What drives membrane fusion in eukaryotes?

The fusion of biological membranes is the terminal step of all vesicular trafficking reactions in eukaryotic cells. Therefore, this fusion is fundamental for the transfer of proteins and lipids between different compartments, for exocytosis and for the structural integrity of organelles. In the past decade, many parts of the molecular machinery involved in fusion have been uncovered. Although the mechanisms responsible for mutual recognition and binding of membranes inside eukaryotes are becoming reasonably well known, there is considerable uncertainty as to what causes the actual merging of the lipid bilayer. Two classes of mechanisms have been proposed. Proximity models postulate that very close apposition of membranes suffices to induce fusion. By contrast, pore models propose that continuous proteinaceous pores between apposed membranes could be the basis for fusion.     

The length–tension curve in muscle depends on lattice spacing

Classic interpretations of the striated muscle length–tension curve focus on how force varies with overlap of thin (actin) and thick (myosin) filaments. New models of sarcomere geometry and experiments with skinned synchronous insect flight muscle suggest that changes in the radial distance between the actin and myosin filaments, the filament lattice spacing, are responsible for between 20% and 50% of the change in force seen between sarcomere lengths of 1.4 and 3.4 µm. Thus, lattice spacing is a significant force regulator, increasing the slope of muscle''s force–length dependence.     

What controls the length of noncoding DNA?

Several recent studies of genome evolution indicate that the rate of DNA loss exceeds that of DNA gain, leading to an underlying mutational pressure towards collapsing the length of noncoding DNA. That such a collapse is not observed suggests opposing mechanisms favoring longer noncoding regions. The presence of transposable elements alone also does not explain observed features of noncoding DNA. At present, a multidisciplinary approach--using population genetics techniques, large-scale genomic analyses, and in silico evolution--is beginning to provide new and valuable insights into the forces that shape the length of noncoding DNA and, ultimately, genome size. Recombination, in a broad sense, might be the missing key parameter for understanding the observed variation in length of noncoding DNA in eukaryotes.     

What drives community dynamics?

The search for general mechanisms of community assembly is a major focus of community ecology. The common practice so far has been to examine alternative assembly theories using dichotomist approaches of the form neutrality versus niche, or compensatory dynamics versus environmental forcing. In reality, all these mechanisms will be operating, albeit with different strengths. While there have been different approaches to community structure and dynamics, including neutrality and niche differentiation, less work has gone into separating out the temporal variation in species abundances into relative contributions from different components. Here we use a refined statistical machinery to decompose temporal fluctuations in species abundances into contributions from environmental stochasticity and inter-/intraspecific interactions, to see which ones dominate. We apply the methodology to community data from a range of taxa. Our results show that communities are largely driven by environmental fluctuations, and that member populations are, to different extents, regulated through intraspecific interactions, the effects of interspecific interactions remaining broadly minor. By decomposing the temporal variation in this way, we have been able to show directly what has been previously inferred indirectly: compensatory dynamics are in fact largely outweighed by environmental forcing, and the latter tends to synchronize the population dynamics.     

What factor drives the fibrillogenic association of beta-sheets?

The identification of the driving factor for fibril formation is paramount to understand the molecular basis of amyloidogenic disease. Recently, an atomic-detail structure of a fibrillogenic aggregate was reported and revealed a tight packing of beta-sheets. However, there is not a single pair-wise interaction of significance between the beta-sheets, no hydrogen bond and no hydrophobic interaction. Instead, there is extensive burial of polar groups at the interface. These observations lead to the question: What factor drives the association of beta-sheets? This issue is addressed by combining all-atom molecular dynamics with an implicit-solvent analysis. The driving force for the association arises from the mechanical equivalent of the dehydration propensity of pre-formed intra-sheet hydrogen bonds and dipole-dipole interactions.     

What drives plant stress genes?

Currently, there is a lot of interest in the plant stress response. Using large-scale genomics approaches, more and more genes are being identified that are involved in or even regulate this complex process. The recent boost in expression profile analyses for several plant stress responses has enabled the identification of new promoter elements as important factors in establishing the expression regulatory network controlling plant stress response.     

