Evolution of life in urban environments Johnson, Marc T. J.; Munshi-South, Jason
Science (American Association for the Advancement of Science),
11/2017, Volume:
358, Issue:
6363
Journal Article
Peer reviewed
Open access
Our planet is an increasingly urbanized landscape, with over half of the human population residing in cities. Despite advances in urban ecology, we do not adequately understand how urbanization ...affects the evolution of organisms, nor how this evolution may affect ecosystems and human health. Here, we review evidence for the effects of urbanization on the evolution of microbes, plants, and animals that inhabit cities. Urbanization affects adaptive and nonadaptive evolutionary processes that shape the genetic diversity within and between populations. Rapid adaptation has facilitated the success of some native species in urban areas, but it has also allowed human pests and disease to spread more rapidly. The nascent field of urban evolution brings together efforts to understand evolution in response to environmental change while developing new hypotheses concerning adaptation to urban infrastructure and human socioeconomic activity. The next generation of research on urban evolution will provide critical insight into the importance of evolution for sustainable interactions between humans and our city environments.
In this brief, the output reachable estimation and safety verification problems for multilayer perceptron (MLP) neural networks are addressed. First, a conception called maximum sensitivity is ...introduced, and for a class of MLPs whose activation functions are monotonic functions, the maximum sensitivity can be computed via solving convex optimization problems. Then, using a simulation-based method, the output reachable set estimation problem for neural networks is formulated into a chain of optimization problems. Finally, an automated safety verification is developed based on the output reachable set estimation result. An application to the safety verification for a robotic arm model with two joints is presented to show the effectiveness of the proposed approaches.
Rice is the primary source of food for billions of people in developing countries, yet the commonly consumed polished grain contains insufficient levels of the key micronutrients iron (Fe), zinc (Zn) ...and Vitamin A to meet daily dietary requirements. Experts estimate that a rice-based diet should contain 14.5 µg g(-1) Fe in endosperm, the main constituent of polished grain, but breeding programs have failed to achieve even half of that value. Transgenic efforts to increase the Fe concentration of rice endosperm include expression of ferritin genes, nicotianamine synthase genes (NAS) or ferritin in conjunction with NAS genes, with results ranging from two-fold increases via single-gene approaches to six-fold increases via multi-gene approaches, yet no approach has reported 14.5 µg g(-1) Fe in endosperm.
Three populations of rice were generated to constitutively overexpress OsNAS1, OsNAS2 or OsNAS3, respectively. Nicotianamine, Fe and Zn concentrations were significantly increased in unpolished grain of all three of the overexpression populations, relative to controls, with the highest concentrations in the OsNAS2 and OsNAS3 overexpression populations. Selected lines from each population had at least 10 µg g(-1) Fe in polished grain and two OsNAS2 overexpression lines had 14 and 19 µg g(-1) Fe in polished grain, representing up to four-fold increases in Fe concentration. Two-fold increases of Zn concentration were also observed in the OsNAS2 population. Synchrotron X-ray fluorescence spectroscopy demonstrated that OsNAS2 overexpression leads to significant enrichment of Fe and Zn in phosphorus-free regions of rice endosperm.
The OsNAS genes, particularly OsNAS2, show enormous potential for Fe and Zn biofortification of rice endosperm. The results demonstrate that rice cultivars overexpressing single rice OsNAS genes could provide a sustainable and genetically simple solution to Fe and Zn deficiency disorders affecting billions of people throughout the world.
Power electronics-intensive dc microgrids use increasingly complex software-based controllers and communication networks. They are evolving into cyber-physical systems (CPS) with sophisticated ...interactions between physical and computational processes, making them vulnerable to cyber attacks. This paper presents a framework to detect possible false-data injection attacks (FDIAs) in cyber-physical dc microgrids. The detection problem is formalized as identifying a change in sets of inferred candidate invariants. Invariants are microgrids properties that do not change over time. Both the physical plant and the software controller of CPS can be described as Simulink/Stateflow (SLSF) diagrams. The dynamic analysis infers the candidate invariants over the input/output variables of SLSF components. The reachability analysis generates the sets of reachable states (reach sets) for the CPS modeled as hybrid automata. The candidate invariants that contain the reach sets are called the actual invariants. The candidate invariants are then compared with the actual invariants, and any mismatch indicates the presence of FDIA. To evaluate the proposed methodology, the hybrid automaton of a dc microgrid, with a distributed cooperative control scheme, is presented. The reachability analysis is performed to obtain the reach sets and, hence, the actual invariants. Moreover, a prototype tool, HYbrid iNvariant GEneratoR, is extended to instrument SLSF models, obtain candidate invariants, and identify FDIA.
Why infectious disease research needs community ecology Johnson, Pieter T. J.; de Roode, Jacobus C.; Fenton, Andy
Science (American Association for the Advancement of Science),
09/2015, Volume:
349, Issue:
6252
Journal Article
Peer reviewed
Open access
Infectious diseases often emerge from interactions among multiple species and across nested levels of biological organization. Threats as diverse as Ebola virus, human malaria, and bat white-nose ...syndrome illustrate the need for a mechanistic understanding of the ecological interactions underlying emerging infections. We describe how recent advances in community ecology can be adopted to address contemporary challenges in disease research. These analytical tools can identify the factors governing complex assemblages of multiple hosts, parasites, and vectors, and reveal how processes link across scales from individual hosts to regions. They can also determine the drivers of heterogeneities among individuals, species, and regions to aid targeting of control strategies. We provide examples where these principles have enhanced disease management and illustrate how they can be further extended.
