Specificity and multiplicity in the recognition of individuals: implications for the evolution of social behaviour.

PubMed

Wiley, R H

2013-02-01

Recognition of conspecifics occurs when individuals classify sets of conspecifics based on sensory input from them and associate these sets with different responses. Classification of conspecifics can vary in specificity (the number of individuals included in a set) and multiplicity (the number of sets differentiated). In other words, the information transmitted varies in complexity. Although recognition of conspecifics has been reported in a wide variety of organisms, few reports have addressed the specificity or multiplicity of this capability. This review discusses examples of these patterns, the mechanisms that can produce them, and the evolution of these mechanisms. Individual recognition is one end of a spectrum of specificity, and binary classification of conspecifics is one end of a spectrum of multiplicity. In some cases, recognition requires no more than simple forms of learning, such as habituation, yet results in individually specific recognition. In other cases, recognition of individuals involves complex associations of multiple cues with multiple previous experiences in particular contexts. Complex mechanisms for recognition are expected to evolve only when simpler mechanisms do not provide sufficient specificity and multiplicity to obtain the available advantages. In particular, the evolution of cooperation and deception is always promoted by specificity and multiplicity in recognition. Nevertheless, there is only one demonstration that recognition of specific individuals contributes to cooperation in animals other than primates. Human capacities for individual recognition probably have a central role in the evolution of complex forms of human cooperation and deception. Although relatively little studied, this capability probably rivals cognitive abilities for language. © 2012 The Author. Biological Reviews © 2012 Cambridge Philosophical Society.

Janus Kinase Antagonists and Other Novel Small Molecules for the Treatment of Crohn's Disease.

PubMed

Boland, Brigid S; Vermeire, Séverine

2017-09-01

There is an ongoing, unmet need for effective therapies for Crohn's disease. Treatments for Crohn's disease continue to evolve from the traditional biologics to novel small molecules, with targeted mechanisms directed toward pathways that are dysregulated in Crohn's disease. There are multiple emerging mechanisms of action, including Janus kinase inhibition, Smad7 inhibition, and sphingosine-1-phosphate receptor modulators, that are administered as oral medications, and small molecules represent the next generation of therapies for Crohn's disease. Copyright © 2017 Elsevier Inc. All rights reserved.

Cell therapy worldwide: an incipient revolution.

PubMed

Rao, Mahendra; Mason, Chris; Solomon, Susan

2015-01-01

The regenerative medicine field is large, diverse and active worldwide. A variety of different organizational and product models have been successful, and pioneering entrepreneurs have shown both what can work and, critically, what does not. Evolving regulations, novel funding mechanisms combined with new technological breakthroughs are keeping the field in a state of flux. The field struggles to cope with the lack of infrastructure and investment, it nevertheless has evolved from its roots in human stem cell therapy and tissue and organ transplants to a field composed of a variety of products from multiple cell sources with approval for use in numerous countries. Currently, tens of thousands of patients have been treated with some kind of cell therapy.

Abscisic-acid-dependent basic leucine zipper (bZIP) transcription factors in plant abiotic stress.

PubMed

Banerjee, Aditya; Roychoudhury, Aryadeep

2017-01-01

One of the major causes of significant crop loss throughout the world is the myriad of environmental stresses including drought, salinity, cold, heavy metal toxicity, and ultraviolet-B (UV-B) rays. Plants as sessile organisms have evolved various effective mechanism which enable them to withstand this plethora of stresses. Most of such regulatory mechanisms usually follow the abscisic-acid (ABA)-dependent pathway. In this review, we have primarily focussed on the basic leucine zipper (bZIP) transcription factors (TFs) activated by the ABA-mediated signalosome. Upon perception of ABA by specialized receptors, the signal is transduced via various groups of Ser/Thr kinases, which phosphorylate the bZIP TFs. Following such post-translational modification of TFs, they are activated so that they bind to specific cis-acting sequences called abscisic-acid-responsive elements (ABREs) or GC-rich coupling elements (CE), thereby influencing the expression of their target downstream genes. Several in silico techniques have been adopted so far to predict the structural features, recognize the regulatory modification sites, undergo phylogenetic analyses, and facilitate genome-wide survey of TF under multiple stresses. Current investigations on the epigenetic regulation that controls greater accessibility of the inducible regions of DNA of the target gene to the bZIP TFs exclusively under stress situations, along with the evolved stress memory responses via genomic imprinting mechanism, have been highlighted. The potentiality of overexpression of bZIP TFs, either in a homologous or in a heterologous background, in generating transgenic plants tolerant to various abiotic stressors have also been addressed by various groups. The present review will provide a coherent documentation on the functional characterization and regulation of bZIP TFs under multiple environmental stresses, with the major goal of generating multiple-stress-tolerant plant cultivars in near future.

Small RNA biology is systems biology.

PubMed

Jost, Daniel; Nowojewski, Andrzej; Levine, Erel

2011-01-01

During the last decade small regulatory RNA (srRNA) emerged as central players in the regulation of gene expression in all kingdoms of life. Multiple pathways for srRNA biogenesis and diverse mechanisms of gene regulation may indicate that srRNA regulation evolved independently multiple times. However, small RNA pathways share numerous properties, including the ability of a single srRNA to regulate multiple targets. Some of the mechanisms of gene regulation by srRNAs have significant effect on the abundance of free srRNAs that are ready to interact with new targets. This results in indirect interactions among seemingly unrelated genes, as well as in a crosstalk between different srRNA pathways. Here we briefly review and compare the major srRNA pathways, and argue that the impact of srRNA is always at the system level. We demonstrate how a simple mathematical model can ease the discussion of governing principles. To demonstrate these points we review a few examples from bacteria and animals.

Cold-loving microbes, plants, and animals—fundamental and applied aspects

NASA Astrophysics Data System (ADS)

Margesin, R.; Neuner, G.; Storey, K. B.

2007-02-01

Microorganisms, plants, and animals have successfully colonized cold environments, which represent the majority of the biosphere on Earth. They have evolved special mechanisms to overcome the life-endangering influence of low temperature and to survive freezing. Cold adaptation includes a complex range of structural and functional adaptations at the level of all cellular constituents, such as membranes, proteins, metabolic activity, and mechanisms to avoid the destructive effect of intracellular ice formation. These strategies offer multiple biotechnological applications of cold-adapted organisms and/or their products in various fields. In this review, we describe the mechanisms of microorganisms, plants, and animals to cope with the cold and the resulting biotechnological perspectives.

Evolution of Influenza A Virus by Mutation and Re-Assortment

PubMed Central

Shao, Wenhan; Li, Xinxin; Goraya, Mohsan Ullah; Wang, Song; Chen, Ji-Long

2017-01-01

Influenza A virus (IAV), a highly infectious respiratory pathogen, has continued to be a significant threat to global public health. To complete their life cycle, influenza viruses have evolved multiple strategies to interact with a host. A large number of studies have revealed that the evolution of influenza A virus is mainly mediated through the mutation of the virus itself and the re-assortment of viral genomes derived from various strains. The evolution of influenza A virus through these mechanisms causes worldwide annual epidemics and occasional pandemics. Importantly, influenza A virus can evolve from an animal infected pathogen to a human infected pathogen. The highly pathogenic influenza virus has resulted in stupendous economic losses due to its morbidity and mortality both in human and animals. Influenza viruses fall into a category of viruses that can cause zoonotic infection with stable adaptation to human, leading to sustained horizontal transmission. The rapid mutations of influenza A virus result in the loss of vaccine optimal efficacy, and challenge the complete eradication of the virus. In this review, we highlight the current understanding of influenza A virus evolution caused by the mutation and re-assortment of viral genomes. In addition, we discuss the specific mechanisms by which the virus evolves. PMID:28783091

In vitro evolution of high-titer, virus-like vesicles containing a single structural protein

PubMed Central

Rose, Nina F.; Buonocore, Linda; Schell, John B.; Chattopadhyay, Anasuya; Bahl, Kapil; Liu, Xinran; Rose, John K.

2014-01-01

Self-propagating, infectious, virus-like vesicles (VLVs) are generated when an alphavirus RNA replicon expresses the vesicular stomatitis virus glycoprotein (VSV G) as the only structural protein. The mechanism that generates these VLVs lacking a capsid protein has remained a mystery for over 20 years. We present evidence that VLVs arise from membrane-enveloped RNA replication factories (spherules) containing VSV G protein that are largely trapped on the cell surface. After extensive passaging, VLVs evolve to grow to high titers through acquisition of multiple point mutations in their nonstructural replicase proteins. We reconstituted these mutations into a plasmid-based system from which high-titer VLVs can be recovered. One of these mutations generates a late domain motif (PTAP) that is critical for high-titer VLV production. We propose a model in which the VLVs have evolved in vitro to exploit a cellular budding pathway that is hijacked by many enveloped viruses, allowing them to bud efficiently from the cell surface. Our results suggest a basic mechanism of propagation that may have been used by primitive RNA viruses lacking capsid proteins. Capsids may have evolved later to allow more efficient packaging of RNA, greater virus stability, and evasion of innate immunity. PMID:25385608

From perception to activation: the molecular-genetic and biochemical landscape of disease resistance signaling in plants.

PubMed

Knepper, Caleb; Day, Brad

2010-01-01

More than 60 years ago, H.H. Flor proposed the "Gene-for-Gene" hypothesis, which described the genetic relationship between host plants and pathogens. In the decades that followed Flor's seminal work, our understanding of the plant-pathogen interaction has evolved into a sophisticated model, detailing the molecular genetic and biochemical processes that control host-range, disease resistance signaling and susceptibility. The interaction between plants and microbes is an intimate exchange of signals that has evolved for millennia, resulting in the modification and adaptation of pathogen virulence strategies and host recognition elements. In total, plants have evolved mechanisms to combat the ever-changing landscape of biotic interactions bombarding their environment, while in parallel, plant pathogens have co-evolved mechanisms to sense and adapt to these changes. On average, the typical plant is susceptible to attack by dozens of microbial pathogens, yet in most cases, remains resistant to many of these challenges. The sum of research in our field has revealed that these interactions are regulated by multiple layers of intimately linked signaling networks. As an evolved model of Flor's initial observations, the current paradigm in host-pathogen interactions is that pathogen effector molecules, in large part, drive the recognition, activation and subsequent physiological responses in plants that give rise to resistance and susceptibility. In this Chapter, we will discuss our current understanding of the association between plants and microbial pathogens, detailing the pressures placed on both host and microbe to either maintain disease resistance, or induce susceptibility and disease. From recognition to transcriptional reprogramming, we will review current data and literature that has advanced the classical model of the Gene-for-Gene hypothesis to our current understanding of basal and effector triggered immunity.

Multi-target drugs to address multiple checkpoints in complex inflammatory pathologies: evolutionary cues for novel "first-in-class" anti-inflammatory drug candidates: a reviewer's perspective.

PubMed

Mathew, Geetha; Unnikrishnan, M K

2015-10-01

Inflammation is a complex, metabolically expensive process involving multiple signaling pathways and regulatory mechanisms which have evolved over evolutionary timescale. Addressing multiple targets of inflammation holistically, in moderation, is probably a more evolutionarily viable strategy, as compared to current therapy which addresses drug targets in isolation. Polypharmacology, addressing multiple targets, is commonly used in complex ailments, suggesting the superior safety and efficacy profile of multi-target (MT) drugs. Phenotypic drug discovery, which generated successful MT and first-in-class drugs in the past, is now re-emerging. A multi-pronged approach, which modulates the evolutionarily conserved, robust and pervasive cellular mechanisms of tissue repair, with AMPK at the helm, regulating the complex metabolic/immune/redox pathways underlying inflammation, is perhaps a more viable strategy than addressing single targets in isolation. Molecules that modulate multiple molecular mechanisms of inflammation in moderation (modulating TH cells toward the anti-inflammatory phenotype, activating AMPK, stimulating Nrf2 and inhibiting NFκB) might serve as a model for a novel Darwinian "first-in-class" therapeutic category that holistically addresses immune, redox and metabolic processes associated with inflammatory repair. Such a multimodal biological activity is supported by the fact that several non-calorific pleiotropic natural products with anti-inflammatory action have been incorporated into diet (chiefly guided by the adaptive development of olfacto-gustatory preferences over evolutionary timescales) rendering such molecules, endowed with evolutionarily privileged molecular scaffolds, naturally oriented toward multiple targets.

The Dilemmas of the Gourmet Fly: The Molecular and Neuronal Mechanisms of Feeding and Nutrient Decision Making in Drosophila

PubMed Central

Itskov, Pavel M.; Ribeiro, Carlos

2012-01-01

To survive and successfully reproduce animals need to maintain a balanced intake of nutrients and energy. The nervous system of insects has evolved multiple mechanisms to regulate feeding behavior. When animals are faced with the choice to feed, several decisions must be made: whether or not to eat, how much to eat, what to eat, and when to eat. Using Drosophila melanogaster substantial progress has been achieved in understanding the neuronal and molecular mechanisms controlling feeding decisions. These feeding decisions are implemented in the nervous system on multiple levels, from alterations in the sensitivity of peripheral sensory organs to the modulation of memory systems. This review discusses methodologies developed in order to study insect feeding, the effects of neuropeptides and neuromodulators on feeding behavior, behavioral evidence supporting the existence of internal energy sensors, neuronal and molecular mechanisms controlling protein intake, and finally the regulation of feeding by circadian rhythms and sleep. From the discussed data a conceptual framework starts to emerge which aims to explain the molecular and neuronal processes maintaining the stability of the internal milieu. PMID:23407678

Levers and linkages: mechanical trade-offs in a power-amplified system.

PubMed

Anderson, Philip S L; Claverie, Thomas; Patek, S N

2014-07-01

Mechanical redundancy within a biomechanical system (e.g., many-to-one mapping) allows morphologically divergent organisms to maintain equivalent mechanical outputs. However, most organisms depend on the integration of more than one biomechanical system. Here, we test whether coupled mechanical systems follow a pattern of amplification (mechanical changes are congruent and evolve toward the same functional extreme) or independence (mechanisms evolve independently). We examined the correlated evolution and evolutionary pathways of the coupled four-bar linkage and lever systems in mantis shrimp (Stomatopoda) ultrafast raptorial appendages. We examined models of character evolution in the framework of two divergent groups of stomatopods-"smashers" (hammer-shaped appendages) and "spearers" (bladed appendages). Smashers tended to evolve toward force amplification, whereas spearers evolved toward displacement amplification. These findings show that coupled biomechanical systems can evolve synergistically, thereby resulting in functional amplification rather than mechanical redundancy. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Dynamics of Implementation and Maintenance of Organizational Health Interventions.

PubMed

Jalali, Mohammad S; Rahmandad, Hazhir; Bullock, Sally Lawrence; Ammerman, Alice

2017-08-15

In this study, we present case studies to explore the dynamics of implementation and maintenance of health interventions. We analyze how specific interventions are built and eroded, how the building and erosion mechanisms are interconnected, and why we can see significantly different erosion rates across otherwise similar organizations. We use multiple comparative obesity prevention case studies to provide empirical information on the mechanisms of interest, and use qualitative systems modeling to integrate our evolving understanding into an internally consistent and transparent theory of the phenomenon. Our preliminary results identify reinforcing feedback mechanisms, including design of organizational processes, motivation of stakeholders, and communication among stakeholders, which influence implementation and maintenance of intervention components. Over time, these feedback mechanisms may drive a wedge between otherwise similar organizations, leading to distinct configurations of implementation and maintenance processes.

Reptile scale paradigm: Evo-Devo, pattern formation and regeneration

PubMed Central

Chang, Cheng; Wu, Ping; Baker, Ruth E.; Maini, Philip K.; Alibardi, Lorenzo; Chuong, Cheng-Ming

2010-01-01

The purpose of this perspective is to highlight the merit of the reptile integument as an experimental model. Reptiles represent the first amniotes. From stem reptiles, extant reptiles, birds and mammals have evolved. Mammal hairs and feathers evolved from Therapsid and Sauropsid reptiles, respectively. The early reptilian integument had to adapt to the challenges of terrestrial life, developing a multi-layered stratum corneum capable of barrier function and ultraviolet protection. For better mechanical protection, diverse reptilian scale types have evolved. The evolution of endothermy has driven the convergent evolution of hair and feather follicles: both form multiple localized growth units with stem cells and transient amplifying cells protected in the proximal follicle. This topological arrangement allows them to elongate, molt and regenerate without structural constraints. Another unique feature of reptile skin is the exquisite arrangement of scales and pigment patterns, making them testable models for mechanisms of pattern formation. Since they face the constant threat of damage on land, different strategies were developed to accommodate skin homeostasis and regeneration. Temporally, they can be under continuous renewal or sloughing cycles. Spatially, they can be diffuse or form discrete localized growth units (follicles). To understand how gene regulatory networks evolved to produce increasingly complex ectodermal organs, we have to study how prototypic scale-forming pathways in reptiles are modulated to produce appendage novelties. Despite the fact that there are numerous studies of reptile scales, molecular analyses have lagged behind. Here, we underscore how further development of this novel experimental model will be valuable in filling the gaps of our understanding of the Evo-Devo of amniote integuments. PMID:19557687

Functional connectivity dynamically evolves on multiple time-scales over a static structural connectome: Models and mechanisms.

PubMed

Cabral, Joana; Kringelbach, Morten L; Deco, Gustavo

2017-10-15

Over the last decade, we have observed a revolution in brain structural and functional Connectomics. On one hand, we have an ever-more detailed characterization of the brain's white matter structural connectome. On the other, we have a repertoire of consistent functional networks that form and dissipate over time during rest. Despite the evident spatial similarities between structural and functional connectivity, understanding how different time-evolving functional networks spontaneously emerge from a single structural network requires analyzing the problem from the perspective of complex network dynamics and dynamical system's theory. In that direction, bottom-up computational models are useful tools to test theoretical scenarios and depict the mechanisms at the genesis of resting-state activity. Here, we provide an overview of the different mechanistic scenarios proposed over the last decade via computational models. Importantly, we highlight the need of incorporating additional model constraints considering the properties observed at finer temporal scales with MEG and the dynamical properties of FC in order to refresh the list of candidate scenarios. Copyright © 2017 Elsevier Inc. All rights reserved.

Urinary tract infection: recent insight into the evolutionary arms race between uropathogenic Escherichia coli and our immune system.

PubMed

Schwab, Sebastian; Jobin, Katarzyna; Kurts, Christian

2017-12-01

Urinary tract infections (UTIs) are among the most common bacterial infections worldwide. Humans evolved various immune-dependent and independent defense mechanisms, while pathogens evolved multiple virulence factors to fight back. This article summarizes recent findings regarding the arms race between hosts and pathogens in UTIs. It was recently reported that macrophage subsets regulate neutrophil-mediated defense in primary UTIs but seem to subvert adaptive immunity upon re-infection. Moreover, some bacterial strains can survive inside macrophages, leading to recurrent infections. Inflammasome activation results in infected host cell death and pathogen release, facilitating the removal of intracellular bacteria. As a counteraction, some bacteria evolved mechanisms to disrupt inflammasome activation. Mucosal-associated invariant T cells are further effectors that can lyse infected epithelial cells and release intracellular bacteria. Once released, the bacteria are phagocytosed by neutrophils. However, some bacteria can inhibit neutrophil migration and deprive neutrophils of nutrients. Furthermore, the complement system, considered generally bactericidal, is exploited by the bacteria for cellular invasion. Another weapon against UTI is antimicrobial peptides, e.g. ribonuclease 7, but its production is inhibited by certain bacterial strains. Thus the arms race in UTI is ongoing, and knowing the enemy's methods can help in developing new drugs to win the race. © The Author 2017. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

Dynamics of Implementation and Maintenance of Organizational Health Interventions

PubMed Central

Rahmandad, Hazhir; Bullock, Sally Lawrence; Ammerman, Alice

2017-01-01

In this study, we present case studies to explore the dynamics of implementation and maintenance of health interventions. We analyze how specific interventions are built and eroded, how the building and erosion mechanisms are interconnected, and why we can see significantly different erosion rates across otherwise similar organizations. We use multiple comparative obesity prevention case studies to provide empirical information on the mechanisms of interest, and use qualitative systems modeling to integrate our evolving understanding into an internally consistent and transparent theory of the phenomenon. Our preliminary results identify reinforcing feedback mechanisms, including design of organizational processes, motivation of stakeholders, and communication among stakeholders, which influence implementation and maintenance of intervention components. Over time, these feedback mechanisms may drive a wedge between otherwise similar organizations, leading to distinct configurations of implementation and maintenance processes. PMID:28809807

Have plants evolved to self-immolate?

PubMed Central

Bowman, David M. J. S.; French, Ben J.; Prior, Lynda D.

2014-01-01

By definition fire prone ecosystems have highly combustible plants, leading to the hypothesis, first formally stated by Mutch in 1970, that community flammability is the product of natural selection of flammable traits. However, proving the “Mutch hypothesis” has presented an enormous challenge for fire ecologists given the difficulty in establishing cause and effect between landscape fire and flammable plant traits. Individual plant traits (such as leaf moisture content, retention of dead branches and foliage, oil rich foliage) are known to affect the flammability of plants but there is no evidence these characters evolved specifically to self-immolate, although some of these traits may have been secondarily modified to increase the propensity to burn. Demonstrating individual benefits from self-immolation is extraordinarily difficult, given the intersection of the physical environmental factors that control landscape fire (fuel production, dryness and ignitions) with community flammability properties that emerge from numerous traits of multiple species (canopy cover and litter bed bulk density). It is more parsimonious to conclude plants have evolved mechanisms to tolerate, but not promote, landscape fire. PMID:25414710

Multiple layers of posttranslational regulation refine circadian clock activity in Arabidopsis.

PubMed

Seo, Pil Joon; Mas, Paloma

2014-01-01

The circadian clock is a cellular time-keeper mechanism that regulates biological rhythms with a period of ~24 h. The circadian rhythms in metabolism, physiology, and development are synchronized by environmental cues such as light and temperature. In plants, proper matching of the internal circadian time with the external environment confers fitness advantages on plant survival and propagation. Accordingly, plants have evolved elaborated regulatory mechanisms that precisely control the circadian oscillations. Transcriptional feedback regulation of several clock components has been well characterized over the past years. However, the importance of additional regulatory mechanisms such as chromatin remodeling, protein complexes, protein phosphorylation, and stability is only starting to emerge. The multiple layers of circadian regulation enable plants to properly synchronize with the environmental cycles and to fine-tune the circadian oscillations. This review focuses on the diverse posttranslational events that regulate circadian clock function. We discuss the mechanistic insights explaining how plants articulate a high degree of complexity in their regulatory networks to maintain circadian homeostasis and to generate highly precise waveforms of circadian expression and activity.

Transhydrogenase Promotes the Robustness and Evolvability of E. coli Deficient in NADPH Production

PubMed Central

Chou, Hsin-Hung; Marx, Christopher J.; Sauer, Uwe

2015-01-01

Metabolic networks revolve around few metabolites recognized by diverse enzymes and involved in myriad reactions. Though hub metabolites are considered as stepping stones to facilitate the evolutionary expansion of biochemical pathways, changes in their production or consumption often impair cellular physiology through their system-wide connections. How does metabolism endure perturbations brought immediately by pathway modification and restore hub homeostasis in the long run? To address this question we studied laboratory evolution of pathway-engineered Escherichia coli that underproduces the redox cofactor NADPH on glucose. Literature suggests multiple possibilities to restore NADPH homeostasis. Surprisingly, genetic dissection of isolates from our twelve evolved populations revealed merely two solutions: (1) modulating the expression of membrane-bound transhydrogenase (mTH) in every population; (2) simultaneously consuming glucose with acetate, an unfavored byproduct normally excreted during glucose catabolism, in two subpopulations. Notably, mTH displays broad phylogenetic distribution and has also played a predominant role in laboratory evolution of Methylobacterium extorquens deficient in NADPH production. Convergent evolution of two phylogenetically and metabolically distinct species suggests mTH as a conserved buffering mechanism that promotes the robustness and evolvability of metabolism. Moreover, adaptive diversification via evolving dual substrate consumption highlights the flexibility of physiological systems to exploit ecological opportunities. PMID:25715029

Immune Ecosystem of Virus-Infected Host Tissues.

PubMed

Maarouf, Mohamed; Rai, Kul Raj; Goraya, Mohsan Ullah; Chen, Ji-Long

2018-05-06

Virus infected host cells serve as a central immune ecological niche during viral infection and replication and stimulate the host immune response via molecular signaling. The viral infection and multiplication process involves complex intracellular molecular interactions between viral components and the host factors. Various types of host cells are also involved to modulate immune factors in delicate and dynamic equilibrium to maintain a balanced immune ecosystem in an infected host tissue. Antiviral host arsenals are equipped to combat or eliminate viral invasion. However, viruses have evolved with strategies to counter against antiviral immunity or hijack cellular machinery to survive inside host tissue for their multiplication. However, host immune systems have also evolved to neutralize the infection; which, in turn, either clears the virus from the infected host or causes immune-mediated host tissue injury. A complex relationship between viral pathogenesis and host antiviral defense could define the immune ecosystem of virus-infected host tissues. Understanding of the molecular mechanism underlying this ecosystem would uncover strategies to modulate host immune function for antiviral therapeutics. This review presents past and present updates of immune-ecological components of virus infected host tissue and explains how viruses subvert the host immune surveillances.

Evolving Concepts in the Pathogenesis of NASH: Beyond Steatosis and Inflammation

PubMed Central

Peverill, William; Powell, Lawrie W.; Skoien, Richard

2014-01-01

Non-alcoholic steatohepatitis (NASH) is characterised by hepatic steatosis and inflammation and, in some patients, progressive fibrosis leading to cirrhosis. An understanding of the pathogenesis of NASH is still evolving but current evidence suggests multiple metabolic factors critically disrupt homeostasis and induce an inflammatory cascade and ensuing fibrosis. The mechanisms underlying these changes and the complex inter-cellular interactions that mediate fibrogenesis are yet to be fully elucidated. Lipotoxicity, in the setting of excess free fatty acids, obesity, and insulin resistance, appears to be the central driver of cellular injury via oxidative stress. Hepatocyte apoptosis and/or senescence contribute to activation of the inflammasome via a variety of intra- and inter-cellular signalling mechanisms leading to fibrosis. Current evidence suggests that periportal components, including the ductular reaction and expansion of the hepatic progenitor cell compartment, may be involved and that the Th17 response may mediate disease progression. This review aims to provide an overview of the pathogenesis of NASH and summarises the evidence pertaining to key mechanisms implicated in the transition from steatosis and inflammation to fibrosis. Currently there are limited treatments for NASH although an increasing understanding of its pathogenesis will likely improve the development and use of interventions in the future. PMID:24830559

Shared and unique responses of plants to multiple individual stresses and stress combinations: physiological and molecular mechanisms

PubMed Central

Pandey, Prachi; Ramegowda, Venkategowda; Senthil-Kumar, Muthappa

2015-01-01

In field conditions, plants are often simultaneously exposed to multiple biotic and abiotic stresses resulting in substantial yield loss. Plants have evolved various physiological and molecular adaptations to protect themselves under stress combinations. Emerging evidences suggest that plant responses to a combination of stresses are unique from individual stress responses. In addition, plants exhibit shared responses which are common to individual stresses and stress combination. In this review, we provide an update on the current understanding of both unique and shared responses. Specific focus of this review is on heat–drought stress as a major abiotic stress combination and, drought–pathogen and heat–pathogen as examples of abiotic–biotic stress combinations. We also comprehend the current understanding of molecular mechanisms of cross talk in relation to shared and unique molecular responses for plant survival under stress combinations. Thus, the knowledge of shared responses of plants from individual stress studies and stress combinations can be utilized to develop varieties with broad spectrum stress tolerance. PMID:26442037

Form follows function: morphological diversification and alternative trapping strategies in carnivorous Nepenthes pitcher plants.

PubMed

Bauer, Ulrike; Clemente, C J; Renner, T; Federle, W

2012-01-01

Carnivorous plants of the genus Nepenthes have evolved a striking diversity of pitcher traps that rely on specialized slippery surfaces for prey capture. With a comparative study of trap morphology, we show that Nepenthes pitcher plants have evolved specific adaptations for the use of either one of two distinct trapping mechanisms: slippery wax crystals on the inner pitcher wall and 'insect aquaplaning' on the wet upper rim (peristome). Species without wax crystals had wider peristomes with a longer inward slope. Ancestral state reconstructions identified wax crystal layers and narrow, symmetrical peristomes as ancestral, indicating that wax crystals have been reduced or lost multiple times independently. Our results complement recent reports of nutrient source specializations in Nepenthes and suggest that these specializations may have driven speciation and rapid diversification in this genus. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Manifestations of classical physics in the quantum evolution of correlated spin states in pulsed NMR experiments.

PubMed

Ligare, Martin

2016-05-01

Multiple-pulse NMR experiments are a powerful tool for the investigation of molecules with coupled nuclear spins. The product operator formalism provides a way to understand the quantum evolution of an ensemble of weakly coupled spins in such experiments using some of the more intuitive concepts of classical physics and semi-classical vector representations. In this paper I present a new way in which to interpret the quantum evolution of an ensemble of spins. I recast the quantum problem in terms of mixtures of pure states of two spins whose expectation values evolve identically to those of classical moments. Pictorial representations of these classically evolving states provide a way to calculate the time evolution of ensembles of weakly coupled spins without the full machinery of quantum mechanics, offering insight to anyone who understands precession of magnetic moments in magnetic fields.

Plasticity of ductile metallic glasses: a self-organized critical state.

PubMed

Sun, B A; Yu, H B; Jiao, W; Bai, H Y; Zhao, D Q; Wang, W H

2010-07-16

We report a close correlation between the dynamic behavior of serrated flow and the plasticity in metallic glasses (MGs) and show that the plastic deformation of ductile MGs can evolve into a self-organized critical state characterized by the power-law distribution of shear avalanches. A stick-slip model considering the interaction of multiple shear bands is presented to reveal complex scale-free intermittent shear-band motions in ductile MGs and quantitatively reproduce the experimental observations. Our studies have implications for understanding the precise plastic deformation mechanism of MGs.

New paradigms in type 2 immunity.

PubMed

Pulendran, Bali; Artis, David

2012-07-27

Nearly half of the world's population harbors helminth infections or suffers from allergic disorders. A common feature of this population is the so-called "type 2 immune response," which confers protection against helminths, but also promotes pathologic responses associated with allergic inflammation. However, the mechanisms that initiate and control type 2 responses remain enigmatic. Recent advances have revealed a role for the innate immune system in orchestrating type 2 responses against a bewildering array of stimuli, from nanometer-sized allergens to 20-meter-long helminth parasites. Here, we review these advances and suggest that the human immune system has evolved multiple mechanisms of sensing such stimuli, from recognition of molecular patterns via innate immune receptors to detecting metabolic changes and tissue damage caused by these stimuli.

Central insulin action in energy and glucose homeostasis.

PubMed

Plum, Leona; Belgardt, Bengt F; Brüning, Jens C

2006-07-01

Insulin has pleiotropic biological effects in virtually all tissues. However, the relevance of insulin signaling in peripheral tissues has been studied far more extensively than its role in the brain. An evolving body of evidence indicates that in the brain, insulin is involved in multiple regulatory mechanisms including neuronal survival, learning, and memory, as well as in regulation of energy homeostasis and reproductive endocrinology. Here we review insulin's role as a central homeostatic signal with regard to energy and glucose homeostasis and discuss the mechanisms by which insulin communicates information about the body's energy status to the brain. Particular emphasis is placed on the controversial current debate about the similarities and differences between hypothalamic insulin and leptin signaling at the molecular level.

Evolutionary optimization of material properties of a tropical seed

PubMed Central

Lucas, Peter W.; Gaskins, John T.; Lowrey, Timothy K.; Harrison, Mark E.; Morrogh-Bernard, Helen C.; Cheyne, Susan M.; Begley, Matthew R.

2012-01-01

Here, we show how the mechanical properties of a thick-shelled tropical seed are adapted to permit them to germinate while preventing their predation. The seed has evolved a complex heterogeneous microstructure resulting in hardness, stiffness and fracture toughness values that place the structure at the intersection of these competing selective constraints. Analyses of different damage mechanisms inflicted by beetles, squirrels and orangutans illustrate that cellular shapes and orientations ensure damage resistance to predation forces imposed across a broad range of length scales. This resistance is shown to be around the upper limit that allows cracking the shell via internal turgor pressure (i.e. germination). Thus, the seed appears to strike an exquisitely delicate adaptive balance between multiple selection pressures. PMID:21613287

A Quantitative Approach to Assessing System Evolvability

NASA Technical Reports Server (NTRS)

Christian, John A., III

2004-01-01

When selecting a system from multiple candidates, the customer seeks the one that best meets his or her needs. Recently the desire for evolvable systems has become more important and engineers are striving to develop systems that accommodate this need. In response to this search for evolvability, we present a historical perspective on evolvability, propose a refined definition of evolvability, and develop a quantitative method for measuring this property. We address this quantitative methodology from both a theoretical and practical perspective. This quantitative model is then applied to the problem of evolving a lunar mission to a Mars mission as a case study.

Water balance in desert Drosophila: lessons from non-charismatic microfauna.

PubMed

Gibbs, Allen G

2002-11-01

Water stress is a particularly important problem for insects and other small organisms in arid environments. Cactophilic fruit flies in the genus Drosophila have invaded deserts on numerous occasions, including multiple independent invasions of North American deserts. Because the evolutionary history of this genus is so well studied, we can investigate the mechanisms of adaptation in a rigorous phylogenetic context. As expected, desert fruit flies lose water less rapidly than their mesic congeners. They are also able to tolerate the loss of a greater percentage of body water, but this difference is mainly due to phylogenetic history, and does not represent an adaptation specifically to desert habitats. A laboratory analogue of desert Drosophila is provided by populations of D. melanogaster that have been subjected to selection for desiccation resistance. Selected populations resemble desert species in that they lose water slowly, relative to control populations, and are not more tolerant of dehydration stress. They differ, however, in having much higher water contents and different behavioral responses to desiccating conditions. Our comparisons of laboratory and natural populations reveal that not all possible adaptive mechanisms evolve in stressful environments. Different physiological and behavioral strategies may evolve depending upon the particular options available in the environment.

Evolution at increased error rate leads to the coexistence of multiple adaptive pathways in an RNA virus.

PubMed

Cabanillas, Laura; Arribas, María; Lázaro, Ester

2013-01-16

When beneficial mutations present in different genomes spread simultaneously in an asexual population, their fixation can be delayed due to competition among them. This interference among mutations is mainly determined by the rate of beneficial mutations, which in turn depends on the population size, the total error rate, and the degree of adaptation of the population. RNA viruses, with their large population sizes and high error rates, are good candidates to present a great extent of interference. To test this hypothesis, in the current study we have investigated whether competition among beneficial mutations was responsible for the prolonged presence of polymorphisms in the mutant spectrum of an RNA virus, the bacteriophage Qβ, evolved during a large number of generations in the presence of the mutagenic nucleoside analogue 5-azacytidine. The analysis of the mutant spectra of bacteriophage Qβ populations evolved at artificially increased error rate shows a large number of polymorphic mutations, some of them with demonstrated selective value. Polymorphisms distributed into several evolutionary lines that can compete among them, making it difficult the emergence of a defined consensus sequence. The presence of accompanying deleterious mutations, the high degree of recurrence of the polymorphic mutations, and the occurrence of epistatic interactions generate a highly complex interference dynamics. Interference among beneficial mutations in bacteriophage Qβ evolved at increased error rate permits the coexistence of multiple adaptive pathways that can provide selective advantages by different molecular mechanisms. In this way, interference can be seen as a positive factor that allows the exploration of the different local maxima that exist in rugged fitness landscapes.

The evolution of jaw protrusion mechanics is tightly coupled to bentho-pelagic divergence in damselfishes (Pomacentridae).

PubMed

Cooper, W James; Carter, Casey B; Conith, Andrew J; Rice, Aaron N; Westneat, Mark W

2017-02-15

Most species-rich lineages of aquatic organisms have undergone divergence between forms that feed from the substrate (benthic feeding) and forms that feed from the water column (pelagic feeding). Changes in trophic niche are frequently accompanied by changes in skull mechanics, and multiple fish lineages have evolved highly specialized biomechanical configurations that allow them to protrude their upper jaws toward the prey during feeding. Damselfishes (family Pomacentridae) are an example of a species-rich lineage with multiple trophic morphologies and feeding ecologies. We sought to determine whether bentho-pelagic divergence in the damselfishes is tightly coupled to changes in jaw protrusion ability. Using high-speed video recordings and kinematic analysis, we examined feeding performance in 10 species that include three examples of convergence on herbivory, three examples of convergence on omnivory and two examples of convergence on planktivory. We also utilized morphometrics to characterize the feeding morphology of an additional 40 species that represent all 29 damselfish genera. Comparative phylogenetic analyses were then used to examine the evolution of trophic morphology and biomechanical performance. We find that pelagic-feeding damselfishes (planktivores) are strongly differentiated from extensively benthic-feeding species (omnivores and herbivores) by their jaw protrusion ability, upper jaw morphology and the functional integration of upper jaw protrusion with lower jaw abduction. Most aspects of cranial form and function that separate these two ecological groups have evolved in correlation with each other and the evolution of the functional morphology of feeding in damselfishes has involved repeated convergence in form, function and ecology. © 2017. Published by The Company of Biologists Ltd.

Ultimate explanations and suboptimal choice.

PubMed

Vasconcelos, Marco; Machado, Armando; Pandeirada, Josefa N S

2018-07-01

Researchers have unraveled multiple cases in which behavior deviates from rationality principles. We propose that such deviations are valuable tools to understand the adaptive significance of the underpinning mechanisms. To illustrate, we discuss in detail an experimental protocol in which animals systematically incur substantial foraging losses by preferring a lean but informative option over a rich but non-informative one. To understand how adaptive mechanisms may fail to maximize food intake, we review a model inspired by optimal foraging principles that reconciles sub-optimal choice with the view that current behavioral mechanisms were pruned by the optimizing action of natural selection. To move beyond retrospective speculation, we then review critical tests of the model, regarding both its assumptions and its (sometimes counterintuitive) predictions, all of which have been upheld. The overall contention is that (a) known mechanisms can be used to develop better ultimate accounts and that (b) to understand why mechanisms that generate suboptimal behavior evolved, we need to consider their adaptive value in the animal's characteristic ecology. Copyright © 2018 Elsevier B.V. All rights reserved.

Learning to Cooperate: The Evolution of Social Rewards in Repeated Interactions.

PubMed

Dridi, Slimane; Akçay, Erol

2018-01-01

Understanding the behavioral and psychological mechanisms underlying social behaviors is one of the major goals of social evolutionary theory. In particular, a persistent question about animal cooperation is to what extent it is supported by other-regarding preferences-the motivation to increase the welfare of others. In many situations, animals adjust their behaviors through learning by responding to the rewards they experience as a consequence of their actions. Therefore, we may ask whether learning in social situations can be driven by evolved other-regarding rewards. Here we develop a mathematical model in order to ask whether the mere act of cooperating with a social partner will evolve to be inherently rewarding. Individuals interact repeatedly in pairs and adjust their behaviors through reinforcement learning. We assume that individuals associate with each game outcome an internal reward value. These perceived rewards are genetically evolving traits. We find that conditionally cooperative rewards that value mutual cooperation positively but the sucker's outcome negatively tend to be evolutionarily stable. Purely other-regarding rewards can evolve only under special parameter combinations. On the other hand, selfish rewards that always lead to pure defection are also evolutionarily successful. These findings are consistent with empirical observations showing that humans tend to display conditionally cooperative behavior and also exhibit a diversity of preferences. Our model also demonstrates the need to further integrate multiple levels of biological causation of behavior.

Predator confusion is sufficient to evolve swarming behaviour

PubMed Central

Olson, Randal S.; Hintze, Arend; Dyer, Fred C.; Knoester, David B.; Adami, Christoph

2013-01-01

Swarming behaviours in animals have been extensively studied owing to their implications for the evolution of cooperation, social cognition and predator–prey dynamics. An important goal of these studies is discerning which evolutionary pressures favour the formation of swarms. One hypothesis is that swarms arise because the presence of multiple moving prey in swarms causes confusion for attacking predators, but it remains unclear how important this selective force is. Using an evolutionary model of a predator–prey system, we show that predator confusion provides a sufficient selection pressure to evolve swarming behaviour in prey. Furthermore, we demonstrate that the evolutionary effect of predator confusion on prey could in turn exert pressure on the structure of the predator's visual field, favouring the frontally oriented, high-resolution visual systems commonly observed in predators that feed on swarming animals. Finally, we provide evidence that when prey evolve swarming in response to predator confusion, there is a change in the shape of the functional response curve describing the predator's consumption rate as prey density increases. Thus, we show that a relatively simple perceptual constraint—predator confusion—could have pervasive evolutionary effects on prey behaviour, predator sensory mechanisms and the ecological interactions between predators and prey. PMID:23740485

Predator confusion is sufficient to evolve swarming behaviour.

PubMed

Olson, Randal S; Hintze, Arend; Dyer, Fred C; Knoester, David B; Adami, Christoph

2013-08-06

Swarming behaviours in animals have been extensively studied owing to their implications for the evolution of cooperation, social cognition and predator-prey dynamics. An important goal of these studies is discerning which evolutionary pressures favour the formation of swarms. One hypothesis is that swarms arise because the presence of multiple moving prey in swarms causes confusion for attacking predators, but it remains unclear how important this selective force is. Using an evolutionary model of a predator-prey system, we show that predator confusion provides a sufficient selection pressure to evolve swarming behaviour in prey. Furthermore, we demonstrate that the evolutionary effect of predator confusion on prey could in turn exert pressure on the structure of the predator's visual field, favouring the frontally oriented, high-resolution visual systems commonly observed in predators that feed on swarming animals. Finally, we provide evidence that when prey evolve swarming in response to predator confusion, there is a change in the shape of the functional response curve describing the predator's consumption rate as prey density increases. Thus, we show that a relatively simple perceptual constraint--predator confusion--could have pervasive evolutionary effects on prey behaviour, predator sensory mechanisms and the ecological interactions between predators and prey.

The evolution of photosynthesis...again?

PubMed

Rothschild, Lynn J

2008-08-27

'Replaying the tape' is an intriguing 'would it happen again?' exercise. With respect to broad evolutionary innovations, such as photosynthesis, the answers are central to our search for life elsewhere. Photosynthesis permits a large planetary biomass on Earth. Specifically, oxygenic photosynthesis has allowed an oxygenated atmosphere and the evolution of large metabolically demanding creatures, including ourselves. There are at least six prerequisites for the evolution of biological carbon fixation: a carbon-based life form; the presence of inorganic carbon; the availability of reductants; the presence of light; a light-harvesting mechanism to convert the light energy into chemical energy; and carboxylating enzymes. All were present on the early Earth. To provide the evolutionary pressure, organic carbon must be a scarce resource in contrast to inorganic carbon. The probability of evolving a carboxylase is approached by creating an inventory of carbon-fixation enzymes and comparing them, leading to the conclusion that carbon fixation in general is basic to life and has arisen multiple times. Certainly, the evolutionary pressure to evolve new pathways for carbon fixation would have been present early in evolution. From knowledge about planetary systems and extraterrestrial chemistry, if organic carbon-based life occurs elsewhere, photosynthesis -- although perhaps not oxygenic photosynthesis -- would also have evolved.

Insights on persistent airway infection by non-typeable Haemophilus influenzae in chronic obstructive pulmonary disease

PubMed Central

Ahearn, Christian P.; Gallo, Mary C.

2017-01-01

Abstract Non-typeable Haemophilus influenzae (NTHi) is the most common bacterial cause of infection of the lower airways in adults with chronic obstructive pulmonary disease (COPD). Infection of the COPD airways causes acute exacerbations, resulting in substantial morbidity and mortality. NTHi has evolved multiple mechanisms to establish infection in the hostile environment of the COPD airways, allowing the pathogen to persist in the airways for months to years. Persistent infection of the COPD airways contributes to chronic airway inflammation that increases symptoms and accelerates the progressive loss of pulmonary function, which is a hallmark of the disease. Persistence mechanisms of NTHi include the expression of multiple redundant adhesins that mediate binding to host cellular and extracellular matrix components. NTHi evades host immune recognition and clearance by invading host epithelial cells, forming biofilms, altering gene expression and displaying surface antigenic variation. NTHi also binds host serum factors that confer serum resistance. Here we discuss the burden of COPD and the role of NTHi infections in the course of the disease. We provide an overview of NTHi mechanisms of persistence that allow the pathogen to establish a niche in the hostile COPD airways. PMID:28449098

Tracking Advanced Planetary Systems (TAPAS) with HARPS-N . I. A multiple planetary system around the red giant star TYC 1422-614-1

NASA Astrophysics Data System (ADS)

Niedzielski, A.; Villaver, E.; Wolszczan, A.; Adamów, M.; Kowalik, K.; Maciejewski, G.; Nowak, G.; García-Hernández, D. A.; Deka, B.; Adamczyk, M.

2015-01-01

Context. Stars that have evolved off the main sequence are crucial for expanding the frontiers of knowledge on exoplanets toward higher stellar masses and for constraining star-planet interaction mechanisms. These stars have an intrinsic activity, however, which complicates the interpretation of precise radial velocity (RV) measurements, and therefore they are often avoided in planet searches. Over the past ten years, we have monitored about 1000 evolved stars for RV variations in search for low-mass companions under the Penn State - Toruń Centre for Astronomy Planet Search program with the Hobby-Eberly Telescope. Selected prospective candidates that required higher RV precision measurements have been followed with HARPS-N at the 3.6 m Telescopio Nazionale Galileo. Aims: We aim to detect planetary systems around evolved stars, to be able to build sound statistics on the frequency and intrinsic nature of these systems, and to deliver in-depth studies of selected planetary systems with evidence of star-planet interaction processes. Methods: We obtained 69 epochs of precise RV measurements for TYC 1422-614-1 collected over 3651 days with the Hobby-Eberly Telescope, and 17 epochs of ultra-precise HARPS-N data collected over 408 days. We complemented these RV data with photometric time-series from the All Sky Automatic Survey archive. Results: We report the discovery of a multiple planetary system around the evolved K2 giant star TYC 1422-614-1. The system orbiting the 1.15 M⊙ star is composed of a planet with mass msini = 2.5 MJ in a 0.69 AU orbit, and a planet or brown dwarf with msini = 10 MJ in an orbit of 1.37 AU. The multiple planetary system orbiting TYC 1422-614-1 is the first finding of the TAPAS project, a HARPS-N monitoring of evolved planetary systems identified with the Hobby-Eberly Telescope. Based on observations obtained with the Hobby-Eberly Telescope, which is a joint project of the University of Texas at Austin, the Pennsylvania State University, Stanford University, Ludwig-Maximilians-Universität München, and Georg-August-Universität Göttingen.Based on observations made with the Italian Telescopio Nazionale Galileo (TNG) operated on the island of La Palma by the Fundación Galileo Galilei of the INAF (Istituto Nazionale di Astrofisica) at the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofísica de Canarias.Tables 2 and 3 are available in electronic form at http://www.aanda.org

Translation system engineering in Escherichia coli enhances non-canonical amino acid incorporation into proteins.

PubMed

Gan, Rui; Perez, Jessica G; Carlson, Erik D; Ntai, Ioanna; Isaacs, Farren J; Kelleher, Neil L; Jewett, Michael C

2017-05-01

The ability to site-specifically incorporate non-canonical amino acids (ncAAs) into proteins has made possible the study of protein structure and function in fundamentally new ways, as well as the bio synthesis of unnatural polymers. However, the task of site-specifically incorporating multiple ncAAs into proteins with high purity and yield continues to present a challenge. At the heart of this challenge lies the lower efficiency of engineered orthogonal translation system components compared to their natural counterparts (e.g., translation elements that specifically use a ncAA and do not interact with the cell's natural translation apparatus). Here, we show that evolving and tuning expression levels of multiple components of an engineered translation system together as a whole enhances ncAA incorporation efficiency. Specifically, we increase protein yield when incorporating multiple p-azido-phenylalanine(pAzF) residues into proteins by (i) evolving the Methanocaldococcus jannaschii p-azido-phenylalanyl-tRNA synthetase anti-codon binding domain, (ii) evolving the elongation factor Tu amino acid-binding pocket, and (iii) tuning the expression of evolved translation machinery components in a single vector. Use of the evolved translation machinery in a genomically recoded organism lacking release factor one enabled enhanced multi-site ncAA incorporation into proteins. We anticipate that our approach to orthogonal translation system development will accelerate and expand our ability to site-specifically incorporate multiple ncAAs into proteins and biopolymers, advancing new horizons for synthetic and chemical biotechnology. Biotechnol. Bioeng. 2017;114: 1074-1086. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Strike-slip fault propagation and linkage via work optimization with application to the San Jacinto fault, California

NASA Astrophysics Data System (ADS)

Madden, E. H.; McBeck, J.; Cooke, M. L.

2013-12-01

Over multiple earthquake cycles, strike-slip faults link to form through-going structures, as demonstrated by the continuous nature of the mature San Andreas fault system in California relative to the younger and more segmented San Jacinto fault system nearby. Despite its immaturity, the San Jacinto system accommodates between one third and one half of the slip along the boundary between the North American and Pacific plates. It therefore poses a significant seismic threat to southern California. Better understanding of how the San Jacinto system has evolved over geologic time and of current interactions between faults within the system is critical to assessing this seismic hazard accurately. Numerical models are well suited to simulating kilometer-scale processes, but models of fault system development are challenged by the multiple physical mechanisms involved. For example, laboratory experiments on brittle materials show that faults propagate and eventually join (hard-linkage) by both opening-mode and shear failure. In addition, faults interact prior to linkage through stress transfer (soft-linkage). The new algorithm GROW (GRowth by Optimization of Work) accounts for this complex array of behaviors by taking a global approach to fault propagation while adhering to the principals of linear elastic fracture mechanics. This makes GROW a powerful tool for studying fault interactions and fault system development over geologic time. In GROW, faults evolve to minimize the work (or energy) expended during deformation, thereby maximizing the mechanical efficiency of the entire system. Furthermore, the incorporation of both static and dynamic friction allows GROW models to capture fault slip and fault propagation in single earthquakes as well as over consecutive earthquake cycles. GROW models with idealized faults reveal that the initial fault spacing and the applied stress orientation control fault linkage propensity and linkage patterns. These models allow the gains in efficiency provided by both hard-linkage and soft-linkage to be quantified and compared. Specialized models of interactions over the past 1 Ma between the Clark and Coyote Creek faults within the San Jacinto system reveal increasing mechanical efficiency as these fault structures change over time. Alongside this increasing efficiency is an increasing likelihood for single, larger earthquakes that rupture multiple fault segments. These models reinforce the sensitivity of mechanical efficiency to both fault structure and the regional tectonic stress orientation controlled by plate motions and provide insight into how slip may have been partitioned between the San Andreas and San Jacinto systems over the past 1 Ma.

Reactive oxygen species-dependent wound responses in animals and plants.

PubMed

Suzuki, Nobuhiro; Mittler, Ron

2012-12-15

Animals and plants evolved sophisticated mechanisms that regulate their responses to mechanical injury. Wound response in animals mainly promotes wound healing processes, nerve cell regeneration, and immune system responses at the vicinity of the wound site. In contrast, wound response in plants is primarily directed at sealing the wound site via deposition of various compounds and generating systemic signals that activate multiple defense mechanisms in remote tissues. Despite these differences between animals and plants, recent studies have shown that reactive oxygen species (ROS) play very common signaling and coordination roles in the wound responses of both systems. This review provides an update on recent findings related to ROS-regulated coordination of intercellular communications and signal transduction during wound response in plants and animals. In particular, differences and similarities in H2O2-dependent long-distance signaling between zebrafish and Arabidopsis thaliana are discussed. Published by Elsevier Inc.

DNA Tumor Virus Regulation of Host DNA Methylation and Its Implications for Immune Evasion and Oncogenesis

PubMed Central

Kuss-Duerkop, Sharon K.; Westrich, Joseph A.

2018-01-01

Viruses have evolved various mechanisms to evade host immunity and ensure efficient viral replication and persistence. Several DNA tumor viruses modulate host DNA methyltransferases for epigenetic dysregulation of immune-related gene expression in host cells. The host immune responses suppressed by virus-induced aberrant DNA methylation are also frequently involved in antitumor immune responses. Here, we describe viral mechanisms and virus–host interactions by which DNA tumor viruses regulate host DNA methylation to evade antiviral immunity, which may contribute to the generation of an immunosuppressive microenvironment during cancer development. Recent trials of immunotherapies have shown promising results to treat multiple cancers; however, a significant number of non-responders necessitate identifying additional targets for cancer immunotherapies. Thus, understanding immune evasion mechanisms of cancer-causing viruses may provide great insights for reversing immune suppression to prevent and treat associated cancers. PMID:29438328

Tissue Engineering and Regenerative Repair in Wound Healing

PubMed Central

Hu, Michael S.; Maan, Zeshaan N.; Wu, Jen-Chieh; Rennert, Robert C.; Hong, Wan Xing; Lai, Tiffany S.; Cheung, Alexander T. M.; Walmsley, Graham G.; Chung, Michael T.; McArdle, Adrian; Longaker, Michael T.; Lorenz, H. Peter

2014-01-01

Wound healing is a highly evolved defense mechanism against infection and further injury. It is a complex process involving multiple cell types and biological pathways. Mammalian adult cutaneous wound healing is mediated by a fibroproliferative response leading to scar formation. In contrast, early to mid-gestational fetal cutaneous wound healing is more akin to regeneration and occurs without scar formation. This early observation has led to extensive research seeking to unlock the mechanism underlying fetal scarless regenerative repair. Building upon recent advances in biomaterials and stem cell applications, tissue engineering approaches are working towards a recapitulation of this phenomenon. In this review, we describe the elements that distinguish fetal scarless and adult scarring wound healing, and discuss current trends in tissue engineering aimed at achieving scarless tissue regeneration. PMID:24788648

Racism, society, and disease: an exploration of the social and biological mechanisms of differential mortality.

PubMed

Cooper, R; Steinhauer, M; Miller, W; David, R; Schatzkin, A

1981-01-01

Racial differentials in mortality provide important insight into the nature of mass disease in capitalist society. Not only are the differentials sizable in magnitude, they are consistent for multiple causes of death and appear to evolve in response to social development. The relationships among social factors and the biological and physical agents of disease can be identified through racial contrasts and a pattern of causation which applies to both the minority and majority populations described. Furthermore, the impact of exploitation as the primary disease-mediating factor under capitalist social relations can be estimated. This paper attempts to combine an analysis of bio-medical mechanisms with Marxist social theory in a comprehensive framework for the study of the social origins of racial differentials.

Study of electromechanical and mechanical properties of bacteria using force microscopy

NASA Astrophysics Data System (ADS)

Reukov, Vladimir; Thompson, Gary; Nikiforov, Maxim; Guo, Senli; Ovchinnikov, Oleg; Jesse, Stephen; Kalinin, Sergei; Vertegel, Alexey

2010-03-01

The application of scanning probe microscopy (SPM) to biological systems has evolved over the past decade into a multimodal and spectroscopic instrument that provides multiple information channels at each spatial pixel acquired. Recently, functional recognition imaging based on differing electromechanical properties between Gram negative and Gram positive bacteria was achieved using artificial neural network analysis of band excitation piezoresponse force microscopy (BEPFM) data. The immediate goal of this project was to study mechanical and electromechanical properties of bacterial systems physiologically-relevant solutions using Band-width Excitation Piezoresponce Force Microscopy (BE PFM) in combination with Force Mapping. Electromechanical imaging in physiological environments will improve the versatility of functional recognition imaging and open the way for application of the rapid BEPFM line mode method to other living cell systems.

Shear response of grain boundaries with metastable structures by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Zhang, Liang; Lu, Cheng; Shibuta, Yasushi

2018-04-01

Grain boundaries (GBs) can play a role as the favored locations to annihilate point defects, such as interstitial atoms and vacancies. It is thus highly probable that different boundary structures can be simultaneously present in equilibrium with each other in the same GB, and thus the GB achieves a metastable state. However, the structural transition and deformation mechanism of such GBs are currently not well understood. In this work, molecular dynamics simulations were carried out to study the multiple structures of a Σ5(310)/[001] GB in bicrystal Al and to investigate the effect of structural multiplicity on the mechanical and kinetic properties of such a GB. Different GB structures were obtained by changing the starting atomic configuration of the bicrystal model, and the GB structures had significantly different atomic density. For the Σ5(310) GB with metastable structures, GB sliding was the dominant mechanism at a low temperature (T = 10 K) under shear stress. The sliding mechanism resulted from the uncoordinated transformation of the inhomogeneous structural units. The nucleation of voids was observed during GB sliding at the low temperature, and the voids subsequently evolved to a nanocrack at the boundary plane. Increasing the temperature can induce the structural transition of local GB structures and can change their overall kinetic properties. GB migration with occasional GB sliding dominated the deformation mechanism at elevated temperatures (T = 300 and 600 K), and the migration process of the metastable GB structures is closely related to the thermally assisted diffusion mechanism.

Experience Modulates the Reproductive Response to Heat Stress in C. elegans via Multiple Physiological Processes

PubMed Central

Gouvêa, Devin Y.; Aprison, Erin Z.; Ruvinsky, Ilya

2015-01-01

Natural environments are considerably more variable than laboratory settings and often involve transient exposure to stressful conditions. To fully understand how organisms have evolved to respond to any given stress, prior experience must therefore be considered. We investigated the effects of individual and ancestral experience on C. elegans reproduction. We documented ways in which cultivation at 15°C or 25°C affects developmental time, lifetime fecundity, and reproductive performance after severe heat stress that exceeds the fertile range of the organism but is compatible with survival and future fecundity. We found that experience modulates multiple aspects of reproductive physiology, including the male and female germ lines and the interaction between them. These responses vary in their environmental sensitivity, suggesting the existence of complex mechanisms for coping with unpredictable and stressful environments. PMID:26713620

Role of Multiple Soliton Interactions in the Generation of Rogue Waves: The Modified Korteweg-de Vries Framework.

PubMed

Slunyaev, A V; Pelinovsky, E N

2016-11-18

The role of multiple soliton and breather interactions in the formation of very high waves is disclosed within the framework of the integrable modified Korteweg-de Vries (MKdV) equation. Optimal conditions for the focusing of many solitons are formulated explicitly. Namely, trains of ordered solitons with alternate polarities evolve to huge strongly localized transient waves. The focused wave amplitude is exactly the sum of the focusing soliton heights; the maximum wave inherits the polarity of the fastest soliton in the train. The focusing of several solitary waves or/and breathers may naturally occur in a soliton gas and will lead to rogue-wave-type dynamics; hence, it represents a new nonlinear mechanism of rogue wave generation. The discovered scenario depends crucially on the soliton polarities (phases), and is not taken into account by existing kinetic theories. The performance of the soliton mechanism of rogue wave generation is shown for the example of the focusing MKdV equation, when solitons possess "frozen" phases (certain polarities), though the approach is efficient in some other integrable systems which admit soliton and breather solutions.

Role of Multiple Soliton Interactions in the Generation of Rogue Waves: The Modified Korteweg-de Vries Framework

NASA Astrophysics Data System (ADS)

Slunyaev, A. V.; Pelinovsky, E. N.

2016-11-01

The role of multiple soliton and breather interactions in the formation of very high waves is disclosed within the framework of the integrable modified Korteweg-de Vries (MKdV) equation. Optimal conditions for the focusing of many solitons are formulated explicitly. Namely, trains of ordered solitons with alternate polarities evolve to huge strongly localized transient waves. The focused wave amplitude is exactly the sum of the focusing soliton heights; the maximum wave inherits the polarity of the fastest soliton in the train. The focusing of several solitary waves or/and breathers may naturally occur in a soliton gas and will lead to rogue-wave-type dynamics; hence, it represents a new nonlinear mechanism of rogue wave generation. The discovered scenario depends crucially on the soliton polarities (phases), and is not taken into account by existing kinetic theories. The performance of the soliton mechanism of rogue wave generation is shown for the example of the focusing MKdV equation, when solitons possess "frozen" phases (certain polarities), though the approach is efficient in some other integrable systems which admit soliton and breather solutions.

Interaction-based evolution: how natural selection and nonrandom mutation work together.

PubMed

Livnat, Adi

2013-10-18

The modern evolutionary synthesis leaves unresolved some of the most fundamental, long-standing questions in evolutionary biology: What is the role of sex in evolution? How does complex adaptation evolve? How can selection operate effectively on genetic interactions? More recently, the molecular biology and genomics revolutions have raised a host of critical new questions, through empirical findings that the modern synthesis fails to explain: for example, the discovery of de novo genes; the immense constructive role of transposable elements in evolution; genetic variance and biochemical activity that go far beyond what traditional natural selection can maintain; perplexing cases of molecular parallelism; and more. Here I address these questions from a unified perspective, by means of a new mechanistic view of evolution that offers a novel connection between selection on the phenotype and genetic evolutionary change (while relying, like the traditional theory, on natural selection as the only source of feedback on the fit between an organism and its environment). I hypothesize that the mutation that is of relevance for the evolution of complex adaptation-while not Lamarckian, or "directed" to increase fitness-is not random, but is instead the outcome of a complex and continually evolving biological process that combines information from multiple loci into one. This allows selection on a fleeting combination of interacting alleles at different loci to have a hereditary effect according to the combination's fitness. This proposed mechanism addresses the problem of how beneficial genetic interactions can evolve under selection, and also offers an intuitive explanation for the role of sex in evolution, which focuses on sex as the generator of genetic combinations. Importantly, it also implies that genetic variation that has appeared neutral through the lens of traditional theory can actually experience selection on interactions and thus has a much greater adaptive potential than previously considered. Empirical evidence for the proposed mechanism from both molecular evolution and evolution at the organismal level is discussed, and multiple predictions are offered by which it may be tested. This article was reviewed by Nigel Goldenfeld (nominated by Eugene V. Koonin), Jürgen Brosius and W. Ford Doolittle.

Quantitative steps in the evolution of metabolic organisation as specified by the Dynamic Energy Budget theory.

PubMed

Kooijman, S A L M; Troost, T A

2007-02-01

The Dynamic Energy Budget (DEB) theory quantifies the metabolic organisation of organisms on the basis of mechanistically inspired assumptions. We here sketch a scenario for how its various modules, such as maintenance, storage dynamics, development, differentiation and life stages could have evolved since the beginning of life. We argue that the combination of homeostasis and maintenance induced the development of reserves and that subsequent increases in the maintenance costs came with increases of the reserve capacity. Life evolved from a multiple reserves - single structure system (prokaryotes, many protoctists) to systems with multiple reserves and two structures (plants) or single reserve and single structure (animals). This had profound consequences for the possible effects of temperature on rates. We present an alternative explanation for what became known as the down-regulation of maintenance at high growth rates in microorganisms; the density of the limiting reserve increases with the growth rate, and reserves do not require maintenance while structure-specific maintenance costs are independent of the growth rate. This is also the mechanism behind the variation of the respiration rate with body size among species. The DEB theory specifies reserve dynamics on the basis of the requirements of weak homeostasis and partitionability. We here present a new and simple mechanism for this dynamics which accounts for the rejection of mobilised reserve by busy maintenance/growth machinery. This module, like quite a few other modules of DEB theory, uses the theory of Synthesising Units; we review recent progress in this field. The plasticity of membranes that evolved in early eukaryotes is a major step forward in metabolic evolution; we discuss quantitative aspects of the efficiency of phagocytosis relative to the excretion of digestive enzymes to illustrate its importance. Some processes of adaptation and gene expression can be understood in terms of allocation linked to the relative workload of metabolic modules in (unicellular) prokaryotes and organs in (multicellular) eukaryotes. We argue that the evolution of demand systems can only be understood in the light of that of supply systems. We illustrate some important points with data from the literature.

Mechanical design of translocating motor proteins.

PubMed

Hwang, Wonmuk; Lang, Matthew J

2009-01-01

Translocating motors generate force and move along a biofilament track to achieve diverse functions including gene transcription, translation, intracellular cargo transport, protein degradation, and muscle contraction. Advances in single molecule manipulation experiments, structural biology, and computational analysis are making it possible to consider common mechanical design principles of these diverse families of motors. Here, we propose a mechanical parts list that include track, energy conversion machinery, and moving parts. Energy is supplied not just by burning of a fuel molecule, but there are other sources or sinks of free energy, by binding and release of a fuel or products, or similarly between the motor and the track. Dynamic conformational changes of the motor domain can be regarded as controlling the flow of free energy to and from the surrounding heat reservoir. Multiple motor domains are organized in distinct ways to achieve motility under imposed physical constraints. Transcending amino acid sequence and structure, physically and functionally similar mechanical parts may have evolved as nature's design strategy for these molecular engines.

Mechanical Design of Translocating Motor Proteins

PubMed Central

Lang, Matthew J.

2013-01-01

Translocating motors generate force and move along a biofilament track to achieve diverse functions including gene transcription, translation, intracellular cargo transport, protein degradation, and muscle contraction. Advances in single molecule manipulation experiments, structural biology, and computational analysis are making it possible to consider common mechanical design principles of these diverse families of motors. Here, we propose a mechanical parts list that include track, energy conversion machinery, and moving parts. Energy is supplied not just by burning of a fuel molecule, but there are other sources or sinks of free energy, by binding and release of a fuel or products, or similarly between the motor and the track. Dynamic conformational changes of the motor domain can be regarded as controlling the flow of free energy to and from the surrounding heat reservoir. Multiple motor domains are organized in distinct ways to achieve motility under imposed physical constraints. Transcending amino acid sequence and structure, physically and functionally similar mechanical parts may have evolved as nature’s design strategy for these molecular engines. PMID:19452133

The Evolution of the Placenta

PubMed Central

Roberts, R Michael; Green, Jonathan A; Schulz, Laura C

2016-01-01

The still apt definition of a placenta is that coined by Mossman, namely apposition or fusion of the fetal membranes to the uterine mucosa for physiological exchange. As such it is a specialized organ whose purpose is to provide continuing support to the developing young. By this definition, placentas have evolved within every vertebrate class other than birds. They have evolved on multiple occasions, often within quite narrow taxonomic groups. As the placenta and the maternal system associate more intimately, such that the conceptus relies extensively on maternal support, the relationship leads to increased conflict that drives adaptive changes on both sides. The story of vertebrate placentation, therefore, is one of convergent evolution at both the macro- and molecular levels. In this short review, we first describe the emergence of placental-like structures in non-mammalian vertebrates and then transition to mammals themselves. We close the review by discussing mechanisms that might have favored diversity and hence evolution of the morphology and physiology of the placentas of eutherian mammals. PMID:27486265

Double-Serine Fluoroquinolone Resistance Mutations Advance Major International Clones and Lineages of Various Multi-Drug Resistant Bacteria.

PubMed

Fuzi, Miklos; Szabo, Dora; Csercsik, Rita

2017-01-01

The major international sequence types/lineages of methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae and ESBL-producing E. coli were demonstrated to have been advanced by favorable fitness balance associated with high-level resistance to fluoroquinolones. The paper shows that favorable fitness in the major STs/lineages of these pathogens was principally attained by the capacity of evolving mutations in the fluoroquinolone-binding serine residues of both the DNA gyrase and topoisomerase IV enzymes. The available information on fitness balance incurred by individual and various combinations of mutations in the enzymes is reviewed in multiple species. Moreover, strong circumstantial evidence is presented that major STs/lineages of other multi-drug resistant bacteria, primarily vancomycin-resistant Enterococcus faecium (VRE), emerged by a similar mechanism. The reason(s) why the major ST/lineage strains of various pathogens proved more adept at evolving favorable mutations than most isolates of the same species remains to be elucidated.