What drives long‐distance movements in the nomadic Grey Teal Anas gracilis in Australia?

In contrast to northern temperate environments, where day length and temperature changes are obvious proximate cues for movement to resource-rich breeding habitats, the cues for movement used by birds in an often resource-poor, stochastic environment are less obvious. We recorded long-distance movements of 23 Grey Teal Anas gracilis using satellite telemetry for up to 879 days and examined the relationship between those movements and environmental factors, such as heavy rainfall and flooding, at the destination site. We identified 32 long-distance (> 150 km) movements that met our criterion for minimally interrupted flight between origin and destination. Thirteen of these flights coincided with rainfall and/or flooding events up to 1050 km from the origin. However, some ducks moved without any clear beneficial conditions at the destination onto small wetlands in regions with little surface water. The data suggest that there are two types of long-distance movement – ranging and directed. These flights occurred over distances up to 1200 km across the arid inland. The rates and distances of movement suggest that long-distance movements of Grey Teal entail high energy costs as in waterfowl elsewhere. We conclude that the proximate controls of directed movements need not be very different from those of their temperate counterparts.     

Experimental determination of sarcomere force–length relationship in type-I human skeletal muscle fibers

The objectives of this study were to measure the active and passive force–length (F–L) relationships in type-I human single muscle fibers and to compare the results to predictions from the sliding filament model (the “standard model”). We measured isometric forces in chemically skinned fibers at different sarcomere lengths (SLs) in separate maximal activations. The experimental tolerance interval for optimal SL was calculated to be (2.37, 2.95 μm), which included the prediction by the standard model (2.64, 2.81 μm). Average passive slack length was 2.22±0.08 μm, and the passive F–L relationship was well described by an exponential function. Best fit lines were used to estimate the ascending and descending limbs from the active F–L data using the average SL obtained from a digital image of the fiber. The experimental descending limb was also estimated using the shortest SL to address the possible effects of sarcomere inhomogeneity (SI). The experimental slopes of the ascending and descending limbs, 0.42 F_o/μm and ?0.52 F_o/μm (vs. ?0.55 F_o/μm with the shortest SL) respectively, F_o being the maximal isometric force, were significantly less in magnitude than those from the standard model. These results suggested that the difference between experimental and standard models was not fully explained by SI and other factors could be important. The broader experimental F–L curve compared to the standard model implies that human muscle has functionally a wider operating length range where its force-generating capacity is not compromised.     

History-dependent properties of skeletal muscle myofibrils contracting along the ascending limb of the force–length relationship

There is a history dependence of skeletal muscle contraction: stretching activated muscles induces a long-lasting force enhancement, while shortening activated muscles induces a long-lasting force depression. These history-dependent properties cannot be explained by the current model of muscle contraction, and its mechanism is unknown. The purposes of this study were (i) to evaluate if force enhancement and force depression are present at short lengths (the ascending limb of the force–length (FL) relationship), (ii) to evaluate if the history-dependent properties are associated with sarcomere length (SL) non-uniformity and (iii) to determine the effects of cross-bridge (de)activation on force depression. Rabbit psoas myofibrils were isolated and attached between two microneedles for force measurements. Images of the myofibrils were projected onto a linear photodiode array for measurements of SL. Myofibrils were activated by either Ca²⁺ or MgADP; the latter induces cross-bridge attachment to actin independently of Ca²⁺. Activated myofibrils were subjected to three stretches or shortenings (approx. 4% SL at approx. 0.07 µm s⁻¹ sarcomere⁻¹) along the ascending limb of the FL relationship separated by periods (approx. 5 s) of isometric contraction. Force after stretch was higher than force after shortening at similar SLs. The differences in force could not be explained by SL non-uniformity. The FL relationship produced by Ca²⁺- and MgADP-activated myofibrils were similar in stretch experiments, but after shortening MgADP activation produced forces that were higher than Ca²⁺ activation. Since MgADP induces the formation of strongly bound cross-bridges, this result suggests that force depression following shortening is associated with cross-bridge deactivation.     

