Development and validation of a novel 15‐CpG‐based signature for predicting prognosis in triple‐negative breast cancer

DNA methylation is an important biological regulatory mechanism that changes gene expression without altering the DNA sequence. Increasing studies have revealed that DNA methylation data play a vital role in the field of oncology. However, the methylation site signature in triple‐negative breast cancer (TNBC) remains unknown. In our research, we analysed 158 TNBC samples and 98 noncancerous samples from The Cancer Genome Atlas (TCGA) in three phases. In the discovery phase, 86 CpGs were identified by univariate Cox proportional hazards regression (CPHR) analyses to be significantly correlated with overall survival (P < 0.01). In the training phase, these candidate CpGs were further narrowed down to a 15‐CpG‐based signature by conducting least absolute shrinkage and selector operator (LASSO) Cox regression in the training set. In the validation phase, the 15‐CpG‐based signature was verified using two different internal sets and one external validation set. Furthermore, a nomogram comprising the CpG‐based signature and TNM stage was generated to predict the 1‐, 3‐ and 5‐year overall survival in the primary set, and it showed excellent performance in the three validation sets (concordance indexes: 0.924, 0.974 and 0.637). This study showed that our nomogram has a precise predictive effect on the prognosis of TNBC and can potentially be implemented for clinical treatment and diagnosis.     

Undertaking large‐scale forest restoration to generate ecosystem services

The global community is seeking to substantially restore the world's forest cover to improve the supply of ecosystem services. However, it is not clear what type of reforestation must be used and there is a risk that the techniques used in industrial timber plantations will become the default methodology. This is unlikely to be sufficient because of the well‐known relationship between biodiversity and ecological functioning. Restoration may be achieved through natural regeneration but this may not always occur at critical locations. Ecological restoration involving species‐rich plantings might also be used but can be difficult to implement at landscape scales. I review here the consequence of planting more limited numbers of species and the effects of this on the delivery of ecosystem services. Evidence suggests many commonly sought ecosystem services—though not all—may be generated by the modest levels of species richness provided these species have appropriate traits. The literature also shows that the alpha diversity of restored forests is not the only driver of functionality and that the location and extent of any reforestation are significant as well; beta and gamma diversity may also affect functionality but these relationships remain unclear. Encouraging the adoption of even moderately diverse plantings at landscape scales and at key locations will require policies and institutions to balance the type, location, and scale of restoration and make the necessary trade‐offs between national and local aspirations. New approaches and metrics will have to be developed to monitor and assess restoration success at these larger scales.     

Modelling responses of pine savannas to climate change and large‐scale disturbance

Global warming can potentially influence ecological communities through altered disturbance regimes in addition to increased temperatures. We investigate the response of pine savannas in the southeastern United States to global warming using a simple Lotka‐Volterra competition model together with predicted changes to fire and hurricane disturbance regimes with global climate change. In the southeastern United States, decreased frequency of both fires and hurricanes with global warming will shift pine savannas toward a forested state. A CO₂ fertilization effect that increases the growth rate of tree populations will also push southeastern landscapes from open savannas towards closed forests. Transient dynamics associated with climate driven changes in vegetation will last on the order of decades to a century. In our model, the sensitivity of savannas to relative changes in the frequency of fire versus hurricanes is linearly dependent on the growth rate and mortality of trees in fire and hurricane disturbances.     

Phenoscope: an automated large‐scale phenotyping platform offering high spatial homogeneity

Increased phenotyping accuracy and throughput are necessary to improve our understanding of quantitative variation and to be able to deconstruct complex traits such as those involved in growth responses to the environment. Still, only a few facilities are known to handle individual plants of small stature for non‐destructive, real‐time phenotype acquisition from plants grown in precisely adjusted and variable experimental conditions. Here, we describe Phenoscope, a high‐throughput phenotyping platform that has the unique feature of continuously rotating 735 individual pots over a table. It automatically adjusts watering and is equipped with a zenithal imaging system to monitor rosette size and expansion rate during the vegetative stage, with automatic image analysis allowing manual correction. When applied to Arabidopsis thaliana, we show that rotating the pots strongly reduced micro‐environmental disparity: heterogeneity in evaporation was cut by a factor of 2.5 and the number of replicates needed to detect a specific mild genotypic effect was reduced by a factor of 3. In addition, by controlling a large proportion of the micro‐environmental variance, other tangible sources of variance become noticeable. Overall, Phenoscope makes it possible to perform large‐scale experiments that would not be possible or reproducible by hand. When applied to a typical quantitative trait loci (QTL) mapping experiment, we show that mapping power is more limited by genetic complexity than phenotyping accuracy. This will help to draw a more general picture as to how genetic diversity shapes phenotypic variation.     

