Large-scale genetic analysis of lethal phenotypes has elucidated the molecular underpinnings of many biological processes. Using the bacterial clustered regularly interspaced short palindromic ...repeats (CRISPR) system, we constructed a genome-wide single-guide RNA library to screen for genes required for proliferation and survival in a human cancer cell line. Our screen revealed the set of cell-essential genes, which was validated with an orthogonal gene-trap–based screen and comparison with yeast gene knockouts. This set is enriched for genes that encode components of fundamental pathways, are expressed at high levels, and contain few inactivating polymorphisms in the human population. We also uncovered a large group of uncharacterized genes involved in RNA processing, a number of whose products localize to the nucleolus. Last, screens in additional cell lines showed a high degree of overlap in gene essentiality but also revealed differences specific to each cell line and cancer type that reflect the developmental origin, oncogenic drivers, paralogous gene expression pattern, and chromosomal structure of each line. These results demonstrate the power of CRISPR-based screens and suggest a general strategy for identifying liabilities in cancer cells.
Interactions between natural selection and environmental change are well recognized and sit at the core of ecology and evolutionary biology. Reciprocal interactions between ecology and evolution, ...eco-evolutionary feedbacks, are less well studied, even though they may be critical for understanding the evolution of biological diversity, the structure of communities and the function of ecosystems. Eco-evolutionary feedbacks require that populations alter their environment (niche construction) and that those changes in the environment feed back to influence the subsequent evolution of the population. There is strong evidence that organisms influence their environment through predation, nutrient excretion and habitat modification, and that populations evolve in response to changes in their environment at time-scales congruent with ecological change (contemporary evolution). Here, we outline how the niche construction and contemporary evolution interact to alter the direction of evolution and the structure and function of communities and ecosystems. We then present five empirical systems that highlight important characteristics of eco-evolutionary feedbacks: rotifer-algae chemostats; alewife-zooplankton interactions in lakes; guppy life-history evolution and nutrient cycling in streams; avian seed predators and plants; and tree leaf chemistry and soil processes. The alewife-zooplankton system provides the most complete evidence for eco-evolutionary feedbacks, but other systems highlight the potential for eco-evolutionary feedbacks in a wide variety of natural systems.
The stable isotopes of nitrogen (Δ15N) and carbon (δ13C) provide powerful tools for estimating the trophic positions of and carbon flow to consumers in food webs; however, the isotopic signature of a ...consumer alone is not generally sufficient to infer trophic position or carbon source without an appropriate isotopic baseline. In this paper, I develop and discuss methods for generating an isotopic baseline and evaluate the assumptions required to estimate the trophic position of consumers using stable isotopes in multiple ecosystem studies. I test the ability of two primary consumers, surface-grazing snails and filter-feeding mussels, to capture the spatial and temporal variation at the base of aquatic food webs. I find that snails reflect the isotopic signature of the base of the littoral food web, mussels reflect the isotopic signature of the pelagic food web, and together they provide a good isotopic baseline for estimating trophic position of secondary or higher trophic level consumers in lake ecosystems. Then, using data from 25 north temperate lakes, I evaluate how δ15N and δ13C of the base of aquatic food webs varies both among lakes and between the littoral and pelagic food webs within lakes. Using data from the literature, I show that the mean trophic fractionation of δ15N is 3.4‰ (1 SD = l‰) and of δ13C is 0.4‰ (1 SD = 1.3‰), and that both, even though variable, are widely applicable. A sensitivity analysis reveals that estimates of trophic position are very sensitive to assumptions about the trophic fractionation of δ15N, moderately sensitive to different methods for generating an isotopic baseline, and not sensitive to assumptions about the trophic fractionation of δ13C when δ13C is used to estimate the proportion of nitrogen in a consumer derived from two sources. Finally, I compare my recommendations for generating an isotopic baseline to an alternative model proposed by M. J. Vander Zanden and J. B. Rasmussen. With an appropriate isotopic baseline and an appreciation of the underlying assumptions and model sensitivity, stable isotopes can help answer some of the most difficult questions in food web ecology.
Context dependency of animal resource subsidies Subalusky, Amanda L.; Post, David M.
