Intra-Site Variability in the Still Bay Fauna at Blombos Cave: Implications for Explanatory Models of the Middle Stone Age Cultural and Technological Evolution

To explain cultural and technological innovations in the Middle Stone Age (MSA) of southern Africa, scholars invoke several factors. A major question in this research theme is whether MSA technocomplexes are adapted to a particular set of environmental conditions and subsistence strategies or, on the contrary, to a wide range of different foraging behaviours. While faunal studies provide key information for addressing these factors, most analyses do not assess intra-technocomplex variability of faunal exploitation (i.e. variability within MSA phases). In this study, we assess the spatial variability of the Still Bay fauna in one phase (M1) of the Blombos Cave sequence. Analyses of taxonomic composition, taphonomic alterations and combustion patterns reveal important faunal variability both across space (lateral variation in the post-depositional history of the deposits, spatial organisation of combustion features) and over time (fine-scale diachronic changes throughout a single phase). Our results show how grouping material prior to zooarchaeological interpretations (e.g. by layer or phase) can induce a loss of information. Finally, we discuss how multiple independent subdivisions of archaeological sequences can improve our understanding of both the timing of different changes (for example in technology, culture, subsistence, environment) and how they may be inter-related.     

Spatial Electron Acceptor Variability: Implications for Assessing Bioremediation Potential

An extensive network of multilevel samplers was established in a hydrocarbon-contaminated wetland aquifer. Results of groundwater sampling for benzene, toluene, ethylbenzene, and xylenes (BTEX), and electron acceptors show that both pristine and contaminated groundwater have spatially variable chemical signatures, owing primarily to microbially mediated oxidation-reduction reactions. Due to these spatial variations, estimates of the efficiency of intrinsic bioremediation can vary significantly depending on how geochemical data are collected. Use of data collected from monitoring wells with screens longer than the vertical extent of the plume will generally underestimate the potential for intrinsic bioremediation for the most chemically active horizon of the plume. A comparison of pristine and contaminated redox patterns demonstrates that, although BTEX exerts the highest demand for electron acceptors, oxidation of natural organic matter also contributes to electron acceptor utilization. If natural and other non-BTEX losses of electron acceptors are ignored, the assimilative capacity, defined as the amount of a contaminant that can potentially be degraded with known amounts of electron acceptors, will be overestimated. Many numerical and analytical models designed to simulate biodegradation are directly or indirectly based on assimilative capacity estimates. Proper estimation of assimilative capacity is crucial if models are to accurately quantify solute concentrations over time and space.     

Fragility of Traditions: The Disturbance Hypothesis for the Loss of Local Traditions in Orangutans

Chimpanzees and orangutans have increasingly well documented local traditions involving learned skillful behaviors, often involving tools, which vary from place to place and are maintained by social transmission. These local traditions are most likely the antecedents of human culture. The complexity of local traditions is thought largely to be a function of the cumulative frequency of opportunities for social learning, and hence of the extent of tolerant gregarious foraging. Data on orangutans and chimpanzees are consistent with this hypothesis. This reliance on continued social transmission makes local traditions vulnerable to interruptions of transmission. I examine the disturbance hypothesis, which suggests that local extinction, hunting pressure, selective logging, and habitat loss in general affect the key parameters of the transmission process—innovation, diffusion, horizontal transmission—and hence will significantly impoverish the repertoire of complex skills for subsistence. Given current trends in orangutan habitats, serious erosion of local traditions is taking place. I also speculate that disturbance in the past has led to a significant loss of orangutan traditions.     