Methyl‐CpG‐binding protein 2 polymorphisms and vulnerability to autism

The methyl‐binding protein gene, MECP2, is a candidate for involvement in autism through its implication as a major causative factor in Rett syndrome that has similarities to autism. Rare mutations in MECP2 have also been identified in autistic individuals. We have examined the possible broader involvement of MECP2 as a predisposing factor in the disorder. Analysis of polymorphic markers spanning the gene and comprising both microsatellites and single nucleotide polymorphisms (SNPs) by the transmission disequilibrium test in two collections of families (219 in total), one in the USA and one in the UK, has provided evidence for significant association (P = 0.009) for a three‐marker SNP haplotype of MECP2 with autism/autism spectrum disorders. This association is supported by association of both Single Sequence Repeat (SSR) and SNP single markers located at the 3′ end of the MECP2 locus and flanking sequence, the most significant being that of an indel marker located in intron 2 (P = 0.001 – Bonferroni corrected P = 0.006). This suggests that one or more functional variants of MECP2 existing at significant frequencies in the population may confer increased risk of autism/autism spectrum disorders and warrants further investigation in additional independent samples.     

Comparison of sample preparation techniques for large‐scale proteomics

Numerous workflows exist for large‐scale bottom‐up proteomics, many of which achieve exceptional proteome depth. Herein, we evaluated the performance of several commonly used sample preparation techniques for proteomic characterization of HeLa lysates [unfractionated in‐solution digests, SDS‐PAGE coupled with in‐gel digestion, gel‐eluted liquid fraction entrapment electrophoresis (GELFrEE) technology, SCX StageTips and high‐/low‐pH reversed phase fractionation (HpH)]. HpH fractionation was found to be superior in terms of proteome depth (>8400 proteins detected) and fractionation efficiency compared to other techniques. SCX StageTip fractionation required minimal sample handling and was also a substantial improvement over SDS‐PAGE separation and GELFrEE technology. Sequence coverage of the HeLa proteome increased to 38% when combining all workflows, however, total proteins detected improved only slightly to 8710. In summary, HpH fractionation and SCX StageTips are robust techniques and highly suited for complex proteome analysis.     

A review of current large‐scale mouse knockout efforts

After the successful completion of the human genome project (HGP), biological research in the postgenome era urgently needs an efficient approach for functional analysis of genes. Utilization of knockout mouse models has been powerful for elucidating the function of genes as well as finding new therapeutic interventions for human diseases. Gene trapping and gene targeting are two independent techniques for making knockout mice from embryonic stem (ES) cells. Gene trapping is high‐throughput, random, and sequence‐tagged while gene targeting enables the knockout of specific genes. It has been about 20 years since the first gene targeting and gene trapping mice were generated. In recent years, new tools have emerged for both gene targeting and gene trapping, and organizations have been formed to knock out genes in the mouse genome using either of the two methods. The knockout mouse project (KOMP) and the international gene trap consortium (IGTC) were initiated to create convenient resources for scientific research worldwide and knock out all the mouse genes. Organizers of KOMP regard it as important as the HGP. Gene targeting methods have changed from conventional gene targeting to high‐throughput conditional gene targeting. The combined advantages of trapping and targeting elements are improving the gene trapping spectrum and gene targeting efficiency. As a newly‐developed insertional mutation system, transposons have some advantages over retrovirus in trapping genes. Emergence of the international knockout mouse consortium (IKMP) is the beginning of a global collaboration to systematically knock out all the genes in the mouse genome for functional genomic research. genesis 48:73–85, 2010. © 2010 Wiley‐Liss, Inc.     

The biology and polymer physics underlying large‐scale chromosome organization

Chromosome large‐scale organization is a beautiful example of the interplay between physics and biology. DNA molecules are polymers and thus belong to the class of molecules for which physicists have developed models and formulated testable hypotheses to understand their arrangement and dynamic properties in solution, based on the principles of polymer physics. Biologists documented and discovered the biochemical basis for the structure, function and dynamic spatial organization of chromosomes in cells. The underlying principles of chromosome organization have recently been revealed in unprecedented detail using high‐resolution chromosome capture technology that can simultaneously detect chromosome contact sites throughout the genome. These independent lines of investigation have now converged on a model in which DNA loops, generated by the loop extrusion mechanism, are the basic organizational and functional units of the chromosome.      