Double-Serine Fluoroquinolone Resistance Mutations Advance Major International Clones and Lineages of Various Multi-Drug Resistant Bacteria

PubMed Central

Fuzi, Miklos; Szabo, Dora; Csercsik, Rita

2017-01-01

The major international sequence types/lineages of methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae and ESBL-producing E. coli were demonstrated to have been advanced by favorable fitness balance associated with high-level resistance to fluoroquinolones. The paper shows that favorable fitness in the major STs/lineages of these pathogens was principally attained by the capacity of evolving mutations in the fluoroquinolone-binding serine residues of both the DNA gyrase and topoisomerase IV enzymes. The available information on fitness balance incurred by individual and various combinations of mutations in the enzymes is reviewed in multiple species. Moreover, strong circumstantial evidence is presented that major STs/lineages of other multi-drug resistant bacteria, primarily vancomycin-resistant Enterococcus faecium (VRE), emerged by a similar mechanism. The reason(s) why the major ST/lineage strains of various pathogens proved more adept at evolving favorable mutations than most isolates of the same species remains to be elucidated. PMID:29250038

Analyzing nature's protective design: The glyptodont body armor.

PubMed

du Plessis, Anton; Broeckhoven, Chris; Yadroitsev, Igor; Yadroitsava, Ina; le Roux, Stephan Gerhard

2018-06-01

Many animal species evolved some form of body armor, such as scales of fish and bony plates or osteoderms of reptiles. Although a protective function is often taken for granted, recent studies show that body armor might comprise multiple functionalities and is shaped by trade-offs among these functionalities. Hence, despite the fact that natural body armor might serve as bio-inspiration for the development of artificial protective materials, focussing on model systems in which body armor serves a solely protective function might be pivotal. In this study, we investigate the osteoderms of Glyptotherium arizonae, an extinct armadillo-like mammal in which body armor evolved as protection against predators and/or tail club blows of conspecifics. By using a combination of micro-computed tomography, reverse-engineering, stress simulations and mechanical testing of 3D printed models, we show that the combination of dense compact layers and porous lattice core might provide an optimized combination of strength and high energy absorption. Copyright © 2018 Elsevier Ltd. All rights reserved.

Specialized Motor-Driven dusp1 Expression in the Song Systems of Multiple Lineages of Vocal Learning Birds

PubMed Central

Horita, Haruhito; Kobayashi, Masahiko; Liu, Wan-chun; Oka, Kotaro; Jarvis, Erich D.; Wada, Kazuhiro

2012-01-01

Mechanisms for the evolution of convergent behavioral traits are largely unknown. Vocal learning is one such trait that evolved multiple times and is necessary in humans for the acquisition of spoken language. Among birds, vocal learning is evolved in songbirds, parrots, and hummingbirds. Each time similar forebrain song nuclei specialized for vocal learning and production have evolved. This finding led to the hypothesis that the behavioral and neuroanatomical convergences for vocal learning could be associated with molecular convergence. We previously found that the neural activity-induced gene dual specificity phosphatase 1 (dusp1) was up-regulated in non-vocal circuits, specifically in sensory-input neurons of the thalamus and telencephalon; however, dusp1 was not up-regulated in higher order sensory neurons or motor circuits. Here we show that song motor nuclei are an exception to this pattern. The song nuclei of species from all known vocal learning avian lineages showed motor-driven up-regulation of dusp1 expression induced by singing. There was no detectable motor-driven dusp1 expression throughout the rest of the forebrain after non-vocal motor performance. This pattern contrasts with expression of the commonly studied activity-induced gene egr1, which shows motor-driven expression in song nuclei induced by singing, but also motor-driven expression in adjacent brain regions after non-vocal motor behaviors. In the vocal non-learning avian species, we found no detectable vocalizing-driven dusp1 expression in the forebrain. These findings suggest that independent evolutions of neural systems for vocal learning were accompanied by selection for specialized motor-driven expression of the dusp1 gene in those circuits. This specialized expression of dusp1 could potentially lead to differential regulation of dusp1-modulated molecular cascades in vocal learning circuits. PMID:22876306

Protecting DNA from errors and damage: an overview of DNA repair mechanisms in plants compared to mammals.

PubMed

Spampinato, Claudia P

2017-05-01

The genome integrity of all organisms is constantly threatened by replication errors and DNA damage arising from endogenous and exogenous sources. Such base pair anomalies must be accurately repaired to prevent mutagenesis and/or lethality. Thus, it is not surprising that cells have evolved multiple and partially overlapping DNA repair pathways to correct specific types of DNA errors and lesions. Great progress in unraveling these repair mechanisms at the molecular level has been made by several talented researchers, among them Tomas Lindahl, Aziz Sancar, and Paul Modrich, all three Nobel laureates in Chemistry for 2015. Much of this knowledge comes from studies performed in bacteria, yeast, and mammals and has impacted research in plant systems. Two plant features should be mentioned. Plants differ from higher eukaryotes in that they lack a reserve germline and cannot avoid environmental stresses. Therefore, plants have evolved different strategies to sustain genome fidelity through generations and continuous exposure to genotoxic stresses. These strategies include the presence of unique or multiple paralogous genes with partially overlapping DNA repair activities. Yet, in spite (or because) of these differences, plants, especially Arabidopsis thaliana, can be used as a model organism for functional studies. Some advantages of this model system are worth mentioning: short life cycle, availability of both homozygous and heterozygous lines for many genes, plant transformation techniques, tissue culture methods and reporter systems for gene expression and function studies. Here, I provide a current understanding of DNA repair genes in plants, with a special focus on A. thaliana. It is expected that this review will be a valuable resource for future functional studies in the DNA repair field, both in plants and animals.

Criticality Is an Emergent Property of Genetic Networks that Exhibit Evolvability

PubMed Central

Torres-Sosa, Christian; Huang, Sui; Aldana, Maximino

2012-01-01

Accumulating experimental evidence suggests that the gene regulatory networks of living organisms operate in the critical phase, namely, at the transition between ordered and chaotic dynamics. Such critical dynamics of the network permits the coexistence of robustness and flexibility which are necessary to ensure homeostatic stability (of a given phenotype) while allowing for switching between multiple phenotypes (network states) as occurs in development and in response to environmental change. However, the mechanisms through which genetic networks evolve such critical behavior have remained elusive. Here we present an evolutionary model in which criticality naturally emerges from the need to balance between the two essential components of evolvability: phenotype conservation and phenotype innovation under mutations. We simulated the Darwinian evolution of random Boolean networks that mutate gene regulatory interactions and grow by gene duplication. The mutating networks were subjected to selection for networks that both (i) preserve all the already acquired phenotypes (dynamical attractor states) and (ii) generate new ones. Our results show that this interplay between extending the phenotypic landscape (innovation) while conserving the existing phenotypes (conservation) suffices to cause the evolution of all the networks in a population towards criticality. Furthermore, the networks produced by this evolutionary process exhibit structures with hubs (global regulators) similar to the observed topology of real gene regulatory networks. Thus, dynamical criticality and certain elementary topological properties of gene regulatory networks can emerge as a byproduct of the evolvability of the phenotypic landscape. PMID:22969419

The Differences between NAD-ME and NADP-ME Subtypes of C4 Photosynthesis: More than Decarboxylating Enzymes.

PubMed

Rao, Xiaolan; Dixon, Richard A

2016-01-01

As an adaptation to changing climatic conditions that caused high rates of photorespiration, C 4 plants have evolved to display higher photosynthetic efficiency than C 3 plants under elevated temperature, high light intensities, and drought. The C 4 plants independently evolved more than 60 times in 19 families of angiosperms to establish similar but not uniform C 4 mechanisms to concentrate CO 2 around the carboxylating enzyme Rubisco (ribulose bisphosphate carboxylase oxygenase). C 4 photosynthesis is divided into at least two basic biochemical subtypes based on the primary decarboxylating enzymes, NAD-dependent malic enzyme (NAD-ME) and NADP-dependent malic enzyme (NADP-ME). The multiple polygenetic origins of these subtypes raise questions about the association of C 4 variation between biochemical subtypes and diverse lineages. This review addresses the differences in evolutionary scenario, leaf anatomy, and especially C 4 metabolic flow, C 4 transporters, and cell-specific function deduced from recently reported cell-specific transcriptomic, proteomic, and metabolic analyses of NAD-ME and NADP-ME subtypes. Current omic analysis has revealed the extent to which component abundances differ between the two biochemical subtypes, leading to a better understanding of C 4 photosynthetic mechanisms in NAD-ME and NADP-ME subtypes.

The Differences between NAD-ME and NADP-ME Subtypes of C4 Photosynthesis: More than Decarboxylating Enzymes

PubMed Central

Rao, Xiaolan; Dixon, Richard A.

2016-01-01

As an adaptation to changing climatic conditions that caused high rates of photorespiration, C4 plants have evolved to display higher photosynthetic efficiency than C3 plants under elevated temperature, high light intensities, and drought. The C4 plants independently evolved more than 60 times in 19 families of angiosperms to establish similar but not uniform C4 mechanisms to concentrate CO2 around the carboxylating enzyme Rubisco (ribulose bisphosphate carboxylase oxygenase). C4 photosynthesis is divided into at least two basic biochemical subtypes based on the primary decarboxylating enzymes, NAD-dependent malic enzyme (NAD-ME) and NADP-dependent malic enzyme (NADP-ME). The multiple polygenetic origins of these subtypes raise questions about the association of C4 variation between biochemical subtypes and diverse lineages. This review addresses the differences in evolutionary scenario, leaf anatomy, and especially C4 metabolic flow, C4 transporters, and cell-specific function deduced from recently reported cell-specific transcriptomic, proteomic, and metabolic analyses of NAD-ME and NADP-ME subtypes. Current omic analysis has revealed the extent to which component abundances differ between the two biochemical subtypes, leading to a better understanding of C4 photosynthetic mechanisms in NAD-ME and NADP-ME subtypes. PMID:27790235

The incidence and selection of multiple mating in plants

PubMed Central

Pannell, John R.; Labouche, Anne-Marie

2013-01-01

Mating with more than one pollen donor, or polyandry, is common in land plants. In flowering plants, polyandry occurs when the pollen from different potential sires is distributed among the fruits of a single individual, or when pollen from more than one donor is deposited on the same stigma. Because polyandry typically leads to multiple paternity among or within fruits, it can be indirectly inferred on the basis of paternity analysis using molecular markers. A review of the literature indicates that polyandry is probably ubiquitous in plants except those that habitually self-fertilize, or that disperse their pollen in pollen packages, such as polyads or pollinia. Multiple mating may increase plants' female component by alleviating pollen limitation or by promoting competition among pollen grains from different potential sires. Accordingly, a number of traits have evolved that should promote polyandry at the flower level from the female's point of view, e.g. the prolongation of stigma receptivity or increases in stigma size. However, many floral traits, such as attractiveness, the physical manipulation of pollinators and pollen-dispensing mechanisms that lead to polyandrous pollination, have probably evolved in response to selection to promote male siring success in general, so that polyandry might often best be seen as a by-product of selection to enhance outcross siring success. In this sense, polyandry in plants is similar to geitonogamy (selfing caused by pollen transfer among flowers of the same plant), because both polyandry and geitonogamy probably result from selection to promote outcross siring success, although geitonogamy is almost always deleterious while polyandry in plants will seldom be so. PMID:23339242

Bispecific antibody targets multiple Pseudomonas aeruginosa evasion mechanisms in the lung vasculature.

PubMed

Thanabalasuriar, Ajitha; Surewaard, Bas Gj; Willson, Michelle E; Neupane, Arpan S; Stover, Charles K; Warrener, Paul; Wilson, George; Keller, Ashley E; Sellman, Bret R; DiGiandomenico, Antonio; Kubes, Paul

2017-06-01

Pseudomonas aeruginosa is a major cause of severe infections that lead to bacteremia and high patient mortality. P. aeruginosa has evolved numerous evasion and subversion mechanisms that work in concert to overcome immune recognition and effector functions in hospitalized and immunosuppressed individuals. Here, we have used multilaser spinning-disk intravital microscopy to monitor the blood-borne stage in a murine bacteremic model of P. aeruginosa infection. P. aeruginosa adhered avidly to lung vasculature, where patrolling neutrophils and other immune cells were virtually blind to the pathogen's presence. This cloaking phenomenon was attributed to expression of Psl exopolysaccharide. Although an anti-Psl mAb activated complement and enhanced neutrophil recognition of P. aeruginosa, neutrophil-mediated clearance of the pathogen was suboptimal owing to a second subversion mechanism, namely the type 3 secretion (T3S) injectisome. Indeed, T3S prevented phagosome acidification and resisted killing inside these compartments. Antibody-mediated inhibition of the T3S protein PcrV did not enhance bacterial phagocytosis but did enhance killing of the few bacteria ingested by neutrophils. A bispecific mAb targeting both Psl and PcrV enhanced neutrophil uptake of P. aeruginosa and also greatly increased inhibition of T3S function, allowing for phagosome acidification and bacterial killing. These data highlight the need to block multiple evasion and subversion mechanisms in tandem to kill P. aeruginosa.

Genomic profiles of low-grade murine gliomas evolve during progression to glioblastoma. | Office of Cancer Genomics

Cancer.gov

Background: Gliomas are diverse neoplasms with multiple molecular subtypes. How tumor-initiating mutations relate to molecular subtypes as these tumors evolve during malignant progression remains unclear.Methods: We used genetically engineered mouse models, histopathology, genetic lineage tracing, expression profiling, and copy number analyses to examine how genomic tumor diversity evolves during the course of malignant progression from low- to high-grade disease.

Evolution and inheritance of early embryonic patterning in D. simulans and D. sechellia

PubMed Central

Lott, Susan E.; Ludwig, Michael Z.; Kreitman, Martin

2010-01-01

Pattern formation in Drosophila is a widely studied example of a robust developmental system. Such robust systems pose a challenge to adaptive evolution, as they mask variation which selection may otherwise act upon. Yet we find variation in the localization of expression domains (henceforth ‘stripe allometry’) in the pattern formation pathway. Specifically, we characterize differences in the gap genes giant and Kruppel, and the pair-rule gene even-skipped, which differ between the sibling species D. simulans and D. sechellia. In a double-backcross experiment, stripe allometry is consistent with maternal inheritance of stripe positioning and multiple genetic factors, with a distinct genetic basis from embryo length. Embryos produced by F1 and F2 backcross mothers exhibit novel spatial patterns of gene expression relative to the parental species, with no measurable increase in positional variance among individuals. Buffering of novel spatial patterns in the backcross genotypes suggests that robustness need not be disrupted in order for the trait to evolve, and perhaps the system is incapable of evolving to prevent the expression of all genetic variation. This limitation, and the ability of natural selection to act on minute genetic differences that are within the “margin of error” for the buffering mechanism, indicates that developmentally buffered traits can evolve without disruption of robustness PMID:21121913

Selective inhibitor of endosomal trafficking pathways exploited by multiple toxins and viruses

PubMed Central

Gillespie, Eugene J.; Ho, Chi-Lee C.; Balaji, Kavitha; Clemens, Daniel L.; Deng, Gang; Wang, Yao E.; Elsaesser, Heidi J.; Tamilselvam, Batcha; Gargi, Amandeep; Dixon, Shandee D.; France, Bryan; Chamberlain, Brian T.; Blanke, Steven R.; Cheng, Genhong; de la Torre, Juan Carlos; Brooks, David G.; Jung, Michael E.; Colicelli, John; Damoiseaux, Robert; Bradley, Kenneth A.

2013-01-01

Pathogenic microorganisms and toxins have evolved a variety of mechanisms to gain access to the host-cell cytosol and thereby exert virulent effects upon the host. One common mechanism of cellular entry requires trafficking to an acidified endosome, which promotes translocation across the host membrane. To identify small-molecule inhibitors that block this process, a library of 30,000 small molecules was screened for inhibitors of anthrax lethal toxin. Here we report that 4-bromobenzaldehyde N-(2,6-dimethylphenyl)semicarbazone, the most active compound identified in the screen, inhibits intoxication by lethal toxin and blocks the entry of multiple other acid-dependent bacterial toxins and viruses into mammalian cells. This compound, which we named EGA, also delays lysosomal targeting and degradation of the EGF receptor, indicating that it targets host-membrane trafficking. In contrast, EGA does not block endosomal recycling of transferrin, retrograde trafficking of ricin, phagolysosomal trafficking, or phagosome permeabilization by Franciscella tularensis. Furthermore, EGA does not neutralize acidic organelles, demonstrating that its mechanism of action is distinct from pH-raising agents such as ammonium chloride and bafilomycin A1. EGA is a powerful tool for the study of membrane trafficking and represents a class of host-targeted compounds for therapeutic development to treat infectious disease. PMID:24191014

Subcutaneous interferon β-1a three times weekly and the natural evolution of gadolinium-enhancing lesions into chronic black holes in relapsing and progressive multiple sclerosis: Analysis of PRISMS and SPECTRIMS trials.

PubMed

Traboulsee, A; Li, Dkb; Tam, R; Zhao, G; Riddehough, A; Fang, J; Dangond, F; Kappos, L

2017-01-01

Evolution of gadolinium-enhancing lesions into chronic black holes (CBH) may be reduced by interferon (IFN) therapy. The objective of this paper is to assess the effect of IFN β-1a and placebo on CBH evolution and disability in patients with relapsing-remitting multiple sclerosis (RRMS), as well as CBH evolution in patients with secondary progressive multiple sclerosis (SPMS). A post hoc, exploratory analysis of patients with RRMS and SPMS with monthly MRI scans (months -1 to 9) from two separate placebo-controlled clinical trials of IFN β-1a was conducted. In RRMS patients, the risk of ≥1 evolved CBH was lower for IFN β-1a versus placebo (odds ratio 0.42; p  = 0.024); volume of newly evolved CBH was numerically reduced. A numerically higher proportion of patients with ≥1 evolving CBH vs no evolving CBH had confirmed three-month disability progression (four-year rate 55.8% vs 43.1%, respectively). Proportion of lesions evolving into CBH (patient level: 34.7% vs 12.6%, p  < 0.0001; lesion level: 28.8% vs 11.0%, p  < 0.0001) and evolved CBH volume (median 33.5 mm 3 (Quartile 1, 0.0; Quartile 3, 173.4) vs 0.0 mm 3 (0.0; 52.4); p  = 0.0008) was higher for SPMS than RRMS patients treated with IFN β-1a. In RRMS, IFN β-1a significantly decreased the proportion of new T1 Gd+ lesions evolving into CBH and the risk of developing a CBH. In patients with SPMS, more lesions develop to CBH, indicating reduced repair capacity, and the natural history of lesion development appears to be unaffected by IFN β-1a treatment.

Risk assessment and adaptive runoff utilization in water resource system considering the complex relationship among water supply, electricity generation and environment

NASA Astrophysics Data System (ADS)

Zhou, J.; Zeng, X.; Mo, L.; Chen, L.; Jiang, Z.; Feng, Z.; Yuan, L.; He, Z.

2017-12-01

Generally, the adaptive utilization and regulation of runoff in the source region of China's southwest rivers is classified as a typical multi-objective collaborative optimization problem. There are grim competitions and incidence relation in the subsystems of water supply, electricity generation and environment, which leads to a series of complex problems represented by hydrological process variation, blocked electricity output and water environment risk. Mathematically, the difficulties of multi-objective collaborative optimization focus on the description of reciprocal relationships and the establishment of evolving model of adaptive systems. Thus, based on the theory of complex systems science, this project tries to carry out the research from the following aspects: the changing trend of coupled water resource, the covariant factor and driving mechanism, the dynamic evolution law of mutual feedback dynamic process in the supply-generation-environment coupled system, the environmental response and influence mechanism of coupled mutual feedback water resource system, the relationship between leading risk factor and multiple risk based on evolutionary stability and dynamic balance, the transfer mechanism of multiple risk response with the variation of the leading risk factor, the multidimensional coupled feedback system of multiple risk assessment index system and optimized decision theory. Based on the above-mentioned research results, the dynamic method balancing the efficiency of multiple objectives in the coupled feedback system and optimized regulation model of water resources is proposed, and the adaptive scheduling mode considering the internal characteristics and external response of coupled mutual feedback system of water resource is established. In this way, the project can make a contribution to the optimal scheduling theory and methodology of water resource management under uncertainty in the source region of Southwest River.

Spatio-Temporal Data Model for Integrating Evolving Nation-Level Datasets

NASA Astrophysics Data System (ADS)

Sorokine, A.; Stewart, R. N.

2017-10-01

Ability to easily combine the data from diverse sources in a single analytical workflow is one of the greatest promises of the Big Data technologies. However, such integration is often challenging as datasets originate from different vendors, governments, and research communities that results in multiple incompatibilities including data representations, formats, and semantics. Semantics differences are hardest to handle: different communities often use different attribute definitions and associate the records with different sets of evolving geographic entities. Analysis of global socioeconomic variables across multiple datasets over prolonged time is often complicated by the difference in how boundaries and histories of countries or other geographic entities are represented. Here we propose an event-based data model for depicting and tracking histories of evolving geographic units (countries, provinces, etc.) and their representations in disparate data. The model addresses the semantic challenge of preserving identity of geographic entities over time by defining criteria for the entity existence, a set of events that may affect its existence, and rules for mapping between different representations (datasets). Proposed model is used for maintaining an evolving compound database of global socioeconomic and environmental data harvested from multiple sources. Practical implementation of our model is demonstrated using PostgreSQL object-relational database with the use of temporal, geospatial, and NoSQL database extensions.

Evolution of kin recognition mechanisms in a fish.

PubMed

Hain, Timothy J A; Garner, Shawn R; Ramnarine, Indar W; Neff, Bryan D

2017-03-01

Both selection and phylogenetic history can influence the evolution of phenotypic traits. Here we used recently characterized variation in kin recognition mechanisms among six guppy populations to explore the phylogenetic history of this trait. Guppies can use two different kin recognition mechanisms: either phenotype matching, in which individuals are identified based on comparison with a recognition template, or familiarity, in which individuals are remembered based on previous interactions. Across the six populations, we identified four transitions in recognition mechanism: phenotype matching evolved once and was subsequently lost in a single population, whereas familiarity evolved twice. Based on a molecular clock, these transitions occurred among populations that had diverged on a timescale of hundreds of thousands of years, which is two orders of magnitude faster than previously documented transitions in recognition mechanisms. A randomization test provided no evidence that recognition mechanisms were constrained by phylogeny, suggesting that recognition mechanisms have the capacity to evolve rapidly, although the specific selection pressures that may be contributing to variation in recognition mechanisms across populations remain unknown.

Richter and Sodium Appetite: from adrenalectomy to molecular biology

PubMed Central

Krause, Eric G.; Sakai, Randall R.

2007-01-01

Nearly three-quarters of a century ago, Curt Richter removed the adrenal glands from rats and noted that the animal's vitality was dependent on its increased consumption of sodium chloride. In doing so, Richter revealed an innate behavioral mechanism that serves to maintain the hydromineral balance of an animal faced with sodium deficit. This experiment and others like it, led to the development of a field of research devoted to the investigation of salt appetite. The following is a discussion of how Richter's initial observations gave birth to an evolving field that incorporates multiple approaches to examine the drive to consume sodium. PMID:17561308

Inhibition and Avoidance of mRNA Degradation by RNA Viruses

PubMed Central

Moon, Stephanie L.; Barnhart, Michael D.; Wilusz, Jeffrey

2012-01-01

The cellular mRNA decay machinery plays a major role in regulating the quality and quantity of gene expression in cells. This machinery involves multiple enzymes and pathways that converge to promote the exonucleolytic decay of mRNAs. The transcripts made by RNA viruses are susceptible to degradation by this machinery and, in fact, can be actively targeted. Thus, to maintain gene expression and replication, RNA viruses have evolved a number of strategies to avoid and/or inactivate aspects of the cellular mRNA decay machinery. Recent work uncovering the mechanisms used by RNA viruses to maintain the stability of their transcripts is described below. PMID:22626865

Adapting the Stress Response: Viral Subversion of the mTOR Signaling Pathway.

PubMed

Le Sage, Valerie; Cinti, Alessandro; Amorim, Raquel; Mouland, Andrew J

2016-05-24

The mammalian target of rapamycin (mTOR) is a central regulator of gene expression, translation and various metabolic processes. Multiple extracellular (growth factors) and intracellular (energy status) molecular signals as well as a variety of stressors are integrated into the mTOR pathway. Viral infection is a significant stress that can activate, reduce or even suppress the mTOR signaling pathway. Consequently, viruses have evolved a plethora of different mechanisms to attack and co-opt the mTOR pathway in order to make the host cell a hospitable environment for replication. A more comprehensive knowledge of different viral interactions may provide fruitful targets for new antiviral drugs.

Brine Migration in Heated Salt: Lessons Learned from Field Experiments

NASA Astrophysics Data System (ADS)

Kuhlman, K. L.; Matteo, E. N.; Mills, M.

2017-12-01

We summarize several interesting brine migration related phenomena hinted at in field experiments from field testing related to salt radioactive waste repositories in Germany and the US. Past heater tests in salt have shown 1) thermal-hydrological-mechanical coupling is quite strong during both heating and cooling; 2) chemical composition of brine evolves during heating, and comprises a mix of several water sources; and 3) acid gas (HCl) generation has been observed during past heater tests and may have multiple mechanisms for formation. We present a heated brine migration test design, formulated with these complexities in mind. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia LLC, a wholly owned subsidiary of Honeywell International Inc. for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Respiratory syncytial virus mechanisms to interfere with type 1 interferons.

PubMed

Barik, Sailen

2013-01-01

Respiratory syncytial virus (RSV) is a member of the Paramyxoviridae family that consists of viruses with nonsegmented negative-strand RNA genome. Infection by these viruses triggers the innate antiviral response of the host, mainly type I interferon (IFN). Essentially all other viruses of this family produce IFN suppressor functions by co-transcriptional RNA editing. In contrast, RSV has evolved two unique nonstructural proteins, NS1 and NS2, to effectively serve this purpose. Together, NS1 and NS2 degrade or sequester multiple signaling proteins that affect both IFN induction and IFN effector functions. While the mechanism of action of NS1 and NS2 is a subject of active research, their effect on adaptive immunity is also being recognized. In this review, we discuss various aspects of NS1 and NS2 function with implications for vaccine design.

Underground tuning: quantitative regulation of root growth.

PubMed

Satbhai, Santosh B; Ristova, Daniela; Busch, Wolfgang

2015-02-01

Plants display a high degree of phenotypic plasticity that allows them to tune their form and function to changing environments. The plant root system has evolved mechanisms to anchor the plant and to efficiently explore soils to forage for soil resources. Key to this is an enormous capacity for plasticity of multiple traits that shape the distribution of roots in the soil. Such root system architecture-related traits are determined by root growth rates, root growth direction, and root branching. In this review, we describe how the root system is constituted, and which mechanisms, pathways, and genes mainly regulate plasticity of the root system in response to environmental variation. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Die Another Day: Inhibition of Cell Death Pathways by Cytomegalovirus.

PubMed

Brune, Wolfram; Andoniou, Christopher E

2017-09-02

Multicellular organisms have evolved multiple genetically programmed cell death pathways that are essential for homeostasis. The finding that many viruses encode cell death inhibitors suggested that cellular suicide also functions as a first line of defence against invading pathogens. This theory was confirmed by studying viral mutants that lack certain cell death inhibitors. Cytomegaloviruses, a family of species-specific viruses, have proved particularly useful in this respect. Cytomegaloviruses are known to encode multiple death inhibitors that are required for efficient viral replication. Here, we outline the mechanisms used by the host cell to detect cytomegalovirus infection and discuss the methods employed by the cytomegalovirus family to prevent death of the host cell. In addition to enhancing our understanding of cytomegalovirus pathogenesis we detail how this research has provided significant insights into the cross-talk that exists between the various cell death pathways.

High times, low sats: diffuse pulmonary infiltrates associated with chronic synthetic cannabinoid use.

PubMed

Alhadi, Sameir; Tiwari, Anupama; Vohra, Rais; Gerona, Roy; Acharya, Janak; Bilello, Kathryn

2013-06-01

In recent years, cases of severe adverse effects from recreational use of synthetic cannabinoids (SC) have established that these agents represent a novel toxicologic hazard. A 21-year-old male presenting as a vehicular trauma victim was noted with diffuse pulmonary infiltrates related to chronic inhalation of multiple synthetic cannabinoid-containing products. Chest imaging revealed bilateral, subacute lung infiltrates; histopathological analysis of bronchial and alveolar tissues revealed an inflammatory process. An extensive workup failed to identify infectious, malignant, autoimmune, or hematologic causes of the syndrome, and toxicological analysis of the blood and body fluids confirmed the presence of multiple synthetic cannabinoids and metabolites. The patient recovered after an 8-day ICU course, wherein he received antibiotics, steroids, and mechanical ventilation. This case contributes to the currently evolving knowledge about SC agents, adding a rarely described pulmonary complication to the growing list of adverse effects associated with these products.

Compositional and Microstructural Evolution of Olivine Under Multiple-Cycle Pulsed Laser Irradiation as Revealed by FIB/Field-Emission TEM

NASA Technical Reports Server (NTRS)

Christoffersen, R.; Loeffler, M. J.; Dukes, C. A.; Keller, L. P.; Baragiola, R. A.

2016-01-01

The use of pulsed laser irradiation to simulate the short duration, high-energy conditions characteristic of micrometeorite impacts is now an established approach in experimental space weathering studies. The laser generates both melt and vapor deposits that contain nanophase metallic Fe (npFe(sup 0)) grains with size distributions and optical properties similar to those in natural impact-generated melt and vapor deposits. There remains uncertainty, however, about how well lasers simulate the mechanical work and internal (thermal) energy partitioning that occurs in actual impacts. We are currently engaged in making a direct comparison between the products of laser irradiation and experimental/natural hypervelocity impacts. An initial step reported here is to use analytical SEM and TEM is to attain a better understanding of how the microstructure and composition of laser deposits evolve over multiple cycles of pulsed laser irradiation.

Growth Control and Disease Mechanisms in Computational Embryogeny

NASA Technical Reports Server (NTRS)

Shapiro, Andrew A.; Yogev, Or; Antonsson, Erik K.

2008-01-01

This paper presents novel approach to applying growth control and diseases mechanisms in computational embryogeny. Our method, which mimics fundamental processes from biology, enables individuals to reach maturity in a controlled process through a stochastic environment. Three different mechanisms were implemented; disease mechanisms, gene suppression, and thermodynamic balancing. This approach was integrated as part of a structural evolutionary model. The model evolved continuum 3-D structures which support an external load. By using these mechanisms we were able to evolve individuals that reached a fixed size limit through the growth process. The growth process was an integral part of the complete development process. The size of the individuals was determined purely by the evolutionary process where different individuals matured to different sizes. Individuals which evolved with these characteristics have been found to be very robust for supporting a wide range of external loads.

Evolving Organizational Structures in Special Education.

ERIC Educational Resources Information Center

McCarthy, Eileen F., Ed.; Sage, Daniel D., Ed.

The monograph addresses evolving organizational structures in special education from the perspectives of theory and practice. The initial paper, "Issues in Organizational Structure" (D. Sage), focuses on how the multiple units and operations of the special education system should be related and how the management authority and responsibility for…

Evolving Nature of Sexual Orientation and Gender Identity

ERIC Educational Resources Information Center

Jourian, T. J.

2015-01-01

This chapter discusses the historical and evolving terminology, constructs, and ideologies that inform the language used by those who are lesbian, gay, bisexual, and same-gender loving, who may identify as queer, as well as those who are members of trans* communities from multiple and intersectional perspectives.

Do Infants Possess an Evolved Spider-Detection Mechanism?

ERIC Educational Resources Information Center

Rakison, David H.; Derringer, Jaime

2008-01-01

Previous studies with various non-human animals have revealed that they possess an evolved predator recognition mechanism that specifies the appearance of recurring threats. We used the preferential looking and habituation paradigms in three experiments to investigate whether 5-month-old human infants have a perceptual template for spiders that…

Research at the Crossroads: How Intellectual Initiatives across Disciplines Evolve

ERIC Educational Resources Information Center

Frost, Susan H.; Jean, Paul M.; Teodorescu, Daniel; Brown, Amy B.

2004-01-01

How do intellectual initiatives across disciplines evolve? This qualitative case study of 11 interdisciplinary research initiatives at Emory University identifies key factors in their development: the passionate commitments of scholarly leaders, the presence of strong collegial networks, access to timely and multiple resources, flexible practices,…

Natural selection promotes antigenic evolvability.

PubMed

Graves, Christopher J; Ros, Vera I D; Stevenson, Brian; Sniegowski, Paul D; Brisson, Dustin

2013-01-01

The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed 'cassettes' that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios) and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish chronic infections.

Natural Selection Promotes Antigenic Evolvability

PubMed Central

Graves, Christopher J.; Ros, Vera I. D.; Stevenson, Brian; Sniegowski, Paul D.; Brisson, Dustin

2013-01-01

The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed ‘cassettes’ that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios) and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish chronic infections. PMID:24244173

Cell-intrinsic mechanisms of temperature compensation in a grasshopper sensory receptor neuron

PubMed Central

Roemschied, Frederic A; Eberhard, Monika JB; Schleimer, Jan-Hendrik; Ronacher, Bernhard; Schreiber, Susanne

2014-01-01

Changes in temperature affect biochemical reaction rates and, consequently, neural processing. The nervous systems of poikilothermic animals must have evolved mechanisms enabling them to retain their functionality under varying temperatures. Auditory receptor neurons of grasshoppers respond to sound in a surprisingly temperature-compensated manner: firing rates depend moderately on temperature, with average Q10 values around 1.5. Analysis of conductance-based neuron models reveals that temperature compensation of spike generation can be achieved solely relying on cell-intrinsic processes and despite a strong dependence of ion conductances on temperature. Remarkably, this type of temperature compensation need not come at an additional metabolic cost of spike generation. Firing rate-based information transfer is likely to increase with temperature and we derive predictions for an optimal temperature dependence of the tympanal transduction process fostering temperature compensation. The example of auditory receptor neurons demonstrates how neurons may exploit single-cell mechanisms to cope with multiple constraints in parallel. DOI: http://dx.doi.org/10.7554/eLife.02078.001 PMID:24843016

Minimizing potential resistance: the molecular view--a comment on Courvalin and Trieu-Cuot.

PubMed

Hooper, D C

2001-09-15

The complexity of bacterial resistance to antimicrobial agents is driven by the interplay of many mechanistic and epidemiologic factors. Mechanistically, resistance by target alteration, reduced permeation, and drug inactivation can occur by both chromosomal mutation and acquisition of new genetic elements. Epidemiologically, exposure to antimicrobial agents provides a growth or persistence advantage for any existing resistant bacteria, generally irrespective of the mechanism. When a single chromosomal mutation is sufficient to cause resistance, any such exposure provides a risk of selection, as long as a sufficiently large bacterial population is exposed. Transmission of resistant bacteria can also amplify resistance of any type, but it is particularly important for complex resistance mechanisms that have evolved over time and for mechanisms that depend on infrequent biological events in nature. Because true biological barriers to the development of resistance are likely to be elusive, multiple approaches that address both the use of antimicrobial agents and transmission are necessary to slow the advance of resistance.

Genetic Parallel Programming: design and implementation.

PubMed

Cheang, Sin Man; Leung, Kwong Sak; Lee, Kin Hong

2006-01-01

This paper presents a novel Genetic Parallel Programming (GPP) paradigm for evolving parallel programs running on a Multi-Arithmetic-Logic-Unit (Multi-ALU) Processor (MAP). The MAP is a Multiple Instruction-streams, Multiple Data-streams (MIMD), general-purpose register machine that can be implemented on modern Very Large-Scale Integrated Circuits (VLSIs) in order to evaluate genetic programs at high speed. For human programmers, writing parallel programs is more difficult than writing sequential programs. However, experimental results show that GPP evolves parallel programs with less computational effort than that of their sequential counterparts. It creates a new approach to evolving a feasible problem solution in parallel program form and then serializes it into a sequential program if required. The effectiveness and efficiency of GPP are investigated using a suite of 14 well-studied benchmark problems. Experimental results show that GPP speeds up evolution substantially.

Cognitive Adaptations for n-person Exchange: The Evolutionary Roots of Organizational Behavior.

PubMed

Tooby, John; Cosmides, Leda; Price, Michael E

2006-03-01

Organizations are composed of stable, predominantly cooperative interactions or n -person exchanges. Humans have been engaging in n -person exchanges for a great enough period of evolutionary time that we appear to have evolved a distinct constellation of species-typical mechanisms specialized to solve the adaptive problems posed by this form of social interaction. These mechanisms appear to have been evolutionarily elaborated out of the cognitive infrastructure that initially evolved for dyadic exchange. Key adaptive problems that these mechanisms are designed to solve include coordination among individuals, and defense against exploitation by free riders. Multi-individual cooperation could not have been maintained over evolutionary time if free riders reliably benefited more than contributors to collective enterprises, and so outcompeted them. As a result, humans evolved mechanisms that implement an aversion to exploitation by free riding, and a strategy of conditional cooperation, supplemented by punitive sentiment towards free riders. Because of the design of these mechanisms, how free riding is treated is a central determinant of the survival and health of cooperative organizations. The mapping of the evolved psychology of n -party exchange cooperation may contribute to the construction of a principled theoretical foundation for the understanding of human behavior in organizations.

Cognitive Adaptations for n-person Exchange: The Evolutionary Roots of Organizational Behavior

PubMed Central

Tooby, John; Cosmides, Leda; Price, Michael E.

2013-01-01

Organizations are composed of stable, predominantly cooperative interactions or n-person exchanges. Humans have been engaging in n-person exchanges for a great enough period of evolutionary time that we appear to have evolved a distinct constellation of species-typical mechanisms specialized to solve the adaptive problems posed by this form of social interaction. These mechanisms appear to have been evolutionarily elaborated out of the cognitive infrastructure that initially evolved for dyadic exchange. Key adaptive problems that these mechanisms are designed to solve include coordination among individuals, and defense against exploitation by free riders. Multi-individual cooperation could not have been maintained over evolutionary time if free riders reliably benefited more than contributors to collective enterprises, and so outcompeted them. As a result, humans evolved mechanisms that implement an aversion to exploitation by free riding, and a strategy of conditional cooperation, supplemented by punitive sentiment towards free riders. Because of the design of these mechanisms, how free riding is treated is a central determinant of the survival and health of cooperative organizations. The mapping of the evolved psychology of n-party exchange cooperation may contribute to the construction of a principled theoretical foundation for the understanding of human behavior in organizations. PMID:23814325

Intestinal crosstalk: a new paradigm for understanding the gut as the "motor" of critical illness.

PubMed

Clark, Jessica A; Coopersmith, Craig M

2007-10-01

For more than 20 years, the gut has been hypothesized to be the "motor" of multiple organ dysfunction syndrome. As critical care research has evolved, there have been multiple mechanisms by which the gastrointestinal tract has been proposed to drive systemic inflammation. Many of these disparate mechanisms have proved to be important in the origin and propagation of critical illness. However, this has led to an unusual situation where investigators describing the gut as a "motor" revving the systemic inflammatory response syndrome are frequently describing wholly different processes to support their claim (i.e., increased apoptosis, altered tight junctions, translocation, cytokine production, crosstalk with commensal bacteria, etc). The purpose of this review is to present a unifying theory as to how the gut drives critical illness. Although the gastrointestinal tract is frequently described simply as "the gut," it is actually made up of (1) an epithelium; (2) a diverse and robust immune arm, which contains most of the immune cells in the body; and (3) the commensal bacteria, which contain more cells than are present in the entire host organism. We propose that the intestinal epithelium, the intestinal immune system, and the intestine's endogenous bacteria all play vital roles driving multiple organ dysfunction syndrome, and the complex crosstalk between these three interrelated portions of the gastrointestinal tract is what cumulatively makes the gut a "motor" of critical illness.

Biomechanical Constraints Underlying Motor Primitives Derived from the Musculoskeletal Anatomy of the Human Arm.

PubMed

Gritsenko, Valeriya; Hardesty, Russell L; Boots, Mathew T; Yakovenko, Sergiy

2016-01-01

Neural control of movement can only be realized though the interaction between the mechanical properties of the limb and the environment. Thus, a fundamental question is whether anatomy has evolved to simplify neural control by shaping these interactions in a beneficial way. This inductive data-driven study analyzed the patterns of muscle actions across multiple joints using the musculoskeletal model of the human upper limb. This model was used to calculate muscle lengths across the full range of motion of the arm and examined the correlations between these values between all pairs of muscles. Musculoskeletal coupling was quantified using hierarchical clustering analysis. Muscle lengths between multiple pairs of muscles across multiple postures were highly correlated. These correlations broadly formed two proximal and distal groups, where proximal muscles of the arm were correlated with each other and distal muscles of the arm and hand were correlated with each other, but not between groups. Using hierarchical clustering, between 11 and 14 reliable muscle groups were identified. This shows that musculoskeletal anatomy does indeed shape the mechanical interactions by grouping muscles into functional clusters that generally match the functional repertoire of the human arm. Together, these results support the idea that the structure of the musculoskeletal system is tuned to solve movement complexity problem by reducing the dimensionality of available solutions.

Age-related changes in the plasticity and toughness of human cortical bone at multiple length-scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zimmermann, Elizabeth A.; Schaible, Eric; Bale, Hrishikesh

2011-08-10

The structure of human cortical bone evolves over multiple length-scales from its basic constituents of collagen and hydroxyapatite at the nanoscale to osteonal structures at nearmillimeter dimensions, which all provide the basis for its mechanical properties. To resist fracture, bone’s toughness is derived intrinsically through plasticity (e.g., fibrillar sliding) at structural-scales typically below a micron and extrinsically (i.e., during crack growth) through mechanisms (e.g., crack deflection/bridging) generated at larger structural-scales. Biological factors such as aging lead to a markedly increased fracture risk, which is often associated with an age-related loss in bone mass (bone quantity). However, we find that age-relatedmore » structural changes can significantly degrade the fracture resistance (bone quality) over multiple lengthscales. Using in situ small-/wide-angle x-ray scattering/diffraction to characterize sub-micron structural changes and synchrotron x-ray computed tomography and in situ fracture-toughness measurements in the scanning electron microscope to characterize effects at micron-scales, we show how these age-related structural changes at differing size-scales degrade both the intrinsic and extrinsic toughness of bone. Specifically, we attribute the loss in toughness to increased non-enzymatic collagen cross-linking which suppresses plasticity at nanoscale dimensions and to an increased osteonal density which limits the potency of crack-bridging mechanisms at micron-scales. The link between these processes is that the increased stiffness of the cross-linked collagen requires energy to be absorbed by “plastic” deformation at higher structural levels, which occurs by the process of microcracking.« less

RNA Splicing: Regulation and Dysregulation in the Heart.

PubMed

van den Hoogenhof, Maarten M G; Pinto, Yigal M; Creemers, Esther E

2016-02-05

RNA splicing represents a post-transcriptional mechanism to generate multiple functional RNAs or proteins from a single transcript. The evolution of RNA splicing is a prime example of the Darwinian function follows form concept. A mutation that leads to a new mRNA (form) that encodes for a new functional protein (function) is likely to be retained, and this way, the genome has gradually evolved to encode for genes with multiple isoforms, thereby creating an enormously diverse transcriptome. Advances in technologies to characterize RNA populations have led to a better understanding of RNA processing in health and disease. In the heart, alternative splicing is increasingly being recognized as an important layer of post-transcriptional gene regulation. Moreover, the recent identification of several cardiac splice factors, such as RNA-binding motif protein 20 and SF3B1, not only provided important insight into the mechanisms underlying alternative splicing but also revealed how these splicing factors impact functional properties of the heart. Here, we review our current knowledge of alternative splicing in the heart, with a particular focus on the major and minor spliceosome, the factors controlling RNA splicing, and the role of alternative splicing in cardiac development and disease. © 2016 American Heart Association, Inc.

Bacterial effectors target the common signaling partner BAK1 to disrupt multiple MAMP receptor-signaling complexes and impede plant immunity.

PubMed

Shan, Libo; He, Ping; Li, Jianming; Heese, Antje; Peck, Scott C; Nürnberger, Thorsten; Martin, Gregory B; Sheen, Jen

2008-07-17

Successful pathogens have evolved strategies to interfere with host immune systems. For example, the ubiquitous plant pathogen Pseudomonas syringae injects two sequence-distinct effectors, AvrPto and AvrPtoB, to intercept convergent innate immune responses stimulated by multiple microbe-associated molecular patterns (MAMPs). However, the direct host targets and precise molecular mechanisms of bacterial effectors remain largely obscure. We show that AvrPto and AvrPtoB bind the Arabidopsis receptor-like kinase BAK1, a shared signaling partner of both the flagellin receptor FLS2 and the brassinosteroid receptor BRI1. This targeting interferes with ligand-dependent association of FLS2 with BAK1 during infection. It also impedes BAK1-dependent host immune responses to diverse other MAMPs and brassinosteroid signaling. Significantly, the structural basis of AvrPto-BAK1 interaction appears to be distinct from AvrPto-Pto association required for effector-triggered immunity. These findings uncover a unique strategy of bacterial pathogenesis where virulence effectors block signal transmission through a key common component of multiple MAMP-receptor complexes.

Multi-gene phylogenetic analysis reveals the multiple origin and evolution of mangrove physiological traits through exaptation

NASA Astrophysics Data System (ADS)

Sahu, Sunil Kumar; Singh, Reena; Kathiresan, Kandasamy

2016-12-01

Mangroves are taxonomically diverse group of salt-tolerant, mainly arboreal, flowering plants that grow in tropical and sub-tropical regions and have adapted themselves to thrive in such obdurate surroundings. While evolution is often understood exclusively in terms of adaptation, innovation often begins when a feature adapted for one function is co-opted for a different purpose and the co-opted features are called exaptations. Thus, one of the fundamental issues is what features of mangroves have evolved through exaptation. We attempt to address these questions through molecular phylogenetic approach using chloroplast and nuclear markers. First, we determined if these mangroves specific traits have evolved multiple times in the phylogeny. Once the multiple origins were established, we then looked at related non-mangrove species for characters that could have been co-opted by mangrove species. We also assessed the efficacy of these molecular sequences in distinguishing mangroves at the species level. This study revealed the multiple origin of mangroves and shed light on the ancestral characters that might have led certain lineages of plants to adapt to estuarine conditions and also traces the evolutionary history of mangroves and hitherto unexplained theory that mangroves traits (aerial roots and viviparous propagules) evolved as a result of exaptation rather than adaptation to saline habitats.

Sex ratio meiotic drive as a plausible evolutionary mechanism for hybrid male sterility.

PubMed

Zhang, Linbin; Sun, Tianai; Woldesellassie, Fitsum; Xiao, Hailian; Tao, Yun

2015-03-01

Biological diversity on Earth depends on the multiplication of species or speciation, which is the evolution of reproductive isolation such as hybrid sterility between two new species. An unsolved puzzle is the exact mechanism(s) that causes two genomes to diverge from their common ancestor so that some divergent genes no longer function properly in the hybrids. Here we report genetic analyses of divergent genes controlling male fertility and sex ratio in two very young fruitfly species, Drosophila albomicans and D. nasuta. A majority of the genetic divergence for both traits is mapped to the same regions by quantitative trait loci mappings. With introgressions, six major loci are found to contribute to both traits. This genetic colocalization implicates that genes for hybrid male sterility have evolved primarily for controlling sex ratio. We propose that genetic conflicts over sex ratio may operate as a perpetual dynamo for genome divergence. This particular evolutionary mechanism may largely contribute to the rapid evolution of hybrid male sterility and the disproportionate enrichment of its underlying genes on the X chromosome--two patterns widely observed across animals.

Sex Ratio Meiotic Drive as a Plausible Evolutionary Mechanism for Hybrid Male Sterility

PubMed Central

Zhang, Linbin; Xiao, Hailian; Tao, Yun

2015-01-01

Biological diversity on Earth depends on the multiplication of species or speciation, which is the evolution of reproductive isolation such as hybrid sterility between two new species. An unsolved puzzle is the exact mechanism(s) that causes two genomes to diverge from their common ancestor so that some divergent genes no longer function properly in the hybrids. Here we report genetic analyses of divergent genes controlling male fertility and sex ratio in two very young fruitfly species, Drosophila albomicans and D. nasuta. A majority of the genetic divergence for both traits is mapped to the same regions by quantitative trait loci mappings. With introgressions, six major loci are found to contribute to both traits. This genetic colocalization implicates that genes for hybrid male sterility have evolved primarily for controlling sex ratio. We propose that genetic conflicts over sex ratio may operate as a perpetual dynamo for genome divergence. This particular evolutionary mechanism may largely contribute to the rapid evolution of hybrid male sterility and the disproportionate enrichment of its underlying genes on the X chromosome – two patterns widely observed across animals. PMID:25822261

Accountable care organizations may have difficulty avoiding the failures of integrated delivery networks of the 1990s.

PubMed

Burns, Lawton R; Pauly, Mark V

2012-11-01

Accountable care organizations are intended to improve the quality and lower the cost of health care through several mechanisms, such as disease management programs, care coordination, and aligning financial incentives for hospitals and physicians. Providers employed several of these mechanisms in forming the integrated delivery networks of the 1990s. The networks failed, however, because of heavy financial losses stemming from hospitals' purchase of physician practices and their inability to align incentives, garner capitated contracts, and develop the infrastructure to manage risk. Although the current mechanisms underlying accountable care organizations continue to evolve, whether and how they will have an impact on quality and costs remains open to question. Care coordination and information technology are proving more complicated and expensive to implement than anticipated, providers may lack the ability to implement these mechanisms, and primary care providers are in short supply. As in the 1990s, success depends on targeting specific populations, such as people with multiple chronic conditions who need and may benefit from coordinated care.

Genetic diversity promotes homeostasis in insect colonies.

PubMed

Oldroyd, Benjamin P; Fewell, Jennifer H

2007-08-01

Although most insect colonies are headed by a singly mated queen, some ant, wasp and bee taxa have evolved high levels of multiple mating or 'polyandry'. We argue here that a contributing factor towards the evolution of polyandry is that the resulting genetic diversity within colonies provides them with a system of genetically based task specialization, enabling them to respond resiliently to environmental perturbation. An alternate view is that genetic contributions to task specialization are a side effect of multiple mating, which evolved through other causes, and that genetically based task specialization now makes little or no contribution to colony fitness.

How Do We Ensure Research and Scientific Integrity? A Diverse Panel Discusses the Critical Components and Challenges of Crafting and Implementing Effective Scientific Integrity Policies.

NASA Astrophysics Data System (ADS)

Werkheiser, W. H.

2016-12-01

10 Years of Scientific Integrity Policy at the U.S. Geological Survey The U.S. Geological Survey implemented its first scientific integrity policy in January 2007. Following the 2009 and 2010 executive memoranda aimed at creating scientific integrity policies throughout the federal government, USGS' policy served as a template to inform the U.S. Department of Interior's policy set forth in January 2011. Scientific integrity policy at the USGS and DOI continues to evolve as best practices come to the fore and the broader Federal scientific integrity community evolves in its understanding of a vital and expanding endeavor. We find that scientific integrity is best served by: formal and informal mechanisms through which to resolve scientific integrity issues; a well-communicated and enforceable code of scientific conduct that is accessible to multiple audiences; an unfailing commitment to the code on the part of all parties; awareness through mandatory training; robust protection to encourage whistleblowers to come forward; and outreach with the scientific integrity community to foster consistency and share experiences.

Evolution of early embryogenesis in rhabditid nematodes

PubMed Central

Brauchle, Michael; Kiontke, Karin; MacMenamin, Philip; Fitch, David H. A.; Piano, Fabio

2009-01-01

The cell biological events that guide early embryonic development occur with great precision within species but can be quite diverse across species. How these cellular processes evolve and which molecular components underlie evolutionary changes is poorly understood. To begin to address these questions, we systematically investigated early embryogenesis, from the one- to the four-cell embryo, in 34 nematode species related to C. elegans. We found 40 cell-biological characters that captured the phenotypic differences between these species. By tracing the evolutionary changes on a molecular phylogeny, we found that these characters evolved multiple times and independently of one another. Strikingly, all these phenotypes are mimicked by single-gene RNAi experiments in C. elegans. We use these comparisons to hypothesize the molecular mechanisms underlying the evolutionary changes. For example, we predict that a cell polarity module was altered during the evolution of the Protorhabditis group and show that PAR-1, a kinase localized asymmetrically in C. elegans early embryos, is symmetrically localized in the one-cell stage of Protorhabditis group species. Our genome-wide approach identifies candidate molecules—and thereby modules—associated with evolutionary changes in cell-biological phenotypes. PMID:19643102

Formation of wide binaries by turbulent fragmentation

NASA Astrophysics Data System (ADS)

Lee, Jeong-Eun; Lee, Seokho; Dunham, Michael M.; Tatematsu, Ken'ichi; Choi, Minho; Bergin, Edwin A.; Evans, Neal J.

2017-08-01

Understanding the formation of wide-binary systems of very low-mass stars (M ≤ 0.1 solar masses, M⊙) is challenging 1,2,3 . The most obvious route is through widely separated low-mass collapsing fragments produced by turbulent fragmentation of a molecular core4,5. However, close binaries or multiples from disk fragmentation can also evolve to wide binaries over a few initial crossing times of the stellar cluster through tidal evolution6. Finding an isolated low-mass wide-binary system in the earliest stage of formation, before tidal evolution could occur, would prove that turbulent fragmentation is a viable mechanism for (very) low-mass wide binaries. Here we report high-resolution ALMA observations of a known wide-separation protostellar binary, showing that each component has a circumstellar disk. The system is too young7 to have evolved from a close binary, and the disk axes are misaligned, providing strong support for the turbulent fragmentation model. Masses of both stars are derived from the Keplerian rotation of the disks; both are very low-mass stars.

How Do We Ensure Research and Scientific Integrity? A Diverse Panel Discusses the Critical Components and Challenges of Crafting and Implementing Effective Scientific Integrity Policies.

NASA Astrophysics Data System (ADS)

Werkheiser, W. H.

2017-12-01

10 Years of Scientific Integrity Policy at the U.S. Geological Survey The U.S. Geological Survey implemented its first scientific integrity policy in January 2007. Following the 2009 and 2010 executive memoranda aimed at creating scientific integrity policies throughout the federal government, USGS' policy served as a template to inform the U.S. Department of Interior's policy set forth in January 2011. Scientific integrity policy at the USGS and DOI continues to evolve as best practices come to the fore and the broader Federal scientific integrity community evolves in its understanding of a vital and expanding endeavor. We find that scientific integrity is best served by: formal and informal mechanisms through which to resolve scientific integrity issues; a well-communicated and enforceable code of scientific conduct that is accessible to multiple audiences; an unfailing commitment to the code on the part of all parties; awareness through mandatory training; robust protection to encourage whistleblowers to come forward; and outreach with the scientific integrity community to foster consistency and share experiences.

Evidence for the speed-value trade-off: human and monkey decision making is magnitude sensitive.

PubMed

Pirrone, Angelo; Azab, Habiba; Hayden, Benjamin Y; Stafford, Tom; Marshall, James A R

2018-04-01

Complex natural systems from brains to bee swarms have evolved to make adaptive multifactorial decisions. Recent theoretical and empirical work suggests that many evolved systems may take advantage of common motifs across multiple domains. We are particularly interested in value sensitivity (i.e., sensitivity to the magnitude or intensity of the stimuli or reward under consideration) as a mechanism to resolve deadlocks adaptively. This mechanism favours long-term reward maximization over accuracy in a simple manner, because it avoids costly delays associated with ambivalence between similar options; speed-value trade-offs have been proposed to be evolutionarily advantageous for many kinds of decision. A key prediction of the value-sensitivity hypothesis is that choices between equally-valued options will proceed faster when the options have a high value than when they have a low value. However, value-sensitivity is not part of idealised choice models such as diffusion to bound. Here we examine two different choice behaviours in two different species, perceptual decisions in humans and economic choices in rhesus monkeys, to test this hypothesis. We observe the same value sensitivity in both human perceptual decisions and monkey value-based decisions. These results endorse the idea that neural decision systems make use of the same basic principle of value-sensitivity in order to resolve costly deadlocks and thus improve long-term reward intake.

Genetic and environmental factors affecting cryptic variations in gene regulatory networks

PubMed Central

2013-01-01

Background Cryptic genetic variation (CGV) is considered to facilitate phenotypic evolution by producing visible variations in response to changes in the internal and/or external environment. Several mechanisms enabling the accumulation and release of CGVs have been proposed. In this study, we focused on gene regulatory networks (GRNs) as an important mechanism for producing CGVs, and examined how interactions between GRNs and the environment influence the number of CGVs by using individual-based simulations. Results Populations of GRNs were allowed to evolve under various stabilizing selections, and we then measured the number of genetic and phenotypic variations that had arisen. Our results showed that CGVs were not depleted irrespective of the strength of the stabilizing selection for each phenotype, whereas the visible fraction of genetic variation in a population decreased with increasing strength of selection. On the other hand, increasing the number of different environments that individuals encountered within their lifetime (i.e., entailing plastic responses to multiple environments) suppressed the accumulation of CGVs, whereas the GRNs with more genes and interactions were favored in such heterogeneous environments. Conclusions Given the findings that the number of CGVs in a population was largely determined by the size (order) of GRNs, we propose that expansion of GRNs and adaptation to novel environments are mutually facilitating and sustainable sources of evolvability and hence the origins of biological diversity and complexity. PMID:23622056

Genetic and environmental factors affecting cryptic variations in gene regulatory networks.

PubMed

Iwasaki, Watal M; Tsuda, Masaki E; Kawata, Masakado

2013-04-26

Cryptic genetic variation (CGV) is considered to facilitate phenotypic evolution by producing visible variations in response to changes in the internal and/or external environment. Several mechanisms enabling the accumulation and release of CGVs have been proposed. In this study, we focused on gene regulatory networks (GRNs) as an important mechanism for producing CGVs, and examined how interactions between GRNs and the environment influence the number of CGVs by using individual-based simulations. Populations of GRNs were allowed to evolve under various stabilizing selections, and we then measured the number of genetic and phenotypic variations that had arisen. Our results showed that CGVs were not depleted irrespective of the strength of the stabilizing selection for each phenotype, whereas the visible fraction of genetic variation in a population decreased with increasing strength of selection. On the other hand, increasing the number of different environments that individuals encountered within their lifetime (i.e., entailing plastic responses to multiple environments) suppressed the accumulation of CGVs, whereas the GRNs with more genes and interactions were favored in such heterogeneous environments. Given the findings that the number of CGVs in a population was largely determined by the size (order) of GRNs, we propose that expansion of GRNs and adaptation to novel environments are mutually facilitating and sustainable sources of evolvability and hence the origins of biological diversity and complexity.

Data collection and analysis strategies for phMRI.

PubMed

Mandeville, Joseph B; Liu, Christina H; Vanduffel, Wim; Marota, John J A; Jenkins, Bruce G

2014-09-01

Although functional MRI traditionally has been applied mainly to study changes in task-induced brain function, evolving acquisition methodologies and improved knowledge of signal mechanisms have increased the utility of this method for studying responses to pharmacological stimuli, a technique often dubbed "phMRI". The proliferation of higher magnetic field strengths and the use of exogenous contrast agent have boosted detection power, a critical factor for successful phMRI due to the restricted ability to average multiple stimuli within subjects. Receptor-based models of neurovascular coupling, including explicit pharmacological models incorporating receptor densities and affinities and data-driven models that incorporate weak biophysical constraints, have demonstrated compelling descriptions of phMRI signal induced by dopaminergic stimuli. This report describes phMRI acquisition and analysis methodologies, with an emphasis on data-driven analyses. As an example application, statistically efficient data-driven regressors were used to describe the biphasic response to the mu-opioid agonist remifentanil, and antagonism using dopaminergic and GABAergic ligands revealed modulation of the mesolimbic pathway. Results illustrate the power of phMRI as well as our incomplete understanding of mechanisms underlying the signal. Future directions are discussed for phMRI acquisitions in human studies, for evolving analysis methodologies, and for interpretative studies using the new generation of simultaneous PET/MRI scanners. This article is part of the Special Issue Section entitled 'Neuroimaging in Neuropharmacology'. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evidence for the speed-value trade-off: human and monkey decision making is magnitude sensitive

PubMed Central

Pirrone, Angelo; Azab, Habiba; Hayden, Benjamin Y.; Stafford, Tom; Marshall, James A. R.

2017-01-01

Complex natural systems from brains to bee swarms have evolved to make adaptive multifactorial decisions. Recent theoretical and empirical work suggests that many evolved systems may take advantage of common motifs across multiple domains. We are particularly interested in value sensitivity (i.e., sensitivity to the magnitude or intensity of the stimuli or reward under consideration) as a mechanism to resolve deadlocks adaptively. This mechanism favours long-term reward maximization over accuracy in a simple manner, because it avoids costly delays associated with ambivalence between similar options; speed-value trade-offs have been proposed to be evolutionarily advantageous for many kinds of decision. A key prediction of the value-sensitivity hypothesis is that choices between equally-valued options will proceed faster when the options have a high value than when they have a low value. However, value-sensitivity is not part of idealised choice models such as diffusion to bound. Here we examine two different choice behaviours in two different species, perceptual decisions in humans and economic choices in rhesus monkeys, to test this hypothesis. We observe the same value sensitivity in both human perceptual decisions and monkey value-based decisions. These results endorse the idea that neural decision systems make use of the same basic principle of value-sensitivity in order to resolve costly deadlocks and thus improve long-term reward intake. PMID:29682592

Neisseria meningitidis: pathogenesis and immunity.

PubMed

Pizza, Mariagrazia; Rappuoli, Rino

2015-02-01

The recent advances in cellular microbiology, genomics, and immunology has opened new horizons in the understanding of meningococcal pathogenesis and in the definition of new prophylactic intervention. It is now clear that Neissera meningitidis has evolved a number of surface structures to mediate interaction with host cells and a number of mechanisms to subvert the immune system and escape complement-mediated killing. In this review we report the more recent findings on meningococcal adhesion and on the bacteria-complement interaction highlighting the redundancy of these mechanisms. An effective vaccine against meningococcus B, based on multiple antigens with different function, has been recently licensed. The antibodies induced by the 4CMenB vaccine could mediate bacterial killing by activating directly the classical complement pathway or, indirectly, by preventing binding of fH on the bacterial surface and interfering with colonization. Copyright © 2014 The Author. Published by Elsevier Ltd.. All rights reserved.

Elucidating Grinding Mechanism by Theoretical and Experimental Investigations

PubMed Central

Kubo, Akihiko; Chowdhury, M. A. K.

2018-01-01

Grinding is one of the essential manufacturing processes for producing brittle or hard materials-based precision parts (e.g., optical lenses). In grinding, a grinding wheel removes the desired amount of material by passing the same area on the workpiece surface multiple times. How the topography of a workpiece surface evolves with these passes is thus an important research issue, which has not yet been addressed elaborately. The present paper tackles this issue from both the theoretical and the experimental points of view. In particular, this paper presents the results of experimental and theoretical investigations on the multi-pass surface grinding operations where the workpiece surface is made of glass and the grinding wheel consists of cBN abrasive grains. Both investigations confirm that a great deal of stochasticity is involved in the grinding mechanism, and the complexity of the workpiece surface gradually increases along with the number of passes. PMID:29425160

Elucidating Grinding Mechanism by Theoretical and Experimental Investigations.

PubMed

Ullah, Amm Sharif; Caggiano, Alessandra; Kubo, Akihiko; Chowdhury, M A K

2018-02-09

Grinding is one of the essential manufacturing processes for producing brittle or hard materials-based precision parts (e.g., optical lenses). In grinding, a grinding wheel removes the desired amount of material by passing the same area on the workpiece surface multiple times. How the topography of a workpiece surface evolves with these passes is thus an important research issue, which has not yet been addressed elaborately. The present paper tackles this issue from both the theoretical and the experimental points of view. In particular, this paper presents the results of experimental and theoretical investigations on the multi-pass surface grinding operations where the workpiece surface is made of glass and the grinding wheel consists of cBN abrasive grains. Both investigations confirm that a great deal of stochasticity is involved in the grinding mechanism, and the complexity of the workpiece surface gradually increases along with the number of passes.

To Cooperate or Not to Cooperate: Why Behavioural Mechanisms Matter

PubMed Central

2016-01-01

Mutualistic cooperation often requires multiple individuals to behave in a coordinated fashion. Hence, while the evolutionary stability of mutualistic cooperation poses no particular theoretical difficulty, its evolutionary emergence faces a chicken and egg problem: an individual cannot benefit from cooperating unless other individuals already do so. Here, we use evolutionary robotic simulations to study the consequences of this problem for the evolution of cooperation. In contrast with standard game-theoretic results, we find that the transition from solitary to cooperative strategies is very unlikely, whether interacting individuals are genetically related (cooperation evolves in 20% of all simulations) or unrelated (only 3% of all simulations). We also observe that successful cooperation between individuals requires the evolution of a specific and rather complex behaviour. This behavioural complexity creates a large fitness valley between solitary and cooperative strategies, making the evolutionary transition difficult. These results reveal the need for research on biological mechanisms which may facilitate this transition. PMID:27148874

Translation Control: A Multifaceted Regulator of Inflammatory Response

PubMed Central

Mazumder, Barsanjit; Li, Xiaoxia; Barik, Sailen

2010-01-01

A robust innate immune response is essential to the protection of all vertebrates from infection, but it often comes with the price tag of acute inflammation. If unchecked, a runaway inflammatory response can cause significant tissue damage, resulting in myriad disorders, such as dermatitis, toxicshock, cardiovascular disease, acute pelvic and arthritic inflammatory diseases, and various infections. To prevent such pathologies, cells have evolved mechanisms to rapidly and specifically shut off these beneficial inflammatory activities before they become detrimental. Our review of recent literature, including our own work, reveals that the most dominant and common mechanism is translational silencing, in which specific regulatory proteins or complexes are recruited to cis-acting RNA structures in the untranslated regions of single or multiple mRNAs that code for the inflammatory protein(s). Enhancement of the silencing function may constitute a novel pharmacological approach to prevent immunity-related inflammation. PMID:20304832

Translation control: a multifaceted regulator of inflammatory response.

PubMed

Mazumder, Barsanjit; Li, Xiaoxia; Barik, Sailen

2010-04-01

A robust innate immune response is essential to the protection of all vertebrates from infection, but it often comes with the price tag of acute inflammation. If unchecked, a runaway inflammatory response can cause significant tissue damage, resulting in myriad disorders, such as dermatitis, toxic shock, cardiovascular disease, acute pelvic and arthritic inflammatory diseases, and various infections. To prevent such pathologies, cells have evolved mechanisms to rapidly and specifically shut off these beneficial inflammatory activities before they become detrimental. Our review of recent literature, including our own work, reveals that the most dominant and common mechanism is translational silencing, in which specific regulatory proteins or complexes are recruited to cis-acting RNA structures in the untranslated regions of single or multiple mRNAs that code for the inflammatory protein(s). Enhancement of the silencing function may constitute a novel pharmacological approach to prevent immunity-related inflammation.

