The BAR-domain family of proteins: a case of bending and binding?

BAR-domains recently took centre stage in science through a report on the crystal structure of this domain in Drosophila Amphiphysin. Though only weakly conserved at the sequence level, the structure of the BAR domain shows striking similarity to the GTPase-binding domain of Arfaptin 2, an effector of Rho- and Arf- GTPases. On the basis of this sequence and structural similarity, these two proteins have been classified as belonging to the same family, the BAR-domain family, and they probably also have similar functional characteristics. Presented here are the results of a database search for the sequence of the BAR domain of Amphiphysin and Arfaptin 2. This search identified a variety of related proteins, most of which are involved in intracellular transport and especially in endocytosis. For example, the BAR-domain family includes Endophilins, GTPase-activating proteins of the Centaurinbeta family and Oligophrenins, the adaptor proteins APPL1 and APPL2 that were recently shown to interact with the small GTPase Rab5, as well as members of the Sorting nexin family. On the basis of the structures of Amphiphysin and Arfaptin 2 and the cellular role of Amphiphysins in the early steps of endocytosis, the functions of the BAR domain have been defined as a dimerization motif and as sensing and inducing membrane curvature. However, data on Arfaptin 2 and now also on the Adaptor proteins APPL1 and 2 suggest that another function of the BAR domain is to bind to small GTPases.     

Do frogs use retinal elevation to measure the distance of a barrier?

Grass frogs, Rana pipiens, will detour around a barrier to reach prey on the other side. However, if the distance between prey and barrier is short, frogs attempt to push through the barrier and reach the prey directly. The relationship between the probability of detouring and the distance between prey and barrier is the same whether the frog's starting position is 4 cm or 8 cm from the barrier. This suggests that frogs measure the absolute separation between the two objects. To discover whether the retinal elevation of the bottom of the barrier contributes to measuring this distance, the relationship between the frequency of detouring and barrier-prey distance was examined in several experiments in which the retinal position of the bottom of the barrier was manipulated. No evidence was obtained that the barrier's retinal elevation helps in gauging distance.On the other hand, retinal elevation influences strongly how far a frog lunges to reach its prey. It is suggested that different cues to distance are applied to the two classes of object because, under natural circumstances, it is difficult to judge where a barrier emerges from the ground. A barrier may be hard to detect below the horizon because of the low contrast between it and the ground, or because vegetation and ground litter mask where the barrier meets the ground. In contrast, the prey's movements make it easily detectable against a stationary background and the prey's short height means that partial occlusion will have little effect on its apparent vertical position in the visual field.     

The Great Wall of China: a physical barrier to gene flow?

One population from each of six plant species along both sides of the Juyong-guan Great Wall, together with one population from each of five species along both sides of a path on a mountain top near Juyong-guan, were selected to study the effect of the Great Wall as a barrier on genetic differentiation between two subpopulations using RAPD markers. Significant genetic differentiation was found between the subpopulations on both sides of the Great Wall. A wind-pollinated woody species, Ulmus pumila, showed less genetic differentiation than four insect-pollinated species: Prunus armeniaca, Ziziphus jujuba, Vitex negundo, and Heteropappus hispidus. Cleistogenes caespitosa, a wind-pollinated perennial herb, displayed more genetic differentiation between subpopulations than the insect-pollinated species because of its propagation strategy. Although AMOVA analysis showed that subpopulations divided by a mountain path had diverged genetically, the variance component between the subpopulations on both sides of the Great Wall was significantly larger than that between the subpopulations at the control site. Therefore, it is reasonable to deduce that the Juyong-guan Great Wall has served as a physical barrier to gene flow between subpopulations separated for more than 600 years.     

The surf zone: a semi-permeable barrier to onshore recruitment of invertebrate larvae?