Ensemble modeling to predict habitat suitability for a large‐scale disturbance specialist

To conserve habitat for disturbance specialist species, ecologists must identify where individuals will likely settle in newly disturbed areas. Habitat suitability models can predict which sites at new disturbances will most likely attract specialists. Without validation data from newly disturbed areas, however, the best approach for maximizing predictive accuracy can be unclear (Northwestern U.S.A.). We predicted habitat suitability for nesting Black‐backed Woodpeckers (Picoides arcticus; a burned‐forest specialist) at 20 recently (≤6 years postwildfire) burned locations in Montana using models calibrated with data from three locations in Washington, Oregon, and Idaho. We developed 8 models using three techniques (weighted logistic regression, Maxent, and Mahalanobis D² models) and various combinations of four environmental variables describing burn severity, the north–south orientation of topographic slope, and prefire canopy cover. After translating model predictions into binary classifications (0 = low suitability to unsuitable, 1 = high to moderate suitability), we compiled “ensemble predictions,” consisting of the number of models (0–8) predicting any given site as highly suitable. The suitability status for 40% of the area burned by eastside Montana wildfires was consistent across models and therefore robust to uncertainty in the relative accuracy of particular models and in alternative ecological hypotheses they described. Ensemble predictions exhibited two desirable properties: (1) a positive relationship with apparent rates of nest occurrence at calibration locations and (2) declining model agreement outside surveyed environments consistent with our reduced confidence in novel (i.e., “no‐analogue”) environments. Areas of disagreement among models suggested where future surveys could help validate and refine models for an improved understanding of Black‐backed Woodpecker nesting habitat relationships. Ensemble predictions presented here can help guide managers attempting to balance salvage logging with habitat conservation in burned‐forest landscapes where black‐backed woodpecker nest location data are not immediately available. Ensemble modeling represents a promising tool for guiding conservation of large‐scale disturbance specialists.     

Trade‐offs between land and water requirements for large‐scale bioenergy production

Bioenergy is expected to play an important role in the future energy mix as it can substitute fossil fuels and contribute to climate change mitigation. However, large‐scale bioenergy cultivation may put substantial pressure on land and water resources. While irrigated bioenergy production can reduce the pressure on land due to higher yields, associated irrigation water requirements may lead to degradation of freshwater ecosystems and to conflicts with other potential users. In this article, we investigate the trade‐offs between land and water requirements of large‐scale bioenergy production. To this end, we adopt an exogenous demand trajectory for bioenergy from dedicated energy crops, targeted at limiting greenhouse gas emissions in the energy sector to 1100 Gt carbon dioxide equivalent until 2095. We then use the spatially explicit global land‐ and water‐use allocation model MAgPIE to project the implications of this bioenergy target for global land and water resources. We find that producing 300 EJ yr^?1 of bioenergy in 2095 from dedicated bioenergy crops is likely to double agricultural water withdrawals if no explicit water protection policies are implemented. Since current human water withdrawals are dominated by agriculture and already lead to ecosystem degradation and biodiversity loss, such a doubling will pose a severe threat to freshwater ecosystems. If irrigated bioenergy production is prohibited to prevent negative impacts of bioenergy cultivation on water resources, bioenergy land requirements for meeting a 300 EJ yr^?1 bioenergy target increase substantially (+ 41%) – mainly at the expense of pasture areas and tropical forests. Thus, avoiding negative environmental impacts of large‐scale bioenergy production will require policies that balance associated water and land requirements.     

Predicting effects of large‐scale reforestation on native and exotic birds

Aim

Ecological restoration is critical for recovering biodiversity and ecosystem services, yet designing interventions to achieve particular outcomes remains fraught with challenges. In the extensive regions where non‐native species are firmly established, it is unlikely that historical conditions can be fully reinstated. To what degree, and how rapidly, can human‐dominated areas be shifted via restoration into regimes that benefit target species, communities or processes?

Location

We explore this question in a >20‐year‐old reforestation effort underway at Hakalau Forest National Wildlife Refuge in montane Hawaii. This large‐scale planting of Acacia koa trees is designed to secure populations of globally threatened bird species by transitioning the site rapidly from pasture to native forest.

Methods

We surveyed all forest birds in multiple corridors of young planted trees, remnant corridors of mature trees along gulches and at sites within mature forest. Using a Bayesian hierarchical approach, we identified which factors (distance from forest, habitat type and surrounding tree cover) had the most important influence on native and exotic bird abundance in the reforestation area.

Results

We found that 90% of native and exotic bird species responded quickly, occupying corridors of native trees approximately a decade after planting. However, native and exotic forest birds responded to markedly different characteristics of the reforested area. Native bird abundance was strongly predicted by proximity to mature forest and remnant corridors; conversely, exotic bird abundance was best predicted by overall tree cover throughout the area reforested.