Mechanisms of viral mutation.

PubMed

Sanjuán, Rafael; Domingo-Calap, Pilar

2016-12-01

The remarkable capacity of some viruses to adapt to new hosts and environments is highly dependent on their ability to generate de novo diversity in a short period of time. Rates of spontaneous mutation vary amply among viruses. RNA viruses mutate faster than DNA viruses, single-stranded viruses mutate faster than double-strand virus, and genome size appears to correlate negatively with mutation rate. Viral mutation rates are modulated at different levels, including polymerase fidelity, sequence context, template secondary structure, cellular microenvironment, replication mechanisms, proofreading, and access to post-replicative repair. Additionally, massive numbers of mutations can be introduced by some virus-encoded diversity-generating elements, as well as by host-encoded cytidine/adenine deaminases. Our current knowledge of viral mutation rates indicates that viral genetic diversity is determined by multiple virus- and host-dependent processes, and that viral mutation rates can evolve in response to specific selective pressures.

Intelligent reservoir operation system based on evolving artificial neural networks

NASA Astrophysics Data System (ADS)

Chaves, Paulo; Chang, Fi-John

2008-06-01

We propose a novel intelligent reservoir operation system based on an evolving artificial neural network (ANN). Evolving means the parameters of the ANN model are identified by the GA evolutionary optimization technique. Accordingly, the ANN model should represent the operational strategies of reservoir operation. The main advantages of the Evolving ANN Intelligent System (ENNIS) are as follows: (i) only a small number of parameters to be optimized even for long optimization horizons, (ii) easy to handle multiple decision variables, and (iii) the straightforward combination of the operation model with other prediction models. The developed intelligent system was applied to the operation of the Shihmen Reservoir in North Taiwan, to investigate its applicability and practicability. The proposed method is first built to a simple formulation for the operation of the Shihmen Reservoir, with single objective and single decision. Its results were compared to those obtained by dynamic programming. The constructed network proved to be a good operational strategy. The method was then built and applied to the reservoir with multiple (five) decision variables. The results demonstrated that the developed evolving neural networks improved the operation performance of the reservoir when compared to its current operational strategy. The system was capable of successfully simultaneously handling various decision variables and provided reasonable and suitable decisions.

Evolution and inheritance of early embryonic patterning in Drosophila simulans and D. sechellia.

PubMed

Lott, Susan E; Ludwig, Michael Z; Kreitman, Martin

2011-05-01

Pattern formation in Drosophila is a widely studied example of a robust developmental system. Such robust systems pose a challenge to adaptive evolution, as they mask variation that selection may otherwise act upon. Yet we find variation in the localization of expression domains (henceforth "stripe allometry") in the pattern formation pathway. Specifically, we characterize differences in the gap genes giant and Kruppel, and the pair-rule gene even-skipped, which differ between the sibling species Drosophila simulans and D. sechellia. In a double-backcross experiment, stripe allometry is consistent with maternal inheritance of stripe positioning and multiple genetic factors, with a distinct genetic basis from embryo length. Embryos produced by F1 and F2 backcross mothers exhibit novel spatial patterns of gene expression relative to the parental species, with no measurable increase in positional variance among individuals. Buffering of novel spatial patterns in the backcross genotypes suggests that robustness need not be disrupted in order for the trait to evolve, and perhaps the system is incapable of evolving to prevent the expression of all genetic variation. This limitation, and the ability of natural selection to act on minute genetic differences that are within the "margin of error" for the buffering mechanism, indicates that developmentally buffered traits can evolve without disruption of robustness. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

Prospective Elementary Teachers Making Sense of Multidigit Multiplication: Leveraging Resources

ERIC Educational Resources Information Center

Whitacre, Ian; Nickerson, Susan D.

2016-01-01

This study examines how collective activity related to multiplication evolved over several class sessions in an elementary mathematics content course that was designed to foster prospective elementary teachers' number-sense development. We document how the class drew on as-if-shared ideas to make sense of multidigit multiplication in terms of…

Interaction-based evolution: how natural selection and nonrandom mutation work together

PubMed Central

2013-01-01

Background The modern evolutionary synthesis leaves unresolved some of the most fundamental, long-standing questions in evolutionary biology: What is the role of sex in evolution? How does complex adaptation evolve? How can selection operate effectively on genetic interactions? More recently, the molecular biology and genomics revolutions have raised a host of critical new questions, through empirical findings that the modern synthesis fails to explain: for example, the discovery of de novo genes; the immense constructive role of transposable elements in evolution; genetic variance and biochemical activity that go far beyond what traditional natural selection can maintain; perplexing cases of molecular parallelism; and more. Presentation of the hypothesis Here I address these questions from a unified perspective, by means of a new mechanistic view of evolution that offers a novel connection between selection on the phenotype and genetic evolutionary change (while relying, like the traditional theory, on natural selection as the only source of feedback on the fit between an organism and its environment). I hypothesize that the mutation that is of relevance for the evolution of complex adaptation—while not Lamarckian, or “directed” to increase fitness—is not random, but is instead the outcome of a complex and continually evolving biological process that combines information from multiple loci into one. This allows selection on a fleeting combination of interacting alleles at different loci to have a hereditary effect according to the combination’s fitness. Testing and implications of the hypothesis This proposed mechanism addresses the problem of how beneficial genetic interactions can evolve under selection, and also offers an intuitive explanation for the role of sex in evolution, which focuses on sex as the generator of genetic combinations. Importantly, it also implies that genetic variation that has appeared neutral through the lens of traditional theory can actually experience selection on interactions and thus has a much greater adaptive potential than previously considered. Empirical evidence for the proposed mechanism from both molecular evolution and evolution at the organismal level is discussed, and multiple predictions are offered by which it may be tested. Reviewers This article was reviewed by Nigel Goldenfeld (nominated by Eugene V. Koonin), Jürgen Brosius and W. Ford Doolittle. PMID:24139515

Nanotechnology use with cosmeceuticals.

PubMed

Golubovic-Liakopoulos, Nevenka; Simon, Sanford R; Shah, Bhavdeep

2011-09-01

The skin is a complex organ and its aging is a complex process. Cutaneous aging is influenced by factors such as sun exposure, genetics, stress and the environment. While skin laxity, rhytides, and dyschromia appear on the surface, these processes originate in deeper layers including the dermis and subcutaneous tissues. Until recently, most topical skin treatments were applied to, and consequently only affected the skin surface. Skin care has evolved to be scientifically based, and as knowledge increases about the physiology of the skin, novel methods of maintaining its health and appearance are developed. New generation skin care products are targeting multiple aging mechanisms by utilizing functional active ingredients in combination with innovative delivery systems. Copyright © 2011 Elsevier Inc. All rights reserved.

Developments in cognitive neuroscience: I. Conflict, compromise, and connectionism.

PubMed

Westen, Drew; Gabbard, Glen O

2002-01-01

The strength of psychoanalysis has always been its understanding of affect and motivation. Contemporary developments in cognitive neuroscience offer possibilities of integrating sophisticated, experimentally informed models of thought and memory with an understanding of dynamically and clinically meaningful processes. Aspects of contemporary theory and research in cognitive neuroscience are integrated with psychoanalytic theory and technique, particularly theories of conflict and compromise. After a description of evolving models of the mind in cognitive neuroscience, several issues relevant to psychoanalytic theory and practice are addressed. These include the nature of representations, the interaction of cognition and affect, and the mechanisms by which the mind unconsciously forges compromise solutions that best fit multiple cognitive and affective-motivational constraints.

Adapting the Stress Response: Viral Subversion of the mTOR Signaling Pathway

PubMed Central

Le Sage, Valerie; Cinti, Alessandro; Amorim, Raquel; Mouland, Andrew J.

2016-01-01

The mammalian target of rapamycin (mTOR) is a central regulator of gene expression, translation and various metabolic processes. Multiple extracellular (growth factors) and intracellular (energy status) molecular signals as well as a variety of stressors are integrated into the mTOR pathway. Viral infection is a significant stress that can activate, reduce or even suppress the mTOR signaling pathway. Consequently, viruses have evolved a plethora of different mechanisms to attack and co-opt the mTOR pathway in order to make the host cell a hospitable environment for replication. A more comprehensive knowledge of different viral interactions may provide fruitful targets for new antiviral drugs. PMID:27231932

Sliding of poly(vinyl chloride) on metals studied by Auger electron spectroscopy

NASA Technical Reports Server (NTRS)

Pepper, S. V.

1974-01-01

The sliding of polyvinyl chloride on nickel, iron and S-Monel has been studied by Auger electron spectroscopy. Polymer was not transferred to the metals, rather shear appeared to take place at the interface. The metal was progressively chlorinated as the polymer made multiple passes on the surface. The thickness of this chlorine film was the order of one atomic layer. Electron-induced desorption studies indicate that the chlorine is chemisorbed to the metal. These results are interpreted as evidence for mechanically induced and/or thermal degradation of the polymer during sliding. Degradation products of HCl and Cl2 which chemisorb to the metal are evolved near the interface.

Symmetry-based reciprocity: evolutionary constraints on a proximate mechanism

PubMed Central

Campennì, Marco

2016-01-01

Background. While the evolution of reciprocal cooperation has attracted an enormous attention, the proximate mechanisms underlying the ability of animals to cooperate reciprocally are comparatively neglected. Symmetry-based reciprocity is a hypothetical proximate mechanism that has been suggested to be widespread among cognitively unsophisticated animals. Methods. We developed two agent-based models of symmetry-based reciprocity (one relying on an arbitrary tag and the other on interindividual proximity) and tested their ability both to reproduce significant emergent features of cooperation in group living animals and to promote the evolution of cooperation. Results. Populations formed by agents adopting symmetry-based reciprocity showed differentiated “social relationships” and a positive correlation between cooperation given and received: two common aspects of animal cooperation. However, when reproduction and selection across multiple generations were added to the models, agents adopting symmetry-based reciprocity were outcompeted by selfish agents that never cooperated. Discussion. In order to evolve, hypothetical proximate mechanisms must be able to stand competition from alternative strategies. While the results of our simulations require confirmation using analytical methods, we provisionally suggest symmetry-based reciprocity is to be abandoned as a possible proximate mechanism underlying the ability of animals to reciprocate cooperative interactions. PMID:26998412

Symmetry-based reciprocity: evolutionary constraints on a proximate mechanism.

PubMed

Campennì, Marco; Schino, Gabriele

2016-01-01

Background. While the evolution of reciprocal cooperation has attracted an enormous attention, the proximate mechanisms underlying the ability of animals to cooperate reciprocally are comparatively neglected. Symmetry-based reciprocity is a hypothetical proximate mechanism that has been suggested to be widespread among cognitively unsophisticated animals. Methods. We developed two agent-based models of symmetry-based reciprocity (one relying on an arbitrary tag and the other on interindividual proximity) and tested their ability both to reproduce significant emergent features of cooperation in group living animals and to promote the evolution of cooperation. Results. Populations formed by agents adopting symmetry-based reciprocity showed differentiated "social relationships" and a positive correlation between cooperation given and received: two common aspects of animal cooperation. However, when reproduction and selection across multiple generations were added to the models, agents adopting symmetry-based reciprocity were outcompeted by selfish agents that never cooperated. Discussion. In order to evolve, hypothetical proximate mechanisms must be able to stand competition from alternative strategies. While the results of our simulations require confirmation using analytical methods, we provisionally suggest symmetry-based reciprocity is to be abandoned as a possible proximate mechanism underlying the ability of animals to reciprocate cooperative interactions.

Pathophysiology of the Gut and the Microbiome in the Host Response.

PubMed

Lyons, John D; Coopersmith, Craig M

2017-03-01

To describe and summarize the data supporting the gut as the motor driving critical illness and multiple organ dysfunction syndrome presented at the National Institute of Child Health and Human Development MODS Workshop (March 26-27, 2015). Summary of workshop keynote presentation. Not applicable. Presented by an expert in the field, the data assessing the role of gastrointestinal dysfunction driving critical illness were described with a focus on identifying knowledge gaps and research priorities. Summary of presentation and discussion supported and supplemented by relevant literature. The understanding of gut dysfunction in critical illness has evolved greatly over time, and the gut is now often considered as the "motor" of critical illness. The association of the gut with critical illness is supported by both animal models and clinical studies. Initially, the association between gut dysfunction and critical illness focused primarily on bacterial translocation into the bloodstream. However, that work has evolved to include other gut-derived products causing distant injury via other routes (e.g., lymphatics). Additionally, alterations in the gut epithelium may be associated with critical illness and influence outcomes. Gut epithelial apoptosis, intestinal hyperpermeability, and perturbations in the intestinal mucus layer have all been associated with critical illness. Finally, there is growing evidence that the intestinal microbiome plays a crucial role in mediating pathology in critical illness. Further research is needed to better understand the role of each of these mechanisms and their contribution to multiple organ dysfunction syndrome in children.

Distinct developmental genetic mechanisms underlie convergently evolved tooth gain in sticklebacks

PubMed Central

Ellis, Nicholas A.; Glazer, Andrew M.; Donde, Nikunj N.; Cleves, Phillip A.; Agoglia, Rachel M.; Miller, Craig T.

2015-01-01

Teeth are a classic model system of organogenesis, as repeated and reciprocal epithelial and mesenchymal interactions pattern placode formation and outgrowth. Less is known about the developmental and genetic bases of tooth formation and replacement in polyphyodonts, which are vertebrates with continual tooth replacement. Here, we leverage natural variation in the threespine stickleback fish Gasterosteus aculeatus to investigate the genetic basis of tooth development and replacement. We find that two derived freshwater stickleback populations have both convergently evolved more ventral pharyngeal teeth through heritable genetic changes. In both populations, evolved tooth gain manifests late in development. Using pulse-chase vital dye labeling to mark newly forming teeth in adult fish, we find that both high-toothed freshwater populations have accelerated tooth replacement rates relative to low-toothed ancestral marine fish. Despite the similar evolved phenotype of more teeth and an accelerated adult replacement rate, the timing of tooth number divergence and the spatial patterns of newly formed adult teeth are different in the two populations, suggesting distinct developmental mechanisms. Using genome-wide linkage mapping in marine-freshwater F2 genetic crosses, we find that the genetic basis of evolved tooth gain in the two freshwater populations is largely distinct. Together, our results support a model whereby increased tooth number and an accelerated tooth replacement rate have evolved convergently in two independently derived freshwater stickleback populations using largely distinct developmental and genetic mechanisms. PMID:26062935

Convergence Is Real

ERIC Educational Resources Information Center

Enyeart, Mike; Staman, E. Michael; Valdes, Jose J., Jr.

2007-01-01

The concept of convergence has evolved significantly during recent years. Today, "convergence" refers to the integration of the communications and computing resources and services that seamlessly traverse multiple infrastructures and deliver content to multiple platforms or appliances. Convergence is real. Those in higher education, and especially…

The Multiple Realities of Curriculum Policy Making.

ERIC Educational Resources Information Center

Hopmann, Stefan

Concerning curriculum making, it is impossible to integrate the different meanings of "curriculum" into a single formula. Read as social constructions, different conceptions reflect varying educational, social-political, and historical contexts. This paper explores how these contexts, or multiple realities, evolved historically and how…

The Voronoi Implicit Interface Method for computing multiphase physics

PubMed Central

Saye, Robert I.; Sethian, James A.

2011-01-01

We introduce a numerical framework, the Voronoi Implicit Interface Method for tracking multiple interacting and evolving regions (phases) whose motion is determined by complex physics (fluids, mechanics, elasticity, etc.), intricate jump conditions, internal constraints, and boundary conditions. The method works in two and three dimensions, handles tens of thousands of interfaces and separate phases, and easily and automatically handles multiple junctions, triple points, and quadruple points in two dimensions, as well as triple lines, etc., in higher dimensions. Topological changes occur naturally, with no surgery required. The method is first-order accurate at junction points/lines, and of arbitrarily high-order accuracy away from such degeneracies. The method uses a single function to describe all phases simultaneously, represented on a fixed Eulerian mesh. We test the method’s accuracy through convergence tests, and demonstrate its applications to geometric flows, accurate prediction of von Neumann’s law for multiphase curvature flow, and robustness under complex fluid flow with surface tension and large shearing forces. PMID:22106269

[Where do the parasites of man come from?].

PubMed

Combes, C

1990-01-01

The Hominids have come in contact, over the last few million years, with the infective stages of many parasites which had up to then evolved in non Primate hosts; this is because Hominids have occupied multiple environments and acquired diversified behaviour. The high number of these lateral transfers explains the multiplicity of current human parasitic diseases whereas their youth on an evolutionary scale accounts for the seriousness of most of these diseases. The basic questions arising from the exceptional opportunities offered to parasites by the evolution of the human lineage concern: the precise role played by human behaviour, the mechanisms of alterations in specificity, the identity of the original host phyla, the dynamic and genetic consequences for parasites, the relationship with the evolutionary history of the ancestors of Homo sapiens sapiens; for instance, it is suggested that man's mastery of fire, allowing him to cook his food, dramatically reduced his contamination by certain parasites and that this contributed to the subsequent success of Hominids.

The Voronoi Implicit Interface Method for computing multiphase physics.

PubMed

Saye, Robert I; Sethian, James A

2011-12-06

We introduce a numerical framework, the Voronoi Implicit Interface Method for tracking multiple interacting and evolving regions (phases) whose motion is determined by complex physics (fluids, mechanics, elasticity, etc.), intricate jump conditions, internal constraints, and boundary conditions. The method works in two and three dimensions, handles tens of thousands of interfaces and separate phases, and easily and automatically handles multiple junctions, triple points, and quadruple points in two dimensions, as well as triple lines, etc., in higher dimensions. Topological changes occur naturally, with no surgery required. The method is first-order accurate at junction points/lines, and of arbitrarily high-order accuracy away from such degeneracies. The method uses a single function to describe all phases simultaneously, represented on a fixed Eulerian mesh. We test the method's accuracy through convergence tests, and demonstrate its applications to geometric flows, accurate prediction of von Neumann's law for multiphase curvature flow, and robustness under complex fluid flow with surface tension and large shearing forces.

The Voronoi Implicit Interface Method for computing multiphase physics

DOE PAGES

Saye, Robert I.; Sethian, James A.

2011-11-21

In this paper, we introduce a numerical framework, the Voronoi Implicit Interface Method for tracking multiple interacting and evolving regions (phases) whose motion is determined by complex physics (fluids, mechanics, elasticity, etc.), intricate jump conditions, internal constraints, and boundary conditions. The method works in two and three dimensions, handles tens of thousands of interfaces and separate phases, and easily and automatically handles multiple junctions, triple points, and quadruple points in two dimensions, as well as triple lines, etc., in higher dimensions. Topological changes occur naturally, with no surgery required. The method is first-order accurate at junction points/lines, and of arbitrarilymore » high-order accuracy away from such degeneracies. The method uses a single function to describe all phases simultaneously, represented on a fixed Eulerian mesh. Finally, we test the method’s accuracy through convergence tests, and demonstrate its applications to geometric flows, accurate prediction of von Neumann’s law for multiphase curvature flow, and robustness under complex fluid flow with surface tension and large shearing forces.« less

Management of status epilepticus.

PubMed

Pichler, M; Hocker, S

2017-01-01

Status epilepticus is a neurologic and medical emergency manifested by prolonged seizure activity or multiple seizures without return to baseline. It is associated with substantial medical cost, morbidity, and mortality. There is a spectrum of severity dependent on the type of seizure, underlying pathology, comorbidities, and appropriate and timely medical management. This chapter discusses the evolving definitions of status epilepticus and multiple patient and clinical factors which influence outcome. The pathophysiology of status epilepticus is reviewed to provide a better understanding of the mechanisms which contribute to status epilepticus, as well as the potential long-term effects. The clinical presentations of different types of status epilepticus in adults are discussed, with emphasis on the hospital course and management of the most dangerous type, generalized convulsive status epilepticus. Strategies for the evaluation and management of status epilepticus are provided based on available evidence from clinical trials and recommendations from the Neurocritical Care Society and the European Federation of Neurological Societies. © 2017 Elsevier B.V. All rights reserved.

Diplomatic Assistance: Can Helminth-Modulated Macrophages Act as Treatment for Inflammatory Disease?

PubMed Central

Steinfelder, Svenja; O’Regan, Noëlle Louise; Hartmann, Susanne

2016-01-01

Helminths have evolved numerous pathways to prevent their expulsion or elimination from the host to ensure long-term survival. During infection, they target numerous host cells, including macrophages, to induce an alternatively activated phenotype, which aids elimination of infection, tissue repair, and wound healing. Multiple animal-based studies have demonstrated a significant reduction or complete reversal of disease by helminth infection, treatment with helminth products, or helminth-modulated macrophages in models of allergy, autoimmunity, and sepsis. Experimental studies of macrophage and helminth therapies are being translated into clinical benefits for patients undergoing transplantation and those with multiple sclerosis. Thus, helminths or helminth-modulated macrophages present great possibilities as therapeutic applications for inflammatory diseases in humans. Macrophage-based helminth therapies and the underlying mechanisms of their therapeutic or curative effects represent an under-researched area with the potential to open new avenues of treatment. This review explores the application of helminth-modulated macrophages as a new therapy for inflammatory diseases. PMID:27101372

Does natalizumab treatment increase the risk of herpes simplex encephalitis in multiple sclerosis? Case and discussion.

PubMed

Sharma, Kanchan; Ballham, Samantha A; Inglis, Kirsty E A; Renowden, Shelley; Cottrell, David A

2013-10-01

This report presents the 4th documented case worldwide of herpes simplex encephalitis in multiple sclerosis (MS) patients treated with natalizumab and the first case in the UK. Natalizumab is licensed for relapsing remitting multiple sclerosis in patients with high disease activity despite treatment with interferon-beta and patients with rapidly evolving severe, multiple sclerosis. Natalizumab is a monoclonal antibody targeted against alpha-4 integrin. Its proposed mechanism is attenuation of the migration of immune cells into the central nervous system. Reactivation of the JC virus causing progressive multifocal leucoencephalopathy (PML) and its association with natalizumab is well documented. This case adds support to the suggestion that natalizumab also increases the reactivation risk of CNS herpes simplex infection. A 34 year old woman was admitted with a generalized tonic-clonic seizure, fever and confusion following her 40th infusion of natalizumab. MRI demonstrated increased signal in the medial temporal lobes and EEG showed focal sharp waves over the temporal lobe. CSF PCR later confirmed herpes simplex virus. The patient made an eventual excellent recovery following 21 days of intravenous acyclovir therapy followed by 14 days of oral treatment. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

A Case Study of the De Novo Evolution of a Complex Odometric Behavior in Digital Organisms

PubMed Central

Grabowski, Laura M.; Bryson, David M.; Dyer, Fred C.; Pennock, Robert T.; Ofria, Charles

2013-01-01

Investigating the evolution of animal behavior is difficult. The fossil record leaves few clues that would allow us to recapitulate the path that evolution took to build a complex behavior, and the large population sizes and long time scales required prevent us from re-evolving such behaviors in a laboratory setting. We present results of a study in which digital organisms–self-replicating computer programs that are subject to mutations and selection–evolved in different environments that required information about past experience for fitness-enhancing behavioral decisions. One population evolved a mechanism for step-counting, a surprisingly complex odometric behavior that was only indirectly related to enhancing fitness. We examine in detail the operation of the evolved mechanism and the evolutionary transitions that produced this striking example of a complex behavior. PMID:23577113

The Evolvement of Automobile Steering System Based on TRIZ

NASA Astrophysics Data System (ADS)

Zhao, Xinjun; Zhang, Shuang

Products and techniques pass through a process of birth, growth, maturity, death and quit the stage like biological evolution process. The developments of products and techniques conform to some evolvement rules. If people know and hold these rules, they can design new kind of products and forecast the develop trends of the products. Thereby, enterprises can grasp the future technique directions of products, and make product and technique innovation. Below, based on TRIZ theory, the mechanism evolvement, the function evolvement and the appearance evolvement of automobile steering system had been analyzed and put forward some new ideas about future automobile steering system.

Tick-Pathogen Interactions and Vector Competence: Identification of Molecular Drivers for Tick-Borne Diseases

PubMed Central

de la Fuente, José; Antunes, Sandra; Bonnet, Sarah; Cabezas-Cruz, Alejandro; Domingos, Ana G.; Estrada-Peña, Agustín; Johnson, Nicholas; Kocan, Katherine M.; Mansfield, Karen L.; Nijhof, Ard M.; Papa, Anna; Rudenko, Nataliia; Villar, Margarita; Alberdi, Pilar; Torina, Alessandra; Ayllón, Nieves; Vancova, Marie; Golovchenko, Maryna; Grubhoffer, Libor; Caracappa, Santo; Fooks, Anthony R.; Gortazar, Christian; Rego, Ryan O. M.

2017-01-01

Ticks and the pathogens they transmit constitute a growing burden for human and animal health worldwide. Vector competence is a component of vectorial capacity and depends on genetic determinants affecting the ability of a vector to transmit a pathogen. These determinants affect traits such as tick-host-pathogen and susceptibility to pathogen infection. Therefore, the elucidation of the mechanisms involved in tick-pathogen interactions that affect vector competence is essential for the identification of molecular drivers for tick-borne diseases. In this review, we provide a comprehensive overview of tick-pathogen molecular interactions for bacteria, viruses, and protozoa affecting human and animal health. Additionally, the impact of tick microbiome on these interactions was considered. Results show that different pathogens evolved similar strategies such as manipulation of the immune response to infect vectors and facilitate multiplication and transmission. Furthermore, some of these strategies may be used by pathogens to infect both tick and mammalian hosts. Identification of interactions that promote tick survival, spread, and pathogen transmission provides the opportunity to disrupt these interactions and lead to a reduction in tick burden and the prevalence of tick-borne diseases. Targeting some of the similar mechanisms used by the pathogens for infection and transmission by ticks may assist in development of preventative strategies against multiple tick-borne diseases. PMID:28439499

Protecting muscle ATP: positive roles for peripheral defense mechanisms-introduction.

PubMed

Myburgh, Kathryn H

2004-01-01

Skeletal muscle has evolved an impressive array of mechanisms for peripherally mediated control of ATP homeostasis. Some of these mechanisms are intracellular, and others are extracellular and include influences on the cross-bridge cycle itself and substrate supply. This paper introduces three distinctly different topics that nevertheless all have ATP defense in common. The role of ADP in fatigue is controversial but has recently been more clearly delineated so that an effect on alleviating force declines during extreme fatigue is plausible. AMP plays its role by activating the protein-kinase, AMPK, which is a key sensor of cellular energy stress. AMPK has different isoforms, is not uniformly distributed in the cell, and its activation is carefully controlled. It has multiple effects including improvements in substrate supply for the metabolic pathways producing ATP and inhibition of anabolic processes to further spare ATP. Red blood cells have the capacity to sense hypoxia and to release vasodilators where there is a locally increased demand for blood supply. The papers in this series emphasize the important positive roles of metabolites and sensors of fatigue in the balance between ATP supply and demand.

Hormonal interactions during root tropic growth: hydrotropism versus gravitropism.

PubMed

Takahashi, Hideyuki; Miyazawa, Yutaka; Fujii, Nobuharu

2009-03-01

Terrestrial plants have evolved remarkable morphological plasticity that enables them to adapt to their surroundings. One of the most important traits that plants have acquired is the ability to sense environmental cues and use them as a basis for governing their growth orientation. The directional growth of plant organs relative to the direction of environmental stimuli is a tropism. The Cholodny-Went theory proposes that auxin plays a key role in several tropisms. Recent molecular genetic studies have strongly supported this hypothesis for gravitropism. However, the molecular mechanisms of other tropisms are far less clear. Hydrotropism is the response of roots to a moisture gradient. Since its re-discovery in 1985, root hydrotropism has been shown to be common among higher plant species. Additionally, in some species, gravitropism interferes with hydrotropism, suggesting that both shared and divergent mechanisms mediating the two tropisms exist. This hypothesis has been supported by recent studies, which provide an understanding of how roots sense multiple environmental cues and exhibit different tropic responses. In this review, we focus on the overlapping and unique mechanisms of the hormonal regulation underlying gravitropism and hydrotropism in roots.

Establishment of Chronic Infection: Brucella's Stealth Strategy

PubMed Central

Ahmed, Waqas; Zheng, Ke; Liu, Zheng-Fei

2016-01-01

Brucella is a facultative intracellular pathogen that causes zoonotic infection known as brucellosis which results in abortion and infertility in natural host. Humans, especially in low income countries, can acquire infection by direct contact with infected animal or by consumption of animal products and show high morbidity, severe economic losses and public health problems. However for survival, host cells develop complex immune mechanisms to defeat and battle against attacking pathogens and maintain a balance between host resistance and Brucella virulence. On the other hand as a successful intracellular pathogen, Brucella has evolved multiple strategies to evade immune response mechanisms to establish persistent infection and replication within host. In this review, we mainly summarize the “Stealth” strategies employed by Brucella to modulate innate and the adaptive immune systems, autophagy, apoptosis and possible role of small noncoding RNA in the establishment of chronic infection. The purpose of this review is to give an overview for recent understanding how this pathogen evades immune response mechanisms of host, which will facilitate to understanding the pathogenesis of brucellosis and the development of novel, more effective therapeutic approaches to treat brucellosis. PMID:27014640

Parallel evolution of Nitric Oxide signaling: Diversity of synthesis & memory pathways

PubMed Central

Moroz, Leonid L.; Kohn, Andrea B.

2014-01-01

The origin of NO signaling can be traceable back to the origin of life with the large scale of parallel evolution of NO synthases (NOSs). Inducible-like NOSs may be the most basal prototype of all NOSs and that neuronal-like NOS might have evolved several times from this prototype. Other enzymatic and non-enzymatic pathways for NO synthesis have been discovered using reduction of nitrites, an alternative source of NO. Diverse synthetic mechanisms can co-exist within the same cell providing a complex NO-oxygen microenvironment tightly coupled with cellular energetics. The dissection of multiple sources of NO formation is crucial in analysis of complex biological processes such as neuronal integration and learning mechanisms when NO can act as a volume transmitter within memory-forming circuits. In particular, the molecular analysis of learning mechanisms (most notably in insects and gastropod molluscs) opens conceptually different perspectives to understand the logic of recruiting evolutionarily conserved pathways for novel functions. Giant uniquely identified cells from Aplysia and related species precent unuque opportunities for integrative analysis of NO signaling at the single cell level. PMID:21622160

[Pneumatosis cystoides intestinalis complicated with intestinal volvulus].

PubMed

Fuenmayor, Carmen Elena; Gainza, Carlos; García, Maryori; Zambrano, Richard; Torres, Gledys; Hernández, Yohanys; García, Anna

2017-01-01

Pneumatosis cystoides intestinalis is a rare condition in which multiple gas-filled cysts are found within the wall of the gastrointestinal tract either in the subserosa or submucosa. Its pathogenesis is uncertain and several pathogenic mechanisms have been proposed to explain its origin. The case of a male patient of 46 years with previous diagnosis of pneumatosis cystic intestinalis, who consulted for abdominal pain, vomiting and fever (39 °C) is presented. By the time of admission ther were signs of peritoneal irritation. The X-ray abdominal reported distension and intestinal hydro-air levels. Exploratory laparotomy was performed and revealed small bowel volvulus with strangulation of some intestinal segment. Histological diagnosis was pneumatosis cystic intestinalis complicated with Infarction trans-mural by intestinal volvulus. The patient evolved satisfactorily.

Evolving models of the immunopathogenesis of T-cell mediated drug allergy: the role of host, pathogens, and drug response

PubMed Central

White, Katie D.; Chung, Wen-Hung; Hung, Shuen-Iu; Mallal, Simon; Phillips, Elizabeth J.

2015-01-01

Immune-mediated adverse drug reactions (IM-ADRs) are an underrecognized source of preventable morbidity, mortality, and cost. Increasingly, genetic variation in the HLA loci is associated with risk of severe reactions, highlighting the importance of T-cell immune responses in the mechanisms of both B-cell mediated and primary T-cell mediated IM-ADRs. In this review, we summarize the role of host genetics, microbes and drugs in the development of IM-ADRs, expand upon the existing models of IM-ADR pathogenesis to address multiple unexplained observations, discuss the implications of this work in clinical practice today, and describe future applications for pre-clinical drug toxicity screening, drug design, and development. PMID:26254049

Enterovirus 71 2C Protein Inhibits NF-κB Activation by Binding to RelA(p65)

PubMed Central

Du, Haiwei; Yin, Peiqi; Yang, Xiaojie; Zhang, Leiliang; Jin, Qi; Zhu, Guofeng

2015-01-01

Viruses evolve multiple ways to interfere with NF-κB signaling, a key regulator of innate and adaptive immunity. Enterovirus 71 (EV71) is one of primary pathogens that cause hand-foot-mouth disease. Here, we identify RelA(p65) as a novel binding partner for EV71 2C protein from yeast two-hybrid screen. By interaction with IPT domain of p65, 2C reduces the formation of heterodimer p65/p50, the predominant form of NF-κB. We also show that picornavirus 2C family proteins inhibit NF-κB activation and associate with p65 and IKKβ. Our findings provide a novel mechanism how EV71 antagonizes innate immunity. PMID:26394554

In vitro resistance to the human immunodeficiency virus type 1 maturation inhibitor PA-457 (Bevirimat).

PubMed

Adamson, Catherine S; Ablan, Sherimay D; Boeras, Ioana; Goila-Gaur, Ritu; Soheilian, Ferri; Nagashima, Kunio; Li, Feng; Salzwedel, Karl; Sakalian, Michael; Wild, Carl T; Freed, Eric O

2006-11-01

3-O-(3',3'-dimethylsuccinyl)betulinic acid (PA-457 or bevirimat) potently inhibits human immunodeficiency virus type 1 (HIV-1) maturation by blocking a late step in the Gag processing pathway, specifically the cleavage of SP1 from the C terminus of capsid (CA). To gain insights into the mechanism(s) by which HIV-1 could evolve resistance to PA-457 and to evaluate the likelihood of such resistance arising in PA-457-treated patients, we sought to identify and characterize a broad spectrum of HIV-1 variants capable of conferring resistance to this compound. Numerous independent rounds of selection repeatedly identified six single-amino-acid substitutions that independently confer PA-457 resistance: three at or near the C terminus of CA (CA-H226Y, -L231F, and -L231M) and three at the first and third residues of SP1 (SP1-A1V, -A3T, and -A3V). We determined that mutations CA-H226Y, CA-L231F, CA-L231M, and SP1-A1V do not impose a significant replication defect on HIV-1 in culture. In contrast, mutations SP1-A3V and -A3T severely impaired virus replication and inhibited virion core condensation. The replication defect imposed by SP1-A3V was reversed by a second-site compensatory mutation in CA (CA-G225S). Intriguingly, high concentrations of PA-457 enhanced the maturation of SP1 residue 3 mutants. The different phenotypes associated with mutations that confer PA-457 resistance suggest the existence of multiple mechanisms by which HIV-1 can evolve resistance to this maturation inhibitor. These findings have implications for the ongoing development of PA-457 to treat HIV-1 infection in vivo.

Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria

PubMed Central

Haft, Rembrandt J. F.; Keating, David H.; Schwaegler, Tyler; Schwalbach, Michael S.; Vinokur, Jeffrey; Tremaine, Mary; Peters, Jason M.; Kotlajich, Matthew V.; Pohlmann, Edward L.; Ong, Irene M.; Grass, Jeffrey A.; Kiley, Patricia J.; Landick, Robert

2014-01-01

The molecular mechanisms of ethanol toxicity and tolerance in bacteria, although important for biotechnology and bioenergy applications, remain incompletely understood. Genetic studies have identified potential cellular targets for ethanol and have revealed multiple mechanisms of tolerance, but it remains difficult to separate the direct and indirect effects of ethanol. We used adaptive evolution to generate spontaneous ethanol-tolerant strains of Escherichia coli, and then characterized mechanisms of toxicity and resistance using genome-scale DNAseq, RNAseq, and ribosome profiling coupled with specific assays of ribosome and RNA polymerase function. Evolved alleles of metJ, rho, and rpsQ recapitulated most of the observed ethanol tolerance, implicating translation and transcription as key processes affected by ethanol. Ethanol induced miscoding errors during protein synthesis, from which the evolved rpsQ allele protected cells by increasing ribosome accuracy. Ribosome profiling and RNAseq analyses established that ethanol negatively affects transcriptional and translational processivity. Ethanol-stressed cells exhibited ribosomal stalling at internal AUG codons, which may be ameliorated by the adaptive inactivation of the MetJ repressor of methionine biosynthesis genes. Ethanol also caused aberrant intragenic transcription termination for mRNAs with low ribosome density, which was reduced in a strain with the adaptive rho mutation. Furthermore, ethanol inhibited transcript elongation by RNA polymerase in vitro. We propose that ethanol-induced inhibition and uncoupling of mRNA and protein synthesis through direct effects on ribosomes and RNA polymerase conformations are major contributors to ethanol toxicity in E. coli, and that adaptive mutations in metJ, rho, and rpsQ help protect these central dogma processes in the presence of ethanol. PMID:24927582

Optical network democratization.

PubMed

Nejabati, Reza; Peng, Shuping; Simeonidou, Dimitra

2016-03-06

The current Internet infrastructure is not able to support independent evolution and innovation at physical and network layer functionalities, protocols and services, while at same time supporting the increasing bandwidth demands of evolving and heterogeneous applications. This paper addresses this problem by proposing a completely democratized optical network infrastructure. It introduces the novel concepts of the optical white box and bare metal optical switch as key technology enablers for democratizing optical networks. These are programmable optical switches whose hardware is loosely connected internally and is completely separated from their control software. To alleviate their complexity, a multi-dimensional abstraction mechanism using software-defined network technology is proposed. It creates a universal model of the proposed switches without exposing their technological details. It also enables a conventional network programmer to develop network applications for control of the optical network without specific technical knowledge of the physical layer. Furthermore, a novel optical network virtualization mechanism is proposed, enabling the composition and operation of multiple coexisting and application-specific virtual optical networks sharing the same physical infrastructure. Finally, the optical white box and the abstraction mechanism are experimentally evaluated, while the virtualization mechanism is evaluated with simulation. © 2016 The Author(s).

Recurrent Innovation at Genes Required for Telomere Integrity in Drosophila.

PubMed

Lee, Yuh Chwen G; Leek, Courtney; Levine, Mia T

2017-02-01

Telomeres are nucleoprotein complexes at the ends of linear chromosomes. These specialized structures ensure genome integrity and faithful chromosome inheritance. Recurrent addition of repetitive, telomere-specific DNA elements to chromosome ends combats end-attrition, while specialized telomere-associated proteins protect naked, double-stranded chromosome ends from promiscuous repair into end-to-end fusions. Although telomere length homeostasis and end-protection are ubiquitous across eukaryotes, there is sporadic but building evidence that the molecular machinery supporting these essential processes evolves rapidly. Nevertheless, no global analysis of the evolutionary forces that shape these fast-evolving proteins has been performed on any eukaryote. The abundant population and comparative genomic resources of Drosophila melanogaster and its close relatives offer us a unique opportunity to fill this gap. Here we leverage population genetics, molecular evolution, and phylogenomics to define the scope and evolutionary mechanisms driving fast evolution of genes required for telomere integrity. We uncover evidence of pervasive positive selection across multiple evolutionary timescales. We also document prolific expansion, turnover, and expression evolution in gene families founded by telomeric proteins. Motivated by the mutant phenotypes and molecular roles of these fast-evolving genes, we put forward four alternative, but not mutually exclusive, models of intra-genomic conflict that may play out at very termini of eukaryotic chromosomes. Our findings set the stage for investigating both the genetic causes and functional consequences of telomere protein evolution in Drosophila and beyond. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Computational structural mechanics methods research using an evolving framework

NASA Technical Reports Server (NTRS)

Knight, N. F., Jr.; Lotts, C. G.; Gillian, R. E.

1990-01-01

Advanced structural analysis and computational methods that exploit high-performance computers are being developed in a computational structural mechanics research activity sponsored by the NASA Langley Research Center. These new methods are developed in an evolving framework and applied to representative complex structural analysis problems from the aerospace industry. An overview of the methods development environment is presented, and methods research areas are described. Selected application studies are also summarized.

Abducting Economics

PubMed Central

Singer, Burton

2018-01-01

Abduction is the process of generating and choosing models, hypotheses and data analyzed in response to surprising findings. All good empirical economists abduct. Explanations usually evolve as studies evolve. The abductive approach challenges economists to step outside the framework of received notions about the “identification problem” that rigidly separates the act of model and hypothesis creation from the act of inference from data. It asks the analyst to engage models and data in an iterative dynamic process, using multiple models and sources of data in a back and forth where both models and data are augmented as learning evolves. PMID:29430020

SparkClouds: visualizing trends in tag clouds.

PubMed

Lee, Bongshin; Riche, Nathalie Henry; Karlson, Amy K; Carpendale, Sheelash

2010-01-01

Tag clouds have proliferated over the web over the last decade. They provide a visual summary of a collection of texts by visually depicting the tag frequency by font size. In use, tag clouds can evolve as the associated data source changes over time. Interesting discussions around tag clouds often include a series of tag clouds and consider how they evolve over time. However, since tag clouds do not explicitly represent trends or support comparisons, the cognitive demands placed on the person for perceiving trends in multiple tag clouds are high. In this paper, we introduce SparkClouds, which integrate sparklines into a tag cloud to convey trends between multiple tag clouds. We present results from a controlled study that compares SparkClouds with two traditional trend visualizations—multiple line graphs and stacked bar charts—as well as Parallel Tag Clouds. Results show that SparkClouds ability to show trends compares favourably to the alternative visualizations.

Molecular marker suggests rapid changes of sex-determining mechanisms in Australian dragon lizards.

PubMed

Ezaz, Tariq; Quinn, Alexander E; Sarre, Stephen D; O'Meally, Denis; Georges, Arthur; Graves, Jennifer A Marshall

2009-01-01

Distribution of sex-determining mechanisms across Australian agamids shows no clear phylogenetic segregation, suggesting multiple transitions between temperature-dependent (TSD) and genotypic sex determination (GSD). These taxa thus present an excellent opportunity for studying the evolution of sex chromosomes, and evolutionary transitions between TSD and GSD. Here we report the hybridization of a 3 kb genomic sequence (PvZW3) that marks the Z and W microchromosomes of the Australian central bearded dragon (Pogona vitticeps) to chromosomes of 12 species of Australian agamids from eight genera using fluorescence in-situ hybridization (FISH). The probe hybridized to a single microchromosome pair in 11 of these species, but to the tip of the long arm of chromosome pair 2 in the twelfth (Physignathus lesueurii), indicating a micro-macro chromosome rearrangement. Three TSD species shared the marked microchromosome, implying that it is a conserved autosome in related species that determine sex by temperature. C-banding identified the marked microchromosome as the heterochromatic W chromosome in two of the three GSD species. However, in Ctenophorus fordi, the probe hybridized to a different microchromosome from that shown by C-banding to be the heterochromatic W, suggesting an independent origin for the ZW chromosome pair in that species. Given the haphazard distribution of GSD and TSD in this group and the existence of at least two sets of sex microchromosomes in GSD species, we conclude that sex-determining mechanisms in this family have evolved independently, multiple times in a short evolutionary period.

Responses to clomazone and 5-ketoclomazone by Echinochloa phyllopogon resistant to multiple herbicides in Californian rice fields.

PubMed

Yasuor, Hagai; TenBrook, Patti L; Tjeerdema, Ronald S; Fischer, Albert J

2008-10-01

Late watergrass [Echinochloa phyllopogon (Stapf.) Koss.] is a major weed of Californian rice that has evolved P450-mediated metabolic resistance to multiple herbicides. Resistant (R) populations are also poorly controlled by the recently introduced herbicide clomazone. The authors assessed whether this cross-resistance was also P450 mediated, and whether R plants also had reduced sensitivity to photooxidation. Understanding mechanism(s) of resistance facilitates the design of herbicide management strategies to delay resistance evolution. Ratios (R/S) of R to susceptible (S) GR(50) were near 2.0. [(14)C]Clomazone uptake was similar in R and S plants. Clomazone and its metabolite 5-ketoclomazone reduced chlorophyll and carotenoids in S more than in R plants. The P450 inhibitors disulfoton and 1-aminobenzo-triazole (ABT) safened clomazone in R and S plants. Disulfoton safened 5-ketoclomazone only in S plants, while ABT synergized 5-ketoclomazone mostly against S plants. Paraquat was more toxic in S than in R plants. Cross-resistance to clomazone explains failures to control R plants in rice fields, and safening by P450 inhibitors suggests that oxidative activation of clomazone is needed for toxicity to E. phyllopogon. Clomazone resistance requires mitigation of 5-ketoclomazone toxicity, but P450 detoxification may not significantly confer resistance, as P450 inhibitors poorly synergized 5-ketoclopmazone in R plants. Responses to paraquat suggest research on mechanisms to mitigate photooxidation in R and S plants is needed.

Walking, running and the evolution of short toes in humans.

PubMed

Rolian, Campbell; Lieberman, Daniel E; Hamill, Joseph; Scott, John W; Werbel, William

2009-03-01

The phalangeal portion of the forefoot is extremely short relative to body mass in humans. This derived pedal proportion is thought to have evolved in the context of committed bipedalism, but the benefits of shorter toes for walking and/or running have not been tested previously. Here, we propose a biomechanical model of toe function in bipedal locomotion that suggests that shorter pedal phalanges improve locomotor performance by decreasing digital flexor force production and mechanical work, which might ultimately reduce the metabolic cost of flexor force production during bipedal locomotion. We tested this model using kinematic, force and plantar pressure data collected from a human sample representing normal variation in toe length (N=25). The effect of toe length on peak digital flexor forces, impulses and work outputs was evaluated during barefoot walking and running using partial correlations and multiple regression analysis, controlling for the effects of body mass, whole-foot and phalangeal contact times and toe-out angle. Our results suggest that there is no significant increase in digital flexor output associated with longer toes in walking. In running, however, multiple regression analyses based on the sample suggest that increasing average relative toe length by as little as 20% doubles peak digital flexor impulses and mechanical work, probably also increasing the metabolic cost of generating these forces. The increased mechanical cost associated with long toes in running suggests that modern human forefoot proportions might have been selected for in the context of the evolution of endurance running.

Systems and Algorithms for Automated Collaborative Observation Using Networked Robotic Cameras

ERIC Educational Resources Information Center

Xu, Yiliang

2011-01-01

The development of telerobotic systems has evolved from Single Operator Single Robot (SOSR) systems to Multiple Operator Multiple Robot (MOMR) systems. The relationship between human operators and robots follows the master-slave control architecture and the requests for controlling robot actuation are completely generated by human operators. …

How does cognition evolve? Phylogenetic comparative psychology

PubMed Central

Matthews, Luke J.; Hare, Brian A.; Nunn, Charles L.; Anderson, Rindy C.; Aureli, Filippo; Brannon, Elizabeth M.; Call, Josep; Drea, Christine M.; Emery, Nathan J.; Haun, Daniel B. M.; Herrmann, Esther; Jacobs, Lucia F.; Platt, Michael L.; Rosati, Alexandra G.; Sandel, Aaron A.; Schroepfer, Kara K.; Seed, Amanda M.; Tan, Jingzhi; van Schaik, Carel P.; Wobber, Victoria

2014-01-01

Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution. PMID:21927850

Evolution of the cytoskeleton

PubMed Central

Erickson, Harold P.

2009-01-01

Summary The eukaryotic cytoskeleton appears to have evolved from ancestral precursors related to prokaryotic FtsZ and MreB. FtsZ and MreB show 40−50% sequence identity across different bacterial and archaeal species. Here I suggest that this represents the limit of divergence that is consistent with maintaining their functions for cytokinesis and cell shape. Previous analyses have noted that tubulin and actin are highly conserved across eukaryotic species, but so divergent from their prokaryotic relatives as to be hardly recognizable from sequence comparisons. One suggestion for this extreme divergence of tubulin and actin is that it occurred as they evolved very different functions from FtsZ and MreB. I will present new arguments favoring this suggestion, and speculate on pathways. Moreover, the extreme conservation of tubulin and actin across eukaryotic species is not due to an intrinsic lack of variability, but is attributed to their acquisition of elaborate mechanisms for assembly dynamics and their interactions with multiple motor and binding proteins. A new structure-based sequence alignment identifies amino acids that are conserved from FtsZ to tubulins. The highly conserved amino acids are not those forming the subunit core or protofilament interface, but those involved in binding and hydrolysis of GTP. PMID:17563102

Evolution of 'smoke' induced seed germination in pyroendemic plants

USGS Publications Warehouse

Keeley, J. E.; Pausas, J.G.

2016-01-01

Pyroendemics are plants in which seedling germination and successful seedling recruitment are restricted to immediate postfire environments. In many fire-prone ecosystems species cue their germination to immediate postfire conditions. Here we address how species have evolved one very specific mechanism, which is using the signal of combustion products from biomass. This is often termed ‘smoke’ stimulated germination although it was first discovered in studies of charred wood effects on germination of species strictly tied to postfire conditions (pyroendemics). Smoke stimulated germination has been reported from a huge diversity of plant species. The fact that the organic compound karrikin (a product of the degradation of cellulose) is a powerful germination cue in many species has led to the assumption that this compound is the only chemical responsible for smoke-stimulated germination. Here we show that smoke-stimulated germination is a complex trait with different compounds involved. We propose that convergent evolution is a more parsimonious model for smoke stimulated germination, suggesting that this trait evolved multiple times in response to a variety of organic and inorganic chemical triggers in smoke. The convergent model is congruent with the evolution of many other fire-related traits.

Selfish cellular networks and the evolution of complex organisms.

PubMed

Kourilsky, Philippe

2012-03-01

Human gametogenesis takes years and involves many cellular divisions, particularly in males. Consequently, gametogenesis provides the opportunity to acquire multiple de novo mutations. A significant portion of these is likely to impact the cellular networks linking genes, proteins, RNA and metabolites, which constitute the functional units of cells. A wealth of literature shows that these individual cellular networks are complex, robust and evolvable. To some extent, they are able to monitor their own performance, and display sufficient autonomy to be termed "selfish". Their robustness is linked to quality control mechanisms which are embedded in and act upon the individual networks, thereby providing a basis for selection during gametogenesis. These selective processes are equally likely to affect cellular functions that are not gamete-specific, and the evolution of the most complex organisms, including man, is therefore likely to occur via two pathways: essential housekeeping functions would be regulated and evolve during gametogenesis within the parents before being transmitted to their progeny, while classical selection would operate on other traits of the organisms that shape their fitness with respect to the environment. Copyright © 2012 Académie des sciences. Published by Elsevier SAS. All rights reserved.

CT scanning and flow measurements of shale fractures after multiple shearing events

DOE PAGES

Crandall, Dustin; Moore, Johnathan; Gill, Magdalena; ...

2017-11-05

A shearing apparatus was used in conjunction with a Hassler-style core holder to incrementally shear fractured shale cores while maintaining various confining pressures. Computed tomography scans were performed after each shearing event, and were used to obtain information on evolving fracture geometry. Fracture transmissivity was measured after each shearing event to understand the hydrodynamic response to the evolving fracture structure. The digital fracture volumes were used to perform laminar single phase flow simulations (local cubic law with a tapered plate correction model) to qualitatively examine small scale flow path variations within the altered fractures. Fractures were found to generally increasemore » in aperture after several shear slip events, with corresponding transmissivity increases. Lower confining pressure resulted in a fracture more prone to episodic mechanical failure and sudden changes in transmissivity. Conversely, higher confining pressures resulted in a system where, after an initial setting of the fracture surfaces, changes to the fracture geometry and transmissivity occurred gradually. Flow paths within the fractures are largely controlled by the location and evolution of zero aperture locations. Lastly, a reduction in the number of primary flow pathways through the fracture, and an increase in their width, was observed during all shearing tests.« less

Classification as clustering: a Pareto cooperative-competitive GP approach.

PubMed

McIntyre, Andrew R; Heywood, Malcolm I

2011-01-01

Intuitively population based algorithms such as genetic programming provide a natural environment for supporting solutions that learn to decompose the overall task between multiple individuals, or a team. This work presents a framework for evolving teams without recourse to prespecifying the number of cooperating individuals. To do so, each individual evolves a mapping to a distribution of outcomes that, following clustering, establishes the parameterization of a (Gaussian) local membership function. This gives individuals the opportunity to represent subsets of tasks, where the overall task is that of classification under the supervised learning domain. Thus, rather than each team member representing an entire class, individuals are free to identify unique subsets of the overall classification task. The framework is supported by techniques from evolutionary multiobjective optimization (EMO) and Pareto competitive coevolution. EMO establishes the basis for encouraging individuals to provide accurate yet nonoverlaping behaviors; whereas competitive coevolution provides the mechanism for scaling to potentially large unbalanced datasets. Benchmarking is performed against recent examples of nonlinear SVM classifiers over 12 UCI datasets with between 150 and 200,000 training instances. Solutions from the proposed coevolutionary multiobjective GP framework appear to provide a good balance between classification performance and model complexity, especially as the dataset instance count increases.

CT scanning and flow measurements of shale fractures after multiple shearing events

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crandall, Dustin; Moore, Johnathan; Gill, Magdalena

A shearing apparatus was used in conjunction with a Hassler-style core holder to incrementally shear fractured shale cores while maintaining various confining pressures. Computed tomography scans were performed after each shearing event, and were used to obtain information on evolving fracture geometry. Fracture transmissivity was measured after each shearing event to understand the hydrodynamic response to the evolving fracture structure. The digital fracture volumes were used to perform laminar single phase flow simulations (local cubic law with a tapered plate correction model) to qualitatively examine small scale flow path variations within the altered fractures. Fractures were found to generally increasemore » in aperture after several shear slip events, with corresponding transmissivity increases. Lower confining pressure resulted in a fracture more prone to episodic mechanical failure and sudden changes in transmissivity. Conversely, higher confining pressures resulted in a system where, after an initial setting of the fracture surfaces, changes to the fracture geometry and transmissivity occurred gradually. Flow paths within the fractures are largely controlled by the location and evolution of zero aperture locations. Lastly, a reduction in the number of primary flow pathways through the fracture, and an increase in their width, was observed during all shearing tests.« less

Advances in the understanding of cancer immunotherapy.

PubMed

Shore, Neal D

2015-09-01

The principal role of the immune system is to prevent and eradicate pathogens and infections. The key characteristics or features of an effective immune response include specificity, trafficking, antigen spread and durability (memory). The immune system is recognised to have a critical role in controlling cancer through a dynamic relationship with tumour cells. Normally, at the early stages of tumour development, the immune system is capable of eliminating tumour cells or keeping tumour growth abated; however, tumour cells may evolve multiple pathways over time to evade immune control. Immunotherapy may be viewed as a treatment designed to boost or restore the ability of the immune system to fight cancer, infections and other diseases. Immunotherapy manifests differently from traditional cancer treatments, eliciting delayed response kinetics and thus may be more effective in patients with lower tumour burden, in whom disease progression may be less rapid, thereby allowing ample time for the immunotherapy to evolve. Because immunotherapies may have a different mechanism of action from traditional cytotoxic or targeted biological agents, immunotherapy techniques have the potential to combine synergistically with traditional therapies. © 2014 The Authors. BJU International © 2014 BJU International Published by John Wiley & Sons Ltd.

Benchmark study on glyphosate-resistant crop systems in the United States. Economics of herbicide resistance management practices in a 5 year field-scale study.

PubMed

Edwards, C Blake; Jordan, David L; Owen, Michael Dk; Dixon, Philip M; Young, Bryan G; Wilson, Robert G; Weller, Steven C; Shaw, David R

2014-12-01

Since the introduction of glyphosate-resistant (GR) crops, growers have often relied on glyphosate-only weed control programs. As a result, multiple weeds have evolved resistance to glyphosate. A 5 year study including 156 growers from Illinois, Iowa, Indiana, Nebraska, North Carolina and Mississippi in the United States was conducted to compare crop yields and net returns between grower standard weed management programs (SPs) and programs containing best management practices (BMPs) recommended by university weed scientists. The BMPs were designed to prevent or mitigate/manage evolved herbicide resistance. Weed management costs were greater for the BMP approach in most situations, but crop yields often increased sufficiently for net returns similar to those of the less expensive SPs. This response was similar across all years, geographical regions, states, crops and tillage systems. Herbicide use strategies that include a diversity of herbicide mechanisms of action will increase the long-term sustainability of glyphosate-based weed management strategies. Growers can adopt herbicide resistance BMPs with confidence that net returns will not be negatively affected in the short term and contribute to resistance management in the long term. © 2014 Society of Chemical Industry.

How does cognition evolve? Phylogenetic comparative psychology.

PubMed

MacLean, Evan L; Matthews, Luke J; Hare, Brian A; Nunn, Charles L; Anderson, Rindy C; Aureli, Filippo; Brannon, Elizabeth M; Call, Josep; Drea, Christine M; Emery, Nathan J; Haun, Daniel B M; Herrmann, Esther; Jacobs, Lucia F; Platt, Michael L; Rosati, Alexandra G; Sandel, Aaron A; Schroepfer, Kara K; Seed, Amanda M; Tan, Jingzhi; van Schaik, Carel P; Wobber, Victoria

2012-03-01

Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution.

Vortex scaling ranges in two-dimensional turbulence

NASA Astrophysics Data System (ADS)

Burgess, B. H.; Dritschel, D. G.; Scott, R. K.

2017-11-01

We survey the role of coherent vortices in two-dimensional turbulence, including formation mechanisms, implications for classical similarity and inertial range theories, and characteristics of the vortex populations. We review early work on the spatial and temporal scaling properties of vortices in freely evolving turbulence and more recent developments, including a spatiotemporal scaling theory for vortices in the forced inverse energy cascade. We emphasize that Kraichnan-Batchelor similarity theories and vortex scaling theories are best viewed as complementary and together provide a more complete description of two-dimensional turbulence. In particular, similarity theory has a continued role in describing the weak filamentary sea between the vortices. Moreover, we locate both classical inertial and vortex scaling ranges within the broader framework of scaling in far-from-equilibrium systems, which generically exhibit multiple fixed point solutions with distinct scaling behaviour. We describe how stationary transport in a range of scales comoving with the dilatation of flow features, as measured by the growth in vortex area, constrains the vortex number density in both freely evolving and forced two-dimensional turbulence. The new theories for coherent vortices reveal previously hidden nontrivial scaling, point to new dynamical understanding, and provide a novel exciting window into two-dimensional turbulence.

Evidence of Multiple Sorption Modes in Layered Double Hydroxides Using Mo As Structural Probe.

PubMed

Ma, Bin; Fernandez-Martinez, Alejandro; Grangeon, Sylvain; Tournassat, Christophe; Findling, Nathaniel; Claret, Francis; Koishi, Ayumi; Marty, Nicolas C M; Tisserand, Delphine; Bureau, Sarah; Salas-Colera, Eduardo; Elkaïm, Erik; Marini, Carlo; Charlet, Laurent

2017-05-16

Layered double hydroxides (LDHs) have been considered as effective phases for the remediation of aquatic environments, to remove anionic contaminants mainly through anion exchange mechanisms. Here, a combination of batch isotherm experiments and X-ray techniques was used to examine molybdate (MoO 4 2- ) sorption mechanisms on CaAl LDHs with increasing loadings of molybdate. Advanced modeling of aqueous data shows that the sorption isotherm can be interpreted by three retention mechanisms, including two types of edge sites complexes, interlayer anion exchange, and CaMoO 4 precipitation. Meanwhile, Mo geometry evolves from tetrahedral to octahedral on the edge, and back to tetrahedral coordination at higher Mo loadings, indicated by Mo K-edge X-ray absorption spectra. Moreover, an anion exchange process on both CaAl LDHs was followed by in situ time-resolved synchrotron-based X-ray diffraction, remarkably agreeing with the sorption isotherm. This detailed molecular view shows that different uptake mechanisms-edge sorption, interfacial dissolution-reprecipitation-are at play and control anion uptake under environmentally relevant conditions, which is contrast to the classical view of anion exchange as the primary retention mechanism. This work puts all these mechanisms in perspective, offering a new insight into the complex interplay of anion uptake mechanisms by LDH phases, by using changes in Mo geometry as powerful molecular-scale probe.

Calcium-manganese oxides as structural and functional models for active site in oxygen evolving complex in photosystem II: lessons from simple models.

PubMed

Najafpour, Mohammad Mahdi

2011-01-01

The oxygen evolving complex in photosystem II which induces the oxidation of water to dioxygen in plants, algae and certain bacteria contains a cluster of one calcium and four manganese ions. It serves as a model to split water by sunlight. Reports on the mechanism and structure of photosystem II provide a more detailed architecture of the oxygen evolving complex and the surrounding amino acids. One challenge in this field is the development of artificial model compounds to study oxygen evolution reaction outside the complicated environment of the enzyme. Calcium-manganese oxides as structural and functional models for the active site of photosystem II are explained and reviewed in this paper. Because of related structures of these calcium-manganese oxides and the catalytic centers of active site of the oxygen evolving complex of photosystem II, the study may help to understand more about mechanism of oxygen evolution by the oxygen evolving complex of photosystem II. Copyright © 2010 Elsevier B.V. All rights reserved.

Has snake fang evolution lost its bite? New insights from a structural mechanics viewpoint.

PubMed

Broeckhoven, Chris; du Plessis, Anton

2017-08-01

Venomous snakes-the pinnacle of snake evolution-are characterized by their possession of venom-conducting fangs ranging from grooved phenotypes characterizing multiple lineages of rear-fanged taxa to tubular phenotypes present in elapids, viperids and atractaspidines. Despite extensive research, controversy still exists on the selective pressures involved in fang phenotype diversification. Here, we test the hypothesis that larger fangs and consequently a shift to an anterior position in the maxilla evolved to compensate for the costs of structural changes, i.e. higher stress upon impact in tubular fangs compared to grooved fangs. Direct voxel-based stress simulations conducted on high-resolution µCT scans, analysed within a phylogenetic framework, showed no differences in stress distribution between the three fang phenotypes, despite differences in (relative) fang length. These findings suggest that additional compensatory mechanisms are responsible for the biomechanical optimization and that fang length might instead be related to differential striking behaviour strategies. © 2017 The Author(s).

Evolution of dispersal and life history interact to drive accelerating spread of an invasive species.

PubMed

Perkins, T Alex; Phillips, Benjamin L; Baskett, Marissa L; Hastings, Alan

2013-08-01

Populations on the edge of an expanding range are subject to unique evolutionary pressures acting on their life-history and dispersal traits. Empirical evidence and theory suggest that traits there can evolve rapidly enough to interact with ecological dynamics, potentially giving rise to accelerating spread. Nevertheless, which of several evolutionary mechanisms drive this interaction between evolution and spread remains an open question. We propose an integrated theoretical framework for partitioning the contributions of different evolutionary mechanisms to accelerating spread, and we apply this model to invasive cane toads in northern Australia. In doing so, we identify a previously unrecognised evolutionary process that involves an interaction between life-history and dispersal evolution during range shift. In roughly equal parts, life-history evolution, dispersal evolution and their interaction led to a doubling of distance spread by cane toads in our model, highlighting the potential importance of multiple evolutionary processes in the dynamics of range expansion. © 2013 John Wiley & Sons Ltd/CNRS.

Complement-mediated neutrophil activation in sepsis- and trauma-related adult respiratory distress syndrome. Clarification with radioaerosol lung scans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tennenberg, S.D.; Jacobs, M.P.; Solomkin, J.S.

Complement-mediated neutrophil activation (CMNA) has been proposed as an important pathogenic mechanism causing acute microvascular lung injury in the adult respiratory distress syndrome (ARDS). To clarify the relationship between CMNA and evolving lung injury, we studied 26 patients with multiple trauma and sepsis within 24 hours of risk establishment for ARDS. Pulmonary alveolar-capillary permeability (PACP) was quantified as the clearance rate of a particulate radioaerosol. Seventeen patients (65%) had increased PACP (six developed ARDS) while nine (35%) had normal PACP (none developed ARDS; clearance rates of 3.4%/min and 1.5%/min, respectively). These patients, regardless of evidence of early lung injury, hadmore » elevated plasma C3adesArg levels and neutrophil chemotactic desensitization to C5a/C5adesArg. Plasma C3adesArg levels correlated weakly, but significantly, with PACP. Thus, CMNA may be a necessary, but not a sufficient, pathogenic mechanism in the evolution of ARDS.« less

Development and Evolution of Character Displacement

PubMed Central

Pfennig, David W.; Pfennig, Karin S.

2012-01-01

Character displacement occurs when competition for either resources or successful reproduction imposes divergent selection on interacting species, causing divergence in traits associated with resource use or reproduction. Here, we describe how character displacement can be mediated either by genetically canalized changes (i.e., changes that reflect allelic or genotype frequency changes) or by phenotypic plasticity. We also discuss how these two mechanisms influence the tempo of character displacement. Specifically, we suggest that, under some conditions, character displacement mediated by phenotypic plasticity might occur more rapidly than that mediated by genetically canalized changes. Finally, we describe how these two mechanisms may act together and determine character displacement’s mode, such that it proceeds through an initial phase in which trait divergence is environmentally induced to a later phase in which divergence becomes genetically canalized. This plasticity-first hypothesis predicts that character displacement should be generally mediated by ancestral plasticity and that it will arise similarly in multiple, independently evolving populations. We conclude by highlighting future directions for research that would test these predictions. PMID:22257002

Emerging insights into resistance to BRAF inhibitors in melanoma.

PubMed

Bucheit, Amanda D; Davies, Michael A

2014-02-01

Melanoma is the most aggressive form of skin cancer. The treatment of patients with advanced melanoma is rapidly evolving due to an improved understanding of molecular drivers of this disease. Somatic mutations in BRAF are the most common genetic alteration found in these tumors. Recently, two different mutant-selective small molecule inhibitors of BRAF, vemurafenib and dabrafenib, have gained regulatory approval based on positive results in randomized phase III trials. While the development of these agents represents a landmark in the treatment of melanoma, the benefit of these agents is limited by the frequent and rapid onset of resistance. The identification of several molecular mechanisms of resistance to BRAF inhibitors is rapidly leading to the clinical testing of combinatorial strategies to improve the clinical benefit of these agents. These mechanisms, and the lessons learned from the initial testing of the BRAF inhibitors, provide multiple insights that may facilitate the development of targeted therapies against other oncogenic mutations in melanoma, as well as in other cancers. Copyright © 2013 Elsevier Inc. All rights reserved.

The contribution of post-copulatory mechanisms to incipient ecological speciation in sticklebacks.