Biological reviews of the Cambridge Philosophical Society,
April 2019, 2019-Apr, 2019-04-00, 20190401, Letnik:
94, Številka:
2
Journal Article
Recenzirano
ABSTRACT
The transport of resource subsidies by animals has been documented across a range of species and ecosystems. Although many of these studies have shown that animal resource subsidies can have ...significant effects on nutrient cycling, ecosystem productivity, and food‐web structure, there is a great deal of variability in the occurrence and strength of these effects. Here we propose a conceptual framework for understanding the context dependency of animal resource subsidies, and for developing and testing predictions about the effects of animal subsidies over space and time. We propose a general framework, in which abiotic characteristics and animal vector characteristics from the donor ecosystem interact to determine the quantity, quality, timing, and duration (QQTD) of an animal input. The animal input is translated through the lens of recipient ecosystem characteristics, which include both abiotic and consumer characteristics, to yield the QQTD of the subsidy. The translated subsidy influences recipient ecosystem dynamics through effects on both trophic structure and ecosystem function, which may both influence the recipient ecosystem's response to further inputs and feed back to influence the donor ecosystem. We present a review of research on animal resource subsidies across ecosystem boundaries, placed within the context of this framework, and we discuss how the QQTD of resource subsidies can influence trophic structure and ecosystem function in recipient ecosystems. We explore the importance of understanding context dependency of animal resource subsidies in increasingly altered ecosystems, in which the characteristics of both animal vectors and donor and recipient ecosystems may be changing rapidly. Finally, we make recommendations for future research on animal resource subsidies, and resource subsidies in general, that will increase our understanding and predictive capacity about their ecosystem effects.
Stable isotope analysis has emerged as one of the primary means for examining the structure and dynamics of food webs, and numerous analytical approaches are now commonly used in the field. ...Techniques range from simple, qualitative inferences based on the isotopic niche, to Bayesian mixing models that can be used to characterize food‐web structure at multiple hierarchical levels. We provide a comprehensive review of these techniques, and thus a single reference source to help identify the most useful approaches to apply to a given data set. We structure the review around four general questions: (1) what is the trophic position of an organism in a food web?; (2) which resource pools support consumers?; (3) what additional information does relative position of consumers in isotopic space reveal about food‐web structure?; and (4) what is the degree of trophic variability at the intrapopulation level? For each general question, we detail different approaches that have been applied, discussing the strengths and weaknesses of each. We conclude with a set of suggestions that transcend individual analytical approaches, and provide guidance for future applications in the field.
The value of biodiversity is widely appreciated, but we are only beginning to understand the interplay of processes that generate biodiversity and their consequences for coevolutionary interactions. ...Whereas predator–prey coevolution is most often analyzed in the context of evolutionary arms races, much less has been written about how predators are affected by, and respond to, evolutionary diversification in their prey. We hypothesize here that adaptive radiation of prey may lead to diversification and potentially speciation in predators, a process that we call an upwards adaptive radiation cascade. In this paper we lay out the conceptual basis for upwards adaptive radiation cascades, explore evidence for such cascades, and finally advocate for intensified research.
Biodiversity is of great cultural and economic value to humans.
We are only beginning to understand how diversification, the interplay of processes that generate biodiversity, works and its consequences for co-evolutionary processes.
Predatory species are affected by prey diversification.
Diversification and speciation at lower trophic levels may affect radiations higher in the food web.
Predator intraspecific diversity and incipient speciation are potentially threatened worldwide.
Root phenology in a changing climate Radville, Laura; McCormack, M. Luke; Post, Eric ...
