Selfish genetic elements favor the evolution of a distinction between soma and germline.

PubMed

Johnson, Louise J

2008-08-01

Many multicellular organisms have evolved a dedicated germline. This can benefit the whole organism, but its advantages to genetic parasites have not been explored. Here I model the evolutionary success of a selfish element, such as a transposable element or endosymbiont, which is capable of creating or strengthening a germline-soma distinction in a primitively multicellular host, and find that it will always benefit the element to do so. Genes causing germline sequestration can therefore spread in a population even if germline sequestration is maladaptive for the host organism. Costly selfish elements are expected to survive only in sexual populations, so sexual species may experience an additional push toward germline-soma distinction, and hence toward cell differentiation and multicellularity.

Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice.

PubMed

Song, Xianwei; Cao, Xiaofeng

2017-04-01

Transposable elements (TEs) have long been regarded as 'selfish DNA', and are generally silenced by epigenetic mechanisms. However, work in the past decade has identified positive roles for TEs in generating genomic novelty and diversity in plants. In particular, recent studies suggested that TE-induced epigenetic alterations and modification of gene expression contribute to phenotypic variation and adaptation to geography or stress. These findings have led many to regard TEs, not as junk DNA, but as sources of control elements and genomic diversity. As a staple food crop and model system for genomic research on monocot plants, rice (Oryza sativa) has a modest-sized genome that harbors massive numbers of DNA transposons (class II transposable elements) scattered across the genome, which may make TE regulation of genes more prevalent. In this review, we summarize recent progress in research on the functions of rice TEs in modulating gene expression and creating new genes. We also examine the contributions of TEs to phenotypic diversity and adaptation to environmental conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Red Queen in mitochondria: cyto-nuclear co-evolution, hybrid breakdown and human disease

PubMed Central

Chou, Jui-Yu; Leu, Jun-Yi

2015-01-01

Cyto-nuclear incompatibility, a specific form of Dobzhansky-Muller incompatibility caused by incompatible alleles between mitochondrial and nuclear genomes, has been suggested to play a critical role during speciation. Several features of the mitochondrial genome (mtDNA), including high mutation rate, dynamic genomic structure, and uniparental inheritance, make mtDNA more likely to accumulate mutations in the population. Once mtDNA has changed, the nuclear genome needs to play catch-up due to the intimate interactions between these two genomes. In two populations, if cyto-nuclear co-evolution is driven in different directions, it may eventually lead to hybrid incompatibility. Although cyto-nuclear incompatibility has been observed in a wide range of organisms, it remains unclear what type of mutations drives the co-evolution. Currently, evidence supporting adaptive mutations in mtDNA remains limited. On the other hand, it has been known that some mutations allow mtDNA to propagate more efficiently but compromise the host fitness (described as selfish mtDNA). Arms races between such selfish mtDNA and host nuclear genomes can accelerate cyto-nuclear co-evolution and lead to a phenomenon called the Red Queen Effect. Here, we discuss how the Red Queen Effect may contribute to the frequent observation of cyto-nuclear incompatibility and be the underlying driving force of some human mitochondrial diseases. PMID:26042149

Humans as Superorganisms: How Microbes, Viruses, Imprinted Genes, and Other Selfish Entities Shape Our Behavior.

PubMed

Kramer, Peter; Bressan, Paola

2015-07-01

Psychologists and psychiatrists tend to be little aware that (a) microbes in our brains and guts are capable of altering our behavior; (b) viral DNA that was incorporated into our DNA millions of years ago is implicated in mental disorders; (c) many of us carry the cells of another human in our brains; and (d) under the regulation of viruslike elements, the paternally inherited and maternally inherited copies of some genes compete for domination in the offspring, on whom they have opposite physical and behavioral effects. This article provides a broad overview, aimed at a wide readership, of the consequences of our coexistence with these selfish entities. The overarching message is that we are not unitary individuals but superorganisms, built out of both human and nonhuman elements; it is their interaction that determines who we are. © The Author(s) 2015.

Alpha3, a transposable element that promotes host sexual reproduction.

PubMed

Barsoum, Emad; Martinez, Paula; Aström, Stefan U

2010-01-01

Theoretical models predict that selfish DNA elements require host sex to persist in a population. Therefore, a transposon that induces sex would strongly favor its own spread. We demonstrate that a protein homologous to transposases, called alpha3, was essential for mating type switch in Kluyveromyces lactis. Mutational analysis showed that amino acids conserved among transposases were essential for its function. During switching, sequences in the 5' and 3' flanking regions of the alpha3 gene were joined, forming a DNA circle, showing that alpha3 mobilized from the genome. The sequences encompassing the alpha3 gene circle junctions in the mating type alpha (MATalpha) locus were essential for switching from MATalpha to MATa, suggesting that alpha3 mobilization was a coupled event. Switching also required a DNA-binding protein, Mating type switch 1 (Mts1), whose binding sites in MATalpha were important. Expression of Mts1 was repressed in MATa/MATalpha diploids and by nutrients, limiting switching to haploids in low-nutrient conditions. A hairpin-capped DNA double-strand break (DSB) was observed in the MATa locus in mre11 mutant strains, indicating that mating type switch was induced by MAT-specific DSBs. This study provides empirical evidence for selfish DNA promoting host sexual reproduction by mediating mating type switch.

Social insects and selfish genes.

PubMed

Bourke, A F

2001-10-01

Sometimes science advances because of a new idea. Sometimes, it's because of a new technique. When both occur together, exciting times result. In the study of social insects, DNA-based methods for measuring relatedness now allow increasingly detailed tests of Hamilton's theory of kin selection.

Haben repetitive DNA-Sequenzen biologische Funktionen?

NASA Astrophysics Data System (ADS)

John, Maliyakal E.; Knöchel, Walter

1983-05-01

By DNA reassociation kinetics it is known that the eucaryotic genome consists of non-repetitive DNA, middle-repetitive DNA and highly repetitive DNA. Whereas the majority of protein-coding genes is located on non-repetitive DNA, repetitive DNA forms a constitutive part of eucaryotic DNA and its amount in most cases equals or even substantially exceeds that of non-repetitive DNA. During the past years a large body of data on repetitive DNA has accumulated and these have prompted speculations ranging from specific roles in the regulation of gene expression to that of a selfish entity with inconsequential functions. The following article summarizes recent findings on structural, transcriptional and evolutionary aspects and, although by no means being proven, some possible biological functions are discussed.

Cell Biology of Cheating-Transmission of Centromeres and Other Selfish Elements Through Asymmetric Meiosis.

PubMed

Chmátal, Lukáš; Schultz, Richard M; Black, Ben E; Lampson, Michael A

2017-01-01

Mendel's First Law of Genetics states that a pair of alleles segregates randomly during meiosis so that one copy of each is represented equally in gametes. Whereas male meiosis produces four equal sperm, in female meiosis only one cell, the egg, survives, and the others degenerate. Meiotic drive is a process in which a selfish DNA element exploits female meiotic asymmetry and segregates preferentially to the egg in violation of Mendel's First Law, thereby increasing its transmission to the offspring and frequency in a population. In principle, the selfish element can consist either of a centromere that increases its transmission via an altered kinetochore connection to the meiotic spindle or a centromere-like element that somehow bypasses the kinetochore altogether in doing so. There are now examples from eukaryotic model systems for both types of meiotic drive. Although meiotic drive has profound evolutionary consequences across many species, relatively little is known about the underlying mechanisms. We discuss examples in various systems and open questions about the underlying cell biology, and propose a mechanism to explain biased segregation in mammalian female meiosis.

Differentiation as symbiosis.

PubMed

Chigira, M; Watanabe, H

1994-07-01

Preservation of the identity of DNA is the ultimate goal of multicellular organisms. An abnormal DNA sequence in cells within an individual means its parasitic nature in cell society as shown in tumors. Somatic gene arrangement and gene mutation in development may be considered as de novo formation of parasites. It is likely that the developmental process with genetic alterations means symbiosis between altered cells and germ line cells preserving genetic information without alterations, when somatic alteration of DNA sequence is a major mechanism of differentiation. According to the selfish gene theory of Dawkins, germ line cells permit symbiosis when somatic cell society derives clear profit for the replication of original DNA copies.

Origins and evolution of viruses of eukaryotes: The ultimate modularity

PubMed Central

Koonin, Eugene V.; Dolja, Valerian V.; Krupovic, Mart

2018-01-01

Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order “Megavirales” that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes. PMID:25771806

Genetic conflict and sex chromosome evolution

PubMed Central

Meiklejohn, Colin D; Tao, Yun

2009-01-01

Chromosomal sex determination systems create the opportunity for the evolution of selfish genetic elements that increase the transmission of one sex chromosome at the expense of its homolog. Because such selfish elements on sex chromosomes can reduce fertility and distort the sex ratio of progeny, unlinked suppressors are expected to evolve, bringing different regions of the genome into conflict over the meiotic transmission of the sex chromosomes. Here we argue that recurrent genetic conflict over sex chromosome transmission is an important evolutionary force that has shaped a wide range of seemingly disparate phenomena including the epigenetic regulation of genes expressed in the germline, the distribution of genes in the genome, and the evolution of hybrid sterility between species. PMID:19931208

Behavior of restriction–modification systems as selfish mobile elements and their impact on genome evolution

PubMed Central

Kobayashi, Ichizo

2001-01-01

Restriction–modification (RM) systems are composed of genes that encode a restriction enzyme and a modification methylase. RM systems sometimes behave as discrete units of life, like viruses and transposons. RM complexes attack invading DNA that has not been properly modified and thus may serve as a tool of defense for bacterial cells. However, any threat to their maintenance, such as a challenge by a competing genetic element (an incompatible plasmid or an allelic homologous stretch of DNA, for example) can lead to cell death through restriction breakage in the genome. This post-segregational or post-disturbance cell killing may provide the RM complexes (and any DNA linked with them) with a competitive advantage. There is evidence that they have undergone extensive horizontal transfer between genomes, as inferred from their sequence homology, codon usage bias and GC content difference. They are often linked with mobile genetic elements such as plasmids, viruses, transposons and integrons. The comparison of closely related bacterial genomes also suggests that, at times, RM genes themselves behave as mobile elements and cause genome rearrangements. Indeed some bacterial genomes that survived post-disturbance attack by an RM gene complex in the laboratory have experienced genome rearrangements. The avoidance of some restriction sites by bacterial genomes may result from selection by past restriction attacks. Both bacteriophages and bacteria also appear to use homologous recombination to cope with the selfish behavior of RM systems. RM systems compete with each other in several ways. One is competition for recognition sequences in post-segregational killing. Another is super-infection exclusion, that is, the killing of the cell carrying an RM system when it is infected with another RM system of the same regulatory specificity but of a different sequence specificity. The capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure and function of RM enzymes. PMID:11557807

Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.

PubMed

Kobayashi, I

2001-09-15

Restriction-modification (RM) systems are composed of genes that encode a restriction enzyme and a modification methylase. RM systems sometimes behave as discrete units of life, like viruses and transposons. RM complexes attack invading DNA that has not been properly modified and thus may serve as a tool of defense for bacterial cells. However, any threat to their maintenance, such as a challenge by a competing genetic element (an incompatible plasmid or an allelic homologous stretch of DNA, for example) can lead to cell death through restriction breakage in the genome. This post-segregational or post-disturbance cell killing may provide the RM complexes (and any DNA linked with them) with a competitive advantage. There is evidence that they have undergone extensive horizontal transfer between genomes, as inferred from their sequence homology, codon usage bias and GC content difference. They are often linked with mobile genetic elements such as plasmids, viruses, transposons and integrons. The comparison of closely related bacterial genomes also suggests that, at times, RM genes themselves behave as mobile elements and cause genome rearrangements. Indeed some bacterial genomes that survived post-disturbance attack by an RM gene complex in the laboratory have experienced genome rearrangements. The avoidance of some restriction sites by bacterial genomes may result from selection by past restriction attacks. Both bacteriophages and bacteria also appear to use homologous recombination to cope with the selfish behavior of RM systems. RM systems compete with each other in several ways. One is competition for recognition sequences in post-segregational killing. Another is super-infection exclusion, that is, the killing of the cell carrying an RM system when it is infected with another RM system of the same regulatory specificity but of a different sequence specificity. The capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure and function of RM enzymes.

Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution

PubMed Central

Krupovic, Mart; Koonin, Eugene V.

2018-01-01

Polintons (also known as Mavericks) are large DNA transposons that are widespread in the genomes of eukaryotes. We have recently shown that Polintons encode virus capsid proteins, which suggests that these transposons might form virions, at least under some conditions. In this Opinion article, we delineate the evolutionary relationships among bacterial tectiviruses, Polintons, adenoviruses, virophages, large and giant DNA viruses of eukaryotes of the proposed order ‘Megavirales’, and linear mitochondrial and cytoplasmic plasmids. We hypothesize that Polintons were the first group of eukaryotic double-stranded DNA viruses to evolve from bacteriophages and that they gave rise to most large DNA viruses of eukaryotes and various other selfish genetic elements. PMID:25534808

Nonequilibrium Phase Transitions Associated with DNA Replication

DTIC Science & Technology

2011-02-11

bioanalysis.org [1] R. Dawkins , The Selfish Gene (Oxford, New York, 1989). [2] F. Jülicher, A. Ajdari, and J. Prost, Rev. Mod. Phys. 69, 1269 (1997). [3...fidelity above a threshold. DOI: 10.1103/PhysRevLett.106.060601 PACS numbers: 05.70.Ln, 87.10.Mn, 87.14.gk The replication of genes by biological

Cellular evidence for selfish spermatogonial selection in aged human testes.

PubMed

Maher, G J; Goriely, A; Wilkie, A O M

2014-05-01

Owing to a recent trend for delayed paternity, the genomic integrity of spermatozoa of older men has become a focus of increased interest. Older fathers are at higher risk for their children to be born with several monogenic conditions collectively termed paternal age effect (PAE) disorders, which include achondroplasia, Apert syndrome and Costello syndrome. These disorders are caused by specific mutations originating almost exclusively from the male germline, in genes encoding components of the tyrosine kinase receptor/RAS/MAPK signalling pathway. These particular mutations, occurring randomly during mitotic divisions of spermatogonial stem cells (SSCs), are predicted to confer a selective/growth advantage on the mutant SSC. This selective advantage leads to a clonal expansion of the mutant cells over time, which generates mutant spermatozoa at levels significantly above the background mutation rate. This phenomenon, termed selfish spermatogonial selection, is likely to occur in all men. In rare cases, probably because of additional mutational events, selfish spermatogonial selection may lead to spermatocytic seminoma. The studies that initially predicted the clonal nature of selfish spermatogonial selection were based on DNA analysis, rather than the visualization of mutant clones in intact testes. In a recent study that aimed to identify these clones directly, we stained serial sections of fixed testes for expression of melanoma antigen family A4 (MAGEA4), a marker of spermatogonia. A subset of seminiferous tubules with an appearance and distribution compatible with the predicted mutant clones were identified. In these tubules, termed 'immunopositive tubules', there is an increased density of spermatogonia positive for markers related to selfish selection (FGFR3) and SSC self-renewal (phosphorylated AKT). Here we detail the properties of the immunopositive tubules and how they relate to the predicted mutant clones, as well as discussing the utility of identifying the potential cellular source of PAE mutations. © 2013 American Society of Andrology and European Academy of Andrology.

Selfishness as second-order altruism

PubMed Central

Eldakar, Omar Tonsi; Wilson, David Sloan

2008-01-01

Selfishness is seldom considered a group-beneficial strategy. In the typical evolutionary formulation, altruism benefits the group, selfishness undermines altruism, and the purpose of the model is to identify mechanisms, such as kinship or reciprocity, that enable altruism to evolve. Recent models have explored punishment as an important mechanism favoring the evolution of altruism, but punishment can be costly to the punisher, making it a form of second-order altruism. This model identifies a strategy called “selfish punisher” that involves behaving selfishly in first-order interactions and altruistically in second-order interactions by punishing other selfish individuals. Selfish punishers cause selfishness to be a self-limiting strategy, enabling altruists to coexist in a stable equilibrium. This polymorphism can be regarded as a division of labor, or mutualism, in which the benefits obtained by first-order selfishness help to “pay” for second-order altruism. PMID:18448681

Selfish Spermatogonial Selection: Evidence from an Immunohistochemical Screen in Testes of Elderly Men

PubMed Central

Turner, Gareth D. H.; Dudka-Ruszkowska, Wioleta; Taylor, Stephen; Meyts, Ewa Rajpert-De; Goriely, Anne; Wilkie, Andrew O. M.

2012-01-01

The dominant congenital disorders Apert syndrome, achondroplasia and multiple endocrine neoplasia–caused by specific missense mutations in the FGFR2, FGFR3 and RET proteins respectively–represent classical examples of paternal age-effect mutation, a class that arises at particularly high frequencies in the sperm of older men. Previous analyses of DNA from randomly selected cadaveric testes showed that the levels of the corresponding FGFR2, FGFR3 and RET mutations exhibit very uneven spatial distributions, with localised hotspots surrounded by large mutation-negative areas. These studies imply that normal testes are mosaic for clusters of mutant cells: these clusters are predicted to have altered growth and signalling properties leading to their clonal expansion (selfish spermatogonial selection), but DNA extraction eliminates the possibility to study such processes at a tissue level. Using a panel of antibodies optimised for the detection of spermatocytic seminoma, a rare tumour of spermatogonial origin, we demonstrate that putative clonal events are frequent within normal testes of elderly men (mean age: 73.3 yrs) and can be classed into two broad categories. We found numerous small (less than 200 cells) cellular aggregations with distinct immunohistochemical characteristics, localised to a portion of the seminiferous tubule, which are of uncertain significance. However more infrequently we identified additional regions where entire seminiferous tubules had a circumferentially altered immunohistochemical appearance that extended through multiple serial sections that were physically contiguous (up to 1 mm in length), and exhibited enhanced staining for antibodies both to FGFR3 and a marker of downstream signal activation, pAKT. These findings support the concept that populations of spermatogonia in individual seminiferous tubules in the testes of older men are clonal mosaics with regard to their signalling properties and activation, thus fulfilling one of the specific predictions of selfish spermatogonial selection. PMID:22879958

The selfish goal meets the selfish gene.

PubMed

Neuberg, Steven L; Schaller, Mark

2014-04-01

The connection between selfish genes and selfish goals is not merely metaphorical. Many goals that shape contemporary cognition and behavior are psychological products of evolutionarily fundamental motivational systems and thus are phenotypic manifestations of genes. An evolutionary perspective can add depth and nuance to our understanding of "selfish goals" and their implications for human cognition and behavior.

Site-specific selfish genes as tools for the control and genetic engineering of natural populations.

PubMed

Burt, Austin

2003-05-07

Site-specific selfish genes exploit host functions to copy themselves into a defined target DNA sequence, and include homing endonuclease genes, group II introns and some LINE-like transposable elements. If such genes can be engineered to target new host sequences, then they can be used to manipulate natural populations, even if the number of individuals released is a small fraction of the entire population. For example, a genetic load sufficient to eradicate a population can be imposed in fewer than 20 generations, if the target is an essential host gene, the knockout is recessive and the selfish gene has an appropriate promoter. There will be selection for resistance, but several strategies are available for reducing the likelihood of it evolving. These genes may also be used to genetically engineer natural populations, by means of population-wide gene knockouts, gene replacements and genetic transformations. By targeting sex-linked loci just prior to meiosis one may skew the population sex ratio, and by changing the promoter one may limit the spread of the gene to neighbouring populations. The proposed constructs are evolutionarily stable in the face of the mutations most likely to arise during their spread, and strategies are also available for reversing the manipulations.

Oxytocin modulates third-party sanctioning of selfish and generous behavior within and between groups.

PubMed

Daughters, Katie; Manstead, Antony S R; Ten Velden, Femke S; De Dreu, Carsten K W

2017-03-01

Human groups function because members trust each other and reciprocate cooperative contributions, and reward others' cooperation and punish their non-cooperation. Here we examined the possibility that such third-party punishment and reward of others' trust and reciprocation is modulated by oxytocin, a neuropeptide generally involved in social bonding and in-group (but not out-group) serving behavior. Healthy males and females (N=100) self-administered a placebo or 24 IU of oxytocin in a randomized, double-blind, between-subjects design. Participants were asked to indicate (incentivized, costly) their level of reward or punishment for in-group (outgroup) investors donating generously or fairly to in-group (outgroup) trustees, who back-transferred generously, fairly or selfishly. Punishment (reward) was higher for selfish (generous) investments and back-transfers when (i) investors were in-group rather than outgroup, and (ii) trustees were in-group rather than outgroup, especially when (iii) participants received oxytocin rather than placebo. It follows, first, that oxytocin leads individuals to ignore out-groups as long as out-group behavior is not relevant to the in-group and, second, that oxytocin contributes to creating and enforcing in-group norms of cooperation and trust. Copyright © 2016 Elsevier Ltd. All rights reserved.

A CRISPR Cas9-based gene drive platform for genetic interaction analysis in Candida albicans

PubMed Central

Shapiro, Rebecca S.; Chavez, Alejandro; Porter, Caroline B. M.; Hamblin, Meagan; Kaas, Christian S.; DiCarlo, James E.; Zeng, Guisheng; Xu, Xiaoli; Revtovich, Alexey V.; Kirienko, Natalia V.; Wang, Yue; Church, George M.; Collins, James J.

2018-01-01

Candida albicans is the leading cause of fungal infections; yet, complex genetic interaction analysis remains cumbersome in this diploid pathogen. Here, we developed a CRISPR-Cas9-based ‘gene drive array’ (GDA) platform to facilitate efficient genetic analysis in C. albicans. In our system, a modified DNA donor molecule acts as a selfish genetic element, replaces the targeted site, and propagates to replace additional wild-type loci. Using mating-competent C. albicans haploids, each carrying a different gene drive disabling a gene of interest, we are able to create diploid strains that are homozygous double-deletion mutants. We generate double-gene deletion libraries to demonstrate this technology, targeting antifungal efflux and biofilm adhesion factors. We screen these libraries to identify virulence regulators and determine how genetic networks shift under diverse conditions. This platform transforms our ability to perform genetic interaction analysis in C. albicans and is readily extended to other fungal pathogens. PMID:29062088

Why Not Charter School Boards?

ERIC Educational Resources Information Center

Schlechty, Phillip C.; Cole, Robert W.

1993-01-01

Claiming that individual school board members act in selfish ways, proposes electing entire school board as a slate. Board would collectively be held responsible for performance of the school system and all of its employees. State legislation would be required to specify how interested groups would select a slate and create a charter, which is the…

Workshop on Self-Determination in Developing and Evolving Systems

DTIC Science & Technology

1994-02-18

processes of duplication (e.g. gene duplication, cell duplication, structural enlargement), responses to selfish DNA (e.g. suppression of outlaw...direct their development, then the genes would need some form of environmental feedback. Are there any plausible mechanisms for such feedback? 3. What is...evolutionary innovation, what is the contribution of random mutations, directed mutation, gene conversion, symbiogenesis, fusion, jumping genes or other

A parasitic selfish gene that affects host promiscuity.

PubMed

Giraldo-Perez, Paulina; Goddard, Matthew R

2013-11-07

Selfish genes demonstrate transmission bias and invade sexual populations despite conferring no benefit to their hosts. While the molecular genetics and evolutionary dynamics of selfish genes are reasonably well characterized, their effects on hosts are not. Homing endonuclease genes (HEGs) are one well-studied family of selfish genes that are assumed to be benign. However, we show that carrying HEGs is costly for Saccharomyces cerevisiae, demonstrating that these genetic elements are not necessarily benign but maybe parasitic. We estimate a selective load of approximately 1-2% in 'natural' niches. The second aspect we examine is the ability of HEGs to affect hosts' sexual behaviour. As all selfish genes critically rely on sex for spread, then any selfish gene correlated with increased host sexuality will enjoy a transmission advantage. While classic parasites are known to manipulate host behaviour, we are not aware of any evidence showing a selfish gene is capable of affecting host promiscuity. The data presented here show a selfish element may increase the propensity of its eukaryote host to undergo sex and along with increased rates of non-Mendelian inheritance, this may counterbalance mitotic selective load and promote spread. Demonstration that selfish genes are correlated with increased promiscuity in eukaryotes connects with ideas suggesting that selfish genes promoted the evolution of sex initially.

A parasitic selfish gene that affects host promiscuity

PubMed Central

Giraldo-Perez, Paulina; Goddard, Matthew R.

2013-01-01

Selfish genes demonstrate transmission bias and invade sexual populations despite conferring no benefit to their hosts. While the molecular genetics and evolutionary dynamics of selfish genes are reasonably well characterized, their effects on hosts are not. Homing endonuclease genes (HEGs) are one well-studied family of selfish genes that are assumed to be benign. However, we show that carrying HEGs is costly for Saccharomyces cerevisiae, demonstrating that these genetic elements are not necessarily benign but maybe parasitic. We estimate a selective load of approximately 1–2% in ‘natural’ niches. The second aspect we examine is the ability of HEGs to affect hosts' sexual behaviour. As all selfish genes critically rely on sex for spread, then any selfish gene correlated with increased host sexuality will enjoy a transmission advantage. While classic parasites are known to manipulate host behaviour, we are not aware of any evidence showing a selfish gene is capable of affecting host promiscuity. The data presented here show a selfish element may increase the propensity of its eukaryote host to undergo sex and along with increased rates of non-Mendelian inheritance, this may counterbalance mitotic selective load and promote spread. Demonstration that selfish genes are correlated with increased promiscuity in eukaryotes connects with ideas suggesting that selfish genes promoted the evolution of sex initially. PMID:24048156

Vitamin D for Cancer Prevention: Global Perspective

DTIC Science & Technology

2009-07-01

selfish gene . New York: Oxford University Press; 2006. 106. Armitage P, Doll R. The two-stage theory of carcinogenesis in relation to the age...cadherin and beta-catenin in the action of vitamin D metabolites against colon cancer cells. in tissue culture and identified several relevant genes ...specific to a particular gene , but its hallmark is persistent alteration in the DNA molecule or in factors that influence the expression of various regions

Mechanism Design for Incentivizing Social Media Contributions

NASA Astrophysics Data System (ADS)

Singh, Vivek K.; Jain, Ramesh; Kankanhalli, Mohan

Despite recent advancements in user-driven social media platforms, tools for studying user behavior patterns and motivations remain primitive. We highlight the voluntary nature of user contributions and that users can choose when (and when not) to contribute to the common media pool. A Game theoretic framework is proposed to study the dynamics of social media networks where contribution costs are individual but gains are common. We model users as rational selfish agents, and consider domain attributes like voluntary participation, virtual reward structure, network effect, and public-sharing to model the dynamics of this interaction. The created model describes the most appropriate contribution strategy from each user's perspective and also highlights issues like 'free-rider' problem and individual rationality leading to irrational (i.e. sub-optimal) group behavior. We also consider the perspective of the system designer who is interested in finding the best incentive mechanisms to influence the selfish end-users so that the overall system utility is maximized. We propose and compare multiple mechanisms (based on optimal bonus payment, social incentive leveraging, and second price auction) to study how a system designer can exploit the selfishness of its users, to design incentive mechanisms which improve the overall task-completion probability and system performance, while possibly still benefiting the individual users.

Immersive Simulation of Complex Social Environments

DTIC Science & Technology

2008-12-01

Complexity, 7, 18–30. Dawkins , R., 1989: The Selfish Gene (2nd ed.). New York: Oxford University Press. Dennett, D. C., 1995: Darwin’s Dangerous...interpretation, bias, and misinformation, which create erroneous versions of what has transpired. Dawkins presents a model for describing knowledge...evolution within a social group through interpersonal exchange (memetics). ( Dawkins , 1987) Where genetic duplication tends to be precise (and mutation

Engineering the genomes of wild insect populations: challenges, and opportunities provided by synthetic Medea selfish genetic elements

PubMed Central

Chen, Chun-Hong; Ward, Catherine M.; Huang, Haixia; Su, Jessica T.; Guo, Ming

2013-01-01

Advances in insect transgenesis and our knowledge of insect physiology and genomics are making it possible to create transgenic populations of beneficial or pest insects that express novel traits. There are contexts in which we may want the transgenes responsible for these traits to spread so that all individuals within a wild population carry them, a process known as population replacement. Transgenes of interest are unlikely to confer an overall fitness benefit on those who carry them. Therefore, an essential component of any population replacement strategy is the presence of a drive mechanism that will ensure the spread of linked transgenes. We discuss contexts in which population replacement might be desirable and the requirements a drive system must satisfy to be both effective and safe. We then describe the creation of synthetic Medea elements, the first selfish genetic elements synthesized de novo, with the capability of driving population replacement, in this case in Drosophila. The strategy used to create Drosophila Medea is applicable to a number of other insect species and the Medea system satisfies key requirements for scientific and social acceptance. Finally, we highlight several challenges to implementing population replacement in the wild. PMID:20570677

Origins and evolution of viruses of eukaryotes: The ultimate modularity

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

Koonin, Eugene V., E-mail: koonin@ncbi.nlm.nih.gov; Dolja, Valerian V., E-mail: doljav@science.oregonstate.edu; Krupovic, Mart, E-mail: krupovic@pasteur.fr

2015-05-15

Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangiblemore » clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order “Megavirales” that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes. - Highlights: • Eukaryotic virome dramatically differs from the viromes of bacteria and archaea. • Eukaryotic virome is dominated by RNA viruses and retroelements. • All classes of eukaryotic viruses evolved by gene module exchange. • Prokaryotic ancestry is traceable for core gene modules of most eukaryotic viruses. • Evolutionary histories of viruses and transposable elements are tightly linked.« less

Endoribonuclease type II toxin-antitoxin systems: functional or selfish?

PubMed

Ramisetty, Bhaskar Chandra Mohan; Santhosh, Ramachandran Sarojini

2017-07-01

Most bacterial genomes have multiple type II toxin-antitoxin systems (TAs) that encode two proteins which are referred to as a toxin and an antitoxin. Toxins inhibit a cellular process, while the interaction of the antitoxin with the toxin attenuates the toxin's activity. Endoribonuclease-encoding TAs cleave RNA in a sequence-dependent fashion, resulting in translational inhibition. To account for their prevalence and retention by bacterial genomes, TAs are credited with clinically significant phenomena, such as bacterial programmed cell death, persistence, biofilms and anti-addiction to plasmids. However, the programmed cell death and persistence hypotheses have been challenged because of conceptual, methodological and/or strain issues. In an alternative view, chromosomal TAs seem to be retained by virtue of addiction at two levels: via a poison-antidote combination (TA proteins) and via transcriptional reprogramming of the downstream core gene (due to integration). Any perturbation in the chromosomal TA operons could cause fitness loss due to polar effects on the downstream genes and hence be detrimental under natural conditions. The endoribonucleases encoding chromosomal TAs are most likely selfish DNA as they are retained by bacterial genomes, even though TAs do not confer a direct advantage via the TA proteins. TAs are likely used by various replicons as 'genetic arms' that allow the maintenance of themselves and associated genetic elements. TAs seem to be the 'selfish arms' that make the best use of the 'arms race' between bacterial genomes and plasmids.

Centromeres Drive a Hard Bargain

PubMed Central

Rosin, Leah F.; Mellone, Barbara G.

2017-01-01

Centromeres are essential chromosomal structures that mediate the accurate distribution of genetic material during meiotic and mitotic cell divisions. In most organisms, centromeres are epigenetically specified and propagated by nucleosomes containing the centromere-specific H3 variant, CENP-A. Although centromeres perform a critical and conserved function, CENP-A and the underlying centromeric DNA are rapidly evolving. This paradox has been explained by the centromere drive hypothesis, which proposes that CENP-A is undergoing an evolutionary tug-of-war with selfish centromeric DNA. Here, we review our current understanding of CENP-A evolution in relation to centromere drive and discuss classical and recent advances, including new evidence implicating CENP-A chaperones in this conflict. PMID:28069312

China Report RED FLAG NO. 4, 16 FEBRUARY 1986.

DTIC Science & Technology

1986-04-14

put forward the idea of genetic determinism is to prove their theory of " selfish human nature." Dawkins in his book "The Selfish Gene " said: "An...while genes are everlasting. Genes are selfish and have a ten- dency to expand themselves without limit. Genes control the organism and genes ...control behavior, and all social behavior can be explained in terms of the theory of selfish genes . From this, they put forward the ideas of the

The dynamics of maternal-effect selfish genetic elements.

PubMed

Smith, N G

1998-03-21

Maternal-effect selfish genes such as Medea or Scat act to kill progeny that do not bear a copy of the selfish gene present in the mother. Previous models of this system allowed for two types of allele, the selfish (killer) type and the sensitive (susceptible) wild-type. These models predict that the invasion conditions of the selfish allele are quite broad and that if invasion is possible a high frequency equilibrium is to be expected. The selfish element is therefore predicted to persist. Here a hypothetical third allele that neither kills nor is killed (i.e. insensitive) is considered. Such an allele could enter a population by recombination, mutation or migration. The incorporation of this third allele profoundly affects the dynamics of the system and, under some parameter values, it is possible for the spread of the insensitive allele to lead, eventually, to the fixation of the wild-type allele (reversible evolution). This is most likely if the death of progeny provides no direct benefit to the surviving sibs (i.e. in the absence of fitness compensation), as in insects without gregarious broods. Under these circumstances the selfish element cannot spread when infinitely rare, only after having risen to some finite frequency. A fitness cost to bearing the killer allele then causes its loss. However, if fitness compensation is found (e.g. in placental mammals) the invasion of the selfish element from an infinitely low level is possible for a wide range of costs and both stable coexistences of all three alleles and limit cycles of all three are then found. It is therefore to be expected that in mammals selfish maternal-effect genes are more likely both to spread and to persist than in insects, due to their different levels of fitness compensation.

Selfishness, Greed, and Counseling.

ERIC Educational Resources Information Center

Farrugia, David

2002-01-01

Although the concepts of greed and selfishness have often been used in discussions about human nature, there seems to be little attention to these characteristics in the disciplines of psychology and counseling. Considers characteristics of greed and selfishness as encountered in counseling from a multidisciplinary perspective and identifies…

Moral actor, selfish agent.

PubMed

Frimer, Jeremy A; Schaefer, Nicola K; Oakes, Harrison

2014-05-01

People are motivated to behave selfishly while appearing moral. This tension gives rise to 2 divergently motivated selves. The actor-the watched self-tends to be moral; the agent-the self as executor-tends to be selfish. Three studies present direct evidence of the actor's and agent's distinct motives. To recruit the self-as-actor, we asked people to rate the importance of various goals. To recruit the self-as-agent, we asked people to describe their goals verbally. In Study 1, actors claimed their goals were equally about helping the self and others (viz., moral); agents claimed their goals were primarily about helping the self (viz., selfish). This disparity was evident in both individualist and collectivist cultures, attesting to the universality of the selfish agent. Study 2 compared actors' and agents' motives to those of people role-playing highly prosocial or selfish exemplars. In content (Study 2a) and in the impressions they made on an outside observer (Study 2b), actors' motives were similar to those of the prosocial role-players, whereas agents' motives were similar to those of the selfish role-players. Study 3 accounted for the difference between the actor and agent: Participants claimed that their agent's motives were the more realistic and that their actor's motives were the more idealistic. The selfish agent/moral actor duality may account for why implicit and explicit measures of the same construct diverge, and why feeling watched brings out the better angels of human nature.

Engineering the genomes of wild insect populations: challenges, and opportunities provided by synthetic Medea selfish genetic elements.

PubMed

Hay, Bruce A; Chen, Chun-Hong; Ward, Catherine M; Huang, Haixia; Su, Jessica T; Guo, Ming

2010-10-01

Advances in insect transgenesis and our knowledge of insect physiology and genomics are making it possible to create transgenic populations of beneficial or pest insects that express novel traits. There are contexts in which we may want the transgenes responsible for these traits to spread so that all individuals within a wild population carry them, a process known as population replacement. Transgenes of interest are unlikely to confer an overall fitness benefit on those who carry them. Therefore, an essential component of any population replacement strategy is the presence of a drive mechanism that will ensure the spread of linked transgenes. We discuss contexts in which population replacement might be desirable and the requirements a drive system must satisfy to be both effective and safe. We then describe the creation of synthetic Medea elements, the first selfish genetic elements synthesized de novo, with the capability of driving population replacement, in this case in Drosophila. The strategy used to create Drosophila Medea is applicable to a number of other insect species and the Medea system satisfies key requirements for scientific and social acceptance. Finally, we highlight several challenges to implementing population replacement in the wild. Copyright 2010 Elsevier Ltd. All rights reserved.

Selfish Gene Algorithm Vs Genetic Algorithm: A Review

NASA Astrophysics Data System (ADS)

Ariff, Norharyati Md; Khalid, Noor Elaiza Abdul; Hashim, Rathiah; Noor, Noorhayati Mohamed

2016-11-01

Evolutionary algorithm is one of the algorithms inspired by the nature. Within little more than a decade hundreds of papers have reported successful applications of EAs. In this paper, the Selfish Gene Algorithms (SFGA), as one of the latest evolutionary algorithms (EAs) inspired from the Selfish Gene Theory which is an interpretation of Darwinian Theory ideas from the biologist Richards Dawkins on 1989. In this paper, following a brief introduction to the Selfish Gene Algorithm (SFGA), the chronology of its evolution is presented. It is the purpose of this paper is to present an overview of the concepts of Selfish Gene Algorithm (SFGA) as well as its opportunities and challenges. Accordingly, the history, step involves in the algorithm are discussed and its different applications together with an analysis of these applications are evaluated.

Does a prosocial-selfish distinction help explain the biological affects? Comment on Buck (1999).

PubMed

Gray, Jeremy R

2002-10-01

R. Buck (1999) argued that a conceptual distinction between prosocial and selfish motivation is necessary to understand the biological affects (consciously experienced feelings and desires having an innate neurochemical basis). However, at a biological level of analysis, a prosocial-selfish distinction is doubtful empirically and conceptually. For this reason, Buck's proposed typology of biological affects is unclear. Moreover, a prosocial-selfish distinction is not necessary to explain hemispheric differences in brain activity associated with affect. In contrast, an approach-withdrawal distinction explains some data uniquely well, although numerous exceptions imply that simple models are inadequate. To extend hemispheric models of experienced emotion, a prosocial-selfish distinction is unlikely to be explanatory, whereas an alternative account based on a distinction between verbal and nonverbal working memory may be useful.

Selfish genetic elements and the gene’s-eye view of evolution

PubMed Central

2016-01-01

During the last few decades, we have seen an explosion in the influx of details about the biology of selfish genetic elements. Ever since the early days of the field, the gene’s-eye view of Richard Dawkins, George Williams, and others, has been instrumental to make sense of new empirical observations and to the generation of new hypotheses. However, the close association between selfish genetic elements and the gene’s-eye view has not been without critics and several other conceptual frameworks have been suggested. In particular, proponents of multilevel selection models have used selfish genetic elements to criticize the gene’s-eye view. In this paper, I first trace the intertwined histories of the study of selfish genetic elements and the gene’s-eye view and then discuss how their association holds up when compared with other proposed frameworks. Next, using examples from transposable elements and the major transitions, I argue that different models highlight separate aspects of the evolution of selfish genetic elements and that the productive way forward is to maintain a plurality of perspectives. Finally, I discuss how the empirical study of selfish genetic elements has implications for other conceptual issues associated with the gene’s-eye view, such as agential thinking, adaptationism, and the role of fitness maximizing models in evolution. PMID:29491953

Reproductive bribing and policing as evolutionary mechanisms for the suppression of within-group selfishness.

PubMed

Reeve, H K; Keller, L

1997-07-01

We show that a new, simple, and robust general mechanism for the social suppression of within-group selfishness follows from Hamilton's rule applied in a multilevel selection approach to asymmetrical, two-person groups: If it pays a group member to behave selfishly (i.e., increase its share of the group's reproduction, at the expense of group productivity), then its partner will virtually always be favored to provide a reproductive "bribe" sufficient to remove the incentive for the selfish behavior. The magnitude of the bribe will vary directly with the number of offspring (or other close kin) potentially gained by the selfish individual and inversely with both the relatedness r between the interactants and the loss in group productivity because of selfishness. This bribe principle greatly extends the scope for cooperation within groups. Reproductive bribing is more likely to be favored over social policing for dominants rather than subordinates and as intragroup relatedness increases. Finally, analysis of the difference between the group optimum for an individual's behavior and the individual's inclusive fitness optimum reveals a paradoxical feedback loop by which bribing and policing, while nullifying particular selfish acts, automatically widen the separation of individual and group optima for other behaviors (i.e., resolution of one conflict intensifies others).

Third-party punishment as a costly signal of high continuation probabilities in repeated games.

PubMed

Jordan, Jillian J; Rand, David G

2017-05-21

Why do individuals pay costs to punish selfish behavior, even as third-party observers? A large body of research suggests that reputation plays an important role in motivating such third-party punishment (TPP). Here we focus on a recently proposed reputation-based account (Jordan et al., 2016) that invokes costly signaling. This account proposed that "trustworthy type" individuals (who are incentivized to cooperate with others) typically experience lower costs of TPP, and thus that TPP can function as a costly signal of trustworthiness. Specifically, it was argued that some but not all individuals face incentives to cooperate, making them high-quality and trustworthy interaction partners; and, because the same mechanisms that incentivize cooperation also create benefits for using TPP to deter selfish behavior, these individuals are likely to experience reduced costs of punishing selfishness. Here, we extend this conceptual framework by providing a concrete, "from-the-ground-up" model demonstrating how this process could work in the context of repeated interactions incentivizing both cooperation and punishment. We show how individual differences in the probability of future interaction can create types that vary in whether they find cooperation payoff-maximizing (and thus make high-quality partners), as well as in their net costs of TPP - because a higher continuation probability increases the likelihood of receiving rewards from the victim of the punished transgression (thus offsetting the cost of punishing). We also provide a simple model of dispersal that demonstrates how types that vary in their continuation probabilities can stably coexist, because the payoff from remaining in one's local environment (i.e. not dispersing) decreases with the number of others who stay. Together, this model demonstrates, from the group up, how TPP can serve as a costly signal of trustworthiness arising from exposure to repeated interactions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Visualizing the origins of selfish de novo mutations in individual seminiferous tubules of human testes

PubMed Central

Maher, Geoffrey J.; McGowan, Simon J.; Giannoulatou, Eleni; Verrill, Clare; Goriely, Anne; Wilkie, Andrew O. M.

2016-01-01

De novo point mutations arise predominantly in the male germline and increase in frequency with age, but it has not previously been possible to locate specific, identifiable mutations directly within the seminiferous tubules of human testes. Using microdissection of tubules exhibiting altered expression of the spermatogonial markers MAGEA4, FGFR3, and phospho-AKT, whole genome amplification, and DNA sequencing, we establish an in situ strategy for discovery and analysis of pathogenic de novo mutations. In 14 testes from men aged 39–90 y, we identified 11 distinct gain-of-function mutations in five genes (fibroblast growth factor receptors FGFR2 and FGFR3, tyrosine phosphatase PTPN11, and RAS oncogene homologs HRAS and KRAS) from 16 of 22 tubules analyzed; all mutations have known associations with severe diseases, ranging from congenital or perinatal lethal disorders to somatically acquired cancers. These results support proposed selfish selection of spermatogonial mutations affecting growth factor receptor-RAS signaling, highlight its prevalence in older men, and enable direct visualization of the microscopic anatomy of elongated mutant clones. PMID:26858415

A selfish DNA element engages a meiosis-specific motor and telomeres for germ-line propagation.

PubMed

Sau, Soumitra; Conrad, Michael N; Lee, Chih-Ying; Kaback, David B; Dresser, Michael E; Jayaram, Makkuni

2014-06-09

The chromosome-like mitotic stability of the yeast 2 micron plasmid is conferred by the plasmid proteins Rep1-Rep2 and the cis-acting locus STB, likely by promoting plasmid-chromosome association and segregation by hitchhiking. Our analysis reveals that stable plasmid segregation during meiosis requires the bouquet proteins Ndj1 and Csm4. Plasmid relocalization from the nuclear interior in mitotic cells to the periphery at or proximal to telomeres rises from early meiosis to pachytene. Analogous to chromosomes, the plasmid undergoes Csm4- and Ndj1-dependent rapid prophase movements with speeds comparable to those of telomeres. Lack of Ndj1 partially disrupts plasmid-telomere association without affecting plasmid colocalization with the telomere-binding protein Rap1. The plasmid appears to engage a meiosis-specific motor that orchestrates telomere-led chromosome movements for its telomere-associated segregation during meiosis I. This hitherto uncharacterized mode of germ-line transmission by a selfish genetic element signifies a mechanistic variation within the shared theme of chromosome-coupled plasmid segregation during mitosis and meiosis. © 2014 Sau et al.

Visualizing the origins of selfish de novo mutations in individual seminiferous tubules of human testes.

