant prey refuge on the dynamics of a ratio-dependent predator–prey system with strong Allee effect in prey growth. The stability analysis of the model has been carried out, and a comprehensive bifurcation analysis is presented. It is found that if prey refuge is less than the Allee threshold, the incorporation of prey refuge increases the threshold values of the predation rate and conversion efficiency at which unconditional extinction occurs. Moreover, if the prey refuge is greater than the Allee threshold, situation of unconditional extinction may not occur. It is found that at a critical value of prey refuge, which is greater than the Allee threshold but less than the carrying capacity of prey population, system undergoes cusp bifurcation and the rich spectrum of dynamics exhibited by the system disappears if the prey refuge is increased further.     

Does Fire Influence the Landscape-Scale Distribution of an Invasive Mesopredator?

Predation and fire shape the structure and function of ecosystems globally. However, studies exploring interactions between these two processes are rare, especially at large spatial scales. This knowledge gap is significant not only for ecological theory, but also in an applied context, because it limits the ability of landscape managers to predict the outcomes of manipulating fire and predators. We examined the influence of fire on the occurrence of an introduced and widespread mesopredator, the red fox (Vulpes vulpes), in semi-arid Australia. We used two extensive and complimentary datasets collected at two spatial scales. At the landscape-scale, we surveyed red foxes using sand-plots within 28 study landscapes – which incorporated variation in the diversity and proportional extent of fire-age classes – located across a 104 000 km² study area. At the site-scale, we surveyed red foxes using camera traps at 108 sites stratified along a century-long post-fire chronosequence (0–105 years) within a 6630 km² study area. Red foxes were widespread both at the landscape and site-scale. Fire did not influence fox distribution at either spatial scale, nor did other environmental variables that we measured. Our results show that red foxes exploit a broad range of environmental conditions within semi-arid Australia. The presence of red foxes throughout much of the landscape is likely to have significant implications for native fauna, particularly in recently burnt habitats where reduced cover may increase prey species’ predation risk.     

What Makes Vocalisation Frequency an Unreliable Signal of Body Size in Birds? A Study on Black Swans

In many animal species, the frequency (pitch) of vocalisations correlates negatively with body size and may thus signal competitive ability. However, this relationship is absent in other species. Understanding why this difference exists across species may help to explain some of the diversity of vocal communication systems. We assessed whether vocalisation frequency signals body size in black swans (Cygnus atratus), and how this is affected by (i) variation in frequency within individuals and (ii) size variation across individuals. Frequency was correlated with body size and mass, with slopes close to the allometry expected if the birds were maximising sound radiation, but the explained variation in frequency was low. Within‐individual variation in vocalisation frequency was greater in male than female swans, and the reliability of frequency as a signal of size in males was correspondingly lower. A review of the literature on the relationship between the frequency of avian vocalisations and body size also showed smaller effect sizes for more variable vocalisations (birdsongs), than for simpler vocalisations. Vocalisation frequency was more reliably correlated with body size when the sexes were pooled (creating a larger range of variation in size) than when the relationship was examined for either sex separately, although male and female data followed the same allometric line. These results show that variation in frequency within individuals and low variation in size across individuals reduce the reliability of vocalisation frequency as a signal of body size, which helps to understand differences among species in the signal value of vocalisation frequency.     

Is the Effect of Aerobic Exercise on Cognition a Placebo Effect?

A number of studies and meta-analyses conclude that aerobic fitness (walking) interventions improve cognition. Such interventions typically compare improvements from these interventions to an active control group in which participants engage in non-aerobic activities (typically stretching and toning) for an equivalent amount of time. However, in the absence of a double-blind design, the presence of an active control group does not necessarily control for placebo effects; participants might expect different amounts of improvement for the treatment and control interventions [1]. We conducted a large survey to explore whether people expect greater cognitive benefits from an aerobic exercise intervention compared to a control intervention. If participants expect greater improvement following aerobic exercise, then the benefits of such interventions might be due in part to a placebo effect. In general, expectations did not differ between aerobic and non-aerobic interventions. If anything, some of the results suggest the opposite (e.g., respondents expected the control, non-aerobic intervention to yield bigger memory gains). These results provide the first evidence that cognitive improvements following aerobic fitness training are not due to differential expectations.     