What drives the positive correlation between human population density and bird species richness in Australia?

Aim To test six hypotheses that could explain or mediate the positive correlation between human population density (HPD) and bird species richness while controlling for biased sampling effort. These hypotheses were labelled as follows: productivity (net primary productivity, NPP); inherent heterogeneity (diversity of vegetation types); anthropogenic heterogeneity (diversity of land uses); conservation policy (proportion of conservation land); increased productivity (human‐induced productivity increases); and the reduced‐slope hypothesis (which predicts that humans have a negative impact on species numbers across the full range of variation in HPD). Location Australia. Methods All data were collected at a spatial resolution of 1° across mainland Australia. Bird species richness was from 2007 atlas data and random subsampling was used to account for biased sampling effort. HPD was from the 2006 census. All other data were from government produced geographic information system layers. The most important biotic or abiotic factors influencing patterns in both species richness and HPD were assessed using simultaneous autoregressive models and an information theoretic approach. Results NPP appeared to be one of the main factors driving spatial congruence between bird species richness and HPD. Inherent habitat heterogeneity was weakly related to richness and HPD, although an interaction between heterogeneity and NPP indicated that the former may be an important determinant of species richness in low‐productivity regions. There was little evidence that anthropogenic landscape heterogeneity or human‐induced changes in productivity influenced the relationship between species richness and HPD, but conservation policy appeared to act as an important mediating factor and species richness was positively related to the proportion of conservation land only in regions of high HPD. Main conclusions The spatial congruence between bird species richness and HPD occurs because both respond positively to productivity and, in certain circumstances, habitat heterogeneity. Our results suggest that conservation policy could mediate this relationship, but further research is required to determine the importance of conservation reserves in supporting species in regions densely populated by humans.     

What drives the binding of minor groove-directed ligands to DNA hairpins?

Understanding the molecular basis of ligand-DNA-binding events, and its application to the rational design of novel drugs, requires knowledge of the structural features and forces that drive the corresponding recognition processes. Existing structural evidence on DNA complexation with classical minor groove-directed ligands and the corresponding studies of binding energetics have suggested that this type of binding can be described as a rigid-body association. In contrast, we show here that the binding-coupled conformational changes may be crucial for the interpretation of DNA (hairpin) association with a classical minor groove binder (netropsin). We found that, although the hairpin form is the only accessible state of ligand-free DNA, its association with the ligand may lead to its transition into a duplex conformation. It appears that formation of the fully ligated duplex from the ligand-free hairpin, occurring via two pathways, is enthalpically driven and accompanied by a significant contribution of the hydrophobic effect. Our thermodynamic and structure-based analysis, together with corresponding theoretical studies, shows that none of the predicted binding steps can be considered as a rigid-body association. In this light we anticipate our thermodynamic approach to be the basis of more sophisticated nucleic acid recognition mechanisms, which take into account the dynamic nature of both the nucleic acid and the ligand molecule.     

What drives the distribution of the bloom-forming cyanobacteria Planktothrix agardhii and Cylindrospermopsis raciborskii?

The cyanobacteria Planktothrix agardhii and Cylindrospermopsis raciborskii are bloom-forming species common in eutrophic freshwaters. These filamentous species share certain physiological traits which imply that they might flourish under similar environmental conditions. We compared the distribution of the two species in a large database (940 samples) covering different climatic regions and the Northern and Southern hemispheres, and carried out laboratory experiments to compare their morphological and physiological responses. The environmental ranges of the two species overlapped with respect to temperature, light and total phosphorus (TP); however, they responded differently to environmental gradients; C.?raciborskii biovolume changed gradually while P. agardhii shifted sharply from being highly dominated to a rare component of the phytoplankton. As expected, P.?agardhii dominates the phytoplankton with high TP and low light availability conditions. Contrary to predictions, C.?raciborskii succeeded in all climates and at temperatures as low as 11?°C. Cylindrospermopsis raciborskii had higher phenotypic plasticity than P.?agardhii in terms of pigments, individual size and growth rates. We conclude that the phenotypic plasticity of C.?raciborskii could explain its ongoing expansion to temperate latitudes and suggest its future predominance under predicted climate-change scenarios.     