Movement of DNA across the chloroplast envelope: Implications for the transfer of promiscuous DNA

Little is known about the mechanistic basis for the movement of promiscuous nucleic acids across cell membranes. To address this problem we sought conditions that would permit the entry of plasmid DNA into isolated, intact pea chloroplasts. DNA uptake did not occur normally, but was induced by hypotonic treatments, by incubation with millimolar levels of Mg²⁺, or by heat shock at 42 °C. These results are consistent with DNA movement being permitted by conditions that transiently alter the permeability of the chloroplast envelope. Plant cells are subject to osmotic tensions and/or conditions inducing polymorphic changes in the membranes, such as those used in the present study, under several environmental stresses. In an evolutionary time frame, these phenomena may provide a mechanism for the transfer of promiscuous nucleic acids between organelles.Abbreviations PEG polyethylene glycol - T-DNA transferred DNATo Dan Arnon; a superb scientist whose findings opened up enormous fields of research in photosynthesis, and a good friend.     

SNX4 in Complex with Clathrin and Dynein: Implications for Endosome Movement

Background

Sorting nexins (SNXs) constitute a family of proteins classified by their phosphatidylinositol (PI) binding Phox homology (PX) domain. Some members regulate intracellular trafficking. We have here investigated mechanisms underlying SNX4 mediated endosome to Golgi transport.

Methodology/Principal Findings

We show that SNX4 forms complexes with clathrin and dynein. The interactions were inhibited by wortmannin, a PI3-kinase inhibitor, suggesting that they form when SNX4 is associated with PI(3)P on endosomes. We further localized the clathrin interacting site on SNX4 to a clathrin box variant. A short peptide containing this motif was sufficient to pull down both clathrin and dynein. Knockdown studies demonstrated that clathrin is not required for the SNX4/dynein interaction. Moreover, clathrin knockdown led to increased Golgi transport of the toxin ricin, as well as redistribution of endosomes.

Conclusions/Significance

We discuss the possibility of clathrin serving as a regulator of SNX4-dependent transport. Upon clathrin release, dynein may bind SNX4 and mediate retrograde movement.     

Quantifying Regional Vegetation Cover Variability in North China during the Holocene: Implications for Climate Feedback

Validating model simulations of vegetation-climate feedback needs information not only on changes in past vegetation types as reconstructed by palynologists, but also on other proxies such as vegetation cover. We present here a quantitative regional vegetation cover reconstruction for North China during the Holocene. The reconstruction was based on 15 high-quality lake sediment profiles selected from 55 published sites in North China, along with their modern remote sensing vegetation index. We used the surface soil pollen percentage to build three pollen-vegetation cover transfer models, and used lake surface sediment pollen data to validate their accuracy. Our results showed that vegetation cover in North China increased slightly before its maximum at 6.5 cal ka BP and has since declined significantly. The vegetation decline since 6.5 cal ka BP has likely induced a regional albedo change and aerosol increase. Further comparison with paleoclimate and paleovegetation dynamics in South China reproduced the regional cooling effect of vegetation cover decline in North China modelled in previous work. Our discussion demonstrates that, instead of reconstructing vegetation type from a single site, reconstructing quantitative regional vegetation cover could offer a broader understanding of regional vegetation-climate feedback.     

Within-Otolith Variability in Chemical Fingerprints: Implications for Sampling Designs and Possible Environmental Interpretation

Largely used as a natural biological tag in studies of dispersal/connectivity of fish, otolith elemental fingerprinting is usually analyzed by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). LA-ICP-MS produces an elemental fingerprint at a discrete time-point in the life of a fish and can generate data on within-otolith variability of that fingerprint. The presence of within-otolith variability has been previously acknowledged but not incorporated into experimental designs on the presumed, but untested, grounds of both its negligibility compared to among-otolith variability and of spatial autocorrelation among multiple ablations within an otolith. Here, using a hierarchical sampling design of spatial variation at multiple scales in otolith chemical fingerprints for two Mediterranean coastal fishes, we explore: 1) whether multiple ablations within an otolith can be used as independent replicates for significance tests among otoliths, and 2) the implications of incorporating within-otolith variability when assessing spatial variability in otolith chemistry at a hierarchy of spatial scales (different fish, from different sites, at different locations on the Apulian Adriatic coast). We find that multiple ablations along the same daily rings do not necessarily exhibit spatial dependency within the otolith and can be used to estimate residual variability in a hierarchical sampling design. Inclusion of within-otolith measurements reveals that individuals at the same site can show significant variability in elemental uptake. Within-otolith variability examined across the spatial hierarchy identifies differences between the two fish species investigated, and this finding leads to discussion of the potential for within-otolith variability to be used as a marker for fish exposure to stressful conditions. We also demonstrate that a ‘cost’-optimal allocation of sampling effort should typically include some level of within-otolith replication in the experimental design. Our findings provide novel evidence to aid the design of future sampling programs and improve our general understanding of the mechanisms regulating elemental fingerprints.     