PubMed

Maher, Geoffrey J; McGowan, Simon J; Giannoulatou, Eleni; Verrill, Clare; Goriely, Anne; Wilkie, Andrew O M

2016-03-01

De novo point mutations arise predominantly in the male germline and increase in frequency with age, but it has not previously been possible to locate specific, identifiable mutations directly within the seminiferous tubules of human testes. Using microdissection of tubules exhibiting altered expression of the spermatogonial markers MAGEA4, FGFR3, and phospho-AKT, whole genome amplification, and DNA sequencing, we establish an in situ strategy for discovery and analysis of pathogenic de novo mutations. In 14 testes from men aged 39-90 y, we identified 11 distinct gain-of-function mutations in five genes (fibroblast growth factor receptors FGFR2 and FGFR3, tyrosine phosphatase PTPN11, and RAS oncogene homologs HRAS and KRAS) from 16 of 22 tubules analyzed; all mutations have known associations with severe diseases, ranging from congenital or perinatal lethal disorders to somatically acquired cancers. These results support proposed selfish selection of spermatogonial mutations affecting growth factor receptor-RAS signaling, highlight its prevalence in older men, and enable direct visualization of the microscopic anatomy of elongated mutant clones.

A selfish DNA element engages a meiosis-specific motor and telomeres for germ-line propagation

PubMed Central

Sau, Soumitra; Conrad, Michael N.; Lee, Chih-Ying; Kaback, David B.; Dresser, Michael E.

2014-01-01

The chromosome-like mitotic stability of the yeast 2 micron plasmid is conferred by the plasmid proteins Rep1-Rep2 and the cis-acting locus STB, likely by promoting plasmid-chromosome association and segregation by hitchhiking. Our analysis reveals that stable plasmid segregation during meiosis requires the bouquet proteins Ndj1 and Csm4. Plasmid relocalization from the nuclear interior in mitotic cells to the periphery at or proximal to telomeres rises from early meiosis to pachytene. Analogous to chromosomes, the plasmid undergoes Csm4- and Ndj1-dependent rapid prophase movements with speeds comparable to those of telomeres. Lack of Ndj1 partially disrupts plasmid–telomere association without affecting plasmid colocalization with the telomere-binding protein Rap1. The plasmid appears to engage a meiosis-specific motor that orchestrates telomere-led chromosome movements for its telomere-associated segregation during meiosis I. This hitherto uncharacterized mode of germ-line transmission by a selfish genetic element signifies a mechanistic variation within the shared theme of chromosome-coupled plasmid segregation during mitosis and meiosis. PMID:24914236

Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes.

PubMed

Lawrence, J

1999-12-01

The Selfish Operon Model postulates that the organization of bacterial genes into operons is beneficial to the constituent genes in that proximity allows horizontal cotransfer of all genes required for a selectable phenotype; eukaryotic operons formed for very different reasons. Horizontal transfer of selfish operons most probably promotes bacterial diversification.

Selfish brain and selfish immune system interplay: A theoretical framework for metabolic comorbidities of mood disorders.

PubMed

Yamagata, Ana Sayuri; Mansur, Rodrigo Barbachan; Rizzo, Lucas Bortolotto; Rosenstock, Tatiana; McIntyre, Roger S; Brietzke, Elisa

2017-01-01

According to the "selfish brain" theory, the brain regulates its own energy supply influencing the peripheral metabolism and food intake according to its needs. The immune system has been likewise "selfish" due to independent energy consumption; and it may compete with the brain (another high energy-consumer) for glucose. In mood disorders, stress in mood episodes or physiological stress activate homeostasis mechanisms from the brain and the immune system to solve the imbalance. The interaction between the selfish brain and the selfish immune system may explain various conditions of medical impairment in mood disorders, such as Metabolic Syndrome (MetS), obesity, type 2 diabetes mellitus (T2DM) and immune dysregulation. The objective of this study is to comprehensively review the literature regarding the competition between the brain and the immune system for energy substrate. Targeting the energetic regulation of the brain and the immune system and their cross-talk open alternative treatments and a different approach in the study of general medical comorbidities in mood disorders, although more investigation is needed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genealogical evidence for epidemics of selfish genes.

PubMed

Ingvarsson, Par K; Taylor, Douglas R

2002-08-20

Some genetic elements spread infectiously in populations by increasing their rate of genetic transmission at the expense of other genes in the genome. These so-called selfish genetic elements comprise a substantial portion of eukaryotic genomes and have long been viewed as a potent evolutionary force. Despite this view, little is known about the evolutionary history of selfish genetic elements in natural populations, or their genetic effects on other portions of the genome. Here we use nuclear and chloroplast gene genealogies in two species of Silene to show the historical pattern of selection on a well known selfish genetic element, cytoplasmic male sterility. We provide evidence that evolution of cytoplasmic male sterility has been characterized by frequent turnovers of mutations in natural populations, thus supporting an epidemic model for the evolution of selfish genes, where new mutations repeatedly arise and rapidly sweep through populations.

Game Theory, Adaptation, and Genetic Programming: Some Perspectives on Operations Research for Counter-IED

DTIC Science & Technology

2011-06-01

Books. Dawkins , R. (1989), The Selfish Gene , 2 nd ed., Oxford University Press. Dekker, A.H. (2010), “Agent-Based Simulation for Counter-IED: A...memes” ( Dawkins , 1989; Gabora, 1995; Boal & Schultz, 2007). As Weeks & Galunic (2003) point out: “Memes are the replicators in cultural evolution...expression) create the macro-level patterns of culture. … Memes are the genes of culture.” Because genetic programs express beliefs, decision

Artificial-life researchers try to create social reality.

PubMed

Flam, F

1994-08-12

Some scientists, among them cosmologist Stephen Hawking, argue that computer viruses are alive. A better case might be made for many of the self-replicating silicon-based creatures featured at the fourth Conference on Artificial Life, held on 5 to 8 July in Boston. Researchers from computer science, biology, and other disciplines presented computer programs that, among other things, evolved cooperative strategies in a selfish world and recreated themselves in ever more complex forms.

Ayn Rand: To be Selfish or Not to be Selfish--That is the Question

ERIC Educational Resources Information Center

Doctor, Tyrus L.; Kritsonis, William Allan

2009-01-01

Ayn Rand's "The Virtue of Selfishness" (1961) is comprised of a philosophy that defies the entire premise of what our education system is and shall be built upon. The "Objectivist" perspective has depicted a clear distinction between the "Have's" and the "Have Not's" or the Bourgeoisie and Proletariat. The "Objectivist" perspective believes that…

Goals are not selfish.

PubMed

von Hippel, William; von Hippel, Frank A

2014-04-01

The metaphor of selfish goals is misguided. Organisms can be considered vessels that further the interests of their genes, but not vessels that further the interests of their goals. Although goals can act at cross-purposes to each other and to longevity, such trade-offs are predicted by evolutionary theory. The metaphor of selfish goals provides no purchase on this problem.

Contagion of Cooperation in Static and Fluid Social Networks.

PubMed

Jordan, Jillian J; Rand, David G; Arbesman, Samuel; Fowler, James H; Christakis, Nicholas A

2013-01-01

Cooperation is essential for successful human societies. Thus, understanding how cooperative and selfish behaviors spread from person to person is a topic of theoretical and practical importance. Previous laboratory experiments provide clear evidence of social contagion in the domain of cooperation, both in fixed networks and in randomly shuffled networks, but leave open the possibility of asymmetries in the spread of cooperative and selfish behaviors. Additionally, many real human interaction structures are dynamic: we often have control over whom we interact with. Dynamic networks may differ importantly in the goals and strategic considerations they promote, and thus the question of how cooperative and selfish behaviors spread in dynamic networks remains open. Here, we address these questions with data from a social dilemma laboratory experiment. We measure the contagion of both cooperative and selfish behavior over time across three different network structures that vary in the extent to which they afford individuals control over their network ties. We find that in relatively fixed networks, both cooperative and selfish behaviors are contagious. In contrast, in more dynamic networks, selfish behavior is contagious, but cooperative behavior is not: subjects are fairly likely to switch to cooperation regardless of the behavior of their neighbors. We hypothesize that this insensitivity to the behavior of neighbors in dynamic networks is the result of subjects' desire to attract new cooperative partners: even if many of one's current neighbors are defectors, it may still make sense to switch to cooperation. We further hypothesize that selfishness remains contagious in dynamic networks because of the well-documented willingness of cooperators to retaliate against selfishness, even when doing so is costly. These results shed light on the contagion of cooperative behavior in fixed and fluid networks, and have implications for influence-based interventions aiming at increasing cooperative behavior.

Sharks shape the geometry of a selfish seal herd: experimental evidence from seal decoys.

PubMed

De Vos, Alta; O'Riain, M Justin

2010-02-23

Many animals respond to predation risk by forming groups. Evolutionary explanations for group formation in previously ungrouped, but loosely associated prey have typically evoked the selfish herd hypothesis. However, despite over 600 studies across a diverse array of taxa, the critical assumptions of this hypothesis have remained collectively untested, owing to several confounding problems in real predator-prey systems. To solve this, we manipulated the domains of danger of Cape fur seal (Arctocephalus pusillus pusillus) decoys to provide evidence that a selfish reduction in a seals' domain of danger results in a proportional reduction in its predation risk from ambush shark attacks. This behaviour confers a survival advantage to individual seals within a group and explains the evolution of selfish herds in a prey species. These findings empirically elevate Hamilton's selfish herd hypothesis to more than a 'theoretical curiosity'.

Sharks shape the geometry of a selfish seal herd: experimental evidence from seal decoys

PubMed Central

De Vos, Alta; O'Riain, M. Justin

2010-01-01

Many animals respond to predation risk by forming groups. Evolutionary explanations for group formation in previously ungrouped, but loosely associated prey have typically evoked the selfish herd hypothesis. However, despite over 600 studies across a diverse array of taxa, the critical assumptions of this hypothesis have remained collectively untested, owing to several confounding problems in real predator–prey systems. To solve this, we manipulated the domains of danger of Cape fur seal (Arctocephalus pusillus pusillus) decoys to provide evidence that a selfish reduction in a seals' domain of danger results in a proportional reduction in its predation risk from ambush shark attacks. This behaviour confers a survival advantage to individual seals within a group and explains the evolution of selfish herds in a prey species. These findings empirically elevate Hamilton's selfish herd hypothesis to more than a ‘theoretical curiosity’. PMID:19793737

Selfish drive can trump function when animal mitochondrial genomes compete.

PubMed

Ma, Hansong; O'Farrell, Patrick H

2016-07-01

Mitochondrial genomes compete for transmission from mother to progeny. We explored this competition by introducing a second genome into Drosophila melanogaster to follow transmission. Competitions between closely related genomes favored those functional in electron transport, resulting in a host-beneficial purifying selection. In contrast, matchups between distantly related genomes often favored those with negligible, negative or lethal consequences, indicating selfish selection. Exhibiting powerful selfish selection, a genome carrying a detrimental mutation displaced a complementing genome, leading to population death after several generations. In a different pairing, opposing selfish and purifying selection counterbalanced to give stable transmission of two genomes. Sequencing of recombinant mitochondrial genomes showed that the noncoding region, containing origins of replication, governs selfish transmission. Uniparental inheritance prevents encounters between distantly related genomes. Nonetheless, in each maternal lineage, constant competition among sibling genomes selects for super-replicators. We suggest that this relentless competition drives positive selection, promoting change in the sequences influencing transmission.

Selfish drive can trump function when animal mitochondrial genomes compete

PubMed Central

Ma, Hansong; O’Farrell, Patrick H.

2016-01-01

Mitochondrial genomes compete for transmission from mother to progeny. We explored this competition by introducing a second genome into Drosophila melanogaster to follow transmission. Competitions between closely related genomes favored those functional in electron transport, resulting in a host-beneficial purifying selection1. Contrastingly, matchups between distant genomes often favored those with negligible, negative or lethal consequences, indicating selfish selection. Exhibiting powerful selfish selection, a genome carrying a detrimental mutation displaced a complementing genome leading to population death after several generations. In a different pairing, opposing selfish and purifying selection counterbalanced to give stable transmission of two genomes. Sequencing of recombinant mitochondrial genomes revealed that the non-coding region, containing origins of replication, governs selfish transmission. Uniparental inheritance prevents encounters between distantly related genomes. Nonetheless, within each maternal lineage, constant competition among sibling genomes selects for super-replicators. We suggest that this relentless competition drives positive selection promoting change in the sequences influencing transmission. PMID:27270106

Evolution of Swarming Behavior Is Shaped by How Predators Attack.

PubMed

Olson, Randal S; Knoester, David B; Adami, Christoph

2016-01-01

Animal grouping behaviors have been widely studied due to their implications for understanding social intelligence, collective cognition, and potential applications in engineering, artificial intelligence, and robotics. An important biological aspect of these studies is discerning which selection pressures favor the evolution of grouping behavior. In the past decade, researchers have begun using evolutionary computation to study the evolutionary effects of these selection pressures in predator-prey models. The selfish herd hypothesis states that concentrated groups arise because prey selfishly attempt to place their conspecifics between themselves and the predator, thus causing an endless cycle of movement toward the center of the group. Using an evolutionary model of a predator-prey system, we show that how predators attack is critical to the evolution of the selfish herd. Following this discovery, we show that density-dependent predation provides an abstraction of Hamilton's original formulation of domains of danger. Finally, we verify that density-dependent predation provides a sufficient selective advantage for prey to evolve the selfish herd in response to predation by coevolving predators. Thus, our work corroborates Hamilton's selfish herd hypothesis in a digital evolutionary model, refines the assumptions of the selfish herd hypothesis, and generalizes the domain of danger concept to density-dependent predation.

[Advances in molecular mechanisms of adaptive immunity mediated by type I-E CRISPR/Cas system--A review].

PubMed

Sun, Dongchang; Qiu, Juanping

2016-01-04

To better adapt to the environment, prokaryocyte can take up exogenous genes (from bacteriophages, plasmids or genomes of other species) through horizontal gene transfer. Accompanied by the acquisition of exogenous genes, prokaryocyte is challenged by the invasion of 'selfish genes'. Therefore, to protect against the risk of gene transfer, prokaryocyte needs to establish mechanisms for selectively taking up or degrading exogenous DNA. In recent years, researchers discovered an adaptive immunity, which is mediated by the small RNA guided DNA degradation, prevents the invasion of exogenous genes in prokaryocyte. During the immune process, partial DNA fragments are firstly integrated.to the clustered regularly interspaced short palindromic repeats (CRISPR) located within the genome DNA, and then the mature CRISPR RNA transcript and the CRISPR associated proteins (Cas) form a complex CRISPR/Cas for degrading exogenous DNA. In this review, we will first briefly describe the CRISPR/Cas systems and then mainly focus on the recent advances of the function mechanism and the regulation mechanism of the type I-E CRISPR/Cas system in Escherichia coli.

Different degree of paternal mtDNA leakage between male and female progeny in interspecific Drosophila crosses

PubMed Central

Dokianakis, Emmanouil; Ladoukakis, Emmanuel D

2014-01-01

Maternal transmission of mitochondrial DNA (mtDNA) in animals is thought to prevent the spread of selfish deleterious mtDNA mutations in the population. Various mechanisms have been evolved independently to prevent the entry of sperm mitochondria in the embryo. However, the increasing number of instances of paternal mtDNA leakage suggests that these mechanisms are not very effective. The destruction of sperm mitochondria in mammalian embryos is mediated by nuclear factors. Also, the destruction of paternal mitochondria in intraspecific crosses is more effective than in interspecific ones. These observations have led to the hypothesis that leakage of paternal mtDNA (and consequently mtDNA recombination owing to ensuing heteroplasmy) might be more common in inter- than in intraspecific crosses and that it should increase with phylogenetic distance of hybridizing species. We checked paternal leakage in inter- and intraspecific crosses in Drosophila and found little evidence for this hypothesis. In addition, we have observed a higher level of leakage among male than among female progeny from the same cross. This is the first report of sex-specific leakage of paternal mtDNA. It suggests that paternal mtDNA leakage might not be a stochastic result of an error-prone mechanism, but rather, it may be under complex genetic control. PMID:25077015

Different degree of paternal mtDNA leakage between male and female progeny in interspecific Drosophila crosses.

PubMed

Dokianakis, Emmanouil; Ladoukakis, Emmanuel D

2014-07-01

Maternal transmission of mitochondrial DNA (mtDNA) in animals is thought to prevent the spread of selfish deleterious mtDNA mutations in the population. Various mechanisms have been evolved independently to prevent the entry of sperm mitochondria in the embryo. However, the increasing number of instances of paternal mtDNA leakage suggests that these mechanisms are not very effective. The destruction of sperm mitochondria in mammalian embryos is mediated by nuclear factors. Also, the destruction of paternal mitochondria in intraspecific crosses is more effective than in interspecific ones. These observations have led to the hypothesis that leakage of paternal mtDNA (and consequently mtDNA recombination owing to ensuing heteroplasmy) might be more common in inter- than in intraspecific crosses and that it should increase with phylogenetic distance of hybridizing species. We checked paternal leakage in inter- and intraspecific crosses in Drosophila and found little evidence for this hypothesis. In addition, we have observed a higher level of leakage among male than among female progeny from the same cross. This is the first report of sex-specific leakage of paternal mtDNA. It suggests that paternal mtDNA leakage might not be a stochastic result of an error-prone mechanism, but rather, it may be under complex genetic control.

Evaluation of Possible Proximate Mechanisms Underlying the Kinship Theory of Intragenomic Conflict in Social Insects.

PubMed

Galbraith, David A; Yi, Soojin V; Grozinger, Christina M

2016-12-01

Kinship theory provides a universal framework in which to understand the evolution of altruism, but there are many molecular and genetic mechanisms that can generate altruistic behaviors. Interestingly, kinship theory specifically predicts intragenomic conflict between maternally-derived alleles (matrigenes) and paternally-derived alleles (patrigenes) over the generation of altruistic behavior in cases where the interests of the matrigenes and patrigenes are not aligned. Under these conditions, individual differences in selfish versus altruistic behavior are predicted to arise from differential expression of the matrigenes and patrigenes (parent-specific gene expression or PSGE) that regulate selfish versus altruistic behaviors. As one of the leading theories to describe PSGE and genomic imprinting, kinship theory has been used to generate predictions to describe the reproductive division of labor in social insect colonies, which represents an excellent model system to test the hypotheses of kinship theory and examine the underlying mechanisms driving it. Recent studies have confirmed the predicted differences in the influence of matrigenes and patrigenes on reproductive division of labor in social insects, and demonstrated that these differences are associated with differences in PSGE of key genes involved in regulating reproductive physiology, providing further support for kinship theory. However, the mechanisms mediating PSGE in social insects, and how PSGE leads to differences in selfish versus altruistic behavior, remain to be determined. Here, we review the available supporting evidence for three possible epigenetic mechanisms (DNA methylation, piRNAs, and histone modification) that may generate PSGE in social insects, and discuss how these may lead to variation in social behavior. © 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.

GTRF: a game theory approach for regulating node behavior in real-time wireless sensor networks.

PubMed

Lin, Chi; Wu, Guowei; Pirozmand, Poria

2015-06-04

The selfish behaviors of nodes (or selfish nodes) cause packet loss, network congestion or even void regions in real-time wireless sensor networks, which greatly decrease the network performance. Previous methods have focused on detecting selfish nodes or avoiding selfish behavior, but little attention has been paid to regulating selfish behavior. In this paper, a Game Theory-based Real-time & Fault-tolerant (GTRF) routing protocol is proposed. GTRF is composed of two stages. In the first stage, a game theory model named VA is developed to regulate nodes' behaviors and meanwhile balance energy cost. In the second stage, a jumping transmission method is adopted, which ensures that real-time packets can be successfully delivered to the sink before a specific deadline. We prove that GTRF theoretically meets real-time requirements with low energy cost. Finally, extensive simulations are conducted to demonstrate the performance of our scheme. Simulation results show that GTRF not only balances the energy cost of the network, but also prolongs network lifetime.

Effect of lie labelling on children's evaluation of selfish, polite, and altruistic lies.

PubMed

Cheung, Him; Chan, Yawen; Tsui, Wan Chi Gigi

2016-09-01

This study investigates how 5- and 6-year-olds' evaluations of selfish, polite, and altruistic lies change as a result of whether these false statements are explicitly labelled as lies. We are also interested in how interpretive theory of mind may correlate with such evaluations with and without a lie label. Our results showed that labelling lowered children's evaluations for the polite and altruistic lies, but not for the selfish lies. Interpretive theory of mind correlated positively with the evaluation difference between the polite and altruistic lies and that between the selfish and altruistic lies in the label, but not in the non-label condition. Correlation between the selfish and altruistic lies and that between the polite and altruistic lies were stronger with than without labelling, after controlling for age, and verbal and non-verbal intelligence. We conclude that lie labelling biases children towards more negative evaluations for non-selfish lies and makes them see lies of different motives as more similar. If a lie label is applied, whether lies of different motives are still evaluated differently depends on interpretive theory of mind, which reflects the child's ability to represent and allow different interpretations of an ambiguous reality. © 2016 The British Psychological Society.

Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences.

PubMed

Martis, Mihaela Maria; Klemme, Sonja; Banaei-Moghaddam, Ali Mohammad; Blattner, Frank R; Macas, Jiří; Schmutzer, Thomas; Scholz, Uwe; Gundlach, Heidrun; Wicker, Thomas; Šimková, Hana; Novák, Petr; Neumann, Pavel; Kubaláková, Marie; Bauer, Eva; Haseneyer, Grit; Fuchs, Jörg; Doležel, Jaroslav; Stein, Nils; Mayer, Klaus F X; Houben, Andreas

2012-08-14

Supernumerary B chromosomes are optional additions to the basic set of A chromosomes, and occur in all eukaryotic groups. They differ from the basic complement in morphology, pairing behavior, and inheritance and are not required for normal growth and development. The current view is that B chromosomes are parasitic elements comparable to selfish DNA, like transposons. In contrast to transposons, they are autonomously inherited independent of the host genome and have their own mechanisms of mitotic or meiotic drive. Although B chromosomes were first described a century ago, little is known about their origin and molecular makeup. The widely accepted view is that they are derived from fragments of A chromosomes and/or generated in response to interspecific hybridization. Through next-generation sequencing of sorted A and B chromosomes, we show that B chromosomes of rye are rich in gene-derived sequences, allowing us to trace their origin to fragments of A chromosomes, with the largest parts corresponding to rye chromosomes 3R and 7R. Compared with A chromosomes, B chromosomes were also found to accumulate large amounts of specific repeats and insertions of organellar DNA. The origin of rye B chromosomes occurred an estimated ∼1.1-1.3 Mya, overlapping in time with the onset of the genus Secale (1.7 Mya). We propose a comprehensive model of B chromosome evolution, including its origin by recombination of several A chromosomes followed by capturing of additional A-derived and organellar sequences and amplification of B-specific repeats.

Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer.

PubMed

Yahara, Koji; Fukuyo, Masaki; Sasaki, Akira; Kobayashi, Ichizo

2009-11-03

Homing endonuclease genes are "selfish" mobile genetic elements whose endonuclease promotes the spread of its own gene by creating a break at a specific target site and using the host machinery to repair the break by copying and inserting the gene at this site. Horizontal transfer across the boundary of a species or population within which mating takes place has been thought to be necessary for their evolutionary persistence. This is based on the assumption that they will become fixed in a host population, where opportunities of homing will disappear, and become susceptible to degeneration. To test this hypothesis, we modeled behavior of a homing endonuclease gene that moves during meiosis through double-strand break repair. We mathematically explored conditions for persistence of the homing endonuclease gene and elucidated their parameter dependence as phase diagrams. We found that, if the cost of the pseudogene is lower than that of the homing endonuclease gene, the 2 forms can persist in a population through autonomous periodic oscillation. If the cost of the pseudogene is higher, 2 types of dynamics appear that enable evolutionary persistence: bistability dependent on initial frequency or fixation irrespective of initial frequency. The prediction of long persistence in the absence of horizontal transfer was confirmed by stochastic simulations in finite populations. The average time to extinction of the endonuclease gene was found to be thousands of meiotic generations or more based on realistic parameter values. These results provide a solid theoretical basis for an understanding of these and other extremely selfish elements.

Selective sweeps of mitochondrial DNA can drive the evolution of uniparental inheritance.

PubMed

Christie, Joshua R; Beekman, Madeleine

2017-08-01

Although the uniparental (or maternal) inheritance of mitochondrial DNA (mtDNA) is widespread, the reasons for its evolution remain unclear. Two main hypotheses have been proposed: selection against individuals containing different mtDNAs (heteroplasmy) and selection against "selfish" mtDNA mutations. Recently, uniparental inheritance was shown to promote adaptive evolution in mtDNA, potentially providing a third hypothesis for its evolution. Here, we explore this hypothesis theoretically and ask if the accumulation of beneficial mutations provides a sufficient fitness advantage for uniparental inheritance to invade a population in which mtDNA is inherited biparentally. In a deterministic model, uniparental inheritance increases in frequency but cannot replace biparental inheritance if only a single beneficial mtDNA mutation sweeps through the population. When we allow successive selective sweeps of mtDNA, however, uniparental inheritance can replace biparental inheritance. Using a stochastic model, we show that a combination of selection and drift facilitates the fixation of uniparental inheritance (compared to a neutral trait) when there is only a single selective mtDNA sweep. When we consider multiple mtDNA sweeps in a stochastic model, uniparental inheritance becomes even more likely to replace biparental inheritance. Our findings thus suggest that selective sweeps of beneficial mtDNA haplotypes can drive the evolution of uniparental inheritance. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

R2d2 Drives Selfish Sweeps in the House Mouse.

PubMed

Didion, John P; Morgan, Andrew P; Yadgary, Liran; Bell, Timothy A; McMullan, Rachel C; Ortiz de Solorzano, Lydia; Britton-Davidian, Janice; Bult, Carol J; Campbell, Karl J; Castiglia, Riccardo; Ching, Yung-Hao; Chunco, Amanda J; Crowley, James J; Chesler, Elissa J; Förster, Daniel W; French, John E; Gabriel, Sofia I; Gatti, Daniel M; Garland, Theodore; Giagia-Athanasopoulou, Eva B; Giménez, Mabel D; Grize, Sofia A; Gündüz, İslam; Holmes, Andrew; Hauffe, Heidi C; Herman, Jeremy S; Holt, James M; Hua, Kunjie; Jolley, Wesley J; Lindholm, Anna K; López-Fuster, María J; Mitsainas, George; da Luz Mathias, Maria; McMillan, Leonard; Ramalhinho, Maria da Graça Morgado; Rehermann, Barbara; Rosshart, Stephan P; Searle, Jeremy B; Shiao, Meng-Shin; Solano, Emanuela; Svenson, Karen L; Thomas-Laemont, Patricia; Threadgill, David W; Ventura, Jacint; Weinstock, George M; Pomp, Daniel; Churchill, Gary A; Pardo-Manuel de Villena, Fernando

2016-06-01

A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether "selfish" genes are capable of fixation-thereby leaving signatures identical to classical selective sweeps-despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2(HC)) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2(HC) rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2(HC) is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A Model of Social Selection and Successful Altruism

DTIC Science & Technology

1989-10-07

D., The evolution of social behavior. Annual Reviews of Ecological Systems, 5:325-383 (1974). 2. Dawkins , R., The selfish gene . Oxford: Oxford...alive and well. it will be important to re- examine this striking historical experience,-not in terms o, oversimplified models of the " selfish gene ," but...Darwinian Analysis The acceptance by many modern geneticists of the axiom that the basic unit of selection Is the " selfish gene " quickly led to the

Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question

PubMed Central

Koonin, Eugene V.; Starokadomskyy, Petro

2016-01-01

The question whether or not “viruses are alive” has caused considerable debate over many years. Yet, the question is effectively without substance because the answer depends entirely on the definition of life or the state of “being alive” that is bound to be arbitrary. In contrast, the status of viruses among biological entities is readily defined within the replicator paradigm. All biological replicators form a continuum along the selfishness-cooperativity axis, from the completely selfish to fully cooperative forms. Within this range, typical, lytic viruses represent the selfish extreme whereas temperate viruses and various mobile elements occupy positions closer to the middle of the range. Selfish replicators not only belong to the biological realm but are intrinsic to any evolving system of replicators. No such system can evolve without the emergence of parasites, and moreover, parasites drive the evolution of biological complexity at multiple levels. The history of life is a story of parasite-host coevolution that includes both the incessant arms race and various forms of cooperation. All organisms are communities of interacting, coevolving replicators of different classes. A complete theory of replicator coevolution remains to be developed, but it appears likely that not only the differentiation between selfish and cooperative replicators but the emergence of the entire range of replication strategies, from selfish to cooperative, is intrinsic to biological evolution. PMID:26965225

Assisted suicide of a selfish gene.

PubMed

Thomson, M S; Beeman, R W

1999-01-01

Medea (M) factors and the hybrid incompatibility factor (H) are involved in two incompatibility systems in flour beetles that were previously thought to be independent. M factors are a novel class of selfish genes that act by maternal lethality to nonself. The H factor causes the death of hybrids with a paternally derived H gene and previously uncharacterized maternal cofactors. We now find that M factors exhibit their selfish behavior only in the absence of the H factor. Furthermore, we show that the previously uncharacterized maternal cofactors required for H-associated hybrid inviability are identical to M factors. We propose that incompatibility between H strains and M strains is due to suppression by the H factor of the self-rescuing activity of the lethal M genes. This interaction has the effect of converting M elements from selfish into self-destructive or "suicidal" genes. M factors are globally widespread, but are conspicuously absent from India, the only country where the H factor is known to occur. Such a mechanism could prevent the spread of selfish M elements by establishing an absolute barrier to hybridization in the boundary between M and non-M zones.

The evolutionary history of Saccharomyces species inferred from completed mitochondrial genomes and revision in the ‘yeast mitochondrial genetic code’

PubMed Central

Szabóová, Dana; Bielik, Peter; Poláková, Silvia; Šoltys, Katarína; Jatzová, Katarína; Szemes, Tomáš

2017-01-01

Abstract The yeast Saccharomyces are widely used to test ecological and evolutionary hypotheses. A large number of nuclear genomic DNA sequences are available, but mitochondrial genomic data are insufficient. We completed mitochondrial DNA (mtDNA) sequencing from Illumina MiSeq reads for all Saccharomyces species. All are circularly mapped molecules decreasing in size with phylogenetic distance from Saccharomyces cerevisiae but with similar gene content including regulatory and selfish elements like origins of replication, introns, free-standing open reading frames or GC clusters. Their most profound feature is species-specific alteration in gene order. The genetic code slightly differs from well-established yeast mitochondrial code as GUG is used rarely as the translation start and CGA and CGC code for arginine. The multilocus phylogeny, inferred from mtDNA, does not correlate with the trees derived from nuclear genes. mtDNA data demonstrate that Saccharomyces cariocanus should be assigned as a separate species and Saccharomyces bayanus CBS 380T should not be considered as a distinct species due to mtDNA nearly identical to Saccharomyces uvarum mtDNA. Apparently, comparison of mtDNAs should not be neglected in genomic studies as it is an important tool to understand the origin and evolutionary history of some yeast species. PMID:28992063

The effect of amount and tangibility of endowment and certainty of recipients on selfishness in a modified dictator game.

PubMed

Chang, Shao-Chuan; Lin, Li-Yun; Horng, Ruey-Yun; Wang, Yau-De

2014-06-01

Taiwanese college students (N = 101) participated in the study to examine the effects of the amount of an endowment, the tangibility of an endowment, and the certainty of the recipient on selfishness in a modified dictator game. Results showed that dictators were more selfish when allocating tangible (money) than less tangible (honor credits) endowments. Selfishness was higher when large amounts of money were involved. The certainty of the recipient was manipulated by whether the recipient was chosen and announced before or after the decision. Unexpectedly, participants were more self-interested in the certain-recipient condition than in the uncertain-recipient condition. In the honor condition, the amount of an endowment and the certainty of the recipient did not affect participants' allocations.

Is there an omission effect in prosocial behavior? A laboratory experiment on passive vs. active generosity

PubMed Central

Gärtner, Manja

2017-01-01

We investigate whether individuals are more prone to act selfishly if they can passively allow for an outcome to be implemented (omission) rather than having to make an active choice (commission). In most settings, active and passive choice alternatives differ in terms of factors such as the presence of a suggested option, costs of taking an action, and awareness. We isolate the omission effect from confounding factors in three experiments, and find no evidence that the distinction between active and passive choices has an independent effect on the propensity to implement selfish outcomes. This suggests that increased selfishness through omission, as observed in various economic choice situations, is driven by other factors than a preference for selfish omissions. PMID:28248979

A family of selfish minicircular chromosomes with jumbled chloroplast gene fragments from a dinoflagellate.

PubMed

Zhang, Z; Cavalier-Smith, T; Green, B R

2001-08-01

Chloroplast genes of several dinoflagellate species are located on unigenic DNA minicircular chromosomes. We have now completely sequenced five aberrant minicircular chromosomes from the dinoflagellate Heterocapsa triquetra. These probably nonfunctional DNA circles lack complete genes, with each being composed of several short fragments of two or three different chloroplast genes and a common conserved region with a tripartite 9G-9A-9G core like the putative replicon origin of functional single-gene circular chloroplast chromosomes. Their sequences imply that all five circles evolved by differential deletions and duplications from common ancestral circles bearing fragments of four genes: psbA, psbC, 16S rRNA, and 23S rRNA. It appears that recombination between separate unigenic chromosomes initially gave intermediate heterodimers, which were subsequently stabilized by deletions that included part or all of one putative replicon origin. We suggest that homologous recombination at the 9G-9A-9G core regions produced a psbA/psbC heterodimer which generated two distinct chimeric circles by differential deletions and duplications. A 23S/16S rRNA heterodimer more likely formed by illegitimate recombination between 16S and 23S rRNA genes. Homologous recombination between the 9G-9A-9G core regions of both heterodimers and additional differential deletions and duplications could then have yielded the other three circles. Near identity of the gene fragments and 9G-9A-9G cores, despite diverging adjacent regions, may be maintained by gene conversion. The conserved organization of the 9G-9A-9G cores alone favors the idea that they are replicon origins and suggests that they may enable the aberrant minicircles to parasitize the chloroplast's replication machinery as selfish circles.

Confirmation of Maslow's Hypothesis of Synergy: Developing an Acceptance of Selfishness at the Workplace Scale.

PubMed

Takaki, Jiro; Taniguchi, Toshiyo; Fujii, Yasuhito

2016-04-30

This study aimed to develop a new Acceptance of Selfishness at the Workplace Scale (ASWS) and to confirm Maslow's hypothesis of synergy: if both a sense of contribution and acceptance of selfishness at the workplace are high, workers are psychologically healthy. In a cross-sectional study with employees of three Japanese companies, 656 workers answered a self-administered questionnaire on paper completely (response rate = 66.8%). Each questionnaire was submitted to us in a sealed envelope and analyzed. The ASWS indicated high internal consistency (Cronbach's alpha = 0.86). Significant (p < 0.001) positive moderate correlations between ASWS scores and job control scores support the ASWS's convergent and discriminant validity. Significant (p < 0.001) associations of ASWS scores with psychological distress and work engagement supported the ASWS's criterion validity. In short, ASWS was a psychometrically satisfactory measure. Significant (p < 0.05) interactions between a sense of contribution and acceptance of selfishness at the workplace in linear regression models showed that when those two factors are low, psychological distress becomes high. However, when a sense of contribution and acceptance of selfishness are high, work engagement also becomes high. Thus, Maslow's hypothesis of synergy was confirmed.

Cooperation and selfishness both occur during molecular evolution.

PubMed

Penny, David

2014-11-26

Perhaps the 'selfish' aspect of evolution has been over-emphasised, and organisms considered as basically selfish. However, at the macromolecular level of genes and proteins the cooperative aspect of evolution is more obvious and balances this self-centred aspect. Thousands of proteins must function together in an integrated manner to use and to produce the many molecules necessary for a functioning cell. The macromolecules have no idea whether they are functioning cooperatively or competitively with other genes and gene products (such as proteins). The cell is a giant cooperative system of thousands of genes/proteins that function together, even if it has to simultaneously resist 'parasites'. There are extensive examples of cooperative behavior among genes and proteins in both functioning cells and in the origin of life, so this cooperative nature, along with selfishness, must be considered part of normal evolution. The principles also apply to very large numbers of examples of 'positive interactions' between organisms, including both eukaryotes and akaryotes (prokaryotes). This does not negate in any way the 'selfishness' of genes - but macromolecules have no idea when they are helping, or hindering, other groups of macromolecules. We need to assert more strongly that genes, and gene products, function together as a cooperative unit.

A synthetic maternal-effect selfish genetic element drives population replacement in Drosophila.

PubMed

Chen, Chun-Hong; Huang, Haixia; Ward, Catherine M; Su, Jessica T; Schaeffer, Lorian V; Guo, Ming; Hay, Bruce A

2007-04-27

One proposed strategy for controlling the transmission of insect-borne pathogens uses a drive mechanism to ensure the rapid spread of transgenes conferring disease refractoriness throughout wild populations. Here, we report the creation of maternal-effect selfish genetic elements in Drosophila that drive population replacement and are resistant to recombination-mediated dissociation of drive and disease refractoriness functions. These selfish elements use microRNA-mediated silencing of a maternally expressed gene essential for embryogenesis, which is coupled with early zygotic expression of a rescuing transgene.

Psychopathy to Altruism: Neurobiology of the Selfish-Selfless Spectrum.

PubMed

Sonne, James W H; Gash, Don M

2018-01-01

The age-old philosophical, biological, and social debate over the basic nature of humans as being "universally selfish" or "universally good" continues today highlighting sharply divergent views of natural social order. Here we analyze advances in biology, genetics and neuroscience increasing our understanding of the evolution, features and neurocircuitry of the human brain underlying behavior in the selfish-selfless spectrum. First, we examine evolutionary pressures for selection of altruistic traits in species with protracted periods of dependence on parents and communities for subsistence and acquisition of learned behaviors. Evidence supporting the concept that altruistic potential is a common feature in human populations is developed. To go into greater depth in assessing critical features of the social brain, the two extremes of selfish-selfless behavior, callous unemotional psychopaths and zealous altruists who take extreme measures to help others, are compared on behavioral traits, structural/functional neural features, and the relative contributions of genetic inheritance versus acquired cognitive learning to their mindsets. Evidence from population groups ranging from newborns, adopted children, incarcerated juveniles, twins and mindfulness meditators point to the important role of neuroplasticity and the dopaminergic reward systems in forming and reforming neural circuitry in response to personal experience and cultural influences in determining behavior in the selfish-selfless spectrum. The underlying neural circuitry differs between psychopaths and altruists with emotional processing being profoundly muted in psychopaths and significantly enhanced in altruists. But both groups are characterized by the reward system of the brain shaping behavior. Instead of rigid assignment of human nature as being "universally selfish" or "universally good," both characterizations are partial truths based on the segments of the selfish-selfless spectrum being examined. In addition, individuals and populations can shift in the behavioral spectrum in response to cognitive therapy and social and cultural experience, and approaches such as mindfulness training for introspection and reward-activating compassion are entering the mainstream of clinical care for managing pain, depression, and stress.

Social Motivation: Costs and Benefits of Selfishness and Otherishness.

PubMed

Crocker, Jennifer; Canevello, Amy; Brown, Ashley A

2017-01-03

We examine recent evidence on the consequences of selfishness and otherishness for psychological well-being, physical health, and relationships. In the first sections, we consider recent evidence regarding the costs and benefits of giving time, money, and support to others and the costs and benefits of taking or receiving those things from others. Then, because the behaviors of giving and taking can be motivated either by selfish or otherish concerns, we next consider the costs and benefits of the motivation underlying giving and taking. We also examine why and for whom selfishness and otherishness have consequences for psychological well-being, physical health, and relationships. We focus on mechanisms identified in research, including intrapsychic mechanisms such as positive and negative affect, self-esteem and self-efficacy, a sense of meaning and purpose in life, and a sense of connectedness to or isolation from others, as well as interpersonal processes such as reciprocation of support and responsiveness.

A maternal-effect selfish genetic element in Caenorhabditis elegans.

PubMed

Ben-David, Eyal; Burga, Alejandro; Kruglyak, Leonid

2017-06-09

Selfish genetic elements spread in natural populations and have an important role in genome evolution. We discovered a selfish element causing embryonic lethality in crosses between wild strains of the nematode Caenorhabditis elegans The element is made up of sup-35 , a maternal-effect toxin that kills developing embryos, and pha-1 , its zygotically expressed antidote. pha-1 has long been considered essential for pharynx development on the basis of its mutant phenotype, but this phenotype arises from a loss of suppression of sup-35 toxicity. Inactive copies of the sup-35/pha-1 element show high sequence divergence from active copies, and phylogenetic reconstruction suggests that they represent ancestral stages in the evolution of the element. Our results suggest that other essential genes identified by genetic screens may turn out to be components of selfish elements. Copyright © 2017, American Association for the Advancement of Science.

Interaction of natural survival instincts and internalized social norms exploring the Titanic and Lusitania disasters.

PubMed

Frey, Bruno S; Savage, David A; Torgler, Benno

2010-03-16

To understand human behavior, it is important to know under what conditions people deviate from selfish rationality. This study explores the interaction of natural survival instincts and internalized social norms using data on the sinking of the Titanic and the Lusitania. We show that time pressure appears to be crucial when explaining behavior under extreme conditions of life and death. Even though the two vessels and the composition of their passengers were quite similar, the behavior of the individuals on board was dramatically different. On the Lusitania, selfish behavior dominated (which corresponds to the classical homo economicus); on the Titanic, social norms and social status (class) dominated, which contradicts standard economics. This difference could be attributed to the fact that the Lusitania sank in 18 min, creating a situation in which the short-run flight impulse dominated behavior. On the slowly sinking Titanic (2 h, 40 min), there was time for socially determined behavioral patterns to reemerge. Maritime disasters are traditionally not analyzed in a comparative manner with advanced statistical (econometric) techniques using individual data of the passengers and crew. Knowing human behavior under extreme conditions provides insight into how widely human behavior can vary, depending on differing external conditions.

Regulation of Small Mitochondrial DNA Replicative Advantage by Ribonucleotide Reductase in Saccharomyces cerevisiae

PubMed Central

Bradshaw, Elliot; Yoshida, Minoru; Ling, Feng

2017-01-01

Small mitochondrial genomes can behave as selfish elements by displacing wild-type genomes regardless of their detriment to the host organism. In the budding yeast Saccharomyces cerevisiae, small hypersuppressive mtDNA transiently coexist with wild-type in a state of heteroplasmy, wherein the replicative advantage of the small mtDNA outcompetes wild-type and produces offspring without respiratory capacity in >95% of colonies. The cytosolic enzyme ribonucleotide reductase (RNR) catalyzes the rate-limiting step in dNTP synthesis and its inhibition has been correlated with increased petite colony formation, reflecting loss of respiratory function. Here, we used heteroplasmic diploids containing wild-type (rho+) and suppressive (rho−) or hypersuppressive (HS rho−) mitochondrial genomes to explore the effects of RNR activity on mtDNA heteroplasmy in offspring. We found that the proportion of rho+ offspring was significantly increased by RNR overexpression or deletion of its inhibitor, SML1, while reducing RNR activity via SML1 overexpression produced the opposite effects. In addition, using Ex Taq and KOD Dash polymerases, we observed a replicative advantage for small over large template DNA in vitro, but only at low dNTP concentrations. These results suggest that dNTP insufficiency contributes to the replicative advantage of small mtDNA over wild-type and cytosolic dNTP synthesis by RNR is an important regulator of heteroplasmy involving small mtDNA molecules in yeast. PMID:28717049

Friend versus foe: Neural correlates of prosocial decisions for liked and disliked peers.

PubMed

Schreuders, Elisabeth; Klapwijk, Eduard T; Will, Geert-Jan; Güroğlu, Berna

2018-02-01

Although the majority of our social interactions are with people we know, few studies have investigated the neural correlates of sharing valuable resources with familiar others. Using an ecologically valid research paradigm, this functional magnetic resonance imaging study examined the neural correlates of prosocial and selfish behavior in interactions with real-life friends and disliked peers in young adults. Participants (N = 27) distributed coins between themselves and another person, where they could make selfish choices that maximized their own gains or prosocial choices that maximized outcomes of the other. Participants were more prosocial toward friends and more selfish toward disliked peers. Individual prosociality levels toward friends were associated negatively with supplementary motor area and anterior insula activity. Further preliminary analyses showed that prosocial decisions involving friends were associated with heightened activity in the bilateral posterior temporoparietal junction, and selfish decisions involving disliked peers were associated with heightened superior temporal sulcus activity, which are brain regions consistently shown to be involved in mentalizing and perspective taking in prior studies. Further, activation of the putamen was observed during prosocial choices involving friends and selfish choices involving disliked peers. These findings provide insights into the modulation of neural processes that underlie prosocial behavior as a function of a positive or negative relationship with the interaction partner.

Arms race between selfishness and policing: two-trait quantitative genetic model for caste fate conflict in eusocial Hymenoptera.