PubMed

Kaufmann, Joshka; Eizaguirre, Christophe; Milinski, Manfred; Lenz, Tobias L

2015-01-01

Ecology can play a major role in species diversification. As individuals are adapting to contrasting habitats, reproductive barriers may evolve at multiple levels. While pre-mating barriers have been extensively studied, the evolution of post-mating reproductive isolation during early stages of ecological speciation remains poorly understood. In diverging three-spined stickleback ecotypes from two lakes and two rivers, we observed differences in sperm traits between lake and river males. Interestingly, these differences did not translate into ecotype-specific gamete precedence for sympatric males in competitive in vitro fertilization experiments, potentially owing to antagonistic compensatory effects. However, we observed indirect evidence for impeded development of inter-ecotype zygotes, possibly suggesting an early stage of genetic incompatibility between ecotypes. Our results show that pre-zygotic post-copulatory mechanisms play a minor role during this first stage of ecotype divergence, but suggest that genetic incompatibilities may arise at early stages of ecological speciation. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Images as drivers of progress in cardiac computational modelling

PubMed Central

Lamata, Pablo; Casero, Ramón; Carapella, Valentina; Niederer, Steve A.; Bishop, Martin J.; Schneider, Jürgen E.; Kohl, Peter; Grau, Vicente

2014-01-01

Computational models have become a fundamental tool in cardiac research. Models are evolving to cover multiple scales and physical mechanisms. They are moving towards mechanistic descriptions of personalised structure and function, including effects of natural variability. These developments are underpinned to a large extent by advances in imaging technologies. This article reviews how novel imaging technologies, or the innovative use and extension of established ones, integrate with computational models and drive novel insights into cardiac biophysics. In terms of structural characterization, we discuss how imaging is allowing a wide range of scales to be considered, from cellular levels to whole organs. We analyse how the evolution from structural to functional imaging is opening new avenues for computational models, and in this respect we review methods for measurement of electrical activity, mechanics and flow. Finally, we consider ways in which combined imaging and modelling research is likely to continue advancing cardiac research, and identify some of the main challenges that remain to be solved. PMID:25117497

Host cell processes that influence the intracellular survival of Legionella pneumophila.

PubMed

Shin, Sunny; Roy, Craig R

2008-06-01

Key to the pathogenesis of intracellular pathogens is their ability to manipulate host cell processes, permitting the establishment of an intracellular replicative niche. In turn, the host cell deploys defence mechanisms that limit intracellular infection. The bacterial pathogen Legionella pneumophila, the aetiological agent of Legionnaire's Disease, has evolved virulence mechanisms that allow it to replicate within protozoa, its natural host. Many of these tactics also enable L. pneumophila's survival and replication inside macrophages within a membrane-bound compartment known as the Legionella-containing vacuole. One of the virulence factors indispensable for L. pneumophila's intracellular survival is a type IV secretion system, which translocates a large repertoire of bacterial effectors into the host cell. These effectors modulate multiple host cell processes and in particular, redirect trafficking of the L. pneumophila phagosome and mediate its conversion into an ER-derived organelle competent for intracellular bacterial replication. In this review, we discuss how L. pneumophila manipulates host cells, as well as host cell processes that either facilitate or impede its intracellular survival.

HIV Maintains an Evolving and Dispersed Population in Multiple Tissues during Suppressive Combined Antiretroviral Therapy in Individuals with Cancer

PubMed Central

Rose, Rebecca; Lamers, Susanna L.; Nolan, David J.; Maidji, Ekaterina; Faria, N. R.; Pybus, Oliver G.; Dollar, James J.; Maruniak, Samuel A.; McAvoy, Andrew C.; Salemi, Marco; Stoddart, Cheryl A.; Singer, Elyse J.

2016-01-01

ABSTRACT While combined antiretroviral therapy (cART) can result in undetectable plasma viral loads, it does not eradicate HIV infection. Furthermore, HIV-infected individuals while on cART remain at an increased risk of developing serious comorbidities, such as cancer, neurological disease, and atherosclerosis, suggesting that during cART, tissue-based HIV may contribute to such pathologies. We obtained DNA and RNA env, nef, and pol sequences using single-genome sequencing from postmortem tissues of three HIV+ cART-treated (cART+) individuals with undetectable viral load and metastatic cancer at death and performed time-scaled Bayesian evolutionary analyses. We used a sensitive in situ hybridization technique to visualize HIV gag-pol mRNA transcripts in cerebellum and lymph node tissues from one patient. Tissue-associated virus evolved at similar rates in cART+ and cART-naive (cART−) patients. Phylogenetic trees were characterized by two distinct features: (i) branching patterns consistent with constant viral evolution and dispersal among tissues and (ii) very recently derived clades containing both DNA and RNA sequences from multiple tissues. Rapid expansion of virus near death corresponded to wide-spread metastasis. HIV RNA+ cells clustered in cerebellum tissue but were dispersed in lymph node tissue, mirroring the evolutionary patterns observed for that patient. Activated, infiltrating macrophages were associated with HIV RNA. Our data provide evidence that tissues serve as a sanctuary for wild-type HIV during cART and suggest the importance of macrophages as an alternative reservoir and mechanism of virus spread. IMPORTANCE Combined antiretroviral therapy (cART) reduces plasma HIV to undetectable levels; however, removal of cART results in plasma HIV rebound, thus highlighting its inability to entirely rid the body of infection. Additionally, HIV-infected individuals on cART remain at high risk of serious diseases, which suggests a contribution from residual HIV. In this study, we isolated and sequenced HIV from postmortem tissues from three HIV+ cART+ individuals who died with metastatic cancer and had no detectable plasma viral load. Using high-resolution evolutionary analyses, we found that tissue-based HIV continues to replicate, evolve, and migrate among tissues during cART. Furthermore, cancer onset and metastasis coincided with increased HIV expansion, suggesting a linked mechanism. HIV-expressing cells were associated with tissue macrophages, a target of HIV infection. Our results suggest the importance of tissues, and macrophages in particular, as a target for novel anti-HIV therapies. PMID:27466425

HIV Maintains an Evolving and Dispersed Population in Multiple Tissues during Suppressive Combined Antiretroviral Therapy in Individuals with Cancer.

PubMed

Rose, Rebecca; Lamers, Susanna L; Nolan, David J; Maidji, Ekaterina; Faria, N R; Pybus, Oliver G; Dollar, James J; Maruniak, Samuel A; McAvoy, Andrew C; Salemi, Marco; Stoddart, Cheryl A; Singer, Elyse J; McGrath, Michael S

2016-10-15

While combined antiretroviral therapy (cART) can result in undetectable plasma viral loads, it does not eradicate HIV infection. Furthermore, HIV-infected individuals while on cART remain at an increased risk of developing serious comorbidities, such as cancer, neurological disease, and atherosclerosis, suggesting that during cART, tissue-based HIV may contribute to such pathologies. We obtained DNA and RNA env, nef, and pol sequences using single-genome sequencing from postmortem tissues of three HIV(+) cART-treated (cART(+)) individuals with undetectable viral load and metastatic cancer at death and performed time-scaled Bayesian evolutionary analyses. We used a sensitive in situ hybridization technique to visualize HIV gag-pol mRNA transcripts in cerebellum and lymph node tissues from one patient. Tissue-associated virus evolved at similar rates in cART(+) and cART-naive (cART(-)) patients. Phylogenetic trees were characterized by two distinct features: (i) branching patterns consistent with constant viral evolution and dispersal among tissues and (ii) very recently derived clades containing both DNA and RNA sequences from multiple tissues. Rapid expansion of virus near death corresponded to wide-spread metastasis. HIV RNA(+) cells clustered in cerebellum tissue but were dispersed in lymph node tissue, mirroring the evolutionary patterns observed for that patient. Activated, infiltrating macrophages were associated with HIV RNA. Our data provide evidence that tissues serve as a sanctuary for wild-type HIV during cART and suggest the importance of macrophages as an alternative reservoir and mechanism of virus spread. Combined antiretroviral therapy (cART) reduces plasma HIV to undetectable levels; however, removal of cART results in plasma HIV rebound, thus highlighting its inability to entirely rid the body of infection. Additionally, HIV-infected individuals on cART remain at high risk of serious diseases, which suggests a contribution from residual HIV. In this study, we isolated and sequenced HIV from postmortem tissues from three HIV(+) cART(+) individuals who died with metastatic cancer and had no detectable plasma viral load. Using high-resolution evolutionary analyses, we found that tissue-based HIV continues to replicate, evolve, and migrate among tissues during cART. Furthermore, cancer onset and metastasis coincided with increased HIV expansion, suggesting a linked mechanism. HIV-expressing cells were associated with tissue macrophages, a target of HIV infection. Our results suggest the importance of tissues, and macrophages in particular, as a target for novel anti-HIV therapies. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Self-organization of intertidal snails facilitates evolution of aggregation behavior.

PubMed

Stafford, Richard; Davies, Mark S; Williams, Gray A

2008-01-01

Many intertidal snails form aggregations during emersion to minimize desiccation stress. Here we investigate possible mechanisms for the evolution of such behavior. Two behavioral traits (following of mucus trails, and crevice occupation), which both provide selective advantages to individuals that possess the traits over individuals that do not, result in self-organization of aggregations in crevices in the rock surface. We suggest that the existence of self-organizing aggregations provides a mechanism by which aggregation behavior can evolve. The inclusion of an explicitly coded third behavior, aggregation, in a simulated population produces patterns statistically similar to those found on real rocky shores. Allowing these three behaviors to evolve using an evolutionary algorithm, however, results in aggregation behavior being selected against on shores with high crevice density. The inclusion of broadcast spawning dispersal mechanisms in the simulation, however, results in aggregation behavior evolving as predicted on shores with both high crevice density and low crevice density (evolving in crevices first, and then both in crevices and on flat rock), indicating the importance of environmental interactions in understanding evolutionary processes. We propose that self-organization can be an important factor in the evolution of group behaviors.

Management of thinned Emory oak coppice for multiple resource benefits

Treesearch

D. Catlow Shipek; Peter F. Ffolliott

2005-01-01

Managers are increasingly moving toward an ecosystem-based, multiple-use approach in managing Emory oak woodlands in the Southwestern United States. Often of particular interest is managing the coppice that evolves from earlier fuelwood harvesting activities. Emory oak (Quercus emoryi) is a prolific sprouting species and, as a consequence, post-...

Using Multiple-Stimulus without Replacement Preference Assessments to Increase Student Engagement and Performance

ERIC Educational Resources Information Center

Weaver, Adam D.; McKevitt, Brian C.; Farris, Allie M.

2017-01-01

Multiple-stimulus without replacement preference assessment is a research-based method for identifying appropriate rewards for students with emotional and behavioral disorders. This article presents a brief history of how this technology evolved and describes a step-by-step approach for conducting the procedure. A discussion of necessary materials…

Environmental Noise, Genetic Diversity and the Evolution of Evolvability and Robustness in Model Gene Networks

PubMed Central

Steiner, Christopher F.

2012-01-01

The ability of organisms to adapt and persist in the face of environmental change is accepted as a fundamental feature of natural systems. More contentious is whether the capacity of organisms to adapt (or “evolvability”) can itself evolve and the mechanisms underlying such responses. Using model gene networks, I provide evidence that evolvability emerges more readily when populations experience positively autocorrelated environmental noise (red noise) compared to populations in stable or randomly varying (white noise) environments. Evolvability was correlated with increasing genetic robustness to effects on network viability and decreasing robustness to effects on phenotypic expression; populations whose networks displayed greater viability robustness and lower phenotypic robustness produced more additive genetic variation and adapted more rapidly in novel environments. Patterns of selection for robustness varied antagonistically with epistatic effects of mutations on viability and phenotypic expression, suggesting that trade-offs between these properties may constrain their evolutionary responses. Evolution of evolvability and robustness was stronger in sexual populations compared to asexual populations indicating that enhanced genetic variation under fluctuating selection combined with recombination load is a primary driver of the emergence of evolvability. These results provide insight into the mechanisms potentially underlying rapid adaptation as well as the environmental conditions that drive the evolution of genetic interactions. PMID:23284934

Co-Evolution of Social Learning and Evolutionary Preparedness in Dangerous Environments

PubMed Central

Lindström, Björn; Selbing, Ida; Olsson, Andreas

2016-01-01

Danger is a fundamental aspect of the lives of most animals. Adaptive behavior therefore requires avoiding actions, objects, and environments associated with danger. Previous research has shown that humans and non-human animals can avoid such dangers through two types of behavioral adaptions, (i) genetic preparedness to avoid certain stimuli or actions, and (ii) social learning. These adaptive mechanisms reduce the fitness costs associated with danger but still allow flexible behavior. Despite the empirical prevalence and importance of both these mechanisms, it is unclear when they evolve and how they interact. We used evolutionary agent-based simulations, incorporating empirically based learning mechanisms, to clarify if preparedness and social learning typically both evolve in dangerous environments, and if these mechanisms generally interact synergistically or antagonistically. Our simulations showed that preparedness and social learning often co-evolve because they provide complimentary benefits: genetic preparedness reduced foraging efficiency, but resulted in a higher rate of survival in dangerous environments, while social learning generally came to dominate the population, especially when the environment was stochastic. However, even in this case, genetic preparedness reliably evolved. Broadly, our results indicate that the relationship between preparedness and social learning is important as it can result in trade-offs between behavioral flexibility and safety, which can lead to seemingly suboptimal behavior if the evolutionary environment of the organism is not taken into account. PMID:27487079

Co-Evolution of Social Learning and Evolutionary Preparedness in Dangerous Environments.

PubMed

Lindström, Björn; Selbing, Ida; Olsson, Andreas

2016-01-01

Danger is a fundamental aspect of the lives of most animals. Adaptive behavior therefore requires avoiding actions, objects, and environments associated with danger. Previous research has shown that humans and non-human animals can avoid such dangers through two types of behavioral adaptions, (i) genetic preparedness to avoid certain stimuli or actions, and (ii) social learning. These adaptive mechanisms reduce the fitness costs associated with danger but still allow flexible behavior. Despite the empirical prevalence and importance of both these mechanisms, it is unclear when they evolve and how they interact. We used evolutionary agent-based simulations, incorporating empirically based learning mechanisms, to clarify if preparedness and social learning typically both evolve in dangerous environments, and if these mechanisms generally interact synergistically or antagonistically. Our simulations showed that preparedness and social learning often co-evolve because they provide complimentary benefits: genetic preparedness reduced foraging efficiency, but resulted in a higher rate of survival in dangerous environments, while social learning generally came to dominate the population, especially when the environment was stochastic. However, even in this case, genetic preparedness reliably evolved. Broadly, our results indicate that the relationship between preparedness and social learning is important as it can result in trade-offs between behavioral flexibility and safety, which can lead to seemingly suboptimal behavior if the evolutionary environment of the organism is not taken into account.

Large variation in mitochondrial DNA of sexual and parthenogenetic Dahlica triquetrella (Lepidoptera: Psychidae) shows multiple origins of parthenogenesis

PubMed Central

2013-01-01

Background Obligate parthenogenesis is relatively rare in animals. Still, in some groups it is quite common and has evolved and persisted multiple times. These groups may provide important clues to help solve the ‘paradox of sex’. Several species in the Psychidae (Lepidoptera) have obligate parthenogenesis. Dahlica triquetrella is one of those species where multiple transitions to parthenogenesis are postulated based on intensive cytological and behavioural studies. This has led to the hypothesis that multiple transitions from sexuals to diploid parthenogens occurred during and after the last glacial period, followed by transitions from parthenogenetic diploids to parthenogenetic tetraploids. Our study is the first to test these hypotheses using a molecular phylogeny based on mtDNA from multiple sexual and parthenogenetic populations from a wide geographic range. Results Parthenogenetic (and sexual) D. triquetrella are not monophyletic, and considerable sequence variation is present suggesting multiple transitions to parthenogenesis. However, we could not establish ancestral sexual haplotypes from our dataset. Our data suggest that some parthenogenetic clades have evolved, indicating origins of parthenogenesis before the last glacial period. Conclusions Multiple transitions to parthenogenesis have taken place in Dahlica triquetrella, confirming previous hypotheses. The number of different parthenogenetic clades, haplotypes and their apparent evolutionary age, clearly show that parthenogenesis has been a very successful reproductive strategy in this species over a long period. PMID:23622052

Large variation in mitochondrial DNA of sexual and parthenogenetic Dahlica triquetrella (Lepidoptera: Psychidae) shows multiple origins of parthenogenesis.

PubMed

Elzinga, Jelmer A; Jokela, Jukka; Shama, Lisa N S

2013-04-26

Obligate parthenogenesis is relatively rare in animals. Still, in some groups it is quite common and has evolved and persisted multiple times. These groups may provide important clues to help solve the 'paradox of sex'. Several species in the Psychidae (Lepidoptera) have obligate parthenogenesis. Dahlica triquetrella is one of those species where multiple transitions to parthenogenesis are postulated based on intensive cytological and behavioural studies. This has led to the hypothesis that multiple transitions from sexuals to diploid parthenogens occurred during and after the last glacial period, followed by transitions from parthenogenetic diploids to parthenogenetic tetraploids. Our study is the first to test these hypotheses using a molecular phylogeny based on mtDNA from multiple sexual and parthenogenetic populations from a wide geographic range. Parthenogenetic (and sexual) D. triquetrella are not monophyletic, and considerable sequence variation is present suggesting multiple transitions to parthenogenesis. However, we could not establish ancestral sexual haplotypes from our dataset. Our data suggest that some parthenogenetic clades have evolved, indicating origins of parthenogenesis before the last glacial period. Multiple transitions to parthenogenesis have taken place in Dahlica triquetrella, confirming previous hypotheses. The number of different parthenogenetic clades, haplotypes and their apparent evolutionary age, clearly show that parthenogenesis has been a very successful reproductive strategy in this species over a long period.

Mechanism of resistance to mesotrione in an Amaranthus tuberculatus population from Nebraska, USA

PubMed Central

Hutchings, Sarah-Jane; Dale, Richard P.; Howell, Anushka; Morris, James A.; Kramer, Vance C.; Shivrain, Vinod K.; Mcindoe, Eddie

2017-01-01

Amaranthus tuberculatus is a troublesome weed in corn and soybean production systems in Midwestern USA, due in part to its ability to evolve multiple resistance to key herbicides including 4-hydroxyphenylpyruvate dioxygenase (HPPD). Here we have investigated the mechanism of resistance to mesotrione, an important chemical for managing broadleaf weeds in corn, in a multiple herbicide resistant population (NEB) from Nebraska. NEB showed a 2.4-fold and 45-fold resistance increase to mesotrione compared to a standard sensitive population (SEN) in pre-emergence and post-emergence dose-response pot tests, respectively. Sequencing of the whole HPPD gene from 12 each of sensitive and resistant plants did not detect any target-site mutations that could be associated with post-emergence resistance to mesotrione in NEB. Resistance was not due to HPPD gene duplication or over-expression before or after herbicide treatment, as revealed by qPCR. Additionally, no difference in mesotrione uptake was detected between NEB and SEN. In contrast, higher levels of mesotrione metabolism via 4-hydroxylation of the dione ring were observed in NEB compared to the sensitive population. Overall, the NEB population was characterised by lower levels of parent mesotrione exported to other parts of the plant, either as a consequence of metabolism in the treated leaves and/or impaired translocation of the herbicide. This study demonstrates another case of non-target-site based resistance to an important class of herbicides in an A. tuberculatus population. The knowledge generated here will help design strategies for managing multiple herbicide resistance in this problematic weed species. PMID:28662111

Repeated cis-regulatory tuning of a metabolic bottleneck gene during evolution.

PubMed

Kuang, Meihua Christina; Kominek, Jacek; Alexander, William G; Cheng, Jan-Fang; Wrobel, Russell L; Hittinger, Chris Todd

2018-05-21

Repeated evolutionary events imply underlying genetic constraints that can make evolutionary mechanisms predictable. Morphological traits are thought to evolve frequently through cis-regulatory changes because these mechanisms bypass constraints in pleiotropic genes that are reused during development. In contrast, the constraints acting on metabolic traits during evolution are less well studied. Here we show how a metabolic bottleneck gene has repeatedly adopted similar cis-regulatory solutions during evolution, likely due to its pleiotropic role integrating flux from multiple metabolic pathways. Specifically, the genes encoding phosphoglucomutase activity (PGM1/PGM2), which connect GALactose catabolism to glycolysis, have gained and lost direct regulation by the transcription factor Gal4 several times during yeast evolution. Through targeted mutations of predicted Gal4-binding sites in yeast genomes, we show this galactose-mediated regulation of PGM1/2 supports vigorous growth on galactose in multiple yeast species, including Saccharomyces uvarum and Lachancea kluyveri. Furthermore, the addition of galactose-inducible PGM1 alone is sufficient to improve the growth on galactose of multiple species that lack this regulation, including Saccharomyces cerevisiae. The strong association between regulation of PGM1/2 by Gal4 even enables remarkably accurate predictions of galactose growth phenotypes between closely related species. This repeated mode of evolution suggests that this specific cis-regulatory connection is a common way that diverse yeasts can govern flux through the pathway, likely due to the constraints imposed by this pleiotropic bottleneck gene. Since metabolic pathways are highly interconnected, we argue that cis-regulatory evolution might be widespread at pleiotropic genes that control metabolic bottlenecks and intersections.

Mechanics governs single-cell signaling and multi-cell robustness in biofilm infections

NASA Astrophysics Data System (ADS)

Gordon, Vernita

In biofilms, bacteria and other microbes are embedded in extracellular polymers (EPS). Multiple types of EPS can be produced by a single bacterial strain - the reasons for this redundancy are not well-understood. Our work suggests that different polymers may confer distinct mechanical benefits. Our model organism is Pseudomonas aeruginosa, an opportunistic human pathogen that forms chronic biofilm infections associated with increased antibiotic resistance and evasion of the immune defense. Biofilms initiate when bacteria attach to a surface, sense the surface, and change their gene expression. Changes in gene expression are regulated by a chemical signal, cyclic-di-GMP. We find that one EPS material, called ``PEL,'' enhances surface sensing by increasing mechanical coupling of single bacteria to the surface. Measurements of bacterial motility suggest that PEL may increase frictional interactions between the surface and the bacteria. Consistent with this, we show that bacteria increase cyclic-di-GMP signaling in response to mechanical shear stress. Mechanosensing has long been known to be important to the function of cells in higher eukaryotes, but this is one of only a handful of studies showing that bacteria can sense and respond to mechanical forces. For the mature biofilm, the embedding polymer matrix can protect bacteria both chemically and mechanically. P. aeruginosa infections in the cystic fibrosis (CF) lung often last for decades, ample time for the infecting strain(s) to evolve. Production of another EPS material, alginate, is well-known to tend to increase over time in CF infections. Alginate chemically protects biofilms, but also makes them softer and weaker. Recently, it is being increasingly recognized that bacteria in chronic CF infections also evolve to increase PSL production. We use oscillatory bulk rheology to determine the unique contributions of EPS materials to biofilm mechanics. Unlike alginate, increased PSL stiffens biofilms. Increasing both PSL and alginate expression increases the energy cost to break the biofilm. We compare the elastic moduli of biofilms to estimated stresses exerted by phagocytotic immune cells, and infer that increased PSL could confer a mechanical fitness benefit. This work was supported by start-up funds from The University of Texas at Austin and a gift from ExxonMobile to VDG, and by Grants from the Human Frontiers Science Program (HFSP RGY0081/2012-GORDON) and the National Science Foundation (NSF 1337670).

The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli.

PubMed

Aziz, Ramy K; Monk, Jonathan M; Andrews, Kathleen A; Nhan, Jenny; Khaw, Valerie L; Wong, Hesper; Palsson, Bernhard O; Charusanti, Pep

2017-01-01

Most Escherichia coli strains are naturally unable to grow on 1,2-propanediol (PDO) as a sole carbon source. Recently, however, a K-12 descendent E. coli strain was evolved to grow on 1,2-PDO, and it was hypothesized that this evolved ability was dependent on the aldehyde dehydrogenase, AldA, which is highly conserved among members of the family Enterobacteriacea. To test this hypothesis, we first performed computational model simulation, which confirmed the essentiality of the aldA gene for 1,2-PDO utilization by the evolved PDO-degrading E. coli. Next, we deleted the aldA gene from the evolved strain, and this deletion was sufficient to abolish the evolved phenotype. On re-introducing the gene on a plasmid, the evolved phenotype was restored. These findings provide experimental evidence for the computationally predicted role of AldA in 1,2-PDO utilization, and represent a good example of E. coli robustness, demonstrated by the bacterial deployment of a generalist enzyme (here AldA) in multiple pathways to survive carbon starvation and to grow on a non-native substrate when no native carbon source is available. Copyright © 2016 Elsevier GmbH. All rights reserved.

Comparative Analysis of Evolutionary Mechanisms of the Hemagglutinin and Three Internal Protein Genes of Influenza B Virus: Multiple Cocirculating Lineages and Frequent Reassortment of the NP, M, and NS Genes

PubMed Central

Lindstrom, Stephen E.; Hiromoto, Yasuaki; Nishimura, Hidekazu; Saito, Takehiko; Nerome, Reiko; Nerome, Kuniaki

1999-01-01

Phylogenetic profiles of the genes coding for the hemagglutinin (HA) protein, nucleoprotein (NP), matrix (M) protein, and nonstructural (NS) proteins of influenza B viruses isolated from 1940 to 1998 were analyzed in a parallel manner in order to understand the evolutionary mechanisms of these viruses. Unlike human influenza A (H3N2) viruses, the evolutionary pathways of all four genes of recent influenza B viruses revealed similar patterns of genetic divergence into two major lineages. Although evolutionary rates of the HA, NP, M, and NS genes of influenza B viruses were estimated to be generally lower than those of human influenza A viruses, genes of influenza B viruses demonstrated complex phylogenetic patterns, indicating alternative mechanisms for generation of virus variability. Topologies of the evolutionary trees of each gene were determined to be quite distinct from one another, showing that these genes were evolving in an independent manner. Furthermore, variable topologies were apparently the result of frequent genetic exchange among cocirculating epidemic viruses. Evolutionary analysis done in the present study provided further evidence for cocirculation of multiple lineages as well as sequestering and reemergence of phylogenetic lineages of the internal genes. In addition, comparison of deduced amino acid sequences revealed a novel amino acid deletion in the HA1 domain of the HA protein of recent isolates from 1998 belonging to the B/Yamagata/16/88-like lineage. It thus became apparent that, despite lower evolutionary rates, influenza B viruses were able to generate genetic diversity among circulating viruses through a combination of evolutionary mechanisms involving cocirculating lineages and genetic reassortment by which new variants with distinct gene constellations emerged. PMID:10196339

Patient with rapidly evolving neurological disease with neuropathological lesions of Creutzfeldt-Jakob disease, Lewy body dementia, chronic subcortical vascular encephalopathy and meningothelial meningioma.

PubMed

Vita, Maria Gabriella; Tiple, Dorina; Bizzarro, Alessandra; Ladogana, Anna; Colaizzo, Elisa; Capellari, Sabina; Rossi, Marcello; Parchi, Piero; Masullo, Carlo; Pocchiari, Maurizio

2017-04-01

We report a case of rapidly evolving neurological disease in a patient with neuropathological lesions of Creutzfeldt-Jakob disease (CJD), Lewy body dementia (LBD), chronic subcortical vascular encephalopathy and meningothelial meningioma. The coexistence of severe multiple pathologies in a single patient strengthens the need to perform accurate clinical differential diagnoses in rapidly progressive dementias. © 2016 Japanese Society of Neuropathology.

The evolution of insecticide resistance in the peach potato aphid, Myzus persicae.

PubMed

Bass, Chris; Puinean, Alin M; Zimmer, Christoph T; Denholm, Ian; Field, Linda M; Foster, Stephen P; Gutbrod, Oliver; Nauen, Ralf; Slater, Russell; Williamson, Martin S

2014-08-01

The peach potato aphid, Myzus persicae is a globally distributed crop pest with a host range of over 400 species including many economically important crop plants. The intensive use of insecticides to control this species over many years has led to populations that are now resistant to several classes of insecticide. Work spanning over 40 years has shown that M. persicae has a remarkable ability to evolve mechanisms that avoid or overcome the toxic effect of insecticides with at least seven independent mechanisms of resistance described in this species to date. The array of novel resistance mechanisms, including several 'first examples', that have evolved in this species represents an important case study for the evolution of insecticide resistance and also rapid adaptive change in insects more generally. In this review we summarise the biochemical and molecular mechanisms underlying resistance in M. persicae and the insights study of this topic has provided on how resistance evolves, the selectivity of insecticides, and the link between resistance and host plant adaptation. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Influential Aspects of the Smart City

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marinovici, Maria C.; Kirkham, Harold; Widergren, Steven E.

2016-01-05

Using millions of sensors in everyday objects, smart cities will generate petabytes of data, and it will be delivered to multiple users via networks. Multi-disciplinary inter-operability is essential. We propose system engineering management, with multidisciplinary teams as an effective way to deliver real change. Their goal is to develop intelligent and integrated services through the use of digital technologies and open collaboration. We also caution that the process cannot be entirely planned ahead of time, it must be allowed to evolve. New technology will change the game (where does a 3-D printer fit into a smart city?). Municipal planning meansmore » central planning – not known for its sensitivity to reality. A successful smart city will include lots of feedback mechanisms for the citizenry.« less

Multiple molecular mechanisms for multidrug resistance transporters.

PubMed

Higgins, Christopher F

2007-04-12

The acquisition of multidrug resistance is a serious impediment to improved healthcare. Multidrug resistance is most frequently due to active transporters that pump a broad spectrum of chemically distinct, cytotoxic molecules out of cells, including antibiotics, antimalarials, herbicides and cancer chemotherapeutics in humans. The paradigm multidrug transporter, mammalian P-glycoprotein, was identified 30 years ago. Nonetheless, success in overcoming or circumventing multidrug resistance in a clinical setting has been modest. Recent structural and biochemical data for several multidrug transporters now provide mechanistic insights into how they work. Organisms have evolved several elegant solutions to ridding the cell of such cytotoxic compounds. Answers are emerging to questions such as how multispecificity for different drugs is achieved, why multidrug resistance arises so readily, and what chance there is of devising a clinical solution.

FAST: A multi-processed environment for visualization of computational fluid dynamics

NASA Technical Reports Server (NTRS)

Bancroft, Gordon V.; Merritt, Fergus J.; Plessel, Todd C.; Kelaita, Paul G.; Mccabe, R. Kevin

1991-01-01

Three-dimensional, unsteady, multi-zoned fluid dynamics simulations over full scale aircraft are typical of the problems being investigated at NASA Ames' Numerical Aerodynamic Simulation (NAS) facility on CRAY2 and CRAY-YMP supercomputers. With multiple processor workstations available in the 10-30 Mflop range, we feel that these new developments in scientific computing warrant a new approach to the design and implementation of analysis tools. These larger, more complex problems create a need for new visualization techniques not possible with the existing software or systems available as of this writing. The visualization techniques will change as the supercomputing environment, and hence the scientific methods employed, evolves even further. The Flow Analysis Software Toolkit (FAST), an implementation of a software system for fluid mechanics analysis, is discussed.

Water Oxidation Catalysis via Size-Selected Iridium Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halder, Avik; Liu, Cong; LIU, ZHUN

The detailed mechanism and efficacy of four electron electrochemical water oxidation depend critically upon the detailed atomic structure of each catalytic site, which are numerous and diverse in most metal oxides anodes. In order to limit the diversity of sites, arrays of discrete iridium clusters with identical metal atom number (Ir-2, Ir-4, or Ir-8) were deposited in submonolayer coverage on conductive oxide supports, and the electrochemical properties and activity of each was evaluated. Exceptional electroactivity for the oxygen evolving reaction (OER) was observed for all cluster samples in acidic electrolyte. Reproducible cluster-size-dependent trends in redox behavior were also resolved. First-principlesmore » computational models of the individual discrete-size clusters allow correlation of catalytic-site structure and multiplicity with redox behavior.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wright, DA; Li, T; Yang, B

Genome editing is the practice of making predetermined and precise changes to a genome by controlling the location of DNA DSBs (double-strand breaks) and manipulating the cell's repair mechanisms. This technology results from harnessing natural processes that have taken decades and multiple lines of inquiry to understand. Through many false starts and iterative technology advances, the goal of genome editing is just now falling under the control of human hands as a routine and broadly applicable method. The present review attempts to define the technique and capture the discovery process while following its evolution from meganucleases and zinc finger nucleasesmore » to the current state of the art: TALEN (transcription-activator-like effector nuclease) technology. We also discuss factors that influence success, technical challenges, and future prospects of this quickly evolving area of study and application.« less

Hearing in Insects.

PubMed

Göpfert, Martin C; Hennig, R Matthias

2016-01-01

Insect hearing has independently evolved multiple times in the context of intraspecific communication and predator detection by transforming proprioceptive organs into ears. Research over the past decade, ranging from the biophysics of sound reception to molecular aspects of auditory transduction to the neuronal mechanisms of auditory signal processing, has greatly advanced our understanding of how insects hear. Apart from evolutionary innovations that seem unique to insect hearing, parallels between insect and vertebrate auditory systems have been uncovered, and the auditory sensory cells of insects and vertebrates turned out to be evolutionarily related. This review summarizes our current understanding of insect hearing. It also discusses recent advances in insect auditory research, which have put forward insect auditory systems for studying biological aspects that extend beyond hearing, such as cilium function, neuronal signal computation, and sensory system evolution.

Corticosterone regulates multiple colour traits in Lacerta [Zootoca] vivipara males.

PubMed

San-Jose, L M; Fitze, P S

2013-12-01

Ornamental colours usually evolve as honest signals of quality, which is supported by the fact that they frequently depend on individual condition. It has generally been suggested that some, but not all types of ornamental colours are condition dependent, indicating that different evolutionary mechanisms underlie the evolution of multiple types of ornamental colours even when these are exhibited by the same species. Stress hormones, which negatively affect condition, have been shown to affect colour traits based on different pigments and structures, suggesting that they mediate condition dependence of multiple ornament types both among and within individuals. However, studies investigating effects of stress hormones on different ornament types within individuals are lacking, and thus, evidence for this hypothesis is scant. Here, we investigated whether corticosterone mediates condition dependence of multiple ornaments by manipulating corticosterone levels and body condition (via food availability) using a two-factorial design and by assessing their effect on multiple colour traits in male common lizards. Corticosterone negatively affected ventral melanin- and carotenoid-based coloration, whereas food availability did not affect coloration, despite its significant effect on body condition. The corticosterone effect on melanin- and carotenoid-based coloration demonstrates the condition dependence of both ornaments. Moreover, corticosterone affected ventral coloration and had no effect on the nonsexually selected dorsal coloration, showing specific effects of corticosterone on ornamental ventral colours. This suggests that corticosterone simultaneously mediates condition dependence of multiple colour traits and that it therefore accounts for covariation among them, which may influence their evolution via correlational selection. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Daclizumab high-yield process reduced the evolution of new gadolinium-enhancing lesions to T1 black holes in patients with relapsing-remitting multiple sclerosis.

PubMed

Radue, E-W; Sprenger, T; Vollmer, T; Giovannoni, G; Gold, R; Havrdova, E; Selmaj, K; Stefoski, D; You, X; Elkins, J

2016-02-01

In the SELECT study, treatment with daclizumab high-yield process (DAC HYP) versus placebo reduced the frequency of gadolinium-enhancing (Gd(+) ) lesions in patients with relapsing-remitting multiple sclerosis (RRMS). The objective of this post hoc analysis of SELECT was to evaluate the effect of DAC HYP on the evolution of new Gd(+) lesions to T1 hypointense lesions (T1 black holes). SELECT was a randomized double-blind study of subcutaneous DAC HYP 150 or 300 mg or placebo every 4 weeks. Magnetic resonance imaging (MRI) scans were performed at baseline and weeks 24, 36 and 52 in all patients and monthly between weeks 4 and 20 in a subset of patients. MRI scans were evaluated for new Gd(+) lesions that evolved to T1 black holes at week 52. Data for the DAC HYP groups were pooled for analysis. Daclizumab high-yield process reduced the number of new Gd(+) lesions present at week 24 (P = 0.005) or between weeks 4 and 20 (P = 0.014) that evolved into T1 black holes at week 52 versus placebo. DAC HYP treatment also reduced the percentage of patients with Gd(+) lesions evolving to T1 black holes versus placebo. Treatment with DAC HYP reduced the evolution of Gd(+) lesions to T1 black holes versus placebo, suggesting that inflammatory lesions that evolved during DAC HYP treatment are less destructive than those evolving during placebo treatment. © 2016 EAN.

Multiple origins of subsociality in crab spiders (Thomisidae).

PubMed

Ruch, Jasmin; Riehl, Torben; May-Collado, Laura J; Agnarsson, Ingi

2015-01-01

Determining factors that facilitate the transition from a solitary to a social lifestyle is a major challenge in evolutionary biology, especially in taxa that are usually aggressive towards conspecifics. Most spiders live solitarily and few species are known to be social. Nevertheless, sociality has evolved multiple times across several families and nearly all studied social lineages have originated from a periodically social (subsocial) ancestor. Group-living crab spiders (Thomisidae) are exclusively found in Australia and differ from most other social spiders because they lack a communal capture web. Three of the group-living species were placed in the genus Diaea and another in the genus Xysticus. Most Australian thomisids are, however, difficult to identify as most descriptions are old and of poor quality, and the genera Diaea and Xysticus may not correspond to monophyletic groups. Here, we clarify the phylogenetic relationships of the four group-living Australian thomisids and conclude that amongst these subsociality has evolved two to three times independently. The subsocial Xysticus bimaculatus is not closely related to any of the social Diaea and an independent origin of subsociality is likely in this case. The presented data indicates that within Diaea two origins of subsociality are possible. Our results help to understand the evolution of sociality in thomisids and support the hypothesis that permanent sociality in spiders has evolved multiple times relatively recently from subsocial ancestors. Copyright © 2014 Elsevier Inc. All rights reserved.

Acid-sensing ion channels: trafficking and synaptic function.

PubMed

Zha, Xiang-ming

2013-01-02

Extracellular acidification occurs in the brain with elevated neural activity, increased metabolism, and neuronal injury. This reduction in pH can have profound effects on brain function because pH regulates essentially every single biochemical reaction. Therefore, it is not surprising to see that Nature evolves a family of proteins, the acid-sensing ion channels (ASICs), to sense extracellular pH reduction. ASICs are proton-gated cation channels that are mainly expressed in the nervous system. In recent years, a growing body of literature has shown that acidosis, through activating ASICs, contributes to multiple diseases, including ischemia, multiple sclerosis, and seizures. In addition, ASICs play a key role in fear and anxiety related psychiatric disorders. Several recent reviews have summarized the importance and therapeutic potential of ASICs in neurological diseases, as well as the structure-function relationship of ASICs. However, there is little focused coverage on either the basic biology of ASICs or their contribution to neural plasticity. This review will center on these topics, with an emphasis on the synaptic role of ASICs and molecular mechanisms regulating the spatial distribution and function of these ion channels.

Parallel evolution of sexual isolation in sticklebacks.

PubMed

Boughman, Janette Wenrick; Rundle, Howard D; Schluter, Dolph

2005-02-01

Mechanisms of speciation are not well understood, despite decades of study. Recent work has focused on how natural and sexual selection cause sexual isolation. Here, we investigate the roles of divergent natural and sexual selection in the evolution of sexual isolation between sympatric species of threespine sticklebacks. We test the importance of morphological and behavioral traits in conferring sexual isolation and examine to what extent these traits have diverged in parallel between multiple, independently evolved species pairs. We use the patterns of evolution in ecological and mating traits to infer the likely nature of selection on sexual isolation. Strong parallel evolution implicates ecologically based divergent natural and/or sexual selection, whereas arbitrary directionality implicates nonecological sexual selection or drift. In multiple pairs we find that sexual isolation arises in the same way: assortative mating on body size and asymmetric isolation due to male nuptial color. Body size and color have diverged in a strongly parallel manner, similar to ecological traits. The data implicate ecologically based divergent natural and sexual selection as engines of speciation in this group.

Survival, gene and metabolite responses of Litoria verreauxii alpina frogs to fungal disease chytridiomycosis

NASA Astrophysics Data System (ADS)

Grogan, Laura F.; Mulvenna, Jason; Gummer, Joel P. A.; Scheele, Ben C.; Berger, Lee; Cashins, Scott D.; McFadden, Michael S.; Harlow, Peter; Hunter, David A.; Trengove, Robert D.; Skerratt, Lee F.

2018-03-01

The fungal skin disease chytridiomycosis has caused the devastating decline and extinction of hundreds of amphibian species globally, yet the potential for evolving resistance, and the underlying pathophysiological mechanisms remain poorly understood. We exposed 406 naïve, captive-raised alpine tree frogs (Litoria verreauxii alpina) from multiple populations (one evolutionarily naïve to chytridiomycosis) to the aetiological agent Batrachochytrium dendrobatidis in two concurrent and controlled infection experiments. We investigated (A) survival outcomes and clinical pathogen burdens between populations and clutches, and (B) individual host tissue responses to chytridiomycosis. Here we present multiple interrelated datasets associated with these exposure experiments, including animal signalment, survival and pathogen burden of 355 animals from Experiment A, and the following datasets related to 61 animals from Experiment B: animal signalment and pathogen burden; raw RNA-Seq reads from skin, liver and spleen tissues; de novo assembled transcriptomes for each tissue type; raw gene expression data; annotation data for each gene; and raw metabolite expression data from skin and liver tissues. These data provide an extensive baseline for future analyses.

Who is 'who' in dissociation?: A plea for psychodynamics in a time of trauma.

PubMed

Gullestad, Siri Erika

2005-06-01

Contemporary theories of dissociation and trauma for the most part have evolved outside of psychoanalysis. Psychoanalytic writings have also been regarded as being in opposition to trauma-based notions of human psychopathology. The specific psychoanalytic contribution--the emphasis on unconscious conflict and meaning--is for the most part excluded from the discourse on dissociation, often resulting in a 'mechanic' conceptualisation of trauma. In this paper, based on clinical material, the author argues in favour of including conflict, unconscious intention and personal meaning in understanding the kind of dissociation we see in cases of multiple personality pathology. Textual analysis of letters written to the analyst illustrates how events of abuse are defensively elaborated. The author demonstrates that patterns of affect regulation and dominant object-relational strategies can be captured through analysis of the discourse structure. She focuses on how an organised character pattern, revealed mainly through narrative style and the analyst's countertransference, serves protective purposes as well as wish-fulfillment. She argues that dissociation in the form of multiple personalities may imply an active, strategic agent.

Modeling misidentification errors that result from use of genetic tags in capture-recapture studies

USGS Publications Warehouse

Yoshizaki, J.; Brownie, C.; Pollock, K.H.; Link, W.A.

2011-01-01

Misidentification of animals is potentially important when naturally existing features (natural tags) such as DNA fingerprints (genetic tags) are used to identify individual animals. For example, when misidentification leads to multiple identities being assigned to an animal, traditional estimators tend to overestimate population size. Accounting for misidentification in capture-recapture models requires detailed understanding of the mechanism. Using genetic tags as an example, we outline a framework for modeling the effect of misidentification in closed population studies when individual identification is based on natural tags that are consistent over time (non-evolving natural tags). We first assume a single sample is obtained per animal for each capture event, and then generalize to the case where multiple samples (such as hair or scat samples) are collected per animal per capture occasion. We introduce methods for estimating population size and, using a simulation study, we show that our new estimators perform well for cases with moderately high capture probabilities or high misidentification rates. In contrast, conventional estimators can seriously overestimate population size when errors due to misidentification are ignored. ?? 2009 Springer Science+Business Media, LLC.

Paternal epigenetic programming: evolving metabolic disease risk.

PubMed

Hur, Suzy S J; Cropley, Jennifer E; Suter, Catherine M

2017-04-01

Parental health or exposures can affect the lifetime health outcomes of offspring, independently of inherited genotypes. Such 'epigenetic' effects occur over a broad range of environmental stressors, including defects in parental metabolism. Although maternal metabolic effects are well documented, it has only recently been established that that there is also an independent paternal contribution to long-term metabolic health. Both paternal undernutrition and overnutrition can induce metabolic phenotypes in immediate offspring, and in some cases, the induced phenotype can affect multiple generations, implying inheritance of an acquired trait. The male lineage transmission of metabolic disease risk in these cases implicates a heritable factor carried by sperm. Sperm-based transmission provides a tractable system to interrogate heritable epigenetic factors influencing metabolism, and as detailed here, animal models of paternal programming have already provided some significant insights. Here, we review the evidence for paternal programming of metabolism in humans and animal models, and the available evidence on potential underlying mechanisms. Programming by paternal metabolism can be observed in multiple species across animal phyla, suggesting that this phenomenon may have a unique evolutionary significance. © 2017 Society for Endocrinology.

Suboptimal nutrient balancing despite dietary choice in glucose-averse German cockroaches, Blattella germanica.

PubMed

Jensen, Kim; Schal, Coby; Silverman, Jules

2015-10-01

Insects have evolved fine-tuned gustatory and post-ingestive physiological mechanisms that enable them to self-select an optimal composition of macronutrients. Their ability to forage optimally among multiple food sources and maximize fitness parameters depends on their ability not only to taste and perceive the nutritional value of potential foods but also to avoid deleterious components; the strength of such avoidance should reflect the severity of the perceived hazard. In German cockroaches (Blattella germanica), glucose aversion has evolved in some populations in response to anthropogenic selection with glucose-containing insecticidal baits. In four feeding treatments, we gave newly eclosed glucose-averse female cockroaches free choice to feed from two artificial, nutritionally complementary foods varying in protein and carbohydrate composition, with glucose or fructose as the sole carbohydrate source in either food. After 6days of feeding, we measured diet consumption and the length of basal oocytes as an estimate of sexual maturation. The females did not compromise on their aversion to glucose in order to balance their protein and carbohydrate intake, and experienced lower sexual maturation rates as a consequence. Nutrient specific hunger via feedback mechanisms, and adjustments to gustatory sensitivity thus do not override the deterrence of glucose, likely due to strong selection against ingesting even small amounts of toxin associated with glucose in baits. In the absence of baits, glucose aversion would be expected to incur a fitness cost compared to wild-type individuals due to lower overall food availability but also to larger difficulty in attaining a nutritionally balanced diet. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein–Protein Interactions

PubMed Central

Bartlett, Madelaine; Thompson, Beth; Brabazon, Holly; Del Gizzi, Robert; Zhang, Thompson; Whipple, Clinton

2016-01-01

Protein–protein interactions (PPIs) have widely acknowledged roles in the regulation of development, but few studies have addressed the timing and mechanism of shifting PPIs over evolutionary history. The B-class MADS-box transcription factors, PISTILLATA (PI) and APETALA3 (AP3) are key regulators of floral development. PI-like (PIL) and AP3-like (AP3L) proteins from a number of plants, including Arabidopsis thaliana (Arabidopsis) and the grass Zea mays (maize), bind DNA as obligate heterodimers. However, a PIL protein from the grass relative Joinvillea can bind DNA as a homodimer. To ascertain whether Joinvillea PIL homodimerization is an anomaly or indicative of broader trends, we characterized PIL dimerization across the Poales and uncovered unexpected evolutionary lability. Both obligate B-class heterodimerization and PIL homodimerization have evolved multiple times in the order, by distinct molecular mechanisms. For example, obligate B-class heterodimerization in maize evolved very recently from PIL homodimerization. A single amino acid change, fixed during domestication, is sufficient to toggle one maize PIL protein between homodimerization and obligate heterodimerization. We detected a signature of positive selection acting on residues preferentially clustered in predicted sites of contact between MADS-box monomers and dimers, and in motifs that mediate MADS PPI specificity in Arabidopsis. Changing one positively selected residue can alter PIL dimerization activity. Furthermore, ectopic expression of a Joinvillea PIL homodimer in Arabidopsis can homeotically transform sepals into petals. Our results provide a window into the evolutionary remodeling of PPIs, and show that novel interactions have the potential to alter plant form in a context-dependent manner. PMID:26908583

Helicobacter pylori oipA, vacA and dupA genetic diversity in individual hosts.

PubMed

Matteo, Mario José; Armitano, Rita Inés; Granados, Gabriela; Wonaga, Andrés Dario; Sánches, Christian; Olmos, Martín; Catalano, Mariana

2010-01-01

Helicobacter pylori putative virulence factors can undergo a continuously evolving mechanism as an approach to bacterial adaptation to the host changing environment during chronic infection. oipA, vacA and dupA genetic diversity among isolates from multiple biopsies (niches) from the antrum and corpus of 40 patients was investigated. A set of 229 isolates was examined. Direct DNA sequence analysis of amplified fragments was used to study oipA 'on/off' expression status as well as the presence of C or T insertion in jhp0917 that originates a continuous (jhp0917-jhp0918) dupA gene. vacA alleles were identified by multiplex PCR. Different inter-niches oipA CT repeat patterns were observed in nine patients; in six of these, 'on' and 'off' mixed patterns were found. In three of these nine patients, different vacA alleles were also observed in a single host. Inter-niche dupA differences involved the absence and presence of jhp0917 and/or jhp0918 or mutations in dupA, including those that may originate a non-functional gene, and they were also present in two patients with mixed oipA CT patterns and in another seven patients. Evidence of mixed infection was observed in two patients only. In conclusion, oipA and dupA genes showed similar inter-niche variability, occurring in approximately 1/4 patients. Conversely, vacA allele microevolution seemed to be a less common event, occurring in approximately 1/10 patients, probably due to the mechanism that this gene evolves 'in vivo'.

Genomewide investigation of adaptation to harmful algal blooms in common bottlenose dolphins (Tursiops truncatus).

PubMed

Cammen, Kristina M; Schultz, Thomas F; Rosel, Patricia E; Wells, Randall S; Read, Andrew J

2015-09-01

Harmful algal blooms (HABs), which can be lethal in marine species and cause illness in humans, are increasing worldwide. In the Gulf of Mexico, HABs of Karenia brevis produce neurotoxic brevetoxins that cause large-scale marine mortality events. The long history of such blooms, combined with the potentially severe effects of exposure, may have produced a strong selective pressure for evolved resistance. Advances in next-generation sequencing, in particular genotyping-by-sequencing, greatly enable the genomic study of such adaptation in natural populations. We used restriction site-associated DNA (RAD) sequencing to investigate brevetoxicosis resistance in common bottlenose dolphins (Tursiops truncatus). To improve our understanding of the epidemiology and aetiology of brevetoxicosis and the potential for evolved resistance in an upper trophic level predator, we sequenced pools of genomic DNA from dolphins sampled from both coastal and estuarine populations in Florida and during multiple HAB-associated mortality events. We sequenced 129 594 RAD loci and analysed 7431 single nucleotide polymorphisms (SNPs). The allele frequencies of many of these polymorphic loci differed significantly between live and dead dolphins. Some loci associated with survival showed patterns suggesting a common genetic-based mechanism of resistance to brevetoxins in bottlenose dolphins along the Gulf coast of Florida, but others suggested regionally specific mechanisms of resistance or reflected differences among HABs. We identified candidate genes that may be the evolutionary target for brevetoxin resistance by searching the dolphin genome for genes adjacent to survival-associated SNPs. © 2015 John Wiley & Sons Ltd.

Multiple Memory Systems Are Unnecessary to Account for Infant Memory Development: An Ecological Model

ERIC Educational Resources Information Center

Rovee-Collier, Carolyn; Cuevas, Kimberly

2009-01-01

How the memory of adults evolves from the memory abilities of infants is a central problem in cognitive development. The popular solution holds that the multiple memory systems of adults mature at different rates during infancy. The "early-maturing system" (implicit or nondeclarative memory) functions automatically from birth, whereas the…

Preliminary Screening Procedures and Criteria for Replacements for Halons 1211 and 1301

DTIC Science & Technology

1991-07-01

suppressants that meet current environmental and toxicological concerns. However, as the multiple and evolving performance constraints tighten, a new...massive trial-and-error study now may find suppressants that meet current environmental and toxicological concerns. However, as the multiple and...Extinguishment Concentration vs. Ratio of Linear Vapor Velocities, Elevated/hot ..................................................... 59 10. NIST PMMA Burner

Do siblings always form and evolve simultaneously? Testing the coevality of multiple protostellar systems through SEDs

NASA Astrophysics Data System (ADS)

Murillo, N. M.; van Dishoeck, E. F.; Tobin, J. J.; Fedele, D.

2016-07-01

Context. Multiplicity is common in field stars and among protostellar systems. Models suggest two paths of formation: turbulent fragmentation and protostellar disk fragmentation. Aims: We attempt to find whether or not the coevality frequency of multiple protostellar systems can help to better understand their formation mechanism. The coevality frequency is determined by constraining the relative evolutionary stages of the components in a multiple system. Methods: Spectral energy distributions (SEDs) for known multiple protostars in Perseus were constructed from literature data. Herschel PACS photometric maps were used to sample the peak of the SED for systems with separations ≥7″, a crucial aspect in determining the evolutionary stage of a protostellar system. Inclination effects and the surrounding envelope and outflows were considered to decouple source geometry from evolution. This together with the shape and derived properties from the SED was used to determine each system's coevality as accurately as possible. SED models were used to examine the frequency of non-coevality that is due to geometry. Results: We find a non-coevality frequency of 33 ± 10% from the comparison of SED shapes of resolved multiple systems. Other source parameters suggest a somewhat lower frequency of non-coevality. The frequency of apparent non-coevality that is due to random inclination angle pairings of model SEDs is 17 ± 0.5%. Observations of the outflow of resolved multiple systems do not suggest significant misalignments within multiple systems. Effects of unresolved multiples on the SED shape are also investigated. Conclusions: We find that one-third of the multiple protostellar systems sampled here are non-coeval, which is more than expected from random geometric orientations. The other two-thirds are found to be coeval. Higher order multiples show a tendency to be non-coeval. The frequency of non-coevality found here is most likely due to formation and enhanced by dynamical evolution.

Function and evolution of sex determination mechanisms, genes and pathways in insects

PubMed Central

Gempe, Tanja; Beye, Martin

2011-01-01

Animals have evolved a bewildering diversity of mechanisms to determine the two sexes. Studies of sex determination genes – their history and function – in non-model insects and Drosophila have allowed us to begin to understand the generation of sex determination diversity. One common theme from these studies is that evolved mechanisms produce activities in either males or females to control a shared gene switch that regulates sexual development. Only a few small-scale changes in existing and duplicated genes are sufficient to generate large differences in sex determination systems. This review summarises recent findings in insects, surveys evidence of how and why sex determination mechanisms can change rapidly and suggests fruitful areas of future research. PMID:21110346

Nonadiabatic one-electron transfer mechanism for the O-O bond formation in the oxygen-evolving complex of photosystem II

NASA Astrophysics Data System (ADS)

Shoji, Mitsuo; Isobe, Hiroshi; Shigeta, Yasuteru; Nakajima, Takahito; Yamaguchi, Kizashi

2018-04-01

The reaction mechanism of the O2 formation in the S4 state of the oxygen-evolving complex of photosystem II was clarified at the quantum mechanics/molecular mechanics (QM/MM) level. After the Yz (Y161) oxidation and the following proton transfer in the S3 state, five reaction steps are required to produce the molecular dioxygen. The highest barrier step is the first proton transfer reaction (0 → 1). The following reactions involving electron transfers were precisely analyzed in terms of their energies, structures and spin densities. We found that the one-electron transfer from the Mn4Ca cluster to Y161 triggers the O-O sigma bond formation.

Heat or cold priming-induced cross-tolerance to abiotic stresses in plants: key regulators and possible mechanisms.

PubMed

Hossain, Mohammad Anwar; Li, Zhong-Guang; Hoque, Tahsina Sharmin; Burritt, David J; Fujita, Masayuki; Munné-Bosch, Sergi

2018-01-01

Plants growing under field conditions are constantly exposed, either simultaneously or sequentially, to more than one abiotic stress factor. Plants have evolved sophisticated sensory systems to perceive a number of stress signals that allow them to activate the most adequate response to grow and survive in a given environment. Recently, cross-stress tolerance (i.e. tolerance to a second, strong stress after a different type of mild primary stress) has gained attention as a potential means of producing stress-resistant crops to aid with global food security. Heat or cold priming-induced cross-tolerance is very common in plants and often results from the synergistic co-activation of multiple stress signalling pathways, which involve reactive nitrogen species (RNS), reactive oxygen species (ROS), reactive carbonyl species (RCS), plant hormones and transcription factors. Recent studies have shown that the signalling functions of ROS, RNS and RCS, most particularly hydrogen peroxide, nitric oxide (NO) and methylglyoxal (MG), provide resistance to abiotic stresses and underpin cross-stress tolerance in plants by modulating the expression of genes as well as the post-translational modification of proteins. The current review highlights the key regulators and mechanisms underlying heat or cold priming-induced cross-stress tolerance in plants, with a focus on ROS, MG and NO signalling, as well as on the role of antioxidant and glyoxalase systems, osmolytes, heat-shock proteins (HSPs) and hormones. Our aim is also to provide a comprehensive idea on the topic for researchers using heat or cold priming-induced cross-tolerance as a mechanism to improve crop yields under multiple abiotic stresses.

Evolutionarily conserved mechanisms for the selection and maintenance of behavioural activity.

PubMed

Fiore, Vincenzo G; Dolan, Raymond J; Strausfeld, Nicholas J; Hirth, Frank

2015-12-19

Survival and reproduction entail the selection of adaptive behavioural repertoires. This selection manifests as phylogenetically acquired activities that depend on evolved nervous system circuitries. Lorenz and Tinbergen already postulated that heritable behaviours and their reliable performance are specified by genetically determined programs. Here we compare the functional anatomy of the insect central complex and vertebrate basal ganglia to illustrate their role in mediating selection and maintenance of adaptive behaviours. Comparative analyses reveal that central complex and basal ganglia circuitries share comparable lineage relationships within clusters of functionally integrated neurons. These clusters are specified by genetic mechanisms that link birth time and order to their neuronal identities and functions. Their subsequent connections and associated functions are characterized by similar mechanisms that implement dimensionality reduction and transition through attractor states, whereby spatially organized parallel-projecting loops integrate and convey sensorimotor representations that select and maintain behavioural activity. In both taxa, these neural systems are modulated by dopamine signalling that also mediates memory-like processes. The multiplicity of similarities between central complex and basal ganglia suggests evolutionarily conserved computational mechanisms for action selection. We speculate that these may have originated from ancestral ground pattern circuitries present in the brain of the last common ancestor of insects and vertebrates. © 2015 The Authors.

Evolutionarily conserved mechanisms for the selection and maintenance of behavioural activity

PubMed Central

Fiore, Vincenzo G.; Dolan, Raymond J.; Strausfeld, Nicholas J.; Hirth, Frank

2015-01-01

Survival and reproduction entail the selection of adaptive behavioural repertoires. This selection manifests as phylogenetically acquired activities that depend on evolved nervous system circuitries. Lorenz and Tinbergen already postulated that heritable behaviours and their reliable performance are specified by genetically determined programs. Here we compare the functional anatomy of the insect central complex and vertebrate basal ganglia to illustrate their role in mediating selection and maintenance of adaptive behaviours. Comparative analyses reveal that central complex and basal ganglia circuitries share comparable lineage relationships within clusters of functionally integrated neurons. These clusters are specified by genetic mechanisms that link birth time and order to their neuronal identities and functions. Their subsequent connections and associated functions are characterized by similar mechanisms that implement dimensionality reduction and transition through attractor states, whereby spatially organized parallel-projecting loops integrate and convey sensorimotor representations that select and maintain behavioural activity. In both taxa, these neural systems are modulated by dopamine signalling that also mediates memory-like processes. The multiplicity of similarities between central complex and basal ganglia suggests evolutionarily conserved computational mechanisms for action selection. We speculate that these may have originated from ancestral ground pattern circuitries present in the brain of the last common ancestor of insects and vertebrates. PMID:26554043

Multiple re-encounter approach to radical pair reactions and the role of nonlinear master equations.

PubMed

Clausen, Jens; Guerreschi, Gian Giacomo; Tiersch, Markus; Briegel, Hans J

2014-08-07

We formulate a multiple-encounter model of the radical pair mechanism that is based on a random coupling of the radical pair to a minimal model environment. These occasional pulse-like couplings correspond to the radical encounters and give rise to both dephasing and recombination. While this is in agreement with the original model of Haberkorn and its extensions that assume additional dephasing, we show how a nonlinear master equation may be constructed to describe the conditional evolution of the radical pairs prior to the detection of their recombination. We propose a nonlinear master equation for the evolution of an ensemble of independently evolving radical pairs whose nonlinearity depends on the record of the fluorescence signal. We also reformulate Haberkorn's original argument on the physicality of reaction operators using the terminology of quantum optics/open quantum systems. Our model allows one to describe multiple encounters within the exponential model and connects this with the master equation approach. We include hitherto neglected effects of the encounters, such as a separate dephasing in the triplet subspace, and predict potential new effects, such as Grover reflections of radical spins, that may be observed if the strength and time of the encounters can be experimentally controlled.

Multimodal signalling in estrildid finches: song, dance and colour are associated with different ecological and life-history traits.

PubMed

Gomes, A C R; Funghi, C; Soma, M; Sorenson, M D; Cardoso, G C

2017-07-01

Sexual traits (e.g. visual ornaments, acoustic signals, courtship behaviour) are often displayed together as multimodal signals. Some hypotheses predict joint evolution of different sexual signals (e.g. to increase the efficiency of communication) or that different signals trade off with each other (e.g. due to limited resources). Alternatively, multiple signals may evolve independently for different functions, or to communicate different information (multiple message hypothesis). We evaluated these hypotheses with a comparative study in the family Estrildidae, one of the largest songbird radiations, and one that includes many model species for research in sexual selection and communication. We found little evidence for either joint evolution or trade-offs between song and colour ornamentation. Some negative correlations between dance repertoire and song traits may suggest a functional compromise, but generally courtship dance also evolved independently from other signals. Instead of correlated evolution, we found that song, dance and colour are each related to different socio-ecological traits. Song complexity evolved together with ecological generalism, song performance with investment in reproduction, dance with commonness and habitat type, whereas colour ornamentation was shown previously to correlate mostly with gregariousness. We conclude that multimodal signals evolve in response to various socio-ecological traits, suggesting the accumulation of distinct signalling functions. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Disaggregating soil erosion processes within an evolving experimental landscape

USDA-ARS?s Scientific Manuscript database

Soil-mantled landscapes subjected to rainfall, runoff events, and downstream base level adjustments will erode and evolve in time and space. Yet the precise mechanisms for soil erosion also will vary, and such variations may not be adequately captured by soil erosion prediction technology. This st...

Proton movement and coupling in the POT family of peptide transporters

PubMed Central

Parker, Joanne L.; Li, Chenghan; Brinth, Allete; Wang, Zhi; Vogeley, Lutz; Solcan, Nicolae; Ledderboge-Vucinic, Gregory; Swanson, Jessica M. J.; Caffrey, Martin; Voth, Gregory A.

2017-01-01

POT transporters represent an evolutionarily well-conserved family of proton-coupled transport systems in biology. An unusual feature of the family is their ability to couple the transport of chemically diverse ligands to an inwardly directed proton electrochemical gradient. For example, in mammals, fungi, and bacteria they are predominantly peptide transporters, whereas in plants the family has diverged to recognize nitrate, plant defense compounds, and hormones. Although recent structural and biochemical studies have identified conserved sites of proton binding, the mechanism through which transport is coupled to proton movement remains enigmatic. Here we show that different POT transporters operate through distinct proton-coupled mechanisms through changes in the extracellular gate. A high-resolution crystal structure reveals the presence of ordered water molecules within the peptide binding site. Multiscale molecular dynamics simulations confirm proton transport occurs through these waters via Grotthuss shuttling and reveal that proton binding to the extracellular side of the transporter facilitates a reorientation from an inward- to outward-facing state. Together these results demonstrate that within the POT family multiple mechanisms of proton coupling have likely evolved in conjunction with variation of the extracellular gate. PMID:29180426

Proton movement and coupling in the POT family of peptide transporters.

PubMed

Parker, Joanne L; Li, Chenghan; Brinth, Allete; Wang, Zhi; Vogeley, Lutz; Solcan, Nicolae; Ledderboge-Vucinic, Gregory; Swanson, Jessica M J; Caffrey, Martin; Voth, Gregory A; Newstead, Simon

2017-12-12

POT transporters represent an evolutionarily well-conserved family of proton-coupled transport systems in biology. An unusual feature of the family is their ability to couple the transport of chemically diverse ligands to an inwardly directed proton electrochemical gradient. For example, in mammals, fungi, and bacteria they are predominantly peptide transporters, whereas in plants the family has diverged to recognize nitrate, plant defense compounds, and hormones. Although recent structural and biochemical studies have identified conserved sites of proton binding, the mechanism through which transport is coupled to proton movement remains enigmatic. Here we show that different POT transporters operate through distinct proton-coupled mechanisms through changes in the extracellular gate. A high-resolution crystal structure reveals the presence of ordered water molecules within the peptide binding site. Multiscale molecular dynamics simulations confirm proton transport occurs through these waters via Grotthuss shuttling and reveal that proton binding to the extracellular side of the transporter facilitates a reorientation from an inward- to outward-facing state. Together these results demonstrate that within the POT family multiple mechanisms of proton coupling have likely evolved in conjunction with variation of the extracellular gate. Copyright © 2017 the Author(s). Published by PNAS.

Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen Bartonella.

PubMed

Engel, Philipp; Salzburger, Walter; Liesch, Marius; Chang, Chao-Chin; Maruyama, Soichi; Lanz, Christa; Calteau, Alexandra; Lajus, Aurélie; Médigue, Claudine; Schuster, Stephan C; Dehio, Christoph

2011-02-10

Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens. Furthermore, our study highlights the remarkable evolvability of T4SSs and their effector proteins, explaining their broad application in bacterial interactions with the environment.

Parallel Evolution of a Type IV Secretion System in Radiating Lineages of the Host-Restricted Bacterial Pathogen Bartonella

PubMed Central

Engel, Philipp; Salzburger, Walter; Liesch, Marius; Chang, Chao-Chin; Maruyama, Soichi; Lanz, Christa; Calteau, Alexandra; Lajus, Aurélie; Médigue, Claudine; Schuster, Stephan C.; Dehio, Christoph

2011-01-01

Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens. Furthermore, our study highlights the remarkable evolvability of T4SSs and their effector proteins, explaining their broad application in bacterial interactions with the environment. PMID:21347280

Genetic and Genomic Architecture of the Evolution of Resistance to Antifungal Drug Combinations

PubMed Central

Hill, Jessica A.; Ammar, Ron; Torti, Dax; Nislow, Corey; Cowen, Leah E.

2013-01-01

The evolution of drug resistance in fungal pathogens compromises the efficacy of the limited number of antifungal drugs. Drug combinations have emerged as a powerful strategy to enhance antifungal efficacy and abrogate drug resistance, but the impact on the evolution of drug resistance remains largely unexplored. Targeting the molecular chaperone Hsp90 or its downstream effector, the protein phosphatase calcineurin, abrogates resistance to the most widely deployed antifungals, the azoles, which inhibit ergosterol biosynthesis. Here, we evolved experimental populations of the model yeast Saccharomyces cerevisiae and the leading human fungal pathogen Candida albicans with azole and an inhibitor of Hsp90, geldanamycin, or calcineurin, FK506. To recapitulate a clinical context where Hsp90 or calcineurin inhibitors could be utilized in combination with azoles to render resistant pathogens responsive to treatment, the evolution experiment was initiated with strains that are resistant to azoles in a manner that depends on Hsp90 and calcineurin. Of the 290 lineages initiated, most went extinct, yet 14 evolved resistance to the drug combination. Drug target mutations that conferred resistance to geldanamycin or FK506 were identified and validated in five evolved lineages. Whole-genome sequencing identified mutations in a gene encoding a transcriptional activator of drug efflux pumps, PDR1, and a gene encoding a transcriptional repressor of ergosterol biosynthesis genes, MOT3, that transformed azole resistance of two lineages from dependent on calcineurin to independent of this regulator. Resistance also arose by mutation that truncated the catalytic subunit of calcineurin, and by mutation in LCB1, encoding a sphingolipid biosynthetic enzyme. Genome analysis revealed extensive aneuploidy in four of the C. albicans lineages. Thus, we identify molecular determinants of the transition of azole resistance from calcineurin dependence to independence and establish multiple mechanisms by which resistance to drug combinations evolves, providing a foundation for predicting and preventing the evolution of drug resistance. PMID:23593013

The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families.