Main conclusions

Our results demonstrate that large‐scale tree planting in corridors adjacent to mature forest can catalyse rapid recovery (both increased abundance and expanded distribution) of forest birds and that it is possible to design reforestation to benefit native species in novel ecosystems.

     

Aesthetic demand of French seniors: a large‐scale study

doi:10.1111/j.1741‐2358.2009.00331.x
Aesthetic demand of French seniors: a large‐scale study Objectives: The needs of seniors for oral health and aesthetics are growing, as are their demands for aesthetics. This large‐scale study aims to identify the demand for aesthetics for a population aged over 55, and the influence of age and gender. Methods: A 15‐item questionnaire was placed on the web in partnership with a major magazine dedicated to seniors. It reflected practitioners’ questions with regard to senior patient expectations: aesthetic demand assessment, most commonly expressed complaints, the importance given to tooth colour, knowledge of available therapeutic treatments and motivation levels for treatment. Results: The survey generated 3868 responses, 61% from women; 77% of respondents declared being satisfied to very satisfied with their smile. Their highest priority to improve their smile was tooth alignment, followed by their shape, length and shade. Although 60% of respondents were satisfied with their current shading, 53% would prefer to have them whitened. Aesthetic treatments were well‐known to seniors. Over four‐fifths of them had heard of dental implants and ceramic crowns. Two‐thirds of those who wished to improve their smile were considering dental treatment. Conclusion: The high number of collected questionnaires confirms the strong interest shown by seniors for dental aesthetics, particularly from women. Baby‐boomers seem more attentive to the appearance of their smile than their elders. However, the importance of appearance decreases with age, as it becomes less of a priority, with attention more focused on general health.     

The invasive bighead goby Ponticola kessleri displays large‐scale genetic similarities and small‐scale genetic differentiation in relation to shipping patterns

Colonization events, range expansions and species invasions leave genetic signatures in the genomes of invasive organisms and produce intricate special patterns. Predictions have been made as to how those patterns arise, but only very rarely, genetic processes can be monitored in real time during range expansions. In an attempt to change that, we track a very recently established invasive population of a fish species, the bighead goby Ponticola kessleri, with high temporal and spatial resolution through 2 years to identify patterns over time. We then compare Swiss and German samples of bighead goby along the river Rhine using microsatellites, mitochondrial D‐loop sequences and geometric morphometrics to investigate geographic patterns. We detect weak temporal and strong geographic patterns in the data, which are inconsistent with isolation by distance and indicate long range transport. In search of an explanation for our observations, we analyse the vector properties and travel patterns of commercial vessels on the river Rhine. We present evidence that freshwater cargo ships and tankers are plausible vectors for larvae of invasive goby species. We also present indications that cargo ships and tankers act as differential vectors for this species. In summary, we present genetic data at unique temporal resolution from a vertebrate invasion front and substantiate the paramount role of commercial shipping in freshwater fish translocations.     

Climate change and large‐scale human population collapses in the pre‐industrial era

Aim It has long been assumed that deteriorating climate (cooling and warming above the norm) could shrink the carrying capacity of agrarian lands, depriving the human population of sufficient food. Population collapses (i.e. negative population growth) follow. However, this human–ecological relationship has rarely been verified scientifically, and evidence of warming‐caused disaster has never been found. This research sought to explore quantitatively the temporal pattern, spatial pattern and triggers of population collapses in relation to climate change at the global scale over 1100 years. Location Various countries/regions in the Northern Hemisphere (NH) during the pre‐industrial era. Methods We performed time‐series analysis to examine the association between temperature change and country‐wide/region‐wide population collapses in different climatic zones. All of the known population collapse incidents in the NH in the period ce 800–1900 were included in our data analysis. Results Nearly 90% of population collapses in various NH countries/regions occurred during periods of climate deterioration characterized by shrinking carrying capacity of the land. In addition, we found that cooling dampened the human ecosystem and brought about 80% of the collapses in warmer humid, cooler humid and dry zones, while warming adversely affected the ecosystems in dry and tropical humid zones. All of the population collapses and growth declines in periods of warm climate occurred in dry and tropical humid zones. Malthusian checks (famines, wars and epidemics) were the dominant triggers of population collapses, which peaked dramatically when climate deteriorated. Main conclusions Global demographic catastrophes and most population collapse incidents occurred in periods with great climate change, owing to overpopulation caused by diminished carrying capacity of the land and the resultant outbreak of Malthusian checks. Impacts of cooling or warming on land carrying capacity varied geographically, as a result of the diversified ecosystems in different parts of the Earth. The observed climate–population synchrony challenges Malthusian theory and demonstrates that it is not population growth alone but climate‐induced subsistence shortage and population growth working synergistically, that cause large‐scale human population collapses on the long‐term scale.     