PubMed

Dobata, Shigeto

2012-12-01

Policing against selfishness is now regarded as the main force maintaining cooperation, by reducing costly conflict in complex social systems. Although policing has been studied extensively in social insect colonies, its coevolution against selfishness has not been fully captured by previous theories. In this study, I developed a two-trait quantitative genetic model of the conflict between selfish immature females (usually larvae) and policing workers in eusocial Hymenoptera over the immatures' propensity to develop into new queens. This model allows for the analysis of coevolution between genomes expressed in immatures and workers that collectively determine the immatures' queen caste fate. The main prediction of the model is that a higher level of polyandry leads to a smaller fraction of queens produced among new females through caste fate policing. The other main prediction of the present model is that, as a result of arms race, caste fate policing by workers coevolves with exaggerated selfishness of the immatures achieving maximum potential to develop into queens. Moreover, the model can incorporate genetic correlation between traits, which has been largely unexplored in social evolution theory. This study highlights the importance of understanding social traits as influenced by the coevolution of conflicting genomes. © 2012 The Author. Evolution© 2012 The Society for the Study of Evolution.

Confirmation of Maslow’s Hypothesis of Synergy: Developing an Acceptance of Selfishness at the Workplace Scale

PubMed Central

Takaki, Jiro; Taniguchi, Toshiyo; Fujii, Yasuhito

2016-01-01

This study aimed to develop a new Acceptance of Selfishness at the Workplace Scale (ASWS) and to confirm Maslow’s hypothesis of synergy: if both a sense of contribution and acceptance of selfishness at the workplace are high, workers are psychologically healthy. In a cross-sectional study with employees of three Japanese companies, 656 workers answered a self-administered questionnaire on paper completely (response rate = 66.8%). Each questionnaire was submitted to us in a sealed envelope and analyzed. The ASWS indicated high internal consistency (Cronbach’s alpha = 0.86). Significant (p < 0.001) positive moderate correlations between ASWS scores and job control scores support the ASWS’s convergent and discriminant validity. Significant (p < 0.001) associations of ASWS scores with psychological distress and work engagement supported the ASWS’s criterion validity. In short, ASWS was a psychometrically satisfactory measure. Significant (p < 0.05) interactions between a sense of contribution and acceptance of selfishness at the workplace in linear regression models showed that when those two factors are low, psychological distress becomes high. However, when a sense of contribution and acceptance of selfishness are high, work engagement also becomes high. Thus, Maslow’s hypothesis of synergy was confirmed. PMID:27144575

R2d2 Drives Selfish Sweeps in the House Mouse

PubMed Central

Didion, John P.; Morgan, Andrew P.; Yadgary, Liran; Bell, Timothy A.; McMullan, Rachel C.; Ortiz de Solorzano, Lydia; Britton-Davidian, Janice; Bult, Carol J.; Campbell, Karl J.; Castiglia, Riccardo; Ching, Yung-Hao; Chunco, Amanda J.; Crowley, James J.; Chesler, Elissa J.; Förster, Daniel W.; French, John E.; Gabriel, Sofia I.; Gatti, Daniel M.; Garland, Theodore; Giagia-Athanasopoulou, Eva B.; Giménez, Mabel D.; Grize, Sofia A.; Gündüz, İslam; Holmes, Andrew; Hauffe, Heidi C.; Herman, Jeremy S.; Holt, James M.; Hua, Kunjie; Jolley, Wesley J.; Lindholm, Anna K.; López-Fuster, María J.; Mitsainas, George; da Luz Mathias, Maria; McMillan, Leonard; Ramalhinho, Maria da Graça Morgado; Rehermann, Barbara; Rosshart, Stephan P.; Searle, Jeremy B.; Shiao, Meng-Shin; Solano, Emanuela; Svenson, Karen L.; Thomas-Laemont, Patricia; Threadgill, David W.; Ventura, Jacint; Weinstock, George M.; Pomp, Daniel; Churchill, Gary A.; Pardo-Manuel de Villena, Fernando

2016-01-01

A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether “selfish” genes are capable of fixation—thereby leaving signatures identical to classical selective sweeps—despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2HC) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2HC rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2HC is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution. PMID:26882987

Selfishness and altruism can coexist when help is subject to diminishing returns.

PubMed

Sibly, R M; Curnow, R N

2011-08-01

Altruism and selfishness are 30-50% heritable in man in both Western and non-Western populations. This genetically based variation in altruism and selfishness requires explanation. In non-human animals, altruism is generally directed towards relatives, and satisfies the condition known as Hamilton's rule. This nepotistic altruism evolves under natural selection only if the ratio of the benefit of receiving help to the cost of giving it exceeds a value that depends on the relatedness of the individuals involved. Standard analyses assume that the benefit provided by each individual is the same but it is plausible in some cases that as more individuals contribute, help is subject to diminishing returns. We analyse this situation using a single-locus two-allele model of selection in a diploid population with the altruistic allele dominant to the selfish allele. The analysis requires calculation of the relationship between the fitnesses of the genotypes and the frequencies of the genes. The fitnesses vary not only with the genotype of the individual but also with the distribution of phenotypes amongst the sibs of the individual and this depends on the genotypes of his parents. These calculations are not possible by direct fitness or ESS methods but are possible using population genetics. Our analysis shows that diminishing returns change the operation of natural selection and the outcome can now be a stable equilibrium between altruistic and selfish alleles rather than the elimination of one allele or the other. We thus provide a plausible genetic model of kin selection that leads to the stable coexistence in the same population of both altruistic and selfish individuals. This may explain reported genetic variation in altruism in man.

A Selfish Constraint Satisfaction Genetic Algorithms for Planning a Long-Distance Transportation Network

NASA Astrophysics Data System (ADS)

Onoyama, Takashi; Maekawa, Takuya; Kubota, Sen; Tsuruta, Setuso; Komoda, Norihisa

To build a cooperative logistics network covering multiple enterprises, a planning method that can build a long-distance transportation network is required. Many strict constraints are imposed on this type of problem. To solve these strict-constraint problems, a selfish constraint satisfaction genetic algorithm (GA) is proposed. In this GA, each gene of an individual satisfies only its constraint selfishly, disregarding the constraints of other genes in the same individuals. Moreover, a constraint pre-checking method is also applied to improve the GA convergence speed. The experimental result shows the proposed method can obtain an accurate solution in a practical response time.

Evidence against the selfish operon theory.

PubMed

Pál, Csaba; Hurst, Laurence D

2004-06-01

According to the selfish operon hypothesis, the clustering of genes and their subsequent organization into operons is beneficial for the constituent genes because it enables the horizontal gene transfer of weakly selected, functionally coupled genes. The majority of these are expected to be non-essential genes. From our analysis of the Escherichia coli genome, we conclude that the selfish operon hypothesis is unlikely to provide a general explanation for clustering nor can it account for the gene composition of operons. Contrary to expectations, essential genes with related functions have an especially strong tendency to cluster, even if they are not in operons. Moreover, essential genes are particularly abundant in operons.

Cancer: a reproductive strategy of "ultra-selfish" genes?

PubMed

Schuiling, G A

2004-01-01

A hypothesis is presented in which the process of "malignant transformation" which ultimately results in the rapidly dividing tumor(s)(cells) causing "cancer", is regarded as an evolved reproductive strategy of "ultra-selfish" (proto-)(onco-) genes, already present in the genome, or introduced by a virus.

The new synthesis in moral psychology.

PubMed

Haidt, Jonathan

2007-05-18

People are selfish, yet morally motivated. Morality is universal, yet culturally variable. Such apparent contradictions are dissolving as research from many disciplines converges on a few shared principles, including the importance of moral intuitions, the socially functional (rather than truth-seeking) nature of moral thinking, and the coevolution of moral minds with cultural practices and institutions that create diverse moral communities. I propose a fourth principle to guide future research: Morality is about more than harm and fairness. More research is needed on the collective and religious parts of the moral domain, such as loyalty, authority, and spiritual purity.

Selfish Routing

DTIC Science & Technology

2002-05-01

traffic models , thereby identifying types of networks for which the cost of routing selfishly is mild. The inefficiency inherent in an uncoordinated outcome...17 1.6 Bibliographic Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 2 Preliminaries 18 2.1 The Model ...to Other Models 68 4.1 Flows at Approximate Nash Equilibrium . . . . . . . . . . . . . . . . 69 4.2 Finitely Many Users: Splittable Flow

Hop limited epidemic-like information spreading in mobile social networks with selfish nodes

NASA Astrophysics Data System (ADS)

Wu, Yahui; Deng, Su; Huang, Hongbin

2013-07-01

Similar to epidemics, information can be transmitted directly among users in mobile social networks. Different from epidemics, we can control the spreading process by adjusting the corresponding parameters (e.g., hop count) directly. This paper proposes a theoretical model to evaluate the performance of an epidemic-like spreading algorithm, in which the maximal hop count of the information is limited. In addition, our model can be used to evaluate the impact of users’ selfish behavior. Simulations show the accuracy of our theoretical model. Numerical results show that the information hop count can have an important impact. In addition, the impact of selfish behavior is related to the information hop count.

Are happier people less judgmental of other people's selfish behaviors? Experimental survey evidence from trust and gift exchange games.

PubMed

Drouvelis, Michalis; Powdthavee, Nattavudh

2015-10-01

What determines people's moral judgments of selfish behaviors? Here we study whether people's normative views in trust and gift exchange games, which underlie many situations of economic and social significance, are themselves functions of positive emotions. We use experimental survey methods to investigate the moral judgments of impartial observers empirically, and explore whether we could influence subsequent judgments by deliberately making some individuals happier. We find that moral judgments of selfish behaviors in the economic context depend strongly on the behavior of the interaction partner of the judged person, but their relationships are significantly moderated by an increase in happiness for the person making the judgment.

The battle of the sexes over seed size: support for both kinship genomic imprinting and interlocus contest evolution.

PubMed

Willi, Yvonne

2013-06-01

Outcrossing creates a venue for parental conflict. When one sex provides parental care to offspring fertilized by several partners, the nonproviding sex is under selection to maximally exploit the caring sex. The caring sex may counteradapt, and a coevolutionary arms race ensues. Genetic models of this conflict include the kinship theory of genomic imprinting (parent-of-origin-specific expression of maternal-care effectors) and interlocus conflict evolution (interaction between male selfish signals and female abatement). Predictions were tested by measuring the sizes of seeds produced by within-population crosses (diallel design) and between-population crosses in outcrossing and selfing populations of Arabidopsis lyrata. Within-population diallel crosses revealed substantial maternal variance in seed size in most populations. The comparison of between- and within-population crosses showed that seeds were larger when pollen came from another outcrossing population than when pollen came from a selfing or the same population, supporting interlocus contest evolution between male selfish genes and female recognition genes. Evidence for kinship genomic imprinting came from complementary trait means of seed size in reciprocal between-population crosses independent of whether populations were predominantly selfing or outcrossing. Hence, both kinship genomic imprinting and interlocus contest are supported in outcrossing Arabidopsis, whereas only kinship genomic imprinting is important in selfing populations.

Interaction of natural survival instincts and internalized social norms exploring the Titanic and Lusitania disasters

PubMed Central

Frey, Bruno S.; Savage, David A.; Torgler, Benno

2010-01-01

To understand human behavior, it is important to know under what conditions people deviate from selfish rationality. This study explores the interaction of natural survival instincts and internalized social norms using data on the sinking of the Titanic and the Lusitania. We show that time pressure appears to be crucial when explaining behavior under extreme conditions of life and death. Even though the two vessels and the composition of their passengers were quite similar, the behavior of the individuals on board was dramatically different. On the Lusitania, selfish behavior dominated (which corresponds to the classical homo economicus); on the Titanic, social norms and social status (class) dominated, which contradicts standard economics. This difference could be attributed to the fact that the Lusitania sank in 18 min, creating a situation in which the short-run flight impulse dominated behavior. On the slowly sinking Titanic (2 h, 40 min), there was time for socially determined behavioral patterns to reemerge. Maritime disasters are traditionally not analyzed in a comparative manner with advanced statistical (econometric) techniques using individual data of the passengers and crew. Knowing human behavior under extreme conditions provides insight into how widely human behavior can vary, depending on differing external conditions. PMID:20194743

A formal theory of the selfish gene.

PubMed

Gardner, A; Welch, J J

2011-08-01

Adaptation is conventionally regarded as occurring at the level of the individual organism. In contrast, the theory of the selfish gene proposes that it is more correct to view adaptation as occurring at the level of the gene. This view has received much popular attention, yet has enjoyed only limited uptake in the primary research literature. Indeed, the idea of ascribing goals and strategies to genes has been highly controversial. Here, we develop a formal theory of the selfish gene, using optimization theory to capture the analogy of 'gene as fitness-maximizing agent' in mathematical terms. We provide formal justification for this view of adaptation by deriving mathematical correspondences that translate the optimization formalism into dynamical population genetics. We show that in the context of social interactions between genes, it is the gene's inclusive fitness that provides the appropriate maximand. Hence, genic selection can drive the evolution of altruistic genes. Finally, we use the formalism to assess the various criticisms that have been levelled at the theory of the selfish gene, dispelling some and strengthening others. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Be nice if you have to--the neurobiological roots of strategic fairness.

PubMed

Strang, Sabrina; Gross, Jörg; Schuhmann, Teresa; Riedl, Arno; Weber, Bernd; Sack, Alexander T

2015-06-01

Social norms, such as treating others fairly regardless of kin relations, are essential for the functioning of human societies. Their existence may explain why humans, among all species, show unique patterns of prosocial behaviour. The maintenance of social norms often depends on external enforcement, as in the absence of credible sanctioning mechanisms prosocial behaviour deteriorates quickly. This sanction-dependent prosocial behaviour suggests that humans strategically adapt their behaviour and act selfishly if possible but control selfish impulses if necessary. Recent studies point at the role of the dorsolateral prefrontal cortex (DLPFC) in controlling selfish impulses. We test whether the DLPFC is indeed involved in the control of selfish impulses as well as the strategic acquisition of this control mechanism. Using repetitive transcranial magnetic stimulation, we provide evidence for the causal role of the right DLPFC in strategic fairness. Because the DLPFC is phylogenetically one of the latest developed neocortical regions, this could explain why complex norm systems exist in humans but not in other social animals. © The Author (2014). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

What Does It Take to Produce Interpretation? Informational, Peircean, and Code-Semiotic Views on Biosemiotics

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

Brier, Soren; Joslyn, Cliff A.

2013-04-01

This paper presents a critical analysis of code-semiotics, which we see as the latest attempt to create paradigmatic foundation for solving the question of the emergence of life and consciousness. We view code semiotics as a an attempt to revise the empirical scientific Darwinian paradigm, and to go beyond the complex systems, emergence, self-organization, and informational paradigms, and also the selfish gene theory of Dawkins and the Peircean pragmaticist semiotic theory built on the simultaneous types of evolution. As such it is a new and bold attempt to use semiotics to solve the problems created by the evolutionary paradigm’s commitmentmore » to produce a theory of how to connect the two sides of the Cartesian dualistic view of physical reality and consciousness in a consistent way.« less

Policing of reproduction by hidden threats in a cooperative mammal.

PubMed

Cant, Michael A; Nichols, Hazel J; Johnstone, Rufus A; Hodge, Sarah J

2014-01-07

The evolution of cooperation in animal and human societies is associated with mechanisms to suppress individual selfishness. In insect societies, queens and workers enforce cooperation by "policing" selfish reproduction by workers. Insect policing typically takes the form of damage limitation after individuals have carried out selfish acts (such as laying eggs). In contrast, human policing is based on the use of threats that deter individuals from acting selfishly in the first place, minimizing the need for damage limitation. Policing by threat could in principle be used to enforce reproductive suppression in animal societies, but testing this idea requires an experimental approach to simulate reproductive transgression and provoke out-of-equilibrium behavior. We carried out an experiment of this kind on a wild population of cooperatively breeding banded mongooses (Mungos mungo) in Uganda. In this species, each group contains multiple female breeders that give birth to a communal litter, usually on the same day. In a 7-y experiment we used contraceptive injections to manipulate the distribution of maternity within groups, triggering hidden threats of infanticide. Our data suggest that older, socially dominant females use the threat of infanticide to deter selfish reproduction by younger females, but that females can escape the threat of infanticide by synchronizing birth to the same day as older females. Our study shows that reproduction in animal societies can be profoundly influenced by threats that remain hidden until they are triggered experimentally. Coercion may thus extend well beyond the systems in which acts of infanticide are common.

Ayn Rand: Effective Educational Leadership Traits Compared to Selfishness

ERIC Educational Resources Information Center

Thompson, Barbara A.; Kritsonis, William Allan

2009-01-01

A man's self-interest cannot be determined by blind desires or random whims, feelings, urges, or wishes. His interest must be discovered and achieved by the guidance of rational principles that he chooses for himself. This selfishness is man's way to individual triumph over hardships. It is a virtue. Man must be guided by his own independent…

Does Asking Make a Difference? Effects of Initiator, Possible Gain, and Risk on Attributed Altruism.

ERIC Educational Resources Information Center

Quigley, Barbara; And Others

1989-01-01

Investigates three variables related to attributed altruism: (1) the effects of initiating prosocial behavior; (2) the potential gain or loss for the prosocial actor; and (3) the possible risk for the prosocial actor. Determines that any evidence of selfish motivation detracts from perceived altruism, and that no evidence of selfish motivation…

Genetic conflicts: the usual suspects and beyond

PubMed Central

McLaughlin, Richard N.

2017-01-01

ABSTRACT Selfishness is pervasive and manifests at all scales of biology, from societies, to individuals, to genetic elements within a genome. The relentless struggle to seek evolutionary advantages drives perpetual cycles of adaptation and counter-adaptation, commonly referred to as Red Queen interactions. In this review, we explore insights gleaned from molecular and genetic studies of such genetic conflicts, both extrinsic (between genomes) and intrinsic (within genomes or cells). We argue that many different characteristics of selfish genetic elements can be distilled into two types of advantages: an over-replication advantage (e.g. mobile genetic elements in genomes) and a transmission distortion advantage (e.g. meiotic drivers in populations). These two general categories may help classify disparate types of selfish genetic elements. PMID:28057823

Are happier people less judgmental of other people’s selfish behaviors? Experimental survey evidence from trust and gift exchange games

PubMed Central

Drouvelis, Michalis; Powdthavee, Nattavudh

2017-01-01

What determines people’s moral judgments of selfish behaviors? Here we study whether people’s normative views in trust and gift exchange games, which underlie many situations of economic and social significance, are themselves functions of positive emotions. We use experimental survey methods to investigate the moral judgments of impartial observers empirically, and explore whether we could influence subsequent judgments by deliberately making some individuals happier. We find that moral judgments of selfish behaviors in the economic context depend strongly on the behavior of the interaction partner of the judged person, but their relationships are significantly moderated by an increase in happiness for the person making the judgment. PMID:28729964

The cultural transmission of cooperative norms

PubMed Central

Zhou, Xinyue; Liu, Yan; Ho, Benjamin

2015-01-01

Cooperative behavior depends on cultural environment, so what happens when people move from to a new culture governed by a new norm? The dynamics of culture-induced cooperation has not been well understood. We expose lab participants to a sequence of different subject pools while playing a constrained Trust Game. We find prior exposure to different subject pools does in fact influence cooperative behavior; first impressions matter—the primacy effect plays a stronger role than the recency effect; and selfish first impressions matter more than cooperative first impressions—observing selfish behavior by others had a longer-lasting and greater influence on behaviors than observing cooperative behavior by others. Moreover, three consecutive exposures to cooperative environments were needed to neutralize one exposure to a selfish environment. PMID:26578993

Centromeres: long intergenic spaces with adaptive features.

PubMed

Kanizay, Lisa; Dawe, R Kelly

2009-08-01

Centromeres are composed of inner kinetochore proteins, which are largely conserved across species, and repetitive DNA, which shows comparatively little sequence conservation. Due to this fundamental paradox the formation and maintenance of centromeres remains largely a mystery. However, it has become increasingly clear that a long-standing balance between epigenetic and genetic control governs the interactions of centromeric DNA and inner kinetochore proteins. The comparison of classical neocentromeres in plants, which are entirely genetic in their mode of operation, and clinical neocentromeres, which are sequence-independent, illustrates the conflict between genetics and epigenetics in regions that control their own transmission to progeny. Tandem repeat arrays present in centromeres may have an origin in meiotic drive or other selfish patterns of evolution, as is the case for the CENP-B box and CENP-B protein in human. In grasses retrotransposons have invaded centromeres to the point of complete domination, consequently breaking genetic regulation at these centromeres. The accumulation of tandem repeats and transposons causes centromeres to expand in size, effectively pushing genes to the sides and opening the centromere to ever fewer constraints on the DNA sequence. On genetic maps centromeres appear as long intergenic spaces that evolve rapidly and apparently without regard to host fitness.

Social insects: from selfish genes to self organisation and beyond.

PubMed

Boomsma, Jacobus J; Franks, Nigel R

2006-06-01

Selfish gene and self-organisation approaches have revolutionised the study of social insects and have provided unparalleled insights into the highly sophisticated nature of insect social evolution. Here, we briefly review the core programs and interfaces with communication and recognition studies that characterise these fields today, and offer an interdisciplinary future perspective for the study of social insect evolutionary biology.

The games economists play: Why economics students behave more selfishly than other students

PubMed Central

Gerlach, Philipp

2017-01-01

Do economics students behave more selfishly than other students? Experiments involving monetary allocations suggest so. This article investigates the underlying motives for the economic students’ more selfish behavior by separating three potential explanatory mechanisms: economics students are less concerned with fairness when making allocation decisions; have a different notion of what is fair in allocations; or are more skeptical about other people’s allocations, which in turn makes them less willing to comply with a shared fairness norm. The three mechanisms were tested by inviting students from various disciplines to participate in a relatively novel experimental game and asking all participants to give reasons for their choices. Compared with students of other disciplines, economics students were about equally likely to mention fairness in their comments; had a similar notion of what was fair in the situation; however, they expected lower offers, made lower offers, and were less willing to enforce compliance with a fair allocation at a cost to themselves. The economics students’ lower expectations mediated their allocation decisions, suggesting that economics students behaved more selfishly because they expected others not to comply with the shared fairness norm. PMID:28873465

The games economists play: Why economics students behave more selfishly than other students.

PubMed

Gerlach, Philipp

2017-01-01

Do economics students behave more selfishly than other students? Experiments involving monetary allocations suggest so. This article investigates the underlying motives for the economic students' more selfish behavior by separating three potential explanatory mechanisms: economics students are less concerned with fairness when making allocation decisions; have a different notion of what is fair in allocations; or are more skeptical about other people's allocations, which in turn makes them less willing to comply with a shared fairness norm. The three mechanisms were tested by inviting students from various disciplines to participate in a relatively novel experimental game and asking all participants to give reasons for their choices. Compared with students of other disciplines, economics students were about equally likely to mention fairness in their comments; had a similar notion of what was fair in the situation; however, they expected lower offers, made lower offers, and were less willing to enforce compliance with a fair allocation at a cost to themselves. The economics students' lower expectations mediated their allocation decisions, suggesting that economics students behaved more selfishly because they expected others not to comply with the shared fairness norm.

Selfish punishment with avoiding mechanism can alleviate both first-order and second-order social dilemma.

PubMed

Cui, Pengbi; Wu, Zhi-Xi

2014-11-21

Punishment, especially selfish punishment, has recently been identified as a potent promoter in sustaining or even enhancing the cooperation among unrelated individuals. However, without other key mechanisms, the first-order social dilemma and second-order social dilemma are still two enduring conundrums in biology and the social sciences even with the presence of punishment. In the present study, we investigate a spatial evolutionary four-strategy prisoner׳s dilemma game model with avoiding mechanism, where the four strategies are cooperation, defection, altruistic and selfish punishment. By introducing the low level of random mutation of strategies, we demonstrate that the presence of selfish punishment with avoiding mechanism can alleviate the two kinds of social dilemmas for various parametrizations. In addition, we propose an extended pair approximation method, whose solutions can essentially estimate the dynamical behaviors and final evolutionary frequencies of the four strategies. At last, considering the analogy between our model and the classical Lotka-Volterra system, we introduce interaction webs based on the spatial replicator dynamics and the transformed payoff matrix to qualitatively characterize the emergent co-exist strategy phases, and its validity are supported by extensive simulations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evolution of double-stranded DNA viruses of eukaryotes: from bacteriophages to transposons to giant viruses

PubMed Central

Koonin, Eugene V; Krupovic, Mart; Yutin, Natalya

2015-01-01

Diverse eukaryotes including animals and protists are hosts to a broad variety of viruses with double-stranded (ds) DNA genomes, from the largest known viruses, such as pandoraviruses and mimiviruses, to tiny polyomaviruses. Recent comparative genomic analyses have revealed many evolutionary connections between dsDNA viruses of eukaryotes, bacteriophages, transposable elements, and linear DNA plasmids. These findings provide an evolutionary scenario that derives several major groups of eukaryotic dsDNA viruses, including the proposed order “Megavirales,” adenoviruses, and virophages from a group of large virus-like transposons known as Polintons (Mavericks). The Polintons have been recently shown to encode two capsid proteins, suggesting that these elements lead a dual lifestyle with both a transposon and a viral phase and should perhaps more appropriately be named polintoviruses. Here, we describe the recently identified evolutionary relationships between bacteriophages of the family Tectiviridae, polintoviruses, adenoviruses, virophages, large and giant DNA viruses of eukaryotes of the proposed order “Megavirales,” and linear mitochondrial and cytoplasmic plasmids. We outline an evolutionary scenario under which the polintoviruses were the first group of eukaryotic dsDNA viruses that evolved from bacteriophages and became the ancestors of most large DNA viruses of eukaryotes and a variety of other selfish elements. Distinct lines of origin are detectable only for herpesviruses (from a different bacteriophage root) and polyoma/papillomaviruses (from single-stranded DNA viruses and ultimately from plasmids). Phylogenomic analysis of giant viruses provides compelling evidence of their independent origins from smaller members of the putative order “Megavirales,” refuting the speculations on the evolution of these viruses from an extinct fourth domain of cellular life. PMID:25727355

Recognizing the enemy within: licensing RNA-guided genome defense

PubMed Central

Dumesic, Phillip A.; Madhani, Hiten D.

2014-01-01

How do cells distinguish normal genes from transposons? Although much has been learned about RNAi-related RNA silencing pathways responsible for genome defense, this fundamental question remains. The literature points to several classes of mechanisms. In some cases, double-stranded RNA structures produced by transposon inverted repeats or antisense integration trigger endo-siRNA biogenesis. In other instances, DNA features associated with transposons—such as their unusual copy number, chromosomal arrangement, and/or chromatin environment—license RNA silencing. Finally, recent studies have identified improper transcript processing events, such as stalled pre-mRNA splicing, as signals for siRNA production. Thus, the suboptimal gene expression properties of selfish elements can enable their identification by RNA silencing pathways. PMID:24280023

Genetic conflicts: the usual suspects and beyond.

PubMed

McLaughlin, Richard N; Malik, Harmit S

2017-01-01

Selfishness is pervasive and manifests at all scales of biology, from societies, to individuals, to genetic elements within a genome. The relentless struggle to seek evolutionary advantages drives perpetual cycles of adaptation and counter-adaptation, commonly referred to as Red Queen interactions. In this review, we explore insights gleaned from molecular and genetic studies of such genetic conflicts, both extrinsic (between genomes) and intrinsic (within genomes or cells). We argue that many different characteristics of selfish genetic elements can be distilled into two types of advantages: an over-replication advantage (e.g. mobile genetic elements in genomes) and a transmission distortion advantage (e.g. meiotic drivers in populations). These two general categories may help classify disparate types of selfish genetic elements. © 2017. Published by The Company of Biologists Ltd.

Fitness effects of a selfish gene (the Mus t complex) are revealed in an ecological context.

PubMed

Carroll, Lara S; Meagher, Shawn; Morrison, Linda; Penn, Dustin J; Potts, Wayne K

2004-06-01

In wild house mice, genes linked to the t transmission distortion complex cause meiotic drive by sabotaging wild-type gametes. The t complex is consequently inherited at frequencies higher than 90%. Yet, for unclear reasons, in wild mouse populations this selfish DNA is found at frequencies much lower than expected. Here, we examine selection on the t complex in 10 seminatural populations of wild mice based on data from 234 founders and nearly 2000 progeny. Eight of the 10 populations decreased in t frequency over one generation, and the overall frequency of t haplotypes across all 10 populations was 48.5% below expectations based on transmission distortion and 34.3% below Mendelian (or Hardy-Weinberg) expectations. Behavioral and reproductive data were collected for 10 months for each population, and microsatellite genotyping was performed on seven of the populations to determine parentage. These combined data show t-associated fitness declines in both males and females. This is the first study to show evidence for a reduction in the ability of +/t males to maintain territories. Because females tend to mate with dominant males, impairment of territorial success can explain much of the selection against t observed in our populations. In nature, selection against heterozygote carriers of the t complex helps solve the puzzlingly low t frequencies found in wild populations. This ecological approach for determining fitness consequences of genetic variants has broad application for the discovery of gene function in general.

Memetics--A Growth Industry in US Military Operations

DTIC Science & Technology

2006-01-01

Ret) and Schmitt John F., presentation to MCCDC, September, 2005. 2 Dawkins , R. (1976), “The Selfish Gene ,” Oxford University Press, Oxford 1...NY: Atlantic Monthly Press; 1995. Brodie, Richard, “Virus of the Mind: The New Science of the Meme” Dawkins , R. (1976), “The Selfish Gene ...interpersonal and societal interaction. Richard Dawkins introduced 1 Van Riper, Paul K., LtGen USMC

What's in a goal? The role of motivational relevance in cognition and action.

PubMed

Eitam, Baruch; Higgins, E Tory

2014-04-01

We argue that it is possible to go beyond the "selfish goal" metaphor and make an even stronger case for the role of unconscious motivation in cognition and action. Through the relevance of a representation (ROAR) framework, we describe how not only value motivation, which relates to "selfish goals," but also truth motivation and control motivation impact cognition and action.

On the Tradeoff Between Altruism and Selfishness in MANET Trust Management

DTIC Science & Technology

2016-04-07

to discourage selfish behaviors, using a hidden Markov model (HMM) to quanti - tatively measure the trustworthiness of nodes. Adams et al. [18...based reliability metric to predict trust-based system survivability. Section 4 analyzes numerical results obtained through the evaluation of our SPN...concepts in MANETs, trust man- agement for MANETs should consider the following design features: trust metrics must be customizable, evaluation of

The outbreak of cooperation among success-driven individuals under noisy conditions

PubMed Central

Helbing, Dirk; Yu, Wenjian

2009-01-01

According to Thomas Hobbes' Leviathan [1651; 2008 (Touchstone, New York), English Ed], “the life of man [is] solitary, poor, nasty, brutish, and short,” and it would need powerful social institutions to establish social order. In reality, however, social cooperation can also arise spontaneously, based on local interactions rather than centralized control. The self-organization of cooperative behavior is particularly puzzling for social dilemmas related to sharing natural resources or creating common goods. Such situations are often described by the prisoner's dilemma. Here, we report the sudden outbreak of predominant cooperation in a noisy world dominated by selfishness and defection, when individuals imitate superior strategies and show success-driven migration. In our model, individuals are unrelated, and do not inherit behavioral traits. They defect or cooperate selfishly when the opportunity arises, and they do not know how often they will interact or have interacted with someone else. Moreover, our individuals have no reputation mechanism to form friendship networks, nor do they have the option of voluntary interaction or costly punishment. Therefore, the outbreak of prevailing cooperation, when directed motion is integrated in a game-theoretical model, is remarkable, particularly when random strategy mutations and random relocations challenge the formation and survival of cooperative clusters. Our results suggest that mobility is significant for the evolution of social order, and essential for its stabilization and maintenance. PMID:19237576

The outbreak of cooperation among success-driven individuals under noisy conditions.

PubMed

Helbing, Dirk; Yu, Wenjian

2009-03-10

According to Thomas Hobbes' Leviathan [1651; 2008 (Touchstone, New York), English Ed], "the life of man [is] solitary, poor, nasty, brutish, and short," and it would need powerful social institutions to establish social order. In reality, however, social cooperation can also arise spontaneously, based on local interactions rather than centralized control. The self-organization of cooperative behavior is particularly puzzling for social dilemmas related to sharing natural resources or creating common goods. Such situations are often described by the prisoner's dilemma. Here, we report the sudden outbreak of predominant cooperation in a noisy world dominated by selfishness and defection, when individuals imitate superior strategies and show success-driven migration. In our model, individuals are unrelated, and do not inherit behavioral traits. They defect or cooperate selfishly when the opportunity arises, and they do not know how often they will interact or have interacted with someone else. Moreover, our individuals have no reputation mechanism to form friendship networks, nor do they have the option of voluntary interaction or costly punishment. Therefore, the outbreak of prevailing cooperation, when directed motion is integrated in a game-theoretical model, is remarkable, particularly when random strategy mutations and random relocations challenge the formation and survival of cooperative clusters. Our results suggest that mobility is significant for the evolution of social order, and essential for its stabilization and maintenance.

The 'selfish brain' is regulated by aquaporins and autophagy under nutrient deprivation.

PubMed

Ye, Qiao; Wu, Yonghong; Gao, Yan; Li, Zhihui; Li, Weiguang; Zhang, Chenggang

2016-05-01

The brain maintains its mass and physiological functional capacity compared with other organs under harsh conditions such as starvation, a mechanism termed the 'selfish brain' theory. To further investigate this phenomenon, mice were examined following water and/or food deprivation. Although the body weights of the mice, the weight of the organs except the brain and blood glucose levels were significantly reduced in the absence of water and/or food, the brain weight maintained its original state. Furthermore, no significant differences in the water content of the brain or its energy balance were observed when the mice were subjected to water and/or food deprivation. To further investigate the mechanism underlying the brain maintenance of water and substance homeostasis, the expression levels of aquaporins (AQPs) and autophagy‑specific protein long‑chain protein 3 (LC3) were examined. During the process of water and food deprivation, no significant differences in the transcriptional levels of AQPs were observed. However, autophagy activity levels were initially stimulated, then suppressed in a time‑dependent manner. LC3 and AQPs have important roles for the survival of the brain under conditions of food and water deprivation, which provided further understanding of the mechanism underlying the 'selfish brain' phenomenon. Although not involved in the energy regulation of the 'selfish brain', AQPs were observed to have important roles in water and food deprivation, specifically with regards to the control of water content. Additionally, the brain exhibits an 'unselfish strategy' using autophagy during water and/or food deprivation. The present study furthered current understanding of the 'selfish brain' theory, and identified additional regulating target genes of AQPs and autophagy, with the aim of providing a basis for the prevention of nutrient shortage in humans and animals.

The 'selfish brain' is regulated by aquaporins and autophagy under nutrient deprivation

PubMed Central

YE, QIAO; WU, YONGHONG; GAO, YAN; LI, ZHIHUI; LI, WEIGUANG; ZHANG, CHENGGANG

2016-01-01

The brain maintains its mass and physiological functional capacity compared with other organs under harsh conditions such as starvation, a mechanism termed the 'selfish brain' theory. To further investigate this phenomenon, mice were examined following water and/or food deprivation. Although the body weights of the mice, the weight of the organs except the brain and blood glucose levels were significantly reduced in the absence of water and/or food, the brain weight maintained its original state. Furthermore, no significant differences in the water content of the brain or its energy balance were observed when the mice were subjected to water and/or food deprivation. To further investigate the mechanism underlying the brain maintenance of water and substance homeostasis, the expression levels of aquaporins (AQPs) and autophagy-specific protein long-chain protein 3 (LC3) were examined. During the process of water and food deprivation, no significant differences in the transcriptional levels of AQPs were observed. However, autophagy activity levels were initially stimulated, then suppressed in a time-dependent manner. LC3 and AQPs have important roles for the survival of the brain under conditions of food and water deprivation, which provided further understanding of the mechanism underlying the 'selfish brain' phenomenon. Although not involved in the energy regulation of the 'selfish brain', AQPs were observed to have important roles in water and food deprivation, specifically with regards to the control of water content. Additionally, the brain exhibits an 'unselfish strategy' using autophagy during water and/or food deprivation. The present study furthered current understanding of the 'selfish brain' theory, and identified additional regulating target genes of AQPs and autophagy, with the aim of providing a basis for the prevention of nutrient shortage in humans and animals. PMID:26986971

Self-Fulfilling Prophecies as a Link between Men’s Facial Width-to-Height Ratio and Behavior

PubMed Central

Haselhuhn, Michael P.; Wong, Elaine M.; Ormiston, Margaret E.

2013-01-01

The facial width-to-height ratio (fWHR) has been identified as a reliable predictor of men’s behavior, with researchers focusing on evolutionary selection pressures as the underlying mechanism explaining these relationships. In this paper, we complement this approach and examine the extent to which social processes also determine the extent to which men’s fWHR serves as a behavioral cue. Specifically, we propose that observers’ treatment of target men based on the targets’ fWHR subsequently affects behavior, leading the targets to behave in ways that are consistent with the observers’ expectations (i.e., a self-fulfilling prophecy). Results from four studies demonstrate that individuals behave more selfishly when interacting with men with greater fWHRs, and this selfish behavior, in turn, elicits selfish behavior in others. PMID:24015226

The Helicobacter pylori HpyAXII restriction–modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components

PubMed Central

Humbert, Olivier; Salama, Nina R.

2008-01-01

The naturally competent organism Helicobacter pylori encodes a large number of restriction–modification (R–M) systems that consist of a restriction endonuclease and a DNA methyltransferase. R–M systems are not only believed to limit DNA exchange among bacteria but may also have other cellular functions. We report a previously uncharacterized H. pylori type II R–M system, M.HpyAXII/R.HpyAXII. We show that this system targets GTAC sites, which are rare in the H. pylori chromosome but numerous in ribosomal RNA genes. As predicted, this type II R–M system showed attributes of a selfish element. Deletion of the methyltransferase M.HpyAXII is lethal when associated with an active endonuclease R.HpyAXII unless compensated by adaptive mutation or gene amplification. R.HpyAXII effectively restricted both unmethylated plasmid and chromosomal DNA during natural transformation and was predicted to belong to the novel ‘half pipe’ structural family of endonucleases. Analysis of a panel of clinical isolates revealed that R.HpyAXII was functional in a small number of H. pylori strains (18.9%, n = 37), whereas the activity of M.HpyAXII was highly conserved (92%, n = 50), suggesting that GTAC methylation confers a selective advantage to H. pylori. However, M.HpyAXII activity did not enhance H. pylori fitness during stomach colonization of a mouse infection model. PMID:18978016

Third-party punishers are rewarded, but third-party helpers even more so.

PubMed

Raihani, Nichola J; Bshary, Redouan

2015-04-01

Punishers can benefit from a tough reputation, where future partners cooperate because they fear repercussions. Alternatively, punishers might receive help from bystanders if their act is perceived as just and other-regarding. Third-party punishment of selfish individuals arguably fits these conditions, but it is not known whether third-party punishers are rewarded for their investments. Here, we show that third-party punishers are indeed rewarded by uninvolved bystanders. Third parties were presented with the outcome of a dictator game in which the dictator was either selfish or fair and were allocated to one of three treatments in which they could choose to do nothing or (1) punish the dictator, (2) help the receiver, or (3) choose between punishment and helping, respectively. A fourth player (bystander) then sees the third-party's decision and could choose to reward the third party or not. Third parties that punished selfish dictators were more likely to be rewarded by bystanders than third parties that took no action in response to a selfish dictator. However, helpful third parties were rewarded even more than third-party punishers. These results suggest that punishment could in principle evolve via indirect reciprocity, but also provide insights into why individuals typically prefer to invest in positive actions. © 2015 The Author(s).

The Selfish Goal: autonomously operating motivational structures as the proximate cause of human judgment and behavior.

PubMed

Huang, Julie Y; Bargh, John A

2014-04-01

We propose the Selfish Goal model, which holds that a person's behavior is driven by psychological processes called goals that guide his or her behavior, at times in contradictory directions. Goals can operate both consciously and unconsciously, and when activated they can trigger downstream effects on a person's information processing and behavioral possibilities that promote only the attainment of goal end-states (and not necessarily the overall interests of the individual). Hence, goals influence a person as if the goals themselves were selfish and interested only in their own completion. We argue that there is an evolutionary basis to believe that conscious goals evolved from unconscious and selfish forms of pursuit. This theoretical framework predicts the existence of unconscious goal processes capable of guiding behavior in the absence of conscious awareness and control (the automaticity principle), the ability of the most motivating or active goal to constrain a person's information processing and behavior toward successful completion of that goal (the reconfiguration principle), structural similarities between conscious and unconscious goal pursuit (the similarity principle), and goal influences that produce apparent inconsistencies or counterintuitive behaviors in a person's behavior extended over time (the inconsistency principle). Thus, we argue that a person's behaviors are indirectly selected at the goal level but expressed (and comprehended) at the individual level.

Congestion schemes and Nash equilibrium in complex networks

NASA Astrophysics Data System (ADS)

Almendral, Juan A.; López, Luis; Cholvi, Vicent; Sanjuán, Miguel A. F.

2005-09-01

Whenever a common resource is scarce, a set of rules are needed to share it in a fairly way. However, most control schemes assume that users will behave in a cooperative way, without taking care of guaranteeing that they will not act in a selfish manner. Then, a fundamental issue is to evaluate the impact of cheating. From the point of view of game theory, a Nash equilibrium implies that nobody can take advantage by unilaterally deviating from this stable state, even in the presence of selfish users. In this paper we prove that any efficient Nash equilibrium strongly depends on the number of users, if the control scheme policy does not record their previous behavior. Since this is a common pattern in real situations, this implies that the system would be always out of equilibrium. Consequently, this result proves that, in practice, oblivious control schemes must be improved to cope with selfish users.

Genes on B chromosomes: old questions revisited with new tools.

PubMed

Banaei-Moghaddam, Ali M; Martis, Mihaela M; Macas, Jiří; Gundlach, Heidrun; Himmelbach, Axel; Altschmied, Lothar; Mayer, Klaus F X; Houben, Andreas

2015-01-01

B chromosomes are supernumerary dispensable parts of the karyotype which appear in some individuals of some populations in some species. Often, they have been considered as 'junk DNA' or genomic parasites without functional genes. Due to recent advances in sequencing technologies, it became possible to investigate their DNA composition, transcriptional activity and effects on the host transcriptome profile in detail. Here, we review the most recent findings regarding the gene content of B chromosomes and their transcriptional activities and discuss these findings in the context of comparable biological phenomena, like sex chromosomes, aneuploidy and pseudogenes. Recent data suggest that B chromosomes carry transcriptionally active genic sequences which could affect the transcriptome profile of their host genome. These findings are gradually changing our view that B chromosomes are solely genetically inert selfish elements without any functional genes. This at one side could partly explain the deleterious effects which are associated with their presence. On the other hand it makes B chromosome a nice model for studying regulatory mechanisms of duplicated genes and their evolutionary consequences. Copyright © 2014 Elsevier B.V. All rights reserved.

The Role of Prosocialness and Trust in the Consumption of Water as a Limited Resource.

PubMed

Cuadrado, Esther; Tabernero, Carmen; García, Rocío; Luque, Bárbara; Seibert, Jan

2017-01-01

This research analyzes the role of prosocialness and trust in the use of water as a limited resource under situations of competition or cooperation. For this purpose, 107 participants played the role of farmers and made decisions about irrigating their fields in the web-based multiplayer game Irrigania. Before the simulation exercise, participants' prosocialness and trust levels were evaluated and they were randomly assigned to an experimental condition (competition or cooperation). Repeated measures analysis, using the 10 fields and the experimental conditions as factors, showed that, in the cooperation condition, farmers and their villages used a less selfish strategy to cultivate their fields, which produced greater benefits. Under competition, benefits to farmers and their villages were reduced over time. Mediational analysis shows that the selfish irrigation strategy fully mediated the relationship between prosocialness and accumulated profits; prosocial individuals choose less selfish irrigation strategies and, in turn, accumulated more benefit. Moreover, moderation analysis shows that trust moderated the link between prosocialness and water use strategy by strengthening the negative effect of prosocialness on selection of selfish strategies. The implications of these results highlight the importance of promoting the necessary trust to develop prosocial strategies in collectives; therefore, the efficacy of interventions, such as the creation of cooperative educational contexts or organization of collective actions with groups affected by water scarcity, are discussed.

The Role of Prosocialness and Trust in the Consumption of Water as a Limited Resource

PubMed Central

Cuadrado, Esther; Tabernero, Carmen; García, Rocío; Luque, Bárbara; Seibert, Jan

2017-01-01

This research analyzes the role of prosocialness and trust in the use of water as a limited resource under situations of competition or cooperation. For this purpose, 107 participants played the role of farmers and made decisions about irrigating their fields in the web-based multiplayer game Irrigania. Before the simulation exercise, participants’ prosocialness and trust levels were evaluated and they were randomly assigned to an experimental condition (competition or cooperation). Repeated measures analysis, using the 10 fields and the experimental conditions as factors, showed that, in the cooperation condition, farmers and their villages used a less selfish strategy to cultivate their fields, which produced greater benefits. Under competition, benefits to farmers and their villages were reduced over time. Mediational analysis shows that the selfish irrigation strategy fully mediated the relationship between prosocialness and accumulated profits; prosocial individuals choose less selfish irrigation strategies and, in turn, accumulated more benefit. Moreover, moderation analysis shows that trust moderated the link between prosocialness and water use strategy by strengthening the negative effect of prosocialness on selection of selfish strategies. The implications of these results highlight the importance of promoting the necessary trust to develop prosocial strategies in collectives; therefore, the efficacy of interventions, such as the creation of cooperative educational contexts or organization of collective actions with groups affected by water scarcity, are discussed. PMID:28533760

Rapid rise and fall of selfish sex-ratio X chromosomes in Drosophila simulans: spatiotemporal analysis of phenotypic and molecular data.

