G4-quadruplex-binding proteins: review and insights into selectivity

There are over 700,000 putative G4-quadruplexes (G4Qs) in the human genome, found largely in promoter regions, telomeres, and other regions of high regulation. Growing evidence links their presence to functionality in various cellular processes, where cellular proteins interact with them, either stabilizing and/or anchoring upon them, or unwinding them to allow a process to proceed. Interest in understanding and manipulating the plethora of processes regulated by these G4Qs has spawned a new area of small-molecule binder development, with attempts to mimic and block the associated G4-binding protein (G4BP). Despite the growing interest and focus on these G4Qs, there is limited data (in particular, high-resolution structural information), on the nature of these G4Q-G4BP interactions and what makes a G4BP selective to certain G4Qs, if in fact they are at all. This review summarizes the current literature on G4BPs with regards to their interactions with G4Qs, providing groupings for binding mode, drawing conclusions around commonalities and highlighting information on specific interactions where available.     

Tight junction biogenesis during early development

The tight junction (TJ) is an essential component of the differentiated epithelial cell required for polarised transport and intercellular integrity and signalling. Whilst much can be learnt about how the TJ is constructed and maintained and how it functions using a wide range of cellular systems, the mechanisms of TJ biogenesis within developmental models must be studied to gain insight into this process as an integral part of epithelial differentiation. Here, we review TJ biogenesis in the early mammalian embryo, mainly considering the mouse but also including the human and other species, and, briefly, within the amphibian embryo. We relate TJ biogenesis to inherent mechanisms of cell differentiation and biosynthesis occurring during cleavage of the egg and the formation of the first epithelium. We also evaluate a wide range of exogenous cues, including cell-cell interactions, protein kinase C signalling, gap junctional communication, Na⁺/K⁺-ATPase and cellular energy status, that may contribute to TJ biogenesis in the embryo and how these may shape the pattern of early morphogenesis.     

The mechanistic basis for higher‐order interactions and non‐additivity in competitive communities

Motivated by both analytical tractability and empirical practicality, community ecologists have long treated the species pair as the fundamental unit of study. This notwithstanding, the challenge of understanding more complex systems has repeatedly generated interest in the role of so‐called higher‐order interactions (HOIs) imposed by species beyond the focal pair. Here we argue that HOIs – defined as non‐additive effects of density on per capita growth – are best interpreted as emergent properties of phenomenological models (e.g. Lotka–Volterra competition) rather than as distinct ‘ecological processes’ in their own right. Using simulations of consumer‐resource models, we explore the mechanisms and system properties that give rise to HOIs in observational data. We demonstrate that HOIs emerge under all but the most restrictive of assumptions, and that incorporating non‐additivity into phenomenological models improves the quantitative and qualitative accuracy of model predictions. Notably, we also observe that HOIs derive primarily from mechanisms and system properties that apply equally to single‐species or pairwise systems as they do to more diverse communities. Consequently, there exists a strong mandate for further recognition of non‐additive effects in both theoretical and empirical research.     

Safety zones for a Sclerotinia sclerotiorum-based mycoherbicide: Accounting for regional and yearly variation in climate

Variation in the width of 'safety zones' for sheep and dairy pasture treated with a Sclerotinia sclerotiorum (Lib.) de Bary-based mycoherbicide was quantified using 10 years of climate data from each of five regions in New Zealand. Acceptable and risk-averse zones were defined as the maximum distances in any direction from a treated pasture where 'added:natural' ratios of air-borne S. sclerotiorum spores are 1:1 and 1:10, respectively. The 10-year mean 1:1 safety zone had zero width for sheep pasture at all locations, and was at most, 50 m wide for dairy pasture. The width of the 10-year mean 1:10 zone varied regionally from 314 to 443 m for sheep and from 175 to 280 m for dairy pasture, and the 90th percentile 1:10 zones were up to 41% wider. Linear relationships between safety zone width and mean wind speed were evident and these could be used to derive region-specific safety zones.     

CHANGES IN PHOTOSYNTHESIS IN RESPONSE TO COMBINED IRRADIANCE AND TEMPERATURE STRESS IN CYANOBACTERIAL SURFACE WATERBLOOMS1

Buoyant cyanobacteria, previously mixed throughout the water column, float to the lake surface and form a surface waterbloom when mixing subsides. At the surface, the cells are exposed to full sunlight, and this abrupt change in photon irradiance may induce photoinhibition; at the same time, temperature rises as well. This study investigated the damaging effects of this increase in temperature as well as the ecologically more relevant combination of both an increased temperature and a high photon irradiance. Analysis of surface blooms with oxygen microelectrodes showed that integrated oxygen contents that are dependent on the balance of photosynthetic oxygen evolution and respiratory oxygen uptake decreased when temperature was raised above the lake temperature. Gross rates of photosynthesis were unaffected by temperatures up to of 35°C; hence, a moderate increase in temperature mainly stimulated oxygen uptake. Preincubation of cells of the cyanobacterium Anabaena flos-aquae (Lyngb.) de Brébisson at temperatures up to 35°C did not affect the subsequent measurement of rates of net photosynthesis. Another 5°C rise in temperature severely damaged the photosynthetic apparatus. Failure to restore net rates of photosynthesis was coupled to a strong quenching of the ratio of variable to maximum fluorescence, F_v/F_m, that was the result of a rise in F_o. A combination of high temperature and high photon irradiance was more damaging than high temperature alone. In contrast, low photon irradiances offered substantial protection against heat injury of the photosynthetic apparatus. I conclude from this study that because cyanobacteria usually are acclimated to low average irradiance prior to bloom formation, there is a reasonable risk of chronic photoinhibition. The increase in temperature will enhance the photodamage of cells in the top layer of the bloom. Low photon irradiances in subsurface layers will offer protection against heat injury. If the high temperatures extend to the deepest, dark layers of the bloom, damage in those layers is likely to occur.     