PubMed

Suplatov, Dmitry; Sharapova, Yana; Timonina, Daria; Kopylov, Kirill; Švedas, Vytas

2018-04-01

The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e.g. a substrate or a crystallographic water molecule), and long-range correlations, annotate and rank binding sites on the protein surface by the presence of statistically significant co-evolving positions. The results of the visualCMAT are organized for a convenient visual analysis and can be downloaded to a local computer as a content-rich all-in-one PyMol session file with multiple layers of annotation corresponding to bioinformatic, statistical and structural analyses of the predicted co-evolution, or further studied online using the built-in interactive analysis tools. The online interactivity is implemented in HTML5 and therefore neither plugins nor Java are required. The visualCMAT web-server is integrated with the Mustguseal web-server capable of constructing large structure-guided sequence alignments of protein families and superfamilies using all available information about their structures and sequences in public databases. The visualCMAT web-server can be used to understand the relationship between structure and function in proteins, implemented at selecting hotspots and compensatory mutations for rational design and directed evolution experiments to produce novel enzymes with improved properties, and employed at studying the mechanism of selective ligand's binding and allosteric communication between topologically independent sites in protein structures. The web-server is freely available at https://biokinet.belozersky.msu.ru/visualcmat and there are no login requirements.

Effortful Control, Explicit Processing, and the Regulation of Human Evolved Predispositions

ERIC Educational Resources Information Center

MacDonald, Kevin B.

2008-01-01

This article analyzes the effortful control of automatic processing related to social and emotional behavior, including control over evolved modules designed to solve problems of survival and reproduction that were recurrent over evolutionary time. The inputs to effortful control mechanisms include a wide range of nonrecurrent…

The burden of proof: The current state of atrial fibrillation prevention and treatment trials

PubMed Central

Zakeri, Rosita; Van Wagoner, David R.; Calkins, Hugh; Wong, Tom; Ross, Heather M.; Heist, E. Kevin; Meyer, Timothy E.; Kowey, Peter R.; Mentz, Robert J.; Cleland, John G.; Pitt, Bertram; Zannad, Faiez; Linde, Cecilia

2017-01-01

Atrial fibrillation (AF) is an age-related arrhythmia of enormous socioeconomic significance. In recent years, our understanding of the basic mechanisms that initiate and perpetuate AF has evolved rapidly, catheter ablation of AF has progressed from concept to reality, and recent studies suggest lifestyle modification may help prevent AF recurrence. Emerging developments in genetics, imaging, and informatics also present new opportunities for personalized care. However, considerable challenges remain. These include a paucity of studies examining AF prevention, modest efficacy of existing antiarrhythmic therapies, diverse ablation technologies and practice, and limited evidence to guide management of high-risk patients with multiple comorbidities. Studies examining the long-term effects of AF catheter ablation on morbidity and mortality outcomes are not yet completed. In many ways, further progress in the field is heavily contingent on the feasibility, capacity, and efficiency of clinical trials to incorporate the rapidly evolving knowledge base and to provide substantive evidence for novel AF therapeutic strategies. This review outlines the current state of AF prevention and treatment trials, including the foreseeable challenges, as discussed by a unique forum of clinical trialists, scientists, and regulatory representatives in a session endorsed by the Heart Rhythm Society at the 12th Global CardioVascular Clinical Trialists Forum in Washington, DC, December 3–5, 2015. PMID:28161513

Heritability of female extra-pair paternity rate in song sparrows (Melospiza melodia)

PubMed Central

Reid, Jane M.; Arcese, Peter; Sardell, Rebecca J.; Keller, Lukas F.

2011-01-01

The forces driving the evolution of extra-pair reproduction in socially monogamous animals remain widely debated and unresolved. One key hypothesis is that female extra-pair reproduction evolves through indirect genetic benefits, reflecting increased additive genetic value of extra-pair offspring. Such evolution requires that a female's propensity to produce offspring that are sired by an extra-pair male is heritable. However, additive genetic variance and heritability in female extra-pair paternity (EPP) rate have not been quantified, precluding accurate estimation of the force of indirect selection. Sixteen years of comprehensive paternity and pedigree data from socially monogamous but genetically polygynandrous song sparrows (Melospiza melodia) showed significant additive genetic variance and heritability in the proportion of a female's offspring that was sired by an extra-pair male, constituting major components of the genetic architecture required for extra-pair reproduction to evolve through indirect additive genetic benefits. However, estimated heritabilities were moderately small (0.12 and 0.18 on the observed and underlying latent scales, respectively). The force of selection on extra-pair reproduction through indirect additive genetic benefits may consequently be relatively weak. However, the additive genetic variance and non-zero heritability observed in female EPP rate allow for multiple further genetic mechanisms to drive and constrain mating system evolution. PMID:20980302

Reduced birth intervals following the birth of children with long-term illness: evidence supporting a conditional evolved response.

PubMed

Waynforth, David

2015-10-01

Human birth interval length is indicative of the level of parental investment that a child will receive: a short interval following birth means that parental resources must be split with a younger sibling during a period when the older sibling remains highly dependent on their parents. From a life-history theoretical perspective, it is likely that there are evolved mechanisms that serve to maximize fitness depending on context. One context that would be expected to result in short birth intervals, and lowered parental investment, is after a child with low expected fitness is born. Here, data drawn from a longitudinal British birth cohort study were used to test whether birth intervals were shorter following the birth of a child with a long-term health problem. Data on the timing of 4543 births were analysed using discrete-time event history analysis. The results were consistent with the hypothesis: birth intervals were shorter following the birth of a child diagnosed by a medical professional with a severe but non-fatal medical condition. Covariates in the analysis were also significantly associated with birth interval length: births of twins or multiple births, and relationship break-up were associated with significantly longer birth intervals. © 2015 The Author(s).

Improving the Transparency of IAEA Safeguards Reporting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toomey, Christopher; Hayman, Aaron M.; Wyse, Evan T.

2011-07-17

In 2008, the Standing Advisory Group on Safeguards Implementation (SAGSI) indicated that the International Atomic Energy Agency's (IAEA) Safeguards Implementation Report (SIR) has not kept pace with the evolution of safeguards and provided the IAEA with a set of recommendations for improvement. The SIR is the primary mechanism for providing an overview of safeguards implementation in a given year and reporting on the annual safeguards findings and conclusions drawn by the Secretariat. As the IAEA transitions to State-level safeguards approaches, SIR reporting must adapt to reflect these evolutionary changes. This evolved report will better reflect the IAEA's transition to amore » more qualitative and information-driven approach, based upon State-as-a-whole considerations. This paper applies SAGSI's recommendations to the development of multiple models for an evolved SIR and finds that an SIR repurposed as a 'safeguards portal' could significantly enhance information delivery, clarity, and transparency. In addition, this paper finds that the 'portal concept' also appears to have value as a standardized information presentation and analysis platform for use by Country Officers, for continuity of knowledge purposes, and the IAEA Secretariat in the safeguards conclusion process. Accompanying this paper is a fully functional prototype of the 'portal' concept, built using commercial software and IAEA Annual Report data.« less

High food abundance permits the evolution of placentotrophy: evidence from a placental lizard, Pseudemoia entrecasteauxii.

PubMed

Van Dyke, James U; Griffith, Oliver W; Thompson, Michael B

2014-08-01

Mechanisms of reproductive allocation are major determinants of fitness because embryos cannot complete development without receiving sufficient nutrition from their parents. The nourishment of offspring via placentas (placentotrophy) has evolved repeatedly in vertebrates, including multiple times in squamate reptiles (lizards and snakes). Placentotrophy has been suggested to evolve only if food is sufficiently abundant throughout gestation to allow successful embryogenesis. If scarcity of food prevents successful embryogenesis, females should recoup nutrients allocated to embryos via abortion, reabsorption, and/or cannibalism. We tested these hypotheses in the placentotrophic southern grass skink Pseudemoia entrecasteauxii. We fed females one of four diets (high constant, high variable, low constant, and low variable) during gestation and tested the effects of both food amount and schedule of feeding on developmental success, cannibalism rate, placental nutrient transport, offspring size, and maternal growth and body condition. Low food availability reduced developmental success, placental nutrient transport, offspring size, and maternal growth and body condition. Cannibalism of offspring also increased when food was scarce. Schedule of feeding did not affect offspring or mothers. We suggest that high food abundance and ability to abort and cannibalize poor-quality offspring are permissive factors necessary for placentotrophy to be a viable strategy of reproductive allocation.

Dynamic Neurovascular Coupling and Uncoupling during Ictal Onset, Propagation, and Termination Revealed by Simultaneous In Vivo Optical Imaging of Neural Activity and Local Blood Volume

PubMed Central

Zhao, Mingrui; Schwartz, Theodore H.

2013-01-01

Traditional models of ictal propagation involve the concept of an initiation site and a progressive outward march of activation. The process of neurovascular coupling, whereby the brain supplies oxygenated blood to metabolically active neurons presumably results in a similar outward cascade of hyperemia. However, ictal neurovascular coupling has never been assessed in vivo using simultaneous measurements of membrane potential change and hyperemia with wide spatial sampling. In an acute rat ictal model, using simultaneous intrinsic optical signal (IOS) and voltage-sensitive dye (VSD) imaging of cerebral blood volume and membrane potential changes, we demonstrate that seizures consist of multiple dynamic multidirectional waves of membrane potential change with variable onset sites that spread through a widespread network. Local blood volume evolves on a much slower spatiotemporal scale. At seizure onset, the VSD waves extend beyond the IOS signal. During evolution, spatial correlation with hemodynamic signal only exists briefly at the maximal spread of the VSD signal. At termination, the IOS signal extends spatially and temporally beyond the VSD waves. Hence, vascular reactivity evolves in a separate but parallel fashion to membrane potential changes resulting in a mechanism of neurovascular coupling and uncoupling, which is as dynamic as the seizure itself. PMID:22499798

Adaptive evolution of baker's yeast in a dough‐like environment enhances freeze and salinity tolerance

PubMed Central

Aguilera, Jaime; Andreu, Pasqual; Randez‐Gil, Francisca; Prieto, Jose Antonio

2010-01-01

Summary We used adaptive evolution to improve freeze tolerance of industrial baker's yeast. Our hypothesis was that adaptation to low temperature is accompanied by enhanced resistance of yeast to freezing. Based on this hypothesis, yeast was propagated in a flour‐free liquid dough model system, which contained sorbitol and NaCl, by successive batch refreshments maintained constantly at 12°C over at least 200 generations. Relative to the parental population, the maximal growth rate (µmax) under the restrictive conditions, increased gradually over the time course of the experiment. This increase was accompanied by enhanced freeze tolerance. However, these changes were not the consequence of genetic adaptation to low temperature, a fact that was confirmed by prolonged selection of yeast cells in YPD at 12°C. Instead, the experimental populations showed a progressive increase in NaCl tolerance. This phenotype was likely achieved at the expense of others traits, since evolved cells showed a ploidy reduction, a defect in the glucose derepression mechanism and a loss in their ability to utilize gluconeogenic carbon sources. We discuss the genetic flexibility of S. cerevisiae in terms of adaptation to the multiple constraints of the experimental design applied to drive adaptive evolution and the technologically advantageous phenotype of the evolved population. PMID:21255321

Evolution and Reconstruction of Learning Cities for Sustainable Actions

ERIC Educational Resources Information Center

Watson, Connie; Wu, Aimee Tiu

2015-01-01

This chapter describes how the concept of learning cities evolved from the "learning society" and the lifelong education and learning movements, and advances multiple forms of communities of learning.

MULTIPLICATION OF DIFFERENT VIRUSES AND EVOLUTION OF VIRAL INFECTION IN CELLULAR CULTURES EXPOSED TO THE ACTION OF HEAVY WATER (in French)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lavillaureix, J.; Reeb, E.; Surjus, A.

1961-03-20

The multiplication of West Nile, Coxsackie B3, and polio type II viruses is considerably increased if they are inoculated on cells cultivated in the presence of heavy water 5 hr before inoculation. The viral infection can not evolve in the presence of heavy water. (tr-auth)

Plant-bacterial pathogen interactions mediated by type III effectors.

PubMed

Feng, Feng; Zhou, Jian-Min

2012-08-01

Effectors secreted by the bacterial type III system play a central role in the interaction between Gram-negative bacterial pathogens and their host plants. Recent advances in the effector studies have helped cementing several key concepts concerning bacterial pathogenesis, plant immunity, and plant-pathogen co-evolution. Type III effectors use a variety of biochemical mechanisms to target specific host proteins or DNA for pathogenesis. The identifications of their host targets led to the identification of novel components of plant innate immune system. Key modules of plant immune signaling pathways such as immune receptor complexes and MAPK cascades have emerged as a major battle ground for host-pathogen adaptation. These modules are attacked by multiple type III effectors, and some components of these modules have evolved to actively sense the effectors and trigger immunity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Time-resolved spectroscopy at surfaces and adsorbate dynamics: Insights from a model-system approach

NASA Astrophysics Data System (ADS)

Boström, Emil; Mikkelsen, Anders; Verdozzi, Claudio

2016-05-01

We introduce a model description of femtosecond laser induced desorption at surfaces. The substrate part of the system is taken into account as a (possibly semi-infinite) linear chain. Here, being especially interested in the early stages of dissociation, we consider a finite-size implementation of the model (i.e., a finite substrate), for which an exact numerical solution is possible. By time-evolving the many-body wave function, and also using results from a time-dependent density functional theory description for electron-nuclear systems, we analyze the competition between several surface-response mechanisms and electronic correlations in the transient and longer time dynamics under the influence of dipole-coupled fields. Our model allows us to explore how coherent multiple-pulse protocols can impact desorption in a variety of prototypical experiments.

Adaptively biased molecular dynamics: An umbrella sampling method with a time-dependent potential

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Karpusenka, Vadzim; Moradi, Mahmoud; Roland, Christopher; Sagui, Celeste

We discuss an adaptively biased molecular dynamics (ABMD) method for the computation of a free energy surface for a set of reaction coordinates. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential. It is characterized by a small number of control parameters and an O(t) numerical cost with simulation time t. The method naturally allows for extensions based on multiple walkers and replica exchange mechanism. The workings of the method are illustrated with a number of examples, including sugar puckering, and free energy landscapes for polymethionine and polyproline peptides, and for a short β-turn peptide. ABMD has been implemented into the latest version (Case et al., AMBER 10; University of California: San Francisco, 2008) of the AMBER software package and is freely available to the simulation community.

Multiple tolerances dilute the second order cooperative dilemma

NASA Astrophysics Data System (ADS)

Sui, Xiukai; Wu, Bin; Wang, Long

2017-12-01

A peer punisher directly imposes fines upon defectors at a cost to himself. It is one of the mechanisms promoting cooperation, which is ubiquitous in nature. Typically, it is assumed that a peer punisher punishes provided that there is one defector in the group. The threshold that triggers punishment, however, is not necessarily one. The larger the threshold is, the more tolerant the peer punisher is. We study the evolutionary dynamics of those diverse tolerant peer punishment strategies in public goods game. We find that, i) less tolerant punishers prevail over tolerant ones; ii) large group size could enhance punishment, in contrast with the case in the first-order cooperative dilemma. Our analytical results are based on weak selection limit and large population size, which are verified by simulations. Our work sheds light on how punishment of diverse tolerance evolves.

Mars Exploration Zones

NASA Image and Video Library

2015-12-22

This concept animation shows just one of many potential concepts for how the first human landing site on Mars might evolve throughout the course of multiple human expeditions to the Red Planet over a decade or more.

Sexual Harassment by Males Reduces Female Fecundity in the Alfalfa Leafcutting Bee (Megachile rotundata)

USDA-ARS?s Scientific Manuscript database

Under sexual conflict, males evolve traits to increase their mating and reproductive success that impose costs on females. Females evolve counter-adaptations to resist males and reduce those costs. Female resistance may instead serve as a mechanism for mate choice if the male-imposed costs are outwe...

Transistor Level Circuit Experiments using Evolvable Hardware

NASA Technical Reports Server (NTRS)

Stoica, A.; Zebulum, R. S.; Keymeulen, D.; Ferguson, M. I.; Daud, Taher; Thakoor, A.

2005-01-01

The Jet Propulsion Laboratory (JPL) performs research in fault tolerant, long life, and space survivable electronics for the National Aeronautics and Space Administration (NASA). With that focus, JPL has been involved in Evolvable Hardware (EHW) technology research for the past several years. We have advanced the technology not only by simulation and evolution experiments, but also by designing, fabricating, and evolving a variety of transistor-based analog and digital circuits at the chip level. EHW refers to self-configuration of electronic hardware by evolutionary/genetic search mechanisms, thereby maintaining existing functionality in the presence of degradations due to aging, temperature, and radiation. In addition, EHW has the capability to reconfigure itself for new functionality when required for mission changes or encountered opportunities. Evolution experiments are performed using a genetic algorithm running on a DSP as the reconfiguration mechanism and controlling the evolvable hardware mounted on a self-contained circuit board. Rapid reconfiguration allows convergence to circuit solutions in the order of seconds. The paper illustrates hardware evolution results of electronic circuits and their ability to perform under 230 C temperature as well as radiations of up to 250 kRad.

New Measurement for Correlation of Co-evolution Relationship of Subsequences in Protein.

PubMed

Gao, Hongyun; Yu, Xiaoqing; Dou, Yongchao; Wang, Jun

2015-12-01

Many computational tools have been developed to measure the protein residues co-evolution. Most of them only focus on co-evolution for pairwise residues in a protein sequence. However, number of residues participate in co-evolution might be multiple. And some co-evolved residues are clustered in several distinct regions in primary structure. Therefore, the co-evolution among the adjacent residues and the correlation between the distinct regions offer insights into function and evolution of the protein and residues. Subsequence is used to represent the adjacent multiple residues in one distinct region. In the paper, co-evolution relationship in each subsequence is represented by mutual information matrix (MIM). Then, Pearson's correlation coefficient: R value is developed to measure the similarity correlation of two MIMs. MSAs from Catalytic Data Base (Catalytic Site Atlas, CSA) are used for testing. R value characterizes a specific class of residues. In contrast to individual pairwise co-evolved residues, adjacent residues without high individual MI values are found since the co-evolved relationship among them is similar to that among another set of adjacent residues. These subsequences possess some flexibility in the composition of side chains, such as the catalyzed environment.

Insights from genomic comparisons of genetically monomorphic bacterial pathogens

PubMed Central

Achtman, Mark

2012-01-01

Some of the most deadly bacterial diseases, including leprosy, anthrax and plague, are caused by bacterial lineages with extremely low levels of genetic diversity, the so-called ‘genetically monomorphic bacteria’. It has only become possible to analyse the population genetics of such bacteria since the recent advent of high-throughput comparative genomics. The genomes of genetically monomorphic lineages contain very few polymorphic sites, which often reflect unambiguous clonal genealogies. Some genetically monomorphic lineages have evolved in the last decades, e.g. antibiotic-resistant Staphylococcus aureus, whereas others have evolved over several millennia, e.g. the cause of plague, Yersinia pestis. Based on recent results, it is now possible to reconstruct the sources and the history of pandemic waves of plague by a combined analysis of phylogeographic signals in Y. pestis plus polymorphisms found in ancient DNA. Different from historical accounts based exclusively on human disease, Y. pestis evolved in China, or the vicinity, and has spread globally on multiple occasions. These routes of transmission can be reconstructed from the genealogy, most precisely for the most recent pandemic that was spread from Hong Kong in multiple independent waves in 1894. PMID:22312053

Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing

PubMed Central

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-01-01

ABSTRACT Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure. PMID:28277933

Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing.

PubMed

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-10-03

Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure.

Plastic and evolutionary responses to climate change in fish

PubMed Central

Crozier, Lisa G; Hutchings, Jeffrey A

2014-01-01

The physical and ecological ‘fingerprints’ of anthropogenic climate change over the past century are now well documented in many environments and taxa. We reviewed the evidence for phenotypic responses to recent climate change in fish. Changes in the timing of migration and reproduction, age at maturity, age at juvenile migration, growth, survival and fecundity were associated primarily with changes in temperature. Although these traits can evolve rapidly, only two studies attributed phenotypic changes formally to evolutionary mechanisms. The correlation-based methods most frequently employed point largely to ‘fine-grained’ population responses to environmental variability (i.e. rapid phenotypic changes relative to generation time), consistent with plastic mechanisms. Ultimately, many species will likely adapt to long-term warming trends overlaid on natural climate oscillations. Considering the strong plasticity in all traits studied, we recommend development and expanded use of methods capable of detecting evolutionary change, such as the long term study of selection coefficients and temporal shifts in reaction norms, and increased attention to forecasting adaptive change in response to the synergistic interactions of the multiple selection pressures likely to be associated with climate change. PMID:24454549

Mechanism-based post-translational modification and inactivation in terpene synthases

DOE PAGES

Kersten, Roland D.; Diedrich, Jolene K.; Yates, III, John R.; ...

2015-09-17

Terpenes are ubiquitous natural chemicals with diverse biological functions spanning all three domains of life. In specialized metabolism, the active sites of terpene synthases (TPSs) evolve in shape and reactivity to direct the biosynthesis of a myriad of chemotypes for organismal fitness. As most terpene biosynthesis mechanistically involves highly reactive carbocationic intermediates, the protein surfaces catalyzing these cascade reactions possess reactive regions possibly prone to premature carbocation capture and potentially enzyme inactivation. Here, we show using proteomic and X-ray crystallographic analyses that cationic intermediates undergo capture by conserved active site residues leading to inhibitory self-alkylation. Furthermore, the level of cation-mediatedmore » inactivation increases with mutation of the active site, upon changes in the size and structure of isoprenoid diphosphate substrates, and alongside increases in reaction temperatures. TPSs that individually synthesize multiple products are less prone to self-alkylation then TPSs possessing relatively high product specificity. In total, the results presented suggest that mechanism-based alkylation represents an overlooked mechanistic pressure during the evolution of cation-derived terpene biosynthesis.« less

Effects of the Ordering of Natural Selection and Population Regulation Mechanisms on Wright-Fisher Models

PubMed Central

He, Zhangyi; Beaumont, Mark; Yu, Feng

2017-01-01

We explore the effect of different mechanisms of natural selection on the evolution of populations for one- and two-locus systems. We compare the effect of viability and fecundity selection in the context of the Wright-Fisher model with selection under the assumption of multiplicative fitness. We show that these two modes of natural selection correspond to different orderings of the processes of population regulation and natural selection in the Wright-Fisher model. We find that under the Wright-Fisher model these two different orderings can affect the distribution of trajectories of haplotype frequencies evolving with genetic recombination. However, the difference in the distribution of trajectories is only appreciable when the population is in significant linkage disequilibrium. We find that as linkage disequilibrium decays the trajectories for the two different models rapidly become indistinguishable. We discuss the significance of these findings in terms of biological examples of viability and fecundity selection, and speculate that the effect may be significant when factors such as gene migration maintain a degree of linkage disequilibrium. PMID:28500051

Multiple mechanisms of MYCN dysregulation in Wilms tumour

PubMed Central

Williams, Richard D.; Chagtai, Tasnim; Alcaide-German, Marisa; Apps, John; Wegert, Jenny; Popov, Sergey; Vujanic, Gordan; van Tinteren, Harm; van den Heuvel-Eibrink, Marry M.; Kool, Marcel; de Kraker, Jan; Gisselsson, David; Graf, Norbert; Gessler, Manfred; Pritchard-Jones, Kathy

2015-01-01

Genomic gain of the proto-oncogene transcription factor gene MYCN is associated with poor prognosis in several childhood cancers. Here we present a comprehensive copy number analysis of MYCN in Wilms tumour (WT), demonstrating that gain of this gene is associated with anaplasia and with poorer relapse-free and overall survival, independent of histology. Using whole exome and gene-specific sequencing, together with methylation and expression profiling, we show that MYCN is targeted by other mechanisms, including a recurrent somatic mutation, P44L, and specific DNA hypomethylation events associated with MYCN overexpression in tumours with high risk histologies. We describe parallel evolution of genomic copy number gain and point mutation of MYCN in the contralateral tumours of a remarkable bilateral case in which independent contralateral mutations of TP53 also evolve over time. We report a second bilateral case in which MYCN gain is a germline aberration. Our results suggest a significant role for MYCN dysregulation in the molecular biology of Wilms tumour. We conclude that MYCN gain is prognostically significant, and suggest that the novel P44L somatic variant is likely to be an activating mutation. PMID:25749049

Herpes simplex virus-1 infection causes the secretion of a type I interferon-antagonizing protein and inhibits signaling at or before Jak-1 activation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Karen E.; Knipe, David M., E-mail: david_knipe@hms.harvard.ed

2010-01-05

Host cells respond to viral infection by the production of type I interferons (IFNs), which induce the expression of antiviral genes. Herpes simplex virus I (HSV-1) encodes many mechanisms that inhibit the type I IFN response, including the ICP27-dependent inhibition of type I IFN signaling. Here we show inhibition of Stat-1 nuclear accumulation in cells that express ICP27. ICP27 expression also induces the secretion of a small, heat-stable type I IFN antagonizing protein that inhibits Stat-1 nuclear accumulation. We show that the inhibition of IFN-induced Stat-1 phosphorylation occurs at or upstream of Jak-1 phosphorylation. Finally, we show that ISG15 expressionmore » is induced after IFNalpha treatment in mock-infected cells, but not cells infected with WT HSV-1 or ICP27{sup -} HSV-1. These data suggest that HSV-1 has evolved multiple mechanisms to inhibit IFN signaling not only in infected cells, but also in neighboring cells, thereby allowing for increased viral replication and spread.« less

Fluorescence Reporter-Based Genome-Wide RNA Interference Screening to Identify Alternative Splicing Regulators.

PubMed

Misra, Ashish; Green, Michael R

2017-01-01

Alternative splicing is a regulated process that leads to inclusion or exclusion of particular exons in a pre-mRNA transcript, resulting in multiple protein isoforms being encoded by a single gene. With more than 90 % of human genes known to undergo alternative splicing, it represents a major source for biological diversity inside cells. Although in vitro splicing assays have revealed insights into the mechanisms regulating individual alternative splicing events, our global understanding of alternative splicing regulation is still evolving. In recent years, genome-wide RNA interference (RNAi) screening has transformed biological research by enabling genome-scale loss-of-function screens in cultured cells and model organisms. In addition to resulting in the identification of new cellular pathways and potential drug targets, these screens have also uncovered many previously unknown mechanisms regulating alternative splicing. Here, we describe a method for the identification of alternative splicing regulators using genome-wide RNAi screening, as well as assays for further validation of the identified candidates. With modifications, this method can also be adapted to study the splicing regulation of pre-mRNAs that contain two or more splice isoforms.

Fitness consequences of parental compatibility in the frog Crinia georgiana.

PubMed

Dziminski, Martin A; Roberts, J Dale; Simmons, Leigh W

2008-04-01

Theory suggests that multiple mating by females can evolve as a mechanism for acquiring compatible genes that promote offspring fitness. Genetic compatibility models predict that differences in fitness among offspring arise from interactions between male and female haplotypes. Using a cross-classified breeding design and in vitro fertilization, we raised families of maternal and paternal half-siblings of the frog Crinia georgiana, a species with a polyandrous breeding system and external fertilization. After controlling for variation in maternal provisioning, we found significant effects of interacting parental haplotypes on fertilization success, and nonadditive genetic effects on measures of offspring fitness such as embryo survival, and survival to, size at, and time to metamorphosis. Additive genetic variation due to males and females was negligible, and not statistically significant for any of the fitness traits measured. Combinations of parental haplotypes that resulted in high rates of fertilization produced offspring with higher embryo survival and rapid juvenile development. We suggest that a gamete recognition mechanism for selective fertilization by compatible sperm may promote offspring fitness in this system.

Phylogenetic context determines the role of competition in adaptive radiation

PubMed Central

Tan, Jiaqi; Slattery, Matthew R.; Yang, Xian; Jiang, Lin

2016-01-01

Understanding ecological mechanisms regulating the evolution of biodiversity is of much interest to ecologists and evolutionary biologists. Adaptive radiation constitutes an important evolutionary process that generates biodiversity. Competition has long been thought to influence adaptive radiation, but the directionality of its effect and associated mechanisms remain ambiguous. Here, we report a rigorous experimental test of the role of competition on adaptive radiation using the rapidly evolving bacterium Pseudomonas fluorescens SBW25 interacting with multiple bacterial species that differed in their phylogenetic distance to the diversifying bacterium. We showed that the inhibitive effect of competitors on the adaptive radiation of P. fluorescens decreased as their phylogenetic distance increased. To explain this phylogenetic dependency of adaptive radiation, we linked the phylogenetic distance between P. fluorescens and its competitors to their niche and competitive fitness differences. Competitive fitness differences, which showed weak phylogenetic signal, reduced P. fluorescens abundance and thus diversification, whereas phylogenetically conserved niche differences promoted diversification. These results demonstrate the context dependency of competitive effects on adaptive radiation, and highlight the importance of past evolutionary history for ongoing evolutionary processes. PMID:27335414

Plastic and evolutionary responses to climate change in fish.

PubMed

Crozier, Lisa G; Hutchings, Jeffrey A

2014-01-01

The physical and ecological 'fingerprints' of anthropogenic climate change over the past century are now well documented in many environments and taxa. We reviewed the evidence for phenotypic responses to recent climate change in fish. Changes in the timing of migration and reproduction, age at maturity, age at juvenile migration, growth, survival and fecundity were associated primarily with changes in temperature. Although these traits can evolve rapidly, only two studies attributed phenotypic changes formally to evolutionary mechanisms. The correlation-based methods most frequently employed point largely to 'fine-grained' population responses to environmental variability (i.e. rapid phenotypic changes relative to generation time), consistent with plastic mechanisms. Ultimately, many species will likely adapt to long-term warming trends overlaid on natural climate oscillations. Considering the strong plasticity in all traits studied, we recommend development and expanded use of methods capable of detecting evolutionary change, such as the long term study of selection coefficients and temporal shifts in reaction norms, and increased attention to forecasting adaptive change in response to the synergistic interactions of the multiple selection pressures likely to be associated with climate change.

Ribonuclease E modulation of the bacterial SOS response.

PubMed

Manasherob, Robert; Miller, Christine; Kim, Kwang-sun; Cohen, Stanley N

2012-01-01

Plants, animals, bacteria, and Archaea all have evolved mechanisms to cope with environmental or cellular stress. Bacterial cells respond to the stress of DNA damage by activation of the SOS response, the canonical RecA/LexA-dependent signal transduction pathway that transcriptionally derepresses a multiplicity of genes-leading to transient arrest of cell division and initiation of DNA repair. Here we report the previously unsuspected role of E. coli endoribonuclease RNase E in regulation of the SOS response. We show that RNase E deletion or inactivation of temperature-sensitive RNase E protein precludes normal initiation of SOS. The ability of RNase E to regulate SOS is dynamic, as down regulation of RNase E following DNA damage by mitomycin C resulted in SOS termination and restoration of RNase E function leads to resumption of a previously aborted response. Overexpression of the RraA protein, which binds to the C-terminal region of RNase E and modulates the actions of degradosomes, recapitulated the effects of RNase E deficiency. Possible mechanisms for RNase E effects on SOS are discussed.

Ribonuclease E Modulation of the Bacterial SOS Response

PubMed Central

Manasherob, Robert; Miller, Christine; Kim, Kwang-sun; Cohen, Stanley N.

2012-01-01

Plants, animals, bacteria, and Archaea all have evolved mechanisms to cope with environmental or cellular stress. Bacterial cells respond to the stress of DNA damage by activation of the SOS response, the canonical RecA/LexA-dependent signal transduction pathway that transcriptionally derepresses a multiplicity of genes–leading to transient arrest of cell division and initiation of DNA repair. Here we report the previously unsuspected role of E. coli endoribonuclease RNase E in regulation of the SOS response. We show that RNase E deletion or inactivation of temperature-sensitive RNase E protein precludes normal initiation of SOS. The ability of RNase E to regulate SOS is dynamic, as down regulation of RNase E following DNA damage by mitomycin C resulted in SOS termination and restoration of RNase E function leads to resumption of a previously aborted response. Overexpression of the RraA protein, which binds to the C-terminal region of RNase E and modulates the actions of degradosomes, recapitulated the effects of RNase E deficiency. Possible mechanisms for RNase E effects on SOS are discussed. PMID:22719885

Iridescent colour production in hairs of blind golden moles (Chrysochloridae).

PubMed

Snyder, Holly K; Maia, Rafael; D'Alba, Liliana; Shultz, Allison J; Rowe, Karen M C; Rowe, Kevin C; Shawkey, Matthew D

2012-06-23

Relative to other metazoans, the mammalian integument is thought to be limited in colour. In particular, while iridescence is widespread among birds and arthropods, it has only rarely been reported in mammals. Here, we examine the colour, morphology and optical mechanisms in hairs from four species of golden mole (Mammalia: Chrysochloridae) that are characterized by sheens ranging from purple to green. Microspectrophotometry reveals that this colour is weak and variable. Iridescent hairs are flattened and have highly reduced cuticular scales, providing a broad and smooth surface for light reflection. These scales form multiple layers of light and dark materials of consistent thickness, strikingly similar to those in the elytra of iridescent beetles. Optical modelling suggests that the multi-layers produce colour through thin-film interference, and that the sensitivity of this mechanism to slight changes in layer thickness and number explains colour variability. While coloured integumentary structures are typically thought to evolve as sexual ornaments, the blindness of golden moles suggests that the colour may be an epiphenomenon resulting from evolution via other selective factors, including the ability to move and keep clean in dirt and sand.

Extinction events can accelerate evolution.

PubMed

Lehman, Joel; Miikkulainen, Risto

2015-01-01

Extinction events impact the trajectory of biological evolution significantly. They are often viewed as upheavals to the evolutionary process. In contrast, this paper supports the hypothesis that although they are unpredictably destructive, extinction events may in the long term accelerate evolution by increasing evolvability. In particular, if extinction events extinguish indiscriminately many ways of life, indirectly they may select for the ability to expand rapidly through vacated niches. Lineages with such an ability are more likely to persist through multiple extinctions. Lending computational support for this hypothesis, this paper shows how increased evolvability will result from simulated extinction events in two computational models of evolved behavior. The conclusion is that although they are destructive in the short term, extinction events may make evolution more prolific in the long term.

The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays

PubMed Central

2011-01-01

Background Ribosomal 5S genes are well known for the critical role they play in ribosome folding and functionality. These genes are thought to evolve in a concerted fashion, with high rates of homogenization of gene copies. However, the majority of previous analyses regarding the evolutionary process of rDNA repeats were conducted in invertebrates and plants. Studies have also been conducted on vertebrates, but these analyses were usually restricted to the 18S, 5.8S and 28S rRNA genes. The recent identification of divergent 5S rRNA gene paralogs in the genomes of elasmobranches and teleost fishes indicate that the eukaryotic 5S rRNA gene family has a more complex genomic organization than previously thought. The availability of new sequence data from lower vertebrates such as teleosts and elasmobranches enables an enhanced evolutionary characterization of 5S rDNA among vertebrates. Results We identified two variant classes of 5S rDNA sequences in the genomes of Potamotrygonidae stingrays, similar to the genomes of other vertebrates. One class of 5S rRNA genes was shared only by elasmobranches. A broad comparative survey among 100 vertebrate species suggests that the 5S rRNA gene variants in fishes originated from rounds of genome duplication. These variants were then maintained or eliminated by birth-and-death mechanisms, under intense purifying selection. Clustered multiple copies of 5S rDNA variants could have arisen due to unequal crossing over mechanisms. Simultaneously, the distinct genome clusters were independently homogenized, resulting in the maintenance of clusters of highly similar repeats through concerted evolution. Conclusions We believe that 5S rDNA molecular evolution in fish genomes is driven by a mixed mechanism that integrates birth-and-death and concerted evolution. PMID:21627815

Unprecedented within-species chromosome number cline in the Wood White butterfly Leptidea sinapis and its significance for karyotype evolution and speciation

PubMed Central

2011-01-01

Background Species generally have a fixed number of chromosomes in the cell nuclei while between-species differences are common and often pronounced. These differences could have evolved through multiple speciation events, each involving the fixation of a single chromosomal rearrangement. Alternatively, marked changes in the karyotype may be the consequence of within-species accumulation of multiple chromosomal fissions/fusions, resulting in highly polymorphic systems with the subsequent extinction of intermediate karyomorphs. Although this mechanism of chromosome number evolution is possible in theory, it has not been well documented. Results We present the discovery of exceptional intraspecific variability in the karyotype of the widespread Eurasian butterfly Leptidea sinapis. We show that within this species the diploid chromosome number gradually decreases from 2n = 106 in Spain to 2n = 56 in eastern Kazakhstan, resulting in a 6000 km-wide cline that originated recently (8,500 to 31,000 years ago). Remarkably, intrapopulational chromosome number polymorphism exists, the chromosome number range overlaps between some populations separated by hundreds of kilometers, and chromosomal heterozygotes are abundant. We demonstrate that this karyotypic variability is intraspecific because in L. sinapis a broad geographical distribution is coupled with a homogenous morphological and genetic structure. Conclusions The discovered system represents the first clearly documented case of explosive chromosome number evolution through intraspecific and intrapopulation accumulation of multiple chromosomal changes. Leptidea sinapis may be used as a model system for studying speciation by means of chromosomally-based suppressed recombination mechanisms, as well as clinal speciation, a process that is theoretically possible but difficult to document. The discovered cline seems to represent a narrow time-window of the very first steps of species formation linked to multiple chromosomal changes that have occurred explosively. This case offers a rare opportunity to study this process before drift, dispersal, selection, extinction and speciation erase the traces of microevolutionary events and just leave the final picture of a pronounced interspecific chromosomal difference. PMID:21507222

[Ego-state Therapy: Psychotherapy for Multiple Personality Disorders].

PubMed

Sugiyama, Toshiro

2018-01-01

The author describes ego-state therapy. This psychotherapy is used for treating multiple personality disorders. The author mentions the theoretical background of this method, and practical points. Initially, ego-state therapy was developed as a type of hypnotherapy, but it evolved as a safe therapeutic method in combination with trauma processing therapies. The author presents a case study, and discusses the clinical significance of this treatment.

Migration Opportunities

NASA Astrophysics Data System (ADS)

Grasselli, Agnese; Vangelista, Alessandro; Bolli, Stefano

Main Players in ICT arena, especially those with multiple assets such as fixed and mobile networks are evolving towards innovative services that leverage on a particular asset's specificity (e.g. mobility, bandwidth, location …) but assure a seamless user experience .

Re-evaluating across-axis geochemical variations at the East Pacific Rise and Juan de Fuca Ridge: on- and off-axis melt delivery

NASA Astrophysics Data System (ADS)

Perfit, M. R.; Walters, R. L.

2014-12-01

High spatial density geochemical data sets from the N-EPR and S-JdFR are used to re-evaluate the across-axis geochemical variations in major and trace elements at mid-ocean ridges (MORs). At two axial melt lens (AML) segments, north and south, at the 9-10°N EPR, N-MORB MgO varies across-axis from the most primitive above the AML to more evolved away from the axis. This trend is distinct at the northern (magmatically more robust) segment with an axial MgO range of 8-9 wt% and off-axis (>2km) range of 6.5-8 wt%. This decrease is also reflected in E-MORB MgO variation. There is more variability at the southern segment but, off-axis progression to more evolved MgO is still evident. Interestingly, the Cleft segment, JdFR, displays similar geochemical behavior to the EPR with an axial MgO range of 7-8.5 wt% and off-axis (>2km) range of 6-7.5 wt%. EPR geochemical studies over the past 30 years have described models of upper crustal accumulation ranging from eruptions limited to the axis, to temporal variation in the composition of magma in the AML, to multiple eruption sites across the ridge crest and flanks (<5km). Eruptions limited to the axis, with topographically controlled flow off-axis, cannot reproduce the observed off-axis change to more evolved N-MORB. Time-dependence could explain one instance of evolved lavas off-axis but, similar geochemical behavior is observed at two separate AML segments. Multiple instances of consistent compositional variability at multiple AML segments, and at different ridges, point to a common process of crustal accretion at MORs. In light of recent geophysical discoveries of Off-axis AMLs (OAMLs) at the EPR and JdFR, we propose that the trend of more evolved lavas for the majority of N-MORB lavas with distance from the axis is controlled by thermal distribution in the underlying crystal mush zone (CMZ). Higher magma flux beneath the axis facilitates higher temperatures and high porosity melt pathways, reducing crustal residence times, and erupting more primitive lava compositions. OAMLs at the edges of the CMZ, where it is cooler, feed more evolved off-axis eruptions. Lower magma flux at the edges increases crustal residence time and the extent to which magmas crystallize. OAMLs outside of the CMZ host magmas that may escaped any central mixing and erupt a greater range of compositions.

The role of sexual preferences in intrasexual female competition

PubMed Central

2012-01-01

Background While search costs have long been understood to affect the evolution of female preference, other costs associated with mating have been the focus of much less attention. Here I consider a novel mate choice cost: female-female intrasexual competition, that is, when females compete with each other for mates. This competition results in cost to female fecundity, such as a reduction in fertility due to decreased direct benefits, sperm limitation, or time and resources spent competing for a mate. I asked if female-female competition affects the evolution of preferences, and further, if the presence of multiple, different, preferences in a population can reduce competitive costs. Results Using population genetic models of preference and trait evolution, I found that intrasexual competition leads to direct selection against female preferences, and restricts the parameter space under which preference may evolve. I also examined how multiple, different, preferences affected preference evolution with female intrasexual competition. Conclusions Multiple preferences primarily serve to increase competitive costs and decrease the range of parameters under which preferences may evolve. PMID:23148567

Comparative genomics and evolution of eukaryotic phospholipidbiosynthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lykidis, Athanasios

2006-12-01

Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymesmore » and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.« less

Evolving microstructure, magnetic properties and phase transition in a mechanically alloyed Ni0.5Zn0.5Fe2O4 single sample

NASA Astrophysics Data System (ADS)

Ismail, Ismayadi; Hashim, Mansor; Kanagesan, Samikannu; Ibrahim, Idza Riati; Nazlan, Rodziah; Wan Ab Rahman, Wan Norailiana; Abdullah, Nor Hapishah; Mohd Idris, Fadzidah; Bahmanrokh, Ghazaleh; Shafie, Mohd Shamsul Ezzad; Manap, Masni

2014-02-01

We report on an investigation to unravel the dependence of magnetic properties on microstructure while they evolve in parallel under the influence of sintering temperature of a single sample of Ni0.5Zn0.5Fe2O4 synthesized via mechanical alloying. A single sample, instead of the normally practiced approach of using multiple samples, was sintered at various sintering temperatures from 500 °C to 1400 °C. The morphology of the samples was studied by means of scanning electron microscopy (SEM) equipped with EDX; density measurement was conducted using the Archimedes principle; and hysteresis measurement was carried out using a B-H hysteresisgraph system. XRD data showed that the first appearance of a single phase was at 800 °C and an amorphous phase was traced at lower sintering temperatures. We correlated the microstructure and the magnetic properties and showed that the important grain-size threshold for the appearance of significant ordered magnetism (mainly ferromagnetism) was about ≥0.3 µm. We found that there were three stages of magnetic phase evolution produced via the sintering process with increasing temperatures. The first stage was dominated by paramagnetic states with some superparamagnetic behavior; the second stage was influenced by moderately ferromagnetic states and some paramagnetic states; and the third stage consisted of strongly ferromagnetic states with negligible paramagnetic states. We found that three factors sensitively influenced the sample's content of ordered magnetism—the ferrite-phase crystallinity degree, the number of grains above the critical grain size and the number of large enough grains for domain wall accommodation.

Evidence for strong intralocus sexual conflict in the Indian meal moth, Plodia interpunctella.

PubMed

Lewis, Zenobia; Wedell, Nina; Hunt, John

2011-07-01

Males and females share a genome and express many shared phenotypic traits, which are often selected in opposite directions. This generates intralocus sexual conflict that may constrain trait evolution by preventing the sexes from reaching their optimal phenotype. Furthermore, if present across multiple loci, intralocus sexual conflict can result in a gender load that may diminish the benefits of sexual selection and help maintain genetic variation for fitness. Despite the importance of intralocus sexual conflict, surprisingly few empirical studies conclusively demonstrate its operation. We show that the pattern of multivariate selection acting on three sexually dimorphic life-history traits (development time, body size, and longevity) in the Indian meal moth, Plodia interpunctella, is opposing for the sexes. Moreover, we combined our estimates of selection with the additive genetic variance-covariance matrix (G) to predict the evolutionary response of the life-history traits in the sexes and showed that the angle between the vector of responses and the vector of sexually antagonistic selection was almost orthogonal at 84.70°. Thus, G biases the predicted response of life-history traits in the sexes away from the direction of sexually antagonistic selection, confirming the presence of strong intralocus sexual conflict in this species. Despite this, sexual dimorphism has evolved in all of the life-history traits examined suggesting that mechanism(s) have evolved to resolve this conflict and allow the sexes to reach their life-history optima. We argue that intralocus sexual conflict is likely to play an important role in the evolution of divergent life-history strategies between the sexes in this species. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

A systems approach defining constraints of the genome architecture on lineage selection and evolvability during somatic cancer evolution

PubMed Central

Rübben, Albert; Nordhoff, Ole

2013-01-01

Summary Most clinically distinguishable malignant tumors are characterized by specific mutations, specific patterns of chromosomal rearrangements and a predominant mechanism of genetic instability but it remains unsolved whether modifications of cancer genomes can be explained solely by mutations and selection through the cancer microenvironment. It has been suggested that internal dynamics of genomic modifications as opposed to the external evolutionary forces have a significant and complex impact on Darwinian species evolution. A similar situation can be expected for somatic cancer evolution as molecular key mechanisms encountered in species evolution also constitute prevalent mutation mechanisms in human cancers. This assumption is developed into a systems approach of carcinogenesis which focuses on possible inner constraints of the genome architecture on lineage selection during somatic cancer evolution. The proposed systems approach can be considered an analogy to the concept of evolvability in species evolution. The principal hypothesis is that permissive or restrictive effects of the genome architecture on lineage selection during somatic cancer evolution exist and have a measurable impact. The systems approach postulates three classes of lineage selection effects of the genome architecture on somatic cancer evolution: i) effects mediated by changes of fitness of cells of cancer lineage, ii) effects mediated by changes of mutation probabilities and iii) effects mediated by changes of gene designation and physical and functional genome redundancy. Physical genome redundancy is the copy number of identical genetic sequences. Functional genome redundancy of a gene or a regulatory element is defined as the number of different genetic elements, regardless of copy number, coding for the same specific biological function within a cancer cell. Complex interactions of the genome architecture on lineage selection may be expected when modifications of the genome architecture have multiple and possibly opposed effects which manifest themselves at disparate times and progression stages. Dissection of putative mechanisms mediating constraints exerted by the genome architecture on somatic cancer evolution may provide an algorithm for understanding and predicting as well as modifying somatic cancer evolution in individual patients. PMID:23336076

Molecular pathways in non-alcoholic fatty liver disease

PubMed Central

Berlanga, Alba; Guiu-Jurado, Esther; Porras, José Antonio; Auguet, Teresa

2014-01-01

Non-alcoholic fatty liver disease (NAFLD) is a clinicopathological change characterized by the accumulation of triglycerides in hepatocytes and has frequently been associated with obesity, type 2 diabetes mellitus, hyperlipidemia, and insulin resistance. It is an increasingly recognized condition that has become the most common liver disorder in developed countries, affecting over one-third of the population and is associated with increased cardiovascular- and liver-related mortality. NAFLD is a spectrum of disorders, beginning as simple steatosis. In about 15% of all NAFLD cases, simple steatosis can evolve into non-alcoholic steatohepatitis, a medley of inflammation, hepatocellular injury, and fibrosis, often resulting in cirrhosis and even hepatocellular cancer. However, the molecular mechanism underlying NAFLD progression is not completely understood. Its pathogenesis has often been interpreted by the “double-hit” hypothesis. The primary insult or the “first hit” includes lipid accumulation in the liver, followed by a “second hit” in which proinflammatory mediators induce inflammation, hepatocellular injury, and fibrosis. Nowadays, a more complex model suggests that fatty acids (FAs) and their metabolites may be the true lipotoxic agents that contribute to NAFLD progression; a multiple parallel hits hypothesis has also been suggested. In NAFLD patients, insulin resistance leads to hepatic steatosis via multiple mechanisms. Despite the excess hepatic accumulation of FAs in NAFLD, it has been described that not only de novo FA synthesis is increased, but FAs are also taken up from the serum. Furthermore, a decrease in mitochondrial FA oxidation and secretion of very-low-density lipoproteins has been reported. This review discusses the molecular mechanisms that underlie the pathophysiological changes of hepatic lipid metabolism that contribute to NAFLD. PMID:25045276

Intestinal crosstalk – a new paradigm for understanding the gut as the “motor” of critical illness

PubMed Central

Clark, Jessica A; Coopersmith, Craig M

2007-01-01

For more than 20 years, the gut has been hypothesized to be the “motor” of multiple organ dysfunction syndrome (MODS). As critical care research has evolved, there have been multiple mechanisms by which the gastrointestinal tract has been proposed to drive systemic inflammation. Many of these disparate mechanisms have proved to be important in the origin and propagation of critical illness. However, this has led to an unusual situation where investigators describing the gut as a “motor” revving the systemic inflammatory response syndrome (SIRS) are frequently describing wholly different processes to support their claim (i.e. increased apoptosis, altered tight junctions, translocation, cytokine production, crosstalk with commensal bacteria, etc). The purpose of this review is to present a unifying theory as to how the gut drives critical illness. Although the gastrointestinal tract is frequently described simply as “the gut,” it is actually made up of a) an epithelium, b) a diverse and robust immune arm, which contains the majority of immune cells in the body, and c) the commensal bacteria, which contain more cells than are present in the entire host organism. We propose that the intestinal epithelium, the intestinal immune system and the intestine’s endogenous bacteria all play vital roles driving MODS, and the complex crosstalk between these three interrelated portions of the gastrointestinal tract are cumulatively what makes the gut a “motor” of critical illness. PMID:17577136

Chromatic illumination discrimination ability reveals that human colour constancy is optimised for blue daylight illuminations.

PubMed

Pearce, Bradley; Crichton, Stuart; Mackiewicz, Michal; Finlayson, Graham D; Hurlbert, Anya

2014-01-01

The phenomenon of colour constancy in human visual perception keeps surface colours constant, despite changes in their reflected light due to changing illumination. Although colour constancy has evolved under a constrained subset of illuminations, it is unknown whether its underlying mechanisms, thought to involve multiple components from retina to cortex, are optimised for particular environmental variations. Here we demonstrate a new method for investigating colour constancy using illumination matching in real scenes which, unlike previous methods using surface matching and simulated scenes, allows testing of multiple, real illuminations. We use real scenes consisting of solid familiar or unfamiliar objects against uniform or variegated backgrounds and compare discrimination performance for typical illuminations from the daylight chromaticity locus (approximately blue-yellow) and atypical spectra from an orthogonal locus (approximately red-green, at correlated colour temperature 6700 K), all produced in real time by a 10-channel LED illuminator. We find that discrimination of illumination changes is poorer along the daylight locus than the atypical locus, and is poorest particularly for bluer illumination changes, demonstrating conversely that surface colour constancy is best for blue daylight illuminations. Illumination discrimination is also enhanced, and therefore colour constancy diminished, for uniform backgrounds, irrespective of the object type. These results are not explained by statistical properties of the scene signal changes at the retinal level. We conclude that high-level mechanisms of colour constancy are biased for the blue daylight illuminations and variegated backgrounds to which the human visual system has typically been exposed.

A Search for Starless Core Substructure in Ophiuchus

NASA Astrophysics Data System (ADS)

Kirk, Helen

2017-06-01

Density substructure is expected in evolved starless cores: a single peak to form a protostar, or multiple peaks from fragmentation. Searches for this substructure have had mixed success. In an ALMA survey of Ophiuchus, we find two starless cores with signs of substructure, consistent with simulation predictions. A similar survey in Chameleon (Dunham et al. 2016) had no detections, despite expecting at least two. Our results suggest that Chamleon may lack a more evolved starless cores. Future ALMA observations will better trace the influence of environment on core substructure formation.

Multifunctionality of chiton biomineralized armor with an integrated visual system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Ling; Connors, Matthew; Kolle, Mathias

2015-11-20

Nature provides a multitude of examples of multifunctional structural materials. There are often trade-offs in these materials because few of them are equally well suited for multiple tasks. One such example is the biomineralized armor of the chiton Acanthopleura granulata, which incorporates an integrated sensory system that includes hundreds of eyes with aragonite-based lens. Here, we used optical experiments to demonstrate directly, for the first time, that these microscopic, mineralized lenses are able to form images. Furthermore, our experiments revealed that the optical performance of these polycrystalline lenses is enhanced by the reduction of spherical aberration through the shape ofmore » the lens and that birefringence scattering is minimized by the use of relatively large, co-aligned grains (~10 μm as compared to ~1 μm in the non-eye regions). Additionally, we used multi-scale mechanical testing techniques to show that A. granulata’s lenses are an integral component of its biomineralized armor, but that both the intrinsic and overall mechanical properties of the lenses are compromised as compared to the primary solid regions of the armor plates. Our results demonstrate that as the size, complexity, and functionality of the integrated sensory elements increases, the local mechanical performance of the armor decreases. But, A. granulata has evolved several strategies to compensate for its local mechanical vulnerabilities to form a multifunctional system with co-optimized overall optical and structural functions.« less

Oxidative and Photosynthetic Phosphorylation Mechanisms

ERIC Educational Resources Information Center

Wang, Jui H.

1970-01-01

Proposes a molecular mechanism for the coupling of phosphorylation to electron transport in both mitochondria and chloroplasts. Justifies the proposed reaction schemes in terms of thermodynamics and biochemical data. Suggests how areobic respiration could have evolved. (EB)

Northeastern conifer research: Multiple species and multiple values

Treesearch

Laura S. Kenefic; John C. Brissette; Richard W. Judd

2014-01-01

The northern conifer, or spruce-fir, forest of the northeastern USA and adjacent Canada has had a defining influence on the economy and culture of the region. The same can be said of the USDA Forest Service’s research in this forest, which began more than 100 years ago. Forest Service research has evolved since that time in response to changes in the needs and...

OUTFLOWS FROM EVOLVED STARS: THE RAPIDLY CHANGING FINGERS OF CRL 618

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balick, Bruce; Huarte-Espinosa, Martin; Frank, Adam

2013-07-20

Our ultimate goal is to probe the nature of the collimator of the outflows in the pre-planetary nebula CRL 618. CRL 618 is uniquely suited for this purpose owing to its multiple, bright, and carefully studied finger-shaped outflows east and west of its nucleus. We compare new Hubble Space Telescope images to images in the same filters observed as much as 11 yr ago to uncover large proper motions and surface brightness changes in its multiple finger-shaped outflows. The expansion age of the ensemble of fingers is close to 100 yr. We find strong brightness variations at the fingertips duringmore » the past decade. Deep IR images reveal a multiple ring-like structure of the surrounding medium into which the outflows propagate and interact. Tightly constrained three-dimensional hydrodynamic models link the properties of the fingers to their possible formation histories. We incorporate previously published complementary information to discern whether each of the fingers of CRL 618 are the results of steady, collimated outflows or a brief ejection event that launched a set of bullets about a century ago. Finally, we argue on various physical grounds that fingers of CRL 618 are likely to be the result of a spray of clumps ejected at the nucleus of CRL 618 since any mechanism that form a sustained set of unaligned jets is unprecedented.« less

Current and Emerging Therapies in Multiple Sclerosis: Implications for the Radiologist, Part 1-Mechanisms, Efficacy, and Safety.

PubMed

McNamara, C; Sugrue, G; Murray, B; MacMahon, P J

2017-09-01

Imaging for the diagnosis and follow-up of patients with suspected or confirmed multiple sclerosis is a common scenario for many general radiologists and subspecialty neuroradiologists. The field of MS therapeutics has rapidly evolved with multiple new agents now being used in routine clinical practice. To provide an informed opinion in discussions concerning newer MS agents, radiologists must have a working understanding of the strengths and limitations of the various novel therapies. The role of imaging in MS has advanced beyond monitoring and surveillance of disease activity to include treatment complications. An understanding of the new generation of MS drugs in conjunction with the key role that MR imaging plays in the detection of disease progression, opportunistic infections, and drug-related adverse events is of vital importance to the radiologist and clinical physician alike. Radiologists are in a unique position to detect many of the described complications well in advance of clinical symptoms. Part 1 of this review outlines recent developments in the treatment of MS and discusses the published clinical data on the efficacy and safety of the currently approved and emerging therapies in this condition as they apply to the radiologist. Part 2 will cover pharmacovigilance and the role the neuroradiologist plays in monitoring patients for signs of opportunistic infection and/or disease progression. © 2017 by American Journal of Neuroradiology.

Consensus Statement on medication use in multiple sclerosis by the Spanish Society of Neurology's study group for demyelinating diseases.

PubMed

García-Merino, A; Fernández, O; Montalbán, X; de Andrés, C; Oreja-Guevara, C; Rodríguez-Antigüedad, A; Arbizu, T

2013-01-01

Treatments for multiple sclerosis therapy are rapidly evolving. It is believed that new drugs will be approved in the near future, thereby changing current indications for treatment. In this context, the Spanish Society of Neurology's study group on demyelinating diseases, which evaluates medication use in MS, has decided to draw up a consensus statement on the current indications and guidelines for multiple sclerosis treatment. Copyright © 2013 Sociedad Española de Neurología. Published by Elsevier Espana. All rights reserved.

Translating Alcohol Research

PubMed Central

Batman, Angela M.; Miles, Michael F.

2015-01-01

Alcohol use disorder (AUD) and its sequelae impose a major burden on the public health of the United States, and adequate long-term control of this disorder has not been achieved. Molecular and behavioral basic science research findings are providing the groundwork for understanding the mechanisms underlying AUD and have identified multiple candidate targets for ongoing clinical trials. However, the translation of basic research or clinical findings into improved therapeutic approaches for AUD must become more efficient. Translational research is a multistage process of streamlining the movement of basic biomedical research findings into clinical research and then to the clinical target populations. This process demands efficient bidirectional communication across basic, applied, and clinical science as well as with clinical practitioners. Ongoing work suggests rapid progress is being made with an evolving translational framework within the alcohol research field. This is helped by multiple interdisciplinary collaborative research structures that have been developed to advance translational work on AUD. Moreover, the integration of systems biology approaches with collaborative clinical studies may yield novel insights for future translational success. Finally, appreciation of genetic variation in pharmacological or behavioral treatment responses and optimal communication from bench to bedside and back may strengthen the success of translational research applications to AUD. PMID:26259085

Translating Alcohol Research: Opportunities and Challenges.

PubMed

Batman, Angela M; Miles, Michael F

2015-01-01

Alcohol use disorder (AUD) and its sequelae impose a major burden on the public health of the United States, and adequate long-term control of this disorder has not been achieved. Molecular and behavioral basic science research findings are providing the groundwork for understanding the mechanisms underlying AUD and have identified multiple candidate targets for ongoing clinical trials. However, the translation of basic research or clinical findings into improved therapeutic approaches for AUD must become more efficient. Translational research is a multistage process of stream-lining the movement of basic biomedical research findings into clinical research and then to the clinical target populations. This process demands efficient bidirectional communication across basic, applied, and clinical science as well as with clinical practitioners. Ongoing work suggests rapid progress is being made with an evolving translational framework within the alcohol research field. This is helped by multiple interdisciplinary collaborative research structures that have been developed to advance translational work on AUD. Moreover, the integration of systems biology approaches with collaborative clinical studies may yield novel insights for future translational success. Finally, appreciation of genetic variation in pharmacological or behavioral treatment responses and optimal communication from bench to bedside and back may strengthen the success of translational research applications to AUD.

Stellar Content and Star Formation in Young Clusters Influenced by Massive Stars

NASA Astrophysics Data System (ADS)

Jose, J.

2014-09-01

Star Formation (SF) in extreme environment is always challenging and can be significantly different from that in quiet environments. This study presents the comprehensive multi-wavelength (optical, NIR, MIR and radio) observational analysis of three Galactic starforming regions associated with H II regions/young clusters and located at > 2 kpc, which are found to be evolving under the influence of massive stars within their vicinity. The candidate massive stars, young stellar objects, their mass, age, age spread, the form of K-band Luminosity Function (KLF), Initial Mass Function (IMF) and a possible formation history of each region are studied. The major results on Sh2-252, an extended H II region that appears to be undergoing multiple episodes of SF, are highlighted. Our analysis shows that all the regions are undergoing complex SF activity and the new generation of stars in each region seem to be an outcome of the influence by the presence of massive stars within them. SF process in these regions are likely to be multi-fold and the results suggest that multiple modes of triggering mechanism and hierarchial modes of SF are a common phenomena within young clusters.

Extinction Events Can Accelerate Evolution

PubMed Central

Lehman, Joel; Miikkulainen, Risto

2015-01-01

Extinction events impact the trajectory of biological evolution significantly. They are often viewed as upheavals to the evolutionary process. In contrast, this paper supports the hypothesis that although they are unpredictably destructive, extinction events may in the long term accelerate evolution by increasing evolvability. In particular, if extinction events extinguish indiscriminately many ways of life, indirectly they may select for the ability to expand rapidly through vacated niches. Lineages with such an ability are more likely to persist through multiple extinctions. Lending computational support for this hypothesis, this paper shows how increased evolvability will result from simulated extinction events in two computational models of evolved behavior. The conclusion is that although they are destructive in the short term, extinction events may make evolution more prolific in the long term. PMID:26266804

Enteroaggregative Escherichia coli have evolved independently as distinct complexes within the E. coli population with varying ability to cause disease.

PubMed

Chattaway, Marie Anne; Jenkins, Claire; Rajendram, Dunstan; Cravioto, Alejandro; Talukder, Kaisar Ali; Dallman, Tim; Underwood, Anthony; Platt, Steve; Okeke, Iruka N; Wain, John

2014-01-01

Enteroaggregative E. coli (EAEC) is an established diarrhoeagenic pathotype. The association with virulence gene content and ability to cause disease has been studied but little is known about the population structure of EAEC and how this pathotype evolved. Analysis by Multi Locus Sequence Typing of 564 EAEC isolates from cases and controls in Bangladesh, Nigeria and the UK spanning the past 29 years, revealed multiple successful lineages of EAEC. The population structure of EAEC indicates some clusters are statistically associated with disease or carriage, further highlighting the heterogeneous nature of this group of organisms. Different clusters have evolved independently as a result of both mutational and recombination events; the EAEC phenotype is distributed throughout the population of E. coli.

Evolving phenotypic networks in silico.

PubMed

François, Paul

2014-11-01

Evolved gene networks are constrained by natural selection. Their structures and functions are consequently far from being random, as exemplified by the multiple instances of parallel/convergent evolution. One can thus ask if features of actual gene networks can be recovered from evolutionary first principles. I review a method for in silico evolution of small models of gene networks aiming at performing predefined biological functions. I summarize the current implementation of the algorithm, insisting on the construction of a proper "fitness" function. I illustrate the approach on three examples: biochemical adaptation, ligand discrimination and vertebrate segmentation (somitogenesis). While the structure of the evolved networks is variable, dynamics of our evolved networks are usually constrained and present many similar features to actual gene networks, including properties that were not explicitly selected for. In silico evolution can thus be used to predict biological behaviours without a detailed knowledge of the mapping between genotype and phenotype. Copyright © 2014 The Author. Published by Elsevier Ltd.. All rights reserved.

Sex determination in flowering plants: papaya as a model system.

PubMed

Aryal, Rishi; Ming, Ray

2014-03-01

Unisexuality in flowering plants evolved from a hermaphrodite ancestor. Transition from hermaphrodite to unisexual flowers has occurred multiple times across the different lineages of the angiosperms. Sexuality in plants is regulated by genetic, epigenetic and physiological mechanisms. The most specialized mechanism of sex determination is sex chromosomes. The sex chromosomes ensure the stable segregation of sexual phenotypes by preventing the recombination of sex determining genes. Despite continuous efforts, sex determining genes of dioecious plants have not yet been cloned. Concerted efforts with various model systems are necessary to understand the complex mechanism of sex determination in plants. Papaya (Carica papaya L.) is a tropical fruit tree with three sex forms, male, hermaphrodite, and female. Sexuality in papaya is determined by an XY chromosome system that is in an early evolutionary stage. The male and hermaphrodite of papaya are controlled by two different types of Y chromosomes: Y and Y(h). Large amounts of information in the area of genetics, genomics, and epigenetics of papaya have been accumulated over the last few decades. Relatively short lifecycle, small genome size, and readily available genetic and genomic resources render papaya an excellent model system to study sex determination and sex chromosomes in flowering plants. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Lake drying and livelihood dynamics in Lake Chad: Unravelling the mechanisms, contexts and responses.

PubMed

Okpara, Uche T; Stringer, Lindsay C; Dougill, Andrew J

2016-11-01

This article examines lake drying and livelihood dynamics in the context of multiple stressors through a case study of the "Small Lake Chad" in the Republic of Chad. Livelihoods research in regions experiencing persistent lake water fluctuations has largely focused on the well-being and security of lakeshore dwellers. Little is known about the mechanisms through which lake drying shapes livelihood drawbacks and opportunities, and whether locally evolved responses are enhancing livelihoods. Here we address these gaps using empirical, mixed-methods field research couched within the framework of livelihoods and human well-being contexts. The analysis demonstrates that limited opportunities outside agriculture, the influx of mixed ethnic migrants and the increasing spate of violence all enhance livelihood challenges. Livelihood opportunities centre on the renewal effects of seasonal flood pulses on lake waters and the learning opportunities triggered by past droughts. Although drying has spurred new adaptive behaviours predicated on seasonality, traditional predictive factors and the availability of assets, responses have remained largely reactive. The article points to where lake drying fits amongst changes in the wider socio-economic landscape in which people live, and suggests that awareness of the particularities of the mechanisms that connect lake drying to livelihoods can offer insights into the ways local people might be assisted by governments and development actors.

Glycogen synthase kinase-3 (GSK3): regulation, actions, and diseases

PubMed Central

Beurel, Eleonore; Grieco, Steven F.; Jope, Richard S.