PubMed

Bastide, Héloïse; Cazemajor, Michel; Ogereau, David; Derome, Nicolas; Hospital, Frédéric; Montchamp-Moreau, Catherine

2011-09-01

Sex-ratio drive, which has been documented in several Drosophila species, is induced by X-linked segregation distorters. Contrary to Mendel's law of independent assortment, the sex-ratio chromosome (X(SR)) is inherited by more than half the offspring of carrier males, resulting in a female-biased sex ratio. This segregation advantage allows X(SR) to spread in populations, even if it is not beneficial for the carriers. In the cosmopolitan species D. simulans, the Paris sex-ratio is caused by recently emerged selfish X(SR) chromosomes. These chromosomes have triggered an intragenomic conflict, and their propagation has been halted over a large area by the evolution of complete drive suppression. Previous molecular population genetics analyses revealed a selective sweep indicating that the invasion of X(SR) chromosomes was very recent in Madagascar (likely less than 100 years ago). Here, we show that X(SR) chromosomes are now declining at this location as well as in Mayotte and Kenya. Drive suppression is complete in the three populations, which display little genetic differentiation and share swept haplotypes, attesting to a common and very recent ancestry of the X(SR) chromosomes. Patterns of DNA sequence variation also indicate a fitness cost of the segmental duplication involved in drive. The data suggest that X(SR) chromosomes started declining first on the African continent, then in Mayotte, and finally in Madagascar and strongly support a scenario of rapid cycling of X chromosomes. Once drive suppression has evolved, standard X(ST) chromosomes locally replace costly X(SR) chromosomes in a few decades.

Quid pro quo: a mechanism for fair collaboration in networked systems.

PubMed

Santos, Agustín; Fernández Anta, Antonio; López Fernández, Luis

2013-01-01

Collaboration may be understood as the execution of coordinated tasks (in the most general sense) by groups of users, who cooperate for achieving a common goal. Collaboration is a fundamental assumption and requirement for the correct operation of many communication systems. The main challenge when creating collaborative systems in a decentralized manner is dealing with the fact that users may behave in selfish ways, trying to obtain the benefits of the tasks but without participating in their execution. In this context, Game Theory has been instrumental to model collaborative systems and the task allocation problem, and to design mechanisms for optimal allocation of tasks. In this paper, we revise the classical assumptions of these models and propose a new approach to this problem. First, we establish a system model based on heterogenous nodes (users, players), and propose a basic distributed mechanism so that, when a new task appears, it is assigned to the most suitable node. The classical technique for compensating a node that executes a task is the use of payments (which in most networks are hard or impossible to implement). Instead, we propose a distributed mechanism for the optimal allocation of tasks without payments. We prove this mechanism to be robust evenevent in the presence of independent selfish or rationally limited players. Additionally, our model is based on very weak assumptions, which makes the proposed mechanisms susceptible to be implemented in networked systems (e.g., the Internet).

Society, Land, Love or Money (A Strategic Model of How to Glue the Generations Together),

DTIC Science & Technology

1981-01-01

carrying of extra capital stock. 33 REFERENCES Dawkins , R. (1976), The Selfish Gene . New York: Oxford University Press. Dubey, P. and N. Shubik (1981...a gene would rapidly disappear. The care for offspring needs to be forthcoming until the last of the new generation is selfsufficient and able to...payoff than the firs:. it is more complicated. 20 4.3. Selfish Individuals and Threat Strategies (Model 1) In this section an example is fully

Constant Price of Anarchy in Network Creation Games via Public Service Advertising

NASA Astrophysics Data System (ADS)

Demaine, Erik D.; Zadimoghaddam, Morteza

Network creation games have been studied in many different settings recently. These games are motivated by social networks in which selfish agents want to construct a connection graph among themselves. Each node wants to minimize its average or maximum distance to the others, without paying much to construct the network. Many generalizations have been considered, including non-uniform interests between nodes, general graphs of allowable edges, bounded budget agents, etc. In all of these settings, there is no known constant bound on the price of anarchy. In fact, in many cases, the price of anarchy can be very large, namely, a constant power of the number of agents. This means that we have no control on the behavior of network when agents act selfishly. On the other hand, the price of stability in all these models is constant, which means that there is chance that agents act selfishly and we end up with a reasonable social cost.

Direct and Indirect Influence of Altruistic Behavior in a Social Network.

PubMed

Liu, Pei-Pei; Safin, Vasiliy; Yang, Barry; Luhmann, Christian C

2015-01-01

Prior research has suggested that recipients of generosity behave more generously themselves (a direct social influence). In contrast, there is conflicting evidence about the existence of indirect influence (i.e., whether interacting with a recipient of generosity causes one to behave more generously), casting doubt on the possibility that altruistic behavior can cascade through social networks. The current study investigated how far selfish and generous behavior can be transmitted through social networks and the cognitive mechanisms that underlie such transmission. Participants played a sequence of public goods games comprising a chain network. This network is advantageous because it permits only a single, unambiguous path of influence. Furthermore, we experimentally manipulated the behavior of the first link in the chain to be either generous or selfish. Results revealed the presence of direct social influence, but no evidence for indirect influence. Results also showed that selfish behavior exerted a substantially greater influence than generous behavior. Finally, expectations about future partners' behavior strongly mediated the observed social influence, suggesting an adaptive basis for such influence.

CSR: Constrained Selfish Routing in Ad-Hoc Networks

NASA Astrophysics Data System (ADS)

Bassem, Christine; Bestavros, Azer

Routing protocols for ad-hoc networks assume that the nodes forming the network are either under a single authority, or else that they would be altruistically forwarding data for other nodes with no expectation of a return. These assumptions are unrealistic since in ad-hoc networks, nodes are likely to be autonomous and rational (selfish), and thus unwilling to help unless they have an incentive to do so. Providing such incentives is an important aspect that should be considered when designing ad-hoc routing protocols. In this paper, we propose a dynamic, decentralized routing protocol for ad-hoc networks that provides incentives in the form of payments to intermediate nodes used to forward data for others. In our Constrained Selfish Routing (CSR) protocol, game-theoretic approaches are used to calculate payments (incentives) that ensure both the truthfulness of participating nodes and the fairness of the CSR protocol. We show through simulations that CSR is an energy efficient protocol and that it provides lower communication overhead in the best and average cases compared to existing approaches.

Selfish genetic elements and sexual selection: their impact on male fertility.

PubMed

Price, Tom A R; Wedell, Nina

2008-03-01

Females of many species mate with more than one male (polyandry), yet the adaptive significance of polyandry is poorly understood. One hypothesis to explain the widespread occurrence of multiple mating is that it may allow females to utilize post-copulatory mechanisms to reduce the risk of fertilizing their eggs with sperm from incompatible males. Selfish genetic elements (SGEs) are ubiquitous in eukaryotes, frequent sources of reproductive incompatibilities, and associated with fitness costs. However, their impact on sexual selection is largely unexplored. In this review we examine the link between SGEs, male fertility and sperm competitive ability. We show there is widespread evidence that SGEs are associated with reduced fertility in both animals and plants, and present some recent data showing that males carrying SGEs have reduced paternity in sperm competition. We also discuss possible reasons why male gametes are particularly vulnerable to the selfish actions of SGEs. The widespread reduction in male fertility caused by SGEs implies polyandry may be a successful female strategy to bias paternity against SGE-carrying males.

Selfish genetic elements and sexual selection: their impact on male fertility.

PubMed

Price, Tom A R; Wedell, Nina

2008-09-01

Females of many species mate with more than one male (polyandry), yet the adaptive significance of polyandry is poorly understood. One hypothesis to explain the widespread occurrence of multiple mating is that it may allow females to utilize post-copulatory mechanisms to reduce the risk of fertilizing their eggs with sperm from incompatible males. Selfish genetic elements (SGEs) are ubiquitous in eukaryotes, frequent sources of reproductive incompatibilities, and associated with fitness costs. However, their impact on sexual selection is largely unexplored. In this review we examine the link between SGEs, male fertility and sperm competitive ability. We show there is widespread evidence that SGEs are associated with reduced fertility in both animals and plants, and present some recent data showing that males carrying SGEs have reduced paternity in sperm competition. We also discuss possible reasons why male gametes are particularly vulnerable to the selfish actions of SGEs. The widespread reduction in male fertility caused by SGEs implies polyandry may be a successful female strategy to bias paternity against SGE-carrying males.

The topography of generosity: asymmetric evaluations of prosocial actions.

PubMed

Klein, Nadav; Epley, Nicholas

2014-12-01

Prosociality is considered a virtue. Those who care for others are admired, whereas those who care only for themselves are despised. For one's reputation, it pays to be nice. Does it pay to be even nicer? Four experiments assess reputational inferences across the entire range of prosocial outcomes in zero-sum interactions, from completely selfish to completely selfless actions. We observed consistent nonlinear evaluations: Participants evaluated selfish actions more negatively than equitable actions, but they did not evaluate selfless actions markedly more favorably than equitable actions. This asymptotic pattern reflected monotonic evaluations for increasingly selfish actions and insensitivity to increasingly selfless actions. It pays to be nice but not to be really nice. Additional experiments suggest that this pattern stems partly from failing to make spontaneous comparisons between varying degrees of selflessness. We suggest that these reputational incentives could guide social norms, encouraging equitable actions but discouraging extremely selfless actions. PsycINFO Database Record (c) 2014 APA, all rights reserved.

The impact of transposable elements on mammalian development

PubMed Central

Garcia-Perez, Jose L.; Widmann, Thomas J.; Adams, Ian R.

2018-01-01

Summary Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that significantly impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues. Importantly, the ongoing domestication and evolution of TEs appears to provide a rich source of regulatory elements, functional modules and genetic variation that fuels the evolution of mammalian developmental processes. Here, we review the functional impact that TEs exert on mammalian developmental processes and how the somatic activity of TEs can influence gene regulatory networks. PMID:27875251

A global optimization algorithm inspired in the behavior of selfish herds.

PubMed

Fausto, Fernando; Cuevas, Erik; Valdivia, Arturo; González, Adrián

2017-10-01

In this paper, a novel swarm optimization algorithm called the Selfish Herd Optimizer (SHO) is proposed for solving global optimization problems. SHO is based on the simulation of the widely observed selfish herd behavior manifested by individuals within a herd of animals subjected to some form of predation risk. In SHO, individuals emulate the predatory interactions between groups of prey and predators by two types of search agents: the members of a selfish herd (the prey) and a pack of hungry predators. Depending on their classification as either a prey or a predator, each individual is conducted by a set of unique evolutionary operators inspired by such prey-predator relationship. These unique traits allow SHO to improve the balance between exploration and exploitation without altering the population size. To illustrate the proficiency and robustness of the proposed method, it is compared to other well-known evolutionary optimization approaches such as Particle Swarm Optimization (PSO), Artificial Bee Colony (ABC), Firefly Algorithm (FA), Differential Evolution (DE), Genetic Algorithms (GA), Crow Search Algorithm (CSA), Dragonfly Algorithm (DA), Moth-flame Optimization Algorithm (MOA) and Sine Cosine Algorithm (SCA). The comparison examines several standard benchmark functions, commonly considered within the literature of evolutionary algorithms. The experimental results show the remarkable performance of our proposed approach against those of the other compared methods, and as such SHO is proven to be an excellent alternative to solve global optimization problems. Copyright © 2017 Elsevier B.V. All rights reserved.

Gene network polymorphism is the raw material of natural selection: the selfish gene network hypothesis.

PubMed

Boldogköi, Zsolt

2004-09-01

Population genetics, the mathematical theory of modern evolutionary biology, defines evolution as the alteration of the frequency of distinct gene variants (alleles) differing in fitness over the time. The major problem with this view is that in gene and protein sequences we can find little evidence concerning the molecular basis of phenotypic variance, especially those that would confer adaptive benefit to the bearers. Some novel data, however, suggest that a large amount of genetic variation exists in the regulatory region of genes within populations. In addition, comparison of homologous DNA sequences of various species shows that evolution appears to depend more strongly on gene expression than on the genes themselves. Furthermore, it has been demonstrated in several systems that genes form functional networks, whose products exhibit interrelated expression profiles. Finally, it has been found that regulatory circuits of development behave as evolutionary units. These data demonstrate that our view of evolution calls for a new synthesis. In this article I propose a novel concept, termed the selfish gene network hypothesis, which is based on an overall consideration of the above findings. The major statements of this hypothesis are as follows. (1) Instead of individual genes, gene networks (GNs) are responsible for the determination of traits and behaviors. (2) The primary source of microevolution is the intraspecific polymorphism in GNs and not the allelic variation in either the coding or the regulatory sequences of individual genes. (3) GN polymorphism is generated by the variation in the regulatory regions of the component genes and not by the variance in their coding sequences. (4) Evolution proceeds through continuous restructuring of the composition of GNs rather than fixing of specific alleles or GN variants.

Transcriptome profiling of Nasonia vitripennis testis reveals novel transcripts expressed from the selfish B chromosome, paternal sex ratio.

PubMed

Akbari, Omar S; Antoshechkin, Igor; Hay, Bruce A; Ferree, Patrick M

2013-09-04

A widespread phenomenon in nature is sex ratio distortion of arthropod populations caused by microbial and genetic parasites. Currently little is known about how these agents alter host developmental processes to favor one sex or the other. The paternal sex ratio (PSR) chromosome is a nonessential, paternally transmitted centric fragment that segregates in natural populations of the jewel wasp, Nasonia vitripennis. To persist, PSR is thought to modify the hereditary material of the developing sperm, with the result that all nuclear DNA other than the PSR chromosome is destroyed shortly after fertilization. This results in the conversion of a fertilized embryo--normally a female--into a male, thereby insuring transmission of the "selfish" PSR chromosome, and simultaneously leading to wasp populations that are male-biased. To begin to understand this system at the mechanistic level, we carried out transcriptional profiling of testis from WT and PSR-carrying males. We identified a number of transcripts that are differentially expressed between these conditions. We also discovered nine transcripts that are uniquely expressed from the PSR chromosome. Four of these PSR-specific transcripts encode putative proteins, whereas the others have very short open reading frames and no homology to known proteins, suggesting that they are long noncoding RNAs. We propose several different models for how these transcripts could facilitate PSR-dependent effects. Our analyses also revealed 15.71 MB of novel transcribed regions in the N. vitripennis genome, thus increasing the current annotation of total transcribed regions by 53.4%. Finally, we detected expression of multiple meiosis-related genes in the wasp testis, despite the lack of conventional meiosis in the male sex.

The partitioning and copy number control systems of the selfish yeast plasmid: an optimized molecular design for stable persistence in host cells

PubMed Central

Yen-Ting-Liu; Sau, Saumitra; Ma, Chien-Hui; Kachroo, Aashiq H; Rowley, Paul A; Chang, Keng-Ming; Fan, Hsiu-Fang; Jayaram, Makkuni

2014-01-01

Summary The multi-copy 2 micron plasmid of Saccharomyces cerevisiae, a resident of the nucleus, is remarkable for its high chromosome-like stability. The plasmid does not appear to contribute to the fitness of the host, nor does it impose a significant metabolic burden on the host at its steady state copy number. The plasmid may be viewed as a highly optimized selfish DNA element whose genome design is devoted entirely towards efficient replication, equal segregation and copy number maintenance. A partitioning system comprised of two plasmid coded proteins, Rep1 and Rep2, and a partitioning locus STB is responsible for equal or nearly equal segregation of plasmid molecules to mother and daughter cells. Current evidence supports a model in which the Rep-STB system promotes the physical association of the plasmid with chromosomes and thus plasmid segregation by a hitchhiking mechanism. The Flp site-specific recombination system housed by the plasmid plays a critical role in maintaining steady state plasmid copy number. A decrease in plasmid population due to rare missegregation events is rectified by plasmid amplification via a recombination induced rolling circle replication mechanism. Appropriate plasmid amplification, without runaway increase in copy number, is ensured by positive and negative regulation of FLP gene expression by plasmid coded proteins and by the control of Flp level/activity through host mediated post-translational modification(s) of Flp. The Flp system has been successfully utilized to understand mechanisms of site-specific recombination, to bring about directed genetic alterations for addressing fundamental problems in biology, and as a tool in biotechnological applications. PMID:25541598

The partitioning and copy number control systems of the selfish yeast plasmid: an optimized molecular design for stable persistence in host cells.

PubMed

Yen-Ting-Liu; Sau, Saumitra; Ma, Chien-Hui; Kachroo, Aashiq H; Rowley, Paul A; Chang, Keng-Ming; Fan, Hsiu-Fang; Jayaram, Makkuni

2014-10-01

The multi-copy 2 micron plasmid of Saccharomyces cerevisiae, a resident of the nucleus, is remarkable for its high chromosome-like stability. The plasmid does not appear to contribute to the fitness of the host, nor does it impose a significant metabolic burden on the host at its steady state copy number. The plasmid may be viewed as a highly optimized selfish DNA element whose genome design is devoted entirely towards efficient replication, equal segregation and copy number maintenance. A partitioning system comprised of two plasmid coded proteins, Rep1 and Rep2, and a partitioning locus STB is responsible for equal or nearly equal segregation of plasmid molecules to mother and daughter cells. Current evidence supports a model in which the Rep-STB system promotes the physical association of the plasmid with chromosomes and thus plasmid segregation by a hitchhiking mechanism. The Flp site-specific recombination system housed by the plasmid plays a critical role in maintaining steady state plasmid copy number. A decrease in plasmid population due to rare missegregation events is rectified by plasmid amplification via a recombination induced rolling circle replication mechanism. Appropriate plasmid amplification, without runaway increase in copy number, is ensured by positive and negative regulation of FLP gene expression by plasmid coded proteins and by the control of Flp level/activity through host mediated post-translational modification(s) of Flp. The Flp system has been successfully utilized to understand mechanisms of site-specific recombination, to bring about directed genetic alterations for addressing fundamental problems in biology, and as a tool in biotechnological applications.

The selfish Segregation Distorter gene complex of Drosophila melanogaster.

PubMed

Larracuente, Amanda M; Presgraves, Daven C

2012-09-01

Segregation Distorter (SD) is an autosomal meiotic drive gene complex found worldwide in natural populations of Drosophila melanogaster. During spermatogenesis, SD induces dysfunction of SD(+) spermatids so that SD/SD(+) males sire almost exclusively SD-bearing progeny rather than the expected 1:1 Mendelian ratio. SD is thus evolutionarily "selfish," enhancing its own transmission at the expense of its bearers. Here we review the molecular and evolutionary genetics of SD. Genetic analyses show that the SD is a multilocus gene complex involving two key loci--the driver, Segregation distorter (Sd), and the target of drive, Responder (Rsp)--and at least three upward modifiers of distortion. Molecular analyses show that Sd encodes a truncated duplication of the gene RanGAP, whereas Rsp is a large pericentromeric block of satellite DNA. The Sd-RanGAP protein is enzymatically wild type but mislocalized within cells and, for reasons that remain unclear, appears to disrupt the histone-to-protamine transition in drive-sensitive spermatids bearing many Rsp satellite repeats but not drive-insensitive spermatids bearing few or no Rsp satellite repeats. Evolutionary analyses show that the Sd-RanGAP duplication arose recently within the D. melanogaster lineage, exploiting the preexisting and considerably older Rsp satellite locus. Once established, the SD haplotype collected enhancers of distortion and suppressors of recombination. Further dissection of the molecular genetic and cellular basis of SD-mediated distortion seems likely to provide insights into several important areas currently understudied, including the genetic control of spermatogenesis, the maintenance and evolution of satellite DNAs, the possible roles of small interfering RNAs in the germline, and the molecular population genetics of the interaction of genetic linkage and natural selection.

Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs.

PubMed

Ichiyanagi, Kenji

2013-01-01

Short interspersed elements (SINEs) are a class of retrotransposons, which amplify their copy numbers in their host genomes by retrotransposition. More than a million copies of SINEs are present in a mammalian genome, constituting over 10% of the total genomic sequence. In contrast to the other two classes of retrotransposons, long interspersed elements (LINEs) and long terminal repeat (LTR) elements, SINEs are transcribed by RNA polymerase III. However, like LINEs and LTR elements, the SINE transcription is likely regulated by epigenetic mechanisms such as DNA methylation, at least for human Alu and mouse B1. Whereas SINEs and other transposable elements have long been thought as selfish or junk DNA, recent studies have revealed that they play functional roles at their genomic locations, for example, as distal enhancers, chromatin boundaries and binding sites of many transcription factors. These activities imply that SINE retrotransposition has shaped the regulatory network and chromatin landscape of their hosts. Whereas it is thought that the epigenetic mechanisms were originated as a host defense system against proliferation of parasitic elements, this review discusses a possibility that the same mechanisms are also used to regulate the SINE-derived functions.

Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer

PubMed Central

Yahara, Koji; Fukuyo, Masaki; Sasaki, Akira; Kobayashi, Ichizo

2009-01-01

Homing endonuclease genes are “selfish” mobile genetic elements whose endonuclease promotes the spread of its own gene by creating a break at a specific target site and using the host machinery to repair the break by copying and inserting the gene at this site. Horizontal transfer across the boundary of a species or population within which mating takes place has been thought to be necessary for their evolutionary persistence. This is based on the assumption that they will become fixed in a host population, where opportunities of homing will disappear, and become susceptible to degeneration. To test this hypothesis, we modeled behavior of a homing endonuclease gene that moves during meiosis through double-strand break repair. We mathematically explored conditions for persistence of the homing endonuclease gene and elucidated their parameter dependence as phase diagrams. We found that, if the cost of the pseudogene is lower than that of the homing endonuclease gene, the 2 forms can persist in a population through autonomous periodic oscillation. If the cost of the pseudogene is higher, 2 types of dynamics appear that enable evolutionary persistence: bistability dependent on initial frequency or fixation irrespective of initial frequency. The prediction of long persistence in the absence of horizontal transfer was confirmed by stochastic simulations in finite populations. The average time to extinction of the endonuclease gene was found to be thousands of meiotic generations or more based on realistic parameter values. These results provide a solid theoretical basis for an understanding of these and other extremely selfish elements. PMID:19837694

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

PubMed Central

Dolja, Valerian V.

2014-01-01

SUMMARY Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus “self” that defines the identity of deep, ancient viral lineages. However, several other widespread viral “hallmark genes” encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host. PMID:24847023

Dopaminergic stimulation increases selfish behavior in the absence of punishment threat.

PubMed

Pedroni, Andreas; Eisenegger, Christoph; Hartmann, Matthias N; Fischbacher, Urs; Knoch, Daria

2014-01-01

People often face decisions that pit self-interested behavior aimed at maximizing personal reward against normative behavior such as acting cooperatively, which benefits others. The threat of social sanctions for defying the fairness norm prevents people from behaving overly selfish. Thus, normative behavior is influenced by both seeking rewards and avoiding punishment. However, the neurochemical processes mediating the impact of these influences remain unknown. Several lines of evidence link the dopaminergic system to reward and punishment processing, respectively, but this evidence stems from studies in non-social contexts. The present study investigates dopaminergic drug effects on individuals' reward seeking and punishment avoidance in social interaction. Two-hundred one healthy male participants were randomly assigned to receive 300 mg of L-3,4-dihydroxyphenylalanine (L-DOPA) or a placebo before playing an economic bargaining game. This game involved two conditions, one in which unfair behavior could be punished and one in which unfair behavior could not be punished. In the absence of punishment threats, L-DOPA administration led to more selfish behavior, likely mediated through an increase in reward seeking. In contrast, L-DOPA administration had no significant effect on behavior when faced with punishment threats. The results of this study broaden the role of the dopaminergic system in reward seeking to human social interactions. We could show that even a single dose of a dopaminergic drug may bring selfish behavior to the fore, which in turn may shed new light on potential causal relationships between the dopaminergic system and norm abiding behaviors in certain clinical subpopulations.

Response time in economic games reflects different types of decision conflict for prosocial and proself individuals.

PubMed

Yamagishi, Toshio; Matsumoto, Yoshie; Kiyonari, Toko; Takagishi, Haruto; Li, Yang; Kanai, Ryota; Sakagami, Masamichi

2017-06-13

Behavioral and neuroscientific studies explore two pathways through which internalized social norms promote prosocial behavior. One pathway involves internal control of impulsive selfishness, and the other involves emotion-based prosocial preferences that are translated into behavior when they evade cognitive control for pursuing self-interest. We measured 443 participants' overall prosocial behavior in four economic games. Participants' predispositions [social value orientation (SVO)] were more strongly reflected in their overall game behavior when they made decisions quickly than when they spent a longer time. Prosocially (or selfishly) predisposed participants behaved less prosocially (or less selfishly) when they spent more time in decision making, such that their SVO prosociality yielded limited effects in actual behavior in their slow decisions. The increase (or decrease) in slower decision makers was prominent among consistent prosocials (or proselfs) whose strong preference for prosocial (or proself) goals would make it less likely to experience conflict between prosocial and proself goals. The strong effect of RT on behavior in consistent prosocials (or proselfs) suggests that conflict between prosocial and selfish goals alone is not responsible for slow decisions. Specifically, we found that contemplation of the risk of being exploited by others (social risk aversion) was partly responsible for making consistent prosocials (but not consistent proselfs) spend longer time in decision making and behave less prosocially. Conflict between means rather than between goals (immediate versus strategic pursuit of self-interest) was suggested to be responsible for the time-related increase in consistent proselfs' prosocial behavior. The findings of this study are generally in favor of the intuitive cooperation model of prosocial behavior.

Omission bias and perceived intention in children and adults.

PubMed

Hayashi, Hajimu

2015-06-01

Omission bias refers to the tendency to judge acts of commission as morally worse than equivalent acts of omission. Children aged 7-8 and 11-12 years, as well as adults, made moral judgements about acts of commission and omission in two conditions in which the protagonist obtained a self-directed benefit. In the antisocial condition, the other person was harmed; in the selfish condition, the other person was not harmed. The results showed that adults and both age groups of children judged that the agent who did something (act of commission) was morally worse than the agent who did nothing (omission) for both antisocial and selfish conditions, although this judgement tendency was clearer in the selfish condition than in the antisocial condition. Agent intention was held constant across commission and omission, but most participants rated the intention of the agent who did something as stronger than that of the agent who did nothing. These results suggest that omission bias occurs regardless of differences in age and situation. In addition, perceived intention appears to change in conjunction with omission bias. © 2015 The British Psychological Society.

Selfish routing equilibrium in stochastic traffic network: A probability-dominant description.

PubMed

Zhang, Wenyi; He, Zhengbing; Guan, Wei; Ma, Rui

2017-01-01

This paper suggests a probability-dominant user equilibrium (PdUE) model to describe the selfish routing equilibrium in a stochastic traffic network. At PdUE, travel demands are only assigned to the most dominant routes in the same origin-destination pair. A probability-dominant rerouting dynamic model is proposed to explain the behavioral mechanism of PdUE. To facilitate applications, the logit formula of PdUE is developed, of which a well-designed route set is not indispensable and the equivalent varitional inequality formation is simple. Two routing strategies, i.e., the probability-dominant strategy (PDS) and the dominant probability strategy (DPS), are discussed through a hypothetical experiment. It is found that, whether out of insurance or striving for perfection, PDS is a better choice than DPS. For more general cases, the conducted numerical tests lead to the same conclusion. These imply that PdUE (rather than the conventional stochastic user equilibrium) is a desirable selfish routing equilibrium for a stochastic network, given that the probability distributions of travel time are available to travelers.

Selfish routing equilibrium in stochastic traffic network: A probability-dominant description

PubMed Central

Zhang, Wenyi; Guan, Wei; Ma, Rui

2017-01-01

This paper suggests a probability-dominant user equilibrium (PdUE) model to describe the selfish routing equilibrium in a stochastic traffic network. At PdUE, travel demands are only assigned to the most dominant routes in the same origin-destination pair. A probability-dominant rerouting dynamic model is proposed to explain the behavioral mechanism of PdUE. To facilitate applications, the logit formula of PdUE is developed, of which a well-designed route set is not indispensable and the equivalent varitional inequality formation is simple. Two routing strategies, i.e., the probability-dominant strategy (PDS) and the dominant probability strategy (DPS), are discussed through a hypothetical experiment. It is found that, whether out of insurance or striving for perfection, PDS is a better choice than DPS. For more general cases, the conducted numerical tests lead to the same conclusion. These imply that PdUE (rather than the conventional stochastic user equilibrium) is a desirable selfish routing equilibrium for a stochastic network, given that the probability distributions of travel time are available to travelers. PMID:28829834

Selfish altruism, fierce cooperation and the predator.

PubMed

Askitas, Nikolaos

2018-12-01

This paper suggests a new way to think about a famous question: what explains cooperation in nature and in particular in humans? I argue that, for an evolutionary biologist as well as a quantitative social scientist, the triangle of two 'teammates' in the presence of a predator (passing and shooting in two-on-one situations) is one of the fundamental conceptual building-blocks for understanding these phenomena because in such a situation the fact that life is packaged in many distinct enclosures (and not in one big monolithic blob) can unfold its comparative advantage. I show how, in the presence of a predator, cooperative equilibria emerge among entirely selfish teammates if we infinitesimally bias the lead player in the selfish direction or assign a computational burden on the predator due to the presence of a teammate. I argue that 'predators' are common in the biological jungle but also in everyday human settings. Intuitively, this paper builds on the simple idea - a familiar one to a biologist observing the natural world but perhaps less so to social scientists - that everybody has enemies.

Genomic patterns associated with paternal/maternal distribution of transposable elements

NASA Astrophysics Data System (ADS)

Jurka, Jerzy

2003-03-01

Transposable elements (TEs) are specialized DNA or RNA fragments capable of surviving in intragenomic niches. They are commonly, perhaps unjustifiably referred to as "selfish" or "parasitic" elements. TEs can be divided in two major classes: retroelements and DNA transposons. The former include non-LTR retrotransposons and retrovirus-like elements, using reverse transriptase for their reproduction prior to integration into host DNA. The latter depend mostly on host DNA replication, with possible exception of rolling-circle transposons recently discovered by our team. I will review basic information on TEs, with emphasis on human Alu and L1 retroelements discussed in the context of genomic organization. TEs are non-randomly distributed in chromosomal DNA. In particular, human Alu elements tend to prefer GC-rich regions, whereas L1 accumulate in AT-rich regions. Current explanations of this phenomenon focus on the so called "target effects" and post-insertional selection. However, the proposed models appear to be unsatisfactory and alternative explanations invoking "channeling" to different chromosomal regions will be a major focus of my presentation. Transposable elements (TEs) can be expressed and integrated into host DNA in the male or female germlines, or both. Different models of expression and integration imply different proportions of TEs on sex chromosomes and autosomes. The density of recently retroposed human Alu elements is around three times higher on chromosome Y than on chromosome X, and over two times higher than the average density for all human autosomes. This implies Alu activity in paternal germlines. Analogous inter-chromosomal proportions for other repeat families should determine their compatibility with one of the three basic models describing the inheritance of TEs. Published evidence indicates that maternally and paternally imprinted genes roughly correspond to GC-rich and AT-rich DNA. This may explain the observed chromosomal distribution of Alu and L1 elements. Finally, paternal models of inheritance predict rapid accumulation of active TEs on chromosome Y. I will discuss potential implications of this phenomenon for evolution of chromosome Y and transposable elements.

The impact of transposable elements on mammalian development.

PubMed

Garcia-Perez, Jose L; Widmann, Thomas J; Adams, Ian R

2016-11-15

Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that have a significant impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues. Importantly, the ongoing domestication and evolution of TEs appears to provide a rich source of regulatory elements, functional modules and genetic variation that fuels the evolution of mammalian developmental processes. Here, we review the functional impact that TEs exert on mammalian developmental processes and discuss how the somatic activity of TEs can influence gene regulatory networks. © 2016. Published by The Company of Biologists Ltd.

Response time in economic games reflects different types of decision conflict for prosocial and proself individuals

PubMed Central

Matsumoto, Yoshie; Kiyonari, Toko; Takagishi, Haruto; Li, Yang; Kanai, Ryota; Sakagami, Masamichi

2017-01-01

Behavioral and neuroscientific studies explore two pathways through which internalized social norms promote prosocial behavior. One pathway involves internal control of impulsive selfishness, and the other involves emotion-based prosocial preferences that are translated into behavior when they evade cognitive control for pursuing self-interest. We measured 443 participants’ overall prosocial behavior in four economic games. Participants’ predispositions [social value orientation (SVO)] were more strongly reflected in their overall game behavior when they made decisions quickly than when they spent a longer time. Prosocially (or selfishly) predisposed participants behaved less prosocially (or less selfishly) when they spent more time in decision making, such that their SVO prosociality yielded limited effects in actual behavior in their slow decisions. The increase (or decrease) in slower decision makers was prominent among consistent prosocials (or proselfs) whose strong preference for prosocial (or proself) goals would make it less likely to experience conflict between prosocial and proself goals. The strong effect of RT on behavior in consistent prosocials (or proselfs) suggests that conflict between prosocial and selfish goals alone is not responsible for slow decisions. Specifically, we found that contemplation of the risk of being exploited by others (social risk aversion) was partly responsible for making consistent prosocials (but not consistent proselfs) spend longer time in decision making and behave less prosocially. Conflict between means rather than between goals (immediate versus strategic pursuit of self-interest) was suggested to be responsible for the time-related increase in consistent proselfs’ prosocial behavior. The findings of this study are generally in favor of the intuitive cooperation model of prosocial behavior. PMID:28559334

Dog’s Discrimination of Human Selfish and Generous Attitudes: The Role of Individual Recognition, Experience, and Experimenters’ Gender

PubMed Central

Carballo, Fabricio; Freidin, Esteban; Putrino, Natalia; Shimabukuro, Carolina; Casanave, Emma; Bentosela, Mariana

2015-01-01

Discrimination of and memory for others’ generous and selfish behaviors could be adaptive abilities in social animals. Dogs have seemingly expressed such skills in both direct and indirect interactions with humans. However, recent studies suggest that their capacity may rely on cues other than people’s individual characteristics, such as the place where the person stands. Thus, the conditions under which dogs recognize individual humans when solving cooperative tasks still remains unclear. With the aim of contributing to this problem, we made dogs interact with two human experimenters, one generous (pointed towards the food, gave ostensive cues, and allowed the dog to eat it) and the other selfish (pointed towards the food, but ate it before the dog could have it). Then subjects could choose between them (studies 1-3). In study 1, dogs took several training trials to learn the discrimination between the generous and the selfish experimenters when both were of the same gender. In study 2, the discrimination was learned faster when the experimenters were of different gender as evidenced both by dogs’ latencies to approach the bowl in training trials as well as by their choices in preference tests. Nevertheless, dogs did not get confused by gender when the experimenters were changed in between the training and the choice phase in study 3. We conclude that dogs spontaneously used human gender as a cue to discriminate between more and less cooperative experimenters. They also relied on some other personal feature which let them avoid being confused by gender when demonstrators were changed. We discuss these results in terms of dogs’ ability to recognize individuals and the potential advantage of this skill for their lives in human environments. PMID:25714915

Virus world as an evolutionary network of viruses and capsidless selfish elements.

PubMed

Koonin, Eugene V; Dolja, Valerian V

2014-06-01

Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus "self" that defines the identity of deep, ancient viral lineages. However, several other widespread viral "hallmark genes" encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Conditions for the Evolution of Gene Clusters in Bacterial Genomes

PubMed Central

Ballouz, Sara; Francis, Andrew R.; Lan, Ruiting; Tanaka, Mark M.

2010-01-01

Genes encoding proteins in a common pathway are often found near each other along bacterial chromosomes. Several explanations have been proposed to account for the evolution of these structures. For instance, natural selection may directly favour gene clusters through a variety of mechanisms, such as increased efficiency of coregulation. An alternative and controversial hypothesis is the selfish operon model, which asserts that clustered arrangements of genes are more easily transferred to other species, thus improving the prospects for survival of the cluster. According to another hypothesis (the persistence model), genes that are in close proximity are less likely to be disrupted by deletions. Here we develop computational models to study the conditions under which gene clusters can evolve and persist. First, we examine the selfish operon model by re-implementing the simulation and running it under a wide range of conditions. Second, we introduce and study a Moran process in which there is natural selection for gene clustering and rearrangement occurs by genome inversion events. Finally, we develop and study a model that includes selection and inversion, which tracks the occurrence and fixation of rearrangements. Surprisingly, gene clusters fail to evolve under a wide range of conditions. Factors that promote the evolution of gene clusters include a low number of genes in the pathway, a high population size, and in the case of the selfish operon model, a high horizontal transfer rate. The computational analysis here has shown that the evolution of gene clusters can occur under both direct and indirect selection as long as certain conditions hold. Under these conditions the selfish operon model is still viable as an explanation for the evolution of gene clusters. PMID:20168992

“Selfish spermatogonial selection”: a novel mechanism for the association between advanced paternal age and neurodevelopmental disorders

PubMed Central

Goriely, Anne; McGrath, John J.; Hultman, Christina M.; Wilkie, Andrew O.M.; Malaspina, Dolores

2014-01-01

Objectives There is robust evidence from epidemiological studies that the offspring of older fathers have an increased risk of neurodevelopmental disorders such as schizophrenia and autism. Here we present a novel mechanism that may contribute to this association. Methods Narrative review. Results Because the male germ cell undergoes many more cell divisions across the reproductive age range, copy-errors taking place in the paternal germline are associated with de novo mutations in the offspring of older men. Recently it has been recognized that somatic mutations in male germ cells that modify proliferation via dysregulation of the RAS pathway can lead to within-testis expansion of mutant clonal lines. First identified in association with rare paternal age-effect disorders (e.g. Apert syndrome, achondroplasia), this process is known as ‘selfish spermatogonial selection’. This mechanism will (a) favor propagation of germ cells carrying pathogenic mutations, (b) increasingly skew the mutational profile of sperm as men age, and (c) result in an enrichment of de novo mutations in the offspring of older fathers that preferentially impact on specific cellular signaling pathways. This mechanism offers a parsimonious explanation not only for the association between advanced paternal age and various neurodevelopmental disorders, but also provides insights into the genetic architecture (role of de novo mutations), neurobiological correlates (altered cell cycle) and some epidemiological features of these disorders. We outline hypotheses to test this model. Conclusions In light of our current understanding of the genetic networks involved in neurocognitive disorders and the principles of selfish spermatogonial selection, we speculate that some pathogenic mutations associated with these disorders are the consequence of a selfish mechanism originating in the aging testis. Given the secular changes for delayed parenthood in most societies, this hypothesis has important public health implications. PMID:23639989

Dog's discrimination of human selfish and generous attitudes: the role of individual recognition, experience, and experimenters' gender.

PubMed

Carballo, Fabricio; Freidin, Esteban; Putrino, Natalia; Shimabukuro, Carolina; Casanave, Emma; Bentosela, Mariana

2015-01-01

Discrimination of and memory for others' generous and selfish behaviors could be adaptive abilities in social animals. Dogs have seemingly expressed such skills in both direct and indirect interactions with humans. However, recent studies suggest that their capacity may rely on cues other than people's individual characteristics, such as the place where the person stands. Thus, the conditions under which dogs recognize individual humans when solving cooperative tasks still remains unclear. With the aim of contributing to this problem, we made dogs interact with two human experimenters, one generous (pointed towards the food, gave ostensive cues, and allowed the dog to eat it) and the other selfish (pointed towards the food, but ate it before the dog could have it). Then subjects could choose between them (studies 1-3). In study 1, dogs took several training trials to learn the discrimination between the generous and the selfish experimenters when both were of the same gender. In study 2, the discrimination was learned faster when the experimenters were of different gender as evidenced both by dogs' latencies to approach the bowl in training trials as well as by their choices in preference tests. Nevertheless, dogs did not get confused by gender when the experimenters were changed in between the training and the choice phase in study 3. We conclude that dogs spontaneously used human gender as a cue to discriminate between more and less cooperative experimenters. They also relied on some other personal feature which let them avoid being confused by gender when demonstrators were changed. We discuss these results in terms of dogs' ability to recognize individuals and the potential advantage of this skill for their lives in human environments.

Suicide and the selfish gene.

PubMed

Satora, Leszek

2005-01-01

The application of an evolutionary perspective to human behaviour generates philosophical, political and scientific controversy. Modern human symbolic consciousness is not the cumulation of the long trend that natural selection would predict. The new archaeological data suggested the anatomical and behavioural innovation has been episodic and rare separated by long periods of stagnate. New behavioural mode and the new skeletal structure of modem human arose as an incidental exaptation. Additionally the genetic basis dysfunction connected with suicide behaviour and growing statistic suicide among teenager is contradictory to the theory that our behaviour are programmed in any detail by selfish genes. In this cases genetically determined suicidal behaviour should be rapidly eliminated by natural selection.

Trust recovery model of Ad Hoc network based on identity authentication scheme

NASA Astrophysics Data System (ADS)

Liu, Jie; Huan, Shuiyuan

2017-05-01

Mobile Ad Hoc network trust model is widely used to solve mobile Ad Hoc network security issues. Aiming at the problem of reducing the network availability caused by the processing of malicious nodes and selfish nodes in mobile Ad Hoc network routing based on trust model, an authentication mechanism based on identity authentication mobile Ad Hoc network is proposed, which uses identity authentication to identify malicious nodes, And trust the recovery of selfish nodes in order to achieve the purpose of reducing network congestion and improving network quality. The simulation results show that the implementation of the mechanism can effectively improve the network availability and security.

Relatedness and the fraternal major transitions.

PubMed Central

Queller, D C

2000-01-01

Many of the major transitions in evolution involved the coalescence of independent lower-level units into a higher organismal level. This paper examines the role of kinship, focusing on the transitions to multicellularity in animals and to coloniality in insects. In both, kin selection based on high relatedness permitted cooperation and a reproductive division of labour. The higher relatedness of haplodiploid females to their sisters than to their offspring might not have been crucial in the origin of insect societies, and the transition to multicellularity shows that such special relationships are not required. When multicellular forms develop from a single cell, selfish conflict is minimal because each selfish mutant obtains only one generation of within-individual advantage in a chimaera. Conditionally expressed traits are particularly immune to within-individual selfishness because such mutations are rarely expressed in chimaeras. Such conditionally expressed altruism genes lead easily to the evolution of the soma, and the germ line might simply be what is left over. In most social insects, differences in relatedness ensure that there will be potential conflicts. Power asymmetries sometimes lead to such decisive settlements of conflicts that social insect colonies can be considered to be fully organismal. PMID:11127911

Resistance to extreme strategies, rather than prosocial preferences, can explain human cooperation in public goods games.

PubMed

Kümmerli, Rolf; Burton-Chellew, Maxwell N; Ross-Gillespie, Adin; West, Stuart A

2010-06-01

The results of numerous economic games suggest that humans behave more cooperatively than would be expected if they were maximizing selfish interests. It has been argued that this is because individuals gain satisfaction from the success of others, and that such prosocial preferences require a novel evolutionary explanation. However, in previous games, imperfect behavior would automatically lead to an increase in cooperation, making it impossible to decouple any form of mistake or error from prosocial cooperative decisions. Here we empirically test between these alternatives by decoupling imperfect behavior from prosocial preferences in modified versions of the public goods game, in which individuals would maximize their selfish gain by completely (100%) cooperating. We found that, although this led to higher levels of cooperation, it did not lead to full cooperation, and individuals still perceived their group mates as competitors. This is inconsistent with either selfish or prosocial preferences, suggesting that the most parsimonious explanation is imperfect behavior triggered by psychological drives that can prevent both complete defection and complete cooperation. More generally, our results illustrate the caution that must be exercised when interpreting the evolutionary implications of economic experiments, especially the absolute level of cooperation in a particular treatment.

Guilty repair sustains cooperation, angry retaliation destroys it

PubMed Central

Skatova, Anya; Spence, Alexa; Leygue, Caroline; Ferguson, Eamonn

2017-01-01

Sustained cooperative social interactions are key to successful outcomes in many real-world contexts (e.g., climate change and energy conservation). We explore the self-regulatory roles of anger and guilt, as well as prosocial or selfish social preferences in a repeated social dilemma game framed around shared electricity use at home. We explore the proposal that for sustained cooperation, guilty repair needs to override angry retaliation. We show that anger is damaging to cooperation as it leads to retaliation and an increase of defection, while, through guilt, cooperation is repaired resulting in higher levels of cooperation. We demonstrate a disconnect between the experience of anger and subsequent retaliation which is a function of participants’ social preferences. While there is no difference in reports of anger between prosocial and selfish individuals after finding out that others use more energy from the communal resource, prosocials are less likely to act on their anger and retaliate. Selfish individuals are motivated by anger to retaliate but not motivated by guilt to repair and contribute disproportionately to the breakdown of cooperation over repeated interactions. We suggest that guilt is a key emotion to appeal to when encouraging cooperation. PMID:28447613

Selfish prion of Rnq1 mutant in yeast.

