Quantifying Structural and Functional Restraints on Amino Acid Substitutions in Evolution of Proteins

One of Oleg Ptitsyn's most important papers (Shakhnovich, E., Abkevich, V., and Ptitsyn, O. (1996) Nature, 379, 96-98) describes how knowledge of structure and function can be used to understand better the nature of amino acid substitutions in families and superfamilies of proteins. The selective advantages of retaining structure and function during evolution can be expressed as restraints on the amino acid substitutions that are accepted.     

Ontogenetic correlates of diet in Malagasy lemurs

There is a well-documented relationship between development and other life-history parameters among anthropoid primates. Smaller-bodied anthropoids tend to mature more rapidly than do larger-bodied species. Among anthropoids of similar body sizes, folivorous species tend to grow and mature more quickly than do frugivorous species, thus attaining adult body size at an earlier age. This pattern conforms to the expectations of Janson and van Schaik's "ecological risk aversion hypothesis," which predicts that rates of growth and maturation should vary in inverse relation to the intensity of intraspecific feeding competition. According to the ecological risk aversion hypothesis (RAH), species experiencing high intraspecific feeding competition will grow and mature slowly to reduce the risk of mortality due to food shortages. Species experiencing low levels of intraspecific feeding competition will shorten the juvenile period to reduce the overall duration of this high-risk portion of the life cycle. This paper focuses on development and maturation in lemurs. We show that folivorous lemurs (such as indriids) grow and mature more slowly than like-sized frugivorous lemurs (e.g., most lemurids), but tend to exhibit faster dental development. Their dental developmental schedules are accelerated on an absolute scale, relative to craniofacial growth, and relative to particular life-history landmarks, such as weaning. Dental development has a strong phylogenetic component: even those lemurids that consume substantial amounts of foliage have slower dental development than those indriids that consume substantial amounts of fruit. Implications of these results for the RAH are discussed, and an explanation for this hypothesis' failure to predict lemur growth schedules is offered. We propose that the differing developmental schedules of folivorous and frugivorous lemurs may reflect different solutions to the ecological problem of environmental instability: some rely on a strategy of low maternal input and slow returns, while others rely on a strategy of high maternal input and fast returns.     

Airborne fungal spores in urban and rural environments in Poland

The concentrations of airborne fungal spores were measured during 2001–2002 in two sites in Poland—one in the city and the other in the countryside. The sites differed in habitat characteristics, such as urbanisation level, vegetation and microclimate. The aim of the study was to determine if, and in which way, land use type would affect spore occurrence. The volumetric method was used, and ten easily identifiable spore types were sampled and anyalysed: Alternaria, Botrytis, Cladosporium, Epiccocum, Ganoderma, Pithomyces, Polythrincium, Stemphylium, Torula and Drechslera. The season of spore occurrence was determined using the 90% method. The fungal spores studied were very frequent in the air (in most instances at a frequency higher than 50%). The most common spores were those of Cladosporium, with a frequency range of 83.1–90.5%. In both years the proportion of Cladosporium spores was statistically significantly higher in the city. In both 2001 and 2002 the total seasonal sum of all the spores was higher in the countryside than in the city as was the Seasonal Fungal Index (SFI) values and average concentrations of Botrytis, Ganoderma and Torula. These latter three genera are usually represented as pathogens of plants. The mean spore concentrations of most taxa were significantly higher in the rural environment. Correlation coefficients between daily concentrations at both sites for most of the taxa studied were significant, but with lower correlation values between variables. Such results indicate that the values from the sites are weakly interdependent. The study confirms that land use type may very likely have an impact on the course of spore occurrence, the mean daily concentrations of spores as well as SFI values.     

Contrasting demographies and persistence of rare annual plants in highly variable environments