Dracula’s ménagerie: A multispecies occupancy analysis of lynx,wildcat, and wolf in the Romanian Carpathians

1. The recovery of terrestrial carnivores in Europe is a conservation success story. Initiatives focused on restoring top predators require information on how resident species may interact with the re‐introduced species as their interactions have the potential to alter food webs, yet such data are scarce for Europe.
2. In this study, we assessed patterns of occupancy and interactions between three carnivore species in the Romanian Carpathians. Romania houses one of the few intact carnivore guilds in Europe, making it an ideal system to assess intraguild interactions and serve as a guide for reintroductions elsewhere.
3. We used camera trap data from two seasons in Transylvanian forests to assess occupancy and co‐occurrence of carnivores using multispecies occupancy models.
4. Mean occupancy in the study area was highest for lynx (Ψ_winter = 0.76 95% CI: 0.42–0.92; Ψ_autumn = 0.71 CI: 0.38–0.84) and wolf (Ψ_winter = 0.60 CI: 0.34–0.78; Ψ_autumn = 0.81 CI: 0.25–0.95) and lowest for wildcat (Ψ_winter = 0.40 CI: 0.19–0.63; Ψ_autumn = 0.52 CI: 0.17–0.78)
5. We found that marginal occupancy predictors for carnivores varied between seasons. We also found differences in predictors of co‐occurrence between seasons for both lynx‐wolf and wildcat‐wolf co‐occurrence. For both seasons, we found that conditional occupancy probabilities of all three species were higher when another species was present.
6. Our results indicate that while there are seasonal differences in predictors of occupancy and co‐occurrence of the three species, co‐occurrence in our study area is high.
7. Terrestrial carnivore recovery efforts are ongoing worldwide. Insights into interspecific relations between carnivore species are critical when considering the depauperate communities they are introduced in. Our work showcases that apex carnivore coexistence is possible, but dependent on protection afforded to forest habitats and their prey base.

     

The role of antipredator behavior in an experimental community of jumping spiders with intraguild predation

 The role of direct and indirect interactions in intraguild predation (IGP) was investigated in a laboratory study. The study system contained two spider species, Phidippus audax and Phidippus octopunctatus, and the fruit fly, Drosophila melanogaster. P. audax and P. octopunctatus eat D. melanogaster. P. audax (top predators) also eat P. octopunctatus (intermediate predators). Thus, P. audax and P. octopunctatus compete for the shared resource and also interact as predator and prey. Experiments consisted of two treatments: risk-IGP and full-IGP. In the risk-IGP treatments, I examined the effects of trait-mediated indirect effects generated by antipredator behavior of P. octopunctatus on the survival of fruit flies. P. audax chelicerae were waxed so that P. audax could not attack a prey. The result indicated a significant positive indirect effect of P. audax on the survival of D. melanogaster due to the antipredator behavior of P. octopunctatus (a trait-mediated indirect effect). In the full-IGP treatments, P. audax chelicerae were not restricted, so that it could attack prey; this resulted in decreased survival of D. melanogaster. Because of predation of P. audax on P. octopunctatus, even stronger positive interactions occurred between P. audax and D. melanogaster in full-IGP than in risk-IGP. Received: May 7, 2002 / Accepted: June 27, 2002     

Population dynamics of three songbird species in a nestbox population in Central Europe show effects of density,climate and competitive interactions

Unravelling the contributions of density‐dependent and density‐independent factors in determining species population dynamics is a challenge, especially if the two factors interact. One approach is to apply stochastic population models to long‐term data, yet few studies have included interactions between density‐dependent and density‐independent factors, or explored more than one type of stochastic population model. However, both are important because model choice critically affects inference on population dynamics and stability. Here, we used a multiple models approach and applied log‐linear and non‐linear stochastic population models to time series (spanning 29 years) on the population growth rates of Blue Tits Cyanistes caeruleus, Great Tits Parus major and Pied Flycatchers Ficedula hypoleuca breeding in two nestbox populations in southern Germany. We focused on the roles of climate conditions and intra‐ and interspecific competition in determining population growth rates. Density dependence was evident in all populations. For Blue Tits in one population and for Great Tits in both populations, addition of a density‐independent factor improved model fit. At one location, Blue Tit population growth rate increased following warmer winters, whereas Great Tit population growth rates decreased following warmer springs. Importantly, Great Tit population growth rate also decreased following years of high Blue Tit abundance, but not vice versa. This finding is consistent with asymmetric interspecific competition and implies that competition could carry over to influence population dynamics. At the other location, Great Tit population growth rate decreased following years of high Pied Flycatcher abundance but only when Great Tit population numbers were low, illustrating that the roles of density‐dependent and density‐independent factors are not necessarily mutually exclusive. The dynamics of this Great Tit population, in contrast to the other populations, were unstable and chaotic, raising the question of whether interactions between density‐dependent and density‐independent factors play a role in determining the (in) stability of the dynamics of species populations.