The supply of larvae to the shore is important for population replenishment and intertidal community dynamics but its variability at most scales is not well understood. We tested the relationship between nearshore mussel larval abundance and intertidal settlement rates over several years at multiple spatiotemporal scales in Oregon and New Zealand. Abundance of competent larvae nearshore and intertidal recruitment rates were simultaneously quantified using collectors mounted at different depths on moorings 50-1100 m from shore, and at adjacent rocky intertidal sites. Total mussel larval abundance and oceanographic conditions were also measured in some locations. At all scales, abundance of nearshore mussel larvae was unrelated to intertidal recruitment rates. In the intertidal, patterns of mussel recruitment were persistent in space, with sites of consistently high or low recruitment. In contrast, nearshore competent larval abundance showed generally similar abundances among sites except for a high, and spatially-inconsistent, variability in Oregon during 1998 only. On moorings, recruitment tended to be greater on midwater collectors than shallower or deeper. Finally, on moorings larval abundance in traps and recruitment on collectors was unrelated. These results suggest that (1) among sites, the size of the nearshore larval pool is relatively uniform while onshore recruitment varies and is unrelated to larval abundance, (2) temporal variability in nearshore larval availability is not strongly expressed onshore, (3) vertical stratification of competent larvae nearshore is strong and may influence transport and recruitment, and (4) within-coast variability in onshore recruitment is strongly driven by processes occurring locally within the surf zone that need to be studied to understand coastal recruitment dynamics.     

What's in a name? The case of cyanobacteria

A redefinition of the cyanobacterial lineage has been proposed based on phylogenomic analysis of distantly related nonphototrophic lineages. We define Cyanobacteria here as “Organisms in the domain bacteria able to carry out oxygenic photosynthesis with water as an electron donor and to reduce carbon dioxide as a source of carbon, or those secondarily evolved from such organisms.”     

Are indirect measures of abundance a useful index of population density? The case of red grouse harvesting

Indirect measures of population abundance, such as harvest data, are often used to make inference on long term population dynamics when direct data are either not available or are logistically difficult to obtain. However, when harvesting records are used, a common concern is that they may not reflect actual population abundance. We investigated the extent to which harvest data reflected changes in population density of the red grouse Lagopus lagopus scoticus in Great Britain. We used 92 independently managed populations over the period 1977–2000 and examined the temporal and spatial variability of the hunting records and independently obtained count data from each of these managed estates. Three different analyses support the conclusion that grouse hunting records are a reliable indicator of grouse abundance: 1) the number of red grouse shot in autumn showed a tendency to be linearly related to the density of individuals counted in the summer prior to the harvesting, 2) the relationships between the variance and the mean in the harvesting and corresponding count data, calculated over different populations at the same time, or the same locations at different times, were not statistically distinguishable, 3) similar direct and delayed density dependence patterns were observed in hunting records and count data. Our results suggest that red grouse hunting time series are a good proxy for population abundance.     

The use of a rare codon specifically during development?

A range of circumstantial evidence suggests that in Streptomyces spp., genes required for vegetative growth do not contain the leucine codon TTA. Instead, the codon seems to be confined to a few genes necessary during differentiation, when the colonies begin to produce aerial hyphae and antibiotics. Thus, mutations in bldA, the structural gene for tRNATTALeu, do not retard vegetative growth, but they prevent normal aerial mycelium and antibiotic production. Most of the known TTA-containing genes specify regulatory or resistance proteins associated with antibiotic-production clusters. Possibly the ability to translate the UUA codons in mRNA from such genes is confined to late stages of colony development. Factors that might have contributed to the evolution of this unusual situation are discussed.     

The CCN family: a new class of inflammation modulators?

Uncontrolled or sustained inflammation is the underlying cause of or actively contributes to the progression of many chronic pathologies such as atherosclerosis, arthritis, or neuroinflammatory diseases. Matricellular proteins of the CCN family (CYR61/CTGF/NOV) have emerged as localized multitasking signal integrators. These structurally conserved secreted proteins specifically interact with and signal through various extracellular partners, in particular integrins, which enable them to play crucial roles in various processes including development, angiogenesis, wound healing and diseases such as fibrosis, vascular disease and cancer. In this review, we discuss the possibility that the CCN family members could represent a putative new class of modulators of inflammation. In this context, we focused on their relationship with cytokines and chemokines. In vitro, CCN expression is finely regulated by diverse inflammatory mediators including cytokines (TNFα, IL1β, TGF-β), small factors such as prostaglandins, nitric oxide, histamine and serotonin, and extracellular matrix enzymes. In addition, CCN proteins acting alone or in concert with their specific partners appear to be potent regulators of the production of cytokines and chemokines in a context-dependent manner. Finally, emerging studies suggest a potential role for CCN proteins in chronic inflammatory diseases such as atherosclerosis, rheumatoid arthritis, inflammatory kidney diseases and neuroinflammatory pathologies such as Alzheimer’s disease. CCN members could therefore represent new potential therapeutic targets for drug development against such diseases.     