PubMed

Kurahashi, Hiroshi; Shibata, Shoichiro; Ishiwata, Masao; Nakamura, Yoshikazu

2009-05-01

[PIN(+)] is a prion form of Rnq1 in Saccharomyces cerevisiae and is necessary for the de novo induction of a second prion, [PSI(+)]. We previously isolated a truncated form of Rnq1, named Rnq1Delta100, as a [PSI(+)]-eliminating factor in S. cerevisiae. Rnq1Delta100 deletes the N-terminal non-prion domain of Rnq1, and eliminates [PSI(+)] in [PIN(+)] yeast. Here we found that [PIN(+)] is transmissible to Rnq1Delta100 in the absence of full-length Rnq1, forming a novel prion variant [RNQ1Delta100(+)]. [RNQ1Delta100(+)] has similar [PIN(+)] properties as it stimulates the de novo induction of [PSI(+)] and is eliminated by the null hsp104Delta mutation, but not by Hsp104 overproduction. In contrast, [RNQ1Delta100(+)] inherits the inhibitory activity and hampers the maintenance of [PSI(+)] though less efficiently than [PIN(+)] made of Rnq1-Rnq1Delta100 co-aggregates. Interestingly, [RNQ1Delta100(+)] prion was eliminated by de novo [PSI(+)] induction. Thus, the [RNQ1Delta100(+)] prion demonstrates selfish activity to eliminate a heterologous prion in S. cerevisiae, showing the first instance of a selfish prion variant in living organisms.

Symmetry warrants rational cooperation by co-action in Social Dilemmas.

PubMed

Sasidevan, V; Sinha, Sitabhra

2015-08-12

Is it rational for selfish individuals to cooperate? The conventional answer based on analysis of games such as the Prisoners Dilemma (PD) is that it is not, even though mutual cooperation results in a better outcome for all. This incompatibility between individual rationality and collective benefit lies at the heart of questions about the evolution of cooperation, as illustrated by PD and similar games. Here, we argue that this apparent incompatibility is due to an inconsistency in the standard Nash framework for analyzing non-cooperative games and propose a new paradigm, that of the co-action equilibrium. As in the Nash solution, agents know that others are just as rational as them and taking this into account lead them to realize that others will independently adopt the same strategy, in contrast to the idea of unilateral deviation central to Nash equilibrium thinking. Co-action equilibrium results in better collective outcomes for games representing social dilemmas, with relatively "nicer" strategies being chosen by rational selfish individuals. In particular, the dilemma of PD gets resolved within this framework, suggesting that cooperation can evolve in nature as the rational outcome even for selfish agents, without having to take recourse to additional mechanisms for promoting it.

To qualify as a social partner, humans hide severe punishment, although their observed cooperativeness is decisive.

PubMed

Rockenbach, Bettina; Milinski, Manfred

2011-11-08

Conflicts of interest between the community and its members are at the core of human social dilemmas. If observed selfishness has future costs, individuals may hide selfish acts but display altruistic ones, and peers aim at identifying the most selfish persons to avoid them as future social partners. An interaction involving hiding and seeking information may be inevitable. We staged an experimental social-dilemma game in which actors could pay to conceal information about their contribution, giving, and punishing decisions from an observer who selects her future social partners from the actors. The observer could pay to conceal her observation of the actors. We found sophisticated dynamic strategies on either side. Actors hide their severe punishment and low contributions but display high contributions. Observers select high contributors as social partners; remarkably, punishment behavior seems irrelevant for qualifying as a social partner. That actors nonetheless pay to conceal their severe punishment adds a further puzzle to the role of punishment in human social behavior. Competition between hiding and seeking information about social behavior may be even more relevant and elaborate in the real world but usually is hidden from our eyes.

Bacteria and game theory: the rise and fall of cooperation in spatially heterogeneous environments.

PubMed

Lambert, Guillaume; Vyawahare, Saurabh; Austin, Robert H

2014-08-06

One of the predictions of game theory is that cooperative behaviours are vulnerable to exploitation by selfish individuals, but this result seemingly contradicts the survival of cooperation observed in nature. In this review, we will introduce game theoretical concepts that lead to this conclusion and show how the spatial competition dynamics between microorganisms can be used to model the survival and maintenance of cooperation. In particular, we focus on how Escherichia coli bacteria with a growth advantage in stationary phase (GASP) phenotype maintain a proliferative phenotype when faced with overcrowding to gain a fitness advantage over wild-type populations. We review recent experimental approaches studying the growth dynamics of competing GASP and wild-type strains of E. coli inside interconnected microfabricated habitats and use a game theoretical approach to analyse the observed inter-species interactions. We describe how the use of evolutionary game theory and the ideal free distribution accurately models the spatial distribution of cooperative and selfish individuals in spatially heterogeneous environments. Using bacteria as a model system of cooperative and selfish behaviours may lead to a better understanding of the competition dynamics of other organisms-including tumour-host interactions during cancer development and metastasis.

nanos-Driven expression of piggyBac transposase induces mobilization of a synthetic autonomous transposon in the malaria vector mosquito, Anopheles stephensi.

PubMed

Macias, Vanessa M; Jimenez, Alyssa J; Burini-Kojin, Bianca; Pledger, David; Jasinskiene, Nijole; Phong, Celine Hien; Chu, Karen; Fazekas, Aniko; Martin, Kelcie; Marinotti, Osvaldo; James, Anthony A

2017-08-01

Transposons are a class of selfish DNA elements that can mobilize within a genome. If mobilization is accompanied by an increase in copy number (replicative transposition), the transposon may sweep through a population until it is fixed in all of its interbreeding members. This introgression has been proposed as the basis for drive systems to move genes with desirable phenotypes into target species. One such application would be to use them to move a gene conferring resistance to malaria parasites throughout a population of vector mosquitos. We assessed the feasibility of using the piggyBac transposon as a gene-drive mechanism to distribute anti-malarial transgenes in populations of the malaria vector, Anopheles stephensi. We designed synthetic gene constructs that express the piggyBac transposase in the female germline using the control DNA of the An. stephensi nanos orthologous gene linked to marker genes to monitor inheritance. Two remobilization events were observed with a frequency of one every 23 generations, a rate far below what would be useful to drive anti-pathogen transgenes into wild mosquito populations. We discuss the possibility of optimizing this system and the impetus to do so. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Yeast cohesin complex embraces 2 micron plasmid sisters in a tri-linked catenane complex

PubMed Central

Ghosh, Santanu K.; Huang, Chu-Chun; Hajra, Sujata; Jayaram, Makkuni

2010-01-01

Sister chromatid cohesion, crucial for faithful segregation of replicated chromosomes in eukaryotes, is mediated by the multi-subunit protein complex cohesin. The Saccharomyces cerevisiae plasmid 2 micron circle mimics chromosomes in assembling cohesin at its partitioning locus. The plasmid is a multi-copy selfish DNA element that resides in the nucleus and propagates itself stably, presumably with assistance from cohesin. In metaphase cell lysates, or fractions enriched for their cohesed state by sedimentation, plasmid molecules are trapped topologically by the protein ring formed by cohesin. They can be released from cohesin’s embrace either by linearizing the DNA or by cleaving a cohesin subunit. Assays using two distinctly tagged cohesin molecules argue against the hand-cuff (an associated pair of monomeric cohesin rings) or the bracelet (a dimeric cohesin ring) model as responsible for establishing plasmid cohesion. Our cumulative results most easily fit a model in which a single monomeric cohesin ring, rather than a series of such rings, conjoins a pair of sister plasmids. These features of plasmid cohesion account for its sister-to-sister mode of segregation by cohesin disassembly during anaphase. The mechanistic similarities of cohesion between mini-chromosome sisters and 2 micron plasmid sisters suggest a potential kinship between the plasmid partitioning locus and centromeres. PMID:19920123

Sperm competition, immunity, selfish genes and cancer.

PubMed

Lewis, Z; Price, T A R; Wedell, N

2008-10-01

Sperm competition is widespread and has played an important role in shaping male reproductive characters such as testis size and numbers of sperm produced, and this is reflected in the rapid evolution of many reproductive genes. Additionally, sperm competition has been implicated in the rapid evolution of seminal fluids. However, our understanding of the molecular basis of many traits thought to be important in sperm competition is rudimentary. Furthermore, links between sperm competition and a range of issues not directly related to reproduction are only just beginning to be explored. These include associations between sperm competition and selfish genes, immunity and diseases such as cancer.We briefly review these topics and suggest areas we consider worthy of additional research.

Selfishness, fraternity, and other-regarding preference in spatial evolutionary games.

PubMed

Szabó, György; Szolnoki, Attila

2012-04-21

Spatial evolutionary games are studied with myopic players whose payoff interest, as a personal character, is tuned from selfishness to other-regarding preference via fraternity. The players are located on a square lattice and collect income from symmetric two-person two-strategy (called cooperation and defection) games with their nearest neighbors. During the elementary steps of evolution a randomly chosen player modifies her strategy in order to maximize stochastically her utility function composed from her own and the co-players' income with weight factors 1-Q and Q. These models are studied within a wide range of payoff parameters using Monte Carlo simulations for noisy strategy updates and by spatial stability analysis in the low noise limit. For fraternal players (Q=1/2) the system evolves into ordered arrangements of strategies in the low noise limit in a way providing optimum payoff for the whole society. Dominance of defectors, representing the "tragedy of the commons", is found within the regions of prisoner's dilemma and stag hunt game for selfish players (Q=0). Due to the symmetry in the effective utility function the system exhibits similar behavior even for Q=1 that can be interpreted as the "lovers' dilemma". Copyright © 2011 Elsevier Ltd. All rights reserved.

Living Emotions, Avoiding Emotions: Behavioral Investigation of the Regulation of Socially Driven Emotions

PubMed Central

Grecucci, Alessandro; Giorgetta, Cinzia; Bonini, Nicolao; Sanfey, Alan G.

2013-01-01

Emotion regulation is important for psychological well-being. Although it is known that alternative regulation strategies may have different emotional consequences, the effectiveness of such strategies for socially driven emotions remains unclear. In this study we investigated the efficacy of different forms of reappraisal on responses to the selfish and altruistic behavior of others in the Dictator Game. In Experiment 1, subjects mentalized the intentions of the other player in one condition, and took distance from the situation in the other. Emotion ratings were recorded after each offer. Compared with a baseline condition, mentalizing led subjects to experience their emotions more positively when receiving both selfish and altruistic proposals, whereas distancing decreased the valence when receiving altruistic offers, but did not affect the perception of selfish behavior. In Experiment 2, subjects played with both computer and human partners while reappraising the meaning of the player’s intentions (with a human partner) or the meaning of the situation (with a computer partner). Results showed that both contexts were effectively modulated by reappraisal, however a stronger effect was observed when the donor was a human partner, as compared to a computer partner. Taken together, these results demonstrate that socially driven emotions can be successfully modulated by reappraisal strategies that focus on the reinterpretation of others’ intentions. PMID:23349645

Selfish evolution of cytonuclear hybrid incompatibility in Mimulus

PubMed Central

Finseth, Findley R.; Barr, Camille M.; Fishman, Lila

2016-01-01

Intraspecific coevolution between selfish elements and suppressors may promote interspecific hybrid incompatibility, but evidence of this process is rare. Here, we use genomic data to test alternative models for the evolution of cytonuclear hybrid male sterility in Mimulus. In hybrids between Iron Mountain (IM) Mimulus guttatus × Mimulus nasutus, two tightly linked M. guttatus alleles (Rf1/Rf2) each restore male fertility by suppressing a local mitochondrial male-sterility gene (IM-CMS). Unlike neutral models for the evolution of hybrid incompatibility loci, selfish evolution predicts that the Rf alleles experienced strong selection in the presence of IM-CMS. Using whole-genome sequences, we compared patterns of population-genetic variation in Rf at IM to a neighbouring population that lacks IM-CMS. Consistent with local selection in the presence of IM-CMS, the Rf region shows elevated FST, high local linkage disequilibrium and a distinct haplotype structure at IM, but not at Cone Peak (CP), suggesting a recent sweep in the presence of IM-CMS. In both populations, Rf2 exhibited lower polymorphism than other regions, but the low-diversity outliers were different between CP and IM. Our results confirm theoretical predictions of ubiquitous cytonuclear conflict in plants and provide a population-genetic mechanism for the evolution of a common form of hybrid incompatibility. PMID:27629037

Sexual selection, genetic conflict, selfish genes, and the atypical patterns of gene expression in spermatogenic cells.

PubMed

Kleene, Kenneth C

2005-01-01

This review proposes that the peculiar patterns of gene expression in spermatogenic cells are the consequence of powerful evolutionary forces known as sexual selection. Sexual selection is generally characterized by intense competition of males for females, an enormous variety of the strategies to maximize male reproductive success, exaggerated male traits at all levels of biological organization, co-evolution of sexual traits in males and females, and conflict between the sexual advantage of the male trait and the reproductive fitness of females and the individual fitness of both sexes. In addition, spermatogenesis is afflicted by selfish genes that promote their transmission to progeny while causing deleterious effects. Sexual selection, selfish genes, and genetic conflict provide compelling explanations for many atypical features of gene expression in spermatogenic cells including the gross overexpression of certain mRNAs, transcripts encoding truncated proteins that cannot carry out basic functions of the proteins encoded by the same genes in somatic cells, the large number of gene families containing paralogous genes encoding spermatogenic cell-specific isoforms, the large number of testis-cancer-associated genes that are expressed only in spermatogenic cells and malignant cells, and the overbearing role of Sertoli cells in regulating the number and quality of spermatozoa.

Centromere-associated meiotic drive and female fitness variation in Mimulus.

PubMed

Fishman, Lila; Kelly, John K

2015-05-01

Female meiotic drive, in which chromosomal variants preferentially segregate to the egg pole during asymmetric female meiosis, is a theoretically pervasive but still mysterious form of selfish evolution. Like other selfish genetic elements, driving chromosomes may be maintained as balanced polymorphisms by pleiotropic or linked fitness costs. A centromere-associated driver (D) with a ∼58:42 female-specific transmission advantage occurs at intermediate frequency (32-40%) in the Iron Mountain population of the yellow monkeyflower, Mimulus guttatus. Previously determined male fertility costs are sufficient to prevent the fixation of D, but predict a higher equilibrium frequency. To better understand the dynamics and effects of D, we developed a new population genetic model and measured genotype-specific lifetime female fitness in the wild. In three of four years, and across all years, D imposed significant recessive seedset costs, most likely due to hitchhiking by deleterious mutations. With both male and female costs as measured, and 58:42 drive, our model predicts an equilibrium frequency of D (38%) very close to the observed value. Thus, D represents a rare selfish genetic element whose local population genetic dynamics have been fully parameterized, and the observation of equilibrium sets the stage for investigations of coevolution with suppressors. © 2015 The Author(s).

Origin, evolution, and population genetics of the selfish Segregation Distorter gene duplication in European and African populations of Drosophila melanogaster.

PubMed

Brand, Cara L; Larracuente, Amanda M; Presgraves, Daven C

2015-05-01

Meiotic drive elements are a special class of evolutionarily "selfish genes" that subvert Mendelian segregation to gain preferential transmission at the expense of homologous loci. Many drive elements appear to be maintained in populations as stable polymorphisms, their equilibrium frequencies determined by the balance between drive (increasing frequency) and selection (decreasing frequency). Here we show that a classic, seemingly balanced, drive system is instead characterized by frequent evolutionary turnover giving rise to dynamic, rather than stable, equilibrium frequencies. The autosomal Segregation Distorter (SD) system of the fruit fly Drosophila melanogaster is a selfish coadapted meiotic drive gene complex in which the major driver corresponds to a partial duplication of the gene Ran-GTPase activating protein (RanGAP). SD chromosomes segregate at similar, low frequencies of 1-5% in natural populations worldwide, consistent with a balanced polymorphism. Surprisingly, our population genetic analyses reveal evidence for parallel, independent selective sweeps of different SD chromosomes in populations on different continents. These findings suggest that, rather than persisting at a single stable equilibrium, SD chromosomes turn over frequently within populations. © 2015 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Promiscuous honey bee queens increase colony productivity by suppressing worker selfishness.

PubMed

Mattila, Heather R; Reeve, H Kern; Smith, Michael L

2012-11-06

Queen monogamy is ancestral among bees, ants, and wasps (Order Hymenoptera), and the close relatedness that it generates within colonies is considered key for the evolution of eusociality in these lineages. Paradoxically, queens of several eusocial species are extremely promiscuous, a derived behavior that decreases relatedness among workers and fitness gained from rearing siblings but benefits queens by enhancing colony productivity and inducing workers to rear queens' sons instead of less related worker-derived males. Selection for promiscuity would be especially strong if productivity in a singly inseminated queen's colony declined because selfish workers invested in personal reproduction at the expense of performing tasks that contribute to colony productivity. We show in honey bees that workers' ovaries are more developed when queens are singly rather than multiply inseminated and that increasing ovary activation is coupled with reductions in task performance by workers and colony-wide rates of foraging and waggle-dance recruitment. Increased investment in reproductive physiology by selfish workers might result from greater incentive for them to favor worker-derived males or because low mating frequency signals a queen's diminished quality or future fecundity. Either possibility fosters selection for queen promiscuity, revealing a novel benefit of it for eusocial insects. Copyright © 2012 Elsevier Ltd. All rights reserved.

The Physical Layer Security Experiments of Cooperative Communication System with Different Relay Behaviors.

PubMed

Su, Yishan; Han, Guangyao; Fu, Xiaomei; Xu, Naishen; Jin, Zhigang

2017-04-06

Physical layer security is an attractive security mechanism, which exploits the randomness characteristics of wireless transmission channel to achieve security. However, it is hampered by the limitation of the channel condition that the main channel must be better than the eavesdropper channel. To alleviate the limitation, cooperative communication is introduced. Few studies have investigated the physical layer security of the relay transmission model. In this paper, we performed some experiments to evaluate the physical layer security of a cooperative communication system, with a relay operating in decode-and-forward (DF) cooperative mode, selfish and malicious behavior in real non-ideal transmission environment. Security performance is evaluated in terms of the probability of non-zero secrecy capacity. Experiments showed some different results compared to theoretical simulation: (1) to achieve the maximum secrecy capacity, the optimal relay power according to the experiments result is larger than that of ideal theoretical results under both cooperative and selfish behavior relay; (2) the relay in malicious behavior who forwards noise to deteriorate the main channel may deteriorate the eavesdropper channel more seriously than the main channel; (3) the optimal relay positions under cooperative and selfish behavior relay cases are both located near the destination because of non-ideal transmission.

Selfish evolution of cytonuclear hybrid incompatibility in Mimulus.

PubMed

Case, Andrea L; Finseth, Findley R; Barr, Camille M; Fishman, Lila

2016-09-14

Intraspecific coevolution between selfish elements and suppressors may promote interspecific hybrid incompatibility, but evidence of this process is rare. Here, we use genomic data to test alternative models for the evolution of cytonuclear hybrid male sterility in Mimulus In hybrids between Iron Mountain (IM) Mimulus guttatus × Mimulus nasutus, two tightly linked M. guttatus alleles (Rf1/Rf2) each restore male fertility by suppressing a local mitochondrial male-sterility gene (IM-CMS). Unlike neutral models for the evolution of hybrid incompatibility loci, selfish evolution predicts that the Rf alleles experienced strong selection in the presence of IM-CMS. Using whole-genome sequences, we compared patterns of population-genetic variation in Rf at IM to a neighbouring population that lacks IM-CMS. Consistent with local selection in the presence of IM-CMS, the Rf region shows elevated FST, high local linkage disequilibrium and a distinct haplotype structure at IM, but not at Cone Peak (CP), suggesting a recent sweep in the presence of IM-CMS. In both populations, Rf2 exhibited lower polymorphism than other regions, but the low-diversity outliers were different between CP and IM. Our results confirm theoretical predictions of ubiquitous cytonuclear conflict in plants and provide a population-genetic mechanism for the evolution of a common form of hybrid incompatibility. © 2016 The Author(s).

Dogs’ recognition of human selfish and generous attitudes requires little but critical experience with people

PubMed Central

Freidin, Esteban; Casanave, Emma B.

2017-01-01

There is some dispute regarding the role of experience in the development of dogs´ socio-cognitive abilities in their interaction with people. We sought to provide new evidence to this debate by comparing dogs with contrasting levels of experience with humans, in a task involving the discrimination of human generous and selfish attitudes. To this end, we compared the performance of adult family dogs against that of adult shelter dogs and puppies living in people´s homes. In training trials, the generous experimenter (G) signaled the bowl with food and allowed the dog to eat, whereas the selfish experimenter (S) also signaled the baited bowl, but she/he ate the food before the dog could have access to it. Then, subjects were allowed to freely choose between G and S in the choice test. The main finding was that adult subjects (both family and shelter dogs) developed a preference for G over S, but puppies did not. We conclude that the quality and/or quantity of everyday-contact with people did not affect the discrimination of human attitudes in the present protocol, but the amount of experience with people (in years) did matter. Finally, we discuss the relative role of domestication and ontogeny in the development of dogs´ socio-cognitive abilities. PMID:29045426

Adherence and the Lie in a HIV Prevention Clinical Trial

PubMed Central

Stadler, Jonathan; Scorgie, Fiona; van der Straten, Ariane; Saethre, Eirik

2016-01-01

The lie has been presented as a performance that protects identities against moral judgment in the context of power imbalances. We explore this assertion from the perspective of a pre-exposure prophylaxis trial to prevent HIV for African women in South Africa, in which context biological evidence of widespread lying about product adherence was produced, resulting in a moral discourse that opposed altruistic and selfish motivations. In this article, we seek to understand the meaning of the lie from the perspective of women trial participants. Seeing the trial as representing a hopeful future, and perfect adherence as sustaining their investment in this, participants recited scripted accounts of adherence and performed the role of the perfect adherer, while identifying other participants as dishonest. Given that clinical trials create moral orders and adherence is key to this, we argue that women embraced the apparatus of the clinical trial to assert their moral subjectivities. PMID:26575611

The tripartite immune conflict in placentals and a hypothesis on fetal-->maternal microchimerism.

PubMed

Apari, Péter; Rózsa, Lajos

2009-01-01

There is a two-way traffic of immune cells through the placenta; and fetal immune cells are often present in the maternal body even long after giving birth. We present an adaptationist theory to interpret fetal-->maternal microchimerism and the diverse set of concomitant medical phenomena. We handle fetal, maternal, and paternal adaptive interests separately and in interaction with one another. Fetuses may benefit from immunological information gathered by migrant cells in the maternal body, and also from improved maternal defence. However, they may be jeopardized by a selfish maternal usage of fetal-->maternal microchimerism - i.e., some mothers get pregnant only to improve their immune system and then to abort. The use of microchimeric cells by the maternal immune system may contribute to the adaptive benefits of female choosiness and polyandry. While fathers may enjoy an indirect benefit from enhanced fetal and maternal health, they also face the risk of wasting sexual efforts due to selfish pregnancies of cheating females. Paternal alleles acting via clones of microchimeric cells in the maternal body could launch an immunological attack against the non-kin sperm in the female genitalia, or against the non-kin fetus in the womb. Furthermore, an intraspecific version of Zahavi's Mafia Hypothesis could explain a potential interaction between the abortion of fetuses and a subsequent rise of an autoimmune disease. We suggest that males may be capable to provoke microchimerism-induced autoimmune-like diseases in the mother in revenge of selfish pregnancies. This hypothetic paternal threat could increase the maternal costs associated to selfish pregnancies. From a medical point of view, we propose new interpretations for autoimmune-like diseases, infertility, miscarriage, and also for the prevailing connections among them. Specifically, we argue that miscarriages may cause autoimmune diseases, a reversed causality as compared to the currently accepted one.

Evolution beyond neo-Darwinism: a new conceptual framework.

PubMed

Noble, Denis

2015-01-01

Experimental results in epigenetics and related fields of biological research show that the Modern Synthesis (neo-Darwinist) theory of evolution requires either extension or replacement. This article examines the conceptual framework of neo-Darwinism, including the concepts of 'gene', 'selfish', 'code', 'program', 'blueprint', 'book of life', 'replicator' and 'vehicle'. This form of representation is a barrier to extending or replacing existing theory as it confuses conceptual and empirical matters. These need to be clearly distinguished. In the case of the central concept of 'gene', the definition has moved all the way from describing a necessary cause (defined in terms of the inheritable phenotype itself) to an empirically testable hypothesis (in terms of causation by DNA sequences). Neo-Darwinism also privileges 'genes' in causation, whereas in multi-way networks of interactions there can be no privileged cause. An alternative conceptual framework is proposed that avoids these problems, and which is more favourable to an integrated systems view of evolution. © 2015. Published by The Company of Biologists Ltd.

Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements.

PubMed

Brunet, Tyler D P; Doolittle, W Ford

2015-08-06

One of several issues at play in the renewed debate over "junk DNA" is the organizational level at which genomic features might be seen as selected, and thus to exhibit function, as etiologically defined. The intuition frequently expressed by molecular geneticists that junk DNA is functional because it serves to "speed evolution" or as an "evolutionary repository" could be recast as a claim about selection between species (or clades) rather than within them, but this is not often done. Here, we review general arguments for the importance of selection at levels above that of organisms in evolution, and develop them further for a common genomic feature: the carriage of transposable elements (TEs). In many species, not least our own, TEs comprise a large fraction of all nuclear DNA, and whether they individually or collectively contribute to fitness--or are instead junk--is a subject of ongoing contestation. Even if TEs generally owe their origin to selfish selection at the lowest level (that of genomes), their prevalence in extant organisms and the prevalence of extant organisms bearing them must also respond to selection within species (on organismal fitness) and between species (on rates of speciation and extinction). At an even higher level, the persistence of clades may be affected (positively or negatively) by TE carriage. If indeed TEs speed evolution, it is at these higher levels of selection that such a function might best be attributed to them as a class. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Resource heterogeneity can facilitate cooperation.

PubMed

Kun, Ádám; Dieckmann, Ulf

2013-01-01

Although social structure is known to promote cooperation, by locally exposing selfish agents to their own deeds, studies to date assumed that all agents have access to the same level of resources. This is clearly unrealistic. Here we find that cooperation can be maintained when some agents have access to more resources than others. Cooperation can then emerge even in populations in which the temptation to defect is so strong that players would act fully selfishly if their resources were distributed uniformly. Resource heterogeneity can thus be crucial for the emergence and maintenance of cooperation. We also show that resource heterogeneity can hinder cooperation once the temptation to defect is significantly lowered. In all cases, the level of cooperation can be maximized by managing resource heterogeneity.

The dynamics of behavior in modified dictator games

PubMed Central

2017-01-01

We investigate the dynamics of individual pro-social behavior over time. The dynamics are tested by running the same experiment with the same subjects at several points in time. To exclude learning and reputation building, we employ non-strategic decision tasks and a sequential prisoners-dilemma as a control treatment. In the first wave, pro-social concerns explain a high share of individual decisions. Pro-social decisions decrease over time, however. In the final wave, most decisions can be accounted for by assuming pure selfishness. Stable behavior in the sense that subjects stick to their decisions over time is observed predominantly for purely selfish subjects. We offer two explanation for our results: diminishing experimenter demand effects and moral self-licensing. PMID:28448506

Selfish genetic elements, genetic conflict, and evolutionary innovation.

PubMed

Werren, John H

2011-06-28

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible "evolutionary functions" of SGEs.

Selfish genetic elements, genetic conflict, and evolutionary innovation

PubMed Central

Werren, John H.

2011-01-01

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible “evolutionary functions” of SGEs. PMID:21690392

Scar-less multi-part DNA assembly design automation

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

Hillson, Nathan J.

The present invention provides a method of a method of designing an implementation of a DNA assembly. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding flanking homology sequences to each of the DNA oligos. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which tomore » assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding optimized overhang sequences to each of the DNA oligos.« less

Replication-dependent and independent mechanisms for the chromosome-coupled persistence of a selfish genome.

PubMed

Liu, Yen-Ting; Chang, Keng-Ming; Ma, Chien-Hui; Jayaram, Makkuni

2016-09-30

The yeast 2-micron plasmid epitomizes the evolutionary optimization of selfish extra-chromosomal genomes for stable persistence without jeopardizing their hosts' fitness. Analyses of fluorescence-tagged single-copy reporter plasmids and/or the plasmid partitioning proteins in native and non-native hosts reveal chromosome-hitchhiking as the likely means for plasmid segregation. The contribution of the partitioning system to equal segregation is bipartite- replication-independent and replication-dependent. The former nearly eliminates 'mother bias' (preferential plasmid retention in the mother cell) according to binomial distribution, thus limiting equal segregation of a plasmid pair to 50%. The latter enhances equal segregation of plasmid sisters beyond this level, elevating the plasmid close to chromosome status. Host factors involved in plasmid partitioning can be functionally separated by their participation in the replication-independent and/or replication-dependent steps. In the hitchhiking model, random tethering of a pair of plasmids to chromosomes signifies the replication-independent component of segregation; the symmetric tethering of plasmid sisters to sister chromatids embodies the replication-dependent component. The 2-micron circle broadly resembles the episomes of certain mammalian viruses in its chromosome-associated propagation. This unifying feature among otherwise widely differing selfish genomes suggests their evolutionary convergence to the common logic of exploiting, albeit via distinct molecular mechanisms, host chromosome segregation machineries for self-preservation. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Replication-dependent and independent mechanisms for the chromosome-coupled persistence of a selfish genome

PubMed Central

Liu, Yen-Ting; Chang, Keng-Ming; Ma, Chien-Hui; Jayaram, Makkuni

2016-01-01

The yeast 2-micron plasmid epitomizes the evolutionary optimization of selfish extra-chromosomal genomes for stable persistence without jeopardizing their hosts’ fitness. Analyses of fluorescence-tagged single-copy reporter plasmids and/or the plasmid partitioning proteins in native and non-native hosts reveal chromosome-hitchhiking as the likely means for plasmid segregation. The contribution of the partitioning system to equal segregation is bipartite- replication-independent and replication-dependent. The former nearly eliminates ‘mother bias’ (preferential plasmid retention in the mother cell) according to binomial distribution, thus limiting equal segregation of a plasmid pair to 50%. The latter enhances equal segregation of plasmid sisters beyond this level, elevating the plasmid close to chromosome status. Host factors involved in plasmid partitioning can be functionally separated by their participation in the replication-independent and/or replication-dependent steps. In the hitchhiking model, random tethering of a pair of plasmids to chromosomes signifies the replication-independent component of segregation; the symmetric tethering of plasmid sisters to sister chromatids embodies the replication-dependent component. The 2-micron circle broadly resembles the episomes of certain mammalian viruses in its chromosome-associated propagation. This unifying feature among otherwise widely differing selfish genomes suggests their evolutionary convergence to the common logic of exploiting, albeit via distinct molecular mechanisms, host chromosome segregation machineries for self-preservation. PMID:27492289

LINE-1 retrotransposons: from 'parasite' sequences to functional elements.

PubMed

Paço, Ana; Adega, Filomena; Chaves, Raquel

2015-02-01

Long interspersed nuclear elements-1 (LINE-1) are the most abundant and active retrotransposons in the mammalian genomes. Traditionally, the occurrence of LINE-1 sequences in the genome of mammals has been explained by the selfish DNA hypothesis. Nevertheless, recently, it has also been argued that these sequences could play important roles in these genomes, as in the regulation of gene expression, genome modelling and X-chromosome inactivation. The non-random chromosomal distribution is a striking feature of these retroelements that somehow reflects its functionality. In the present study, we have isolated and analysed a fraction of the open reading frame 2 (ORF2) LINE-1 sequence from three rodent species, Cricetus cricetus, Peromyscus eremicus and Praomys tullbergi. Physical mapping of the isolated sequences revealed an interspersed longitudinal AT pattern of distribution along all the chromosomes of the complement in the three genomes. A detailed analysis shows that these sequences are preferentially located in the euchromatic regions, although some signals could be detected in the heterochromatin. In addition, a coincidence between the location of imprinted gene regions (as Xist and Tsix gene regions) and the LINE-1 retroelements was also observed. According to these results, we propose an involvement of LINE-1 sequences in different genomic events as gene imprinting, X-chromosome inactivation and evolution of repetitive sequences located at the heterochromatic regions (e.g. satellite DNA sequences) of the rodents' genomes analysed.

Programmable molecular recognition based on the geometry of DNA nanostructures.

PubMed

Woo, Sungwook; Rothemund, Paul W K

2011-07-10

From ligand-receptor binding to DNA hybridization, molecular recognition plays a central role in biology. Over the past several decades, chemists have successfully reproduced the exquisite specificity of biomolecular interactions. However, engineering multiple specific interactions in synthetic systems remains difficult. DNA retains its position as the best medium with which to create orthogonal, isoenergetic interactions, based on the complementarity of Watson-Crick binding. Here we show that DNA can be used to create diverse bonds using an entirely different principle: the geometric arrangement of blunt-end stacking interactions. We show that both binary codes and shape complementarity can serve as a basis for such stacking bonds, and explore their specificity, thermodynamics and binding rules. Orthogonal stacking bonds were used to connect five distinct DNA origami. This work, which demonstrates how a single attractive interaction can be developed to create diverse bonds, may guide strategies for molecular recognition in systems beyond DNA nanostructures.

Synthetic Biology: Knowledge Accessed by Everyone (Open Sources)

ERIC Educational Resources Information Center

Sánchez Reyes, Patricia Margarita

2016-01-01

Using the principles of biology, along with engineering and with the help of computer, scientists manage to copy. DNA sequences from nature and use them to create new organisms. DNA is created through engineering and computer science managing to create life inside a laboratory. We cannot dismiss the role that synthetic biology could lead in…

Ha-Mah-Tsa

ERIC Educational Resources Information Center

Johnston, Basil

1978-01-01

Describing the values and moral orientations associated with the Cannibal Dance Ceremony, this article emphasizes the Kwahiutl's belief in the free will to choose between good or selflessness and evil or selfishness. (JC)

A fault-tolerant small world topology control model in ad hoc networks for search and rescue

NASA Astrophysics Data System (ADS)

Tan, Mian; Fang, Ling; Wu, Yue; Zhang, Bo; Chang, Bowen; Holme, Petter; Zhao, Jing

2018-02-01

Due to their self-organized, multi-hop and distributed characteristics, ad hoc networks are useful in search and rescue. Topology control models need to be designed for energy-efficient, robust and fast communication in ad hoc networks. This paper proposes a topology control model which specializes for search and rescue-Compensation Small World-Repeated Game (CSWRG)-which integrates mobility models, constructing small world networks and a game-theoretic approach to the allocation of resources. Simulation results show that our mobility models can enhance the communication performance of the constructed small-world networks. Our strategy, based on repeated game, can suppress selfish behavior and compensate agents that encounter selfish or faulty neighbors. This model could be useful for the design of ad hoc communication networks.

Creating metamaterial building blocks with directed photochemical metallization of silver onto DNA origami templates.

PubMed

Hossen, Md Mir; Bendickson, Lee; Palo, Pierre E; Yao, Zhiqi; Nilsen-Hamilton, Marit; Hillier, Andrew C

2018-08-31

DNA origami can be used to create a variety of complex and geometrically unique nanostructures that can be further modified to produce building blocks for applications such as in optical metamaterials. We describe a method for creating metal-coated nanostructures using DNA origami templates and a photochemical metallization technique. Triangular DNA origami forms were fabricated and coated with a thin metal layer by photochemical silver reduction while in solution or supported on a surface. The DNA origami template serves as a localized photosensitizer to facilitate reduction of silver ions directly from solution onto the DNA surface. The metallizing process is shown to result in a conformal metal coating, which grows in height to a self-limiting value with increasing photoreduction steps. Although this coating process results in a slight decrease in the triangle dimensions, the overall template shape is retained. Notably, this coating method exhibits characteristics of self-limiting and defect-filling growth, which results in a metal nanostructure that maps the shape of the original DNA template with a continuous and uniform metal layer and stops growing once all available DNA sites are exhausted.

Biomaterial-based Memory Device Development by Conducting Metallic DNA

DTIC Science & Technology

2013-05-28

time. Therefore, we have created a multiple-states memory system . This is the first multi-states resistance memory device by using bio-nanowire of the...world. Based on this achievement, logic device and application will be developed in the near future, too. Moreover, by using Ni-DNA detection system ...ions in DNA can change the resistance of Ni-DNA by applying different polar bias and time. Therefore, we have created a multiple-states memory system

Narcissistic personality disorder

MedlinePlus

... An extreme preoccupation with themselves A lack of empathy for others Causes Cause of this disorder is ... of others, and have little ability to feel empathy Have obsessive self-interest Pursue mainly selfish goals ...

Creating Cost-Effective DNA Size Standards for Use in Teaching and Research Laboratories

ERIC Educational Resources Information Center

Shultz, Jeff

2011-01-01

I have devised a method with which a molecular size standard can be readily manufactured using Lambda DNA and PCR. This method allows the production of specific sized DNA fragments and is easily performed in a standard molecular biology laboratory. The material required to create these markers can also be used to provide a highly robust and…

The Economics of Fair Play.

ERIC Educational Resources Information Center

Sigmund, Karl; Fehr, Ernst; Nowak, Martin A.

2002-01-01

Reports on the field of experimental economics and speculates about why we value fairness and cooperation over the seemingly more rational selfishness. Illustrates a typical decision making situation using the Ultimatum game. (DDR)

Creating complex molecular topologies by configuring DNA four-way junctions

NASA Astrophysics Data System (ADS)

Liu, Di; Chen, Gang; Akhter, Usman; Cronin, Timothy M.; Weizmann, Yossi

2016-10-01

The realization of complex topologies at the molecular level represents a grand challenge in chemistry. This necessitates the manipulation of molecular interactions with high precision. Here we show that single-stranded DNA (ssDNA) knots and links can be created by utilizing the inherent topological properties that pertain to the DNA four-way junction, at which the two helical strands form a node and can be configured conveniently and connected for complex topological construction. Using this strategy, we produced series of ssDNA topoisomers with the same sequences. By finely designing the curvature and torsion, double-stranded DNA knots were accessed by hybridizing and ligating the complementary strands with the knotted ssDNA templates. Furthermore, we demonstrate the use of a constructed ssDNA knot both to probe the topological conversion catalysed by DNA topoisomerase and to study the DNA replication under topological constraint.

Selfish play increases during high-stakes NBA games and is rewarded with more lucrative contracts.

PubMed

Uhlmann, Eric Luis; Barnes, Christopher M

2014-01-01

High-stakes team competitions can present a social dilemma in which participants must choose between concentrating on their personal performance and assisting teammates as a means of achieving group objectives. We find that despite the seemingly strong group incentive to win the NBA title, cooperative play actually diminishes during playoff games, negatively affecting team performance. Thus team cooperation decreases in the very high stakes contexts in which it is most important to perform well together. Highlighting the mixed incentives that underlie selfish play, personal scoring is rewarded with more lucrative future contracts, whereas assisting teammates to score is associated with reduced pay due to lost opportunities for personal scoring. A combination of misaligned incentives and psychological biases in performance evaluation bring out the "I" in "team" when cooperation is most critical.

Selfish Play Increases during High-Stakes NBA Games and Is Rewarded with More Lucrative Contracts

PubMed Central

Uhlmann, Eric Luis; Barnes, Christopher M.

2014-01-01

High-stakes team competitions can present a social dilemma in which participants must choose between concentrating on their personal performance and assisting teammates as a means of achieving group objectives. We find that despite the seemingly strong group incentive to win the NBA title, cooperative play actually diminishes during playoff games, negatively affecting team performance. Thus team cooperation decreases in the very high stakes contexts in which it is most important to perform well together. Highlighting the mixed incentives that underlie selfish play, personal scoring is rewarded with more lucrative future contracts, whereas assisting teammates to score is associated with reduced pay due to lost opportunities for personal scoring. A combination of misaligned incentives and psychological biases in performance evaluation bring out the “I” in “team” when cooperation is most critical. PMID:24763384

Unifying perspectives on cooperation under social viscosity. Comment on "Universal scaling for the dilemma strength in evolutionary games" by Z. Wang et al.

NASA Astrophysics Data System (ADS)

Bauch, Chris T.

2015-09-01

How cooperation evolved in populations of self-interested agents puzzled Charles Darwin, who portrayed the paradox in The Descent of Man as such: "He who was ready to sacrifice his life, as many a savage has been, rather than betray his comrades, would often leave no offspring to inherit his noble nature" [1]. Darwin invoked group selection to explain cooperation: if groups of cooperating individuals could work together to outcompete groups of selfish individuals, cooperation could thrive. Fundamentally, this mechanism works by allowing cooperators to interact preferentially with one another: cooperators tend to interact with other co-operators whereas selfish "defectors" tend to interact with other defectors. Since cooperators cooperate and defectors defect, groups of cooperators should do better, on average.

Game Theory Meets Wireless Sensor Networks Security Requirements and Threats Mitigation: A Survey.

PubMed

Abdalzaher, Mohamed S; Seddik, Karim; Elsabrouty, Maha; Muta, Osamu; Furukawa, Hiroshi; Abdel-Rahman, Adel

2016-06-29

We present a study of using game theory for protecting wireless sensor networks (WSNs) from selfish behavior or malicious nodes. Due to scalability, low complexity and disseminated nature of WSNs, malicious attacks can be modeled effectively using game theory. In this study, we survey the different game-theoretic defense strategies for WSNs. We present a taxonomy of the game theory approaches based on the nature of the attack, whether it is caused by an external attacker or it is the result of an internal node acting selfishly or maliciously. We also present a general trust model using game theory for decision making. We, finally, identify the significant role of evolutionary games for WSNs security against intelligent attacks; then, we list several prospect applications of game theory to enhance the data trustworthiness and node cooperation in different WSNs.

Are maternal mitochondria the selfish entities that are masters of the cells of eukaryotic multicellular organisms?

PubMed Central

Barlow, Peter W; Baldelli, E; Baluška, Frantisek

2009-01-01

The Energide concept, as well as the endosymbiotic theory of eukaryotic cell organization and evolution, proposes that present-day cells of eukaryotic organisms are mosaics of specialized and cooperating units, or organelles. Some of these units were originally free-living prokaryotes, which were engulfed during evolutionary time. Mitochondria represent one of these types of previously independent organisms, the Energide, is another type. This new perspective on the organization of the cell has been further expanded to reveal the concept of a public milieu, the cytosol, in which Energides and mitochondria live, each with their own private internal milieu. The present paper discusses how the endosymbiotic theory implicates a new hypothesis about the hierarchical and communicational organization of the integrated prokaryotic components of the eukaryotic cell and provides a new angle from which to consider the theory of evolution and its bearing upon cellular complexity. Thus, it is proposed that the “selfish gene” hypothesis of Dawkins1 is not the only possible perspective for comprehending genomic and cellular evolution. Our proposal is that maternal mitochondria are the selfish “master” entities of the eukaryotic cell with respect not only to their propagation from cell-to-cell and from generation-to-generation but also to their regulation of all other cellular functions. However, it should be recognized that the concept of “master” and “servant” cell components is a metaphor; in present-day living organisms their organellar components are considered to be interdependent and inseparable. PMID:19513277

Social class, power, and selfishness: when and why upper and lower class individuals behave unethically.

PubMed

Dubois, David; Rucker, Derek D; Galinsky, Adam D

2015-03-01

Are the rich more unethical than the poor? To answer this question, the current research introduces a key conceptual distinction between selfish and unethical behavior. Based on this distinction, the current article offers 2 novel findings that illuminate the relationship between social class and unethical behavior. First, the effects of social class on unethical behavior are not invariant; rather, the effects of social class are moderated by whether unethical behavior benefits the self or others. Replicating past work, social class positively predicted unethical behavior; however, this relationship was only observed when that behavior was self-beneficial. When unethical behavior was performed to benefit others, social class negatively predicted unethical behavior; lower class individuals were more likely than upper class individuals to engage in unethical behavior. Overall, social class predicts people's tendency to behave selfishly, rather than predicting unethical behavior per se. Second, individuals' sense of power drove the effects of social class on unethical behavior. Evidence for this relationship was provided in three forms. First, income, but not education level, predicted unethical behavior. Second, feelings of power mediated the effect of social class on unethical behavior, but feelings of status did not. Third, two distinct manipulations of power produced the same moderation by self-versus-other beneficiary as was found with social class. The current theoretical framework and data both synthesize and help to explain a range of findings in the social class and power literatures. PsycINFO Database Record (c) 2015 APA, all rights reserved.

Selfish genes, pleiotropy and the origin of recombination.