Journal of experimental botany,
06/2016, Letnik:
67, Številka:
12
Journal Article
Recenzirano
Odprti dostop
Plant phenology is one of the strongest indicators of ecological responses to climate change, and altered phenology can have pronounced effects on net primary production, species composition in local ...communities, greenhouse gas fluxes, and ecosystem processes. Although many studies have shown that aboveground plant phenology advances with warmer temperatures, demonstration of a comparable association for belowground phenology has been lacking because the factors that influence root phenology are poorly understood. Because roots can constitute a large fraction of plant biomass, and root phenology may not respond to warming in the same way as shoots, this represents an important knowledge gap in our understanding of how climate change will influence phenology and plant performance. We review studies of root phenology and provide suggestions to direct future research. Only 29% of examined studies approached root phenology quantitatively, strongly limiting interpretation of results across studies. Therefore, we suggest that researchers emphasize quantitative analyses in future phenological studies. We suggest that root initiation, peak growth, and root cessation may be under different controls. Root initiation and cessation may be more constrained by soil temperature and the timing of carbon availability, whereas the timing of peak root growth may represent trade-offs among competing plant sinks. Roots probably do not experience winter dormancy in the same way as shoots: 89% of the studies that examined winter phenology found evidence of growth during winter months. More research is needed to observe root phenology, and future studies should be careful to capture winter and early season phenology. This should be done quantitatively, with direct observations of root growth utilizing rhizotrons or minirhizotrons.
Human activity is causing wild populations to experience rapid trait change and local extirpation. The resulting effects on intraspecific variation could have substantial consequences for ecological ...processes and ecosystem services. Although researchers have long acknowledged that variation among species influences the surrounding environment, only recently has evidence accumulated for the ecological importance of variation within species. We conducted a meta-analysis comparing the ecological effects of variation within a species (intraspecific effects) with the effects of replacement or removal of that species (species effects). We evaluated direct and indirect ecological responses, including changes in abundance (or biomass), rates of ecological processes and changes in community composition. Our results show that intraspecific effects are often comparable to, and sometimes stronger than, species effects. Species effects tend to be larger for direct ecological responses (for example, through consumption), whereas intraspecific effects and species effects tend to be similar for indirect responses (for example, through trophic cascades). Intraspecific effects are especially strong when indirect interactions alter community composition. Our results summarize data from the first generation of studies examining the relative ecological effects of intraspecific variation. Our conclusions can help inform the design of future experiments and the formulation of strategies to quantify and conserve biodiversity.
Food- chain length is a central characteristic of ecological communities because of its strong influence on community structure and ecosystem function. While recent studies have started to better ...clarify the relationship between food-chain length and environmental gradients such as resource availability and ecosystem size, much less progress has been made in isolating the ultimate and proximate mechanisms that determine food-chain length. Progress has been slow, in part, because research has paid little attention to the proximate changes in food web structure that must link variation in food-chain length to the ultimate dynamic mechanism. Here we outline the structural mechanisms that determine variation in food- chain length. We explore the implications of these mechanisms for understanding how changes in food- web structure influence food-chain length using both an intraguild predation community model and data from natural ecosystems. The resulting framework provides the mechanisms for linking ultimate dynamic mechanisms to variation in food- chain length. It also suggests that simple linear food-chain models may make misleading predictions about patterns of variation in food-chain length because they are unable to incorporate important structural mechanisms that alter food-web dynamics and cause non-linear shifts in food-web structure. Intraguild predation models provide a more appropriate theoretical framework for understanding food- chain length in most natural ecosystems because they accommodate all of the proximate structural mechanisms identified here.
To confirm that neoplastic monocyte-derived collagen- and fibronectin-producing fibrocytes induce bone marrow (BM) fibrosis in primary myelofibrosis (PMF), we injected PMF BM-derived ...fibrocyte-precursor CD14+/CD34- monocytes into the tail vein of NOD-SCID-γ (NSG) mice. PMF BM-derived CD14+/CD34- monocytes engrafted and induced a PMF-like phenotype with splenomegaly, myeloid hyperplasia with clusters of atypical megakaryocytes, persistence of the JAK2V617F mutation, and BM and spleen fibrosis. As control we used normal human BM-derived CD14+/CD34- monocytes. These monocytes also engrafted and gave rise to normal megakaryocytes that, like PMF CD14+/CD34--derived megakaryocytes, expressed HLA-ABC and human CD42b antigens. Using 2 clonogenic assays we confirmed that PMF and normal BM-derived CD14+/CD34- monocytes give rise to megakaryocyte colony-forming cells, suggesting that a subpopulation BM monocytes harbors megakaryocyte progenitor capacity. Taken together, our data suggest that PMF monocytes induce myelofibrosis-like phenotype in immunodeficient mice and that PMF and normal BM-derived CD14+/CD34- monocytes give rise to megakaryocyte progenitor cells.
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