Inter-Individual Variability of Stone Marten Behavioral Responses to a Highway

Efforts to reduce the negative impacts of roads on wildlife may be hindered if individuals within the population vary widely in their responses to roads and mitigation strategies ignore this variability. This knowledge is particularly important for medium-sized carnivores as they are vulnerable to road mortality, while also known to use available road passages (e.g., drainage culverts) for safely crossing highways. Our goal in this study was to assess whether this apparently contradictory pattern of high road-kill numbers associated with a regular use of road passages is attributable to the variation in behavioral responses toward the highway between individuals. We investigated the responses of seven radio-tracked stone martens (Martes foina) to a highway by measuring their utilization distribution, response turning angles and highway crossing patterns. We compared the observed responses to simulated movement parameterized by the observed space use and movement characteristics of each individual, but naïve to the presence of the highway. Our results suggested that martens demonstrate a diversity of responses to the highway, including attraction, indifference, or avoidance. Martens also varied in their highway crossing patterns, with some crossing repeatedly at the same location (often coincident with highway passages). We suspect that the response variability derives from the individual''s familiarity of the landscape, including their awareness of highway passage locations. Because of these variable yet potentially attributable responses, we support the use of exclusionary fencing to guide transient (e.g., dispersers) individuals to existing passages to reduce the road-kill risk.     

Characterizing the Microbial Colonization of a Dolostone Quarry: Implications for Stone Biodeterioration and Response to Biocide Treatments

This study examines the microbial colonization of three fronts of an abandoned dolostone quarry (Redueña, Madrid, Spain) exposed to atmospheric conditions for different time periods since Roman times to the present. Through scanning electron microscopy in backscattered electron mode (SEM-BSE), endolithic colonization was predominantly detected in the most recently exposed front, while in the longer exposed quarry fronts, epilithic forms of growth were most often observed. These observations were confirmed by denaturing gradient gel electrophoresis (DGGE) analysis. Based on the distribution pattern of microbial colonization in the different quarry fronts, we then established a sequence of colonization events that took place over this long time frame. Bioalteration processes related to this sequential colonization were also identified. Characterizing these sequential processes can be useful for interpreting biodeterioration processes in historic dolostone monuments, especially those affecting constructions in the area of the Redueña stone quarry. In a second experimental stage, different biocide treatments were tested on this quarry rock to find the best way to avoid the microbial colonization effects identified. Through combined SEM-BSE/DGGE analysis, the efficacy of several biocides against the microorganisms inhabiting the dolostones was assessed after 4 and 16 months treatment. In general, all treatments were effective at reducing around 80% of the lichen cover, although effects on endolithic lithobiontic communities were dependant on how well the rock surface had been mechanically cleaned prior to treatment and gradually disappeared over time.     

Stone handling by Japanese macaques (Macaca fuscata): Implications for tool use of stone

Stone-play, a newly innovated cultural behavior, has been observed among the free-ranging Arashiyama B troop Japanese macaques near Kyoto, Japan since 1979. Conditions in which the non-purposeful handling of stones might possibly give rise to tool behavior are discussed. The progression of this behavior is traced through three phases: transmission, tradition, and transformation. During the first two phases, through social learning, the behavior was established within the group as a regular item of their behavioral repertoire and was most frequently observed after eating provisioned grain. In the third phase, observations suggest a “faddish” shift in the practice of certain behavioral sub-types between 1984 and 1985. During this period young individuals increasingly began to carry stones away from the feeding station, mixing stone manipulation with forage-feeding activities in the forest. Observations suggest under such conditions, stone handling is likely to lead to the occasional use of stone as a tool. This conclusion probably can be applied to species other thanMacaca fuscata. Consideration of the eco-setting and social learning correlates of stone handling suggests how the instrumental use of stone might emerge from a tradition of non-instrumental manipulation.     