CRISPR-Cas gene editing and messenger RNA-based protein replacement therapy hold tremendous potential to effectively treat disease-causing mutations with diverse cellular origin. However, it is ...currently impossible to rationally design nanoparticles that selectively target specific tissues. Here, we report a strategy termed selective organ targeting (SORT) wherein multiple classes of lipid nanoparticles are systematically engineered to exclusively edit extrahepatic tissues via addition of a supplemental SORT molecule. Lung-, spleen- and liver-targeted SORT lipid nanoparticles were designed to selectively edit therapeutically relevant cell types including epithelial cells, endothelial cells, B cells, T cells and hepatocytes. SORT is compatible with multiple gene editing techniques, including mRNA, Cas9 mRNA/single guide RNA and Cas9 ribonucleoprotein complexes, and is envisioned to aid the development of protein replacement and gene correction therapeutics in targeted tissues.
The a–x relations recently presented in White et al. (, Journal of Metamorphic Geology, 32, 261–286) are extended to include MnO. This provides a set of internally consistent a–x relations for ...metapelitic rocks in the MnO–Na2O–CaO–K2O–FeO–MgO–Al2O3–SiO2–H2O–TiO2–O2 (MnNCKFMASHTO) system. The mixing parameters for the Mn‐bearing minerals were estimated using the micro‐ϕ approach of Powell et al. (, Journal of Metamorphic Geology, 32, 245–260). Then the Mn‐end‐member thermodynamic properties were calibrated using a database of co‐existing minerals involving literature data from rocks and from experiments on natural materials. Mn‐end‐members were calibrated for orthopyroxene, cordierite, staurolite, chloritoid, chlorite, biotite, ilmenite and hematite, assuming known properties for the garnet end‐member spessartine. The addition of MnO to phase diagram calculations results in a marked expansion of the stability of garnet‐bearing assemblages. At greenschist facies conditions garnet stability is extended down temperature. At amphibolite facies conditions, the garnet‐in boundary shifts to lower pressure. While the addition of MnO greatly influences the stability of garnet, it has relatively little effect on the stability of other common metapelitic minerals, with the resultant diagrams being topologically very similar to those calculated without MnO. Furthermore, the addition of MnO in the amounts measured in most metapelites has only a small effect on the mode of garnet, with calculated garnet modes remaining smaller than 1% in the P–T range outside its predicted Mn‐free P–T range.
Inhibition of the chemokine receptor CXCR4 in combination with blockade of the PD-1/PD-L1 T cell checkpoint induces T cell infiltration and anticancer responses in murine and human pancreatic cancer. ...Here we elucidate the mechanism by which CXCR4 inhibition affects the tumor immune microenvironment. In human immune cell-based chemotaxis assays, we find that CXCL12-stimulated CXCR4 inhibits the directed migration mediated by CXCR1, CXCR3, CXCR5, CXCR6, and CCR2, respectively, chemokine receptors expressed by all of the immune cell types that participate in an integrated immune response. Inhibiting CXCR4 in an experimental cancer medicine study by 1-wk continuous infusion of the small-molecule inhibitor AMD3100 (plerixafor) induces an integrated immune response that is detected by transcriptional analysis of paired biopsies of metastases from patients with microsatellite stable colorectal and pancreatic cancer. This integrated immune response occurs in three other examples of immunemediated damage to noninfected tissues: Rejecting renal allografts, melanomas clinically responding to anti-PD1 antibody therapy, and microsatellite instable colorectal cancers. Thus, signaling by CXCR4 causes immune suppression in human pancreatic ductal adenocarcinoma and colorectal cancer by impairing the function of the chemokine receptors that mediate the intratumoral accumulation of immune cells.
Evolution caused by extreme events Grant, Peter R.; Grant, B. Rosemary; Huey, Raymond B. ...
Philosophical transactions of the Royal Society of London. Series B. Biological sciences,
06/2017, Volume:
372, Issue:
1723
Journal Article
Peer reviewed
Open access
Extreme events can be a major driver of evolutionary change over geological and contemporary timescales. Outstanding examples are evolutionary diversification following mass extinctions caused by ...extreme volcanism or asteroid impact. The evolution of organisms in contemporary time is typically viewed as a gradual and incremental process that results from genetic change, environmental perturbation or both. However, contemporary environments occasionally experience strong perturbations such as heat waves, floods, hurricanes, droughts and pest outbreaks. These extreme events set up strong selection pressures on organisms, and are small-scale analogues of the dramatic changes documented in the fossil record. Because extreme events are rare, almost by definition, they are difficult to study. So far most attention has been given to their ecological rather than to their evolutionary consequences. We review several case studies of contemporary evolution in response to two types of extreme environmental perturbations, episodic (pulse) or prolonged (press). Evolution is most likely to occur when extreme events alter community composition. We encourage investigators to be prepared for evolutionary change in response to rare events during long-term field studies.
This article is part of the themed issue ‘Behavioural, ecological and evolutionary responses to extreme climatic events’.
Insect herbivores are hypothesized to be major factors affecting the ecology and evolution of plants. We tested this prediction by suppressing insects in replicated field populations of a native ...plant, Oenothera biennis, which reduced seed predation, altered interspecific competitive dynamics, and resulted in rapid evolutionary divergence. Comparative genotyping and phenotyping of nearly 12,000 O. biennis individuals revealed that in plots protected from insects, resistance to herbivores declined through time owing to changes in flowering time and lower defensive ellagitannins in fruits, whereas plant competitive ability increased. This independent real-time evolution of plant resistance and competitive ability in the field resulted from the relaxation of direct selective effects of insects on plant defense and through indirect effects due to reduced herbivory on plant competitors.
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