2014-01-01

Glycogen synthase kinase-3 (GSK3) may be the busiest kinase in most cells, with over 100 known substrates to deal with. How does GSK3 maintain control to selectively phosphorylate each substrate, and why was it evolutionarily favorable for GSK3 to assume such a large responsibility? GSK3 must be particularly adaptable for incorporating new substrates into its repertoire, and we discuss the distinct properties of GSK3 that may contribute to its capacity to fulfill its roles in multiple signaling pathways. The mechanisms regulating GSK3 (predominantly post-translational modifications, substrate priming, cellular trafficking, protein complexes) have been reviewed previously, so here we focus on newly identified complexities in these mechanisms, how each of these regulatory mechanism contributes to the ability of GSK3 to select which substrates to phosphorylate, and how these mechanisms may have contributed to its adaptability as new substrates evolved. The current understanding of the mechanisms regulating GSK3 is reviewed, as are emerging topics in the actions of GSK3, particularly its interactions with receptors and receptor-coupled signal transduction events, and differential actions and regulation of the two GSK3 isoforms, GSK3α and GSK3β. Another remarkable characteristic of GSK3 is its involvement in many prevalent disorders, including psychiatric and neurological diseases, inflammatory diseases, cancer, and others. We address the feasibility of targeting GSK3 therapeutically, and provide an update of its involvement in the etiology and treatment of several disorders. PMID:25435019

Controlled disulfonated poly(arylene ether sulfone) multiblock copolymers for direct methanol fuel cells.

PubMed

Li, Qing; Chen, Yu; Rowlett, Jarrett R; McGrath, James E; Mack, Nathan H; Kim, Yu Seung

2014-04-23

Structure-property-performance relationships of disulfonated poly(arylene ether sulfone) multiblock copolymer membranes were investigated for their use in direct methanol fuel cell (DMFC) applications. Multiple series of reactive polysulfone, polyketone, and polynitrile hydrophobic block segments having different block lengths and molecular composition were synthesized and reacted with a disulfonated poly(arylene ether sulfone) hydrophilic block segment by a coupling reaction. Large-scale morphological order of the multiblock copolymers evolved with the increase of block size that gave notable influence on mechanical toughness, water uptake, and proton/methanol transport. Chemical structural changes of the hydrophobic blocks through polar group, fluorination, and bisphenol type allowed further control of the specific properties. DMFC performance was analyzed to elicit the impact of structural variations of the multiblock copolymers. Finally, DMFC performances of selected multiblock copolymers were compared against that of the industrial standard Nafion in the DMFC system.

Why are sec-alkylperoxyl bimolecular self-reactions orders of magnitude faster than the analogous reactions of tert-alkylperoxyls? The unanticipated role of CH hydrogen bond donation.

PubMed

Lee, Richmond; Gryn'ova, Ganna; Ingold, K U; Coote, Michelle L

2016-08-24

High-level ab initio calculations are used to identify the mechanism of secondary (and primary) alkylperoxyl radical termination and explain why their reactions are much faster than their tertiary counterparts. Contrary to existing literature, the decomposition of both tertiary and non-tertiary tetroxides follows the same asymmetric two-step bond cleavage pathway to form a caged intermediate of overall singlet multiplicity comprising triplet oxygen and two alkoxyl radicals. The alpha hydrogen atoms of non-tertiary species facilitate this process by forming unexpected CHO hydrogen bonds to the evolving O2. For non-tertiary peroxyls, subsequent alpha hydrogen atom transfer then yields the experimentally observed non-radical products, ketone, alcohol and O2, whereas for tertiary species, this reaction is precluded and cage escape of the (unpaired) alkoxyl radicals is a likely outcome with important consequences for autoxidation.

Enhancing a slow and weak optomechanical nonlinearity with delayed quantum feedback

PubMed Central

Wang, Zhaoyou; Safavi-Naeini, Amir H.

2017-01-01

A central goal of quantum optics is to generate large interactions between single photons so that one photon can strongly modify the state of another one. In cavity optomechanics, photons interact with the motional degrees of freedom of an optical resonator, for example, by imparting radiation pressure forces on a movable mirror or sensing minute fluctuations in the position of the mirror. Here, we show that the optical nonlinearity arising from these effects, typically too small to operate on single photons, can be sufficiently enhanced with feedback to generate large interactions between single photons. We propose a protocol that allows photons propagating in a waveguide to interact with each other through multiple bounces off an optomechanical system. The protocol is analysed by evolving the full many-body quantum state of the waveguide-coupled system, illustrating that large photon–photon interactions mediated by mechanical motion may be within experimental reach. PMID:28677674

Exceptional fossil preservation demonstrates a new mode of axial skeleton elongation in early ray-finned fishes.

PubMed

Maxwell, Erin E; Furrer, Heinz; Sánchez-Villagra, Marcelo R

2013-01-01

Elongate body plans have evolved independently multiple times in vertebrates, and involve either an increase in the number or in the length of the vertebrae. Here, we describe a new mechanism of body elongation in saurichthyids, an extinct group of elongate early ray-finned fishes. The rare preservation of soft tissue in a specimen of Saurichthys curionii from the Middle Triassic (Ladinian) of Switzerland provides significant new information on the relationship between the musculature and the skeleton. This new fossil material shows that elongation in these fishes results from doubling the number of neural arch-like elements per myomeric segment. This unique way of generating an elongate body plan demonstrates the evolutionary lability of the vertebral column in non-teleostean fishes. The shape and arrangement of preserved myosepta suggest that S. curionii was not a highly flexible fish, in spite of the increase in the number of neural arch-like elements.

Cis-regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans

PubMed Central

Miller, Craig T.; Beleza, Sandra; Pollen, Alex A.; Schluter, Dolph; Kittles, Rick A.; Shriver, Mark D.; Kingsley, David M.

2010-01-01

SUMMARY Dramatic pigmentation changes have evolved within most vertebrate groups, including fish and humans. Here we use genetic crosses in sticklebacks to investigate the parallel origin of pigmentation changes in natural populations. High-resolution mapping and expression experiments show that light gills and light ventrums map to a divergent regulatory allele of the Kit ligand (Kitlg) gene. The divergent allele reduces expression in gill and skin tissue, and is shared by multiple derived freshwater populations with reduced pigmentation. In humans, Europeans and East Asians also share derived alleles at the KITLG locus. Strong signatures of selection map to regulatory regions surrounding the gene, and admixture mapping shows that the KITLG genomic region has a significant effect on human skin color. These experiments suggest that regulatory changes in Kitlg contribute to natural variation in vertebrate pigmentation, and that similar genetic mechanisms may underlie rapid evolutionary change in fish and humans. PMID:18083106

Medical photography: current technology, evolving issues and legal perspectives.

PubMed

Harting, M T; DeWees, J M; Vela, K M; Khirallah, R T

2015-04-01

Medical photographic image capture and data management has undergone a rapid and compelling change in complexity over the last 20 years. This is because of multiple factors, including significant advances in ease of photograph capture, alongside an evolution of mechanisms of data portability/dissemination, combined with governmental focus on health information privacy. Literature to guide medical, legal, governmental and business professionals when dealing with issues related to medical photography is virtually nonexistent. Herein, we will address the breadth of uses of medical photography, device properties/specific devices utilised for image capture, methods of data transfer and dissemination and patient perceptions and attitudes regarding photography in a medical setting. In addition, we will address the legal implications, including legal precedent, copyright and privacy law, informed consent, protected health information and the Health Insurance Portability and Accountability Act (HIPAA), as they pertain to medical photography. © 2015 John Wiley & Sons Ltd.

Adaptive evolution of complex innovations through stepwise metabolic niche expansion.

PubMed

Szappanos, Balázs; Fritzemeier, Jonathan; Csörgő, Bálint; Lázár, Viktória; Lu, Xiaowen; Fekete, Gergely; Bálint, Balázs; Herczeg, Róbert; Nagy, István; Notebaart, Richard A; Lercher, Martin J; Pál, Csaba; Papp, Balázs

2016-05-20

A central challenge in evolutionary biology concerns the mechanisms by which complex metabolic innovations requiring multiple mutations arise. Here, we propose that metabolic innovations accessible through the addition of a single reaction serve as stepping stones towards the later establishment of complex metabolic features in another environment. We demonstrate the feasibility of this hypothesis through three complementary analyses. First, using genome-scale metabolic modelling, we show that complex metabolic innovations in Escherichia coli can arise via changing nutrient conditions. Second, using phylogenetic approaches, we demonstrate that the acquisition patterns of complex metabolic pathways during the evolutionary history of bacterial genomes support the hypothesis. Third, we show how adaptation of laboratory populations of E. coli to one carbon source facilitates the later adaptation to another carbon source. Our work demonstrates how complex innovations can evolve through series of adaptive steps without the need to invoke non-adaptive processes.

Adaptive evolution of complex innovations through stepwise metabolic niche expansion

PubMed Central

Szappanos, Balázs; Fritzemeier, Jonathan; Csörgő, Bálint; Lázár, Viktória; Lu, Xiaowen; Fekete, Gergely; Bálint, Balázs; Herczeg, Róbert; Nagy, István; Notebaart, Richard A.; Lercher, Martin J.; Pál, Csaba; Papp, Balázs

2016-01-01

A central challenge in evolutionary biology concerns the mechanisms by which complex metabolic innovations requiring multiple mutations arise. Here, we propose that metabolic innovations accessible through the addition of a single reaction serve as stepping stones towards the later establishment of complex metabolic features in another environment. We demonstrate the feasibility of this hypothesis through three complementary analyses. First, using genome-scale metabolic modelling, we show that complex metabolic innovations in Escherichia coli can arise via changing nutrient conditions. Second, using phylogenetic approaches, we demonstrate that the acquisition patterns of complex metabolic pathways during the evolutionary history of bacterial genomes support the hypothesis. Third, we show how adaptation of laboratory populations of E. coli to one carbon source facilitates the later adaptation to another carbon source. Our work demonstrates how complex innovations can evolve through series of adaptive steps without the need to invoke non-adaptive processes. PMID:27197754

Learning During Stressful Times

PubMed Central

Shors, Tracey J.

2012-01-01

Stressful life events can have profound effects on our cognitive and motor abilities, from those that could be construed as adaptive to those not so. In this review, I discuss the general notion that acute stressful experience necessarily impairs our abilities to learn and remember. The effects of stress on operant conditioning, that is, learned helplessness, as well as those on classical conditioning procedures are discussed in the context of performance and adaptation. Studies indicating sex differences in learning during stressful times are discussed, as are those attributing different responses to the existence of multiple memory systems and nonlinear relationships. The intent of this review is to highlight the apparent plasticity of the stress response, how it might have evolved to affect both performance and learning processes, and the potential problems with interpreting stress effects on learning as either good or bad. An appreciation for its plasticity may provide new avenues for investigating its underlying neuronal mechanisms. PMID:15054128

Enhancing a slow and weak optomechanical nonlinearity with delayed quantum feedback

NASA Astrophysics Data System (ADS)

Wang, Zhaoyou; Safavi-Naeini, Amir H.

2017-07-01

A central goal of quantum optics is to generate large interactions between single photons so that one photon can strongly modify the state of another one. In cavity optomechanics, photons interact with the motional degrees of freedom of an optical resonator, for example, by imparting radiation pressure forces on a movable mirror or sensing minute fluctuations in the position of the mirror. Here, we show that the optical nonlinearity arising from these effects, typically too small to operate on single photons, can be sufficiently enhanced with feedback to generate large interactions between single photons. We propose a protocol that allows photons propagating in a waveguide to interact with each other through multiple bounces off an optomechanical system. The protocol is analysed by evolving the full many-body quantum state of the waveguide-coupled system, illustrating that large photon-photon interactions mediated by mechanical motion may be within experimental reach.

Treatment of ALK-rearranged non-small cell lung cancer: A review of the landscape and approach to emerging patterns of treatment resistance in the Australian context.

PubMed

Itchins, M; Chia, P L; Hayes, S A; Howell, V M; Gill, A J; Cooper, W A; John, T; Mitchell, P; Millward, M; Clarke, S J; Solomon, B; Pavlakis, N

2017-08-01

Since the identification of anaplastic lymphoma kinase (ALK) gene rearrangements in non-small cell lung cancer (NSCLC) in 2005, the treatment of ALK-rearranged NSCLC (ALK+ NSCLC) has evolved at a rapid pace. This molecularly distinct subset of NSCLC has uniquely important biology, clinicopathologic features and mechanisms of drug resistance which impact on the choice of treatment for a patient with this disease. There are multiple ALK tyrosine kinase inhibitors now available in clinical practice with efficacy data continuing to emerge and guide the optimal treatment algorithm. A detailed search of medical databases and clinical trial registries was conducted to capture all relevant articles on this topic enabling an updated detailed overview of the landscape of management of ALK-rearranged NSCLC. © 2017 John Wiley & Sons Australia, Ltd.

Catalytic Oxygen Evolution by a Bioinorganic Model of the Photosystem II Oxygen-Evolving Complex

ERIC Educational Resources Information Center

Howard, Derrick L.; Tinoco, Arthur D.; Brudvig, Gary W.; Vrettos, John S.; Allen, Bertha Connie

2005-01-01

Bioinorganic models of the manganese Mn4 cluster are important not only as aids in understanding the structure and function of the oxygen-evolving complex (OEC), but also in developing artificial water-oxidation catalysts. The mechanism of water oxidation by photosystem II (PSII) is thought to involve the formation of a high-valent terminal Mn-oxo…

Modeling misidentification errors in capture-recapture studies using photographic identification of evolving marks

USGS Publications Warehouse

Yoshizaki, J.; Pollock, K.H.; Brownie, C.; Webster, R.A.

2009-01-01

Misidentification of animals is potentially important when naturally existing features (natural tags) are used to identify individual animals in a capture-recapture study. Photographic identification (photoID) typically uses photographic images of animals' naturally existing features as tags (photographic tags) and is subject to two main causes of identification errors: those related to quality of photographs (non-evolving natural tags) and those related to changes in natural marks (evolving natural tags). The conventional methods for analysis of capture-recapture data do not account for identification errors, and to do so requires a detailed understanding of the misidentification mechanism. Focusing on the situation where errors are due to evolving natural tags, we propose a misidentification mechanism and outline a framework for modeling the effect of misidentification in closed population studies. We introduce methods for estimating population size based on this model. Using a simulation study, we show that conventional estimators can seriously overestimate population size when errors due to misidentification are ignored, and that, in comparison, our new estimators have better properties except in cases with low capture probabilities (<0.2) or low misidentification rates (<2.5%). ?? 2009 by the Ecological Society of America.

Genomics and the making of yeast biodiversity

USDA-ARS?s Scientific Manuscript database

Yeasts are unicellular fungi that do not form fruiting bodies. Although the yeast lifestyle has evolved multiple times, most known species belong to the subphylum Saccharomycotina (syn. Hemiascomycota, hereafter yeasts). This diverse group includes the premier eukaryotic model system, Saccharomyces ...

Peripheral genetic structure of Helicoverpa zea indicates asymmetrical panmixia

USDA-ARS?s Scientific Manuscript database

Seasonal climatic shifts create peripheral habitats that alternate between habitable and uninhabitable for migratory species. Such dynamic peripheral habitats are potential sites where migratory species could evolve high genetic diversity resulting from convergence of immigrants from multiple region...

Multiple Resistances and Complex Mechanisms of Anopheles sinensis Mosquito: A Major Obstacle to Mosquito-Borne Diseases Control and Elimination in China

PubMed Central

Fang, Qiang; Hartsel, Joshua; Zhou, Guofa; Shi, Linna; Fang, Fujin; Zhu, Changliang; Yan, Guiyun

2014-01-01

Malaria, dengue fever, and filariasis are three of the most common mosquito-borne diseases worldwide. Malaria and lymphatic filariasis can occur as concomitant human infections while also sharing common mosquito vectors. The overall prevalence and health significance of malaria and filariasis have made them top priorities for global elimination and control programmes. Pyrethroid resistance in anopheline mosquito vectors represents a highly significant problem to malaria control worldwide. Several methods have been proposed to mitigate insecticide resistance, including rotational use of insecticides with different modes of action. Anopheles sinensis, an important malaria and filariasis vector in Southeast Asia, represents an interesting mosquito species for examining the consequences of long-term insecticide rotation use on resistance. We examined insecticide resistance in two An. Sinensis populations from central and southern China against pyrethroids, organochlorines, organophosphates, and carbamates, which are the major classes of insecticides recommended for indoor residual spray. We found that the mosquito populations were highly resistant to the four classes of insecticides. High frequency of kdr mutation was revealed in the central population, whereas no kdr mutation was detected in the southern population. The frequency of G119S mutation in the ace-1 gene was moderate in both populations. The classification and regression trees (CART) statistical analysis found that metabolic detoxification was the most important resistance mechanism, whereas target site insensitivity of L1014 kdr mutation played a less important role. Our results indicate that metabolic detoxification was the dominant mechanism of resistance compared to target site insensitivity, and suggests that long-term rotational use of various insecticides has led An. sinensis to evolve a high insecticide resistance. This study highlights the complex network of mechanisms conferring multiple resistances to chemical insecticides in mosquito vectors and it has important implication for designing and implementing vector resistance management strategies. PMID:24852174

The burden of proof: The current state of atrial fibrillation prevention and treatment trials.

PubMed

Zakeri, Rosita; Van Wagoner, David R; Calkins, Hugh; Wong, Tom; Ross, Heather M; Heist, E Kevin; Meyer, Timothy E; Kowey, Peter R; Mentz, Robert J; Cleland, John G; Pitt, Bertram; Zannad, Faiez; Linde, Cecilia

2017-05-01

Atrial fibrillation (AF) is an age-related arrhythmia of enormous socioeconomic significance. In recent years, our understanding of the basic mechanisms that initiate and perpetuate AF has evolved rapidly, catheter ablation of AF has progressed from concept to reality, and recent studies suggest lifestyle modification may help prevent AF recurrence. Emerging developments in genetics, imaging, and informatics also present new opportunities for personalized care. However, considerable challenges remain. These include a paucity of studies examining AF prevention, modest efficacy of existing antiarrhythmic therapies, diverse ablation technologies and practice, and limited evidence to guide management of high-risk patients with multiple comorbidities. Studies examining the long-term effects of AF catheter ablation on morbidity and mortality outcomes are not yet completed. In many ways, further progress in the field is heavily contingent on the feasibility, capacity, and efficiency of clinical trials to incorporate the rapidly evolving knowledge base and to provide substantive evidence for novel AF therapeutic strategies. This review outlines the current state of AF prevention and treatment trials, including the foreseeable challenges, as discussed by a unique forum of clinical trialists, scientists, and regulatory representatives in a session endorsed by the Heart Rhythm Society at the 12th Global CardioVascular Clinical Trialists Forum in Washington, DC, December 3-5, 2015. Copyright © 2017 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife

USGS Publications Warehouse

Velotta, Jonathan P.; Wegrzyn, Jill L.; Ginzburg, Samuel; Kang, Lin; Czesny, Sergiusz J.; O'Neill, Rachel J.; McCormick, Stephen; Michalak, Pawel; Schultz, Eric T.

2017-01-01

Comparative approaches in physiological genomics offer an opportunity to understand the functional importance of genes involved in niche exploitation. We used populations of Alewife (Alosa pseudoharengus) to explore the transcriptional mechanisms that underlie adaptation to fresh water. Ancestrally anadromous Alewives have recently formed multiple, independently derived, landlocked populations, which exhibit reduced tolerance of saltwater and enhanced tolerance of fresh water. Using RNA-seq, we compared transcriptional responses of an anadromous Alewife population to two landlocked populations after acclimation to fresh (0 ppt) and saltwater (35 ppt). Our results suggest that the gill transcriptome has evolved in primarily discordant ways between independent landlocked populations and their anadromous ancestor. By contrast, evolved shifts in the transcription of a small suite of well-characterized osmoregulatory genes exhibited a strong degree of parallelism. In particular, transcription of genes that regulate gill ion exchange has diverged in accordance with functional predictions: freshwater ion-uptake genes (most notably, the ‘freshwater paralog’ of Na+/K+-ATPase α-subunit) were more highly expressed in landlocked forms, whereas genes that regulate saltwater ion secretion (e.g. the ‘saltwater paralog’ of NKAα) exhibited a blunted response to saltwater. Parallel divergence of ion transport gene expression is associated with shifts in salinity tolerance limits among landlocked forms, suggesting that changes to the gill's transcriptional response to salinity facilitate freshwater adaptation.

Improving Transparency in the Reporting of Safeguards Implementation: FY11 Update

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toomey, Christopher; Odlaug, Christopher S.; Wyse, Evan T.

2011-09-30

In 2008, the Standing Advisory Group on Safeguards Implementation (SAGSI) indicated that the International Atomic Energy Agency's (IAEA) Safeguards Implementation Report (SIR) has not kept pace with the evolution of safeguards and provided the IAEA with a set of recommendations for improvement. The SIR is the primary mechanism for providing an overview of safeguards implementation in a given year and reporting on the annual safeguards findings and conclusions drawn by the Secretariat. As the IAEA transitions to State-level safeguards approaches, SIR reporting must adapt to reflect these evolutionary changes. This evolved report will better reflect the IAEA's transition to amore » more qualitative and information-driven approach, based upon State-as-a-whole considerations. This paper applies SAGSI's recommendations to the development of multiple models for an evolved SIR and finds that an SIR repurposed as a 'safeguards portal' could significantly enhance information delivery, clarity, and transparency. In addition, this paper finds that the 'portal concept' also appears to have value as a standardized information presentation and analysis platform for use by Country Officers, for continuity of knowledge purposes, and the IAEA Secretariat in the safeguards conclusion process. Accompanying this paper is a fully functional prototype of the 'portal' concept, built using commercial software and IAEA Annual Report data and available for viewing at http://safeguardsportal.pnnl.gov.« less

Multiple Vaccinations: Friend or Foe

PubMed Central

Church, Sarah E.; Jensen, Shawn M.; Twitty, Chris; Bahjat, Keith; Hu, Hong-Ming; Urba, Walter J.; Fox, Bernard A.

2013-01-01

Few immunotherapists would accept the concept of a single vaccination inducing a therapeutic anti-cancer immune response in a patient with advanced cancer. But what is the evidence to support the “more-is-better” approach of multiple vaccinations? Since we are unaware of trials comparing the effect of a single vaccine versus multiple vaccinations on patient outcome, we considered that an anti-cancer immune response might provide a surrogate measure of the effectiveness of vaccination strategies. Since few large trials include immunological monitoring, the majority of information is gleaned from smaller trials in which an evaluation of immune responses to vaccine or tumor, before and at one or more times following the first vaccine was performed. In some studies there is convincing evidence that repeated administration of a specific vaccine can augment the immune response to antigens contained in the vaccine. In other settings multiple vaccinations can significantly reduce the immune response to one or more targets. Results from three large adjuvant vaccine studies support the potential detrimental effect of multiple vaccinations as clinical outcomes in the control arms were significantly better than that for treatment groups. Recent research has provided insights into mechanisms that are likely responsible for the reduced responses in the studies noted above, but supporting evidence from clinical specimens is generally lacking. Interpretation of these results is further complicated by the possibility that the dominant immune response may evolve to recognize epitopes not present in the vaccine. Nonetheless, the FDA-approval of the first therapeutic cancer vaccine and recent developments from preclinical models and clinical trials provide a substantial basis for optimism and a critical evaluation of cancer vaccine strategies. PMID:21952289

Quantifying selection in evolving populations using time-resolved genetic data

NASA Astrophysics Data System (ADS)

Illingworth, Christopher J. R.; Mustonen, Ville

2013-01-01

Methods which uncover the molecular basis of the adaptive evolution of a population address some important biological questions. For example, the problem of identifying genetic variants which underlie drug resistance, a question of importance for the treatment of pathogens, and of cancer, can be understood as a matter of inferring selection. One difficulty in the inference of variants under positive selection is the potential complexity of the underlying evolutionary dynamics, which may involve an interplay between several contributing processes, including mutation, recombination and genetic drift. A source of progress may be found in modern sequencing technologies, which confer an increasing ability to gather information about evolving populations, granting a window into these complex processes. One particularly interesting development is the ability to follow evolution as it happens, by whole-genome sequencing of an evolving population at multiple time points. We here discuss how to use time-resolved sequence data to draw inferences about the evolutionary dynamics of a population under study. We begin by reviewing our earlier analysis of a yeast selection experiment, in which we used a deterministic evolutionary framework to identify alleles under selection for heat tolerance, and to quantify the selection acting upon them. Considering further the use of advanced intercross lines to measure selection, we here extend this framework to cover scenarios of simultaneous recombination and selection, and of two driver alleles with multiple linked neutral, or passenger, alleles, where the driver pair evolves under an epistatic fitness landscape. We conclude by discussing the limitations of the approach presented and outlining future challenges for such methodologies.

Evolution of Collective Behaviors for a Real Swarm of Aquatic Surface Robots.

PubMed

Duarte, Miguel; Costa, Vasco; Gomes, Jorge; Rodrigues, Tiago; Silva, Fernando; Oliveira, Sancho Moura; Christensen, Anders Lyhne

2016-01-01

Swarm robotics is a promising approach for the coordination of large numbers of robots. While previous studies have shown that evolutionary robotics techniques can be applied to obtain robust and efficient self-organized behaviors for robot swarms, most studies have been conducted in simulation, and the few that have been conducted on real robots have been confined to laboratory environments. In this paper, we demonstrate for the first time a swarm robotics system with evolved control successfully operating in a real and uncontrolled environment. We evolve neural network-based controllers in simulation for canonical swarm robotics tasks, namely homing, dispersion, clustering, and monitoring. We then assess the performance of the controllers on a real swarm of up to ten aquatic surface robots. Our results show that the evolved controllers transfer successfully to real robots and achieve a performance similar to the performance obtained in simulation. We validate that the evolved controllers display key properties of swarm intelligence-based control, namely scalability, flexibility, and robustness on the real swarm. We conclude with a proof-of-concept experiment in which the swarm performs a complete environmental monitoring task by combining multiple evolved controllers.

Evolution of Collective Behaviors for a Real Swarm of Aquatic Surface Robots

PubMed Central

Duarte, Miguel; Costa, Vasco; Gomes, Jorge; Rodrigues, Tiago; Silva, Fernando; Oliveira, Sancho Moura; Christensen, Anders Lyhne

2016-01-01

Swarm robotics is a promising approach for the coordination of large numbers of robots. While previous studies have shown that evolutionary robotics techniques can be applied to obtain robust and efficient self-organized behaviors for robot swarms, most studies have been conducted in simulation, and the few that have been conducted on real robots have been confined to laboratory environments. In this paper, we demonstrate for the first time a swarm robotics system with evolved control successfully operating in a real and uncontrolled environment. We evolve neural network-based controllers in simulation for canonical swarm robotics tasks, namely homing, dispersion, clustering, and monitoring. We then assess the performance of the controllers on a real swarm of up to ten aquatic surface robots. Our results show that the evolved controllers transfer successfully to real robots and achieve a performance similar to the performance obtained in simulation. We validate that the evolved controllers display key properties of swarm intelligence-based control, namely scalability, flexibility, and robustness on the real swarm. We conclude with a proof-of-concept experiment in which the swarm performs a complete environmental monitoring task by combining multiple evolved controllers. PMID:26999614

Sensory basis of lepidopteran migration: Focus on the monarch butterfly

PubMed Central

Guerra, Patrick A.; Reppert, Steven M.

2015-01-01

In response to seasonal habitats, migratory lepidopterans, exemplified by the monarch butterfly, have evolved migration to deal with dynamic conditions. During migration, monarchs use orientation mechanisms, exploiting a time-compensated sun compasses and a light-sensitive inclination magnetic compass to facilitate fall migration south. The sun compass is bidirectional with overwintering coldness triggering the change in orientation direction for remigration northward in the spring. The timing of the remigration and milkweed emergence in the southern US have co-evolved for propagation of the migration. Current research is uncovering the anatomical and molecular substrates that underlie migratory-relevant sensory mechanisms with the antennae being critical components. Orientation mechanisms may be detrimentally affected by environmental factors such as climate change and sensory interference from human-generated sources. PMID:25625216

Sensory basis of lepidopteran migration: focus on the monarch butterfly.

PubMed

Guerra, Patrick A; Reppert, Steven M

2015-10-01

In response to seasonal habitats, migratory lepidopterans, exemplified by the monarch butterfly, have evolved migration to deal with dynamic conditions. During migration, monarchs use orientation mechanisms, exploiting a time-compensated sun compass and a light-sensitive inclination magnetic compass to facilitate fall migration south. The sun compass is bidirectional with overwintering coldness triggering the change in orientation direction for remigration northward in the spring. The timing of the remigration and milkweed emergence in the southern US have co-evolved for propagation of the migration. Current research is uncovering the anatomical and molecular substrates that underlie migratory-relevant sensory mechanisms with the antennae being critical components. Orientation mechanisms may be detrimentally affected by environmental factors such as climate change and sensory interference from human-generated sources. Copyright © 2015 Elsevier Ltd. All rights reserved.

Forward selection for multiple resistance across the non-selective glyphosate, glufosinate and oxyfluorfen herbicides in Lolium weed species.

PubMed

Fernández, Pablo; Alcántara, Ricardo; Osuna, María D; Vila-Aiub, Martin M; Prado, Rafael De

2017-05-01

In the Mediterranean area, Lolium species have evolved resistance to glyphosate after decades of continual use without other alternative chemicals in perennial crops (olive, citrus and vineyards). In recent years, oxyfluorfen alone or mixed with glyphosate and glufosinate has been introduced as a chemical option to control dicot and grass weeds. Dose-response studies confirmed that three glyphosate-resistant Lolium weed species (L. rigidum, L. perenne, L. multiflorum) collected from perennial crops in the Iberian Peninsula have also evolved resistance to glufosinate and oxyfluorfen herbicides, despite their recent introduction. Based on the LD 50 resistance parameter, the resistance factor was similar among Lolium species and ranged from 14- to 21-fold and from ten- to 12-fold for oxyfluorfen and glufosinate respectively. Similarly, about 14-fold resistance to both oxyfluorfen and glufosinate was estimated on average for the three Lolium species when growth reduction (GR 50 ) was assessed. This study identified oxyfluorfen resistance in a grass species for the first time. A major threat to sustainability of perennial crops in the Iberian Peninsula is evident, as multiple resistance to non-selective glyphosate, glufosinate and oxyfluorfen herbicides has evolved in L. rigidum, L. perenne and L. multiflorum weeds. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

PubMed Central

Kingwell, Callum J.; Wcislo, William T.; Robinson, Gene E.

2017-01-01

Developmental plasticity may accelerate the evolution of phenotypic novelty through genetic accommodation, but studies of genetic accommodation often lack knowledge of the ancestral state to place selected traits in an evolutionary context. A promising approach for assessing genetic accommodation involves using a comparative framework to ask whether ancestral plasticity is related to the evolution of a particular trait. Bees are an excellent group for such comparisons because caste-based societies (eusociality) have evolved multiple times independently and extant species exhibit different modes of eusociality. We measured brain and abdominal gene expression in a facultatively eusocial bee, Megalopta genalis, and assessed whether plasticity in this species is functionally linked to eusocial traits in other bee lineages. Caste-biased abdominal genes in M. genalis overlapped significantly with caste-biased genes in obligately eusocial bees. Moreover, caste-biased genes in M. genalis overlapped significantly with genes shown to be rapidly evolving in multiple studies of 10 bee species, particularly for genes in the glycolysis pathway and other genes involved in metabolism. These results provide support for the idea that eusociality can evolve via genetic accommodation, with plasticity in facultatively eusocial species like M. genalis providing a substrate for selection during the evolution of caste in obligately eusocial lineages. PMID:28053060

Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality.

PubMed

Jones, Beryl M; Kingwell, Callum J; Wcislo, William T; Robinson, Gene E

2017-01-11

Developmental plasticity may accelerate the evolution of phenotypic novelty through genetic accommodation, but studies of genetic accommodation often lack knowledge of the ancestral state to place selected traits in an evolutionary context. A promising approach for assessing genetic accommodation involves using a comparative framework to ask whether ancestral plasticity is related to the evolution of a particular trait. Bees are an excellent group for such comparisons because caste-based societies (eusociality) have evolved multiple times independently and extant species exhibit different modes of eusociality. We measured brain and abdominal gene expression in a facultatively eusocial bee, Megalopta genalis, and assessed whether plasticity in this species is functionally linked to eusocial traits in other bee lineages. Caste-biased abdominal genes in M. genalis overlapped significantly with caste-biased genes in obligately eusocial bees. Moreover, caste-biased genes in M. genalis overlapped significantly with genes shown to be rapidly evolving in multiple studies of 10 bee species, particularly for genes in the glycolysis pathway and other genes involved in metabolism. These results provide support for the idea that eusociality can evolve via genetic accommodation, with plasticity in facultatively eusocial species like M. genalis providing a substrate for selection during the evolution of caste in obligately eusocial lineages. © 2017 The Author(s).

Evidence of refractory organic matter preserved in the mudstones of Yellowknife Bay and the Murray Formations

NASA Astrophysics Data System (ADS)

Eigenbrode, J. L.; Steele, A.; Summons, R. E.; Sutter, B.; McAdam, A.; Franz, H. B.; Mahaffy, P. R.; Conrad, P. G.; Freissinet, C.; Glavin, D. P.; Millan, M.; Ming, D. W.

2015-12-01

Volatiles from high-temperature (above 500°C) pyrolysis of drilled and sieved deltaic/lacustrine mudstones at Yellowknife Bay and Pahrump Hills were detected by the Sample Analysis at Mars (SAM) instrument's evolved gas analysis experiment onboard the Curiosity rover in Gale Crater, Mars. Mass fragments detected from the mudstones are consistent with C1-C4 alkyl and single-ring aromatic components that evolve at different temperatures and often in multiple phases. Concurrent release of oxidized sulfur (sulfur dioxide and sulfur trioxide), sulfide gases (hydrogen sulfide, carbonyl sulfide, carbon disulfide, dimethylsulfide or thiol, and thiophene) suggest that either these gases are evolving directly from the mudstone or are products of gas phase reactions in the SAM oven, or both. Multiple chlorohydrocarbon releases are also observed in analysis of the Mojave mudstone indicating punctuated organic releases from the sample. The organic signatures observed are unique to specific samples and are not observed in blanks or all samples, nor can the SAM background explain them. These results suggest that geologically refractory organic matter has been preserved in some Hesperian mudstones despite possible acid-sulfate weathering (as suggested by jarosite in Mojave) and exposure to ionizing cosmic rays after exhumation. We will report on ongoing study of these samples.

Quantum mechanics/molecular mechanics structural models of the oxygen-evolving complex of photosystem II.

PubMed

Sproviero, Eduardo M; Gascón, José A; McEvoy, James P; Brudvig, Gary W; Batista, Victor S

2007-04-01

The annual production of 260 Gtonnes of oxygen, during the process of photosynthesis, sustains life on earth. Oxygen is produced in the thylakoid membranes of green-plant chloroplasts and the internal membranes of cyanobacteria by photocatalytic water oxidation at the oxygen-evolving complex (OEC) of photosystem II (PSII). Recent breakthroughs in X-ray crystallography and advances in quantum mechanics/molecular mechanics (QM/MM) hybrid methods have enabled the construction of chemically sensible models of the OEC of PSII. The resulting computational structural models suggest the complete ligation of the catalytic center by amino acid residues, water, hydroxide and chloride, as determined from the intrinsic electronic properties of the oxomanganese core and the perturbational influence of the surrounding protein environment. These structures are found to be consistent with available mechanistic data, and are also compatible with X-ray diffraction models and extended X-ray absorption fine structure measurements. It is therefore conjectured that these OEC models are particularly relevant for the elucidation of the catalytic mechanism of water oxidation.

Effects of ambient temperature on mechanomyography of resting quadriceps muscle.

PubMed

McKay, William P; Vargo, Michael; Chilibeck, Philip D; Daku, Brian L

2013-03-01

It has been speculated that resting muscle mechanical activity, also known as minor tremor, microvibration, and thermoregulatory tonus, has evolved to maintain core temperature in homeotherms, and may play a role in nonshivering thermogenesis. This experiment was done to determine whether resting muscle mechanical activity increases with decreasing ambient temperature. We cooled 20 healthy, human, resting, supine subjects from an ambient temperature of 40° to 12 °C over 65 min. Core temperature, midquadriceps mechanomyography, surface electromyography, and oxygen consumption (VO2) were recorded. Resting muscle mechanical and electrical activity in the absence of shivering increased significantly at temperatures below 21.5 °C. Women defended core temperature more effectively than men, and showed increased resting muscle activity earlier than men. Metabolism measured by VO2 correlated with resting muscle mechanical activity (R = 0.65; p = 0.01). Resting muscle mechanical activity may have evolved, in part, to maintain core temperature in the face of mild cooling.

A Method to Determine an Organization’s Compatibility with Hybrid Workspaces

DTIC Science & Technology

2014-03-27

workers were present and assumed to be working. As early as the 1980s , private sector organizations began to evolve from task-based work to process...fact that people may utilize multiple physical spaces to conduct work ( Hislop & Axtell 2007). This is an important difference to consider when...on a flexible basis (Kunkle, 2000). Hislop and Axtell (2007) discovered that multiple studies compared the performances of teleworkers to those

Child abuse and the balance of power in parental relationships: an evolved domain-independent mental mechanism that accounts for behavioral variation.

PubMed

Handwerker, W P

2001-01-01

Previous studies use zero-order analyses to show a link between child abuse and exposure to "stepfathers." These studies rest on a proposed evolved, domain-specific cognitive mechanism that induces adult males to abuse or kill offspring not their own and, so, contribute directly to reproductive success. However, child abuse may reflect an evolved neurological mechanism that creates behavioral plasticity and adaptability by assigning emotional weights (which in consciousness appear rationalized as costs and benefits) to choice alternatives in all behavioral domains. This mechanism should act as a selective mechanism to create enhanced ability to avoid predation (social exploitation) and to obtain access to resources, given the properties of specific ecosystems, and should control behavioral responses to variation in the balance of power in social relationships. Power equalities should elicit good treatment for both parties; power inequalities, by contrast, should elicit exploitative and coercive behavior on the part of those who hold the balance of power. This paper reports a test of both hypotheses simultaneously, controlling for a standard social science risk factor (growing up in poverty). Once we control for the balance of power in parental relationships, exposure to a stepfather and growing up in poverty show no effect on the intensity of child abuse. Powerful women negotiated affectionate behavior from their partners for both themselves and their children; powerless women's negotiations with partners usually left both themselves and their children open to violence.

Behavioral responses in structured populations pave the way to group optimality.

PubMed

Akçay, Erol; Van Cleve, Jeremy

2012-02-01

An unresolved controversy regarding social behaviors is exemplified when natural selection might lead to behaviors that maximize fitness at the social-group level but are costly at the individual level. Except for the special case of groups of clones, we do not have a general understanding of how and when group-optimal behaviors evolve, especially when the behaviors in question are flexible. To address this question, we develop a general model that integrates behavioral plasticity in social interactions with the action of natural selection in structured populations. We find that group-optimal behaviors can evolve, even without clonal groups, if individuals exhibit appropriate behavioral responses to each other's actions. The evolution of such behavioral responses, in turn, is predicated on the nature of the proximate behavioral mechanisms. We model a particular class of proximate mechanisms, prosocial preferences, and find that such preferences evolve to sustain maximum group benefit under certain levels of relatedness and certain ecological conditions. Thus, our model demonstrates the fundamental interplay between behavioral responses and relatedness in determining the course of social evolution. We also highlight the crucial role of proximate mechanisms such as prosocial preferences in the evolution of behavioral responses and in facilitating evolutionary transitions in individuality.

OSD CALS Architecture Master Plan Study. Concept Paper. Indexing. Volume 30

DOT National Transportation Integrated Search

1989-06-01

An index identifies and reference information which is exchanged between multiple users and systems. The increased automation that will take place as CALS evolves will dictate an increased use of indexes for the successful exchange of information. Th...

Fog : a review of the literature pertaining to highway problems and possible solutions.

DOT National Transportation Integrated Search

1972-01-01

1. Fogs are significant contributors to multiple car accidents that often result in fatalities. 2. Systems that adequately abate fogs or lighting systems that provide minimum visibility requirements have not evolved. 3. Most abatement techniques stem...

Loblolly Pine Responds to Mechanical Wounding with Increased Resin Flow

Treesearch

Jonathan J. Ruel; Matthew P. Ayres; Peter L. Lorio

1998-01-01

The oleoresin produced by many conifers has a deleterious effect on numerous associated herbivores, including bark beetles (Coleoptera: Scolytidae), and may have evolved as a plant defense mechanism. Three experiments with juvenile loblolly pine (Pinus taeda L.) used mechanical wounding to drain resin reserves and assess the effects of prior bark wounding on...

Melt Compositional Diversities in Early Ignimbrite from the 2.08 Ma Huckleberry Ridge Eruption, Yellowstone

NASA Astrophysics Data System (ADS)

Swallow, E. J.; Wilson, C. J. N.; Myers, M.; Collins, K. S.

2016-12-01

Detailed, stratigraphically-constrained geochemical analyses can shed light on the nature of magma systems and mechanisms behind the initiation and escalation of large caldera-forming eruptions1,2. The 2.08 Ma, ˜2,500 km3 Huckleberry Ridge Tuff is the first of three caldera-forming eruptions in the Yellowstone area3, and consists of a widespread initial fall deposit3,4 followed by three ignimbrite members3: A, B and C. Myers et al.2 demonstrated the episodic and multi-vent initiation of the HRT event during eruption of the initial fall deposits, with sequential tapping of three discrete melt bodies, the last of which becomes dominant within the later fall deposits. Here, we build on their dataset to consider glass compositions in the earliest-erupted parts of the overlying ignimbrite (member A). Trace element analyses of ignimbrite shards reveals clustering of compositions and signifies a continuation of the tapping of multiple melt domains. Principal component and cluster analysis indicate at least seven clusters, separated out by crystal fractionation processes. These early flows tapped a range of melts (paralleled by whole-rock magma compositions), from highly evolved (as in the fall deposits) to hotter, less evolved material not represented in the fall deposits. Variations are greatest in Ba (10-900 ppm), Rb/Sr ratios (10-210) and degrees of LREE depletion. However there is an absence of geographical variation, with locations north and south of the subsequent caldera, and in proximal and distal regions, exhibiting similar ranges of glass composition from inferred contemporaneous flow deposition. These observations suggest complexities in the early stages of the tapping of a heterogeneous magma chamber (comprising multiple melt/magma domains), possibly accompanying the onset of caldera collapse. We also consider that external controls, such as rifting, were at least initially important as an eruption trigger2 but understanding of the mechanisms controlling the onset of ignimbrite generation is complicated by the apparent lack of a compositionally coherent melt-dominant magma body. 1Pistolesi et al. (2016): Geology 44, 487-490; 2Myers et al. (2016): Earth Planet Sci Lett (in press); 3Christiansen (2001): USGS Prof Paper 729-G; 4Izett & Wilcox (1982), USGS Map I-1325.

A single origin of extreme matrotrophy in African mabuyine skinks

PubMed Central

Metallinou, Margarita; Karin, Benjamin R.; Conradie, Werner; Wagner, Philipp; Schmitz, Andreas; Jackman, Todd R.; Bauer, Aaron M.

2016-01-01

Most mammals and approximately 20% of squamates (lizards and snakes) are viviparous, whereas all crocodilians, birds and turtles are oviparous. Viviparity evolved greater than 100 times in squamates, including multiple times in Mabuyinae (Reptilia: Scincidae), making this group ideal for studying the evolution of nutritional patterns associated with viviparity. Previous studies suggest that extreme matrotrophy, the support of virtually all of embryonic development by maternal nutrients, evolved as many as three times in Mabuyinae: in Neotropical Mabuyinae (63 species), Eumecia (2 species; Africa) and Trachylepis ivensii (Africa). However, no explicit phylogenetic hypotheses exist for understanding the evolution of extreme matrotrophy. Using multilocus DNA data, we inferred a species tree for Mabuyinae that implies that T. ivensii (here assigned to the resurrected genus Lubuya) is sister to Eumecia, suggesting that extreme matrotrophy evolved only once in African mabuyine skinks. PMID:27555650

Evolution of vertebrate visual pigments.

PubMed

Bowmaker, James K

2008-09-01

The visual pigments of vertebrates evolved about 500 million years ago, before the major evolutionary step of the development of jaws. Four spectrally distinct classes of cone opsin evolved through gene duplication, followed by the rod opsin class that arose from the duplication of the middle-wave-sensitive cone opsin. All four cone classes are present in many extant teleost fish, reptiles and birds, but one or more classes have been lost in primitive fish, amphibians and mammals. Gene duplication within the cone classes, especially in teleosts, has resulted in multiple opsins being available, both temporally and spatially, during development.

Metadata Evaluation and Improvement: Evolving Analysis and Reporting

NASA Technical Reports Server (NTRS)

Habermann, Ted; Kozimor, John; Gordon, Sean

2017-01-01

ESIP Community members create and manage a large collection of environmental datasets that span multiple decades, the entire globe, and many parts of the solar system. Metadata are critical for discovering, accessing, using and understanding these data effectively and ESIP community members have successfully created large collections of metadata describing these data. As part of the White House Big Earth Data Initiative (BEDI), ESDIS has developed a suite of tools for evaluating these metadata in native dialects with respect to recommendations from many organizations. We will describe those tools and demonstrate evolving techniques for sharing results with data providers.

Highly-Parallel, Highly-Compact Computing Structures Implemented in Nanotechnology

NASA Technical Reports Server (NTRS)

Crawley, D. G.; Duff, M. J. B.; Fountain, T. J.; Moffat, C. D.; Tomlinson, C. D.

1995-01-01

In this paper, we describe work in which we are evaluating how the evolving properties of nano-electronic devices could best be utilized in highly parallel computing structures. Because of their combination of high performance, low power, and extreme compactness, such structures would have obvious applications in spaceborne environments, both for general mission control and for on-board data analysis. However, the anticipated properties of nano-devices mean that the optimum architecture for such systems is by no means certain. Candidates include single instruction multiple datastream (SIMD) arrays, neural networks, and multiple instruction multiple datastream (MIMD) assemblies.

How cancer shapes evolution, and how evolution shapes cancer

PubMed Central

Casás-Selves, Matias; DeGregori, James

2013-01-01

Evolutionary theories are critical for understanding cancer development at the level of species as well as at the level of cells and tissues, and for developing effective therapies. Animals have evolved potent tumor suppressive mechanisms to prevent cancer development. These mechanisms were initially necessary for the evolution of multi-cellular organisms, and became even more important as animals evolved large bodies and long lives. Indeed, the development and architecture of our tissues were evolutionarily constrained by the need to limit cancer. Cancer development within an individual is also an evolutionary process, which in many respects mirrors species evolution. Species evolve by mutation and selection acting on individuals in a population; tumors evolve by mutation and selection acting on cells in a tissue. The processes of mutation and selection are integral to the evolution of cancer at every step of multistage carcinogenesis, from tumor genesis to metastasis. Factors associated with cancer development, such as aging and carcinogens, have been shown to promote cancer evolution by impacting both mutation and selection processes. While there are therapies that can decimate a cancer cell population, unfortunately, cancers can also evolve resistance to these therapies, leading to the resurgence of treatment-refractory disease. Understanding cancer from an evolutionary perspective can allow us to appreciate better why cancers predominantly occur in the elderly, and why other conditions, from radiation exposure to smoking, are associated with increased cancers. Importantly, the application of evolutionary theory to cancer should engender new treatment strategies that could better control this dreaded disease. PMID:23705033

Cellular packing, mechanical stress and the evolution of multicellularity

NASA Astrophysics Data System (ADS)

Jacobeen, Shane; Pentz, Jennifer T.; Graba, Elyes C.; Brandys, Colin G.; Ratcliff, William C.; Yunker, Peter J.

2018-03-01

The evolution of multicellularity set the stage for sustained increases in organismal complexity1-5. However, a fundamental aspect of this transition remains largely unknown: how do simple clusters of cells evolve increased size when confronted by forces capable of breaking intracellular bonds? Here we show that multicellular snowflake yeast clusters6-8 fracture due to crowding-induced mechanical stress. Over seven weeks ( 291 generations) of daily selection for large size, snowflake clusters evolve to increase their radius 1.7-fold by reducing the accumulation of internal stress. During this period, cells within the clusters evolve to be more elongated, concomitant with a decrease in the cellular volume fraction of the clusters. The associated increase in free space reduces the internal stress caused by cellular growth, thus delaying fracture and increasing cluster size. This work demonstrates how readily natural selection finds simple, physical solutions to spatial constraints that limit the evolution of group size—a fundamental step in the evolution of multicellularity.

Convergence: Human Intelligence The Next 100 Years

ERIC Educational Resources Information Center

Fluellen, Jerry E., Jr.

2005-01-01

How might human intelligence evolve over the next 100 years? This issue paper explores that idea. First, the paper summarizes five emerging perspectives about human intelligence: Howard Gardner's multiple intelligences theory, Robert Sternberg's triarchic theory of intelligence, Ellen Langer's mindfulness theory, David Perkins' learnable…

Evolutionary Processes in Multiple Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eggleton, P P; Kisseleva-Eggleton, L

There are several ways in which triple stars can evolve in somewhat unusual ways. They discuss two situations where Case A Roche-lobe overflow, followed by a merger, can produce anomalous wide binaries such as {gamma} Per; and Kozai cycles in triples with non-parallel orbits, which can produce merged rapidly-rotating stars like AB Dor, and which can also lead to the delayed ejection of one component of a multiple, as may have been observed in T Tau in 1998.

The mechanism of sound production in túngara frogs and its role in sexual selection and speciation.

PubMed

Ryan, Michael J; Guerra, Mónica A

2014-10-01

Sexual communication can evolve in response to sexual selection, and it can also cause behavioral reproductive isolation between populations and thus drive speciation. Anurans are an excellent system to investigate these links between behavior and evolution because we have detailed knowledge of how neural mechanisms generate behavioral preferences for calls and how these preferences then generate selection on call variation. But we know far less about the physical mechanisms of call production, especially how different laryngeal morphologies generate call variation. Here we review studies of a group of species that differ in the presence of a secondary call component that evolved under sexual selection. We discuss how the larynx produces this call component, and how laryngeal morphology generates sexual selection and can contribute to speciation. Copyright © 2014. Published by Elsevier Ltd.

Cloak and Dagger: Alternative Immune Evasion and Modulation Strategies of Poxviruses

PubMed Central

Bidgood, Susanna R.; Mercer, Jason

2015-01-01

As all viruses rely on cellular factors throughout their replication cycle, to be successful they must evolve strategies to evade and/or manipulate the defence mechanisms employed by the host cell. In addition to their expression of a wide array of host modulatory factors, several recent studies have suggested that poxviruses may have evolved unique mechanisms to shunt or evade host detection. These potential mechanisms include mimicry of apoptotic bodies by mature virions (MVs), the use of viral sub-structures termed lateral bodies for the packaging and delivery of host modulators, and the formation of a second, “cloaked” form of infectious extracellular virus (EVs). Here we discuss these various strategies and how they may facilitate poxvirus immune evasion. Finally we propose a model for the exploitation of the cellular exosome pathway for the formation of EVs. PMID:26308043

Undermining and Strengthening Social Networks through Network Modification

PubMed Central

Mellon, Jonathan; Yoder, Jordan; Evans, Daniel

2016-01-01

Social networks have well documented effects at the individual and aggregate level. Consequently it is often useful to understand how an attempt to influence a network will change its structure and consequently achieve other goals. We develop a framework for network modification that allows for arbitrary objective functions, types of modification (e.g. edge weight addition, edge weight removal, node removal, and covariate value change), and recovery mechanisms (i.e. how a network responds to interventions). The framework outlined in this paper helps both to situate the existing work on network interventions but also opens up many new possibilities for intervening in networks. In particular use two case studies to highlight the potential impact of empirically calibrating the objective function and network recovery mechanisms as well as showing how interventions beyond node removal can be optimised. First, we simulate an optimal removal of nodes from the Noordin terrorist network in order to reduce the expected number of attacks (based on empirically predicting the terrorist collaboration network from multiple types of network ties). Second, we simulate optimally strengthening ties within entrepreneurial ecosystems in six developing countries. In both cases we estimate ERGM models to simulate how a network will endogenously evolve after intervention. PMID:27703198

Type IV Collagens and Basement Membrane Diseases: Cell Biology and Pathogenic Mechanisms.

PubMed

Mao, Mao; Alavi, Marcel V; Labelle-Dumais, Cassandre; Gould, Douglas B

2015-01-01

Basement membranes are highly specialized extracellular matrices. Once considered inert scaffolds, basement membranes are now viewed as dynamic and versatile environments that modulate cellular behaviors to regulate tissue development, function, and repair. Increasing evidence suggests that, in addition to providing structural support to neighboring cells, basement membranes serve as reservoirs of growth factors that direct and fine-tune cellular functions. Type IV collagens are a major component of all basement membranes. They evolved along with the earliest multicellular organisms and have been integrated into diverse fundamental biological processes as time and evolution shaped the animal kingdom. The roles of basement membranes in humans are as complex and diverse as their distributions and molecular composition. As a result, basement membrane defects result in multisystem disorders with ambiguous and overlapping boundaries that likely reflect the simultaneous interplay and integration of multiple cellular pathways and processes. Consequently, there will be no single treatment for basement membrane disorders, and therapies are likely to be as varied as the phenotypes. Understanding tissue-specific pathology and the underlying molecular mechanism is the present challenge; personalized medicine will rely upon understanding how a given mutation impacts diverse cellular functions. Copyright © 2015 Elsevier Inc. All rights reserved.

Mechanisms of regulation of SNF1/AMPK/SnRK1 protein kinases.

PubMed

Crozet, Pierre; Margalha, Leonor; Confraria, Ana; Rodrigues, Américo; Martinho, Cláudia; Adamo, Mattia; Elias, Carlos A; Baena-González, Elena

2014-01-01

The SNF1 (sucrose non-fermenting 1)-related protein kinases 1 (SnRKs1) are the plant orthologs of the budding yeast SNF1 and mammalian AMPK (AMP-activated protein kinase). These evolutionarily conserved kinases are metabolic sensors that undergo activation in response to declining energy levels. Upon activation, SNF1/AMPK/SnRK1 kinases trigger a vast transcriptional and metabolic reprograming that restores energy homeostasis and promotes tolerance to adverse conditions, partly through an induction of catabolic processes and a general repression of anabolism. These kinases typically function as a heterotrimeric complex composed of two regulatory subunits, β and γ, and an α-catalytic subunit, which requires phosphorylation of a conserved activation loop residue for activity. Additionally, SNF1/AMPK/SnRK1 kinases are controlled by multiple mechanisms that have an impact on kinase activity, stability, and/or subcellular localization. Here we will review current knowledge on the regulation of SNF1/AMPK/SnRK1 by upstream components, post-translational modifications, various metabolites, hormones, and others, in an attempt to highlight both the commonalities of these essential eukaryotic kinases and the divergences that have evolved to cope with the particularities of each one of these systems.

Mechanisms of regulation of SNF1/AMPK/SnRK1 protein kinases

PubMed Central

Crozet, Pierre; Margalha, Leonor; Confraria, Ana; Rodrigues, Américo; Martinho, Cláudia; Adamo, Mattia; Elias, Carlos A.; Baena-González, Elena

2014-01-01

The SNF1 (sucrose non-fermenting 1)-related protein kinases 1 (SnRKs1) are the plant orthologs of the budding yeast SNF1 and mammalian AMPK (AMP-activated protein kinase). These evolutionarily conserved kinases are metabolic sensors that undergo activation in response to declining energy levels. Upon activation, SNF1/AMPK/SnRK1 kinases trigger a vast transcriptional and metabolic reprograming that restores energy homeostasis and promotes tolerance to adverse conditions, partly through an induction of catabolic processes and a general repression of anabolism. These kinases typically function as a heterotrimeric complex composed of two regulatory subunits, β and γ, and an α-catalytic subunit, which requires phosphorylation of a conserved activation loop residue for activity. Additionally, SNF1/AMPK/SnRK1 kinases are controlled by multiple mechanisms that have an impact on kinase activity, stability, and/or subcellular localization. Here we will review current knowledge on the regulation of SNF1/AMPK/SnRK1 by upstream components, post-translational modifications, various metabolites, hormones, and others, in an attempt to highlight both the commonalities of these essential eukaryotic kinases and the divergences that have evolved to cope with the particularities of each one of these systems. PMID:24904600

Undermining and Strengthening Social Networks through Network Modification.

PubMed

Mellon, Jonathan; Yoder, Jordan; Evans, Daniel

2016-10-05

Social networks have well documented effects at the individual and aggregate level. Consequently it is often useful to understand how an attempt to influence a network will change its structure and consequently achieve other goals. We develop a framework for network modification that allows for arbitrary objective functions, types of modification (e.g. edge weight addition, edge weight removal, node removal, and covariate value change), and recovery mechanisms (i.e. how a network responds to interventions). The framework outlined in this paper helps both to situate the existing work on network interventions but also opens up many new possibilities for intervening in networks. In particular use two case studies to highlight the potential impact of empirically calibrating the objective function and network recovery mechanisms as well as showing how interventions beyond node removal can be optimised. First, we simulate an optimal removal of nodes from the Noordin terrorist network in order to reduce the expected number of attacks (based on empirically predicting the terrorist collaboration network from multiple types of network ties). Second, we simulate optimally strengthening ties within entrepreneurial ecosystems in six developing countries. In both cases we estimate ERGM models to simulate how a network will endogenously evolve after intervention.

Undermining and Strengthening Social Networks through Network Modification

NASA Astrophysics Data System (ADS)

Mellon, Jonathan; Yoder, Jordan; Evans, Daniel

2016-10-01

Social networks have well documented effects at the individual and aggregate level. Consequently it is often useful to understand how an attempt to influence a network will change its structure and consequently achieve other goals. We develop a framework for network modification that allows for arbitrary objective functions, types of modification (e.g. edge weight addition, edge weight removal, node removal, and covariate value change), and recovery mechanisms (i.e. how a network responds to interventions). The framework outlined in this paper helps both to situate the existing work on network interventions but also opens up many new possibilities for intervening in networks. In particular use two case studies to highlight the potential impact of empirically calibrating the objective function and network recovery mechanisms as well as showing how interventions beyond node removal can be optimised. First, we simulate an optimal removal of nodes from the Noordin terrorist network in order to reduce the expected number of attacks (based on empirically predicting the terrorist collaboration network from multiple types of network ties). Second, we simulate optimally strengthening ties within entrepreneurial ecosystems in six developing countries. In both cases we estimate ERGM models to simulate how a network will endogenously evolve after intervention.

Transport and homeostasis of potassium and phosphate: limiting factors for sustainable crop production.

PubMed

Luan, Mingda; Tang, Ren-Jie; Tang, Yumei; Tian, Wang; Hou, Congong; Zhao, Fugeng; Lan, Wenzhi; Luan, Sheng

2017-06-01

Potassium (K) and phosphate (Pi) are both macronutrients essential for plant growth and crop production, but the unrenewable resources of phosphorus rock and potash have become limiting factors for food security. One critical measure to help solve this problem is to improve nutrient use efficiency (NUE) in plants by understanding and engineering genetic networks for ion uptake, translocation, and storage. Plants have evolved multiple systems to adapt to various nutrient conditions for growth and production. Within the NUE networks, transport proteins and their regulators are the primary players for maintaining nutrient homeostasis and could be utilized to engineer high NUE traits in crop plants. A large number of publications have detailed K+ and Pi transport proteins in plants over the past three decades. Meanwhile, the discovery and validation of their regulatory mechanisms are fast-track topics for research. Here, we provide an overview of K+ and Pi transport proteins and their regulatory mechanisms, which participate in the uptake, translocation, storage, and recycling of these nutrients in plants. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Simulations and Experiments of Dynamic Granular Compaction in Non-ideal Geometries

NASA Astrophysics Data System (ADS)

Homel, Michael; Herbold, Eric; Lind, John; Crum, Ryan; Hurley, Ryan; Akin, Minta; Pagan, Darren; LLNL Team

2017-06-01

Accurately describing the dynamic compaction of granular materials is a persistent challenge in computational mechanics. Using a synchrotron x-ray source we have obtained detailed imaging of the evolving compaction front in synthetic olivine powder impacted at 300 - 600 m / s . To facilitate imaging, a non-traditional sample geometry is used, producing multiple load paths within the sample. We demonstrate that (i) commonly used models for porous compaction may produce inaccurate results for complex loading, even if the 1 - D , uniaxial-strain compaction response is reasonable, and (ii) the experimental results can be used along with simulations to determine parameters for sophisticated constitutive models that more accurately describe the strength, softening, bulking, and poroelastic response. Effects of experimental geometry and alternative configurations are discussed. Our understanding of the material response is further enhanced using mesoscale simulations that allow us to relate the mechanisms of grain fracture, contact, and comminution to the macroscale continuum response. Numerical considerations in both continuum and mesoscale simulations are described. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LDRD#16-ERD-010. LLNL-ABS-725113.

Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations

PubMed Central

Perron, Gabriel G.; Lee, Alexander E. G.; Wang, Yun; Huang, Wei E.; Barraclough, Timothy G.

2012-01-01

Bacterial recombination is believed to be a major factor explaining the prevalence of multi-drug-resistance (MDR) among pathogenic bacteria. Despite extensive evidence for exchange of resistance genes from retrospective sequence analyses, experimental evidence for the evolutionary benefits of bacterial recombination is scarce. We compared the evolution of MDR between populations of Acinetobacter baylyi in which we manipulated both the recombination rate and the initial diversity of strains with resistance to single drugs. In populations lacking recombination, the initial presence of multiple strains resistant to different antibiotics inhibits the evolution of MDR. However, in populations with recombination, the inhibitory effect of standing diversity is alleviated and MDR evolves rapidly. Moreover, only the presence of DNA harbouring resistance genes promotes the evolution of resistance, ruling out other proposed benefits for recombination. Together, these results provide direct evidence for the fitness benefits of bacterial recombination and show that this occurs by mitigation of functional interference between genotypes resistant to single antibiotics. Although analogous to previously described mechanisms of clonal interference among alternative beneficial mutations, our results actually highlight a different mechanism by which interactions among co-occurring strains determine the benefits of recombination for bacterial evolution. PMID:22048956

The Exosome Associates Cotranscriptionally with the Nascent Pre-mRNP through Interactions with Heterogeneous Nuclear Ribonucleoproteins

PubMed Central

Hessle, Viktoria; Björk, Petra; Sokolowski, Marcus; de Valdivia, Ernesto González; Silverstein, Rebecca; Artemenko, Konstantin; Tyagi, Anu; Maddalo, Gianluca; Ilag, Leopold; Helbig, Roger; Zubarev, Roman A.

2009-01-01

Eukaryotic cells have evolved quality control mechanisms to degrade aberrant mRNA molecules and prevent the synthesis of defective proteins that could be deleterious for the cell. The exosome, a protein complex with ribonuclease activity, is a key player in quality control. An early quality checkpoint takes place cotranscriptionally but little is known about the molecular mechanisms by which the exosome is recruited to the transcribed genes. Here we study the core exosome subunit Rrp4 in two insect model systems, Chironomus and Drosophila. We show that a significant fraction of Rrp4 is associated with the nascent pre-mRNPs and that a specific mRNA-binding protein, Hrp59/hnRNP M, interacts in vivo with multiple exosome subunits. Depletion of Hrp59 by RNA interference reduces the levels of Rrp4 at transcription sites, which suggests that Hrp59 is needed for the exosome to stably interact with nascent pre-mRNPs. Our results lead to a revised mechanistic model for cotranscriptional quality control in which the exosome is constantly recruited to newly synthesized RNAs through direct interactions with specific hnRNP proteins. PMID:19494042

Hemoglobin: A Nitric-Oxide Dioxygenase

PubMed Central

Gardner, Paul R.

2012-01-01

Members of the hemoglobin superfamily efficiently catalyze nitric-oxide dioxygenation, and when paired with native electron donors, function as NO dioxygenases (NODs). Indeed, the NOD function has emerged as a more common and ancient function than the well-known role in O2 transport-storage. Novel hemoglobins possessing a NOD function continue to be discovered in diverse life forms. Unique hemoglobin structures evolved, in part, for catalysis with different electron donors. The mechanism of NOD catalysis by representative single domain hemoglobins and multidomain flavohemoglobin occurs through a multistep mechanism involving O2 migration to the heme pocket, O2 binding-reduction, NO migration, radical-radical coupling, O-atom rearrangement, nitrate release, and heme iron re-reduction. Unraveling the physiological functions of multiple NODs with varying expression in organisms and the complexity of NO as both a poison and signaling molecule remain grand challenges for the NO field. NOD knockout organisms and cells expressing recombinant NODs are helping to advance our understanding of NO actions in microbial infection, plant senescence, cancer, mitochondrial function, iron metabolism, and tissue O2 homeostasis. NOD inhibitors are being pursued for therapeutic applications as antibiotics and antitumor agents. Transgenic NOD-expressing plants, fish, algae, and microbes are being developed for agriculture, aquaculture, and industry. PMID:24278729

Recanalization Therapies in Acute Ischemic Stroke: Pharmacological Agents, Devices, and Combinations

PubMed Central

Sharma, Vijay K.; Teoh, Hock Luen; Wong, Lily Y. H.; Su, Jie; Ong, Benjamin K. C.; Chan, Bernard P. L.

2010-01-01

The primary aim of thrombolysis in acute ischemic stroke is recanalization of an occluded intracranial artery. Recanalization is an important predictor of stroke outcome as timely restoration of regional cerebral perfusion helps salvage threatened ischemic tissue. At present, intravenously administered tissue plasminogen activator (IV-TPA) remains the only FDA-approved therapeutic agent for the treatment of ischemic stroke within 3 hours of symptom onset. Recent studies have demonstrated safety as well as efficacy of IV-TPA even in an extended therapeutic window. However, the short therapeutic window, low rates of recanalization, and only modest benefits with IV-TPA have prompted a quest for alternative approaches to restore blood flow in an occluded artery in acute ischemic stroke. Although intra-arterial delivery of the thrombolytic agent seems effective, various logistic constraints limit its routine use and as yet no lytic agent have not received full regulatory approval for intra-arterial therapy. Mechanical devices and approaches can achieve higher rates of recanalization but their safety and efficacy still need to be established in larger clinical trials. The field of acute revascularization is rapidly evolving, and various combinations of pharmacologic agents, mechanical devices, and novel microbubble/ultrasound technologies are being tested in multiple clinical trials. PMID:20798838

An oral exam model for teaching advanced "Batchelor-level" fluid mechanics in the US

NASA Astrophysics Data System (ADS)

Freund, Jonathan

2016-11-01

A teaching model is developed to meet the challenge of teaching fluid mechanics at what might be considered a high level, at least by the current norms in the US. The initial goal was to avoid loss of concepts amidst the challenge of particular mathematical manipulations on particular assignments. However, it evolved toward fostering facile working knowledge of challenging material, such as in the books by Batchelor (e.g. streaming flow), Whitham (e.g. ship waves), and van Dyke (e.g. second-order boundary layer). To this end, the course model forgoes traditional assigned problems to focus on completion, augmentation, and in-depth understanding of the lecture material. The lectures are relatively traditional in structure, albeit with somewhat more interactive examples. The main unusual feature-again, by modern US standards-was assessment via multiple half-hour oral exams. This model has now been successful over 8 semesters for 3 different graduate courses in 2 departments. For all, students were assume to have already completed a full course at a "Navier-Stokes level". The presentation will include specifics of the course and exam structure, impressions of positive outcomes from the instructor, and a summary of the overwhelmingly positive student feedback.

