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Highlights • We explore a simple quantitative model of selection by survival - the hypothesis that biospheres can acquire persistence-enhancing adaptations by chance over time. • We compare the survival rates of a set of biospheres undergoing selection by survival to a null hypothesis of survival by pure chance, and to biospheres with added feedback from the environment to the biosphere. • We find that selection by survival alone can increase a biosphere's survival probability. • We find that feedback can either hinder or enhance the persistence of a biosphere depending on the strength of the feedback and how closely initial conditions match those ideal for life. Abstract A long-standing objection to the Gaia hypothesis has been a perceived lack of plausible mechanisms by which life on Earth could come to regulate its abiotic environment. A null hypothesis is survival by pure chance, by which any appearance of regulation on Earth is illusory and the persistence of life simply reflects the weak anthropic principle - it must have occurred for intelligent observers to ask the question. Recent work has proposed that persistence alone increases the chance that a biosphere will acquire further persistence-enhancing properties. Here we use a simple quantitative model to show that such 'selection by survival alone' can indeed increase the probability that a biosphere will persist in the future, relative to a baseline of pure chance. Adding environmental feedback to this model shows either an increased or decreased survival probability depending on the initial conditions. Feedback can hinder early life becoming established if initial conditions are poor, but feedback can also prevent systems from diverging too far from optimum environmental conditions and thus increase survival rates. The outstanding question remains the relative importance of each mechanism for the historical and continued persistence of life on Earth. [ABSTRACT FROM AUTHOR]

The analysis of 87Sr/86Sr isotope ratios in human and nonhuman tooth enamel is used worldwide for archaeological and forensic purposes to establish if an individual is likely to have grown up in the area from which their remains were excavated. The English Peak District has produced an unusually high proportion of archaeological humans who, based on Sr isotope ratios, appear to have come from elsewhere. We have used modern plant samples from the Peak to show that the current understanding of Sr isotope ratios for this area is incomplete – we found many plant samples growing on gritstone sediments had higher Sr values than would be expected based on the current literature. In addition we demonstrated that the taxonomy of the plant does not appear to affect the Sr isotope values (we also found that mycorrhizal type did not determine Sr isotope values in these plants), rather it is the substrate on which it is growing that is important. In terms of human movement, our work suggests it is likely that many archaeological individuals found in the Peak District are indeed local, rather than migrants. It is also possible that the expansion of blanket peat in the Peak has over time reduced the amount of Sr entering the food chain from mineral soils, reducing the radiogenic Sr isotope values in more recent teeth. While our case study is the Peak District, our findings have implications for anomalously high archaeological 87Sr/86Sr isotope values in other upland regions with similar geologies and blanket peats. • Analysis of plant remains in from the Peak District, England identified 87Sr/86Sr isotope values, greater than those expected in the local biosphere. • Neither plant species or mycorrhizal type were related to high Sr isotope ratios, instead plants yielding these values are growing on mineral soils directly overlying gritstones. • These mineral soils have been covered by peat during the Holocene, reducing their availability for grazing and agriculture. This long-term change may indicate why some of the Peak prehistoric sites appear to have high levels of migrants compared to the present day. [ABSTRACT FROM AUTHOR]

The Gaia hypothesis postulates that life influences Earth's feedback mechanisms to form a self regulating system. This provokes the question: how can global self-regulation evolve? Most models demonstrating environmental regulation involving life have relied on alignment between local selection and global regulation. In these models environment-improving individuals or communities spread to outcompete environment degrading individuals/communities, leading to global regulation, but this depends on local differences in environmental conditions. In contrast, well-mixed components of the Earth system, such as the atmosphere, lack local environmental differentiation. These previous models do not explain how global regulation can emerge in a system with no well defined local environment, or where the local environment is overwhelmed by global effects. We present a model of self-regulation by ‘microbes’ in an environment with no spatial structure. These microbes affect an abiotic ‘temperature’ as a byproduct of metabolism. We demonstrate that global self-regulation can arise in the absence of spatial structure in a diverse ecosystem without localised environmental effects. We find that systems can exhibit nutrient limitation and two temperature limitation regimes where the temperature is maintained at a near constant value. During temperature regulation, the total temperature change caused by the microbes is kept near constant by the total population expanding or contracting to absorb the impacts of new mutants on the average affect on the temperature per microbe. Dramatic shifts between low temperature regulation and high temperature regulation can occur when a mutant arises that causes the sign of the temperature effect to change. This result implies that self-regulating feedback loops can arise without the need for spatial structure, weakening criticisms of the Gaia hypothesis that state that with just one Earth, global regulation has no mechanism for developing because natural selection requires selection between multiple entities. [ABSTRACT FROM AUTHOR]