PubMed Central

Hey, J

1998-01-01

If multiple linked polymorphisms are under natural selection, then conflicts arise and the efficiency of natural selection is hindered relative to the case of no linkage. This simple interaction between linkage and natural selection creates an opportunity for mutations that raise the level of recombination to increase in frequency and have an enhanced chance of fixation. This important finding by S. Otto and N. Barton means that mutations that raise the recombination rate, but are otherwise neutral, will be selectively favored under fairly general circumstances of multilocus selection and linkage. The effect described by Otto and Barton, which was limited to neutral modifiers, can also be extended to include all modifiers of recombination, both beneficial and deleterious. Computer simulations show that beneficial mutations that also increase recombination have an increased chance of fixation. Similarly, deleterious mutations that also decrease recombination have an increased chance of fixation. The results suggest that a simple model of recombination modifiers, including both neutral and pleiotropic modifiers, is a necessary explanation for the evolutionary origin of recombination. PMID:9691060

Why would I help my coworker? Exploring asymmetric task dependence and the self-determination theory internalization process.

PubMed

Poile, Christopher

2017-09-01

Research on power suggests asymmetric task dependence (sending work resources to a coworker and receiving little in return) should create a power imbalance and promote selfishness. In contrast, work design theory suggests asymmetry can lead to felt responsibility, but this link has not been tested and its theory remains underdeveloped. Drawing on self-determination theory (SDT), this article argues that work design characteristics can encourage the SDT internalization process-the transformation of external reasons for behavior into internal reasons. Two experiments demonstrate asymmetry encourages felt responsibility for the dependent's task, which helps explain the amount of help provided to the dependent. The author proposes felt responsibility indicates the extent to which an external task has been internalized as a self-directed motivation. This article clarifies how task dependence is different from power and develops an important and understudied aspect of SDT: how work design characteristics are transformed into internalized motivations. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Self-extinction through optimizing selection.

PubMed

Parvinen, Kalle; Dieckmann, Ulf

2013-09-21

Evolutionary suicide is a process in which selection drives a viable population to extinction. So far, such selection-driven self-extinction has been demonstrated in models with frequency-dependent selection. This is not surprising, since frequency-dependent selection can disconnect individual-level and population-level interests through environmental feedback. Hence it can lead to situations akin to the tragedy of the commons, with adaptations that serve the selfish interests of individuals ultimately ruining a population. For frequency-dependent selection to play such a role, it must not be optimizing. Together, all published studies of evolutionary suicide have created the impression that evolutionary suicide is not possible with optimizing selection. Here we disprove this misconception by presenting and analyzing an example in which optimizing selection causes self-extinction. We then take this line of argument one step further by showing, in a further example, that selection-driven self-extinction can occur even under frequency-independent selection. Copyright © 2013 Elsevier Ltd. All rights reserved.

A virocentric perspective on the evolution of life

PubMed Central

Koonin, Eugene V.; Dolja, Valerian V.

2015-01-01

Viruses and/or virus-like selfish elements are associated with all cellular life forms and are the most abundant biological entities on Earth, with the number of virus particles in many environments exceeding the number of cells by one to two orders of magnitude. The genetic diversity of viruses is commensurately enormous and might substantially exceed the diversity of cellular organisms. Unlike cellular organisms with their uniform replication-expression scheme, viruses possess either RNA or DNA genomes and exploit all conceivable replication-expression strategies. Although viruses extensively exchange genes with their hosts, there exists a set of viral hallmark genes that are shared by extremely diverse groups of viruses to the exclusion of cellular life forms. Coevolution of viruses and host defense systems is a key aspect in the evolution of both viruses and cells, and viral genes are often recruited for cellular functions. Together with the fundamental inevitability of the emergence of genomic parasites in any evolving replicator system, these multiple lines of evidence reveal the central role of viruses in the entire evolution of life. PMID:23850169

How gene order is influenced by the biophysics of transcription regulation

PubMed Central

Kolesov, Grigory; Wunderlich, Zeba; Laikova, Olga N.; Gelfand, Mikhail S.; Mirny, Leonid A.

2007-01-01

What are the forces that shape the structure of prokaryotic genomes: the order of genes, their proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are believed to promote the proximity of functionally related genes and the formation of operons. However, forces that influence the structure of the genome beyond the level of a single operon remain unknown. Here, we show that the biophysical mechanism by which regulatory proteins search for their sites on DNA can impose constraints on genome structure. Using simulations, we demonstrate that rapid and reliable gene regulation requires that the transcription factor (TF) gene be close to the site on DNA the TF has to bind, thus promoting the colocalization of TF genes and their targets on the genome. We use parameters that have been measured in recent experiments to estimate the relevant length and times scales of this process and demonstrate that the search for a cognate site may be prohibitively slow if a TF has a low copy number and is not colocalized. We also analyze TFs and their sites in a number of bacterial genomes, confirm that they are colocalized significantly more often than expected, and show that this observation cannot be attributed to the pressure for coregulation or formation of selfish gene clusters, thus supporting the role of the biophysical constraint in shaping the structure of prokaryotic genomes. Our results demonstrate how spatial organization can influence timing and noise in gene expression. PMID:17709750

Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements

PubMed Central

Brunet, Tyler D.P.; Doolittle, W. Ford

2015-01-01

One of several issues at play in the renewed debate over “junk DNA” is the organizational level at which genomic features might be seen as selected, and thus to exhibit function, as etiologically defined. The intuition frequently expressed by molecular geneticists that junk DNA is functional because it serves to “speed evolution” or as an “evolutionary repository” could be recast as a claim about selection between species (or clades) rather than within them, but this is not often done. Here, we review general arguments for the importance of selection at levels above that of organisms in evolution, and develop them further for a common genomic feature: the carriage of transposable elements (TEs). In many species, not least our own, TEs comprise a large fraction of all nuclear DNA, and whether they individually or collectively contribute to fitness—or are instead junk— is a subject of ongoing contestation. Even if TEs generally owe their origin to selfish selection at the lowest level (that of genomes), their prevalence in extant organisms and the prevalence of extant organisms bearing them must also respond to selection within species (on organismal fitness) and between species (on rates of speciation and extinction). At an even higher level, the persistence of clades may be affected (positively or negatively) by TE carriage. If indeed TEs speed evolution, it is at these higher levels of selection that such a function might best be attributed to them as a class. PMID:26253318

Darwinian Evolution of Mutualistic RNA Replicators with Different Genes

NASA Astrophysics Data System (ADS)

Mizuuchi, R.; Ichihashi, N.

2017-07-01

We report a sustainable long-term replication and evolution of two distinct cooperative RNA replicators encoding different genes. One of the RNAs evolved to maintain or increase the cooperativity, despite selective advantage of selfish mutations.

When giving is good: Ventromedial prefrontal cortex activation for others’ intentions

PubMed Central

Cooper, Jeffrey C.; Kreps, Tamar A.; Wiebe, Taylor; Pirkl, Tristana; Knutson, Brian

2010-01-01

Summary In social decision-making, people care both about others’ outcomes and their intentions to help or harm. How the brain integrates representations of others’ intentions with their outcomes, however, is unknown. In this study, participants inferred others’ decisions in an economic game during functional magnetic resonance imaging. When the game was described in terms of donations, ventromedial prefrontal cortex (VMPFC) activation increased for inferring generous play and decreased for inferring selfish play. When the game was described in terms of individual savings, however, VMPFC activation did not distinguish between strategies. Distinct medial prefrontal regions also encoded consistency with situational norms. A separate network, including right temporoparietal junction and parahippocampal gyrus, was more activated for inferential errors in the donation than in the savings condition. These results for the first time demonstrate that neural responses to others’ generosity or selfishness depend not only on their actions but also on their perceived intentions. PMID:20696386

Game Theory Meets Wireless Sensor Networks Security Requirements and Threats Mitigation: A Survey

PubMed Central

Abdalzaher, Mohamed S.; Seddik, Karim; Elsabrouty, Maha; Muta, Osamu; Furukawa, Hiroshi; Abdel-Rahman, Adel

2016-01-01

We present a study of using game theory for protecting wireless sensor networks (WSNs) from selfish behavior or malicious nodes. Due to scalability, low complexity and disseminated nature of WSNs, malicious attacks can be modeled effectively using game theory. In this study, we survey the different game-theoretic defense strategies for WSNs. We present a taxonomy of the game theory approaches based on the nature of the attack, whether it is caused by an external attacker or it is the result of an internal node acting selfishly or maliciously. We also present a general trust model using game theory for decision making. We, finally, identify the significant role of evolutionary games for WSNs security against intelligent attacks; then, we list several prospect applications of game theory to enhance the data trustworthiness and node cooperation in different WSNs. PMID:27367700

The maternal-effect, selfish genetic element Medea is associated with a composite Tc1 transposon.

PubMed

Lorenzen, Marcé D; Gnirke, Andreas; Margolis, Jonathan; Garnes, Jeffrey; Campbell, Margie; Stuart, Jeffrey J; Aggarwal, Rajat; Richards, Stephen; Park, Yoonseong; Beeman, Richard W

2008-07-22

Maternal-Effect Dominant Embryonic Arrest ("Medea") factors are selfish nuclear elements that combine maternal-lethal and zygotic-rescue activities to gain a postzygotic survival advantage. We show that Medea(1) activity in Tribolium castaneum is associated with a composite Tc1 transposon inserted just downstream of the neurotransmitter reuptake symporter bloated tubules (blot), whose Drosophila ortholog has both maternal and zygotic functions. The 21.5-kb insertion contains defective copies of elongation initiation factor-3, ATP synthase subunit C, and an RNaseD-related gene, as well as a potentially intact copy of a prokaryotic DUF1703 gene. Sequence comparisons suggest that the current distribution of Medea(1) reflects global emanation after a single transpositional event in recent evolutionary time. The Medea system in Tribolium represents an unusual type of intragenomic conflict and could provide a useful vehicle for driving desirable genes into populations.

wtf genes are prolific dual poison-antidote meiotic drivers.

PubMed

Nuckolls, Nicole L; Bravo Núñez, María Angélica; Eickbush, Michael T; Young, Janet M; Lange, Jeffrey J; Yu, Jonathan S; Smith, Gerald R; Jaspersen, Sue L; Malik, Harmit S; Zanders, Sarah E

2017-06-20

Meiotic drivers are selfish genes that bias their transmission into gametes, defying Mendelian inheritance. Despite the significant impact of these genomic parasites on evolution and infertility, few meiotic drive loci have been identified or mechanistically characterized. Here, we demonstrate a complex landscape of meiotic drive genes on chromosome 3 of the fission yeasts Schizosaccharomyces kambucha and S. pombe . We identify S. kambucha wtf4 as one of these genes that acts to kill gametes (known as spores in yeast) that do not inherit the gene from heterozygotes. wtf4 utilizes dual, overlapping transcripts to encode both a gamete-killing poison and an antidote to the poison. To enact drive, all gametes are poisoned, whereas only those that inherit wtf4 are rescued by the antidote. Our work suggests that the wtf multigene family proliferated due to meiotic drive and highlights the power of selfish genes to shape genomes, even while imposing tremendous costs to fertility.

The maternal-effect, selfish genetic element Medea is associated with a composite Tc1 transposon

PubMed Central

Lorenzen, Marcé D.; Gnirke, Andreas; Margolis, Jonathan; Garnes, Jeffrey; Campbell, Margie; Stuart, Jeffrey J.; Aggarwal, Rajat; Richards, Stephen; Park, Yoonseong; Beeman, Richard W.

2008-01-01

Maternal-Effect Dominant Embryonic Arrest (“Medea”) factors are selfish nuclear elements that combine maternal-lethal and zygotic-rescue activities to gain a postzygotic survival advantage. We show that Medea1 activity in Tribolium castaneum is associated with a composite Tc1 transposon inserted just downstream of the neurotransmitter reuptake symporter bloated tubules (blot), whose Drosophila ortholog has both maternal and zygotic functions. The 21.5-kb insertion contains defective copies of elongation initiation factor-3, ATP synthase subunit C, and an RNaseD-related gene, as well as a potentially intact copy of a prokaryotic DUF1703 gene. Sequence comparisons suggest that the current distribution of Medea1 reflects global emanation after a single transpositional event in recent evolutionary time. The Medea system in Tribolium represents an unusual type of intragenomic conflict and could provide a useful vehicle for driving desirable genes into populations. PMID:18621706

Homing endonuclease genes: the rise and fall and rise again of a selfish element.

PubMed

Burt, Austin; Koufopanou, Vassiliki

2004-12-01

Homing endonuclease genes (HEGs) are selfish genetic elements that spread by first cleaving chromosomes that do not contain them and then getting copied across to the broken chromosome as a byproduct of the repair process. The success of this strategy will depend on the opportunities for homing--in other words, the frequency with which HEG(+) and HEG(-) chromosomes come into contact--which varies widely among host taxa. HEGs are also unusual in that the selection pressure for endonuclease function disappears if they become fixed in a population, which makes them susceptible to degeneration and imposes a need for regular horizontal transmission between species. HEGs will be selected to reduce the harm done to the host organism, and this is expected to influence the evolution of their sequence specificity and maturase functions. HEGs may also be domesticated by their hosts, and are currently being put to human uses.

Humans choose representatives who enforce cooperation in social dilemmas through extortion

NASA Astrophysics Data System (ADS)

Milinski, Manfred; Hilbe, Christian; Semmann, Dirk; Sommerfeld, Ralf; Marotzke, Jochem

2016-03-01

Social dilemmas force players to balance between personal and collective gain. In many dilemmas, such as elected governments negotiating climate-change mitigation measures, the decisions are made not by individual players but by their representatives. However, the behaviour of representatives in social dilemmas has not been investigated experimentally. Here inspired by the negotiations for greenhouse-gas emissions reductions, we experimentally study a collective-risk social dilemma that involves representatives deciding on behalf of their fellow group members. Representatives can be re-elected or voted out after each consecutive collective-risk game. Selfish players are preferentially elected and are hence found most frequently in the `representatives' treatment. Across all treatments, we identify the selfish players as extortioners. As predicted by our mathematical model, their steadfast strategies enforce cooperation from fair players who finally compensate almost completely the deficit caused by the extortionate co-players. Everybody gains, but the extortionate representatives and their groups gain the most.

Probabilistic monitoring in intrusion detection module for energy efficiency in mobile ad hoc networks

NASA Astrophysics Data System (ADS)

De Rango, Floriano; Lupia, Andrea

2016-05-01

MANETs allow mobile nodes communicating to each other using the wireless medium. A key aspect of these kind of networks is the security, because their setup is done without an infrastructure, so external nodes could interfere in the communication. Mobile nodes could be compromised, misbehaving during the multi-hop transmission of data, or they could have a selfish behavior to save energy, which is another important constraint in MANETs. The detection of these behaviors need a framework that takes into account the latest interactions among nodes, so malicious or selfish nodes could be detected also if their behavior is changed over time. The monitoring activity increases the energy consumption, so our proposal takes into account this issue reducing the energy required by the monitoring system, keeping the effectiveness of the intrusion detection system. The results show an improvement in the saved energy, improving the detection performance too.

SEX-RATIO MEIOTIC DRIVE AND INTERSPECIFIC COMPETITION

PubMed Central

Unckless, Robert L.; Clark, Andrew G.

2014-01-01

It has long been known that processes occurring within a species may impact the interactions between species. For example, since competitive ability is sensitive to parameters including reproductive rate, carrying capacity and competition efficiency, the outcome of interspecific competition may be influenced by any process that alters these attributes. While several such scenarios have been discussed, the influence of selfish genetic elements within one species on competition between species has not received theoretical treatment. We show that, with strong competition, sex-ratio meiotic drive systems can result in a significant shift in community composition because the effective birth rate in the population may be increased by a female-biased sex-ratio. Using empirical data we attempt to estimate the magnitude of this effect in several Drosophila species. We infer that meiotic drive elements, selfish genetic elements within species, can provide a substantial competitive advantage to that species within a community. PMID:24835887

Active DNA gels

NASA Astrophysics Data System (ADS)

Saleh, Omar A.; Fygenson, Deborah K.; Bertrand, Olivier J. N.; Park, Chang Young

2013-02-01

Research into the mechanics and fluctuations of living cells has revealed the key role played by the cytoskeleton, a gel of stiff filaments driven out of equilibrium by force-generating motor proteins. Inspired by the extraordinary mechanical functions that the cytoskeleton imparts to the cell, we sought to create an artificial gel with similar characteristics. We identified DNA, and DNA-based motor proteins, as functional counterparts to the constituents of the cytoskeleton. We used DNA selfassembly to create a gel, and characterized its fluctuations and mechanics both before and after activation by the motor. We found that certain aspects of the DNA gel quantitatively match those of cytoskeletal networks, indicating the universal features of motor-driven, non-equilibrium networks.

[cDNA library construction from panicle meristem of finger millet].

PubMed

Radchuk, V; Pirko, Ia V; Isaenkov, S V; Emets, A I; Blium, Ia B

2014-01-01

The protocol for production of full-size cDNA using SuperScript Full-Length cDNA Library Construction Kit II (Invitrogen) was tested and high quality cDNA library from meristematic tissue of finger millet panicle (Eleusine coracana (L.) Gaertn) was created. The titer of obtained cDNA library comprised 3.01 x 10(5) CFU/ml in avarage. In average the length of cDNA insertion consisted about 1070 base pairs, the effectivity of cDNA fragment insertions--99.5%. The selective sequencing of cDNA clones from created library was performed. The sequences of cDNA clones were identified with usage of BLAST-search. The results of cDNA library analysis and selective sequencing represents prove good functionality and full length character of inserted cDNA clones. Obtained cDNA library from meristematic tissue of finger millet panicle represents good and valuable source for isolation and identification of key genes regulating metabolism and meristematic development and for mining of new molecular markers to conduct out high quality genetic investigations and molecular breeding as well.

Detection of sub-femtomolar DNA based on double potential electrodeposition of electrocatalytic platinum nanoparticles.

PubMed

Spain, Elaine; McArdle, Hazel; Keyes, Tia E; Forster, Robert J

2013-08-07

Suspensions of electrocatalytic platinum nanoparticles with radii as small as 78.9 ± 3.5 nm that are functionalised with DNA only in one region have been created using templated electrodeposition. The integrity of the bound DNA following nanoparticle desorption from the electrode is demonstrated by detecting attomolar concentrations of DNA without the need for molecular, e.g., PCR or NASBA, amplification. Double potential step approaches coupled with interface engineering via nucleation sites allows PtNPs to be created with controlled particle size and density in a facile and reproducible manner.

Brain activity and prosocial behavior in a simulated life-threatening situation.

PubMed

Zanon, Marco; Novembre, Giovanni; Zangrando, Nicola; Chittaro, Luca; Silani, Giorgia

2014-09-01

To study the neuronal basis of altruistic behavior, we investigated functional connectivity within brain networks of participants who exhibited either a self-benefit behavior or an altruistic one in a life-threatening situation simulated in a virtual environment. In particular, participants were asked to evacuate a virtual building on fire and, without being previously informed, they were faced with a decision on whether to stop and help a trapped virtual human, at the possible cost of losing their own life in the virtual experience. Group independent component analysis (gICA) applied on blood-oxygen-level-dependent (BOLD) functional images revealed significant differences between the group of participants who showed selfish behavior and those who acted prosocially. Specifically, an increased functional connectivity in the salience network, comprising the anterior insula (AI) and the anterior mid cingulate cortex (aMCC), was observed in the selfish group compared to the prosocial one. Conversely, higher ICA weights in the medial prefrontal cortex and temporo-parietal junction (TPJ), were observed in the prosocial group. The findings show that an increased functional connectivity of the salience network, which suggests an enhanced sensitivity to the threatening situation and potential danger for the individual, resulted in more selfish choices, while the engagement of the medial prefrontal and temporo-parietal cortices subserved prosocial behavior, possibly due to their role in perspective-taking. The study provides the first online neurophysiological measurement of prosocial decision-making during threatening situations, opening new avenues to the investigation of neuronal substrates of complex social behaviors. Copyright © 2014 Elsevier Inc. All rights reserved.

Contributions of intrinsic mutation rate and selfish selection to levels of de novo HRAS mutations in the paternal germline

PubMed Central

Giannoulatou, Eleni; McVean, Gilean; Taylor, Indira B.; McGowan, Simon J.; Maher, Geoffrey J.; Iqbal, Zamin; Pfeifer, Susanne P.; Turner, Isaac; Burkitt Wright, Emma M. M.; Shorto, Jennifer; Itani, Aysha; Turner, Karen; Gregory, Lorna; Buck, David; Rajpert-De Meyts, Ewa; Looijenga, Leendert H. J.; Kerr, Bronwyn; Wilkie, Andrew O. M.; Goriely, Anne

2013-01-01

The RAS proto-oncogene Harvey rat sarcoma viral oncogene homolog (HRAS) encodes a small GTPase that transduces signals from cell surface receptors to intracellular effectors to control cellular behavior. Although somatic HRAS mutations have been described in many cancers, germline mutations cause Costello syndrome (CS), a congenital disorder associated with predisposition to malignancy. Based on the epidemiology of CS and the occurrence of HRAS mutations in spermatocytic seminoma, we proposed that activating HRAS mutations become enriched in sperm through a process akin to tumorigenesis, termed selfish spermatogonial selection. To test this hypothesis, we quantified the levels, in blood and sperm samples, of HRAS mutations at the p.G12 codon and compared the results to changes at the p.A11 codon, at which activating mutations do not occur. The data strongly support the role of selection in determining HRAS mutation levels in sperm, and hence the occurrence of CS, but we also found differences from the mutation pattern in tumorigenesis. First, the relative prevalence of mutations in sperm correlates weakly with their in vitro activating properties and occurrence in cancers. Second, specific tandem base substitutions (predominantly GC>TT/AA) occur in sperm but not in cancers; genomewide analysis showed that this same mutation is also overrepresented in constitutional pathogenic and polymorphic variants, suggesting a heightened vulnerability to these mutations in the germline. We developed a statistical model to show how both intrinsic mutation rate and selfish selection contribute to the mutational burden borne by the paternal germline. PMID:24259709

Contributions of intrinsic mutation rate and selfish selection to levels of de novo HRAS mutations in the paternal germline.

PubMed

Giannoulatou, Eleni; McVean, Gilean; Taylor, Indira B; McGowan, Simon J; Maher, Geoffrey J; Iqbal, Zamin; Pfeifer, Susanne P; Turner, Isaac; Burkitt Wright, Emma M M; Shorto, Jennifer; Itani, Aysha; Turner, Karen; Gregory, Lorna; Buck, David; Rajpert-De Meyts, Ewa; Looijenga, Leendert H J; Kerr, Bronwyn; Wilkie, Andrew O M; Goriely, Anne

2013-12-10

The RAS proto-oncogene Harvey rat sarcoma viral oncogene homolog (HRAS) encodes a small GTPase that transduces signals from cell surface receptors to intracellular effectors to control cellular behavior. Although somatic HRAS mutations have been described in many cancers, germline mutations cause Costello syndrome (CS), a congenital disorder associated with predisposition to malignancy. Based on the epidemiology of CS and the occurrence of HRAS mutations in spermatocytic seminoma, we proposed that activating HRAS mutations become enriched in sperm through a process akin to tumorigenesis, termed selfish spermatogonial selection. To test this hypothesis, we quantified the levels, in blood and sperm samples, of HRAS mutations at the p.G12 codon and compared the results to changes at the p.A11 codon, at which activating mutations do not occur. The data strongly support the role of selection in determining HRAS mutation levels in sperm, and hence the occurrence of CS, but we also found differences from the mutation pattern in tumorigenesis. First, the relative prevalence of mutations in sperm correlates weakly with their in vitro activating properties and occurrence in cancers. Second, specific tandem base substitutions (predominantly GC>TT/AA) occur in sperm but not in cancers; genomewide analysis showed that this same mutation is also overrepresented in constitutional pathogenic and polymorphic variants, suggesting a heightened vulnerability to these mutations in the germline. We developed a statistical model to show how both intrinsic mutation rate and selfish selection contribute to the mutational burden borne by the paternal germline.

Rolling Circle Amplification For Spatially Directed Synthesis Of A Solid Phase Anchored Single-Stranded DNA Molecule

NASA Astrophysics Data System (ADS)

Reiß, Edda; Hölzel, Ralph; von Nickisch-Rosenegk, Markus; Bier, Frank F.

2006-09-01

In this article the usefulness of the enzyme phi29 DNA polymerase and the principle of rolling circle amplification (RCA) for creating single-stranded DNA (ssDNA) nanostructures is described. Currently we are working on the spatial orientation of a growing ssDNA molecule during its RCA-based synthesis by the application of a hydrodynamic force. Starting at an immobilized primer at single molecule level, the aim is to construct a nanostructure of known location and orientation, providing multiple repeating binding sites that can be addressed via complementary base-pairing. Proof-of-principle experiments demonstrate the potential of the enzymatic reaction. ssDNA molecules of more than 20 μm length were created at an immobilized primer and detected by means of fluorescence microscopy.

Structure of Escherichia coli dGTP Triphosphohydrolase: A Hexameric Enzyme with DNA Effector Molecules

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

Singh, Deepa; Gawel, Damian; Itsko, Mark

The Escherichia coli dgt gene encodes a dGTP triphosphohydrolase whose detailed role still remains to be determined. Deletion of dgt creates a mutator phenotype, indicating that the dGTPase has a fidelity role, possibly by affecting the cellular dNTP pool. In the present paper, we have investigated the structure of the Dgt protein at 3.1-Å resolution. One of the obtained structures revealed a protein hexamer that contained two molecules of single-stranded DNA. The presence of DNA caused significant conformational changes in the enzyme, including in the catalytic site of the enzyme. Dgt preparations lacking DNA were able to bind single-stranded DNAmore » with high affinity (K d ~ 50 nM). DNA binding positively affected the activity of the enzyme: dGTPase activity displayed sigmoidal (cooperative) behavior without DNA but hyperbolic (Michaelis-Menten) kinetics in its presence, consistent with a specific lowering of the apparent K m for dGTP. A mutant Dgt enzyme was also created containing residue changes in the DNA binding cleft. This mutant enzyme, whereas still active, was incapable of DNA binding and could no longer be stimulated by addition of DNA. We also created an E. coli strain containing the mutant dgt gene on the chromosome replacing the wild-type gene. The mutant also displayed a mutator phenotype. Finally, our results provide insight into the allosteric regulation of the enzyme and support a physiologically important role of DNA binding.« less

Structure of Escherichia coli dGTP Triphosphohydrolase: A Hexameric Enzyme with DNA Effector Molecules

DOE PAGES

Singh, Deepa; Gawel, Damian; Itsko, Mark; ...

2015-02-18

The Escherichia coli dgt gene encodes a dGTP triphosphohydrolase whose detailed role still remains to be determined. Deletion of dgt creates a mutator phenotype, indicating that the dGTPase has a fidelity role, possibly by affecting the cellular dNTP pool. In the present paper, we have investigated the structure of the Dgt protein at 3.1-Å resolution. One of the obtained structures revealed a protein hexamer that contained two molecules of single-stranded DNA. The presence of DNA caused significant conformational changes in the enzyme, including in the catalytic site of the enzyme. Dgt preparations lacking DNA were able to bind single-stranded DNAmore » with high affinity (K d ~ 50 nM). DNA binding positively affected the activity of the enzyme: dGTPase activity displayed sigmoidal (cooperative) behavior without DNA but hyperbolic (Michaelis-Menten) kinetics in its presence, consistent with a specific lowering of the apparent K m for dGTP. A mutant Dgt enzyme was also created containing residue changes in the DNA binding cleft. This mutant enzyme, whereas still active, was incapable of DNA binding and could no longer be stimulated by addition of DNA. We also created an E. coli strain containing the mutant dgt gene on the chromosome replacing the wild-type gene. The mutant also displayed a mutator phenotype. Finally, our results provide insight into the allosteric regulation of the enzyme and support a physiologically important role of DNA binding.« less

Genes Are Us

ERIC Educational Resources Information Center

Keller, Alexandra; Smith, David; Harrop, Brenda; Lamit, Louis; Schroer, Melanie; Wymore, Adam; Ueckert, Catherine

2012-01-01

Almost all living organisms, including plants, fungi, insects, and humans, have DNA. Variation in DNA, or genetic variation, is responsible for most of the diversity one sees in nature. By analyzing DNA, it is possible to create a DNA fingerprint that is unique to an organism. DNA fingerprinting is used in several disciplines of science, including…

Public Education, Public Good.

ERIC Educational Resources Information Center

Tomlinson, John

1986-01-01

Criticizes policies which would damage or destroy a public education system. Examines the relationship between government-provided education and democracy. Concludes that privatization of public education would emphasize self-interest and selfishness, further jeopardizing the altruism and civic mindedness necessary for the public good. (JDH)

When gene medication is also genetic modification--regulating DNA treatment.

PubMed

Foss, Grethe S; Rogne, Sissel

2007-07-26

The molecular methods used in DNA vaccination and gene therapy resemble in many ways the methods applied in genetic modification of organisms. In some regulatory regimes, this creates an overlap between 'gene medication' and genetic modification. In Norway, an animal injected with plasmid DNA, in the form of DNA vaccine or gene therapy, currently is viewed as being genetically modified for as long as the added DNA is present in the animal. However, regulating a DNA-vaccinated animal as genetically modified creates both regulatory and practical challenges. It is also counter-intuitive to many biologists. Since immune responses can be elicited also to alter traits, the borderline between vaccination and the modification of properties is no longer distinct. In this paper, we discuss the background for the Norwegian interpretation and ways in which the regulatory challenge can be handled.

DNA nanostructure-directed assembly of metal nanoparticle superlattices

NASA Astrophysics Data System (ADS)

Julin, Sofia; Nummelin, Sami; Kostiainen, Mauri A.; Linko, Veikko

2018-05-01

Structural DNA nanotechnology provides unique, well-controlled, versatile, and highly addressable motifs and templates for assembling materials at the nanoscale. These methods to build from the bottom-up using DNA as a construction material are based on programmable and fully predictable Watson-Crick base pairing. Researchers have adopted these techniques to an increasing extent for creating numerous DNA nanostructures for a variety of uses ranging from nanoelectronics to drug-delivery applications. Recently, an increasing effort has been put into attaching nanoparticles (the size range of 1-20 nm) to the accurate DNA motifs and into creating metallic nanostructures (typically 20-100 nm) using designer DNA nanoshapes as molds or stencils. By combining nanoparticles with the superior addressability of DNA-based scaffolds, it is possible to form well-ordered materials with intriguing and completely new optical, plasmonic, electronic, and magnetic properties. This focused review discusses the DNA structure-directed nanoparticle assemblies covering the wide range of different one-, two-, and three-dimensional systems.

A review of state legislation on DNA forensic data banking.

PubMed Central

McEwen, J. E.; Reilly, P. R.

1994-01-01

Recent advances in DNA identification technology are making their way into the criminal law. States across the country are enacting legislation to create repositories for the storage both of DNA samples collected from convicted offenders and of the DNA profiles derived from them. These data banks will be used to assist in the resolution of future crimes. This study surveys existing state statues, pending legislation, and administrative regulations that govern these DNA forensic data banks. We critically analyzed these laws with respect to their treatment of the collection, storage, analysis, retrieval, and use of DNA and DNA data. We found much variation among data-banking laws and conclude that, while DNA forensic data banking carries tremendous potential for law enforcement, many states, in their rush to create data banks, have paid little attention to issues of quality control, quality assurance, and privacy. In addition, the sweep of some laws is unnecessarily broad. Legislative modifications are needed in many states to better safeguard civil liberties and individual privacy. PMID:8198138

How We Make DNA Origami.

PubMed

Wagenbauer, Klaus F; Engelhardt, Floris A S; Stahl, Evi; Hechtl, Vera K; Stömmer, Pierre; Seebacher, Fabian; Meregalli, Letizia; Ketterer, Philip; Gerling, Thomas; Dietz, Hendrik

2017-10-05

DNA origami has attracted substantial attention since its invention ten years ago, due to the seemingly infinite possibilities that it affords for creating customized nanoscale objects. Although the basic concept of DNA origami is easy to understand, using custom DNA origami in practical applications requires detailed know-how for designing and producing the particles with sufficient quality and for preparing them at appropriate concentrations with the necessary degree of purity in custom environments. Such know-how is not readily available for newcomers to the field, thus slowing down the rate at which new applications outside the field of DNA nanotechnology may emerge. To foster faster progress, we share in this article the experience in making and preparing DNA origami that we have accumulated over recent years. We discuss design solutions for creating advanced structural motifs including corners and various types of hinges that expand the design space for the more rigid multilayer DNA origami and provide guidelines for preventing undesired aggregation and on how to induce specific oligomerization of multiple DNA origami building blocks. In addition, we provide detailed protocols and discuss the expected results for five key methods that allow efficient and damage-free preparation of DNA origami. These methods are agarose-gel purification, filtration through molecular cut-off membranes, PEG precipitation, size-exclusion chromatography, and ultracentrifugation-based sedimentation. The guide for creating advanced design motifs and the detailed protocols with their experimental characterization that we describe here should lower the barrier for researchers to accomplish the full DNA origami production workflow. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

In Defence of Competition.

ERIC Educational Resources Information Center

Prvulovich, Zika Rad

1982-01-01

Examines objections to competition as presented by educational philosopher Michael Fielding and others. The two major types of criticism of competition are that it is unfair and divisive and that it is selfish and immoral. The author advocates educational experiences which combine self-competition with cooperation. (AM)

Communicative genes in the evolution of empathy and altruism.

PubMed

Buck, Ross

2011-11-01

This paper discusses spontaneous communication and its implications for understanding empathy and altruism. The question of the possibility of "true" altruism-giving up one's genetic potential in favor of the genetic potential of another-is a fundamental issue common to the biological, behavioral, and social sciences. Darwin regarded "social instincts and sympathies" to be critical to the social order, but the possibility of biologically-based prosocial motives and emotions was questioned when selection was interpreted as operating at the level of the gene. In the selfish gene hypothesis, Dawkins argued that the unit of evolutionary selection must be an active, germ-line replicator: a unit whose activities determine whether copies of it are made across evolutionary timescales. He argued that the only active replicator existing across evolutionary timescales is the gene, so that the "selfish gene" is a replicator motivated only to make copies of itself. The communicative gene hypothesis notes that genes function by communicating, and the phenotype communication involves not only the individual sending and receiving abilities of the individual genes involved, but also the relationship between them relative to other genes. Therefore the selection of communication as phenotype involves the selection of individual genes and also their relationship. Relationships become replicators, and are selected across evolutionary timescales including social relationships (e.g., sex, nurturance, dominance-submission). An interesting implication of this view: apparent altruism has been interpreted by selfish gene theorists as due to kin selection and reciprocity, in which the survival of kin and comrade indirectly favor the genetic potential of the altruist. From the viewpoint of the communicative gene hypothesis, rather than underlying altruism, kin selection and reciprocity are ways of restricting altruism to kin and comrade: they are mechanisms not of altruism but of xenophobia.

The restriction-modification genes of Escherichia coli K-12 may not be selfish: they do not resist loss and are readily replaced by alleles conferring different specificities.

PubMed

O'Neill, M; Chen, A; Murray, N E

1997-12-23

Type II restriction and modification (R-M) genes have been described as selfish because they have been shown to impose selection for the maintenance of the plasmid that encodes them. In our experiments, the type I R-M system EcoKI does not behave in the same way. The genes specifying EcoKI are, however, normally residents of the chromosome and therefore our analyses were extended to monitor the deletion of chromosomal genes rather than loss of plasmid vector. If EcoKI were to behave in the same way as the plasmid-encoded type II R-M systems, the loss of the relevant chromosomal genes by mutation or recombination should lead to cell death because the cell would become deficient in modification enzyme and the bacterial chromosome would be vulnerable to the restriction endonuclease. Our data contradict this prediction; they reveal that functional type I R-M genes in the chromosome are readily replaced by mutant alleles and by alleles encoding a type I R-M system of different specificity. The acquisition of allelic genes conferring a new sequence specificity, but not the loss of the resident genes, is dependent on the product of an unlinked gene, one predicted [Prakash-Cheng, A., Chung, S. S. & Ryu, J. (1993) Mol. Gen. Genet. 241, 491-496] to be relevant to control of expression of the genes that encode EcoKI. Our evidence suggests that not all R-M systems are evolving as "selfish" units; rather, the diversity and distribution of the family of type I enzymes we have investigated require an alternative selective pressure.

Student Relationships Ethical and Legal Implications.

ERIC Educational Resources Information Center

Haney, Gerald L.

Due process, legal rights, invasion of privacy, right-to-decide, majorities, minorities, pressure groups, individual egos, domain building, selfishness, ignorance, and incompetency are only a few of the considerations facing educators today. School boards, administrators, teachers, support-personnel, and others who come in contact with student…

wtf genes are prolific dual poison-antidote meiotic drivers

PubMed Central

Nuckolls, Nicole L; Bravo Núñez, María Angélica; Eickbush, Michael T; Young, Janet M; Lange, Jeffrey J; Yu, Jonathan S; Smith, Gerald R; Jaspersen, Sue L; Malik, Harmit S; Zanders, Sarah E

2017-01-01

Meiotic drivers are selfish genes that bias their transmission into gametes, defying Mendelian inheritance. Despite the significant impact of these genomic parasites on evolution and infertility, few meiotic drive loci have been identified or mechanistically characterized. Here, we demonstrate a complex landscape of meiotic drive genes on chromosome 3 of the fission yeasts Schizosaccharomyces kambucha and S. pombe. We identify S. kambucha wtf4 as one of these genes that acts to kill gametes (known as spores in yeast) that do not inherit the gene from heterozygotes. wtf4 utilizes dual, overlapping transcripts to encode both a gamete-killing poison and an antidote to the poison. To enact drive, all gametes are poisoned, whereas only those that inherit wtf4 are rescued by the antidote. Our work suggests that the wtf multigene family proliferated due to meiotic drive and highlights the power of selfish genes to shape genomes, even while imposing tremendous costs to fertility. DOI: http://dx.doi.org/10.7554/eLife.26033.001 PMID:28631612

Humans choose representatives who enforce cooperation in social dilemmas through extortion

PubMed Central

Milinski, Manfred; Hilbe, Christian; Semmann, Dirk; Sommerfeld, Ralf; Marotzke, Jochem

2016-01-01

Social dilemmas force players to balance between personal and collective gain. In many dilemmas, such as elected governments negotiating climate-change mitigation measures, the decisions are made not by individual players but by their representatives. However, the behaviour of representatives in social dilemmas has not been investigated experimentally. Here inspired by the negotiations for greenhouse-gas emissions reductions, we experimentally study a collective-risk social dilemma that involves representatives deciding on behalf of their fellow group members. Representatives can be re-elected or voted out after each consecutive collective-risk game. Selfish players are preferentially elected and are hence found most frequently in the ‘representatives' treatment. Across all treatments, we identify the selfish players as extortioners. As predicted by our mathematical model, their steadfast strategies enforce cooperation from fair players who finally compensate almost completely the deficit caused by the extortionate co-players. Everybody gains, but the extortionate representatives and their groups gain the most. PMID:26948250

In search of Homo economicus.

PubMed

Yamagishi, Toshio; Li, Yang; Takagishi, Haruto; Matsumoto, Yoshie; Kiyonari, Toko

2014-09-01

Homo economicus, a model for humans in neoclassical economics, is a rational maximizer of self-interest. However, many social scientists regard such a person as a mere imaginary creature. We found that 31 of 446 residents of relatively wealthy Tokyo suburbs met the behavioral definition of Homo economicus. In several rounds of economic games, participants whose behavior was consistent with this model always apportioned the money endowed by the experimenter to themselves, leaving no share for their partners. These participants had high IQs and a deliberative decision style. An additional 39 participants showed a similar disregard for other people's welfare, although they were slightly more altruistic than those in the Homo economicus group. The psychological composition of these quasi-Homo economicus participants was distinct from that of participants in the Homo economicus group. Although participants in the latter group behaved selfishly on the basis of rational calculations, those in the former group made selfish choices impulsively. The implications of these findings concerning the two types of extreme noncooperators are discussed. © The Author(s) 2014.

Why Do Corals Bleach? Conflict and Conflict Mediation in a Host/Symbiont Community.

PubMed

Blackstone, Neil W; Golladay, Jeff M

2018-06-26

Coral bleaching has attracted considerable study, yet one central question remains unanswered: given that corals and their Symbiodinium symbionts have co-evolved for millions of years, why does this clearly maladaptive process occur? Bleaching may result from evolutionary conflict between the host corals and their symbionts. Selection at the level of the individual symbiont favors using the products of photosynthesis for selfish replication, while selection at the higher level favors using these products for growth of the entire host/symbiont community. To hold the selfish lower-level units in check, mechanisms of conflict mediation must evolve. Fundamental features of photosynthesis have been co-opted into conflict mediation so that symbionts that fail to export these products produce high levels of reactive oxygen species and undergo programmed cell death. These mechanisms function very well under most environmental conditions, but under conditions particularly detrimental to photosynthesis, it is these mechanisms of conflict mediation that trigger bleaching. © 2018 WILEY Periodicals, Inc.

Bacterial toxin-antitoxin systems: more than selfish entities?

PubMed

Van Melderen, Laurence; Saavedra De Bast, Manuel

2009-03-01

Bacterial toxin-antitoxin (TA) systems are diverse and widespread in the prokaryotic kingdom. They are composed of closely linked genes encoding a stable toxin that can harm the host cell and its cognate labile antitoxin, which protects the host from the toxin's deleterious effect. TA systems are thought to invade bacterial genomes through horizontal gene transfer. Some TA systems might behave as selfish elements and favour their own maintenance at the expense of their host. As a consequence, they may contribute to the maintenance of plasmids or genomic islands, such as super-integrons, by post-segregational killing of the cell that loses these genes and so suffers the stable toxin's destructive effect. The function of the chromosomally encoded TA systems is less clear and still open to debate. This Review discusses current hypotheses regarding the biological roles of these evolutionarily successful small operons. We consider the various selective forces that could drive the maintenance of TA systems in bacterial genomes.

Bacterial Toxin–Antitoxin Systems: More Than Selfish Entities?

PubMed Central

Van Melderen, Laurence; Saavedra De Bast, Manuel

2009-01-01

Bacterial toxin–antitoxin (TA) systems are diverse and widespread in the prokaryotic kingdom. They are composed of closely linked genes encoding a stable toxin that can harm the host cell and its cognate labile antitoxin, which protects the host from the toxin's deleterious effect. TA systems are thought to invade bacterial genomes through horizontal gene transfer. Some TA systems might behave as selfish elements and favour their own maintenance at the expense of their host. As a consequence, they may contribute to the maintenance of plasmids or genomic islands, such as super-integrons, by post-segregational killing of the cell that loses these genes and so suffers the stable toxin's destructive effect. The function of the chromosomally encoded TA systems is less clear and still open to debate. This Review discusses current hypotheses regarding the biological roles of these evolutionarily successful small operons. We consider the various selective forces that could drive the maintenance of TA systems in bacterial genomes. PMID:19325885

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism.

PubMed

Cuskin, Fiona; Lowe, Elisabeth C; Temple, Max J; Zhu, Yanping; Cameron, Elizabeth; Pudlo, Nicholas A; Porter, Nathan T; Urs, Karthik; Thompson, Andrew J; Cartmell, Alan; Rogowski, Artur; Hamilton, Brian S; Chen, Rui; Tolbert, Thomas J; Piens, Kathleen; Bracke, Debby; Vervecken, Wouter; Hakki, Zalihe; Speciale, Gaetano; Munōz-Munōz, Jose L; Day, Andrew; Peña, Maria J; McLean, Richard; Suits, Michael D; Boraston, Alisdair B; Atherly, Todd; Ziemer, Cherie J; Williams, Spencer J; Davies, Gideon J; Abbott, D Wade; Martens, Eric C; Gilbert, Harry J

2015-01-08

Yeasts, which have been a component of the human diet for at least 7,000 years, possess an elaborate cell wall α-mannan. The influence of yeast mannan on the ecology of the human microbiota is unknown. Here we show that yeast α-mannan is a viable food source for the Gram-negative bacterium Bacteroides thetaiotaomicron, a dominant member of the microbiota. Detailed biochemical analysis and targeted gene disruption studies support a model whereby limited cleavage of α-mannan on the surface generates large oligosaccharides that are subsequently depolymerized to mannose by the action of periplasmic enzymes. Co-culturing studies showed that metabolism of yeast mannan by B. thetaiotaomicron presents a 'selfish' model for the catabolism of this difficult to breakdown polysaccharide. Genomic comparison with B. thetaiotaomicron in conjunction with cell culture studies show that a cohort of highly successful members of the microbiota has evolved to consume sterically-restricted yeast glycans, an adaptation that may reflect the incorporation of eukaryotic microorganisms into the human diet.

A selfish genetic element confers non-Mendelian inheritance in rice.