Cell assembly sequences arising from spike threshold adaptation keep track of time in the hippocampus

PubMed Central

Itskov, Vladimir; Curto, Carina; Pastalkova, Eva; Buzsáki, György

2011-01-01

Hippocampal neurons can display reliable and long-lasting sequences of transient firing patterns, even in the absence of changing external stimuli. We suggest that time-keeping is an important function of these sequences, and propose a network mechanism for their generation. We show that sequences of neuronal assemblies recorded from rat hippocampal CA1 pyramidal cells can reliably predict elapsed time (15-20 sec) during wheel running with a precision of 0.5sec. In addition, we demonstrate the generation of multiple reliable, long-lasting sequences in a recurrent network model. These sequences are generated in the presence of noisy, unstructured inputs to the network, mimicking stationary sensory input. Identical initial conditions generate similar sequences, whereas different initial conditions give rise to distinct sequences. The key ingredients responsible for sequence generation in the model are threshold-adaptation and a Mexican-hat-like pattern of connectivity among pyramidal cells. This pattern may arise from recurrent systems such as the hippocampal CA3 region or the entorhinal cortex. We hypothesize that mechanisms that evolved for spatial navigation also support tracking of elapsed time in behaviorally relevant contexts. PMID:21414904

Learned recognition of maternal signature odors mediates the first suckling episode in mice

PubMed Central

Logan, Darren W.; Brunet, Lisa J.; Webb, William R.; Cutforth, Tyler; Ngai, John; Stowers, Lisa

2012-01-01

Summary Background Soon after birth all mammals must initiate milk suckling to survive. In rodents, this innate behavior is critically dependent on uncharacterized maternally-derived chemosensory ligands. Recently the first pheromone sufficient to initiate suckling was isolated from the rabbit. Identification of the olfactory cues that trigger first suckling in the mouse would provide the means to determine the neural mechanisms that generate innate behavior. Results Here we use behavioral analysis, metabolomics, and calcium imaging of primary sensory neurons and find no evidence of ligands with intrinsic bioactivity, such as pheromones, acting to promote first suckling in the mouse. Instead, we find that the initiation of suckling is dependent on variable blends of maternal ‘signature odors’ that are learned and recognized prior to first suckling. Conclusions As observed with pheromone-mediated behavior, the response to signature odors releases innate behavior. However, this mechanism tolerates variability in both the signaling ligands and sensory neurons which may maximize the probability that this first essential behavior is successfully initiated. These results suggest that mammalian species have evolved multiple strategies to ensure the onset of this critical behavior. PMID:23041191

The Association between Endometriomas and Ovarian Cancer: Preventive Effect of Inhibiting Ovulation and Menstruation during Reproductive Life

PubMed Central

Grandi, Giovanni; Toss, Angela; Cortesi, Laura; Botticelli, Laura; Volpe, Annibale; Cagnacci, Angelo

2015-01-01

Although endometriosis frequently involves multiple sites in the pelvis, malignancies associated with this disease are mostly confined to the ovaries, evolving from an endometrioma. Endometriomas present a 2-3-fold increased risk of transformation in clear-cell, endometrioid, and possibly low-grade serous ovarian cancers, but not in mucinous ovarian cancers. These last cancers are, in some aspects, different from the other epithelial ovarian cancers, as they do not appear to be decreased by the inhibition of ovulation and menstruation. The step by step process of transformation from typical endometrioma, through atypical endometrioma, finally to ovarian cancer seems mainly related to oxidative stress, inflammation, hyperestrogenism, and specific molecular alterations. Particularly, activation of oncogenic KRAS and PI3K pathways and inactivation of tumor suppressor genes PTEN and ARID1A are suggested as major pathogenic mechanisms for endometriosis associated clear-cell and endometrioid ovarian cancer. Both the risk for endometriomas and their associated ovarian cancers seems to be highly and similarly decreased by the inhibition of ovulation and retrograde menstruation, suggesting a common pathogenetic mechanism and common possible preventive strategies during reproductive life. PMID:26413541

The Association between Endometriomas and Ovarian Cancer: Preventive Effect of Inhibiting Ovulation and Menstruation during Reproductive Life.

PubMed

Grandi, Giovanni; Toss, Angela; Cortesi, Laura; Botticelli, Laura; Volpe, Annibale; Cagnacci, Angelo

2015-01-01

Although endometriosis frequently involves multiple sites in the pelvis, malignancies associated with this disease are mostly confined to the ovaries, evolving from an endometrioma. Endometriomas present a 2-3-fold increased risk of transformation in clear-cell, endometrioid, and possibly low-grade serous ovarian cancers, but not in mucinous ovarian cancers. These last cancers are, in some aspects, different from the other epithelial ovarian cancers, as they do not appear to be decreased by the inhibition of ovulation and menstruation. The step by step process of transformation from typical endometrioma, through atypical endometrioma, finally to ovarian cancer seems mainly related to oxidative stress, inflammation, hyperestrogenism, and specific molecular alterations. Particularly, activation of oncogenic KRAS and PI3K pathways and inactivation of tumor suppressor genes PTEN and ARID1A are suggested as major pathogenic mechanisms for endometriosis associated clear-cell and endometrioid ovarian cancer. Both the risk for endometriomas and their associated ovarian cancers seems to be highly and similarly decreased by the inhibition of ovulation and retrograde menstruation, suggesting a common pathogenetic mechanism and common possible preventive strategies during reproductive life.

Catabolite repression by intracellular succinate in Campylobacter jejuni

USDA-ARS?s Scientific Manuscript database

Bacteria have evolved different mechanisms to catabolize carbon sources from a mixture of nutrients. They first consume their preferred carbon source, before others are used. Regulatory mechanisms adapt the metabolism accordingly to maximize growth and to outcompete other organisms. The human patho...

A case study for effects of operational taxonomic units from intracellular endoparasites and ciliates on the eukaryotic phylogeny: phylogenetic position of the haptophyta in analyses of multiple slowly evolving genes.

PubMed

Nozaki, Hisayoshi; Yang, Yi; Maruyama, Shinichiro; Suzaki, Toshinobu

2012-01-01

Recent multigene phylogenetic analyses have contributed much to our understanding of eukaryotic phylogeny. However, the phylogenetic positions of various lineages within the eukaryotes have remained unresolved or in conflict between different phylogenetic studies. These phylogenetic ambiguities might have resulted from mixtures or integration from various factors including limited taxon sampling, missing data in the alignment, saturations of rapidly evolving genes, mixed analyses of short- and long-branched operational taxonomic units (OTUs), intracellular endoparasite and ciliate OTUs with unusual substitution etc. In order to evaluate the effects from intracellular endoparasite and ciliate OTUs co-analyzed on the eukaryotic phylogeny and simplify the results, we here used two different sets of data matrices of multiple slowly evolving genes with small amounts of missing data and examined the phylogenetic position of the secondary photosynthetic chromalveolates Haptophyta, one of the most abundant groups of oceanic phytoplankton and significant primary producers. In both sets, a robust sister relationship between Haptophyta and SAR (stramenopiles, alveolates, rhizarians, or SA [stramenopiles and alveolates]) was resolved when intracellular endoparasite/ciliate OTUs were excluded, but not in their presence. Based on comparisons of character optimizations on a fixed tree (with a clade composed of haptophytes and SAR or SA), disruption of the monophyly between haptophytes and SAR (or SA) in the presence of intracellular endoparasite/ciliate OTUs can be considered to be a result of multiple evolutionary reversals of character positions that supported the synapomorphy of the haptophyte and SAR (or SA) clade in the absence of intracellular endoparasite/ciliate OTUs.

The chicken or the egg? Adaptation to desiccation and salinity tolerance in a lineage of water beetles.

PubMed

Pallarés, Susana; Arribas, Paula; Bilton, David T; Millán, Andrés; Velasco, Josefa; Ribera, Ignacio

2017-10-01

Transitions from fresh to saline habitats are restricted to a handful of insect lineages, as the colonization of saline waters requires specialized mechanisms to deal with osmotic stress. Previous studies have suggested that tolerance to salinity and desiccation could be mechanistically and evolutionarily linked, but the temporal sequence of these adaptations is not well established for individual lineages. We combined molecular, physiological and ecological data to explore the evolution of desiccation resistance, hyporegulation ability (i.e., the ability to osmoregulate in hyperosmotic media) and habitat transitions in the water beetle genus Enochrus subgenus Lumetus (Hydrophilidae). We tested whether enhanced desiccation resistance evolved before increases in hyporegulation ability or vice versa, or whether the two mechanisms evolved in parallel. The most recent ancestor of Lumetus was inferred to have high desiccation resistance and moderate hyporegulation ability. There were repeated shifts between habitats with differing levels of salinity in the radiation of the group, those to the most saline habitats generally occurring more rapidly than those to less saline ones. Significant and accelerated changes in hyporegulation ability evolved in parallel with smaller and more progressive increases in desiccation resistance across the phylogeny, associated with the colonization of meso- and hypersaline waters during global aridification events. All species with high hyporegulation ability were also desiccation-resistant, but not vice versa. Overall, results are consistent with the hypothesis that desiccation resistance mechanisms evolved first and provided the physiological basis for the development of hyporegulation ability, allowing these insects to colonize and diversify across meso- and hypersaline habitats. © 2017 John Wiley & Sons Ltd.

Chromatic Illumination Discrimination Ability Reveals that Human Colour Constancy Is Optimised for Blue Daylight Illuminations

PubMed Central

Pearce, Bradley; Crichton, Stuart; Mackiewicz, Michal; Finlayson, Graham D.; Hurlbert, Anya

2014-01-01

The phenomenon of colour constancy in human visual perception keeps surface colours constant, despite changes in their reflected light due to changing illumination. Although colour constancy has evolved under a constrained subset of illuminations, it is unknown whether its underlying mechanisms, thought to involve multiple components from retina to cortex, are optimised for particular environmental variations. Here we demonstrate a new method for investigating colour constancy using illumination matching in real scenes which, unlike previous methods using surface matching and simulated scenes, allows testing of multiple, real illuminations. We use real scenes consisting of solid familiar or unfamiliar objects against uniform or variegated backgrounds and compare discrimination performance for typical illuminations from the daylight chromaticity locus (approximately blue-yellow) and atypical spectra from an orthogonal locus (approximately red-green, at correlated colour temperature 6700 K), all produced in real time by a 10-channel LED illuminator. We find that discrimination of illumination changes is poorer along the daylight locus than the atypical locus, and is poorest particularly for bluer illumination changes, demonstrating conversely that surface colour constancy is best for blue daylight illuminations. Illumination discrimination is also enhanced, and therefore colour constancy diminished, for uniform backgrounds, irrespective of the object type. These results are not explained by statistical properties of the scene signal changes at the retinal level. We conclude that high-level mechanisms of colour constancy are biased for the blue daylight illuminations and variegated backgrounds to which the human visual system has typically been exposed. PMID:24586299

DOE Office of Scientific and Technical Information (OSTI.GOV)

Millar, A. P.; Behrmann, G.; Bernardt, C.

With over ten years in production use dCache data storage system has evolved to match ever changing lansdcape of continually evolving storage technologies with new solutions to both existing problems and new challenges. In this paper, we present three areas of innovation in dCache: providing efficient access to data with NFS v4.1 pNFS, adoption of CDMI and WebDAV as an alternative to SRM for managing data, and integration with alternative authentication mechanisms.

Synaptic Plasticity and Spike Synchronisation in Neuronal Networks

NASA Astrophysics Data System (ADS)

Borges, Rafael R.; Borges, Fernando S.; Lameu, Ewandson L.; Protachevicz, Paulo R.; Iarosz, Kelly C.; Caldas, Iberê L.; Viana, Ricardo L.; Macau, Elbert E. N.; Baptista, Murilo S.; Grebogi, Celso; Batista, Antonio M.

2017-12-01

Brain plasticity, also known as neuroplasticity, is a fundamental mechanism of neuronal adaptation in response to changes in the environment or due to brain injury. In this review, we show our results about the effects of synaptic plasticity on neuronal networks composed by Hodgkin-Huxley neurons. We show that the final topology of the evolved network depends crucially on the ratio between the strengths of the inhibitory and excitatory synapses. Excitation of the same order of inhibition revels an evolved network that presents the rich-club phenomenon, well known to exist in the brain. For initial networks with considerably larger inhibitory strengths, we observe the emergence of a complex evolved topology, where neurons sparsely connected to other neurons, also a typical topology of the brain. The presence of noise enhances the strength of both types of synapses, but if the initial network has synapses of both natures with similar strengths. Finally, we show how the synchronous behaviour of the evolved network will reflect its evolved topology.

Jomtien to Jomtien: The Evolving Coordination Process of Education for All 1990-2011

ERIC Educational Resources Information Center

Ito, Hiroshi

2012-01-01

UNESCO's EFA coordination mechanisms have been serving political platforms for EFA stakeholders for over 20 years. During the Ninth Meeting of the High-Level Group on EFA (HLG) in 2010, however, UNESCO was called on to enhance the effectiveness of the coordination mechanisms. This paper examines the EFA coordination mechanisms between the World…

Nanoscale imaging of fundamental Li battery chemistry: solid-electrolyte interphase formation and preferential growth of lithium metal nanoclusters

DOE PAGES

Sacci, Robert L; Black, Jennifer M.; Wisinger, Nina; ...

2015-02-23

The performance characteristics of Li-ion batteries are intrinsically linked to evolving nanoscale interfacial electrochemical reactions. To probe the mechanisms of solid electrolyte interphase formation and Li electrodeposition from a standard battery electrolyte, we use in situ electrochemical scanning transmission electron microscopy for controlled potential sweep-hold electrochemical measurements with simultaneous BF and ADF STEM image acquisition. Through a combined quantitative electrochemical measurement and quantitative STEM imaging approach, based upon electron scattering theory, we show that chemically sensitive ADF STEM imaging can be used to estimate the density of evolving SEI constituents and distinguish contrast mechanisms of Li-bearing components in the liquidmore » cell.« less

Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Aifen; Lau, Rebecca; Baran, Richard

ABSTRACT. Rapid genetic and phenotypic adaptation of the sulfate-reducing bacteriumDesulfovibrio vulgarisHildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, inmore » addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance inD. vulgaris. The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection. IMPORTANCE. High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for experimental evolutionary studies.Desulfovibrio vulgarisHildenborough is a model sulfate-reducing bacterium (SRB) that is important in biogeochemical cycling of sulfur, carbon, and nitrogen, potentially for bio-corrosion, and for bioremediation of toxic heavy metals and radionuclides. The coexistence of SRB and high salinity in natural habitats and heavy metal-contaminated field sites laid the foundation for the study of salt adaptation ofD. vulgarisHildenborough with experimental evolution. Here in this paper, we analyzed a clone that evolved under salt stress for 5,000 generations and compared it to a clone evolved under the same condition for 1,200 generations. The results indicated the key roles of glutamate for osmoprotection and of i17:1ω9c for increasing membrane fluidity during salt adaptation. The findings provide valuable insights about the salt adaptation mechanism changes during long-term experimental evolution.« less

Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris.

PubMed

Zhou, Aifen; Lau, Rebecca; Baran, Richard; Ma, Jincai; von Netzer, Frederick; Shi, Weiling; Gorman-Lewis, Drew; Kempher, Megan L; He, Zhili; Qin, Yujia; Shi, Zhou; Zane, Grant M; Wu, Liyou; Bowen, Benjamin P; Northen, Trent R; Hillesland, Kristina L; Stahl, David A; Wall, Judy D; Arkin, Adam P; Zhou, Jizhong

2017-11-14

Rapid genetic and phenotypic adaptation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, in addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance in D. vulgaris The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection. IMPORTANCE High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for experimental evolutionary studies. Desulfovibrio vulgaris Hildenborough is a model sulfate-reducing bacterium (SRB) that is important in biogeochemical cycling of sulfur, carbon, and nitrogen, potentially for bio-corrosion, and for bioremediation of toxic heavy metals and radionuclides. The coexistence of SRB and high salinity in natural habitats and heavy metal-contaminated field sites laid the foundation for the study of salt adaptation of D. vulgaris Hildenborough with experimental evolution. Here, we analyzed a clone that evolved under salt stress for 5,000 generations and compared it to a clone evolved under the same condition for 1,200 generations. The results indicated the key roles of glutamate for osmoprotection and of i17:1ω9c for increasing membrane fluidity during salt adaptation. The findings provide valuable insights about the salt adaptation mechanism changes during long-term experimental evolution. Copyright © 2017 Zhou et al.

Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris

DOE PAGES

Zhou, Aifen; Lau, Rebecca; Baran, Richard; ...

2017-11-14

ABSTRACT. Rapid genetic and phenotypic adaptation of the sulfate-reducing bacteriumDesulfovibrio vulgarisHildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, inmore » addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance inD. vulgaris. The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection. IMPORTANCE. High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for experimental evolutionary studies.Desulfovibrio vulgarisHildenborough is a model sulfate-reducing bacterium (SRB) that is important in biogeochemical cycling of sulfur, carbon, and nitrogen, potentially for bio-corrosion, and for bioremediation of toxic heavy metals and radionuclides. The coexistence of SRB and high salinity in natural habitats and heavy metal-contaminated field sites laid the foundation for the study of salt adaptation ofD. vulgarisHildenborough with experimental evolution. Here in this paper, we analyzed a clone that evolved under salt stress for 5,000 generations and compared it to a clone evolved under the same condition for 1,200 generations. The results indicated the key roles of glutamate for osmoprotection and of i17:1ω9c for increasing membrane fluidity during salt adaptation. The findings provide valuable insights about the salt adaptation mechanism changes during long-term experimental evolution.« less

Continuing progress toward controlled intracellular delivery of semiconductor quantum dots

PubMed Central

Breger, Joyce; Delehanty, James B; Medintz, Igor L

2015-01-01

The biological applications of luminescent semiconductor quantum dots (QDs) continue to grow at a nearly unabated pace. This growth is driven, in part, by their unique photophysical and physicochemical properties which have allowed them to be used in many different roles in cellular biology including: as superior fluorophores for a wide variety of cellular labeling applications; as active platforms for assembly of nanoscale sensors; and, more recently, as a powerful tool to understand the mechanisms of nanoparticle mediated drug delivery. Given that controlled cellular delivery is at the intersection of all these applications, the latest progress in delivering QDs to cells is examined here. A brief discussion of relevant considerations including the importance of materials preparation and bioconjugation along with the continuing issue of endosomal sequestration is initially provided for context. Methods for the cellular delivery of QDs are then highlighted including those based on passive exposure, facilitated strategies that utilize peptides or polymers and fully active modalities such as electroporation and other mechanically based methods. Following on this, the exciting advent of QD cellular delivery using multiple or combined mechanisms is then previewed. Several recent methods reporting endosomal escape of QD materials in cells are also examined in detail with a focus on the mechanisms by which access to the cytosol is achieved. The ongoing debate over QD cytotoxicity is also discussed along with a perspective on how this field will continue to evolve in the future. PMID:25154379

Blended Learning: An Evolving Praxis

ERIC Educational Resources Information Center

Fogal, Gary G.; Graham, Floyd H., III.; Lavigne, Anthony G.

2014-01-01

TED (Technology Entertainment Design), a collection of regularly updated talks, offers a web-based platform that is easily accessible. This platform affords language learners across multiple proficiency levels an opportunity to develop autonomy and critical thinking skills alongside their second language (L2) development. With an international…

Accelerated Learning: Madness with a Method.

ERIC Educational Resources Information Center

Zemke, Ron

1995-01-01

Accelerated learning methods have evolved into a variety of holistic techniques that involve participants in the learning process and overcome negative attitudes about learning. These components are part of the mix: the brain, learning environment, music, imaginative activities, suggestion, positive mental state, the arts, multiple intelligences,…

A Dialogical Approach to Conceptualizing Teacher Identity

ERIC Educational Resources Information Center

Akkerman, Sanne F.; Meijer, Paulien C.

2011-01-01

In recent attempts to address the notion of teacher identity, scholars have stressed how identity is dynamically evolving, intrinsically related to others, and consists of multiple identities. Though these postmodern characterizations represent radically new perceptions of identity, they are not extensively discussed in relation to previous…

Evolved differences in larval social behavior mediated by novel pheromones

USDA-ARS?s Scientific Manuscript database

Pheromones, chemical signals that convey social information, mediate many insect social behaviors in both adult and immature stages. Multiple pheromones and neural pathways that underlie adult social behavior have been described in the genetic model organism, Drosophila melanogaster, but there is no...

A Balanced Mixture of Antagonistic Pressures Promotes the Evolution of Parallel Movement

NASA Astrophysics Data System (ADS)

Demšar, Jure; Štrumbelj, Erik; Lebar Bajec, Iztok

2016-12-01

A common hypothesis about the origins of collective behaviour suggests that animals might live and move in groups to increase their chances of surviving predator attacks. This hypothesis is supported by several studies that use computational models to simulate natural evolution. These studies, however, either tune an ad-hoc model to ‘reproduce’ collective behaviour, or concentrate on a single type of predation pressure, or infer the emergence of collective behaviour from an increase in prey density. In nature, prey are often targeted by multiple predator species simultaneously and this might have played a pivotal role in the evolution of collective behaviour. We expand on previous research by using an evolutionary rule-based system to simulate the evolution of prey behaviour when prey are subject to multiple simultaneous predation pressures. We analyse the evolved behaviour via prey density, polarization, and angular momentum. Our results suggest that a mixture of antagonistic external pressures that simultaneously steer prey towards grouping and dispersing might be required for prey individuals to evolve dynamic parallel movement.

On the Evolution of Behaviors through Embodied Imitation.

PubMed

Erbas, Mehmet D; Bull, Larry; Winfield, Alan F T

2015-01-01

This article describes research in which embodied imitation and behavioral adaptation are investigated in collective robotics. We model social learning in artificial agents with real robots. The robots are able to observe and learn each others' movement patterns using their on-board sensors only, so that imitation is embodied. We show that the variations that arise from embodiment allow certain behaviors that are better adapted to the process of imitation to emerge and evolve during multiple cycles of imitation. As these behaviors are more robust to uncertainties in the real robots' sensors and actuators, they can be learned by other members of the collective with higher fidelity. Three different types of learned-behavior memory have been experimentally tested to investigate the effect of memory capacity on the evolution of movement patterns, and results show that as the movement patterns evolve through multiple cycles of imitation, selection, and variation, the robots are able to, in a sense, agree on the structure of the behaviors that are imitated.

Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus.

PubMed

Moncla, Louise H; Zhong, Gongxun; Nelson, Chase W; Dinis, Jorge M; Mutschler, James; Hughes, Austin L; Watanabe, Tokiko; Kawaoka, Yoshihiro; Friedrich, Thomas C

2016-02-10

Avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among mammals by acquiring mutations in hemagglutinin (HA) and polymerase. Using the ferret model, we trace the evolutionary pathway by which an avian-like virus evolves the capacity for mammalian replication and airborne transmission. During initial infection, within-host HA diversity increased drastically. Then, airborne transmission fixed two polymerase mutations that do not confer a detectable replication advantage. In later transmissions, selection fixed advantageous HA1 variants. Transmission initially involved a "loose" bottleneck, which became strongly selective after additional HA mutations emerged. The stringency and evolutionary forces governing between-host bottlenecks may therefore change throughout host adaptation. Mutations occurred in multiple combinations in transmitted viruses, suggesting that mammalian transmissibility can evolve through multiple genetic pathways despite phenotypic constraints. Our data provide a glimpse into avian influenza virus adaptation in mammals, with broad implications for surveillance on potentially zoonotic viruses. Copyright © 2016 Elsevier Inc. All rights reserved.

Multiresolution multiscale active mask segmentation of fluorescence microscope images

NASA Astrophysics Data System (ADS)

Srinivasa, Gowri; Fickus, Matthew; Kovačević, Jelena

2009-08-01

We propose an active mask segmentation framework that combines the advantages of statistical modeling, smoothing, speed and flexibility offered by the traditional methods of region-growing, multiscale, multiresolution and active contours respectively. At the crux of this framework is a paradigm shift from evolving contours in the continuous domain to evolving multiple masks in the discrete domain. Thus, the active mask framework is particularly suited to segment digital images. We demonstrate the use of the framework in practice through the segmentation of punctate patterns in fluorescence microscope images. Experiments reveal that statistical modeling helps the multiple masks converge from a random initial configuration to a meaningful one. This obviates the need for an involved initialization procedure germane to most of the traditional methods used to segment fluorescence microscope images. While we provide the mathematical details of the functions used to segment fluorescence microscope images, this is only an instantiation of the active mask framework. We suggest some other instantiations of the framework to segment different types of images.

MSAT signalling and network management architectures

NASA Technical Reports Server (NTRS)

Garland, Peter; Keelty, J. Malcolm

1989-01-01

Spar Aerospace has been active in the design and definition of Mobile Satellite Systems since the mid 1970's. In work sponsored by the Canadian Department of Communications, various payload configurations have evolved. In addressing the payload configuration, the requirements of the mobile user, the service provider and the satellite operator have always been the most important consideration. The current Spar 11 beam satellite design is reviewed, and its capabilities to provide flexibility and potential for network growth within the WARC87 allocations are explored. To enable the full capabilities of the payload to be realized, a large amount of ground based Switching and Network Management infrastructure will be required, when space segment becomes available. Early indications were that a single custom designed Demand Assignment Multiple Access (DAMA) switch should be implemented to provide efficient use of the space segment. As MSAT has evolved into a multiple service concept, supporting many service providers, this architecture should be reviewed. Some possible signalling and Network Management solutions are explored.

Convergent evolution of mechanically optimal locomotion in aquatic invertebrates and vertebrates.

PubMed

Bale, Rahul; Neveln, Izaak D; Bhalla, Amneet Pal Singh; MacIver, Malcolm A; Patankar, Neelesh A

2015-04-01

Examples of animals evolving similar traits despite the absence of that trait in the last common ancestor, such as the wing and camera-type lens eye in vertebrates and invertebrates, are called cases of convergent evolution. Instances of convergent evolution of locomotory patterns that quantitatively agree with the mechanically optimal solution are very rare. Here, we show that, with respect to a very diverse group of aquatic animals, a mechanically optimal method of swimming with elongated fins has evolved independently at least eight times in both vertebrate and invertebrate swimmers across three different phyla. Specifically, if we take the length of an undulation along an animal's fin during swimming and divide it by the mean amplitude of undulations along the fin length, the result is consistently around twenty. We call this value the optimal specific wavelength (OSW). We show that the OSW maximizes the force generated by the body, which also maximizes swimming speed. We hypothesize a mechanical basis for this optimality and suggest reasons for its repeated emergence through evolution.

Physical Model of the Genotype-to-Phenotype Map of Proteins

NASA Astrophysics Data System (ADS)

Tlusty, Tsvi; Libchaber, Albert; Eckmann, Jean-Pierre

2017-04-01

How DNA is mapped to functional proteins is a basic question of living matter. We introduce and study a physical model of protein evolution which suggests a mechanical basis for this map. Many proteins rely on large-scale motion to function. We therefore treat protein as learning amorphous matter that evolves towards such a mechanical function: Genes are binary sequences that encode the connectivity of the amino acid network that makes a protein. The gene is evolved until the network forms a shear band across the protein, which allows for long-range, soft modes required for protein function. The evolution reduces the high-dimensional sequence space to a low-dimensional space of mechanical modes, in accord with the observed dimensional reduction between genotype and phenotype of proteins. Spectral analysis of the space of 1 06 solutions shows a strong correspondence between localization around the shear band of both mechanical modes and the sequence structure. Specifically, our model shows how mutations are correlated among amino acids whose interactions determine the functional mode.

Developmental mechanisms underlying variable, invariant and plastic phenotypes

PubMed Central

Abley, Katie; Locke, James C. W.; Leyser, H. M. Ottoline

2016-01-01

Background Discussions of phenotypic robustness often consider scenarios where invariant phenotypes are optimal and assume that developmental mechanisms have evolved to buffer the phenotypes of specific traits against stochastic and environmental perturbations. However, plastic plant phenotypes that vary between environments or variable phenotypes that vary stochastically within an environment may also be advantageous in some scenarios. Scope Here the conditions under which invariant, plastic and variable phenotypes of specific traits may confer a selective advantage in plants are examined. Drawing on work from microbes and multicellular organisms, the mechanisms that may give rise to each type of phenotype are discussed. Conclusion In contrast to the view of robustness as being the ability of a genotype to produce a single, invariant phenotype, changes in a phenotype in response to the environment, or phenotypic variability within an environment, may also be delivered consistently (i.e. robustly). Thus, for some plant traits, mechanisms have probably evolved to produce plasticity or variability in a reliable manner. PMID:27072645

Estimation and Analysis of Nonlinear Stochastic Systems. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Marcus, S. I.

1975-01-01

The algebraic and geometric structures of certain classes of nonlinear stochastic systems were exploited in order to obtain useful stability and estimation results. The class of bilinear stochastic systems (or linear systems with multiplicative noise) was discussed. The stochastic stability of bilinear systems driven by colored noise was considered. Approximate methods for obtaining sufficient conditions for the stochastic stability of bilinear systems evolving on general Lie groups were discussed. Two classes of estimation problems involving bilinear systems were considered. It was proved that, for systems described by certain types of Volterra series expansions or by certain bilinear equations evolving on nilpotent or solvable Lie groups, the optimal conditional mean estimator consists of a finite dimensional nonlinear set of equations. The theory of harmonic analysis was used to derive suboptimal estimators for bilinear systems driven by white noise which evolve on compact Lie groups or homogeneous spaces.

Volatile, isotope, and organic analysis of martian fines with the Mars Curiosity rover.

PubMed

Leshin, L A; Mahaffy, P R; Webster, C R; Cabane, M; Coll, P; Conrad, P G; Archer, P D; Atreya, S K; Brunner, A E; Buch, A; Eigenbrode, J L; Flesch, G J; Franz, H B; Freissinet, C; Glavin, D P; McAdam, A C; Miller, K E; Ming, D W; Morris, R V; Navarro-González, R; Niles, P B; Owen, T; Pepin, R O; Squyres, S; Steele, A; Stern, J C; Summons, R E; Sumner, D Y; Sutter, B; Szopa, C; Teinturier, S; Trainer, M G; Wray, J J; Grotzinger, J P

2013-09-27

Samples from the Rocknest aeolian deposit were heated to ~835°C under helium flow and evolved gases analyzed by Curiosity's Sample Analysis at Mars instrument suite. H2O, SO2, CO2, and O2 were the major gases released. Water abundance (1.5 to 3 weight percent) and release temperature suggest that H2O is bound within an amorphous component of the sample. Decomposition of fine-grained Fe or Mg carbonate is the likely source of much of the evolved CO2. Evolved O2 is coincident with the release of Cl, suggesting that oxygen is produced from thermal decomposition of an oxychloride compound. Elevated δD values are consistent with recent atmospheric exchange. Carbon isotopes indicate multiple carbon sources in the fines. Several simple organic compounds were detected, but they are not definitively martian in origin.

Clear: Composition of Likelihoods for Evolve and Resequence Experiments.

PubMed

Iranmehr, Arya; Akbari, Ali; Schlötterer, Christian; Bafna, Vineet

2017-06-01

The advent of next generation sequencing technologies has made whole-genome and whole-population sampling possible, even for eukaryotes with large genomes. With this development, experimental evolution studies can be designed to observe molecular evolution "in action" via evolve-and-resequence (E&R) experiments. Among other applications, E&R studies can be used to locate the genes and variants responsible for genetic adaptation. Most existing literature on time-series data analysis often assumes large population size, accurate allele frequency estimates, or wide time spans. These assumptions do not hold in many E&R studies. In this article, we propose a method-composition of likelihoods for evolve-and-resequence experiments (Clear)-to identify signatures of selection in small population E&R experiments. Clear takes whole-genome sequences of pools of individuals as input, and properly addresses heterogeneous ascertainment bias resulting from uneven coverage. Clear also provides unbiased estimates of model parameters, including population size, selection strength, and dominance, while being computationally efficient. Extensive simulations show that Clear achieves higher power in detecting and localizing selection over a wide range of parameters, and is robust to variation of coverage. We applied the Clear statistic to multiple E&R experiments, including data from a study of adaptation of Drosophila melanogaster to alternating temperatures and a study of outcrossing yeast populations, and identified multiple regions under selection with genome-wide significance. Copyright © 2017 by the Genetics Society of America.

Cooperation, conflict, and the evolution of queen pheromones.

PubMed

Kocher, Sarah D; Grozinger, Christina M

2011-11-01

While chemical communication regulates individual behavior in a wide variety of species, these communication systems are most elaborated in insect societies. In these complex systems, pheromones produced by the reproductive individuals (queens) are critical in establishing and maintaining dominant reproductive status over hundreds to thousands of workers. The proximate and ultimate mechanisms by which these intricate pheromone communication systems evolved are largely unknown, though there has been much debate over whether queen pheromones function as a control mechanism or as an honest signal facilitating cooperation. Here, we summarize results from recent studies in honey bees, bumble bees, wasps, ants and termites. We further discuss evolutionary mechanisms by which queen pheromone communication systems may have evolved. Overall, these studies suggest that queen-worker pheromone communication is a multi-component, labile dialog between the castes, rather than a simple, fixed signal-response system. We also discuss future approaches that can shed light on the proximate and ultimate mechanisms that underlie these complex systems by focusing on the development of increasingly sophisticated genomic tools and their potential applications to examine the molecular mechanisms that regulate pheromone production and perception.

Mini-Tn7 Insertion in Bacteria With Multiple glmS-Linked attTn7 Sites: Example Burkholderia Mallei ATCC 23344

DTIC Science & Technology

2006-06-27

INTRODUCTION Burkholderia mallei is the etiological agent of glanders and a highly evolved obligate zoonotic mammalian pathogen that naturally affects horses...mini-Tn7 insertion in bacteria with multiple glmS-linked attTn7 sites: example Burkholderia mallei ATCC 23344 Kyoung-Hee Choi1, David DeShazer2... glanders is a rare disease, B. mallei has received renewed attention because of its listing as a category B agent by the Centers for Disease Control

Structural characterization of a novel full-length transcript promoter from Horseradish Latent Virus (HRLV) and its transcriptional regulation by multiple stress responsive transcription factors.

PubMed

Khan, Ahamed; Shrestha, Ankita; Bhuyan, Kashyap; Maiti, Indu B; Dey, Nrisingha

2018-01-01

The promoter fragment described in this study can be employed for strong transgene expression under both biotic and abiotic stress conditions. Plant-infecting Caulimoviruses have evolved multiple regulatory mechanisms to address various environmental stimuli during the course of evolution. One such mechanism involves the retention of discrete stress responsive cis-elements which are required for their survival and host-specificity. Here we describe the characterization of a novel Caulimoviral promoter isolated from Horseradish Latent Virus (HRLV) and its regulation by multiple stress responsive Transcription factors (TFs) namely DREB1, AREB1 and TGA1a. The activity of full length transcript (Flt-) promoter from HRLV (- 677 to + 283) was investigated in both transient and transgenic assays where we identified H12 (- 427 to + 73) as the highest expressing fragment having ~ 2.5-fold stronger activity than the CaMV35S promoter. The H12 promoter was highly active and near-constitutive in the vegetative and reproductive parts of both Tobacco and Arabidopsis transgenic plants. Interestingly, H12 contains a distinct cluster of cis-elements like dehydration-responsive element (DRE-core; GCCGAC), an ABA-responsive element (ABRE; ACGTGTC) and as-1 element (TGACG) which are known to be induced by cold, drought and pathogen/SA respectively. The specific binding of DREB1, AREB1 and TGA1a to DRE, ABRE and as-1 elements respectively were confirmed by the gel-binding assays using H12 promoter-specific probes. Detailed mutational analysis of the H12 promoter suggested that the presence of DRE-core and as-1 element was indispensable for its activity which was further confirmed by the transactivation assays. Our studies imply that H12 could be a valuable genetic tool for regulated transgene expression under diverse environmental conditions.

Evolution of Perianth and Stamen Characteristics with Respect to Floral Symmetry in Ranunculales

PubMed Central

Damerval, Catherine; Nadot, Sophie

2007-01-01

Background and Aims Floral symmetry presents two main states in angiosperms, namely polysymmetry and monosymmetry. Monosymmetry is thought to have evolved several times independently from polysymmetry, possibly in co-adaptation with specialized pollinators. Monosymmetry commonly refers to the perianth, even though associated androecium modifications have been reported. The evolution of perianth symmetry is examined with respect to traits of flower architecture in the Ranunculales, the sister group to all other eudicots, which present a large diversity of floral forms. Methods Characters considered were perianth merism, calyx, corolla and androecium symmetry, number of stamens and spurs. Character evolution was optimized on a composite phylogenetic tree of Ranunculales using maximum parsimony. Key Results The ancestral state for merism could not be inferred because the basalmost Eupteleaceae lack a perianth and have a variable number of stamens. The Papaveraceae are dimerous, and the five other families share a common trimerous ancestor. Shifts from trimery to dimery (or reverse) are observed. Pentamery evolved in Ranunculaceae. Ranunculales except Eupteleaceae, present a polysymmetric ancestral state. Monosymmetry evolved once within Papaveraceae, Ranunculaceae and Menispermaceae (female flowers only). Oligandry is the ancestral state for all Ranunculales, and polyandry evolved several times independently, in Papaveraceae, Menispermaceae, Berberidaceae and Ranunculaceae, with two reversions to oligandry in the latter. The ancestral state for androecium symmetry is ambiguous for the Ranunculales, while polysymmetry evolved immediately after the divergence of Eupteleaceae. A disymmetric androecium evolved in Papaveraceae. The ancestral state for spurs is none. Multiple spurs evolved in Papaveraceae, Berberidaceae and Ranunculaceae, and single spurs occur in Papaveraceae and Ranunculaceae. Conclusions The evolution of symmetry appears disconnected from changes in merism and stamen number, although monosymmetry never evolved in the context of an open ground plan. In bisexual species, monosymmetry evolved coincidently with single spurs, allowing us to propose an evolutionary scenario for Papaveraceae. PMID:17428835

Dissecting the impact of CO2 and pH on the mechanisms of photosynthesis and calcification in the coccolithophore Emiliania huxleyi.

PubMed

Bach, Lennart T; Mackinder, Luke C M; Schulz, Kai G; Wheeler, Glen; Schroeder, Declan C; Brownlee, Colin; Riebesell, Ulf

2013-07-01

Coccolithophores are important calcifying phytoplankton predicted to be impacted by changes in ocean carbonate chemistry caused by the absorption of anthropogenic CO2 . However, it is difficult to disentangle the effects of the simultaneously changing carbonate system parameters (CO2 , bicarbonate, carbonate and protons) on the physiological responses to elevated CO2 . Here, we adopted a multifactorial approach at constant pH or CO2 whilst varying dissolved inorganic carbon (DIC) to determine physiological and transcriptional responses to individual carbonate system parameters. We show that Emiliania huxleyi is sensitive to low CO2 (growth and photosynthesis) and low bicarbonate (calcification) as well as low pH beyond a limited tolerance range, but is much less sensitive to elevated CO2 and bicarbonate. Multiple up-regulated genes at low DIC bear the hallmarks of a carbon-concentrating mechanism (CCM) that is responsive to CO2 and bicarbonate but not to pH. Emiliania huxleyi appears to have evolved mechanisms to respond to limiting rather than elevated CO2 . Calcification does not function as a CCM, but is inhibited at low DIC to allow the redistribution of DIC from calcification to photosynthesis. The presented data provides a significant step in understanding how E. huxleyi will respond to changing carbonate chemistry at a cellular level. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Targeting Leukemia Stem Cells in the Bone Marrow Niche

PubMed Central

Bornhäuser, Martin

2018-01-01

The bone marrow (BM) niche encompasses multiple cells of mesenchymal and hematopoietic origin and represents a unique microenvironment that is poised to maintain hematopoietic stem cells. In addition to its role as a primary lymphoid organ through the support of lymphoid development, the BM hosts various mature lymphoid cell types, including naïve T cells, memory T cells and plasma cells, as well as mature myeloid elements such as monocyte/macrophages and neutrophils, all of which are crucially important to control leukemia initiation and progression. The BM niche provides an attractive milieu for tumor cell colonization given its ability to provide signals which accelerate tumor cell proliferation and facilitate tumor cell survival. Cancer stem cells (CSCs) share phenotypic and functional features with normal counterparts from the tissue of origin of the tumor and can self-renew, differentiate and initiate tumor formation. CSCs possess a distinct immunological profile compared with the bulk population of tumor cells and have evolved complex strategies to suppress immune responses through multiple mechanisms, including the release of soluble factors and the over-expression of molecules implicated in cancer immune evasion. This chapter discusses the latest advancements in understanding of the immunological BM niche and highlights current and future immunotherapeutic strategies to target leukemia CSCs and overcome therapeutic resistance in the clinic. PMID:29466292

Effects of multiple spreaders in community networks

NASA Astrophysics Data System (ADS)

Hu, Zhao-Long; Ren, Zhuo-Ming; Yang, Guang-Yong; Liu, Jian-Guo

2014-12-01

Human contact networks exhibit the community structure. Understanding how such community structure affects the epidemic spreading could provide insights for preventing the spreading of epidemics between communities. In this paper, we explore the spreading of multiple spreaders in community networks. A network based on the clustering preferential mechanism is evolved, whose communities are detected by the Girvan-Newman (GN) algorithm. We investigate the spreading effectiveness by selecting the nodes as spreaders in the following ways: nodes with the largest degree in each community (community hubs), the same number of nodes with the largest degree from the global network (global large-degree) and randomly selected one node within each community (community random). The experimental results on the SIR model show that the spreading effectiveness based on the global large-degree and community hubs methods is the same in the early stage of the infection and the method of community random is the worst. However, when the infection rate exceeds the critical value, the global large-degree method embodies the worst spreading effectiveness. Furthermore, the discrepancy of effectiveness for the three methods will decrease as the infection rate increases. Therefore, we should immunize the hubs in each community rather than those hubs in the global network to prevent the outbreak of epidemics.

Antimicrobial Peptides from Plants

PubMed Central

Tam, James P.; Wang, Shujing; Wong, Ka H.; Tan, Wei Liang

2015-01-01

Plant antimicrobial peptides (AMPs) have evolved differently from AMPs from other life forms. They are generally rich in cysteine residues which form multiple disulfides. In turn, the disulfides cross-braced plant AMPs as cystine-rich peptides to confer them with extraordinary high chemical, thermal and proteolytic stability. The cystine-rich or commonly known as cysteine-rich peptides (CRPs) of plant AMPs are classified into families based on their sequence similarity, cysteine motifs that determine their distinctive disulfide bond patterns and tertiary structure fold. Cystine-rich plant AMP families include thionins, defensins, hevein-like peptides, knottin-type peptides (linear and cyclic), lipid transfer proteins, α-hairpinin and snakins family. In addition, there are AMPs which are rich in other amino acids. The ability of plant AMPs to organize into specific families with conserved structural folds that enable sequence variation of non-Cys residues encased in the same scaffold within a particular family to play multiple functions. Furthermore, the ability of plant AMPs to tolerate hypervariable sequences using a conserved scaffold provides diversity to recognize different targets by varying the sequence of the non-cysteine residues. These properties bode well for developing plant AMPs as potential therapeutics and for protection of crops through transgenic methods. This review provides an overview of the major families of plant AMPs, including their structures, functions, and putative mechanisms. PMID:26580629

Sepsis: Multiple Abnormalities, Heterogeneous Responses, and Evolving Understanding

PubMed Central

Iskander, Kendra N.; Osuchowski, Marcin F.; Stearns-Kurosawa, Deborah J.; Kurosawa, Shinichiro; Stepien, David; Valentine, Catherine

2013-01-01

Sepsis represents the host's systemic inflammatory response to a severe infection. It causes substantial human morbidity resulting in hundreds of thousands of deaths each year. Despite decades of intense research, the basic mechanisms still remain elusive. In either experimental animal models of sepsis or human patients, there are substantial physiological changes, many of which may result in subsequent organ injury. Variations in age, gender, and medical comorbidities including diabetes and renal failure create additional complexity that influence the outcomes in septic patients. Specific system-based alterations, such as the coagulopathy observed in sepsis, offer both potential insight and possible therapeutic targets. Intracellular stress induces changes in the endoplasmic reticulum yielding misfolded proteins that contribute to the underlying pathophysiological changes. With these multiple changes it is difficult to precisely classify an individual's response in sepsis as proinflammatory or immunosuppressed. This heterogeneity also may explain why most therapeutic interventions have not improved survival. Given the complexity of sepsis, biomarkers and mathematical models offer potential guidance once they have been carefully validated. This review discusses each of these important factors to provide a framework for understanding the complex and current challenges of managing the septic patient. Clinical trial failures and the therapeutic interventions that have proven successful are also discussed. PMID:23899564

Integrative studies of cultural evolution: crossing disciplinary boundaries to produce new insights

PubMed Central

2018-01-01

Culture evolves according to dynamics on multiple temporal scales, from individuals' minute-by-minute behaviour to millennia of cultural accumulation that give rise to population-level differences. These dynamics act on a range of entities—including behavioural sequences, ideas and artefacts as well as individuals, populations and whole species—and involve mechanisms at multiple levels, from neurons in brains to inter-population interactions. Studying such complex phenomena requires an integration of perspectives from a diverse array of fields, as well as bridging gaps between traditionally disparate areas of study. In this article, which also serves as an introduction to the current special issue, we highlight some specific respects in which the study of cultural evolution has benefited and should continue to benefit from an integrative approach. We showcase a number of pioneering studies of cultural evolution that bring together numerous disciplines. These studies illustrate the value of perspectives from different fields for understanding cultural evolution, such as cognitive science and neuroanatomy, behavioural ecology, population dynamics, and evolutionary genetics. They also underscore the importance of understanding cultural processes when interpreting research about human genetics, neuroscience, behaviour and evolution. This article is part of the theme issue ‘Bridging cultural gaps: interdisciplinary studies in human cultural evolution’. PMID:29440515

Integrative studies of cultural evolution: crossing disciplinary boundaries to produce new insights.

PubMed

Kolodny, Oren; Feldman, Marcus W; Creanza, Nicole

2018-04-05

Culture evolves according to dynamics on multiple temporal scales, from individuals' minute-by-minute behaviour to millennia of cultural accumulation that give rise to population-level differences. These dynamics act on a range of entities-including behavioural sequences, ideas and artefacts as well as individuals, populations and whole species-and involve mechanisms at multiple levels, from neurons in brains to inter-population interactions. Studying such complex phenomena requires an integration of perspectives from a diverse array of fields, as well as bridging gaps between traditionally disparate areas of study. In this article, which also serves as an introduction to the current special issue, we highlight some specific respects in which the study of cultural evolution has benefited and should continue to benefit from an integrative approach. We showcase a number of pioneering studies of cultural evolution that bring together numerous disciplines. These studies illustrate the value of perspectives from different fields for understanding cultural evolution, such as cognitive science and neuroanatomy, behavioural ecology, population dynamics, and evolutionary genetics. They also underscore the importance of understanding cultural processes when interpreting research about human genetics, neuroscience, behaviour and evolution.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

Polylactic acid (PLA) controlled delivery carriers for biomedical applications.

PubMed

Tyler, Betty; Gullotti, David; Mangraviti, Antonella; Utsuki, Tadanobu; Brem, Henry

2016-12-15

Polylactic acid (PLA) and its copolymers have a long history of safety in humans and an extensive range of applications. PLA is biocompatible, biodegradable by hydrolysis and enzymatic activity, has a large range of mechanical and physical properties that can be engineered appropriately to suit multiple applications, and has low immunogenicity. Formulations containing PLA have also been Food and Drug Administration (FDA)-approved for multiple applications making PLA suitable for expedited clinical translatability. These biomaterials can be fashioned into sutures, scaffolds, cell carriers, drug delivery systems, and a myriad of fabrications. PLA has been the focus of a multitude of preclinical and clinical testing. Three-dimensional printing has expanded the possibilities of biomedical engineering and has enabled the fabrication of a myriad of platforms for an extensive variety of applications. PLA has been widely used as temporary extracellular matrices in tissue engineering. At the other end of the spectrum, PLA's application as drug-loaded nanoparticle drug carriers, such as liposomes, polymeric nanoparticles, dendrimers, and micelles, can encapsulate otherwise toxic hydrophobic anti-tumor drugs and evade systemic toxicities. The clinical translation of these technologies from preclinical experimental settings is an ever-evolving field with incremental advancements. In this review, some of the biomedical applications of PLA and its copolymers are highlighted and briefly summarized. Copyright © 2016 Elsevier B.V. All rights reserved.

Management of EGFR-mutated non-small-cell lung cancer: practical implications from a clinical and pathology perspective

PubMed Central

Cabanero, M.; Sangha, R.; Sheffield, B.S.; Sukhai, M.; Pakkal, M.; Kamel-Reid, S.; Karsan, A.; Ionescu, D.; Juergens, R.A.; Butts, C.; Tsao, M.S.

2017-01-01

Starting in the early 2000s, non-small-cell lung cancer (nsclc) subtypes have evolved from being histologically described to molecularly defined. Management of lung adenocarcinomas now generally requires multiple molecular tests at baseline to define the optimal treatment strategy. More recently, second biopsies performed at progression in patients treated with tyrosine kinase inhibitors (tkis) have further defined the continued use of molecularly targeted therapy. In the present article, we focus on one molecular subtype: EGFR-mutated nsclc. For that patient population, multiple lines of tki therapy are now available either clinically or in clinical trials. Each line of treatment is guided by the specific mutations (for example, L858R, T790M, C797S) identified in EGFR. We first describe the various mechanisms of acquired resistance to EGFR tki treatment. We then focus on strategies that clinicians and pathologists can both use during tissue acquisition and handling to optimize patient results. We also discuss future directions for the molecular characterization of lung cancers with driver mutations, including liquid biopsies. Finally, we provide an algorithm to guide treating physicians managing patients with EGFR-mutated nsclc. The same framework can also be applied to other molecularly defined nsclc subgroups as resistance patterns are elucidated and additional lines of treatment are developed. PMID:28490925

Deducing multiple interfacial dynamics during polymeric foaming.

PubMed

Chandan, Mohammed Rehaan; Naskar, Nilanjon; Das, Anuja; Mukherjee, Rabibrata; Harikrishnan, Gopalakrishna Pillai

2018-06-15

Several interfacial phenomena are active during polymeric foaming, the dynamics of which significantly influence terminal stability, cell structure and in turn the thermo-mechanical properties of temporally evolved foam. Understanding these dynamics is important in achieving desired foam properties. Here, we introduce a method to simultaneously portray the time evolution of bubble growth, lamella thinning and Plateau border drainage, occurring during reactive polymeric foaming. In this method, we initially conduct bulk and surface shear rheology under polymerizing and non-foaming conditions. In a subsequent step, foaming experiments were conducted in a rheometer. The microscopic structural dimensions pertaining to the terminal values of the dynamics of each interfacial phenomena are then measured using a combination of scanning electron microscopy, optical microscopy and imaging ellipsometry, after the foaming is over. The measured surface and bulk rheological parameters are incorporated in time evolution equations that are derived from mass and momentum transport occurring when a model viscoelastic fluid is foamed by gas dispersion. Analytical and numerical solutions to these equations portray the dynamics. We demonstrate this method for a series of reactive polyurethane foams generated from different chemical sources. The effectiveness of our method is in simultaneously obtaining these dynamics that are difficult to directly monitor due to short active durations over multiple length scales.

SMART USE OF COMPUTER-AIDED SPERM ANALYSIS (CASA) TO CHARACTERIZE SPERM MOTION

EPA Science Inventory

Computer-aided sperm analysis (CASA) has evolved over the past fifteen years to provide an objective, practical means of measuring and characterizing the velocity and parttern of sperm motion. CASA instruments use video frame-grabber boards to capture multiple images of spermato...

Sex determination: why so many ways of doing it?

PubMed

Bachtrog, Doris; Mank, Judith E; Peichel, Catherine L; Kirkpatrick, Mark; Otto, Sarah P; Ashman, Tia-Lynn; Hahn, Matthew W; Kitano, Jun; Mayrose, Itay; Ming, Ray; Perrin, Nicolas; Ross, Laura; Valenzuela, Nicole; Vamosi, Jana C

2014-07-01

Sexual reproduction is an ancient feature of life on earth, and the familiar X and Y chromosomes in humans and other model species have led to the impression that sex determination mechanisms are old and conserved. In fact, males and females are determined by diverse mechanisms that evolve rapidly in many taxa. Yet this diversity in primary sex-determining signals is coupled with conserved molecular pathways that trigger male or female development. Conflicting selection on different parts of the genome and on the two sexes may drive many of these transitions, but few systems with rapid turnover of sex determination mechanisms have been rigorously studied. Here we survey our current understanding of how and why sex determination evolves in animals and plants and identify important gaps in our knowledge that present exciting research opportunities to characterize the evolutionary forces and molecular pathways underlying the evolution of sex determination.

Is the political animal politically ignorant? Applying evolutionary psychology to the study of political attitudes.

PubMed

Petersen, Michael Bang; Aarøe, Lene

2012-12-20

As evidenced by research in evolutionary psychology, humans have evolved sophisticated psychological mechanisms tailored to solve enduring adaptive problems of social life. Many of these social problems are political in nature and relate to the distribution of costs and benefits within and between groups. In that sense, evolutionary psychology suggests that humans are, by nature, political animals. By implication, a straightforward application of evolutionary psychology to the study of public opinion seems to entail that modern individuals find politics intrinsically interesting. Yet, as documented by more than fifty years of research in political science, people lack knowledge of basic features of the political process and the ability to form consistent political attitudes. By reviewing and integrating research in evolutionary psychology and public opinion, we describe (1) why modern mass politics often fail to activate evolved mechanisms and (2) the conditions in which these mechanisms are in fact triggered.

Sex Determination: Why So Many Ways of Doing It?

PubMed Central

Bachtrog, Doris; Mank, Judith E.; Peichel, Catherine L.; Kirkpatrick, Mark; Otto, Sarah P.; Ashman, Tia-Lynn; Hahn, Matthew W.; Kitano, Jun; Mayrose, Itay; Ming, Ray; Perrin, Nicolas; Ross, Laura; Valenzuela, Nicole; Vamosi, Jana C.

2014-01-01

Sexual reproduction is an ancient feature of life on earth, and the familiar X and Y chromosomes in humans and other model species have led to the impression that sex determination mechanisms are old and conserved. In fact, males and females are determined by diverse mechanisms that evolve rapidly in many taxa. Yet this diversity in primary sex-determining signals is coupled with conserved molecular pathways that trigger male or female development. Conflicting selection on different parts of the genome and on the two sexes may drive many of these transitions, but few systems with rapid turnover of sex determination mechanisms have been rigorously studied. Here we survey our current understanding of how and why sex determination evolves in animals and plants and identify important gaps in our knowledge that present exciting research opportunities to characterize the evolutionary forces and molecular pathways underlying the evolution of sex determination. PMID:24983465

Dosage Compensation of the Sex Chromosomes

PubMed Central

Disteche, Christine M.

2013-01-01

Differentiated sex chromosomes evolved because of suppressed recombination once sex became genetically controlled. In XX/XY and ZZ/ZW systems, the heterogametic sex became partially aneuploid after degeneration of the Y or W. Often, aneuploidy causes abnormal levels of gene expression throughout the entire genome. Dosage compensation mechanisms evolved to restore balanced expression of the genome. These mechanisms include upregulation of the heterogametic chromosome as well as repression in the homogametic sex. Remarkably, strategies for dosage compensation differ between species. In organisms where more is known about molecular mechanisms of dosage compensation, specific protein complexes containing noncoding RNAs are targeted to the X chromosome. In addition, the dosage-regulated chromosome often occupies a specific nuclear compartment. Some genes escape dosage compensation, potentially resulting in sex-specific differences in gene expression. This review focuses on dosage compensation in mammals, with comparisons to fruit flies, nematodes, and birds. PMID:22974302

Dosage compensation of the sex chromosomes and autosomes

PubMed Central

Disteche, Christine M.

2016-01-01

Males are XY and females are XX in most mammalian species. Other species such as birds have a different sex chromosome make-up: ZZ in males and ZW in females. In both types of organisms one of the sex chromosomes, Y or W, has degenerated due to lack of recombination with its respective homolog X or Z. Since autosomes are present in two copies in diploid organisms the heterogametic sex has become a natural "aneuploid" with haploinsufficiency for X- or Z-linked genes. Specific mechanisms have evolved to restore a balance between critical gene products throughout the genome and between males and females. Some of these mechanisms were co-opted from and/or added to compensatory processes that alleviate autosomal aneuploidy. Surprisingly, several modes of dosage compensation have evolved. In this review we will consider the evidence for dosage compensation and the molecular mechanisms implicated. PMID:27112542

Harmonic Hopping, and Both Punctuated and Gradual Evolution of Acoustic Characters in Selasphorus Hummingbird Tail-Feathers

PubMed Central

Clark, Christopher James

2014-01-01

Models of character evolution often assume a single mode of evolutionary change, such as continuous, or discrete. Here I provide an example in which a character exhibits both types of change. Hummingbirds in the genus Selasphorus produce sound with fluttering tail-feathers during courtship. The ancestral character state within Selasphorus is production of sound with an inner tail-feather, R2, in which the sound usually evolves gradually. Calliope and Allen's Hummingbirds have evolved autapomorphic acoustic mechanisms that involve feather-feather interactions. I develop a source-filter model of these interactions. The ‘source’ comprises feather(s) that are both necessary and sufficient for sound production, and are aerodynamically coupled to neighboring feathers, which act as filters. Filters are unnecessary or insufficient for sound production, but may evolve to become sources. Allen's Hummingbird has evolved to produce sound with two sources, one with feather R3, another frequency-modulated sound with R4, and their interaction frequencies. Allen's R2 retains the ancestral character state, a ∼1 kHz “ghost” fundamental frequency masked by R3, which is revealed when R3 is experimentally removed. In the ancestor to Allen's Hummingbird, the dominant frequency has ‘hopped’ to the second harmonic without passing through intermediate frequencies. This demonstrates that although the fundamental frequency of a communication sound may usually evolve gradually, occasional jumps from one character state to another can occur in a discrete fashion. Accordingly, mapping acoustic characters on a phylogeny may produce misleading results if the physical mechanism of production is not known. PMID:24722049

Evolvable mathematical models: A new artificial Intelligence paradigm

NASA Astrophysics Data System (ADS)

Grouchy, Paul

We develop a novel Artificial Intelligence paradigm to generate autonomously artificial agents as mathematical models of behaviour. Agent/environment inputs are mapped to agent outputs via equation trees which are evolved in a manner similar to Symbolic Regression in Genetic Programming. Equations are comprised of only the four basic mathematical operators, addition, subtraction, multiplication and division, as well as input and output variables and constants. From these operations, equations can be constructed that approximate any analytic function. These Evolvable Mathematical Models (EMMs) are tested and compared to their Artificial Neural Network (ANN) counterparts on two benchmarking tasks: the double-pole balancing without velocity information benchmark and the challenging discrete Double-T Maze experiments with homing. The results from these experiments show that EMMs are capable of solving tasks typically solved by ANNs, and that they have the ability to produce agents that demonstrate learning behaviours. To further explore the capabilities of EMMs, as well as to investigate the evolutionary origins of communication, we develop NoiseWorld, an Artificial Life simulation in which interagent communication emerges and evolves from initially noncommunicating EMM-based agents. Agents develop the capability to transmit their x and y position information over a one-dimensional channel via a complex, dialogue-based communication scheme. These evolved communication schemes are analyzed and their evolutionary trajectories examined, yielding significant insight into the emergence and subsequent evolution of cooperative communication. Evolved agents from NoiseWorld are successfully transferred onto physical robots, demonstrating the transferability of EMM-based AIs from simulation into physical reality.

Assessing five evolving microbial enzyme models against field measurements from a semiarid savannah—What are the mechanisms of soil respiration pulses?

NASA Astrophysics Data System (ADS)

Zhang, Xia; Niu, Guo-Yue; Elshall, Ahmed S.; Ye, Ming; Barron-Gafford, Greg A.; Pavao-Zuckerman, Mitch

2014-09-01

Soil microbial respiration pulses in response to episodic rainfall pulses (the "Birch effect") are poorly understood. We developed and assessed five evolving microbial enzyme models against field measurements from a semiarid savannah characterized by pulsed precipitation to understand the mechanisms to generate the Birch pulses. The five models evolve from an existing four-carbon (C) pool model to models with additional C pools and explicit representations of soil moisture controls on C degradation and microbial uptake rates. Assessing the models using techniques of model selection and model averaging suggests that models with additional C pools for accumulation of degraded C in the dry zone of the soil pore space result in a higher probability of reproducing the observed Birch pulses. Degraded C accumulated in dry soil pores during dry periods becomes immediately accessible to microbes in response to rainstorms, providing a major mechanism to generate respiration pulses. Explicitly representing the transition of degraded C and enzymes between dry and wet soil pores in response to soil moisture changes and soil moisture controls on C degradation and microbial uptake rates improve the models' efficiency and robustness in simulating the Birch effect. Assuming that enzymes in the dry soil pores facilitate degradation of complex C during dry periods (though at a lower rate) results in a greater accumulation of degraded C and thus further improves the models' performance. However, the actual mechanism inducing the greater accumulation of labile C needs further experimental studies.

Cytogenetics in the management of multiple myeloma: an update by the Groupe francophone de cytogénétique hématologique (GFCH).

PubMed

Daudignon, Agnès; Quilichini, Benoît; Ameye, Geneviève; Poirel, Hélène; Bastard, Christian; Terré, Christine

2016-10-01

Cytogenetics of multiple myeloma has evolved in recent years by the emergence of Interphasic fluorescence in situ hybridization (FISH) performed on sorted plasma cells detecting abnormalities independently of a proliferative and infiltrative index. Cytogenetic analysis plays a major part in the risk stratification of myeloma diagnosis due to prognostic impact of various cytogenetic abnormalities as well as to the association between emerging therapeutic approaches in MM. Thus, practice guidelines now recommend interphasic FISH or alternative molecular technics as the initial analysis for multiple myeloma. The Groupe francophone de cytogénétique hématologique (GFCH) proposes in this issue an update of managing multiple myeloma cytogenetics.

How Hierarchical Topics Evolve in Large Text Corpora.

PubMed

Cui, Weiwei; Liu, Shixia; Wu, Zhuofeng; Wei, Hao

2014-12-01

Using a sequence of topic trees to organize documents is a popular way to represent hierarchical and evolving topics in text corpora. However, following evolving topics in the context of topic trees remains difficult for users. To address this issue, we present an interactive visual text analysis approach to allow users to progressively explore and analyze the complex evolutionary patterns of hierarchical topics. The key idea behind our approach is to exploit a tree cut to approximate each tree and allow users to interactively modify the tree cuts based on their interests. In particular, we propose an incremental evolutionary tree cut algorithm with the goal of balancing 1) the fitness of each tree cut and the smoothness between adjacent tree cuts; 2) the historical and new information related to user interests. A time-based visualization is designed to illustrate the evolving topics over time. To preserve the mental map, we develop a stable layout algorithm. As a result, our approach can quickly guide users to progressively gain profound insights into evolving hierarchical topics. We evaluate the effectiveness of the proposed method on Amazon's Mechanical Turk and real-world news data. The results show that users are able to successfully analyze evolving topics in text data.

Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage.

PubMed

Rockah-Shmuel, Liat; Tawfik, Dan S

2012-12-01

DNA-binding and modifying proteins show high specificity but also exhibit a certain level of promiscuity. Such latent promiscuous activities comprise the starting points for new protein functions, but this hypothesis presents a paradox: a new activity can only evolve if it already exists. How then, do novel activities evolve? DNA methyltransferases, for example, are highly divergent in their target sites, but how transitions toward novel sites occur remains unknown. We performed laboratory evolution of the DNA methyltransferase M.HaeIII. We found that new target sites emerged primarily through expansion of the original site, GGCC, and the subsequent shrinkage of evolved expanded sites. Variants evolved for sites that are promiscuously methylated by M.HaeIII [GG((A)/(T))CC and GGCGCC] carried mutations in 'gate-keeper' residues. They could thereby methylate novel target sites such as GCGC and GGATCC that were neither selected for nor present in M.HaeIII. These 'generalist' intermediates were further evolved to obtain variants with novel target specificities. Our results demonstrate the ease by which new DNA-binding and modifying specificities evolve and the mechanism by which they occur at both the protein and DNA levels.

Beyond the Eye: Molecular Evolution of Extraocular Photoreception.

PubMed

Porter, Megan L

2016-11-01

The molecular mechanisms used by biological systems to detect light are diverse, with at least 10 classes of photosensor proteins and additional photosensitive domains characterized. At least six of these protein classes-Type I microbial opsins, Type II animal opsins, cryptochromes, gustatory-related receptors (GRRs), transient receptor potential A1 ion channels, and euglenoid photoactivated adenylyl cylases-can be considered as playing a role in extraocular systems (e.g., expressed outside of the eye in organisms with a visual system). These six classes of extraocular photosensor proteins consist of four broad groups: (1) seven transmembrane proteins, (2) cryptochromes, (3) ion channels, and (4) adenylyl cyclases. The light-driven functions of these extraocular photoreceptors are diverse, ranging from circadian entrainment to phototactic behavior. There are surprising similarities in structural motifs, with at least three independent families-the GRRs and Types I and II opsins-evolving a seven transmembrane helical tertiary structure for light sensing. When considering all of the photosensitive proteins, particularly those in microbial lineages, an image of evolutionary flexibility is emerging, with examples of fusion proteins from multiple types of photosensors and photosensitive domains shared among diverse arrays of proteins. In general, large questions remain for most of these photosensor proteins about exactly how the protein evolved light sensitivity, how light interacts with the protein, and how the photosensitive protein is transducing the signal. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Hair Follicle Bulge Stem Cells Appear Dispensable for the Acute Phase of Wound Re‐epithelialization

PubMed Central

Garcin, Clare L.; Ansell, David M.; Headon, Denis J.; Paus, Ralf

2016-01-01

Abstract The cutaneous healing response has evolved to occur rapidly, in order to minimize infection and to re‐establish epithelial homeostasis. Rapid healing is achieved through complex coordination of multiple cell types, which importantly includes specific cell populations within the hair follicle (HF). Under physiological conditions, the epithelial compartments of HF and interfollicular epidermis remain discrete, with K15+ve bulge stem cells contributing progeny for HF reconstruction during the hair cycle and as a basis for hair shaft production during anagen. Only upon wounding do HF cells migrate from the follicle to contribute to the neo‐epidermis. However, the identity of the first‐responding cells, and in particular whether this process involves a direct contribution of K15+ve bulge cells to the early stage of epidermal wound repair remains unclear. Here we demonstrate that epidermal injury in murine skin does not induce bulge activation during early epidermal wound repair. Specifically, bulge cells of uninjured HFs neither proliferate nor appear to migrate out of the bulge niche upon epidermal wounding. In support of these observations, Diphtheria toxin‐mediated partial ablation of K15+ve bulge cells fails to delay wound healing. Our data suggest that bulge cells only respond to epidermal wounding during later stages of repair. We discuss that this response may have evolved as a protective safeguarding mechanism against bulge stem cell exhaust and tumorigenesis. Stem Cells 2016;34:1377–1385 PMID:26756547

Thermal Analyzer for Planetary Soil (TAPS): an in Situ Instrument for Mineral and Volatile-element Measurements

NASA Technical Reports Server (NTRS)

Gooding, J. L.; Ming, D. W.; Gruener, J. E.; Gibbons, F. L.; Allton, J. H.