The normal distribution remains the most widely used statistical model, so it is only natural that researchers will frequently be required to consider whether a sample of data appears to have been drawn from a normal distribution. Commonly used statistical packages offer a range of alternative formal statistical tests of the null hypothesis of normality, with inference being drawn on the basis of a calculated P value. Here we review the statistical literature on the performance of these tests and briefly survey current usage of them in recently published papers, with a view to offering advice on good practice. We find that authors in Animal Behaviour seem to be using such testing most commonly in situations in which it is inadvisable (or at best unnecessary) involving pretesting to select parametric or nonparametric analyses, and making little use of it in model-fitting situations in which it might be of value. Of the many alternative tests, we recommend the routine use of either the Shapiro–Wilk or Chen–Shapiro tests; these are almost always superior to commonly used alternatives such as the Kolmogorov–Smirnov test, often by a substantial margin. We describe how both our recommended tests can be implemented. In contrast to current practice as indicated by our survey, we recommend that the results of these tests are reported in more detail (providing both the calculated sample statistic and the associated P value). Finally, we emphasize that even the higher-performing tests of normality have low power (generally below 0.5 and often much lower) when sample sizes are less than 50, as is often the case in our field. [ABSTRACT FROM AUTHOR]

Abstract: We modify an existing model of the population trajectory on an island after the first arrival of a group of hominins to compare the potential success rates of accidental arrival (e.g., on vegetation rafts following major floods or a tsunami) against planned colonisation by watercraft. Our model predicts that colonisation through the accidental arrival of a group of individuals on an island should be around half as likely to be successful as colonisation through the arrival of a planned voyaging party of the same size, but that this difference could be entirely counteracted by the infrequent arrival of small numbers of individuals by similar accidental circumstances in the centuries after the initial colonisation. We argue that our model investigations strengthen the plausibility that especially early island colonisation (such as Homo erectus on Flores) may have occurred as a result of highly anomalous natural events (such as a tsunami), and thus hominin colonisation of islands outside swimming range of continents should not be seen as necessarily indicating the existences of seafaring technologies and skills. [Copyright &y& Elsevier]

Abstract: Thermoregulation is often cited as a potentially important influence on the evolution of hominins, thanks to a highly influential series of papers in the Journal of Human Evolution in the 1980s and 1990s by Peter Wheeler. These papers developed quantitative modeling of heat balance between different potential hominins and their environment. Here, we return to these models, update them in line with new developments and measurements in animal thermal biology, and modify them to represent a running hominin rather than the stationary form considered previously. In particular, we use our modified Wheeler model to investigate thermoregulatory aspects of the evolution of endurance running ability. Our model suggests that for endurance running to be possible, a hominin would need locomotive efficiency, sweating rates, and areas of hairless skin similar to modern humans. We argue that these restrictions suggest that endurance running may have been possible (from a thermoregulatory viewpoint) for Homo erectus, but is unlikely for any earlier hominins. [Copyright &y& Elsevier]

Abstract: Morpholino antisense oligonucleotides (MOs) are widely used as a tool to achieve loss of gene function, but many have off-target effects mediated by activation of Tp53 and associated apoptosis. Here, we re-examine our previous MO-based loss-of-function studies that had suggested that Wnt1 expressed at hindbrain boundaries in zebrafish promotes neurogenesis and inhibits boundary marker gene expression in the adjacent para-boundary regions. We find that Tp53 is highly activated and apoptosis is frequently induced by the MOs used in these studies. Co-knockdown of Tp53 rescues the decrease in proneural and neuronal marker expression, which is thus an off-target effect of MOs. While loss of gene expression can be attributed to cell loss through apoptotic cell death, surprisingly we find that the ectopic expression of hindbrain boundary markers is also dependent on Tp53 activity and its downstream apoptotic effectors. We examine whether this non-specific activation of hindbrain boundary gene expression provides insight into the endogenous mechanisms underlying boundary cell specification. We find that the pro-apoptotic Bcl genes puma and bax-a are required for hindbrain boundary marker expression, and that gain of function of the Bcl-caspase pathway leads to ectopic boundary marker expression. These data reveal a non-apoptotic role for pro-apoptotic genes in the regulation of gene expression at hindbrain boundaries. In light of these findings, we discuss the precautions needed in performing morpholino knockdowns and in interpreting the data derived from their use. [Copyright &y& Elsevier]