What drives proteins into the major or minor grooves of DNA?

The energetic profiles of a significant number of protein-DNA systems at 20 °C reveal that, despite comparable Gibbs free energies, association with the major groove is primarily an enthalpy-driven process, whereas binding to the minor groove is characterized by an unfavorable enthalpy that is compensated by favorable entropic contributions. These distinct energetic signatures for major versus minor groove binding are irrespective of the magnitude of DNA bending and/or the extent of binding-induced protein refolding. The primary determinants of their different energetic profiles appear to be the distinct hydration properties of the major and minor grooves; namely, that the water in the A+T-rich minor groove is in a highly ordered state and its removal results in a substantial positive contribution to the binding entropy. Since the entropic forces driving protein binding into the minor groove are a consequence of displacing water ordered by the regular arrangement of polar contacts, they cannot be regarded as hydrophobic.     

Internode length in pisum: do the internode length genes effect growth in dark-grown plants?

Internode length in light-grown peas (Pisum sativum L.) is controlled by the interaction of genes occupying at least five major loci, Le, La, Cry, Na, and Lm. The present work shows that the genes at all of the loci examined (Le, Cry, and Na) also exert an effect on internode length in plants grown in complete darkness. Preliminary results using pure lines were verified using either segregating progenies or near isogenic lines. The major cause of the differences was due to a change in the number of cells per internode rather than to an alteration of the cell length. Since the genes occupying at least two of these loci, Le and Na, have been shown to be directly involved with gibberellin metabolism, it appears that gibberellins are not only essential for elongation in the dark but are limiting for elongation in the nana (extremely short, na), dwarf (Na le), and tall (Na Le) phenotypes. These results are supported by the large inhibitory effects of AMO 1618 treatments on stem elongation in dwarf and tall lines grown in the dark and the fact that applied gibberellic acid could overcome this inhibition and greatly promote elongation in a gibberellin-deficient na line. It is clear that the internode length genes, and in particular the alleles at the Le locus, are not acting by simply controlling the sensitivity of the plant to light.     

What drives the evolution of body size in ectotherms? A global analysis across the amphibian tree of life

Aim

The emergence of large-scale patterns of animal body size is the central expectation of a wide range of (macro)ecological and evolutionary hypotheses. The drivers shaping these patterns include climate (e.g. Bergmann's rule), resource availability (e.g. ‘resource rule’), biogeographic settings and niche partitioning (e.g. adaptive radiation). However, these hypotheses often make opposing predictions about the trajectories of body size evolution. Therefore, whether underlying drivers of body size evolution can be identified remains an open question. Here, we employ the most comprehensive global dataset of body size in amphibians, to address multiple hypotheses that predict patterns of body size evolution based on climatic factors, ecology and biogeographic settings to identify underlying drivers and their generality across lineages.

Location

Global.

Time Period

Present.

Major Taxa Studied

Amphibians.

Methods

Using a global dataset spanning 7270 (>87% of) species of Anura, Caudata and Gymnophiona, we employed phylogenetic Bayesian modelling to test the roles of climate, resource availability, insularity, elevation, habitat use and diel activity on body size.

Results

Only climate and elevation drive body size patterns, and these processes are order-specific. Seasonality in precipitation and in temperature predict body size clines in anurans, whereas caecilian body size increases with aridity. However, neither of these drivers explained variation in salamander body size. In both anurans and caecilians, size increases with elevational range and with midpoint elevation in caecilians only. No effects of mean temperature, resource abundance, insularity, time of activity or habitat use were found.