Spatial and temporal variation in critical life history traits differ markedly between two co-occurring, rare and endangered annual plants, Gilia tenuiflora arenaria and Chorizanthe pungens pungens, that have restricted, but overlapping geographic distributions in coastal habitats of central California, USA. Environmental variation was extreme during the 6-year study (1997–2002), with the greatest differences between an intense wet, warm El Niño year (1998), followed by a very dry, cool La Niña (1999). Both species have similar increases in adult survival and seed set with wetter, warmer weather in spring, but they differed in other traits: more Gilia germinated in years with high rainfall and temperature, while more Chorizanthe germinated in dry, cooler years; Gilia abundance increased with the number of years since the previous large El Niño event, while Chorizanthe abundance declined; and Gilia abundance was independent of the previous year’s seed set, while Chorizanthe density was directly related to the previous year’s seed set. The strong negative associations of Chorizanthe abundance with warm, wet weather and with time since the previous El Niño probably reflect the particular sequence of annual weather patterns from 1997 through 2002, especially the extremes in 1998 and 1999. Since it germinates readily in most years under a wide range of winter conditions and does not develop a long-lived seed bank, Chorizanthe seedling abundance reflects recent additions and depletions of its seed bank, rather than prevailing weather, per se. In contrast, Gilia seeds may remain in the seed bank for many years, until relatively rare winter conditions trigger significant germination. These species-specific demographies enhance persistence and coexistence of these species, but the mechanisms differ from each other and from those described for annuals in other highly variable environments.     

Thermal Energy and the Origin of Life

Life has evolved on Earth with electromagnetic radiation (light), fermentable organic molecules, and oxidizable chemicals as sources of energy. Biological use of thermal energy has not been observed although heat, and the thermal gradients required to convert it into free energy, are ubiquitous and were even more abundant at the time of the origin of life on Earth. Nevertheless, Earth-organisms sense thermal energy, and in suitable environments may have gained the capability to use it as energy source. It has been proposed that the first organisms obtained their energy by a first protein named pF₁ that worked on a thermal variation of the binding change mechanism of today's ATP sythase enzyme. Organisms using thermosynthesis may still live where light or chemical energy sources are not available. Possible suitable examples are subsurface environments on Earth and in the outer Solar System, in particular the subsurface oceans of the icy satellites of Jupiter and Saturn.     

Wind-chill-equivalent temperatures: regarding the impact due to the variability of the environmental convective heat transfer coefficient

The wind-chill index (WCI), developed in Antarctica in the 1940s and recently updated by the weather services in the USA and Canada, expresses the enhancement of heat loss in cold climates from exposed body parts, e.g., face, due to wind. The index provides a simple and practical means for assessing the thermal effects of wind on humans outdoors. It is also used for indicating weather conditions that may pose adverse risks of freezing at subfreezing environmental temperatures. Values of the WCI depend on a number of parameters, i.e, temperatures, physical properties of the air, wind speed, etc., and on insolation and evaporation. This paper focuses on the effects of various empirical correlations used in the literature for calculating the convective heat transfer coefficients between humans and their environment. Insolation and evaporation are not included in the presentation. Large differences in calculated values among these correlations are demonstrated and quantified. Steady-state wind-chill-equivalent temperatures (WCETs) are estimated by a simple, one-dimensional heat-conducting hollow-cylindrical model using these empirical correlations. Partial comparison of these values with the published “new” WCETs is presented. The variability of the estimated WCETs, due to different correlations employed to calculate them, is clearly demonstrated. The results of this study clearly suggest the need for establishing a “gold standard” for estimating convective heat exchange between exposed body elements and the cold and windy environment. This should be done prior to the introduction and adoption of further modifications to WCETs and indices. Correlations to estimate the convective heat transfer coefficients between exposed body parts of humans in windy and cold environments influence the WCETs and need to be standardized.     

New ages for Middle and Later Stone Age deposits at Mumba rockshelter, Tanzania: optically stimulated luminescence dating of quartz and feldspar grains