What changed the demography of an introduced population of an herbivorous lady beetle?

1. The population dynamics of an introduced population of Epilachna niponica (Lewis) (Coleoptera: Coccinellidae) was investigated for a 7-year period following its introduction to a site outside of its natural range. A population from Asiu Experimental Forest was introduced to Kyoto University Botanical Garden, 10 km south of its natural distribution.
2. Arthropod predation was much lower in the introduced than in the source population. As a result of the lower predation in the Botanical Garden, larvae reached densities five times higher than in the Asiu Forest and host plants were frequently defoliated. Food shortage caused larval deaths from starvation and increased dispersal.
3. The density of the introduced population was much more variable than that of the source population. The variation in population density in both the introduced and source populations is limited by density-dependent reduction in fecundity and female survival. However, variation in the introduced population's density was increased due to host plant defoliation that resulted in overcompensating density-dependent mortality. In years with high larval density plants were defoliated and this increased adult mortality during the prehibernation period. Besides, the density-dependent regulatory mechanisms that produce population stability were weaker in the introduced population than in the source population.     

What is the function of MSP-I on the malaria merozoite?

In the absence o f any clear enzymatic activity, attempts to define the role of merozoite surface protein-I have focused mainly on analysis of its structure, on its interaction with the immune system and on binding assays. But how does our knowledge of the structure o f this protein contribute to functional studies? Are there data to suggest a role in the evasion of effective host immune responses? Binding studies have used the intact protein or various fragments and peptides, but do such approaches provide a reliable indicator of function? In this article, Tony Holder and Mike Blackman review these areas.     

Predator Inspection Behaviour in a Characin Fish: an Interaction between Chemical and Visual Information?

Recent evidence suggests that predator inspection behaviour by Ostariophysan prey fishes is regulated by both the chemical and visual cues of potential predators. In laboratory trials, we assessed the relative importance of chemical and visual information during inspection visits by varying both ambient light (visual cues) and predator odour (chemical cues) in a 2 × 2 experimental design. Shoals of glowlight tetras (Hemigrammus erythrozonus) were exposed to a live convict cichlid (Archocentrus nigrofasciatus) predator under low (3 lux) or high (50 lux) light levels and in the presence of the odour of a cichild fed tetras (with an alarm cue) or swordtails (Xiphophorus helleri, with an alarm cue not recognized by tetras). Tetras exhibited threat‐sensitive inspection behaviour (increased latency to inspect, reduced frequency of inspection, smaller inspecting group sizes and increased minimum approach distance) towards a predator paired with a tetra‐fed diet cue, regardless of light levels. Similar threat‐sensitive inspection patterns were observed towards cichlids paired with a swordtail‐fed diet cue only under high light conditions. Our data suggest that chemical cues in the form of prey alarm cues in the diet of the predator, are the primary source of information regarding local predation risk during inspection behaviour, and that visual cues are used when chemical information is unavailable or ambiguous.     

Auxins or Sugars: What Makes the Difference in the Adventitious Rooting of Stored Carnation Cuttings?

Cold storage of cuttings is frequently applied in the vegetative propagation of ornamental plants. Dianthus caryophyllus was used to study the limiting influences of auxin and sugars on adventitious root formation (ARF) in cuttings stored at 5°C. Carbohydrate levels during storage were modulated by exposing cuttings to low light or darkness. The resulting cuttings were treated (or not) with auxin and planted, and then ARF was evaluated. Carbohydrate levels in the cuttings were monitored and the influence of light treatment on indole-3-acetic acid (IAA) and zeatin (Z) in the basal stem was investigated. Dark storage for up to 4 weeks increased the percentage of early rooted cuttings and the final number and length of adventitious roots, despite decreased sugar levels in the stem base. Light during cold storage greatly enhanced sugar levels, particularly in the stem base where the Z/IAA ratio was higher and ARF was lower than observed in the corresponding dark-stored cuttings. Sugar levels in nonstored and dark-stored cuttings increased during the rooting period, and auxin application enhanced the accumulation of sugars in the stem base of nonstored cuttings. Auxin stimulated ARF most strongly in nonstored, less so in light-stored, and only marginally in dark-stored cuttings. A model of auxin-sugar interactions in ARF in carnation is proposed: cold storage brings forward root induction and sink establishment, both of which are promoted by the accumulation of auxin but not of sugars, whereas high levels of sugars and probably also of cytokinins act as inhibitors. Subsequent root differentiation and growth depend on current photosynthesis.     