Main Conclusions

Precipitation and temperature seasonality are the dominant climatic drivers of body size variation in amphibians overall. Bergmann's rule is consistently rejected, and so are other alternative hypotheses. We suggest that the rationale sustaining existing macroecological rules of body size is unrealistic in amphibians and discuss our findings in the context of the emerging hypothesis that climate change can drive body size shifts.     

What drives bacteria to produce a biofilm?

Nearly 40 years ago, Dr. R.J. Gibbons made the first reports of the clinical relevance of what we now know as bacterial biofilms when he published his observations of the role of polysaccharide glycocalyx formation on teeth by Streptococcus mutans [Sci. Am. 238 (1978) 86]. As the clinical relevance of bacterial biofilm formation became increasingly apparent, interest in the phenomenon exploded. Studies are rapidly shedding light on the biomolecular pathways leading to this sessile mode of growth but many fundamental questions remain. The intent of this review is to consider the reasons why bacteria switch from a free-floating to a biofilm mode of growth. The currently available wealth of data pertaining to the molecular genetics of biofilm formation in commonly studied, clinically relevant, single-species biofilms will be discussed in an effort to decipher the motivation behind the transition from planktonic to sessile growth in the human body. Four potential incentives behind the formation of biofilms by bacteria during infection are considered: (1) protection from harmful conditions in the host (defense), (2) sequestration to a nutrient-rich area (colonization), (3) utilization of cooperative benefits (community), (4) biofilms normally grow as biofilms and planktonic cultures are an in vitro artifact (biofilms as the default mode of growth).     

Predators,fire or resources: What drives the distribution of herbivores in fragmented mesic forests?

Trophic interactions and disturbance events can shape the structure and function of ecosystems. However, the effects of drivers such as predation, fire and climatic variables on species distributions are rarely considered concurrently. We used a replicated landscape‐scale predator management experiment to compare the effects of red fox Vulpes vulpes control, time‐since‐fire, vegetation type and other environmental variables on native herbivore distributions. Occurrence data for four native herbivores and an invasive predator – the red fox – were collected from 240 sites across three baited (for lethal fox control) and three unbaited forest blocks (4659–9750 ha) in south‐western Victoria, Australia, and used to build species distribution models. The herbivore taxa were as follows: red‐necked wallaby Macropus rufogriseus, black wallaby Wallabia bicolour, grey kangaroo Macropus fuligenosus and Macropus giganteus and common brushtail possum Trichosurus vulpecula. Fox control and fire had little effect on herbivore occurrence, despite the literature suggesting it can influence abundance, while climate, proximity to farmland and topography were more influential. This may be because the region’s high productivity and agricultural pastures subsidise food resources for both predators and prey within the forest blocks and so dampen trophic interactions. Alternatively, these drivers may affect herbivore abundance, but not herbivore occurrence. Understanding the drivers of herbivore distributions is an important step in predicting the effects of herbivory on other species, particularly after management interventions such as predator control and prescribed burns.     

Obesity and food away from home: What drives the socioeconomic gradient in excess body weight?

Rising obesity rates are one of the most challenging public health issues in many emerging economies. To what extent food away from home (FAFH) and its nutritional components are behind this rise is not yet well understood. To address the issue, this paper combines a representative restaurant survey that includes detailed information on the diet quality of the most widely consumed meals and their nutritional components from 1605 restaurants and a representative household survey with anthropometric measures of adult women living in 40 neighborhoods in the Lima Metropolitan Area. One important advantage of the dataset is the fact that nutrition professionals observed the preparation of the meals and that they were subject to a detailed laboratory analysis. Exploiting this data, we examine the differences in nutritional quality of FAFH among 40 neighborhoods of various socioeconomic groups and explore whether these differences can explain part of the observed socioeconomic gradient in excess body weight. The findings indicate that less healthy food in restaurants located in the food environment of the households is significantly associated with higher rates of obesity and overweight. In particular, the high supply and intake of sodium potentially drives higher excess body weight. The study also finds that up to 15 percent of the socioeconomic gradient in obesity is attributable to the restaurant food quality in the food environment of the households.