The co‐evolution of social institutions,demography, and large‐scale human cooperation

Human cooperation is typically coordinated by institutions, which determine the outcome structure of the social interactions individuals engage in. Explaining the Neolithic transition from small‐ to large‐scale societies involves understanding how these institutions co‐evolve with demography. We study this using a demographically explicit model of institution formation in a patch‐structured population. Each patch supports both social and asocial niches. Social individuals create an institution, at a cost to themselves, by negotiating how much of the costly public good provided by cooperators is invested into sanctioning defectors. The remainder of their public good is invested in technology that increases carrying capacity, such as irrigation systems. We show that social individuals can invade a population of asocials, and form institutions that support high levels of cooperation. We then demonstrate conditions where the co‐evolution of cooperation, institutions, and demographic carrying capacity creates a transition from small‐ to large‐scale social groups.     

Cooperation,collective action,and the archeology of large‐scale societies

Archeologists investigating the emergence of large‐scale societies in the past have renewed interest in examining the dynamics of cooperation as a means of understanding societal change and organizational variability within human groups over time. Unlike earlier approaches to these issues, which used models designated voluntaristic or managerial, contemporary research articulates more explicitly with frameworks for cooperation and collective action used in other fields, thereby facilitating empirical testing through better definition of the costs, benefits, and social mechanisms associated with success or failure in coordinated group action. Current scholarship is nevertheless bifurcated along lines of epistemology and scale, which is understandable but problematic for forging a broader, more transdisciplinary field of cooperation studies. Here, we point to some areas of potential overlap by reviewing archeological research that places the dynamics of social cooperation and competition in the foreground of the emergence of large‐scale societies, which we define as those having larger populations, greater concentrations of political power, and higher degrees of social inequality. We focus on key issues involving the communal‐resource management of subsistence and other economic goods, as well as the revenue flows that undergird political institutions. Drawing on archeological cases from across the globe, with greater detail from our area of expertise in Mesoamerica, we offer suggestions for strengthening analytical methods and generating more transdisciplinary research programs that address human societies across scalar and temporal spectra.     

An evolutionary theory of large‐scale human warfare: Group‐structured cultural selection

When humans wage war, it is not unusual for battlefields to be strewn with dead warriors. These warriors typically were men in their reproductive prime who, had they not died in battle, might have gone on to father more children. Typically, they are also genetically unrelated to one another. We know of no other animal species in which reproductively capable, genetically unrelated individuals risk their lives in this manner. Because the immense private costs borne by individual warriors create benefits that are shared widely by others in their group, warfare is a stark evolutionary puzzle that is difficult to explain. Although several scholars have posited models of the evolution of human warfare, 1 - 6 these models do not adequately explain how humans solve the problem of collective action in warfare at the evolutionarily novel scale of hundreds of genetically unrelated individuals. We propose that group‐structured cultural selection explains this phenomenon.     

A large‐scale survey of heterochrony in anuran cranial ossification patterns

Most anurans have a biphasic life cycle, which includes metamorphosis from a tadpole stage to an adult frog. This process involves extensive transformations of the cranial skeleton, which have been of long‐standing interest with respect to anuran skeletal evolution and taxonomy. In this study, large‐scale patterns of anuran skeletal ossification are assessed by collecting the most comprehensive data set on anuran cranial ossification to date from the literature, including data for 45 anuran and one caudate outgroup species. Ossification sequences were translated into event‐pair matrices for explorative phylogenetic analysis and phylogenetically informed parsimony search for heterochrony using the Parsimov algorithm. Rank variability of single bones across species was also analysed. Little phylogenetic signal was retrieved from a parsimony‐based phylogenetic analysis of event‐pairs, and only a few species that are generally agreed to be closely related are placed close to each other (e.g. some Pipidae and Costata). Parsimov analysis revealed some clade‐specific heterochrony in anuran clades of varying inclusiveness. Our results show that relating heterochronic changes in anuran cranial ontogeny to parameters such as direct development or miniaturization is problematic because of the high evolvability of cranial ossification sequences. Rank variation analysis suggests that anuran cranial bones are highly variable in their sequence positioning, possibly because tadpole and adult cranial morphology do not co‐evolve. Elements which are lost in some species ossify at the end of the sequence, providing evidence for the notion that failure of anuran cranial elements to ossify is due to processes of paedomorphosis.