What Makes Socio-ecological Systems Robust? An Institutional Analysis of the 2,000 Year-Old Ifugao Society

Scholars have often puzzled over why ancient socio-ecological systems (SES) have collapsed or survived overtime. This paper examines the case of the 2,000-year old Ifugao SES in the northern Philippines and the contemporary challenges they now face. Five observations can be drawn. First, the Ifugao case does not fit some of the conventional theoretical explanations for the collapse or survival of SES. Second, the Ifugao’s primogeniture system of property rights along with the their customary laws and practices have played important roles in maintaining the robustness of their SES through their effects on ecological integrity. Third, the Ifugao SES today is faced with contemporary challenges with varying effects on its robustness: integration into a post-colonial social order, the effects of tourism and agricultural development, migration, urbanization and the introduction of Christianity and mass education. Fourth, despite these changes, it is not a certainty that the Ifugao will shift to a new domain of attraction that cannot support a human population, or that will induce a transition that causes long-term human suffering. Finally, the Ifugao case study adds to our understanding of robust SES.     

What is the role of thermodynamics on protein stability?

The most challenging and emerging field of biotechnology is the tailoring of proteins to attain the desired characteristic properties. In order to increase the stability of proteins and to study the function of proteins, the mechanism by which proteins fold and unfold should be known. It has been debated for a long time how exactly the linear form of a protein is converted into a stable 3-dimensional structure. The literature showed that many theories support the fact that protein folding is a thermodynamically controlled process. It is also possible to predict the mechanism of protein deactivation and stability to an extent from thermodynamic studies. This article reviewed various theories that have been proposed to explain the process of protein folding after its biosynthesis in ribosomes. The theories of the determination of the thermodynamic properties and the interpretation of thermodynamic data of protein stability are also discussed in this article.     

Dynamics of a Prey–Predator System with Herd Behaviour in Both and Strong Allee Effect in Prey

Biophysics - This paper mainly deals with the prey?predator dynamics where both the prey and predator exhibit herd behavior. Positivity, boundedness, some extinction criteria, stability of...     

Effect of γ-butyrolactone derivative on an artificial membrane

trans-2-(6'Methylheptanol-1'-yl)-3-hydroxymethyl-4-butanolide(II) was shown to increase the passive flux of cations such as Co²⁺ through a black lipid membrane made from ox brain phospholipids. This membranotropic effect appears to be involved in the activity of II towards blocked mutants of streptomycetes as an autoregulator of cytodifferentiation.     

Do People Agree on What Makes One Feel Loved? A Cognitive Psychometric Approach to the Consensus on Felt Love

This pragmatic study examines love as a mode of communication. Our focus is on the receiver side: what makes an individual feel loved and how felt love is defined through daily interactions. Our aim is to explore everyday life scenarios in which people might experience love, and to consider people’s converging and diverging judgments about which scenarios indicate felt love. We apply a cognitive psychometric approach to quantify a receiver’s ability to detect, understand, and know that they are loved. Through crowd-sourcing, we surveyed lay participants about whether various scenarios were indicators of felt love. We thus quantify these responses to make inference about consensus judgments of felt love, measure individual levels of agreement with consensus, and assess individual response styles. More specifically, we (1) derive consensus judgments on felt love; (2) describe its characteristics in qualitative and quantitative terms, (3) explore individual differences in both (a) participant agreement with consensus, and (b) participant judgment when uncertain about shared knowledge, and (4) test whether individual differences can be meaningfully linked to explanatory variables. Results indicate that people converge towards a shared cognitive model of felt love. Conversely, respondents showed heterogeneity in knowledge of consensus, and in dealing with uncertainty. We found that, when facing uncertainty, female respondents and people in relationships more frequently judge scenarios as indicators of felt love. Moreover, respondents from smaller households tend to know more about consensus judgments of felt love, while respondents from larger households are more willing to guess when unsure of consensus.