Abstract: A network of molecular interactions is required in the developing vertebrate hindbrain for the formation and anterior–posterior patterning of the rhombomeres. FGF signaling is required in this network to upregulate the expression of the Krox20 and Kreisler segmentation genes, but little is known of how FGF gene expression is regulated in the hindbrain. We show that the dynamic expression of FGF3 in chick hindbrain segments and boundaries is similar to that of the BMP antagonist, follistatin. Consistent with a regulatory relationship between BMP signaling and FGF3 expression, we find that an increase in BMP activity due to blocking of follistatin translation by morpholino antisense oligonucleotides or overexpression of BMP results in strong inhibition of FGF3 expression. Conversely, addition of follistatin leads to an increase in the level of FGF3 expression. Furthermore, the segmental inhibition of BMP activity by follistatin is required for the expression of Krox20, Hoxb1 and EphA4 in the hindbrain. In addition, we show that the maintenance of FGF3 gene expression requires FGF activity, suggestive of an autoregulatory loop. These results reveal an antagonistic relationship between BMP activity and FGF3 expression that is required for correct segmental gene expression in the chick hindbrain, in which follistatin enables FGF3 expression by inhibiting BMP activity. [Copyright &y& Elsevier]

Many geometric shapes retain their symmetry when bisected, but appear asymmetrical when misbisected. We have previously shown that this correspondence can guide the accuracy and speed of perceptual bisection (Landmark) judgments. Using event-related fMRI, here we examined whether the behavioural effects of symmetry are also evident at the neural level. The data showed that the presence/absence of symmetry modulates the activity of right anterior cingulate gyrus, an area associated with a variety of higher level attentional functions. A previous visual half-field study also showed that bisected lines are apprehended more quickly and accurately than misbisected lines in right, but not left, visual field. We were able to localise this advantage to right superior temporal gyrus. Significantly, we found no evidence that symmetry played a role in apprehending the midpoint of the line stimuli traditionally used to assess visual neglect. The data clarify the effects of visual symmetry on bisection behaviour, and highlight novel dissociations within the neural systems thought to underline Landmark performance. [Copyright &y& Elsevier]

The superior parietal lobe has been associated with the spatial integration of visual features, an important step in the detection of particular form conjunctions. However, behavioral research has indicated that when target items can be segmented from neighboring distracters via similarity grouping, detection may not rely on spatial integration. The question therefore arises as to whether the superior parietal cortex is an integral component of conjunction search or only important in the absence of certain grouping relations. Here, we acquired measures of reaction time and event-related fMRI, while subjects searched for conjunction targets in displays containing either homogeneous or heterogeneous distracters. We confirm that under conditions of low distracter similarity, search involves parietal-motor areas associated with spatial selection. However, we also demonstrate that under conditions of high distracter similarity, search is instead associated with activation of right temporal-parietal cortex. These results suggest that the superior parietal cortex is not a necessary component of visual conjunction search and highlight a new role for the right temporal-parietal cortex in perceptual grouping. [Copyright &y& Elsevier]

Fungi are a common part of modern human diets, but are rarely discussed in an archaeological context. Power et al. (2015) published data on bolete spores in human tooth calculus, suggesting that Upper Palaeolithic peoples ate mushrooms. Here we briefly consider the likelihood of mushroom consumption in the past, and examine whether or not stable isotopes may provide a way of seeing this in archaeological populations. We also consider the complexities of fungal stable isotopes using our own data and that from the literature. We conclude that fungi are highly variable isotopically, and are an additional dietary factor that should be considered when trying to interpret ‘terrestrial’ carbon isotope signatures combined with relatively high nitrogen isotope values in humans and other animals. Substantial mushroom ingestion could, in some cases, result in isotope values that may be interpreted as considerable meat consumption. [ABSTRACT FROM AUTHOR]