PubMed

Yu, Xiaowen; Zhao, Zhigang; Zheng, Xiaoming; Zhou, Jiawu; Kong, Weiyi; Wang, Peiran; Bai, Wenting; Zheng, Hai; Zhang, Huan; Li, Jing; Liu, Jiafan; Wang, Qiming; Zhang, Long; Liu, Kai; Yu, Yang; Guo, Xiuping; Wang, Jiulin; Lin, Qibing; Wu, Fuqing; Ren, Yulong; Zhu, Shanshan; Zhang, Xin; Cheng, Zhijun; Lei, Cailin; Liu, Shijia; Liu, Xi; Tian, Yunlu; Jiang, Ling; Ge, Song; Wu, Chuanyin; Tao, Dayun; Wang, Haiyang; Wan, Jianmin

2018-06-08

Selfish genetic elements are pervasive in eukaryote genomes, but their role remains controversial. We show that qHMS7 , a major quantitative genetic locus for hybrid male sterility between wild rice ( Oryza meridionalis ) and Asian cultivated rice ( O. sativa ), contains two tightly linked genes [ Open Reading Frame 2 ( ORF2 ) and ORF3 ]. ORF2 encodes a toxic genetic element that aborts pollen in a sporophytic manner, whereas ORF3 encodes an antidote that protects pollen in a gametophytic manner. Pollens lacking ORF3 are selectively eliminated, leading to segregation distortion in the progeny. Analysis of the genetic sequence suggests that ORF3 arose first, followed by gradual functionalization of ORF2 Furthermore, this toxin-antidote system may have promoted the differentiation and/or maintained the genome stability of wild and cultivated rice. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Social penalty promotes cooperation in a cooperative society.

PubMed

Ito, Hiromu; Yoshimura, Jin

2015-08-04

Why cooperation is well developed in human society is an unsolved question in biological and human sciences. Vast studies in game theory have revealed that in non-cooperative games selfish behavior generally dominates over cooperation and cooperation can be evolved only under very limited conditions. These studies ask the origin of cooperation; whether cooperation can evolve in a group of selfish individuals. In this paper, instead of asking the origin of cooperation, we consider the enhancement of cooperation in a small already cooperative society. We ask whether cooperative behavior is further promoted in a small cooperative society in which social penalty is devised. We analyze hawk-dove game and prisoner's dilemma introducing social penalty. We then expand it for non-cooperative games in general. The results indicate that cooperation is universally favored if penalty is further imposed. We discuss the current result in terms of the moral, laws, rules and regulations in a society, e.g., criminology and traffic violation.

Packet error rate analysis of decode-and-forward free-space optical cooperative networks in the presence of random link blockage

NASA Astrophysics Data System (ADS)

Zdravković, Nemanja; Cvetkovic, Aleksandra; Milic, Dejan; Djordjevic, Goran T.

2017-09-01

This paper analyses end-to-end packet error rate (PER) of a free-space optical decode-and-forward cooperative network over a gamma-gamma atmospheric turbulence channel in the presence of temporary random link blockage. Closed-form analytical expressions for PER are derived for the cases with and without transmission links being prone to blockage. Two cooperation protocols (denoted as 'selfish' and 'pilot-adaptive') are presented and compared, where the latter accounts for the presence of blockage and adapts transmission power. The influence of scintillation, link distance, average transmitted signal power, network topology and probability of an uplink and/or internode link being blocked are discussed when the destination applies equal gain combining. The results show that link blockage caused by obstacles can degrade system performance, causing an unavoidable PER floor. The implementation of the pilot-adaptive protocol improves performance when compared to the selfish protocol, diminishing internode link blockage and lowering the PER floor, especially for larger networks.

Statics and Dynamics of Selfish Interactions in Distributed Service Systems

PubMed Central

Altarelli, Fabrizio; Braunstein, Alfredo; Dall’Asta, Luca

2015-01-01

We study a class of games which models the competition among agents to access some service provided by distributed service units and which exhibits congestion and frustration phenomena when service units have limited capacity. We propose a technique, based on the cavity method of statistical physics, to characterize the full spectrum of Nash equilibria of the game. The analysis reveals a large variety of equilibria, with very different statistical properties. Natural selfish dynamics, such as best-response, usually tend to large-utility equilibria, even though those of smaller utility are exponentially more numerous. Interestingly, the latter actually can be reached by selecting the initial conditions of the best-response dynamics close to the saturation limit of the service unit capacities. We also study a more realistic stochastic variant of the game by means of a simple and effective approximation of the average over the random parameters, showing that the properties of the average-case Nash equilibria are qualitatively similar to the deterministic ones. PMID:26177449

Social penalty promotes cooperation in a cooperative society

PubMed Central

Ito, Hiromu; Yoshimura, Jin

2015-01-01

Why cooperation is well developed in human society is an unsolved question in biological and human sciences. Vast studies in game theory have revealed that in non-cooperative games selfish behavior generally dominates over cooperation and cooperation can be evolved only under very limited conditions. These studies ask the origin of cooperation; whether cooperation can evolve in a group of selfish individuals. In this paper, instead of asking the origin of cooperation, we consider the enhancement of cooperation in a small already cooperative society. We ask whether cooperative behavior is further promoted in a small cooperative society in which social penalty is devised. We analyze hawk-dove game and prisoner’s dilemma introducing social penalty. We then expand it for non-cooperative games in general. The results indicate that cooperation is universally favored if penalty is further imposed. We discuss the current result in terms of the moral, laws, rules and regulations in a society, e.g., criminology and traffic violation. PMID:26238521

Mariner and the ITm Superfamily of Transposons.

PubMed

Tellier, Michael; Bouuaert, Corentin Claeys; Chalmers, Ronald

2015-04-01

The IS630-Tc1-mariner (ITm) family of transposons is one of the most widespread in nature. The phylogenetic distribution of its members shows that they do not persist for long in a given lineage, but rely on frequent horizontal transfer to new hosts. Although they are primarily selfish genomic-parasites, ITm transposons contribute to the evolution of their hosts because they generate variation and contribute protein domains and regulatory regions. Here we review the molecular mechanism of ITm transposition and its regulation. We focus mostly on the mariner elements, which are understood in the greatest detail owing to in vitro reconstitution and structural analysis. Nevertheless, the most important characteristics are probably shared across the grouping. Members of the ITm family are mobilized by a cut-and-paste mechanism and integrate at 5'-TA dinucleotide target sites. The elements encode a single transposase protein with an N-terminal DNA-binding domain and a C-terminal catalytic domain. The phosphoryl-transferase reactions during the DNA-strand breaking and joining reactions are performed by the two metal-ion mechanism. The metal ions are coordinated by three or four acidic amino acid residues located within an RNase H-like structural fold. Although all of the strand breaking and joining events at a given transposon end are performed by a single molecule of transposase, the reaction is coordinated by close communication between transpososome components. During transpososome assembly, transposase dimers compete for free transposon ends. This helps to protect the host by dampening an otherwise exponential increase in the rate of transposition as the copy number increases.

Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle

DOE PAGES

Walworth, Nathan; Pfreundt, Ulrike; Nelson, William C.; ...

2015-03-23

Understanding the evolution of the free-living, cyanobacterial, diazotroph Trichodesmium is of great importance because of its critical role in oceanic biogeochemistry and primary production. Unlike the other >150 available genomes of free-living cyanobacteria, only 63.8% of the Trichodesmium erythraeum (strain IMS101) genome is predicted to encode protein, which is 20–25% less than the average for other cyanobacteria and nonpathogenic, free-living bacteria. In this paper, we use distinctive isolates and metagenomic data to show that low coding density observed in IMS101 is a common feature of the Trichodesmium genus, both in culture and in situ. Transcriptome analysis indicates that 86% ofmore » the noncoding space is expressed, although the function of these transcripts is unclear. The density of noncoding, possible regulatory elements predicted in Trichodesmium, when normalized per intergenic kilobase, was comparable and twofold higher than that found in the gene-dense genomes of the sympatric cyanobacterial genera Synechococcus and Prochlorococcus, respectively. Conserved Trichodesmium noncoding RNA secondary structures were predicted between most culture and metagenomic sequences, lending support to the structural conservation. Conservation of these intergenic regions in spatiotemporally separated Trichodesmium populations suggests possible genus-wide selection for their maintenance. These large intergenic spacers may have developed during intervals of strong genetic drift caused by periodic blooms of a subset of genotypes, which may have reduced effective population size. Finally, our data suggest that transposition of selfish DNA, low effective population size, and high-fidelity replication allowed the unusual “inflation” of noncoding sequence observed in Trichodesmium despite its oligotrophic lifestyle.« less

Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle

DOE PAGES

Walworth, Nathan G.; Pfreundt, Ulrike; Nelson, William C.; ...

2015-04-07

Understanding the evolution of the free-living, cyanobacterial, diazotroph Trichodesmium is of great importance due to its critical role in oceanic biogeochemistry and primary production. Unlike the other >150 available genomes of free-living cyanobacteria, only 63.8% of the Trichodesmium erythraeum (strain IMS101) genome is predicted to encode protein, which is 20-25% less than the average for other cyanobacteria and non-pathogenic, free-living bacteria. We use distinctive isolates and metagenomic data to show that low coding density observed in IMS101 is a common feature of the Trichodesmium genus both in culture and in situ. Transcriptome analysis indicates that 86% of the non-coding spacemore » is expressed, although the function of these transcripts is unclear. The density of noncoding, possible regulatory elements predicted in Trichodesmium, when normalized per intergenic kilobase, was comparable and two fold higher than that found in the gene dense genomes of the sympatric cyanobacterial genera Synechococcus and Prochlorococcus, respectively. Conserved Trichodesmium ncRNA secondary structures were predicted between most culture and metagenomic sequences lending support to the structural conservation. Conservation of these intergenic regions in spatiotemporally separated Trichodesmium populations suggests possible genus-wide selection for their maintenance. These large intergenic spacers may have developed during intervals of strong genetic drift caused by periodic blooms of a subset of genotypes, which may have reduced effective population size. Our data suggest that transposition of selfish DNA, low effective population size, and high fidelity replication allowed the unusual ‘inflation’ of noncoding sequence observed in Trichodesmium despite its oligotrophic lifestyle.« less

Evolution of animal and plant dicers: early parallel duplications and recurrent adaptation of antiviral RNA binding in plants.

PubMed

Mukherjee, Krishanu; Campos, Henry; Kolaczkowski, Bryan

2013-03-01

RNA interference (RNAi) is a eukaryotic molecular system that serves two primary functions: 1) gene regulation and 2) protection against selfish elements such as viruses and transposable DNA. Although the biochemistry of RNAi has been detailed in model organisms, very little is known about the broad-scale patterns and forces that have shaped RNAi evolution. Here, we provide a comprehensive evolutionary analysis of the Dicer protein family, which carries out the initial RNA recognition and processing steps in the RNAi pathway. We show that Dicer genes duplicated and diversified independently in early animal and plant evolution, coincident with the origins of multicellularity. We identify a strong signature of long-term protein-coding adaptation that has continually reshaped the RNA-binding pocket of the plant Dicer responsible for antiviral immunity, suggesting an evolutionary arms race with viral factors. We also identify key changes in Dicer domain architecture and sequence leading to specialization in either gene-regulatory or protective functions in animal and plant paralogs. As a whole, these results reveal a dynamic picture in which the evolution of Dicer function has driven elaboration of parallel RNAi functional pathways in animals and plants.

Flipping chromosomes in deep-sea archaea

PubMed Central

Catchpole, Ryan; Gadelle, Danièle; Marguet, Evelyne; Barbe, Valérie; Forterre, Patrick

2017-01-01

One of the major mechanisms driving the evolution of all organisms is genomic rearrangement. In hyperthermophilic Archaea of the order Thermococcales, large chromosomal inversions occur so frequently that even closely related genomes are difficult to align. Clearly not resulting from the native homologous recombination machinery, the causative agent of these inversions has remained elusive. We present a model in which genomic inversions are catalyzed by the integrase enzyme encoded by a family of mobile genetic elements. We characterized the integrase from Thermococcus nautili plasmid pTN3 and showed that besides canonical site-specific reactions, it catalyzes low sequence specificity recombination reactions with the same outcome as homologous recombination events on DNA segments as short as 104bp both in vitro and in vivo, in contrast to other known tyrosine recombinases. Through serial culturing, we showed that the integrase-mediated divergence of T. nautili strains occurs at an astonishing rate, with at least four large-scale genomic inversions appearing within 60 generations. Our results and the ubiquitous distribution of pTN3-like integrated elements suggest that a major mechanism of evolution of an entire order of Archaea results from the activity of a selfish mobile genetic element. PMID:28628615

Transposable elements and insecticide resistance.

PubMed

Rostant, Wayne G; Wedell, Nina; Hosken, David J

2012-01-01

Transposable elements (TEs) are mobile DNA sequences that are able to copy themselves within a host genome. They were initially characterized as selfish genes because of documented or presumed costs to host fitness, but it has become increasingly clear that not all TEs reduce host fitness. A good example of TEs benefiting hosts is seen with insecticide resistance, where in a number of cases, TE insertions near specific genes confer resistance to these man-made products. This is particularly true of Accord and associated TEs in Drosophila melanogaster and Doc insertions in Drosophila simulans. The first of these insertions also has sexually antagonistic fitness effects in the absence of insecticides, and although the magnitude of this effect depends on the genetic background in which Accord finds itself, this represents an excellent example of intralocus sexual conflict where the precise allele involved is well characterized. We discuss this finding and the role of TEs in insecticide resistance. We also highlight areas for further research, including the need for surveys of the prevalence and fitness consequences of the Doc insertion and how Drosophila can be used as models to investigate resistance in pest species. Copyright © 2012 Elsevier Inc. All rights reserved.

Partner choice creates fairness in humans.

PubMed

Debove, Stéphane; André, Jean-Baptiste; Baumard, Nicolas

2015-06-07

Many studies demonstrate that partner choice has played an important role in the evolution of human cooperation, but little work has tested its impact on the evolution of human fairness. In experiments involving divisions of money, people become either over-generous or over-selfish when they are in competition to be chosen as cooperative partners. Hence, it is difficult to see how partner choice could result in the evolution of fair, equal divisions. Here, we show that this puzzle can be solved if we consider the outside options on which partner choice operates. We conduct a behavioural experiment, run agent-based simulations and analyse a game-theoretic model to understand how outside options affect partner choice and fairness. All support the conclusion that partner choice leads to fairness only when individuals have equal outside options. We discuss how this condition has been met in our evolutionary history, and the implications of these findings for our understanding of other aspects of fairness less specific than preferences for equal divisions of resources. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

FastID: Extremely Fast Forensic DNA Comparisons

DTIC Science & Technology

2017-05-19

FastID: Extremely Fast Forensic DNA Comparisons Darrell O. Ricke, PhD Bioengineering Systems & Technologies Massachusetts Institute of...Technology Lincoln Laboratory Lexington, MA USA Darrell.Ricke@ll.mit.edu Abstract—Rapid analysis of DNA forensic samples can have a critical impact on...time sensitive investigations. Analysis of forensic DNA samples by massively parallel sequencing is creating the next gold standard for DNA

Building a Phylogenetic Tree of the Human and Ape Superfamily Using DNA-DNA Hybridization Data

ERIC Educational Resources Information Center

Maier, Caroline Alexander

2004-01-01

The study describes the process of DNA-DNA hybridization and the history of its use by Sibley and Alquist in simple, straightforward, and interesting language that students easily understand to create their own phylogenetic tree of the hominoid superfamily. They calibrate the DNA clock and use it to estimate the divergence dates of the various…

Easi-CRISPR for creating knock-in and conditional knockout mouse models using long ssDNA donors.

PubMed

Miura, Hiromi; Quadros, Rolen M; Gurumurthy, Channabasavaiah B; Ohtsuka, Masato

2018-01-01

CRISPR/Cas9-based genome editing can easily generate knockout mouse models by disrupting the gene sequence, but its efficiency for creating models that require either insertion of exogenous DNA (knock-in) or replacement of genomic segments is very poor. The majority of mouse models used in research involve knock-in (reporters or recombinases) or gene replacement (e.g., conditional knockout alleles containing exons flanked by LoxP sites). A few methods for creating such models have been reported that use double-stranded DNA as donors, but their efficiency is typically 1-10% and therefore not suitable for routine use. We recently demonstrated that long single-stranded DNAs (ssDNAs) serve as very efficient donors, both for insertion and for gene replacement. We call this method efficient additions with ssDNA inserts-CRISPR (Easi-CRISPR) because it is a highly efficient technology (efficiency is typically 30-60% and reaches as high as 100% in some cases). The protocol takes ∼2 months to generate the founder mice.

Mechanical properties of DNA-like polymers

PubMed Central

Peters, Justin P.; Yelgaonkar, Shweta P.; Srivatsan, Seergazhi G.; Tor, Yitzhak; James Maher, L.

2013-01-01

The molecular structure of the DNA double helix has been known for 60 years, but we remain surprisingly ignorant of the balance of forces that determine its mechanical properties. The DNA double helix is among the stiffest of all biopolymers, but neither theory nor experiment has provided a coherent understanding of the relative roles of attractive base stacking forces and repulsive electrostatic forces creating this stiffness. To gain insight, we have created a family of double-helical DNA-like polymers where one of the four normal bases is replaced with various cationic, anionic or neutral analogs. We apply DNA ligase-catalyzed cyclization kinetics experiments to measure the bending and twisting flexibilities of these polymers under low salt conditions. Interestingly, we show that these modifications alter DNA bending stiffness by only 20%, but have much stronger (5-fold) effects on twist flexibility. We suggest that rather than modifying DNA stiffness through a mechanism easily interpretable as electrostatic, the more dominant effect of neutral and charged base modifications is their ability to drive transitions to helical conformations different from canonical B-form DNA. PMID:24013560

Programmable DNA tile self-assembly using a hierarchical sub-tile strategy.

PubMed

Shi, Xiaolong; Lu, Wei; Wang, Zhiyu; Pan, Linqiang; Cui, Guangzhao; Xu, Jin; LaBean, Thomas H

2014-02-21

DNA tile based self-assembly provides a bottom-up approach to construct desired nanostructures. DNA tiles have been directly constructed from ssDNA and readily self-assembled into 2D lattices and 3D superstructures. However, for more complex lattice designs including algorithmic assemblies requiring larger tile sets, a more modular approach could prove useful. This paper reports a new DNA 'sub-tile' strategy to easily create whole families of programmable tiles. Here, we demonstrate the stability and flexibility of our sub-tile structures by constructing 3-, 4- and 6-arm DNA tiles that are subsequently assembled into 2D lattices and 3D nanotubes according to a hierarchical design. Assembly of sub-tiles, tiles, and superstructures was analyzed using polyacrylamide gel electrophoresis and atomic force microscopy. DNA tile self-assembly methods provide a bottom-up approach to create desired nanostructures; the sub-tile strategy adds a useful new layer to this technique. Complex units can be made from simple parts. The sub-tile approach enables the rapid redesign and prototyping of complex DNA tile sets and tiles with asymmetric designs.

Sharing, Discounting, and Selfishness: A Japanese-American Comparison

ERIC Educational Resources Information Center

Ito, Masato; Saeki, Daisuke; Green, Leonard

2011-01-01

Social discounting rates were compared between Japanese and American college students. In a series of psychophysical questionnaire tasks, participants chose between a hypothetical unshared monetary reward and a hypothetical monetary reward to be shared with other people (relatives or strangers), to determine amounts of the unshared reward…

PriC-mediated DNA replication restart requires PriC complex formation with the single-stranded DNA-binding protein.

PubMed

Wessel, Sarah R; Marceau, Aimee H; Massoni, Shawn C; Zhou, Ruobo; Ha, Taekjip; Sandler, Steven J; Keck, James L

2013-06-14

Frequent collisions between cellular DNA replication complexes (replisomes) and obstacles such as damaged DNA or frozen protein complexes make DNA replication fork progression surprisingly sporadic. These collisions can lead to the ejection of replisomes prior to completion of replication, which, if left unrepaired, results in bacterial cell death. As such, bacteria have evolved DNA replication restart mechanisms that function to reload replisomes onto abandoned DNA replication forks. Here, we define a direct interaction between PriC, a key Escherichia coli DNA replication restart protein, and the single-stranded DNA-binding protein (SSB), a protein that is ubiquitously associated with DNA replication forks. PriC/SSB complex formation requires evolutionarily conserved residues from both proteins, including a pair of Arg residues from PriC and the C terminus of SSB. In vitro, disruption of the PriC/SSB interface by sequence changes in either protein blocks the first step of DNA replication restart, reloading of the replicative DnaB helicase onto an abandoned replication fork. Consistent with the critical role of PriC/SSB complex formation in DNA replication restart, PriC variants that cannot bind SSB are non-functional in vivo. Single-molecule experiments demonstrate that PriC binding to SSB alters SSB/DNA complexes, exposing single-stranded DNA and creating a platform for other proteins to bind. These data lead to a model in which PriC interaction with SSB remodels SSB/DNA structures at abandoned DNA replication forks to create a DNA structure that is competent for DnaB loading.

Design of Availability-Dependent Distributed Services in Large-Scale Uncooperative Settings

ERIC Educational Resources Information Center

Morales, Ramses Victor

2009-01-01

Thesis Statement: "Availability-dependent global predicates can be efficiently and scalably realized for a class of distributed services, in spite of specific selfish and colluding behaviors, using local and decentralized protocols". Several types of large-scale distributed systems spanning the Internet have to deal with availability variations…

A Glimpse into the Cultural Foundations of Open Innovation

ERIC Educational Resources Information Center

Formica, Piero

2018-01-01

In the knowledge economy, greater togetherness is the prerequisite for innovating and having more: selflessness extends scope while selfishness increases limitations. But human beings are not automatically attracted to innovation: between the two lies culture, and cultural values vary widely, with the egoistic accent or the altruistic intonation…

Designing an Advanced Instructional Design Advisor: Possibilities for Automation. Volume 3

DTIC Science & Technology

1991-05-01

system (Spec. Rep. NPRDC- SR-83-13). San Diego, CA: Navy Personnel Research and Development Center. Dawkins , R. (1976). The selfish gene . Oxford...instructional methods that keep the idea alive will change in corresponding ways. (See Dawkins (1976) for a discussion of related ideas.) The implications of

Suicide Terrorism: Deadly Tactic or Operational Art at Work?

DTIC Science & Technology

2009-05-04

clerical leader, opined in a 1996 interview printed in an Egyptian newspaper that “suicide puts an end to his life out of selfish considerations...attacks in support of their strategic objectives. Following the February 1994 massacre in the Tomb of the Patriarchs-Khalili Mosque perpetrated by

Friends Helping Friends: A Manual for Peer Counselors.

ERIC Educational Resources Information Center

Painter, Carol

This manual presents a training program for peer counselors which focuses on three areas: helper development, skills development, and topic development. The first chapter focuses on helper development. Pitfalls on the path to helping are discussed. Being your own best friend, selfishness, responsibility, feelings, advice-giving, being healthy,…

Altered nuclear transport and the most selfish of genes.

PubMed

Hawley, R S

2001-09-01

The Segregation Distorter System in Drosophila is one of the best-known and genetically characterized systems of meiotic drive. A recent paper by Kusano et al. (2001) provides a key molecular insight into the molecular mechanism by which one chromosome can ensure the destruction of its partner.

Hard Times for American Youth: A Look at the Reasons.

ERIC Educational Resources Information Center

Uhlenberg, Peter; Eggebeen, David

1988-01-01

According to national statistics on death rates, criminal behavior, and other indicators, the well-being of White adolescents has declined markedly between 1960 and 1980, despite certain improvements in families, schools, and youth programs. American culture seems geared to a selfish individualism inconsistent with maintaining strong families and…

Adolescent Psychopathy and the Big Five: Results from Two Samples

ERIC Educational Resources Information Center

Lynam, Donald R.; Caspi, Avshalom; Moffitt, Terrie E.; Raine, Adrian; Loeber, Rolf; Stouthamer-Loeber, Magda

2005-01-01

The present study examines the relation between psychopathy and the Big Five dimensions of personality in two samples of adolescents. Specifically, the study tests the hypothesis that the aspect of psychopathy representing selfishness, callousness, and interpersonal manipulation (Factor 1) is most strongly associated with low Agreeableness,…

Being Selfish: Taking Personal Responsibility for Excellence

ERIC Educational Resources Information Center

Johnson, Larry

2013-01-01

Nordstrom department stores, Disney, Lands' End, and the Merck pharmaceutical company to name a few. Many books and articles have been written in the past 20 years about the factors that such companies have in common. The oft-named factors are (1) a focus on the customer,…

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

USDA-ARS?s Scientific Manuscript database

The architecture of the human distal gut microbiota (microbiota) is sculpted by the complex carbohydrates delivered in the diet. Yeasts, which are among the earliest domesticated microorganisms and have been a component of the human diet for at least 7000 years, possess an elaborate cell wall alpha-...

On Tradeoffs between Trust Accuracy and Resource Consumption in Communications and Social Networks

DTIC Science & Technology

2016-04-11

length, the use of indirect information to establish trust values, and the impact of misbehaving nodes on both communication overhead and the...evaluated). We consider the impact of misbehaving (selfish or malicious) nodes on the evaluation of trust. We also consider the interaction between

Sequencing and molecular dissection of Sk-2 in Neurospora

USDA-ARS?s Scientific Manuscript database

Neurospora Spore killer-2 is a selfish meiotic drive element that kills its non-Sk-2 siblings during sexual sporulation. Although the location of Sk-2 has been mapped to a large recombination-suppressed region of chromosome III, the physical length and exact borders of the element have remained unde...

Imaging and sizing of single DNA molecules on a mobile phone.

PubMed

Wei, Qingshan; Luo, Wei; Chiang, Samuel; Kappel, Tara; Mejia, Crystal; Tseng, Derek; Chan, Raymond Yan Lok; Yan, Eddie; Qi, Hangfei; Shabbir, Faizan; Ozkan, Haydar; Feng, Steve; Ozcan, Aydogan

2014-12-23

DNA imaging techniques using optical microscopy have found numerous applications in biology, chemistry and physics and are based on relatively expensive, bulky and complicated set-ups that limit their use to advanced laboratory settings. Here we demonstrate imaging and length quantification of single molecule DNA strands using a compact, lightweight and cost-effective fluorescence microscope installed on a mobile phone. In addition to an optomechanical attachment that creates a high contrast dark-field imaging setup using an external lens, thin-film interference filters, a miniature dovetail stage and a laser-diode for oblique-angle excitation, we also created a computational framework and a mobile phone application connected to a server back-end for measurement of the lengths of individual DNA molecules that are labeled and stretched using disposable chips. Using this mobile phone platform, we imaged single DNA molecules of various lengths to demonstrate a sizing accuracy of <1 kilobase-pairs (kbp) for 10 kbp and longer DNA samples imaged over a field-of-view of ∼2 mm2.

3D DNA Crystals and Nanotechnology

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

Paukstelis, Paul; Seeman, Nadrian

DNA's molecular recognition properties have made it one of the most widely used biomacromolecular construction materials. The programmed assembly of DNA oligonucleotides has been used to create complex 2D and 3D self-assembled architectures and to guide the assembly of other molecules. The origins of DNA nanotechnology are rooted in the goal of assembling DNA molecules into designed periodic arrays, i.e., crystals. Here, we highlight several DNA crystal structures, the progress made in designing DNA crystals, and look at the current prospects and future directions of DNA crystals in nanotechnology.

3D DNA Crystals and Nanotechnology

DOE PAGES

Paukstelis, Paul; Seeman, Nadrian

2016-08-18

DNA's molecular recognition properties have made it one of the most widely used biomacromolecular construction materials. The programmed assembly of DNA oligonucleotides has been used to create complex 2D and 3D self-assembled architectures and to guide the assembly of other molecules. The origins of DNA nanotechnology are rooted in the goal of assembling DNA molecules into designed periodic arrays, i.e., crystals. Here, we highlight several DNA crystal structures, the progress made in designing DNA crystals, and look at the current prospects and future directions of DNA crystals in nanotechnology.

Disentangling DNA molecules

NASA Astrophysics Data System (ADS)

Vologodskii, Alexander

2016-09-01

The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.

DNA-based construction at the nanoscale: emerging trends and applications

NASA Astrophysics Data System (ADS)

Lourdu Xavier, P.; Chandrasekaran, Arun Richard

2018-02-01

The field of structural DNA nanotechnology has evolved remarkably—from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes—in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.

DNA-based construction at the nanoscale: emerging trends and applications.

PubMed

Xavier, P Lourdu; Chandrasekaran, Arun Richard

2018-02-09

The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.

Initial analysis of sperm DNA methylome in Holstein bulls

USDA-ARS?s Scientific Manuscript database

Aberrant DNA methylation patterns have been associated with abnormal semen parameters, idiopathic male infertility and early embryonic loss in mammals. Using Holstein bulls with high (Bull1) or low (Bull2) fertility rates, we created two representative sperm DNA methylomes at a single-base resolutio...

A 3D Model of Double-Helical DNA Showing Variable Chemical Details

ERIC Educational Resources Information Center

Cady, Susan G.

2005-01-01

Since the first DNA model was created approximately 50 years ago using molecular models, students and teachers have been building simplified DNA models from various practical materials. A 3D double-helical DNA model, made by placing beads on a wire and stringing beads through holes in plastic canvas, is described. Suggestions are given to enhance…

A difference in the pattern of repair in a large genomic region in UV-irradiated normal human and Cockayne syndrome cells.

PubMed

Shanower, G A; Kantor, G J

1997-11-01

Xeroderma pigmentosum group C cells repair DNA damaged by ultraviolet radiation in an unusual pattern throughout the genome. They remove cyclobutane pyrimidine dimers only from the DNA of transcriptionally active chromatin regions and only from the strand that contains the transcribed strand. The repair proceeds in a manner that creates damage-free islands which are in some cases much larger than the active gene associated with them. For example, the small transcriptionally active beta-actin gene (3.5 kb) is repaired as part of a 50 kb single-stranded region. The repair responsible for creating these islands requires active transcription, suggesting that the two activities are coupled. A preferential repair pathway in normal human cells promotes repair of actively transcribed DNA strands and is coupled to transcription. It is not known if similar large islands, referred to as repair domains, are preferentially created as a result of the coupling. Data are presented showing that in normal cells, preferential repair in the beta-actin region is associated with the creation of a large, completely repaired region in the partially repaired genome. Repair at other genomic locations which contain inactive genes (insulin, 754) does not create similar large regions as quickly. In contrast, repair in Cockayne syndrome cells, which are defective in the preferential repair pathway but not in genome-overall repair, proceeds in the beta-actin region by a mechanism which does not create preferentially a large repaired region. Thus a correlation between the activity required to preferentially repair active genes and that required to create repaired domains is detected. We propose an involvement of the transcription-repair coupling factor in a coordinated repair pathway for removing DNA damage from entire transcription units.

Cutaneous gene expression of plasmid DNA in excised human skin following delivery via microchannels created by radio frequency ablation.

PubMed

Birchall, James; Coulman, Sion; Anstey, Alexander; Gateley, Chris; Sweetland, Helen; Gershonowitz, Amikam; Neville, Lewis; Levin, Galit

2006-04-07

The skin is a valuable organ for the development and exploitation of gene medicines. Delivering genes to skin is restricted however by the physico-chemical properties of DNA and the stratum corneum (SC) barrier. In this study, we demonstrate the utility of an innovative technology that creates transient microconduits in human skin, allowing DNA delivery and resultant gene expression within the epidermis and dermis layers. The radio frequency (RF)-generated microchannels were of sufficient morphology and depth to permit the epidermal delivery of 100 nm diameter nanoparticles. Model fluorescent nanoparticles were used to confirm the capacity of the channels for augmenting diffusion of macromolecules through the SC. An ex vivo human organ culture model was used to establish the gene expression efficiency of a beta-galactosidase reporter plasmid DNA applied to ViaDerm treated skin. Skin treated with ViaDerm using 50 microm electrode arrays promoted intense levels of gene expression in the viable epidermis. The intensity and extent of gene expression was superior when ViaDerm was used following a prior surface application of the DNA formulation. In conclusion, the RF-microchannel generator (ViaDerm) creates microchannels amenable for delivery of nanoparticles and gene therapy vectors to the viable region of skin.

Passing On: Personal Attributes Associated with Midlife Expressions of Intended Legacies

ERIC Educational Resources Information Center

Newton, Nicky J.; Jones, Brady K.

2016-01-01

Expressions of the intent to leave behind something when we die can contain elements of both selflessness and selfishness. In this paper, we identify 3 different types of expressed legacy (personal, broader, and composite), and distinguish between them by examining their correlates (generativity, narcissism, and community involvement), as well as…

Profit Is Not a Dirty Word: The Role of Money in Education.

ERIC Educational Resources Information Center

Payne, James L.

1996-01-01

In "Corporate School Takeovers," the National Education Association expresses indignation over profit making by private companies providing services to schools. Argues that profits are a way of recognizing costs that exist in all school settings. The seeking of profits is no more selfish than the seeking of higher salaries, promotions,…

"They Sit Selfishly." Beginning STEM Educators' Expectations of Young Adolescent Students

ERIC Educational Resources Information Center

Jordan, Robert; DiCicco, Mike; Sabella, Laura

2017-01-01

To meet the demand for certified math and science teachers, alternative certification programs attempt to provide fast-track training and licensure of STEM-area educators (Goldhaber, Kreig, Theobald, & Brown, 2014). Teachers prepared in programs with a middle level specialization have been shown to participate in effective practices such as…

The Architecture of Interdependent Minds: A Motivation-Management Theory of Mutual Responsiveness

ERIC Educational Resources Information Center

Murray, Sandra L.; Holmes, John G.

2009-01-01

A model of mutual responsiveness in adult romantic relationships is proposed. Behaving responsively in conflict-of-interest situations requires one partner to resist the temptation to be selfish and the other partner to resist the temptation to protect against exploitation. Managing risk and the attendant temptations of self-interest require the…

Giving Education a Bad Name: Bookish Boys in Contemporary American School Stories

ERIC Educational Resources Information Center

Aitchison, David

2018-01-01

This article discusses contemporary American school stories that appear to advocate learning and literacy as a democratic good, but actually undermine democratic possibilities by teaching young readers to think of academic inquiry as a means to selfish, petty ends. Since "learning" and "literacy" are catchwords for educators…

Purposes and Effects of Lying.

ERIC Educational Resources Information Center

Hample, Dale

Three exploratory studies were aimed at describing the purposes of lies and the consequences of lying. Data were collected through a partly open-ended questionnaire, a content analysis of several tape-recorded interviews, and a large-scale survey. The results showed that two of every three lies were told for selfish reasons, while three of every…

Midlife Women in Continuing Education: A Comparative Study.

ERIC Educational Resources Information Center

Traupmann, Jane

Developmental theorists have suggested recently that at midlife women often want to reduce responsibilities to family and concentrate on self-development and growth, which earlier in their lives would have seemed to them selfish and therefore not acceptable. The aim of this comparative study was to determine if women returning to school at midlife…

The Strategic Revolution.

PubMed

Gardner, Andy

2016-09-08

On the 40(th) anniversary of the publication of Richard Dawkins's The Selfish Gene, we explore the origins of cynical, strategic thinking in evolutionary biology, investigate how this illuminated the sexual and social lives of animals, and assess Dawkins's suggestion that evolution is best understood by taking the gene's-eye view. Copyright © 2016 Elsevier Inc. All rights reserved.

Leadership and the Force of Love: Six Keys to Motivating with Love.

ERIC Educational Resources Information Center

Hoyle, John R.

Although educators are frequently faced with the challenges of politics, hostility, selfishness, and violence, this book demonstrates that these obstacles can be overcome through vision, teamwork, motivation, empowerment, and communication. By using love as a guiding force in the daily interactions with others, the way one conducts business is…

Sports and Competition in Higher Education: A Search for Values and Ethics

ERIC Educational Resources Information Center

Sciarabba, Davide

2012-01-01

The issue of competition in sports is controversial in certain philosophies of education, especially among the more conservative, often religious, educators. Some understand competition negatively, as opposed to ideal human solidarity, and therefore argue that the practice of sports conveys dangerous attitudes of violence, pride, selfishness, etc.…

Development and Psychometric Evaluation of the Military Suicide Attitudes Questionnaire (MSAQ)

DTIC Science & Technology

2015-05-12

selfish 42 People who kill themselves will burn in hell 43 Someone who kills themselves must not believe in an afterlife 44 Those who attempt suicide...who attempt suicide will be punished in the afterlife 62 God will forgive those who take their own life 63 Chaplains should be required to report

Homosexuals' and Lesbians' Philosophies of Human Nature.

ERIC Educational Resources Information Center

Weller, Leonard; Benozio, Motti

1987-01-01

Compared 57 homosexual men and 45 lesbians on six dimensions of beliefs about human nature. On only one dimension was significant difference found: lesbians saw people as more altruistic and less selfish than did homosexual men. Findings are consistent with the few personality studies which report no differences between homosexuals and lesbians.…

Moderating Effects of Social Value Orientation on the Effect of Social Influence in Prosocial Decisions

PubMed Central

Wei, Zhenyu; Zhao, Zhiying; Zheng, Yong

2016-01-01

Prosocial behaviors are susceptible to individuals’ preferences regarding payoffs and social context. In the present study, we combined individual differences with social influence and attempted to discover the effect of social value orientation (SVO) and social influence on prosocial behavior in a trust game and a dictator game. Prosocial behavior in the trust game could be motivated by strategic considerations whereas individuals’ decisions in the dictator game could be associated with their social preference. In the trust game, prosocials were less likely than proselfs to conform to the behavior of other group members when the majority of group members distrusted the trustee. In the dictator game, the results of the three-way ANOVA indicated that, irrespective of the type of offer, in contrast to proselfs, prosocials were influenced more by others’ generous choices than their selfish choices, even if the selfish choices were beneficial to themselves. The overall results demonstrated that the effect of social influence appears to depend on individuals’ SVO: that is, prosocials tend to conform to prosocial rather than proself behaviors. PMID:27445917

Genetic addiction: selfish gene's strategy for symbiosis in the genome.

PubMed

Mochizuki, Atsushi; Yahara, Koji; Kobayashi, Ichizo; Iwasa, Yoh

2006-02-01

The evolution and maintenance of the phenomenon of postsegregational host killing or genetic addiction are paradoxical. In this phenomenon, a gene complex, once established in a genome, programs death of a host cell that has eliminated it. The intact form of the gene complex would survive in other members of the host population. It is controversial as to why these genetic elements are maintained, due to the lethal effects of host killing, or perhaps some other properties are beneficial to the host. We analyzed their population dynamics by analytical methods and computer simulations. Genetic addiction turned out to be advantageous to the gene complex in the presence of a competitor genetic element. The advantage is, however, limited in a population without spatial structure, such as that in a well-mixed liquid culture. In contrast, in a structured habitat, such as the surface of a solid medium, the addiction gene complex can increase in frequency, irrespective of its initial density. Our demonstration that genomes can evolve through acquisition of addiction genes has implications for the general question of how a genome can evolve as a community of potentially selfish genes.

Ubiquitin--conserved protein or selfish gene?

PubMed

Catic, André; Ploegh, Hidde L

2005-11-01

The posttranslational modifier ubiquitin is encoded by a multigene family containing three primary members, which yield the precursor protein polyubiquitin and two ubiquitin moieties, Ub(L40) and Ub(S27), that are fused to the ribosomal proteins L40 and S27, respectively. The gene encoding polyubiquitin is highly conserved and, until now, those encoding Ub(L40) and Ub(S27) have been generally considered to be equally invariant. The evolution of the ribosomal ubiquitin moieties is, however, proving to be more dynamic. It seems that the genes encoding Ub(L40) and Ub(S27) are actively maintained by homologous recombination with the invariant polyubiquitin locus. Failure to recombine leads to deterioration of the sequence of the ribosomal ubiquitin moieties in several phyla, although this deterioration is evidently constrained by the structural requirements of the ubiquitin fold. Only a few amino acids in ubiquitin are vital for its function, and we propose that conservation of all three ubiquitin genes is driven not only by functional properties of the ubiquitin protein, but also by the propensity of the polyubiquitin locus to act as a 'selfish gene'.

Non-transferable signals on ant queen eggs

NASA Astrophysics Data System (ADS)

D'Ettorre, Patrizia; Tofilski, Adam; Heinze, Jürgen; Ratnieks, Francis L. W.

2006-03-01

How biological systems resolve internal conflicts is a major evolutionary question. Social insect workers cooperate but also pursue individual interests, such as laying male eggs. The rewards of this individual selfishness can be reduced by policing, such as by killing worker-laid eggs. However, selfish individuals may evade policing. What factors prevent individuals from being able to evade policing? In the ant Pachycondyla inversa, workers kill (police) worker-laid eggs. Because the colony keeps eggs in piles and worker-laid and queen-laid eggs are chemically distinct, worker-laid eggs might become more acceptable once placed in the egg pile by odour transfer from touching queen-laid eggs. Here, we show that such “cue scrambling” does not occur. Worker-laid eggs that were sandwiched between three queen-laid eggs for 45 min were not more acceptable in a policing bioassay than control worker-laid eggs. Chemical analyses also showed that the surface hydrocarbon profile of these eggs was unchanged. Policing, therefore, is stable against this potential cheating mechanism probably because queen-laid eggs are made chemically distinct using chemicals, that are not easily transferred by physical contact.

Non-transferable signals on ant queen eggs.

PubMed

D'Ettorre, Patrizia; Tofilski, Adam; Heinze, Jürgen; Ratnieks, Francis L W

2006-03-01

How biological systems resolve internal conflicts is a major evolutionary question. Social insect workers cooperate but also pursue individual interests, such as laying male eggs. The rewards of this individual selfishness can be reduced by policing, such as by killing worker-laid eggs. However, selfish individuals may evade policing. What factors prevent individuals from being able to evade policing? In the ant Pachycondyla inversa, workers kill (police) worker-laid eggs. Because the colony keeps eggs in piles and worker-laid and queen-laid eggs are chemically distinct, worker-laid eggs might become more acceptable once placed in the egg pile by odour transfer from touching queen-laid eggs. Here, we show that such "cue scrambling" does not occur. Worker-laid eggs that were sandwiched between three queen-laid eggs for 45 min were not more acceptable in a policing bioassay than control worker-laid eggs. Chemical analyses also showed that the surface hydrocarbon profile of these eggs was unchanged. Policing, therefore, is stable against this potential cheating mechanism probably because queen-laid eggs are made chemically distinct using chemicals, that are not easily transferred by physical contact.

A selfish genetic element influencing longevity correlates with reactive behavioural traits in female house mice (Mus domesticus).

PubMed

Auclair, Yannick; König, Barbara; Lindholm, Anna K

2013-01-01

According to theory in life-history and animal personality, individuals with high fitness expectations should be risk-averse, while individuals with low fitness expectations should be more bold. In female house mice, a selfish genetic element, the t haplotype, is associated with increased longevity under natural conditions, representing an appropriate case study to investigate this recent theory empirically. Following theory, females heterozygous for the t haplotype (+/t) are hypothesised to express more reactive personality traits and be more shy, less explorative and less active compared to the shorter-lived homozygous wildtype females (+/+). As males of different haplotype do not differ in survival, no similar pattern is expected. We tested these predictions by quantifying boldness, exploration, activity, and energetic intake in both +/t and +/+ mice. +/t females, unlike +/+ ones, expressed some reactive-like personality traits: +/t females were less active, less prone to form an exploratory routine and tended to ingest less food. Taken together these results suggest that differences in animal personality may contribute to the survival advantage observed in +/t females but fail to provide full empirical support for recent theory.

Out of Control!? How Loss of Self-Control Influences Prosocial Behavior: The Role of Power and Moral Values

PubMed Central

Joosten, Anne; van Dijke, Marius; Van Hiel, Alain; De Cremer, David

2015-01-01

Lack of self-control has been suggested to facilitate norm-transgressing behaviors because of the operation of automatic selfish impulses. Previous research, however, has shown that people having a high moral identity may not show such selfish impulses when their self-control resources are depleted. In the present research, we extended this effect to prosocial behavior. Moreover, we investigated the role of power in the interaction between moral identity and self-control depletion. More specifically, we expected that power facilitates the externalization of internal states, which implies that for people who feel powerful, rather than powerless, depletion decreases prosocial behavior especially for those low in moral identity. A laboratory experiment and a multisource field study supported our predictions. The present finding that the interaction between self-control depletion and moral identity is contingent upon people’s level of power suggests that power may enable people to refrain from helping behavior. Moreover, the findings suggest that if organizations want to improve prosocial behaviors, it may be effective to situationally induce moral values in their employees. PMID:26024380

Reach a nonlinear consensus for MAS via doubly stochastic quadratic operators

NASA Astrophysics Data System (ADS)

Abdulghafor, Rawad; Turaev, Sherzod; Zeki, Akram; Al-Shaikhli, Imad

2018-06-01

This technical note addresses the new nonlinear protocol class of doubly stochastic quadratic operators (DSQOs) for coordination of consensus problem in multi-agent systems (MAS). We derive the conditions for ensuring that every agent reaches consensus on a desired rate of the group's decision where the group decision value in its agent's initial statuses varies. Besides that, we investigate a nonlinear protocol sub-class of extreme DSQO (EDSQO) to reach a consensus for MAS to a common value with nonlinear low-complexity rules and fast time convergence if the interactions for each agent are not selfish. In addition, to extend the results to reach a consensus and to avoid the selfish case we specify a general class of DSQO for reaching a consensus under any given case of initial states. The case that MAS reach a consensus by DSQO is if each member of the agent group has positive interactions of DSQO (PDSQO) with the others. The convergence of both EDSQO and PDSQO classes is found to be directed towards the centre point. Finally, experimental simulations are given to support the analysis from theoretical aspect.