The archaeological deposits at Mumba rockshelter, northern Tanzania, have been excavated for more than 70 years, starting with Margit and Ludwig Köhl-Larsen in the 1930s. The assemblages of Middle Stone Age (MSA) and Later Stone Age (LSA) artefacts collected from this site constitute the type sequences for these cultural phases in East Africa. Despite its archaeological importance, however, the chronology of the site is poorly constrained, despite the application since the 1980s of several dating methods (radiocarbon, uranium-series and amino acid racemisation) to a variety of materials recovered from the deposits. Here, we review these previous chronologies for Mumba and report new ages obtained from optically stimulated luminescence (OSL) and infrared stimulated luminescence (IRSL) measurements on single grains of quartz and multi-grain aliquots of potassium (K) feldspar from the MSA and LSA deposits. Measurements of single grains of quartz allowed the rejection of unrepresentative grains and the application of appropriate statistical models to obtain the most reliable age estimates, while measurements of K-feldspars allowed the chronology to be extended to older deposits. The seven quartz ages and four K-feldspar ages provide improved temporal constraints on the archaeological sequence at Mumba. The deposits associated with the latest Kisele Industry (Bed VI-A) and the earliest Mumba Industry (Bed V) are dated to 63.4 ± 5.7 and 56.9 ± 4.8 ka (thousands of years ago), respectively, thus constraining the time of transition between these two archaeological phases to ∼60 ka. An age of 49.1 ± 4.3 ka has been obtained for the latest deposits associated with the Mumba Industry, which show no evidence for post-depositional mixing and contain ostrich eggshell (OES) beads and abundant microlithics. The Nasera Industry deposits (Bed III) contain large quantities of OES beads and date to 36.8 ± 3.4 ka. We compare the luminescence ages with the previous chronologies for Mumba, and briefly discuss how the revised chronology fits in the context of existing archaeological records and palaeoclimatic reconstructions for East Africa.     

Is my hand connected to my body? The impact of body continuity and arm alignment on the virtual hand illusion

When a rubber hand is placed on a table top in a plausible position as if part of a person’s body, and is stroked synchronously with the person’s corresponding hidden real hand, an illusion of ownership over the rubber hand can occur (Botvinick and Cohen 1998). A similar result has been found with respect to a virtual hand portrayed in a virtual environment, a virtual hand illusion (Slater et al. 2008). The conditions under which these illusions occur have been the subject of considerable study. Here we exploited the flexibility of virtual reality to examine four contributory factors: visuo-tactile synchrony while stroking the virtual and the real arms, body continuity, alignment between the real and virtual arms, and the distance between them. We carried out three experiments on a total of 32 participants where these factors were varied. The results show that the subjective illusion of ownership over the virtual arm and the time to evoke this illusion are highly dependent on synchronous visuo-tactile stimulation and on connectivity of the virtual arm with the rest of the virtual body. The alignment between the real and virtual arms and the distance between these were less important. It was found that proprioceptive drift was not a sensitive measure of the illusion, but was only related to the distance between the real and virtual arms.

Electronic supplementary material

The online version of this article (doi:10.1007/s11571-011-9178-5) contains supplementary material, which is available to authorized users.     

Alteration of protein patterns in black rock inhabiting fungi as a response to different temperatures

Rock inhabiting fungi are among the most stress tolerant organisms on Earth. They are able to cope with different stressors determined by the typical conditions of bare rocks in hot and cold extreme environments. In this study first results of a system biological approach based on two-dimensional protein profiles are presented. Protein patterns of extremotolerant black fungi – Coniosporium perforans, Exophiala jeanselmei – and of the extremophilic fungus – Friedmanniomyces endolithicus – were compared with the cosmopolitan and mesophilic hyphomycete Penicillium chrysogenum in order to follow and determine changes in the expression pattern under different temperatures. The 2D protein gels indicated a temperature dependent qualitative change in all the tested strains. Whereas the reference strain P. chrysogenum expressed the highest number of proteins at 40 °C, thus exhibiting real signs of temperature induced reaction, black fungi, when exposed to temperatures far above their growth optimum, decreased the number of proteins indicating a down-regulation of their metabolism. Temperature of 1 °C led to an increased number of proteins in all of the analysed strains, with the exception of P. chrysogenum. These first results on temperature dependent reactions in rock inhabiting black fungi indicate a rather different strategy to cope with non-optimal temperature than in the mesophilic hyphomycete P. chrysogenum.     

Life history traits variation in heterogeneous environment: The case of a freshwater snail resistance to pond drying

Ecologists and population geneticists have long suspected that the diversity of living organisms was connected to the structure of their environment. In heterogeneous environments, diversifying selection combined to restricted gene flow may indeed lead to locally adapted populations. The freshwater snail, Galba truncatula, is a good model to address this question because it is present in a heterogeneous environment composed of temporary and permanent waters. In order to test the selective importance of those environments, we proposed here to measure survival of lineages from both habitats during drought episodes. To this purpose, we experimentally submitted adults and juveniles individuals from both habitats to drought. We found a difference in desiccation resistance between temporary and permanents waters only for adults. Adults from temporary habitats were found more resistant to drought. This divergence in desiccation resistance seems to explain the unexpected life history traits differences between habitats observed.