Selectivity and Variability in the Diet of Milne-Edwards' Sifakas (Propithecus diadema edwardsi): Implications for Folivory and Seed-Eating

Propithecus diadema edwardsi combines a strategy of high selectivity for many food items with the use of more readily available and abundant foods. Selectivity is seen in relation to taxonomic affiliations of plants eaten, forest composition, and phenological patterns. Feeding time is concentrated on relatively uncommon species as indicated by high selection ratios. Annual and monthly dietary diversity is low, with food choices restricted to a relatively narrow set of species: a total of 82 and 73 plant species were eaten by the two groups of which, only 22 and 16% contributed >1% feeding time, however, these values fall with commonly reported ranges. Plant parts eaten varied widely from month to month, with overall variance in seed-eating higher than variance in young or mature leaf feeding. No correlation between percentage feeding time and food availability is significant; instead, monthly feeding patterns are better explained by the availability of particular plant species, which also supports a view of high selectivity in food choice. In contrast to selectivity for many seed, whole fruit, and new leaf sources, reliably abundant food sources appear to be leaves from lianas, epiphytes, and parasites, which were eaten in all focal months. While dramatic interannual differences in dietary composition in response to the absence of a preferred seed source highlight the interpretation of folivores as surviving food crunches by turning to readily available, poor quality resources, this strategy is not unique to folivores.     

Spatial and Temporal Variability in the Amount and Source of Dissolved Organic Carbon: Implications for Ultraviolet Exposure in Amphibian Habitats

The amount, chemical composition, and source of dissolved organic carbon (DOC), together with in situ ultraviolet (UV-B) attenuation, were measured at 1–2 week intervals throughout the summers of 1999, 2000, and 2001 at four sites in Rocky Mountain National Park (Colorado). Eight additional sites, four in Sequoia and Kings Canyon National Park/John Muir Wilderness (California) and four in Glacier National Park (Montana), were sampled during the summer of 2000. Attenuation of UV-B was significantly related to DOC concentrations over the three years in Rocky Mountain (R² = 0.39, F = 25.71, P < 0.0001) and across all parks in 2000 (R² = 0.44, F = 38.25, P < 0.0001). The relatively low R² values, however, reflect significant temporal and spatial variability in the specific attenuation per unit DOC. Fluorescence analysis of the fulvic acid DOC fraction (roughly 600–2,000 Daltons) indicated that the source of DOC significantly affected the attenuation of UV-B. Sites in Sequoia–Kings Canyon were characterized by DOC derived primarily from algal sources and showed much deeper UV-B penetration, whereas sites in Glacier and Rocky Mountain contained a mix of algal and terrestrial DOC-dominated sites, with more terrestrially dominated sites characterized by greater UV-B attenuation per unit DOC. In general, site characteristics that promoted the accumulation of terrestrially derived DOC showed greater attenuation of UV-B per unit DOC; however, catchment vegetation and soil characteristics, precipitation, and local hydrology interacted to make it difficult to predict potential exposure from DOC concentrations.     

Functional Variability of Snake Venom Metalloproteinases: Adaptive Advantages in Targeting Different Prey and Implications for Human Envenomation