What is a category? The case of rough-and-tumble play

The intent of this paper is to outline a process by which we redefined an ambiguous behavioral category, rough-and-tumble play (R&T), using ethological and ethnographic methods (i.e., factor analyses, motivational/functional analyses, and interviews). Results suggest that sociometrically rejected and popular elementary school children have different concepts of R&T. For the former group, R&T and aggression seem to be interrelated and serve similar functions, while for the latter group R&T is a playful, social affiliative category. Interview results suggest that a cognitive processing difference between the groups may be at the root of this difference.     

Are the pH-sensitive mutants members of theVMA family?

This work was supported by Grant 7S 203 013 07.     

Can a barrier zone stop invasion of a population?

Journal of Mathematical Biology - We consider an integro-difference model to study the effect of a stationary barrier zone on invasion of a population with a strong Allee effect. It is assumed that...     

Are two South-Western Atlantic wrasses involved in a case of social mimicry?

Journal of Ethology - We investigated whether two South-Western Atlantic wrasses [Halichoeres penrosei (models) and Thalassoma noronhanum (mimics)] were involved in social mimicry. In mixed shoals,...     

How Many Nucleotides Are Required to Resolve a Phylogenetic Problem? The Use of a New Statistical Method Applicable to Available Sequences

The evolution of bootstrap proportions (BP) with sequence length was studied using a 28S ribosomal RNA data set. For different sequence lengths, informative sites were jackknifed several times. Bootstrapping was subsequently performed on each of these subsamples. For each node, BPs so obtained were plotted against sequence length, showing the evolution of the robustness with increasing number of informative sites. For robust nodes (BP of 100%), the pattern of BPs is unvarying and is described by a simple function BP = 100(1− e^{−b(x − x′)}), where x is the number of informative sites and b and x′ are two parameters estimated using a nonlinear regression procedure. When a node has a BP <100% and the pattern of BPs fits this function, it is possible to estimate the number of informative sites required to obtain a given average BP. The method also identifies nonrobust nodes (nonascending clusters of BP dots), for which it seems to be more cost effective and fruitful to turn to other species and/or genes rather than to continue sequencing longer gene lengths from the same species to reach a BP of 95%.     

The novel cytochrome c6 of chloroplasts: a case of evolutionary bricolage?

Cytochrome c6 has long been known as a redox carrier of the thylakoid lumen of cyanobacteria and some eukaryotic algae that can substitute for plastocyanin in electron transfer. Until recently, it was widely accepted that land plants lack a cytochrome c6. However, a homologue of the protein has now been identified in several plant species together with an additional isoform in the green alga Chlamydomonas reinhardtii. This form of the protein, designated cytochrome c6A, differs from the 'conventional' cytochrome c6 in possessing a conserved insertion of 12 amino acids that includes two absolutely conserved cysteine residues. There are conflicting reports of whether cytochrome c6A can substitute for plastocyanin in photosynthetic electron transfer. The evidence for and against this is reviewed and the likely evolutionary history of cytochrome c6A is discussed. It is suggested that it has been converted from a primary role in electron transfer to one in regulation within the chloroplast, and is an example of evolutionary 'bricolage'.     

The effect of maternal and child health and family planning services on mortality: is prevention enough?

OBJECTIVE--To examine the impact on mortality of a child survival strategy, mostly based on preventive interventions. DESIGN--Cross sectional comparison of cause specific mortality in two communities differing in the type, coverage, and quality of maternal and child health and family planning services. In the intervention area the services were mainly preventive, community based, and home delivered. SUBJECTS--Neonates, infants, children, and mothers in two contiguous areas of rural Bangladesh. INTERVENTIONS--In the intervention area community health workers provided advice on contraception and on feeding and weaning babies; distributed oral rehydration solution, vitamin A tablets for children under 5, and ferrous fumarate and folic acid during pregnancy; immunised children; trained birth attendants in safe delivery and when to refer; treated minor ailments; and referred seriously ill people and malnourished children to a central clinic. MAIN OUTCOME MEASURES--Overall and age and cause specific death rates, obtained by a multiple step "verbal autopsy" process. RESULTS--During the two years covered by the study overall mortality was 17% lower among neonates, 9% lower among infants aged 1-5 months, 30% lower among children aged 6-35 months, and 19% lower among women living in the study area than in those living in the control area. These differences were mainly due to fewer deaths from neonatal tetanus, measles, persistent diarrhoea with severe malnutrition among children, and fewer abortions among women. CONCLUSIONS--The programme was effective in preventing some deaths. In addition to preventive components such as tetanus and measles immunisation, health and nutrition education, and family planning, curative services are needed to reduce mortality further.