The formation of sharp borders, across which cell intermingling is restricted, has a crucial role in the establishment and maintenance of organized tissues. Signaling of Eph receptors and ephrins underlies formation of a number of boundaries between and within tissues during vertebrate development. Eph–ephrin signaling can regulate several types of cell response—adhesion, repulsion and tension—that can in principle underlie the segregation of cells and formation of sharp borders. Recent studies have implicated each of these cell responses as having important roles at different boundaries: repulsion at the mesoderm–ectoderm border, decreased adhesion at the notochord–presomitic mesoderm border, and tension at boundaries within the hindbrain and forebrain. These distinct responses to Eph receptor and ephrin activation may in part be due to the adhesive properties of the tissue. [ABSTRACT FROM AUTHOR]

Transcript variants of the same gene may play distinct functions in the tissue where they are expressed. Absolute quantitation of different transcript variants in malignant and normal tissues can address the specific role of each particular isoform in cancer development and progression. We have recently demonstrated differential expression of the wild-type Wilms’ tumor transcript (wtWT1) and a novel truncated WT1 transcript (trWT1) which lacks the first five exons of wtWT1, among human prostate cancer, leukemia, and breast cancer cell lines. Here we report the analytical validation of a real-time RT-PCR assay for the absolute quantitation of these two different WT1 transcripts with specific primers and probes that ensure specificity for each WT1 variant. By cloning each WT1 transcript in a T3 promoter-containing plasmid, we obtained two WT1 transcript-specific in vitro-generated RNA calibrators for absolute quantitation. Serial dilution of each RNA calibrator demonstrated a 5 log linear dynamic range (5×101 to 5×106 copies/reaction, R2=0.9963 for wtWT1 and R2=0.9993 for trWT1). Dilution of the calibrators in total RNA from 1×103 non-WT1-expressing cells showed a decreased sensitivity without affecting the linear dynamic range. Precision studies for values within the linear dynamic range showed a coefficient of variation of less than 4% for both transcripts. The described method provides a sensitive and reliable technique for quantitating different WT1 mRNA transcripts. [Copyright &y& Elsevier]

Eph receptor and ephrin signaling has a major role in segregating distinct cell populations to form sharp borders. Expression of interacting Ephs and ephrins typically occurs in complementary regions, such that polarised activation of both components occurs at the interface. Forward signaling through Eph receptors can drive cell segregation, but it is unclear whether reverse signaling through ephrins can also contribute. We have tested the role of reverse signaling, and of polarised versus non-polarised activation, in assays in which contact repulsion drives cell segregation and border sharpening. We find that polarised forward signaling drives stronger segregation than polarised reverse signaling. Nevertheless, reverse signaling contributes since bidirectional Eph and ephrin activation drives stronger segregation than unidirectional forward signaling alone. In contrast, non-polarised Eph activation drives little segregation. We propose that although polarised forward signaling is the principal driver of segregation, reverse signaling enables bidirectional repulsion which prevents mingling of each population into the other. • Polarised forward and reverse signaling by EphB2 and ephrinB1 drives strong cell segregation and border sharpening. • Disruption of reverse signaling in ephrinB1-6F mutant leads to decrease in cell segregation. • Polarised forward signaling drives stronger cell segregation than polarised reverse signaling. • Non-polarised EphB2 activation leads to little if any cell segregation. • Bidirectional forward and reverse signaling drives strong segregation by preventing intermingling in both directions. [ABSTRACT FROM AUTHOR]