Snake venom metalloproteinases (SVMPs) are major components in most viperid venoms that induce disturbances in the hemostatic system and tissues of animals envenomated by snakes. These disturbances are involved in human pathology of snake bites and appear to be essential for the capture and digestion of snake''s prey and avoidance of predators. SVMPs are a versatile family of venom toxins acting on different hemostatic targets which are present in venoms in distinct structural forms. However, the reason why a large number of different SVMPs are expressed in some venoms is still unclear. In this study, we evaluated the interference of five isolated SVMPs in blood coagulation of humans, birds and small rodents. P-III class SVMPs (fractions Ic, IIb and IIc) possess gelatinolytic and hemorrhagic activities, and, of these, two also show fibrinolytic activity. P-I class SVMPs (fractions IVa and IVb) are only fibrinolytic. P-III class SVMPs reduced clotting time of human plasma. Fraction IIc was characterized as prothrombin activator and fraction Ic as factor X activator. In the absence of Ca²⁺, a firm clot was observed in chicken blood samples with fractions Ic, IIb and partially with fraction IIc. In contrast, without Ca²⁺, only fraction IIc was able to induce a firm clot in rat blood. In conclusion, functionally distinct forms of SVMPs were found in B. neuwiedi venom that affect distinct mechanisms in the coagulation system of humans, birds and small rodents. Distinct SVMPs appear to be more specialized to rat or chicken blood, strengthening the current hypothesis that toxin diversity enhances the possibilities of the snakes for hunting different prey or evading different predators. This functional diversity also impacts the complexity of human envenoming since different hemostatic mechanisms will be targeted by SVMPs accounting for the complexity of the response of humans to venoms.     

Individual Nuclei Differ in Their Sensitivity to the Cytoplasmic Inducers of DNA Synthesis: Implications for the Origin of Cell Cycle Variability

Nuclei of multinucleate cells generally initiate DNA synthesis simultaneously, suggesting that the timing of DNA synthesis depends upon the appearance of a cytoplasmic signal. In contrast, intact nuclei from quiescent mammalian cells initiate DNA synthesisasynchronouslyin cell-free extracts ofXenopuseggs, despite the common environment. Here we show that the two nuclei of permeabilized binucleate cells enter DNA synthesis coordinately in egg extracts, as they doin vivo,with different pairs of nuclei initiating replication at different times. This indicates that the two nuclei of a binucleate cell are identical in their sensitivity to the inducers of DNA synthesis in egg extracts; this sensitivity varies in general between the nuclei of unrelated cells. The asynchrony of DNA synthesis shown by unrelated nuclei in egg extracts is therefore not an artifact of the cell-free system but a reflection of genuine differences preexisting within the intact cell. Evidence that these differences between nuclei are responsible for a substantial fraction of G₁variability in living cells is presented.     

Correlated Variability in the Breathing Pattern and End-Expiratory Lung Volumes in Conscious Humans

In order to characterize the variability and correlation properties of spontaneous breathing in humans, the breathing pattern of 16 seated healthy subjects was studied during 40 min of quiet breathing using opto-electronic plethysmography, a contactless technology that measures total and compartmental chest wall volumes without interfering with the subjects breathing. From these signals, tidal volume (V_T), respiratory time (T_TOT) and the other breathing pattern parameters were computed breath-by-breath together with the end-expiratory total and compartmental (pulmonary rib cage and abdomen) chest wall volume changes. The correlation properties of these variables were quantified by detrended fluctuation analysis, computing the scaling exponentα. V_T, T_TOT and the other breathing pattern variables showed α values between 0.60 (for minute ventilation) to 0.71 (for respiratory rate), all significantly lower than the ones obtained for end-expiratory volumes, that ranged between 1.05 (for rib cage) and 1.13 (for abdomen) with no significant differences between compartments. The much stronger long-range correlations of the end expiratory volumes were interpreted by a neuromechanical network model consisting of five neuron groups in the brain respiratory center coupled with the mechanical properties of the respiratory system modeled as a simple Kelvin body. The model-based α for V_T is 0.57, similar to the experimental data. While the α for T_TOT was slightly lower than the experimental values, the model correctly predicted α for end-expiratory lung volumes (1.045). In conclusion, we propose that the correlations in the timing and amplitude of the physiological variables originate from the brain with the exception of end-expiratory lung volume, which shows the strongest correlations largely due to the contribution of the viscoelastic properties of the tissues. This cycle-by-cycle variability may have a significant impact on the functioning of adherent cells in the respiratory system.