1993-01-01

Thermal Analyzer for Planetary Soil (TAPS) offers a specific implementation for the generic thermal analyzer/evolved-gas analyzer (TA/EGA) function included in the Mars Environmental Survey (MESUR) strawman payload; applications to asteroids and comets are also possible. The baseline TAPS is a single-sample differential scanning calorimeter (DSC), backed by a capacitive-polymer humidity sensor, with an integrated sampling mechanism. After placement on a planetary surface, TAPS acquires 10-50 mg of soil or sediment and heats the sample from ambient temperature to 1000-1300 K. During heating, DSC data are taken for the solid and evolved gases are swept past the water sensor. Through ground based data analysis, multicomponent DSC data are deconvolved and correlated with the water release profile to quantitatively determine the types and relative proportions of volatile-bearing minerals such as clays and other hydrates, carbonates, and nitrates. The rapid-response humidity sensors also achieve quantitative analysis of total water. After conclusion of soil-analysis operations, the humidity sensors become available for meteorology. The baseline design fits within a circular-cylindrical volume less than 1000 cm(sup 3), occupies 1.2 kg mass, and consumes about 2 Whr of power per analysis. Enhanced designs would acquire and analyze multiple samples and employ additional microchemical sensors for analysis of CO2, SO2, NO(x), and other gaseous species. Atmospheric pumps are also being considered as alternatives to pressurized purge gas.

Thermal Analyzer for Planetary Soil (TAPS): an in situ instrument for mineral and volatile-element measurements

NASA Astrophysics Data System (ADS)

Gooding, J. L.; Ming, D. W.; Gruener, J. E.; Gibbons, F. L.; Allton, J. H.

Thermal Analyzer for Planetary Soil (TAPS) offers a specific implementation for the generic thermal analyzer/evolved-gas analyzer (TA/EGA) function included in the Mars Environmental Survey (MESUR) strawman payload; applications to asteroids and comets are also possible. The baseline TAPS is a single-sample differential scanning calorimeter (DSC), backed by a capacitive-polymer humidity sensor, with an integrated sampling mechanism. After placement on a planetary surface, TAPS acquires 10-50 mg of soil or sediment and heats the sample from ambient temperature to 1000-1300 K. During heating, DSC data are taken for the solid and evolved gases are swept past the water sensor. Through ground based data analysis, multicomponent DSC data are deconvolved and correlated with the water release profile to quantitatively determine the types and relative proportions of volatile-bearing minerals such as clays and other hydrates, carbonates, and nitrates. The rapid-response humidity sensors also achieve quantitative analysis of total water. After conclusion of soil-analysis operations, the humidity sensors become available for meteorology. The baseline design fits within a circular-cylindrical volume less than 1000 cm3, occupies 1.2 kg mass, and consumes about 2 Whr of power per analysis. Enhanced designs would acquire and analyze multiple samples and employ additional microchemical sensors for analysis of CO2, SO2, NO(x), and other gaseous species. Atmospheric pumps are also being considered as alternatives to pressurized purge gas.

Three-dimensional flow structure and patterns of bed shear stress in an evolving compound meander bend

USGS Publications Warehouse

Engel, Frank; Rhoads, Bruce L.

2016-01-01

Compound meander bends with multiple lobes of maximum curvature are common in actively evolving lowland rivers. Interaction among spatial patterns of mean flow, turbulence, bed morphology, bank failures and channel migration in compound bends is poorly understood. In this paper, acoustic Doppler current profiler (ADCP) measurements of the three-dimensional (3D) flow velocities in a compound bend are examined to evaluate the influence of channel curvature and hydrologic variability on the structure of flow within the bend. Flow structure at various flow stages is related to changes in bed morphology over the study timeframe. Increases in local curvature within the upstream lobe of the bend reduce outer bank velocities at morphologically significant flows, creating a region that protects the bank from high momentum flow and high bed shear stresses. The dimensionless radius of curvature in the upstream lobe is one-third less than that of the downstream lobe, with average bank erosion rates less than half of the erosion rates for the downstream lobe. Higher bank erosion rates within the downstream lobe correspond to the shift in a core of high velocity and bed shear stresses toward the outer bank as flow moves through the two lobes. These erosion patterns provide a mechanism for continued migration of the downstream lobe in the near future. Bed material size distributions within the bend correspond to spatial patterns of bed shear stress magnitudes, indicating that bed material sorting within the bend is governed by bed shear stress. Results suggest that patterns of flow, sediment entrainment, and planform evolution in compound meander bends are more complex than in simple meander bends. Moreover, interactions among local influences on the flow, such as woody debris, local topographic steering, and locally high curvature, tend to cause compound bends to evolve toward increasing planform complexity over time rather than stable configurations.

EarthCube as an information resource marketplace; the GEAR Project conceptual design

NASA Astrophysics Data System (ADS)

Richard, S. M.; Zaslavsky, I.; Gupta, A.; Valentine, D.

2015-12-01

Geoscience Architecture for Research (GEAR) is approaching EarthCube design as a complex and evolving socio-technical federation of systems. EarthCube is intended to support the science research enterprise, for which there is no centralized command and control, requirements are a moving target, the function and behavior of the system must evolve and adapt as new scientific paradigms emerge, and system participants are conducting research that inherently implies seeking new ways of doing things. EarthCube must address evolving user requirements and enable domain and project systems developed under different management and for different purposes to work together. The EC architecture must focus on creating a technical environment that enables new capabilities by combining existing and newly developed resources in various ways, and encourages development of new resource designs intended for re-use and interoperability. In a sense, instead of a single architecture design, GEAR provides a way to accommodate multiple designs tuned to different tasks. This agile, adaptive, evolutionary software development style is based on a continuously updated portfolio of compatible components that enable new sub-system architecture. System users make decisions about which components to use in this marketplace based on performance, satisfaction, and impact metrics collected continuously to evaluate components, determine priorities, and guide resource allocation decisions by the system governance agency. EC is designed as a federation of independent systems, and although the coordinator of the EC system may be named an enterprise architect, the focus of the role needs to be organizing resources, assessing their readiness for interoperability with the existing EC component inventory, managing dependencies between transient subsystems, mechanisms of stakeholder engagement and inclusion, and negotiation of standard interfaces, rather than actual specification of components. Composition of components will be developed by projects that involve both domain scientists and CI experts for specific research problems. We believe an agile, marketplace type approach is an essential architectural strategy for EarthCube.

Storytelling, behavior planning, and language evolution in context.

PubMed

McBride, Glen

2014-01-01

An attempt is made to specify the structure of the hominin bands that began steps to language. Storytelling could evolve without need for language yet be strongly subject to natural selection and could provide a major feedback process in evolving language. A storytelling model is examined, including its effects on the evolution of consciousness and the possible timing of language evolution. Behavior planning is presented as a model of language evolution from storytelling. The behavior programming mechanism in both directions provide a model of creating and understanding behavior and language. Culture began with societies, then family evolution, family life in troops, but storytelling created a culture of experiences, a final step in the long process of achieving experienced adults by natural selection. Most language evolution occurred in conversations where evolving non-verbal feedback ensured mutual agreements on understanding. Natural language evolved in conversations with feedback providing understanding of changes.

Implications of a Culturally Evolved Self for Notions of Free Will

PubMed Central

Robertson, Lloyd Hawkeye

2017-01-01

Most schools in psychology have emphasized individual choice despite evidence of genetic and cultural determinism. It is suggested in this paper that the rejection of classical behaviorism by psychology and other humanities flowed from deeply held cultural assumptions about volition and free will. While compatibilists have suggested that notions of free will and determinism are not mutually exclusive, the psychological mechanisms by which such an accommodation could be explained have been inadequately explored. Drawing on research into classical cultures, this paper builds an argument that the notion of free will was adaptive flowing from culturally evolved changes to the self, and that this “evolved self,” containing assumptions of personal volition, continuity, and reason, became benchmarks of what it means to be human. The paper proposes a model of a culturally evolved self that is compatible with understandings of free will and determinism. Implications for therapeutic practice and future research are discussed. PMID:29163273

Storytelling, behavior planning, and language evolution in context

PubMed Central

McBride, Glen

2014-01-01

An attempt is made to specify the structure of the hominin bands that began steps to language. Storytelling could evolve without need for language yet be strongly subject to natural selection and could provide a major feedback process in evolving language. A storytelling model is examined, including its effects on the evolution of consciousness and the possible timing of language evolution. Behavior planning is presented as a model of language evolution from storytelling. The behavior programming mechanism in both directions provide a model of creating and understanding behavior and language. Culture began with societies, then family evolution, family life in troops, but storytelling created a culture of experiences, a final step in the long process of achieving experienced adults by natural selection. Most language evolution occurred in conversations where evolving non-verbal feedback ensured mutual agreements on understanding. Natural language evolved in conversations with feedback providing understanding of changes. PMID:25360123

OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY SHOWS INNER CHOROIDAL ISCHEMIA IN ACUTE POSTERIOR MULTIFOCAL PLACOID PIGMENT EPITHELIOPATHY.

PubMed

Dolz-Marco, Rosa; Sarraf, David; Giovinazzo, Vincent; Freund, K Bailey

2017-01-01

To describe multimodal imaging findings of an evolving case of acute posterior multifocal placoid pigment epitheliopathy occurring in a young healthy male. Case report of a patient with acute posterior multifocal placoid pigment epitheliopathy including comprehensive systemic and ocular examinations. Ultra-widefield autofluorescence, fluorescein angiography, indocyanine green angiography, and serial optical coherence tomography angiography were performed. A 34-year-old male presented with acute vision loss in his left eye for 2 weeks. His best-corrected visual acuity was 20/20 in his right eye and 20/200 in his left eye. Dilated funduscopic examination revealed multiple creamy white deep retinal lesions showing macular involvement of the left eye with a diffuse area of pigmentary changes. The presence of multiple areas of hypoperfusion of the inner choroid were demonstrated with fluorescein and indocyanine green angiography. Serial optical coherence tomography angiography showed multiple evolving areas of decreased flow at the level of the inner choroid. Although the pathogenesis of acute posterior multifocal placoid pigment epitheliopathy remains unknown, there is growing evidence of a primary choroidal involvement with secondary damage to the overlying retinal pigment epithelium and the outer retinal layers. Optical coherence tomography angiography may provide valuable information for the diagnosis and follow-up of this condition avoiding invasive angiographic procedures.

Disease-modifying treatments for early and advanced multiple sclerosis: a new treatment paradigm.

PubMed

Giovannoni, Gavin

2018-06-01

The treatment of multiple sclerosis is evolving rapidly with 11 classes of disease-modifying therapies (DMTs). This article provides an overview of a new classification system for DMTs and treatment paradigm for using these DMTs effectively and safely. A summary of research into the use of more active approaches to early and effective treatment of multiple sclerosis with defined treatment targets of no evident disease activity (NEDA). New insights are discussed that is allowing the field to begin to tackle more advanced multiple sclerosis, including people with multiple sclerosis using wheelchairs. However, the need to modify expectations of what can be achieved in more advanced multiple sclerosis are discussed; in particular, the focus on neuronal systems with reserve capacity, for example, upper limb, bulbar and visual function. The review describes a new more active way of managing multiple sclerosis and concludes with a call to action in solving the problem of slow adoption of innovations and the global problem of untreated, or undertreated, multiple sclerosis.

Molecular and physiological mechanisms of plant tolerance to toxic metals

USDA-ARS?s Scientific Manuscript database

Plants have evolved a myriad of adaptive mechanisms based on a number of genes to deal with the different toxic metals they encounter in the soils worldwide. These genes encode a range of different metal and organic compound transporters and enzyme pathways for the synthesis of metal detoxifying lig...

75 FR 60089 - Final Environmental Impact Statement (EIS) Addressing Campus Development at Fort Meade

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-29

... Intelligence Community's continually evolving requirements. The purpose of the Proposed Action is to provide facilities that fully support the Intelligence Community's mission. The need for the action is to consolidate multiple agencies' efforts to ensure capabilities for current and future missions as directed by Congress...

Chapter 8: The future

Treesearch

Peter F. Ffolliott

1999-01-01

Research in the vegetation types of the Central Arizona Highlands has evolved, for the most part, from single resource evaluations (increased water yield) to evaluations that consider the multiple benefits of vegetation management treatments. The papers presented in this publication have demonstrated that vegetation can be managed to increase water yields, while...

Using Machine Learning to Increase Research Efficiency: A New Approach in Environmental Sciences

USDA-ARS?s Scientific Manuscript database

Data collection has evolved from tedious in-person fieldwork to automatic data gathering from multiple sensor remotely. Scientist in environmental sciences have not fully exploited this data deluge, including legacy and new data, because the traditional scientific method is focused on small, high qu...

Navigating the Complexity of Qualitative Research in Postmodern Contexts: Assemblage, Critical Reflexivity, and Communion as Guides

ERIC Educational Resources Information Center

Bettez, Silvia Cristina

2015-01-01

For graduate students and other emerging qualitative researchers, the ever-evolving and sometimes conflicting perspectives, methodologies, and practices within various post-positivist frameworks (e.g. feminist, critical, Indigenous, participatory) can be overwhelming. Qualitative researchers working within postmodern contexts of multiplicity and…

Relational Inquiry: Generating New Knowledge with Adolescent Girls Who Use Crystal Meth

ERIC Educational Resources Information Center

Newbury, Janet; Hoskins, Marie

2010-01-01

Qualitative research is continuously evolving and expanding as researchers seek methodologies that reflect the intersubjective nature of experience. "Relational inquiry" is an approach which considers the relationships (a) between researchers and participants, (b) among multiple dimensions of the participant's lived experience, and (c) between the…

The Changing Job of the President.

ERIC Educational Resources Information Center

McPhail, Irving P.

The multiple roles of a contemporary Black college president are discussed and defined, focusing on the changing role of the president. Like their White counterparts, presidents of the nation's 117 historically Black colleges have seen their roles evolve as they have become savvy promoters, competing aggressively for students and philanthropic…

Contextualised Skill Acquisition Research: A New Framework to Study the Development of Sport Expertise

ERIC Educational Resources Information Center

Uehara, Luiz; Button, Chris; Falcous, Mark; Davids, Keith

2016-01-01

Background: Under the view of dynamical system theory, expertise in sports emerges from the interaction of multiple constraints. At an individual level, important interactions amongst constraints could include the relationships that evolve between one's family, playmates/coaches, and specific training activities. Or more broadly, other…

Digitized Special Collections and Multiple User Groups

ERIC Educational Resources Information Center

Gueguen, Gretchen

2010-01-01

Many organizations have evolved since their early attempts to mount digital exhibits on the Web and are experimenting with ways to increase the scale of their digitized collections by utilizing archival finding aid description rather than resource-intensive collections and exhibits. This article examines usability research to predict how such…

Evolving Approaches to the Study of Childhood Poverty and Education

ERIC Educational Resources Information Center

Hannum, Emily; Liu, Ran; Alvarado-Urbina, Andrea

2017-01-01

Social scientists have conceptualised poverty in multiple ways, with measurement approaches that seek to identify absolute, relative, subjective, and multi-dimensional poverty. The concept of poverty is central in the comparative education field, but has been empirically elusive in many large, international educational surveys: these studies have…

Insect sex determination: it all evolves around transformer.

PubMed

Verhulst, Eveline C; van de Zande, Louis; Beukeboom, Leo W

2010-08-01

Insects exhibit a variety of sex determining mechanisms including male or female heterogamety and haplodiploidy. The primary signal that starts sex determination is processed by a cascade of genes ending with the conserved switch doublesex that controls sexual differentiation. Transformer is the doublesex splicing regulator and has been found in all examined insects, indicating its ancestral function as a sex-determining gene. Despite this conserved function, the variation in transformer nucleotide sequence, amino acid composition and protein structure can accommodate a multitude of upstream sex determining signals. Transformer regulation of doublesex and its taxonomic distribution indicate that the doublesex-transformer axis is conserved among all insects and that transformer is the key gene around which variation in sex determining mechanisms has evolved.

Identifying multiple submissions in Internet research: preserving data integrity.

PubMed

Bowen, Anne M; Daniel, Candice M; Williams, Mark L; Baird, Grayson L

2008-11-01

Internet-based sexuality research with hidden populations has become increasingly popular. Respondent anonymity may encourage participation and lower social desirability, but associated disinhibition may promote multiple submissions, especially when incentives are offered. The goal of this study was to identify the usefulness of different variables for detecting multiple submissions from repeat responders and to explore incentive effects. The data included 1,900 submissions from a three-session Internet intervention with a pretest and three post-test questionnaires. Participants were men who have sex with men and incentives were offered to rural participants for completing each questionnaire. The final number of submissions included 1,273 "unique", 132 first submissions by "repeat responders" and 495 additional submissions by the "repeat responders" (N = 1,900). Four categories of repeat responders were identified: "infrequent" (2-5 submissions), "persistent" (6-10 submissions), "very persistent" (11-30 submissions), and "hackers" (more than 30 submissions). Internet Provider (IP) addresses, user names, and passwords were the most useful for identifying "infrequent" repeat responders. "Hackers" often varied their IP address and identifying information to prevent easy identification, but investigating the data for small variations in IP, using reverse telephone look up, and patterns across usernames and passwords were helpful. Incentives appeared to play a role in stimulating multiple submissions, especially from the more sophisticated "hackers". Finally, the web is ever evolving and it will be necessary to have good programmers and staff who evolve as fast as "hackers".

Acute transfusion-related abdominal injury in trauma patients: a case report.

PubMed

Michel, P; Wähnert, D; Freistühler, M; Laukoetter, M G; Rehberg, S; Raschke, M J; Garcia, P

2016-10-19

Secondary abdominal compartment syndrome is well known as a life-threatening complication in critically ill patients in an intensive care unit. Massive crystalloid fluid resuscitation has been identified as the most important risk factor. The time interval from hospital admittance to the development of manifest abdominal compartment syndrome is usually greater than 24 hours. In the absence of any direct abdominal trauma, we observed a rapidly evolving secondary abdominal compartment syndrome shortly after hospital admittance associated with massive transfusion of blood products and only moderate crystalloid resuscitation. We report the case of an acute secondary abdominal compartment syndrome developing within 3 to 4 hours in a 74-year-old polytraumatized white woman. Although multiple fractures of her extremities and a B-type pelvic ring fracture were diagnosed by a full body computed tomography scan, no intra-abdominal injury could be detected. Hemorrhagic shock with a drop in her hemoglobin level to 5.7 g/dl was treated by massive transfusion of blood products and high doses of catecholamines. Shortly afterwards, her pulmonary gas exchange progressively deteriorated and mechanical ventilation became almost impossible with peak airway pressures of up to 60 cmH 2 O. Her abdomen appeared rigid and tense accompanied by a progressive hemodynamic decompensation necessitating mechanic cardiopulmonary resuscitation. Although preoperative computed tomography scans showed no signs of intra-abdominal fluid, a decompressive laparotomy under cardiopulmonary resuscitation conditions was performed and 2 liters of ascites-like fluid disgorged. Her hemodynamics and pulmonary ventilation improved immediately. This case report describes for the first time acute secondary abdominal compartment syndrome in a trauma patient, evolving in a very short time period. We hypothesize that the massive transfusion of blood products along with high doses of catecholamines triggered the acute development of abdominal compartment syndrome. Trauma teams need to consider a rapidly developing secondary abdominal compartment syndrome to be a potential cause of hemodynamic decompensation not only in the later phase of treatment but also in the emergency phase of treatment.

The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation

PubMed Central

Mayer, Melanie G.; Rödelsperger, Christian; Witte, Hanh; Riebesell, Metta; Sommer, Ralf J.

2015-01-01

Many nematodes form dauer larvae when exposed to unfavorable conditions, representing an example of phenotypic plasticity and a major survival and dispersal strategy. In Caenorhabditis elegans, the regulation of dauer induction is a model for pheromone, insulin, and steroid-hormone signaling. Recent studies in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development, i.e. pheromone production and sensing and dauer longevity and fitness. One intriguing example is a strain from Ohio, having extremely long-lived dauers associated with very high fitness and often forming the most dauers in response to other strains´ pheromones, including the reference strain from California. While such examples have been suggested to represent intraspecific competition among strains, the molecular mechanisms underlying these dauer-associated patterns are currently unknown. We generated recombinant-inbred-lines between the Californian and Ohioan strains and used quantitative-trait-loci analysis to investigate the molecular mechanism determining natural variation in dauer development. Surprisingly, we discovered that the orphan gene dauerless controls dauer formation by copy number variation. The Ohioan strain has one dauerless copy causing high dauer formation, whereas the Californian strain has two copies, resulting in strongly reduced dauer formation. Transgenic animals expressing multiple copies do not form dauers. dauerless is exclusively expressed in CAN neurons, and both CAN ablation and dauerless mutations increase dauer formation. Strikingly, dauerless underwent several duplications and acts in parallel or downstream of steroid-hormone signaling but upstream of the nuclear-hormone-receptor daf-12. We identified the novel or fast-evolving gene dauerless as inhibitor of dauer development. Our findings reveal the importance of gene duplications and copy number variations for orphan gene function and suggest daf-12 as major target for dauer regulation. We discuss the consequences of the novel vs. fast-evolving nature of orphans for the evolution of developmental networks and their role in natural variation and intraspecific competition. PMID:26087034

The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation.

PubMed

Mayer, Melanie G; Rödelsperger, Christian; Witte, Hanh; Riebesell, Metta; Sommer, Ralf J

2015-06-01

Many nematodes form dauer larvae when exposed to unfavorable conditions, representing an example of phenotypic plasticity and a major survival and dispersal strategy. In Caenorhabditis elegans, the regulation of dauer induction is a model for pheromone, insulin, and steroid-hormone signaling. Recent studies in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development, i.e. pheromone production and sensing and dauer longevity and fitness. One intriguing example is a strain from Ohio, having extremely long-lived dauers associated with very high fitness and often forming the most dauers in response to other strains' pheromones, including the reference strain from California. While such examples have been suggested to represent intraspecific competition among strains, the molecular mechanisms underlying these dauer-associated patterns are currently unknown. We generated recombinant-inbred-lines between the Californian and Ohioan strains and used quantitative-trait-loci analysis to investigate the molecular mechanism determining natural variation in dauer development. Surprisingly, we discovered that the orphan gene dauerless controls dauer formation by copy number variation. The Ohioan strain has one dauerless copy causing high dauer formation, whereas the Californian strain has two copies, resulting in strongly reduced dauer formation. Transgenic animals expressing multiple copies do not form dauers. dauerless is exclusively expressed in CAN neurons, and both CAN ablation and dauerless mutations increase dauer formation. Strikingly, dauerless underwent several duplications and acts in parallel or downstream of steroid-hormone signaling but upstream of the nuclear-hormone-receptor daf-12. We identified the novel or fast-evolving gene dauerless as inhibitor of dauer development. Our findings reveal the importance of gene duplications and copy number variations for orphan gene function and suggest daf-12 as major target for dauer regulation. We discuss the consequences of the novel vs. fast-evolving nature of orphans for the evolution of developmental networks and their role in natural variation and intraspecific competition.

Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering

PubMed Central

Prescott, Thomas P.; Lang, Moritz; Papachristodoulou, Antonis

2015-01-01

Large, naturally evolved biomolecular networks typically fulfil multiple functions. When modelling or redesigning such systems, functional subsystems are often analysed independently first, before subsequent integration into larger-scale computational models. In the design and analysis process, it is therefore important to quantitatively analyse and predict the dynamics of the interactions between integrated subsystems; in particular, how the incremental effect of integrating a subsystem into a network depends on the existing dynamics of that network. In this paper we present a framework for simulating the contribution of any given functional subsystem when integrated together with one or more other subsystems. This is achieved through a cascaded layering of a network into functional subsystems, where each layer is defined by an appropriate subset of the reactions. We exploit symmetries in our formulation to exhaustively quantify each subsystem’s incremental effects with minimal computational effort. When combining subsystems, their isolated behaviour may be amplified, attenuated, or be subject to more complicated effects. We propose the concept of mutual dynamics to quantify such nonlinear phenomena, thereby defining the incompatibility and cooperativity between all pairs of subsystems when integrated into any larger network. We exemplify our theoretical framework by analysing diverse behaviours in three dynamic models of signalling and metabolic pathways: the effect of crosstalk mechanisms on the dynamics of parallel signal transduction pathways; reciprocal side-effects between several integral feedback mechanisms and the subsystems they stabilise; and consequences of nonlinear interactions between elementary flux modes in glycolysis for metabolic engineering strategies. Our analysis shows that it is not sufficient to just specify subsystems and analyse their pairwise interactions; the environment in which the interaction takes place must also be explicitly defined. Our framework provides a natural representation of nonlinear interaction phenomena, and will therefore be an important tool for modelling large-scale evolved or synthetic biomolecular networks. PMID:25933116

Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish.

PubMed

Meng, Fanwei; Braasch, Ingo; Phillips, Jennifer B; Lin, Xiwen; Titus, Tom; Zhang, Chunguang; Postlethwait, John H

2013-07-01

In adaptating to perpetual darkness, cave species gradually lose eyes and body pigmentation and evolve alternatives for exploring their environments. Although troglodyte features evolved independently many times in cavefish, we do not yet know whether independent evolution of these characters involves common genetic mechanisms. Surface-dwelling and many cave-dwelling species make the freshwater teleost genus Sinocyclocheilus an excellent model for studying the evolution of adaptations to life in constant darkness. We compared the mature retinal histology of surface and cave species in Sinocyclocheilus and found that adult cavefish showed a reduction in the number and length of photoreceptor cells. To identify genes and genetic pathways that evolved in constant darkness, we used RNA-seq to compare eyes of surface and cave species. De novo transcriptome assemblies were developed for both species, and contigs were annotated with gene ontology. Results from cave-dwelling Sinocyclocheilus revealed reduced transcription of phototransduction and other genes important for retinal function. In contrast to the blind Mexican tetra cavefish Astyanax mexicanus, our results on morphologies and gene expression suggest that evolved retinal reduction in cave-dwelling Sinocyclocheilus occurs in a lens-independent fashion by the reduced proliferation and downregulation of transcriptional factors shown to have direct roles in retinal development and maintenance, including cone-rod homeobox (crx) and Wnt pathway members. These results show that the independent evolution of retinal degeneration in cavefish can occur by different developmental genetic mechanisms.

Insecticide Resistance Mechanisms in the Green Peach Aphid Myzus persicae (Hemiptera: Aphididae) II: Costs and Benefits

PubMed Central

Silva, Andrea X.; Bacigalupe, Leonardo D.; Luna-Rudloff, Manuela; Figueroa, Christian C.

2012-01-01

Background Among herbivorous insects that have exploited agro-ecosystems, the peach-potato aphid, Myzus persicae, is recognized as one of the most important agricultural pests worldwide. Uses over 400 plant species and has evolved different insecticides resistance mechanisms. As M. persicae feeds upon a huge diversity of hosts, it has been exposed to a wide variety of plant allelochemicals, which probably have promoted a wide range of detoxification systems. Methodology/Principal Findings In this work we (i) evaluated whether insecticide resistance mutations (IRM) in M. persicae can give an advantage in terms of reproductive fitness when aphids face two hosts, pepper (Capsicum annuum) a suitable host and radish (Raphanus sativus) the unfavorable host and (ii) examined the transcriptional expression of six genes that are known to be up-regulated in response to insecticides. Our results show a significant interaction between host and IRM on the intrinsic rate of increase (rm). Susceptible genotypes (not carrying insensitivity mutations) had a higher rm on pepper, and the transcriptional levels of five genes increased on radish. The rm relationship was reversed on the unfavorable host; genotypes with multiple IRM exhibited higher rm, without altering the transcriptional levels of the studied genes. Genotypes with one IRM kept a similar rm on both hosts, but they increased the transcriptional levels of two genes. Conclusions/Significance Although we have studied only nine genotypes, overall our results are in agreement with the general idea that allelochemical detoxification systems could constitute a pre-adaptation for the development of insecticide resistance. Genotypes carrying IRM exhibited a higher rm than susceptible genotypes on radish, the more unfavorable host. Susceptible genotypes should be able to tolerate the defended host by up-regulating some metabolic genes that are also responding to insecticides. Hence, our results suggest that the trade-off among resistance mechanisms might be quite complex, with a multiplicity of costs and benefits depending on the environment. PMID:22685539

Investigation of Vapor Cooling Enhancements for Applications on Large Cryogenic Systems

NASA Technical Reports Server (NTRS)

Ameen, Lauren; Zoeckler, Joseph

2017-01-01

The need to demonstrate and evaluate the effectiveness of heat interception methods for use on a relevant cryogenic propulsion stage at a system level has been identified. Evolvable Cryogenics (eCryo) Structural Heat Intercept, Insulation and Vibration Evaluation Rig (SHIIVER) will be designed with vehicle specific geometries (SLS Exploration Upper Stage (EUS) as guidance) and will be subjected to simulated space environments. One method of reducing structure-born heat leak being investigated utilizes vapor-based heat interception. Vapor-based heat interception could potentially reduce heat leak into liquid hydrogen propulsion tanks, increasing potential mission length or payload capability. Due to the high number of unknowns associated with the heat transfer mechanism and integration of vapor-based heat interception on a realistic large-scale skirt design, a sub-scale investigation was developed. The sub-project effort is known as the Small-scale Laboratory Investigation of Cooling Enhancements (SLICE). The SLICE aims to study, design, and test sub-scale multiple attachments and flow configuration concepts for vapor-based heat interception of structural skirts. SLICE will focus on understanding the efficiency of the heat transfer mechanism to the boil-off hydrogen vapor by varying the fluid network designs and configurations. Various analyses were completed in MATLAB, Excel VBA, and COMSOL Multiphysics to understand the optimum flow pattern for heat transfer and fluid dynamics. Results from these analyses were used to design and fabricate test article subsections of a large forward skirt with vapor cooling applied. The SLICE testing is currently being performed to collect thermal mechanical performance data on multiple skirt heat removal designs while varying inlet vapor conditions necessary to intercept a specified amount of heat for a given system. Initial results suggest that applying vapor-cooling provides a 50 heat reduction in conductive heat transmission along the skirt to the tank. The information obtained by SLICE will be used by the SHIIVER engineering team to design and implement vapor-based heat removal technology into the SHIIVER forward skirt hardware design.

Energy-latitude dispersion patterns near the isotropy boundaries of energetic protons

NASA Astrophysics Data System (ADS)

Sergeev, V. A.; Chernyaeva, S. A.; Apatenkov, S. V.; Ganushkina, N. Y.; Dubyagin, S. V.

2015-08-01

Non-adiabatic motion of plasma sheet protons causes pitch-angle scattering and isotropic precipitation to the ionosphere, which forms the proton auroral oval. This mechanism related to current sheet scattering (CSS) provides a specific energy-latitude dispersion pattern near the equatorward boundary of proton isotropic precipitation (isotropy boundary, IB), with precipitation sharply decreasing at higher (lower) latitude for protons with lower (higher) energy. However, this boundary maps to the inner magnetosphere, where wave-induced scattering may provide different dispersion patterns as recently demonstrated by Liang et al. (2014). Motivated by the potential usage of the IBs for the magnetotail monitoring as well as by the need to better understand the mechanisms forming the proton IB, we investigate statistically the details of particle flux patterns near the proton IB using NOAA-POES polar spacecraft observations made during September 2009. By comparing precipitated-to-trapped flux ratio (J0/J90) at >30 and >80 keV proton energies, we found a relatively small number of simple CSS-type dispersion events (only 31 %). The clear reversed (wave-induced) dispersion patterns were very rare (5 %). The most frequent pattern had nearly coinciding IBs at two energies (63 %). The structured precipitation with multiple IBs was very frequent (60 %), that is, with two or more significant J0/J90 dropouts. The average latitudinal width of multiple IB structures was about 1°. Investigation of dozens of paired auroral zone crossings of POES satellites showed that the IB pattern is stable on a timescale of less than 2 min (a few proton bounce periods) but can evolve on a longer (several minutes) scale, suggesting temporal changes in some mesoscale structures in the equatorial magnetosphere. We discuss the possible role of CSS-related and wave-induced mechanisms and their possible coupling to interpret the emerging complicated patterns of proton isotropy boundaries.

Science of Integrated Approaches to Natural Resources Management

NASA Astrophysics Data System (ADS)

Tengberg, Anna; Valencia, Sandra

2017-04-01

To meet multiple environmental objectives, integrated programming is becoming increasingly important for the Global Environmental Facility (GEF), the financial mechanism of the multilateral environmental agreements, including the United Nations Convention to Combat Desertification (UNCCD). Integration of multiple environmental, social and economic objectives also contributes to the achievement of the Sustainable Development Goals (SDGs) in a timely and cost-effective way. However, integration is often not well defined. This paper therefore focuses on identifying key aspects of integration and assessing their implementation in natural resources management (NRM) projects. To that end, we draw on systems thinking literature, and carry out an analysis of a random sample of GEF integrated projects and in-depth case studies demonstrating lessons learned and good practices in addressing land degradation and other NRM challenges. We identify numerous challenges and opportunities of integrated approaches that need to be addressed in order to maximise the catalytic impact of the GEF during problem diagnosis, project design, implementation and governance. We highlight the need for projects to identify clearer system boundaries and main feedback mechanisms within those boundaries, in order to effectively address drivers of environmental change. We propose a theory of change for Integrated Natural Resources Management (INRM) projects, where short-term environmental and socio-economic benefits will first accrue at the local level. Implementation of improved INRM technologies and practices at the local level can be extended through spatial planning, strengthening of innovation systems, and financing and incentive mechanisms at the watershed and/or landscape/seascape level to sustain and enhance ecosystem services at larger scales and longer time spans. We conclude that the evolving scientific understanding of factors influencing social, technical and institutional innovations and transitions towards sustainable management of natural resources should be harnessed and integrated into GEF's influencing models and theory of change, and be coupled with updated approaches for learning, adaptive management and scaling up.

Studies of compatibility in Betula

Treesearch

Knud E. Clausen

1966-01-01

Heterozygosity appears necessary to maintain fitness in many plant populations, and mechanisms favoring or enforcing cross pollination have evolved. Most important among the latter are dioecism and incompatibility.

A major gene controls mimicry and crypsis in butterflies and moths

PubMed Central

Nadeau, Nicola J.; Pardo-Diaz, Carolina; Whibley, Annabel; Supple, Megan; Saenko, Suzanne V.; Wallbank, Richard W. R.; Wu, Grace C.; Maroja, Luana; Ferguson, Laura; Hanly, Joseph J.; Hines, Heather; Salazar, Camilo; Merrill, Richard; Dowling, Andrea; ffrench-Constant, Richard; Llaurens, Violaine; Joron, Mathieu; McMillan, W. Owen; Jiggins, Chris D.

2016-01-01

The wing patterns of butterflies and moths (Lepidoptera) are diverse and striking examples of evolutionary diversification by natural selection1,2. Lepidopteran wing colour patterns are a key innovation, consisting of arrays of coloured scales. We still lack a general understanding of how these patterns are controlled and if there is any commonality across the 160,000 moth and 17,000 butterfly species. Here, we identify a gene, cortex, through fine-scale mapping using population genomics and gene expression analyses, which regulates pattern switches in multiple species across the mimetic radiation in Heliconius butterflies. cortex belongs to a fast evolving subfamily of the otherwise highly conserved fizzy family of cell cycle regulators3, suggesting that it most likely regulates pigmentation patterning through regulation of scale cell development. In parallel with findings in the peppered moth (Biston betularia)4, our results suggest that this mechanism is common within Lepidoptera and that cortex has become a major target for natural selection acting on colour and pattern variation in this group of insects. PMID:27251285

Climate change and pastoralism: impacts, consequences and adaptation.

PubMed

Herrero, M; Addison, J; Bedelian, C; Carabine, E; Havlík, P; Henderson, B; Van De Steeg, J; Thornton, P K

2016-11-01

The authors discuss the main climate change impacts on pastoralist societies, including those on rangelands, livestock and other natural resources, and their extended repercussions on food security, incomes and vulnerability. The impacts of climate change on the rangelands of the globe and on the vulnerability of the people who inhabit them will be severe and diverse, and will require multiple, simultaneous responses. In higher latitudes, the removal of temperature constraints might increase pasture production and livestock productivity, but in tropical arid lands, the impacts are highly location specific, but mostly negative. The authors outline several adaptation options, ranging from implementing new technical practices and diversifying income sources to finding institutional support and introducing new market mechanisms, all of which are pivotal for enhancing the capacity of pastoralists to adapt to climate variability and change. Due to the dynamism of all the changes affecting pastoral societies, strategies that lock pastoral societies into specified development pathways could be maladaptive. Flexible and evolving combinations of practices and policies are the key to successful pastoral adaptation.

Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast

PubMed Central

Zanders, Sarah E; Eickbush, Michael T; Yu, Jonathan S; Kang, Ji-Won; Fowler, Kyle R; Smith, Gerald R; Malik, Harmit Singh

2014-01-01

Hybrid sterility is one of the earliest postzygotic isolating mechanisms to evolve between two recently diverged species. Here we identify causes underlying hybrid infertility of two recently diverged fission yeast species Schizosaccharomyces pombe and S. kambucha, which mate to form viable hybrid diploids that efficiently complete meiosis, but generate few viable gametes. We find that chromosomal rearrangements and related recombination defects are major but not sole causes of hybrid infertility. At least three distinct meiotic drive alleles, one on each S. kambucha chromosome, independently contribute to hybrid infertility by causing nonrandom spore death. Two of these driving loci are linked by a chromosomal translocation and thus constitute a novel type of paired meiotic drive complex. Our study reveals how quickly multiple barriers to fertility can arise. In addition, it provides further support for models in which genetic conflicts, such as those caused by meiotic drive alleles, can drive speciation. DOI: http://dx.doi.org/10.7554/eLife.02630.001 PMID:24963140

Steric antisense inhibition of AMPA receptor Q/R editing reveals tight coupling to intronic editing sites and splicing

PubMed Central

Penn, Andrew C.; Balik, Ales; Greger, Ingo H.

2013-01-01

Adenosine-to-Inosine (A-to-I) RNA editing is a post-transcriptional mechanism, evolved to diversify the transcriptome in metazoa. In addition to wide-spread editing in non-coding regions protein recoding by RNA editing allows for fine tuning of protein function. Functional consequences are only known for some editing sites and the combinatorial effect between multiple sites (functional epistasis) is currently unclear. Similarly, the interplay between RNA editing and splicing, which impacts on post-transcriptional gene regulation, has not been resolved. Here, we describe a versatile antisense approach, which will aid resolving these open questions. We have developed and characterized morpholino oligos targeting the most efficiently edited site—the AMPA receptor GluA2 Q/R site. We show that inhibition of editing closely correlates with intronic editing efficiency, which is linked to splicing efficiency. In addition to providing a versatile tool our data underscore the unique efficiency of a physiologically pivotal editing site. PMID:23172291

[Progressive cerebral infraction initially presenting with pseudo-ulnar nerve palsy in a patient with severe internal carotid artery stenosis].

PubMed

Kakinuma, Kanako; Nakajima, Masashi; Hieda, Soutarou; Ichikawa, Hiroo; Kawamura, Mitsuru

2010-09-01

A 63-year-old man with hypercholesterolemia developed sensory and motor disturbances in the ulnar side of the right hand, and over three days the weakness evolved to entire right arm. Examination on the 6th day after onset showed mild lower facial palsy in addition to the upper limb weakness on the right. The weakness involved entire right arm sparing shoulder girdle muscles, which was worse in the 4th and 5th digits with claw hand deformity of the hand. Magnetic resonance imaging showed multiple small infracts in the centrum semiovale as well as in the medial side of the precentral knob on the left. Magnetic resonance angiography, ultrasonography, and 3D-CT angiography of the neck showed severe stenosis associated with unstable plaque of the left internal carotid artery. Hemodynamic mechanisms including microemboli and hypoperfusion associated with severe internal carotid artery stenosis are likely to cause stroke in evolution after initial presentation of pseudo-ulnar palsy in the present case.

Synonymous Mutations at the Beginning of the Influenza A Virus Hemagglutinin Gene Impact Experimental Fitness.

PubMed

Canale, Aneth S; Venev, Sergey V; Whitfield, Troy W; Caffrey, Daniel R; Marasco, Wayne A; Schiffer, Celia A; Kowalik, Timothy F; Jensen, Jeffrey D; Finberg, Robert W; Zeldovich, Konstantin B; Wang, Jennifer P; Bolon, Daniel N A

2018-04-13

The fitness effects of synonymous mutations can provide insights into biological and evolutionary mechanisms. We analyzed the experimental fitness effects of all single-nucleotide mutations, including synonymous substitutions, at the beginning of the influenza A virus hemagglutinin (HA) gene. Many synonymous substitutions were deleterious both in bulk competition and for individually isolated clones. Investigating protein and RNA levels of a subset of individually expressed HA variants revealed that multiple biochemical properties contribute to the observed experimental fitness effects. Our results indicate that a structural element in the HA segment viral RNA may influence fitness. Examination of naturally evolved sequences in human hosts indicates a preference for the unfolded state of this structural element compared to that found in swine hosts. Our overall results reveal that synonymous mutations may have greater fitness consequences than indicated by simple models of sequence conservation, and we discuss the implications of this finding for commonly used evolutionary tests and analyses. Copyright © 2018. Published by Elsevier Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Y Cao; X Jin; H Huang

The TrkH/TrkG/KtrB proteins mediate K{sup +} uptake in bacteria and probably evolved from simple K{sup +} channels by multiple gene duplications or fusions. Here we present the crystal structure of a TrkH from Vibrio parahaemolyticus. TrkH is a homodimer, and each protomer contains an ion permeation pathway. A selectivity filter, similar in architecture to those of K{sup +} channels but significantly shorter, is lined by backbone and side-chain oxygen atoms. Functional studies showed that TrkH is selective for permeation of K{sup +} and Rb{sup +} over smaller ions such as Na{sup +} or Li{sup +}. Immediately intracellular to the selectivitymore » filter are an intramembrane loop and an arginine residue, both highly conserved, which constrict the permeation pathway. Substituting the arginine with an alanine significantly increases the rate of K{sup +} flux. These results reveal the molecular basis of K{sup +} selectivity and suggest a novel gating mechanism for this large and important family of membrane transport proteins.« less

3D Bioprinting for Organ Regeneration

PubMed Central

Cui, Haitao; Nowicki, Margaret; Fisher, John P.; Zhang, Lijie Grace

2017-01-01

Regenerative medicine holds the promise of engineering functional tissues or organs to heal or replace abnormal and necrotic tissues/organs, offering hope for filling the gap between organ shortage and transplantation needs. Three-dimensional (3D) bioprinting is evolving into an unparalleled bio-manufacturing technology due to its high-integration potential for patient-specific designs, precise and rapid manufacturing capabilities with high resolution, and unprecedented versatility. It enables precise control over multiple compositions, spatial distributions, and architectural accuracy/complexity, therefore achieving effective recapitulation of microstructure, architecture, mechanical properties, and biological functions of target tissues and organs. Here we provide an overview of recent advances in 3D bioprinting technology, as well as design concepts of bioinks suitable for the bioprinting process. We focus on the applications of this technology for engineering living organs, focusing more specifically on vasculature, neural networks, the heart and liver. We conclude with current challenges and the technical perspective for further development of 3D organ bioprinting. PMID:27995751

Conserved versatile master regulators in signalling pathways in response to stress in plants

PubMed Central

Balderas-Hernández, Victor E.; Alvarado-Rodríguez, Miguel; Fraire-Velázquez, Saúl

2013-01-01

From the first land plants to the complex gymnosperms and angiosperms of today, environmental conditions have forced plants to develop molecular strategies to surpass natural obstacles to growth and proliferation, and these genetic gains have been transmitted to the following generations. In this long natural process, novel and elaborate mechanisms have evolved to enable plants to cope with environmental limitations. Elements in many signalling cascades enable plants to sense different, multiple and simultaneous ambient cues. A group of versatile master regulators of gene expression control plant responses to stressing conditions. For crop breeding purposes, the task is to determine how to activate these key regulators to enable accurate and optimal reactions to common stresses. In this review, we discuss how plants sense biotic and abiotic stresses, how and which master regulators are implied in the responses to these stresses, their evolution in the life kingdoms, and the domains in these proteins that interact with other factors to lead to a proper and efficient plant response. PMID:24147216

Glycosylation-dependent galectin-receptor interactions promote Chlamydia trachomatis infection.

PubMed

Lujan, Agustin L; Croci, Diego O; Gambarte Tudela, Julián A; Losinno, Antonella D; Cagnoni, Alejandro J; Mariño, Karina V; Damiani, María T; Rabinovich, Gabriel A

2018-06-11

Chlamydia trachomatis ( Ct ) constitutes the most prevalent sexually transmitted bacterium worldwide. Chlamydial infections can lead to severe clinical sequelae including pelvic inflammatory disease, ectopic pregnancy, and tubal infertility. As an obligate intracellular pathogen, Ct has evolved multiple strategies to promote adhesion and invasion of host cells, including those involving both bacterial and host glycans. Here, we show that galectin-1 (Gal1), an endogenous lectin widely expressed in female and male genital tracts, promotes Ct infection. Through glycosylation-dependent mechanisms involving recognition of bacterial glycoproteins and N -glycosylated host cell receptors, Gal1 enhanced Ct attachment to cervical epithelial cells. Exposure to Gal1, mainly in its dimeric form, facilitated bacterial entry and increased the number of infected cells by favoring Ct - Ct and Ct -host cell interactions. These effects were substantiated in vivo in mice lacking Gal1 or complex β1-6-branched N -glycans. Thus, disrupting Gal1- N -glycan interactions may limit the severity of chlamydial infection by inhibiting bacterial invasion of host cells.

Treatment of severe lupus nephritis: the new horizon.

PubMed

Chan, Tak Mao

2015-01-01

Lupus nephritis is a common and severe manifestation of systemic lupus erythematosus, and an important cause of both acute kidney injury and end-stage renal disease. Despite its aggressive course, lupus nephritis is amenable to treatment in the majority of patients. The paradigm of immunosuppressive treatment for lupus nephritis has evolved over the past few decades from corticosteroids alone to corticosteroids combined with cyclophosphamide. Sequential treatment regimens using various agents have been formulated for induction and long-term maintenance therapy, and mycophenolate mofetil has emerged as a standard of care option for both induction and maintenance immunosuppressive treatment. The current era has witnessed the emergence of multiple novel therapeutic options, such as calcineurin inhibitors and biologic agents that target key pathogenetic mechanisms of lupus nephritis. Clinical outcomes have improved in parallel with these therapeutic advances. This Review discusses the evidence in support of current standard of care immunosuppressive treatments and emerging therapies, and describes their roles and relative merits in the management of patients with lupus nephritis.

Multiple transcription factor codes activate epidermal wound–response genes in Drosophila

PubMed Central

Pearson, Joseph C.; Juarez, Michelle T.; Kim, Myungjin; Drivenes, Øyvind; McGinnis, William

2009-01-01

Wounds in Drosophila and mouse embryos induce similar genetic pathways to repair epidermal barriers. However, the transcription factors that transduce wound signals to repair epidermal barriers are largely unknown. We characterize the transcriptional regulatory enhancers of 4 genes—Ddc, ple, msn, and kkv—that are rapidly activated in epidermal cells surrounding wounds in late Drosophila embryos and early larvae. These epidermal wound enhancers all contain evolutionarily conserved sequences matching binding sites for JUN/FOS and GRH transcription factors, but vary widely in trans- and cis-requirements for these inputs and their binding sites. We propose that the combination of GRH and FOS is part of an ancient wound–response pathway still used in vertebrates and invertebrates, but that other mechanisms have evolved that result in similar transcriptional output. A common, but largely untested assumption of bioinformatic analyses of gene regulatory networks is that transcription units activated in the same spatial and temporal patterns will require the same cis-regulatory codes. Our results indicate that this is an overly simplistic view. PMID:19168633

Cancer Stem Cells: Dynamic Entities in an Ever-Evolving Paradigm.

PubMed

Lopez-Bertoni, Hernando; Li, Yunqing; Laterra, John

2015-11-01

The cancer stem cell (CSC) hypothesis postulates that there is a hierarchy of cellular differentiation within cancers and that the bulk population of tumor cells is derived from a relatively small population of multi-potent neoplastic stem-like cells (CSCs). This tumor-initiating cell population plays an important role in maintaining tumor growth through their unlimited self-renewal, therapeutic resistance, and capacity to propagate tumors through asymmetric cell division. Recent findings from multiple laboratories show that cancer progenitor cells have the capacity to de-differentiate and acquire a stem-like phenotype in response to either genetic manipulation or environmental cues. These findings suggest that CSCs and relatively differentiated progenitors coexist in dynamic equilibrium and are subject to bidirectional conversion. In this review, we discuss emerging concepts regarding the stem-like phenotype, its acquisition by cancer progenitor cells, and the molecular mechanisms involved. Understanding the dynamic equilibrium between CSCs and cancer progenitor cells is critical for the development of novel therapeutic strategies that focus on depleting tumors of their tumor-propagating cell population.

Quantitative analysis reveals how EGFR activation and downregulation are coupled in normal but not in cancer cells

PubMed Central

Capuani, Fabrizio; Conte, Alexia; Argenzio, Elisabetta; Marchetti, Luca; Priami, Corrado; Polo, Simona; Di Fiore, Pier Paolo; Sigismund, Sara; Ciliberto, Andrea

2015-01-01

Ubiquitination of the epidermal growth factor receptor (EGFR) that occurs when Cbl and Grb2 bind to three phosphotyrosine residues (pY1045, pY1068 and pY1086) on the receptor displays a sharp threshold effect as a function of EGF concentration. Here we use a simple modelling approach together with experiments to show that the establishment of the threshold requires both the multiplicity of binding sites and cooperative binding of Cbl and Grb2 to the EGFR. While the threshold is remarkably robust, a more sophisticated model predicted that it could be modulated as a function of EGFR levels on the cell surface. We confirmed experimentally that the system has evolved to perform optimally at physiological levels of EGFR. As a consequence, this system displays an intrinsic weakness that causes—at the supraphysiological levels of receptor and/or ligand associated with cancer—uncoupling of the mechanisms leading to signalling through phosphorylation and attenuation through ubiquitination. PMID:26264748

Is the Gut Microbiota a New Factor Contributing to Obesity and Its Metabolic Disorders?

PubMed Central

Harris, Kristina; Kassis, Amira; Major, Geneviève; Chou, Chieh J.

2012-01-01

The gut microbiota refers to the trillions of microorganisms residing in the intestine and is integral in multiple physiological processes of the host. Recent research has shown that gut bacteria play a role in metabolic disorders such as obesity, diabetes, and cardiovascular diseases. The mechanisms by which the gut microbiota affects metabolic diseases are by two major routes: (1) the innate immune response to the structural components of bacteria (e.g., lipopolysaccharide) resulting in inflammation and (2) bacterial metabolites of dietary compounds (e.g., SCFA from fiber), which have biological activities that regulate host functions. Gut microbiota has evolved with humans as a mutualistic partner, but dysbiosis in a form of altered gut metagenome and collected microbial activities, in combination with classic genetic and environmental factors, may promote the development of metabolic disorders. This paper reviews the available literature about the gut microbiota and aforementioned metabolic disorders and reveals the gaps in knowledge for future study. PMID:22315672

Pathways to extinction: beyond the error threshold.

PubMed

Manrubia, Susanna C; Domingo, Esteban; Lázaro, Ester

2010-06-27

Since the introduction of the quasispecies and the error catastrophe concepts for molecular evolution by Eigen and their subsequent application to viral populations, increased mutagenesis has become a common strategy to cause the extinction of viral infectivity. Nevertheless, the high complexity of virus populations has shown that viral extinction can occur through several other pathways apart from crossing an error threshold. Increases in the mutation rate enhance the appearance of defective forms and promote the selection of mechanisms that are able to counteract the accelerated appearance of mutations. Current models of viral evolution take into account more realistic scenarios that consider compensatory and lethal mutations, a highly redundant genotype-to-phenotype map, rough fitness landscapes relating phenotype and fitness, and where phenotype is described as a set of interdependent traits. Further, viral populations cannot be understood without specifying the characteristics of the environment where they evolve and adapt. Altogether, it turns out that the pathways through which viral quasispecies go extinct are multiple and diverse.

Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast.

PubMed

Zanders, Sarah E; Eickbush, Michael T; Yu, Jonathan S; Kang, Ji-Won; Fowler, Kyle R; Smith, Gerald R; Malik, Harmit Singh

2014-06-24

Hybrid sterility is one of the earliest postzygotic isolating mechanisms to evolve between two recently diverged species. Here we identify causes underlying hybrid infertility of two recently diverged fission yeast species Schizosaccharomyces pombe and S. kambucha, which mate to form viable hybrid diploids that efficiently complete meiosis, but generate few viable gametes. We find that chromosomal rearrangements and related recombination defects are major but not sole causes of hybrid infertility. At least three distinct meiotic drive alleles, one on each S. kambucha chromosome, independently contribute to hybrid infertility by causing nonrandom spore death. Two of these driving loci are linked by a chromosomal translocation and thus constitute a novel type of paired meiotic drive complex. Our study reveals how quickly multiple barriers to fertility can arise. In addition, it provides further support for models in which genetic conflicts, such as those caused by meiotic drive alleles, can drive speciation.DOI: http://dx.doi.org/10.7554/eLife.02630.001. Copyright © 2014, Zanders et al.

3D Bioprinting for Organ Regeneration.

PubMed

Cui, Haitao; Nowicki, Margaret; Fisher, John P; Zhang, Lijie Grace

2017-01-01

Regenerative medicine holds the promise of engineering functional tissues or organs to heal or replace abnormal and necrotic tissues/organs, offering hope for filling the gap between organ shortage and transplantation needs. Three-dimensional (3D) bioprinting is evolving into an unparalleled biomanufacturing technology due to its high-integration potential for patient-specific designs, precise and rapid manufacturing capabilities with high resolution, and unprecedented versatility. It enables precise control over multiple compositions, spatial distributions, and architectural accuracy/complexity, therefore achieving effective recapitulation of microstructure, architecture, mechanical properties, and biological functions of target tissues and organs. Here we provide an overview of recent advances in 3D bioprinting technology, as well as design concepts of bioinks suitable for the bioprinting process. We focus on the applications of this technology for engineering living organs, focusing more specifically on vasculature, neural networks, the heart and liver. We conclude with current challenges and the technical perspective for further development of 3D organ bioprinting. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The trans-kingdom identification of negative regulators of pathogen hypervirulence.

PubMed

Brown, Neil A; Urban, Martin; Hammond-Kosack, Kim E

2016-01-01

Modern society and global ecosystems are increasingly under threat from pathogens, which cause a plethora of human, animal, invertebrate and plant diseases. Of increasing concern is the trans-kingdom tendency for increased pathogen virulence that is beginning to emerge in natural, clinical and agricultural settings. The study of pathogenicity has revealed multiple examples of convergently evolved virulence mechanisms. Originally described as rare, but increasingly common, are interactions where a single gene deletion in a pathogenic species causes hypervirulence. This review utilised the pathogen-host interaction database (www.PHI-base.org) to identify 112 hypervirulent mutations from 37 pathogen species, and subsequently interrogates the trans-kingdom, conserved, molecular, biochemical and cellular themes that cause hypervirulence. This study investigates 22 animal and 15 plant pathogens including 17 bacterial and 17 fungal species. Finally, the evolutionary significance and trans-kingdom requirement for negative regulators of hypervirulence and the implication of pathogen hypervirulence and emerging infectious diseases on society are discussed. © FEMS 2015.

Effects of Animal Venoms and Toxins on Hallmarks of Cancer

PubMed Central

Chaisakul, Janeyuth; Hodgson, Wayne C.; Kuruppu, Sanjaya; Prasongsook, Naiyarat

2016-01-01

Animal venoms are a cocktail of proteins and peptides, targeting vital physiological processes. Venoms have evolved to assist in the capture and digestion of prey. Key venom components often include neurotoxins, myotoxins, cardiotoxins, hematoxins and catalytic enzymes. The pharmacological activities of venom components have been investigated as a source of potential therapeutic agents. Interestingly, a number of animal toxins display profound anticancer effects. These include toxins purified from snake, bee and scorpion venoms effecting cancer cell proliferation, migration, invasion, apoptotic activity and neovascularization. Indeed, the mechanism behind the anticancer effect of certain toxins is similar to that of agents currently used in chemotherapy. For example, Lebein is a snake venom disintegrin which generates anti-angiogenic effects by inhibiting vascular endothelial growth factors (VEGF). In this review article, we highlight the biological activities of animal toxins on the multiple steps of tumour formation or hallmarks of cancer. We also discuss recent progress in the discovery of lead compounds for anticancer drug development from venom components. PMID:27471574

Experimental studies of animal social learning in the wild: Trying to untangle the mystery of human culture.

PubMed

Hill, Kim

2010-08-01

Here I discuss how studies on animal social learning may help us understand human culture. It is an evolutionary truism that complex biological adaptations always evolve from less complex but related adaptations, but occasionally evolutionary transitions lead to major biological changes whose end products are difficult to anticipate. Language-based cumulative adaptive culture in humans may represent an evolutionary transition of this type. Most of the social learning observed in animals (and even plants) may be due to mechanisms that cannot produce cumulative cultural adaptations. Likewise, much of the critical content of socially transmitted human culture seems to show no parallel in nonhuman species. Thus, with regard to the uniquely human extent and quality of culture, we are forced to ask: Are other species only a few small steps away from this transition, or do they lack multiple critical features that make us the only truly cultural species? Only future research into animal social learning can answer these questions.

The gene cortex controls mimicry and crypsis in butterflies and moths.

PubMed

Nadeau, Nicola J; Pardo-Diaz, Carolina; Whibley, Annabel; Supple, Megan A; Saenko, Suzanne V; Wallbank, Richard W R; Wu, Grace C; Maroja, Luana; Ferguson, Laura; Hanly, Joseph J; Hines, Heather; Salazar, Camilo; Merrill, Richard M; Dowling, Andrea J; ffrench-Constant, Richard H; Llaurens, Violaine; Joron, Mathieu; McMillan, W Owen; Jiggins, Chris D

2016-06-02

The wing patterns of butterflies and moths (Lepidoptera) are diverse and striking examples of evolutionary diversification by natural selection. Lepidopteran wing colour patterns are a key innovation, consisting of arrays of coloured scales. We still lack a general understanding of how these patterns are controlled and whether this control shows any commonality across the 160,000 moth and 17,000 butterfly species. Here, we use fine-scale mapping with population genomics and gene expression analyses to identify a gene, cortex, that regulates pattern switches in multiple species across the mimetic radiation in Heliconius butterflies. cortex belongs to a fast-evolving subfamily of the otherwise highly conserved fizzy family of cell-cycle regulators, suggesting that it probably regulates pigmentation patterning by regulating scale cell development. In parallel with findings in the peppered moth (Biston betularia), our results suggest that this mechanism is common within Lepidoptera and that cortex has become a major target for natural selection acting on colour and pattern variation in this group of insects.

Earthquake hypocenters and focal mechanisms in central Oklahoma reveal a complex system of reactivated subsurface strike-slip faulting

USGS Publications Warehouse

McNamara, Daniel E.; Benz, Harley M.; Herrmann, Robert B.; Bergman, Eric A.; Earle, Paul S.; Holland, Austin F.; Baldwin, Randy W.; Gassner, A.

2015-01-01

The sharp increase in seismicity over a broad region of central Oklahoma has raised concern regarding the source of the activity and its potential hazard to local communities and energy industry infrastructure. Since early 2010, numerous organizations have deployed temporary portable seismic stations in central Oklahoma in order to record the evolving seismicity. In this study, we apply a multiple-event relocation method to produce a catalog of 3,639 central Oklahoma earthquakes from late 2009 through 2014. RMT source parameters were determined for 195 of the largest and best-recorded earthquakes. Combining RMT results with relocated seismicity enabled us to determine the length, depth and style-of-faulting occurring on reactivated subsurface fault systems. Results show that the majority of earthquakes occur on near vertical, optimally oriented (NE-SW and NW-SE), strike-slip faults in the shallow crystalline basement. These are necessary first order observations required to assess the potential hazards of individual faults in Oklahoma.

Recent Development of Prebiotic Research—Statement from an Expert Workshop

PubMed Central

La Fata, Giorgio; Rastall, Robert A.; Lacroix, Christophe; Harmsen, Hermie J. M.; Mohajeri, M. Hasan; Weber, Peter

2017-01-01

A dietary prebiotic is defined as ‘a substrate that is selectively utilized by host microorganisms conferring a health benefit’. Although this definition evolved concomitantly with the knowledge and technological developments that accrued in the last twenty years, what qualifies as prebiotic continues to be a matter of debate. In this statement, we report the outcome of a workshop where academic experts working in the field of prebiotic research met with scientists from industry. The workshop covered three main topics: (i) evolution of the prebiotic concept/definition; (ii) the gut modeling in vitro technology PolyFermS to study prebiotic effects; and (iii) the potential novel microbiome-modulating effects associated with vitamins. The future of prebiotic research is very promising. Indeed, the technological developments observed in recent years provide scientists with powerful tools to investigate the complex ecosystem of gut microbiota. Combining multiple in vitro approaches with in vivo studies is key to understanding the mechanisms of action of prebiotics consumption and their potential beneficial effects on the host. PMID:29261110

Properties of branching exponential flights in bounded domains

NASA Astrophysics Data System (ADS)

Zoia, A.; Dumonteil, E.; Mazzolo, A.

2012-11-01

In a series of recent works, important results have been reported concerning the statistical properties of exponential flights evolving in bounded domains, a widely adopted model for finite-speed transport phenomena (Blanco S. and Fournier R., Europhys. Lett., 61 (2003) 168; Mazzolo A., Europhys. Lett., 68 (2004) 350; Bénichou O. et al., Europhys. Lett., 70 (2005) 42). Motivated by physical and biological systems where random spatial displacements are coupled with Galton-Watson birth-death mechanisms, such as neutron multiplication, diffusion of reproducing bacteria or spread of epidemics, in this letter we extend those results in two directions, via a Feynman-Kac formalism. First, we characterize the occupation statistics of exponential flights in the presence of absorption and branching, and give explicit moment formulas for the total length travelled by the walker and the number of performed collisions in a given domain. Then, we show that the survival and escape probability can be derived as well by resorting to a similar approach.

DNA Damage Responses in Prokaryotes: Regulating Gene Expression, Modulating Growth Patterns, and Manipulating Replication Forks

PubMed Central

Kreuzer, Kenneth N.

2013-01-01

Recent advances in the area of bacterial DNA damage responses are reviewed here. The SOS pathway is still the major paradigm of bacterial DNA damage response, and recent studies have clarified the mechanisms of SOS induction and key physiological roles of SOS including a very major role in genetic exchange and variation. When considering diverse bacteria, it is clear that SOS is not a uniform pathway with one purpose, but rather a platform that has evolved for differing functions in different bacteria. Relating in part to the SOS response, the field has uncovered multiple apparent cell-cycle checkpoints that assist cell survival after DNA damage and remarkable pathways that induce programmed cell death in bacteria. Bacterial DNA damage responses are also much broader than SOS, and several important examples of LexA-independent regulation will be reviewed. Finally, some recent advances that relate to the replication and repair of damaged DNA will be summarized. PMID:24097899

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kersten, Roland D.; Diedrich, Jolene K.; Yates, III, John R.

Terpenes are ubiquitous natural chemicals with diverse biological functions spanning all three domains of life. In specialized metabolism, the active sites of terpene synthases (TPSs) evolve in shape and reactivity to direct the biosynthesis of a myriad of chemotypes for organismal fitness. As most terpene biosynthesis mechanistically involves highly reactive carbocationic intermediates, the protein surfaces catalyzing these cascade reactions possess reactive regions possibly prone to premature carbocation capture and potentially enzyme inactivation. Here, we show using proteomic and X-ray crystallographic analyses that cationic intermediates undergo capture by conserved active site residues leading to inhibitory self-alkylation. Furthermore, the level of cation-mediatedmore » inactivation increases with mutation of the active site, upon changes in the size and structure of isoprenoid diphosphate substrates, and alongside increases in reaction temperatures. TPSs that individually synthesize multiple products are less prone to self-alkylation then TPSs possessing relatively high product specificity. In total, the results presented suggest that mechanism-based alkylation represents an overlooked mechanistic pressure during the evolution of cation-derived terpene biosynthesis.« less

Mapping behavioural evolution onto brain evolution: the strategic roles of conserved organization in individuals and species.

PubMed

Finlay, Barbara L; Hinz, Flora; Darlington, Richard B

2011-07-27

The pattern of individual variation in brain component structure in pigs, minks and laboratory mice is very similar to variation across species in the same components, at a reduced scale. This conserved pattern of allometric scaling resembles robotic architectures designed to be robust to changes in computing power and task demands, and may reflect the mechanism by which both growing and evolving brains defend basic sensory, motor and homeostatic functions at multiple scales. Conserved scaling rules also have implications for species-specific sensory and social communication systems, motor competencies and cognitive abilities. The role of relative changes in neuron number in the central nervous system in producing species-specific behaviour is thus highly constrained, while changes in the sensory and motor periphery, and in motivational and attentional systems increase in probability as the principal loci producing important changes in functional neuroanatomy between species. By their nature, these loci require renewed attention to development and life history in the initial organization and production of species-specific behavioural abilities.

The trans-kingdom identification of negative regulators of pathogen hypervirulence

PubMed Central

Brown, Neil A.; Urban, Martin; Hammond-Kosack, Kim E.

2015-01-01

Modern society and global ecosystems are increasingly under threat from pathogens, which cause a plethora of human, animal, invertebrate and plant diseases. Of increasing concern is the trans-kingdom tendency for increased pathogen virulence that is beginning to emerge in natural, clinical and agricultural settings. The study of pathogenicity has revealed multiple examples of convergently evolved virulence mechanisms. Originally described as rare, but increasingly common, are interactions where a single gene deletion in a pathogenic species causes hypervirulence. This review utilised the pathogen–host interaction database (www.PHI-base.org) to identify 112 hypervirulent mutations from 37 pathogen species, and subsequently interrogates the trans-kingdom, conserved, molecular, biochemical and cellular themes that cause hypervirulence. This study investigates 22 animal and 15 plant pathogens including 17 bacterial and 17 fungal species. Finally, the evolutionary significance and trans-kingdom requirement for negative regulators of hypervirulence and the implication of pathogen hypervirulence and emerging infectious diseases on society are discussed. PMID:26468211

Finding the genes to build C4 rice.

PubMed

Wang, Peng; Vlad, Daniela; Langdale, Jane A

2016-06-01

Rice, a C3 crop, is a staple food for more than half of the world's population, with most consumers living in developing countries. Engineering C4 photosynthetic traits into rice is increasingly suggested as a way to meet the 50% yield increase that is predicted to be needed by 2050. Advances in genome-wide deep-sequencing, gene discovery and genome editing platforms have brought the possibility of engineering a C3 to C4 conversion closer than ever before. Because C4 plants have evolved independently multiple times from C3 origins, it is probably that key genes and gene regulatory networks that regulate C4 were recruited from C3 ancestors. In the past five years there have been over 20 comparative transcriptomic studies published that aimed to identify these recruited C4 genes and regulatory mechanisms. Here we present an overview of what we have learned so far and preview the efforts still needed to provide a practical blueprint for building C4 rice. Copyright © 2016 Elsevier Ltd. All rights reserved.