UV-irradiated fluidized bed reactor system and Pt-loaded TiO 2 spheres were developed for photocatalytic water splitting. This novel approach was explored as a means to minimize the parasitic back reaction, mass transport and radiation distribution effects that limit the performance and scalability of immobilized-film and suspended slurry photocatalysts typically employed for photocatalytic hydrogen production. By fluidizing Pt-loaded TiO 2 spheres in a 2.2 M Na 2 CO 3 solution, steady hydrogen production rates up to 211 μmol/h with an apparent quantum efficiency of 1.33% were achieved upon UV-irradiation. This demonstrates a marked 44% increase in the apparent quantum efficiency when compared to the performance of a traditional Pt-loaded TiO 2 suspended slurry photocatalyst in the same reactor. It is hypothesized that this enhanced performance is primarily due to improved separation of the evolved H 2 and O 2 from the Pt-loaded photocatalyst particles, thus reducing the parasitic back reaction. [ABSTRACT FROM AUTHOR]

High-density oligonucleotide microarray analysis has proven to be an excellent approach for gene expression profiling in human cancers. This technique assesses the expression of thousands of genes simultaneously, from at least 5 μg of total RNA per sample per experiment. This total RNA requirement poses a challenge when studying small, unique clinical samples, like biopsies. Recently, a new standardized protocol for small samples was released by Affymetrix, which includes a linear amplification step. To evaluate the impact of such amplification in the gene expression profiling of human ovarian cancer, we compared results obtained from 5 μg and 100 ng of total RNA from the same tumor sample, using the standard Affymetrix protocol and the new linear RNA amplification protocol, respectively. We identified a small bias in gene expression data caused by linear amplification, potentially due to shorter elongation products leading to misclassification of probe sets directed to the middle-5′ region of the transcripts. Interestingly, the magnitude of the bias varied when different normalization and expression summary algorithms were used. However, this bias does not affect tumor gene expression profiling. Consequently, linear amplification may be of utility in cases of extremely low RNA recovery from critical and unique samples, such as small biopsies. [Copyright &y& Elsevier]

Within the developing vertebrate head, the migration of neural tube-derived neural crest cells (NCCs) through the cranial mesenchyme is patterned into three streams, with mesenchyme adjacent to rhombomeres (r)3 and r5 maintained NCC-free. The receptor tyrosine kinase erbB4 is expressed within r3 and r5 and is required to maintain the r3-adjacent NCC-free zone in mouse embryos. In this study, we demonstrate that the extent of r3 involvement in patterning mouse NCC migration is restricted to the same dorsolateral region regulated by erbB4. In chick embryos, we show that erbB4 signaling similarly maintains the r3-adjacent NCC-free zone. However, although r5 expresses erbB4, this is insufficient to maintain the r3-adjacent NCC-free zone in grafting experiments where r5 replaced r3, indicating that erbB4 requires additional factors at the A–P level of r3 to pattern NCC migration. Furthermore, we show that the r5-adjacent NCC-free zone is maintained independently of r5, but requires surface ectoderm. Finally, we demonstrate that avian cranial surface ectoderm is patterned molecularly, with dorsolateral surface ectoderm at the levels of r2/3 and r7 expressing the sulfatase QSulf1 in quail, or the orthologue CSulf1 in chick. Aberrant NCC migration into r3-adjacent mesenchyme correlated with more focused QSulf1 expression in r2/3 surface ectoderm. [Copyright &y& Elsevier]

Loss of heterozygosity (LOH) of chromosomal regions is crucial in tumor progression. In this study we assessed the potential of the Affymetrix GeneChip HuSNP mapping assay for detecting genome-wide LOH in prostate tumors. We analyzed two human prostate cell lines, P69SV40Tag (P69) and its tumorigenic subline, M12, and 11 prostate cancer cases. The M12 cells showed LOH in chromosomes 3p12.1-p22.1, 11q22.1-q24.2, 19p13.12, and 19q13.42. All of the prostate cases with informative single-nucleotide polymorphism (SNP) markers showed LOH in 1p31.2, 10q11.21, 12p13.1, 16q23.1-q23.2, 17p13.3, 17q21.31, and 21q21.2. Additionally, a high percentage of cases showed LOH at 6p25.1-p25.3 (75%), 8p22-p23.2, and 10q22.1 (70%). Several tumor suppressor genes (TSGs) have been mapped in these loci. These results demonstrate that the HuSNP mapping assay can serve as an alternative to comparative genomic hybridization for assessing genome-wide LOH and can identify chromosomal regions harboring candidate TSGs implicated in prostate cancer. [Copyright &y& Elsevier]