Out of control!? How loss of self-control influences prosocial behavior: the role of power and moral values.

PubMed

Joosten, Anne; van Dijke, Marius; Van Hiel, Alain; De Cremer, David

2015-01-01

Lack of self-control has been suggested to facilitate norm-transgressing behaviors because of the operation of automatic selfish impulses. Previous research, however, has shown that people having a high moral identity may not show such selfish impulses when their self-control resources are depleted. In the present research, we extended this effect to prosocial behavior. Moreover, we investigated the role of power in the interaction between moral identity and self-control depletion. More specifically, we expected that power facilitates the externalization of internal states, which implies that for people who feel powerful, rather than powerless, depletion decreases prosocial behavior especially for those low in moral identity. A laboratory experiment and a multisource field study supported our predictions. The present finding that the interaction between self-control depletion and moral identity is contingent upon people's level of power suggests that power may enable people to refrain from helping behavior. Moreover, the findings suggest that if organizations want to improve prosocial behaviors, it may be effective to situationally induce moral values in their employees.

Selfishness- and Selflessness-based models of pedestrian room evacuation

NASA Astrophysics Data System (ADS)

Song, Xiao; Ma, Liang; Ma, Yaofei; Yang, Chen; Ji, Hang

2016-04-01

Some pedestrian evacuation studies have employed game strategy to deal with moving conflicts involving two or three pedestrians. However, most of these have simply presented game strategies for pedestrians without analyzing the reasons why they choose to defect or cooperate. We believe that selfish and selfless behaviors are two main factors that should be considered in evacuation. In addition to these behaviors, human emotions such as sympathy and behaviors such as vying were also taken into account to investigate their impacts on pedestrians' strategies. Moreover, an essential objective factor, the building design factor of door width was tested and analyzed. Experimental results showed that the sense of self leads to more defectors and a longer evacuation time. However, sympathy does some good, leading to more cooperators and a shorter evacuation time. Moreover, the exit door width is an essential factor of the evacuation efficiency. When the width was less than 6 cells in a rectangular room with a size greater than 50 × 50, the evacuation time greatly decreased when the width increased. However, this effect was less obvious when the width increased.

Can editors save peer review from peer reviewers?

PubMed

D'Andrea, Rafael; O'Dwyer, James P

2017-01-01

Peer review is the gold standard for scientific communication, but its ability to guarantee the quality of published research remains difficult to verify. Recent modeling studies suggest that peer review is sensitive to reviewer misbehavior, and it has been claimed that referees who sabotage work they perceive as competition may severely undermine the quality of publications. Here we examine which aspects of suboptimal reviewing practices most strongly impact quality, and test different mitigating strategies that editors may employ to counter them. We find that the biggest hazard to the quality of published literature is not selfish rejection of high-quality manuscripts but indifferent acceptance of low-quality ones. Bypassing or blacklisting bad reviewers and consulting additional reviewers to settle disagreements can reduce but not eliminate the impact. The other editorial strategies we tested do not significantly improve quality, but pairing manuscripts to reviewers unlikely to selfishly reject them and allowing revision of rejected manuscripts minimize rejection of above-average manuscripts. In its current form, peer review offers few incentives for impartial reviewing efforts. Editors can help, but structural changes are more likely to have a stronger impact.

Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies.

PubMed

Yutin, Natalya; Raoult, Didier; Koonin, Eugene V

2013-05-23

Recent advances of genomics and metagenomics reveal remarkable diversity of viruses and other selfish genetic elements. In particular, giant viruses have been shown to possess their own mobilomes that include virophages, small viruses that parasitize on giant viruses of the Mimiviridae family, and transpovirons, distinct linear plasmids. One of the virophages known as the Mavirus, a parasite of the giant Cafeteria roenbergensis virus, shares several genes with large eukaryotic self-replicating transposon of the Polinton (Maverick) family, and it has been proposed that the polintons evolved from a Mavirus-like ancestor. We performed a comprehensive phylogenomic analysis of the available genomes of virophages and traced the evolutionary connections between the virophages and other selfish genetic elements. The comparison of the gene composition and genome organization of the virophages reveals 6 conserved, core genes that are organized in partially conserved arrays. Phylogenetic analysis of those core virophage genes, for which a sufficient diversity of homologs outside the virophages was detected, including the maturation protease and the packaging ATPase, supports the monophyly of the virophages. The results of this analysis appear incompatible with the origin of polintons from a Mavirus-like agent but rather suggest that Mavirus evolved through recombination between a polinton and an unknown virus. Altogether, virophages, polintons, a distinct Tetrahymena transposable element Tlr1, transpovirons, adenoviruses, and some bacteriophages form a network of evolutionary relationships that is held together by overlapping sets of shared genes and appears to represent a distinct module in the vast total network of viruses and mobile elements. The results of the phylogenomic analysis of the virophages and related genetic elements are compatible with the concept of network-like evolution of the virus world and emphasize multiple evolutionary connections between bona fide viruses and other classes of capsid-less mobile elements.

Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies

PubMed Central

2013-01-01

Background Recent advances of genomics and metagenomics reveal remarkable diversity of viruses and other selfish genetic elements. In particular, giant viruses have been shown to possess their own mobilomes that include virophages, small viruses that parasitize on giant viruses of the Mimiviridae family, and transpovirons, distinct linear plasmids. One of the virophages known as the Mavirus, a parasite of the giant Cafeteria roenbergensis virus, shares several genes with large eukaryotic self-replicating transposon of the Polinton (Maverick) family, and it has been proposed that the polintons evolved from a Mavirus-like ancestor. Results We performed a comprehensive phylogenomic analysis of the available genomes of virophages and traced the evolutionary connections between the virophages and other selfish genetic elements. The comparison of the gene composition and genome organization of the virophages reveals 6 conserved, core genes that are organized in partially conserved arrays. Phylogenetic analysis of those core virophage genes, for which a sufficient diversity of homologs outside the virophages was detected, including the maturation protease and the packaging ATPase, supports the monophyly of the virophages. The results of this analysis appear incompatible with the origin of polintons from a Mavirus-like agent but rather suggest that Mavirus evolved through recombination between a polinton and an unknownvirus. Altogether, virophages, polintons, a distinct Tetrahymena transposable element Tlr1, transpovirons, adenoviruses, and some bacteriophages form a network of evolutionary relationships that is held together by overlapping sets of shared genes and appears to represent a distinct module in the vast total network of viruses and mobile elements. Conclusions The results of the phylogenomic analysis of the virophages and related genetic elements are compatible with the concept of network-like evolution of the virus world and emphasize multiple evolutionary connections between bona fide viruses and other classes of capsid-less mobile elements. PMID:23701946

Identification of Proteins Required for Repair of Double-Strand Chromosome Breaks, a Predisposing Factor in Breast Cancer

DTIC Science & Technology

2001-06-01

enzymatic apparatus needed to initiate DNA replication on recombination intermediates. Escherichia coli PriA protein was found to play a critical function in...the transition from recombination to DNA replication . PriA specifically binds to forked DNA structures created by recombination or replication fork

Lesion bypass by S. cerevisiae Pol ζ alone

PubMed Central

Stone, Jana E.; Kumar, Dinesh; Binz, Sara K.; Inase, Aki; Iwai, Shigenori; Chabes, Andrei; Burgers, Peter M.; Kunkel, Thomas A.

2011-01-01

DNA polymerase zeta (Pol ζ) participates in translesion synthesis (TLS) of DNA adducts that stall replication fork progression. Previous studies have led to the suggestion that the primary role of Pol ζ in TLS is to extend primers created when another DNA polymerase inserts nucleotides opposite lesions. Here we test the non-exclusive possibility that Pol ζ can sometimes perform TLS in the absence of any other polymerase. To do so, we quantified the efficiency with which S. cerevisiae Pol ζ bypasses abasic sites, cis-syn cyclobutane pyrimidine dimers and (6-4) photoproducts. In reactions containing dNTP concentrations that mimic those induced by DNA damage, a Pol ζ derivative with phenylalanine substituted for leucine 979 at the polymerase active site bypasses all three lesions at efficiencies between 27–73%. Wild-type Pol ζ also bypasses these lesions, with efficiencies that are lower and depend on the sequence context in which the lesion resides. The results are consistent with the hypothesis that, in addition to extending aberrant termini created by other DNA polymerases, Pol ζ has the potential to be the sole DNA polymerase involved in TLS. PMID:21622032

Computational DNA hole spectroscopy: A new tool to predict mutation hotspots, critical base pairs, and disease ‘driver’ mutations

PubMed Central

Suárez, Martha Y.; Villagrán; Miller, John H.

2015-01-01

We report on a new technique, computational DNA hole spectroscopy, which creates spectra of electron hole probabilities vs. nucleotide position. A hole is a site of positive charge created when an electron is removed. Peaks in the hole spectrum depict sites where holes tend to localize and potentially trigger a base pair mismatch during replication. Our studies of mitochondrial DNA reveal a correlation between L-strand hole spectrum peaks and spikes in the human mutation spectrum. Importantly, we also find that hole peak positions that do not coincide with large variant frequencies often coincide with disease-implicated mutations and/or (for coding DNA) encoded conserved amino acids. This enables combining hole spectra with variant data to identify critical base pairs and potential disease ‘driver’ mutations. Such integration of DNA hole and variance spectra could ultimately prove invaluable for pinpointing critical regions of the vast non-protein-coding genome. An observed asymmetry in correlations, between the spectrum of human mtDNA variations and the L- and H-strand hole spectra, is attributed to asymmetric DNA replication processes that occur for the leading and lagging strands. PMID:26310834

Computational DNA hole spectroscopy: A new tool to predict mutation hotspots, critical base pairs, and disease 'driver' mutations.

PubMed

Villagrán, Martha Y Suárez; Miller, John H

2015-08-27

We report on a new technique, computational DNA hole spectroscopy, which creates spectra of electron hole probabilities vs. nucleotide position. A hole is a site of positive charge created when an electron is removed. Peaks in the hole spectrum depict sites where holes tend to localize and potentially trigger a base pair mismatch during replication. Our studies of mitochondrial DNA reveal a correlation between L-strand hole spectrum peaks and spikes in the human mutation spectrum. Importantly, we also find that hole peak positions that do not coincide with large variant frequencies often coincide with disease-implicated mutations and/or (for coding DNA) encoded conserved amino acids. This enables combining hole spectra with variant data to identify critical base pairs and potential disease 'driver' mutations. Such integration of DNA hole and variance spectra could ultimately prove invaluable for pinpointing critical regions of the vast non-protein-coding genome. An observed asymmetry in correlations, between the spectrum of human mtDNA variations and the L- and H-strand hole spectra, is attributed to asymmetric DNA replication processes that occur for the leading and lagging strands.

Nanopore with Transverse Nanoelectrodes for Electrical Characterization and Sequencing of DNA

PubMed Central

Gierhart, Brian C.; Howitt, David G.; Chen, Shiahn J.; Zhu, Zhineng; Kotecki, David E.; Smith, Rosemary L.; Collins, Scott D.

2009-01-01

A DNA sequencing device which integrates transverse conducting electrodes for the measurement of electrode currents during DNA translocation through a nanopore has been nanofabricated and characterized. A focused electron beam (FEB) milling technique, capable of creating features on the order of 1 nm in diameter, was used to create the nanopore. The device was characterized electrically using gold nanoparticles as an artificial analyte with both DC and AC measurement methods. Single nanoparticle/electrode interaction events were recorded. A low-noise, high-speed transimpedance current amplifier for the detection of nano to picoampere currents at microsecond time scales was designed, fabricated and tested for future integration with the nanopore device. PMID:19584949

Nanopore with Transverse Nanoelectrodes for Electrical Characterization and Sequencing of DNA.

PubMed

Gierhart, Brian C; Howitt, David G; Chen, Shiahn J; Zhu, Zhineng; Kotecki, David E; Smith, Rosemary L; Collins, Scott D

2008-06-16

A DNA sequencing device which integrates transverse conducting electrodes for the measurement of electrode currents during DNA translocation through a nanopore has been nanofabricated and characterized. A focused electron beam (FEB) milling technique, capable of creating features on the order of 1 nm in diameter, was used to create the nanopore. The device was characterized electrically using gold nanoparticles as an artificial analyte with both DC and AC measurement methods. Single nanoparticle/electrode interaction events were recorded. A low-noise, high-speed transimpedance current amplifier for the detection of nano to picoampere currents at microsecond time scales was designed, fabricated and tested for future integration with the nanopore device.

Active, motor-driven mechanics in a DNA gel.

PubMed

Bertrand, Olivier J N; Fygenson, Deborah Kuchnir; Saleh, Omar A

2012-10-23

Cells are capable of a variety of dramatic stimuli-responsive mechanical behaviors. These capabilities are enabled by the pervading cytoskeletal network, an active gel composed of structural filaments (e.g., actin) that are acted upon by motor proteins (e.g., myosin). Here, we describe the synthesis and characterization of an active gel using noncytoskeletal components. We use methods of base-pair-templated DNA self assembly to create a hybrid DNA gel containing stiff tubes and flexible linkers. We then activate the gel by adding the motor FtsK50C, a construct derived from the bacterial protein FtsK that, in vitro, has a strong and processive DNA contraction activity. The motors stiffen the gel and create stochastic contractile events that affect the positions of attached beads. We quantify the fluctuations of the beads and show that they are comparable both to measurements of cytoskeletal systems and to theoretical predictions for active gels. Thus, we present a DNA-based active gel whose behavior highlights the universal aspects of nonequilibrium, motor-driven networks.

Semiotic systems with duality of patterning and the issue of cultural replicators.

PubMed

Schaden, Gerhard; Patin, Cédric

2017-11-14

Two major works in recent evolutionary biology have in different ways touched upon the issue of cultural replicators in language, namely Dawkins' Selfish Gene and Maynard Smith and Szathmáry's Major Transitions in Evolution. In the latter, the emergence of language is referred to as the last major transition in evolution (for the time being), a claim we argue to be derived from a crucial property of language, called Duality of Patterning. Prima facie, this property makes natural language look like a structural equivalent to DNA, and its peer in terms of expressive power. We will argue that, if one takes seriously Maynard Smith and Szathmáry's outlook and examines what has been proposed as linguistic replicators, amongst others phonemes and words, the analogy meme-gene becomes problematic. A key issue is the fact that genes and memes are assumed to carry and transmit information, while what has been described as the best candidate for replicatorhood in language, i.e. the phoneme, does by definition not carry meaning. We will argue that semiotic systems with Duality of Pattering (like natural languages) force us to reconsider either the analogy between replicators in the biological and the cultural domain, or what it is to be a replicator in linguistics.

Consumption, supply and transport: self-organization without direct communication

NASA Technical Reports Server (NTRS)

Kessler, J. O.

1996-01-01

Swimming bacteria of the species Bacillus subtilis require and consume oxygen. In static liquid cultures the cells' swimming behaviour leads them to accumulate up oxygen concentration gradients generated by consumption and supply. Since the density of bacterial cells exceeds that of the fluid in which they live, fluid regions where cells have accumulated are denser than depleted regions. These density variations cause convection. The fluid motion is dynamically maintained by the swimming of the cells toward regions of attraction: the air-fluid interface and the fluctuating advecting attractors, gradients of oxygen concentration that are embedded in the convecting fluid. Because of the fluid dynamical conservation laws, these complex physical and biological factors generate patterns ordered over distances > 10000 bacterial cell diameters. The convection enhances long-range transport and mixing of oxygen, cells and extracellular products by orders of magnitude. Thus, through the interplay of physical and biological factors, a population of undifferentiated selfish cells creates functional dynamic patterns. Populations of bacteria that have organised themselves into regularly patterned regions of vigorous convection and varying cell concentration interact with their environment as if they were one purposeful, coherent multicellular individual. The mathematical and experimental ingredients of these remarkable phenomena are presented here.

Dynamics of prebiotic RNA reproduction illuminated by chemical game theory

PubMed Central

Yeates, Jessica A. M.; Hilbe, Christian; Zwick, Martin; Nowak, Martin A.; Lehman, Niles

2016-01-01

Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. We also demonstrate that three RNA genotypes can stably coexist in a rock–paper–scissors analog. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world. PMID:27091972

The virtues of gossip: reputational information sharing as prosocial behavior.

PubMed

Feinberg, Matthew; Willer, Robb; Stellar, Jennifer; Keltner, Dacher

2012-05-01

Reputation systems promote cooperation and deter antisocial behavior in groups. Little is known, however, about how and why people share reputational information. Here, we seek to establish the existence and dynamics of prosocial gossip, the sharing of negative evaluative information about a target in a way that protects others from antisocial or exploitative behavior. We present a model of prosocial gossip and the results of 4 studies testing the model's claims. Results of Studies 1 through 3 demonstrate that (a) individuals who observe an antisocial act experience negative affect and are compelled to share information about the antisocial actor with a potentially vulnerable person, (b) sharing such information reduces negative affect created by observing the antisocial behavior, and (c) individuals possessing more prosocial orientations are the most motivated to engage in such gossip, even at a personal cost, and exhibit the greatest reduction in negative affect as a result. Study 4 demonstrates that prosocial gossip can effectively deter selfishness and promote cooperation. Taken together these results highlight the roles of prosocial motivations and negative affective reactions to injustice in maintaining reputational information sharing in groups. We conclude by discussing implications for reputational theories of the maintenance of cooperation in human groups.

Dynamics of prebiotic RNA reproduction illuminated by chemical game theory.

PubMed

Yeates, Jessica A M; Hilbe, Christian; Zwick, Martin; Nowak, Martin A; Lehman, Niles

2016-05-03

Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. We also demonstrate that three RNA genotypes can stably coexist in a rock-paper-scissors analog. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world.

So Many Zebras, So Little Time: Ecological Models and Counterinsurgency Operations (Defense Horizons, Number 62, February 2008)

DTIC Science & Technology

2008-02-01

Starfish and the Spider (New York: Penguin Group, 2006); Richard Dawkins , The Selfish Gene (Oxford: Oxford Univer- sity Press, 1976). See also Nassim...with a certain combination of genes . In COIN, it is even harder to estimate the payoff associated with killing one rebellion member or winning over one

An Analysis of the Objectivist Ethics in Educational Leadership through Ayn Rand's "The Virtues of Selfishness" (1964)

ERIC Educational Resources Information Center

Jacobs, Karen Dupre; Kritsonis, William Allan

2007-01-01

Educational leadership is vital to sustain quality educational institutions. It is the role of the school leader to indoctrinate stakeholders with the objectivist ethics-embracing egoism and relinquishing altruistic ideals when it comes to invigorating the system with sustainable change. Ayn Rand's timeless piece of literature "The Virtue of…

Between the Social and the Selfish: Learner Autonomy in Online Environments

ERIC Educational Resources Information Center

Lewis, Tim

2013-01-01

This paper explores what it means to be an autonomous learner in an online social context. Using distinctions originally drawn by Jürgen Habermas, it argues that classic accounts of learner autonomy as teleological action are inadequate to explain learner activity in group settings. It points out that learners in such settings display attitudes…

Tragedy of the commons in Melipona bees.

PubMed Central

Wenseleers, Tom; Ratnieks, Francis L W

2004-01-01

In human society selfish use of common resources can lead to disaster, a situation known as the 'tragedy of the commons' (TOC). Although a TOC is usually prevented by coercion, theory predicts that close kinship ties can also favour reduced exploitation. We test this prediction using data on a TOC occurring in Melipona bee societies. PMID:15504003

Why be nice? Better not think about it.

PubMed

Tomasello, Michael

2012-12-01

Are people more likely to be cooperative if they must act quickly or if they have more time to mull it over? The results of a recent series of studies suggest that peoples' initial impulse is to cooperate, but that with more time and reflection they become more selfish. Copyright © 2012 Elsevier Ltd. All rights reserved.

Words and Deeds about Altruism and the Subsequent Reinforcement Power of the Model.

ERIC Educational Resources Information Center

Bryan, James H.; And Others

Ninety-six second and third grade children were exposed to one of six types of videotaped models. Children witnessed an adult female practice either charitable or selfish behavior. One-third of the subjects in each group heard the model exhort either charity or greed or verbalize normatively neutral material. Following this exposure, half the…

The veil of ignorance can favour biological cooperation.

PubMed

Queller, David C; Strassmann, Joan E

2013-01-01

Lack of information is a constraint but ignorance can sometimes assist the evolution of cooperation by constraining selfishness. We discuss examples involving both ignorance of role or pay-off and ignorance of relatedness. Ignorance can favour cooperative traits like grouping and warning coloration and reduce conflicts from meiotic drive, imprinting, greenbeards and various forms of nepotism.

The veil of ignorance can favour biological cooperation

PubMed Central

Queller, David C.; Strassmann, Joan E.

2013-01-01

Lack of information is a constraint but ignorance can sometimes assist the evolution of cooperation by constraining selfishness. We discuss examples involving both ignorance of role or pay-off and ignorance of relatedness. Ignorance can favour cooperative traits like grouping and warning coloration and reduce conflicts from meiotic drive, imprinting, greenbeards and various forms of nepotism. PMID:24132090

Leadership for Development. Farm House Dialogue (1st, Ota, Nigeria, May 13-14, 1988).

ERIC Educational Resources Information Center

Africa Leadership Forum.

This document summarizes discussions at an invitational workshop on leadership for development in Nigeria. The following views on the essence of leadership were expressed: (1) the majority of current leaders tend to be selfish, self-centered, and incapable of performing their jobs effectively; (2) most current leaders have impeded the growth of…

DNA origami based Au-Ag-core-shell nanoparticle dimers with single-molecule SERS sensitivity

NASA Astrophysics Data System (ADS)

Prinz, J.; Heck, C.; Ellerik, L.; Merk, V.; Bald, I.

2016-03-01

DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 1010, which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled.DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 1010, which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled. Electronic supplementary information (ESI) available: Additional information about materials and methods, designs of DNA origami templates, height profiles, additional SERS spectra, assignment of DNA bands, SEM images, additional AFM images, FDTD simulations, additional reference spectra for Cy3 and detailed description of EF estimation, simulated absorption and scattering spectra. See DOI: 10.1039/c5nr08674d

Final Report: The DNA Files: Unraveling the mysteries of genetics, January 1, 1998-March 31, 1999

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

Scott, Bari

1999-05-01

The DNA Files is an award-winning radio documentary series on genetics created by SoundVision Productions. The DNA Files was hosted by John Hockenberry and was presented in documentary and discussion format. The programs covered a range of topics from prenatal and predictive gene testing, gene therapy, and commercialization of genetic information to new evolutionary genetic evidence, transgenic vegetables and use of DNA in forensics.

Cancer Risks Associated With Inherited Mutations in Ovarian Cancer Susceptibility Genes Beyond BRCA1 and BRCA2

DTIC Science & Technology

2017-05-01

TERMS Ovarian cancer, drug resistance, rucaparib, phase 2, DNA repair, homologous recombination, nonhomologous end-joining (NHEJ), poly(ADP-ribose...tissues from AA patients with OC. This should add 50 AA OC patients. We are also requesting anonymized DNA from AA OC patients who participated on...extracts DNA and creates library pretps for DNA sequencing. He performs Sanger sequencing validations. Funding Support: Has there been a change

Functionalized patchy particles using colloidal lenses

NASA Astrophysics Data System (ADS)

Middleton, Christine

2014-03-01

Colloidal assembly had been limited by the isotropic, nonspecific nature of interactions between spherical colloidal particles. By giving particles patches functionalized with single stranded DNA, these interactions can be made both directional and specific. We create patchy particles by adding patches to spherical emulsion droplets using the depletion interaction. First we make polystyrene particles in the shape of contact lenses to be the patches. The lenses are functionalized with single stranded DNA on their convex side. Then we put the lenses on the surface of oil emulsion droplets using the depletion interaction, creating a patch (or multiple patches) on the surface of each emulsion droplet. The emulsion droplets can now interact with each other in a specific, directional way through DNA functionalized patches.

TH-CD-201-11: Optimizing the Response and Cost of a DNA Double-Strand Break Dosimeter

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

Obeidat, M; Cline, K; Stathakis, S

Purpose: A DNA double-strand break (DSB) dosimeter was developed to measure the biological effect of radiation. The goal here is to refine the fabrication method of this dosimeter to reproducibly create a low coefficient of variation (CoV) and reduce the cost for the dosimeter. Methods: Our dosimeter consists of 4 kilo-base pair DNA strands (labeled on one end with biotin and on the other with fluorescein) attached to streptavidin magnetic beads. The final step of the DNA dosimeter fabrication is to suspend these attached beads in phosphate-buffered saline (PBS). The amount of PBS used to suspend the attached beads andmore » the relative volume of the DNA strands to the beads both affect the CoV and dosimeter cost. We diluted the beads attached with DNA in different volumes of PBS (100, 200, and 400 µL) to create different concentrations of the DNA dosimeter. Then we irradiated these dosimeters (50 µL samples) in a water-equivalent plastic phantom at 25 and 50 Gy (three samples per dose) and calculated the CoV for each dosimeter concentration. Also, we used different masses of DNA strands (1, 2, 8, 16, 24, and 32 µg) to attach to the same volume of magnetic beads (100 µL) to explore how this affects the cost of the dosimeter. Results: The lowest CoV was produced for the highest concentration of dosimeter (100 µL of PBS), which created CoV of 2.0 and 1.0% for 25 and 50 Gy, respectively. We found that the lowest production cost for the dosimeter occurs by attaching 16 µg of DNA strands with 100 µL of beads. Conclusion: : We optimized the fabrication of the DNA dosimeter to produce low CoV and cost, but we still need to explore ways to further improve the dosimeter for use at lower doses. This work was supported in part by Yarmouk University (Irbid, Jordan) and CPRIT (RP140105)« less

Creation of reference DNA barcode library and authentication of medicinal plant raw drugs used in Ayurvedic medicine.

PubMed

Vassou, Sophie Lorraine; Nithaniyal, Stalin; Raju, Balaji; Parani, Madasamy

2016-07-18

Ayurveda is a system of traditional medicine that originated in ancient India, and it is still in practice. Medicinal plants are the backbone of Ayurveda, which heavily relies on the plant-derived therapeutics. While Ayurveda is becoming more popular in several countries throughout the World, lack of authenticated medicinal plant raw drugs is a growing concern. Our aim was to DNA barcode the medicinal plants that are listed in the Ayurvedic Pharmacopoeia of India (API) to create a reference DNA barcode library, and to use the same to authenticate the raw drugs that are sold in markets. We have DNA barcoded 347 medicinal plants using rbcL marker, and curated rbcL DNA barcodes for 27 medicinal plants from public databases. These sequences were used to create Ayurvedic Pharmacopoeia of India - Reference DNA Barcode Library (API-RDBL). This library was used to authenticate 100 medicinal plant raw drugs, which were in the form of powders (82) and seeds (18). Ayurvedic Pharmacopoeia of India - Reference DNA Barcode Library (API-RDBL) was created with high quality and authentic rbcL barcodes for 374 out of the 395 medicinal plants that are included in the API. The rbcL DNA barcode differentiated 319 species (85 %) with the pairwise divergence ranging between 0.2 and 29.9 %. PCR amplification and DNA sequencing success rate of rbcL marker was 100 % even for the poorly preserved medicinal plant raw drugs that were collected from local markets. DNA barcoding revealed that only 79 % raw drugs were authentic, and the remaining 21 % samples were adulterated. Further, adulteration was found to be much higher with powders (ca. 25 %) when compared to seeds (ca. 5 %). The present study demonstrated the utility of DNA barcoding in authenticating medicinal plant raw drugs, and found that approximately one fifth of the market samples were adulterated. Powdered raw drugs, which are very difficult to be identified by taxonomists as well as common people, seem to be the easy target for adulteration. Developing a quality control protocol for medicinal plant raw drugs by incorporating DNA barcoding as a component is essential to ensure safety to the consumers.

Unifying the DNA End-processing Roles of the Artemis Nuclease

PubMed Central

Chang, Howard H. Y.; Watanabe, Go; Lieber, Michael R.

2015-01-01

Artemis is a member of the metallo-β-lactamase protein family of nucleases. It is essential in vertebrates because, during V(D)J recombination, the RAG complex generates hairpins when it creates the double strand breaks at V, D, and J segments, and Artemis is required to open the hairpins so that they can be joined. Artemis is a diverse endo- and exonuclease, and creating a unified model for its wide range of nuclease properties has been challenging. Here we show that Artemis resects iteratively into blunt DNA ends with an efficiency that reflects the AT-richness of the DNA end. GC-rich ends are not cut by Artemis alone because of a requirement for DNA end breathing (and confirmed using fixed pseudo-Y structures). All DNA ends are cut when both the DNA-dependent protein kinase catalytic subunit and Ku accompany Artemis but not when Ku is omitted. These are the first biochemical data demonstrating a Ku dependence of Artemis action on DNA ends of any configuration. The action of Artemis at blunt DNA ends is slower than at overhangs, consistent with a requirement for a slow DNA end breathing step preceding the cut. The AT sequence dependence, the order of strand cutting, the length of the cuts, and the Ku-dependence of Artemis action at blunt ends can be reconciled with the other nucleolytic properties of both Artemis and Artemis·DNA-PKcs in a model incorporating DNA end breathing of blunt ends to form transient single to double strand boundaries that have structural similarities to hairpins and fixed 5′ and 3′ overhangs. PMID:26276388

Programmable Quantitative DNA Nanothermometers.

PubMed

Gareau, David; Desrosiers, Arnaud; Vallée-Bélisle, Alexis

2016-07-13

Developing molecules, switches, probes or nanomaterials that are able to respond to specific temperature changes should prove of utility for several applications in nanotechnology. Here, we describe bioinspired strategies to design DNA thermoswitches with programmable linear response ranges that can provide either a precise ultrasensitive response over a desired, small temperature interval (±0.05 °C) or an extended linear response over a wide temperature range (e.g., from 25 to 90 °C). Using structural modifications or inexpensive DNA stabilizers, we show that we can tune the transition midpoints of DNA thermometers from 30 to 85 °C. Using multimeric switch architectures, we are able to create ultrasensitive thermometers that display large quantitative fluorescence gains within small temperature variation (e.g., > 700% over 10 °C). Using a combination of thermoswitches of different stabilities or a mix of stabilizers of various strengths, we can create extended thermometers that respond linearly up to 50 °C in temperature range. Here, we demonstrate the reversibility, robustness, and efficiency of these programmable DNA thermometers by monitoring temperature change inside individual wells during polymerase chain reactions. We discuss the potential applications of these programmable DNA thermoswitches in various nanotechnology fields including cell imaging, nanofluidics, nanomedecine, nanoelectronics, nanomaterial, and synthetic biology.

D1/D2 domain of large-subunit ribosomal DNA for differentiation of Orpinomyces spp.

PubMed

Dagar, Sumit S; Kumar, Sanjay; Mudgil, Priti; Singh, Rameshwar; Puniya, Anil K

2011-09-01

This study presents the suitability of D1/D2 domain of large-subunit (LSU) ribosomal DNA (rDNA) for differentiation of Orpinomyces joyonii and Orpinomyces intercalaris based on PCR-restriction fragment length polymorphism (RFLP). A variation of G/T in O. intercalaris created an additional restriction site for AluI, which was used as an RFLP marker. The results demonstrate adequate heterogeneity in the LSU rDNA for species-level differentiation.

Silicon Dioxide Thin Film Mediated Single Cell Nucleic Acid Isolation

PubMed Central

Bogdanov, Evgeny; Dominova, Irina; Shusharina, Natalia; Botman, Stepan; Kasymov, Vitaliy; Patrushev, Maksim

2013-01-01

A limited amount of DNA extracted from single cells, and the development of single cell diagnostics make it necessary to create a new highly effective method for the single cells nucleic acids isolation. In this paper, we propose the DNA isolation method from biomaterials with limited DNA quantity in sample, and from samples with degradable DNA based on the use of solid-phase adsorbent silicon dioxide nanofilm deposited on the inner surface of PCR tube. PMID:23874571

Canonical DNA Repair Pathways Influence R-Loop-Driven Genome Instability.

PubMed

Stirling, Peter C; Hieter, Philip

2017-10-27

DNA repair defects create cancer predisposition in humans by fostering a higher rate of mutations. While DNA repair is quite well characterized, recent studies have identified previously unrecognized relationships between DNA repair and R-loop-mediated genome instability. R-loops are three-stranded nucleic acid structures in which RNA binds to genomic DNA to displace a loop of single-stranded DNA. Mutations in homologous recombination, nucleotide excision repair, crosslink repair, and DNA damage checkpoints have all now been linked to formation and function of transcription-coupled R-loops. This perspective will summarize recent literature linking DNA repair to R-loop-mediated genomic instability and discuss how R-loops may contribute to mutagenesis in DNA-repair-deficient cancers. Copyright © 2016 Elsevier Ltd. All rights reserved.

Explicit Building Block Multiobjective Evolutionary Computation: Methods and Applications

DTIC Science & Technology

2005-06-16

which is introduced in 1990 by Richard Dawkins in his book ”The Selfish Gene .” [34] 356 E.5.7 Pareto Envelop-based Selection Algorithm I and II...IGC Intelligent Gene Collector . . . . . . . . . . . . . . . . . 59 OED Orthogonal Experimental Design . . . . . . . . . . . . . 59 MED Main Effect...complete one experiment 74 `′ The string length hold within the computer (can be longer than number of genes

Intelligence Revisited

DTIC Science & Technology

2005-05-01

Harvest (Harcourt), San Diego, 1999. Dawkins , Richard, The Selfish Gene , ISBN 0192860925, Oxford University Press, Oxford, 1990. Dennett, Daniel C... genes we inherit from our parents, for better or worse. Others argue that social factors are the more dominant influence; our surrounding...a function of our genes , and where we actually wind up across the full spectrum of human possibilities is determined by how these genes interact with

An Open Epistle to Dr. Traditional Cherokee of the Nonexistent Bear Clan

ERIC Educational Resources Information Center

Redsteer, Robert W.

2003-01-01

Having grown up in the Native American Church culture in the time when Navajo people were persecuted for practicing this religion, the author states that a great price has been paid to date that allows him to practice his religious freedom and his way of life. Because non native people are selfishly imitating sacred Indigenous ceremonies, they put…

Implementation Strategy Cooperative Learning Type of Student Achievement Division Team (STAD) to Improve Social Skills Students on Learning Morals in Man 2 Pontianak Learning the Year 2016/2017

ERIC Educational Resources Information Center

Rianawati

2017-01-01

Background doing the research is Social skills is an individual's ability to communicate effectively with others, both verbally and nonverbally. Facts social attitudes such selfishness, individualism, indifferent, no responsible attitude, miss communication and interaction with others. One Cooperative-learning strategy to develop cooperation…

Critically Evaluating Competing Theories: An Exercise Based on the Kitty Genovese Murder

ERIC Educational Resources Information Center

Sagarin, Brad J.; Lawler-Sagarin, Kimberly A.

2005-01-01

We describe an exercise based on the 1964 murder of Catherine Genovese--a murder observed by 38 witnesses, none of whom called the police. Students read a summary of the murder and worked in small groups to design an experiment to test the competing theories for the inaction of the witnesses (Americans' selfishness and insensitivity vs. diffusion…

Dopamine D4 receptor gene and religious affiliation correlate with dictator game altruism in males and not females: evidence for gender-sensitive gene × culture interaction.

PubMed

Jiang, Yushi; Bachner-Melman, Rachel; Chew, Soo Hong; Ebstein, Richard P

2015-01-01

On a large sample of 2288 Han Chinese undergraduates, we investigated how religion and DRD4 are related to human altruistic giving behavior as measured with the Andreoni-Miller Dictator Game. This game enables us to clearly specify (non-)selfishness, efficiency, and fairness motives for sharing. Participants were further classified into religious categories (Christian, Buddhist-Tao, and No Religion) based on self-reports, and genotyped for the dopamine D4 receptor (DRD4) gene exon III VNTR. Our analysis revealed a significant interaction between religion and DRD4 correlated with giving behavior solely among males: Whereas no significant association between religion and sharing decisions was observed in the majority 4R/4R genotype group, a significant difference in giving behavior between Christian and non-Christian males was seen in the non-4R/4R group, with Christian men being overall more altruistic (less selfish and fairer) than non-Christian men. These results support the vantage sensitivity hypothesis regarding DRD4 that the non-4R/4R "susceptibility" genotype is more responsive to a positive environment provided by some religions.

Viruses and mobile elements as drivers of evolutionary transitions

PubMed Central

2016-01-01

The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of ‘public goods’. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host–parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431520

Genetic control of invasive plants species using selfish genetic elements

PubMed Central

Hodgins, Kathryn A; Rieseberg, Loren; Otto, Sarah P

2009-01-01

Invasive plants cause substantial environmental damage and economic loss. Here, we explore the possibility that a selfish genetic element found in plants called cytoplasmic male sterility (CMS) could be exploited for weed control. CMS is caused by mutations in the mitochondrial genome that sterilize male reproductive organs. We developed an analytical model and a spatial simulation to assess the use of CMS alleles to manage weed populations. Specifically, we examined how fertility, selfing, pollen limitation and dispersal influenced extinction rate and time until extinction in populations where CMS arises. We found that the introduction of a CMS allele can cause rapid population extinction, but only under a restricted set of conditions. Both models suggest that the CMS strategy will be appropriate for species where pollen limitation is negligible, inbreeding depression is high and the fertility advantage of females over hermaphrodites is substantial. In general, spatial structure did not have a strong influence on the simulation outcome, although low pollen dispersal and intermediate levels of seed dispersal tended to reduce population extinction rates. Given these results, the introduction of CMS alleles into a population of invasive plants probably represents an effective control method for only a select number of species. PMID:25567898

Perceived Gaze Direction Modulates Neural Processing of Prosocial Decision Making

PubMed Central

Sun, Delin; Shao, Robin; Wang, Zhaoxin; Lee, Tatia M. C.

2018-01-01

Gaze direction is a common social cue implying potential interpersonal interaction. However, little is known about the neural processing of social decision making influenced by perceived gaze direction. Here, we employed functional magnetic resonance imaging (fMRI) method to investigate 27 females when they were engaging in an economic exchange game task during which photos of direct or averted eye gaze were shown. We found that, when averted but not direct gaze was presented, prosocial vs. selfish choices were associated with stronger activations in the right superior temporal gyrus (STG) as well as larger functional couplings between right STG and the posterior cingulate cortex (PCC). Moreover, stronger activations in right STG was associated with quicker actions for making prosocial choice accompanied with averted gaze. The findings suggest that, when the cue implying social contact is absent, the processing of understanding others’ intention and the relationship between self and others is more involved for making prosocial than selfish decisions. These findings could advance our understanding of the roles of subtle cues in influencing prosocial decision making, as well as shedding lights on deficient social cue processing and functioning among individuals with autism spectrum disorder (ASD). PMID:29487516

Social discounting involves modulation of neural value signals by temporoparietal junction

PubMed Central

Strombach, Tina; Weber, Bernd; Hangebrauk, Zsofia; Kenning, Peter; Karipidis, Iliana I.; Tobler, Philippe N.; Kalenscher, Tobias

2015-01-01

Most people are generous, but not toward everyone alike: generosity usually declines with social distance between individuals, a phenomenon called social discounting. Despite the pervasiveness of social discounting, social distance between actors has been surprisingly neglected in economic theory and neuroscientific research. We used functional magnetic resonance imaging (fMRI) to study the neural basis of this process to understand the neural underpinnings of social decision making. Participants chose between selfish and generous alternatives, yielding either a large reward for the participant alone, or smaller rewards for the participant and another individual at a particular social distance. We found that generous choices engaged the temporoparietal junction (TPJ). In particular, the TPJ activity was scaled to the social-distance–dependent conflict between selfish and generous motives during prosocial choice, consistent with ideas that the TPJ promotes generosity by facilitating overcoming egoism bias. Based on functional coupling data, we propose and provide evidence for a biologically plausible neural model according to which the TPJ supports social discounting by modulating basic neural value signals in the ventromedial prefrontal cortex to incorporate social-distance–dependent other-regarding preferences into an otherwise exclusively own-reward value representation. PMID:25605887

Dopamine D4 receptor gene and religious affiliation correlate with dictator game altruism in males and not females: evidence for gender-sensitive gene × culture interaction

PubMed Central

Jiang, Yushi; Bachner-Melman, Rachel; Chew, Soo Hong; Ebstein, Richard P.

2015-01-01

On a large sample of 2288 Han Chinese undergraduates, we investigated how religion and DRD4 are related to human altruistic giving behavior as measured with the Andreoni-Miller Dictator Game. This game enables us to clearly specify (non-)selfishness, efficiency, and fairness motives for sharing. Participants were further classified into religious categories (Christian, Buddhist-Tao, and No Religion) based on self-reports, and genotyped for the dopamine D4 receptor (DRD4) gene exon III VNTR. Our analysis revealed a significant interaction between religion and DRD4 correlated with giving behavior solely among males: Whereas no significant association between religion and sharing decisions was observed in the majority 4R/4R genotype group, a significant difference in giving behavior between Christian and non-Christian males was seen in the non-4R/4R group, with Christian men being overall more altruistic (less selfish and fairer) than non-Christian men. These results support the vantage sensitivity hypothesis regarding DRD4 that the non-4R/4R “susceptibility” genotype is more responsive to a positive environment provided by some religions. PMID:26441510

Viruses and mobile elements as drivers of evolutionary transitions.

PubMed

Koonin, Eugene V

2016-08-19

The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of 'public goods'. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host-parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions.This article is part of the themed issue 'The major synthetic evolutionary transitions'. © 2016 The Authors.

Selfish mothers indeed! Resource-dependent conflict over extended parental care in free-ranging dogs

PubMed Central

2015-01-01

Parent–offspring conflict (POC) theory provides an interesting premise for understanding social dynamics in facultatively social species. In free-ranging dogs, mothers increase conflict over extended parental care with their pups beyond the weaning stage. In this study, we investigated whether resource quality affects POC in the dogs that typically live in a highly competitive environment as scavengers. We built a theoretical model to predict the alternative options available to the mother in the context of food sharing with her pups when protein-rich food (meat) is provided, as compared to carbohydrate-rich food (biscuits). We fit the mothers’ response from experimental data to the model and show that the mothers choose a selfish strategy, which can in turn ensure higher lifetime reproductive success, while depriving the current litter access to better resources. These results have interesting implications for understanding the social dynamics of the dogs, and the emergence of facultative sociality in a species that evolved from strongly social ancestors. We speculate that the tendency of increased conflict in resource-rich conditions might have driven the process of domestication in the ancestors of dogs which defected from their groups in favour of richer resources around human settlements. PMID:27019741

Effects of Oxytocin and Prosocial Behavior on Brain Responses to Direct and Vicariously Experienced Pain

PubMed Central

Singer, Tania; Snozzi, Romana; Bird, Geoffrey; Petrovic, Predrag; Silani, Giorgia; Heinrichs, Markus; Dolan, Raymond J.

2008-01-01

In this study, we tested the validity of 2 popular assumptions about empathy: (a) empathy can be enhanced by oxytocin, a neuropeptide known to be crucial in affiliative behavior, and (b) individual differences in prosocial behavior are positively associated with empathic brain responses. To do so, we measured brain activity in a double-blind placebo-controlled study of 20 male participants either receiving painful stimulation to their own hand (self condition) or observing their female partner receiving painful stimulation to her hand (other condition). Prosocial behavior was measured using a monetary economic interaction game with which participants classified as prosocial (N = 12) or selfish (N = 6), depending on whether they cooperated with another player. Empathy-relevant brain activation (anterior insula) was neither enhanced by oxytocin nor positively associated with prosocial behavior. However, oxytocin reduced amygdala activation when participants received painful stimulation themselves (in the nonsocial condition). Surprisingly, this effect was driven by “selfish” participants. The results suggest that selfish individuals may not be as rational and unemotional as usually suggested, their actions being determined by their feeling anxious rather than by reason. PMID:19102589

Lack of prosociality in great apes, capuchin monkeys and spider monkeys: convergent evidence from two different food distribution tasks

PubMed Central

Amici, Federica; Visalberghi, Elisabetta; Call, Josep

2014-01-01

Prosociality can be defined as any behaviour performed to alleviate the needs of others or to improve their welfare. Prosociality has probably played an essential role in the evolution of cooperative behaviour and several studies have already investigated it in primates to understand the evolutionary origins of human prosociality. Two main tasks have been used to test prosociality in a food context. In the Platforms task, subjects can prosocially provide food to a partner by selecting a prosocial platform over a selfish one. In the Tokens task, subjects can prosocially provide food to a partner by selecting a prosocial token over a selfish one. As these tasks have provided mixed results, we used both tasks to test prosociality in great apes, capuchin monkeys and spider monkeys. Our results provided no compelling evidence of prosociality in a food context in any of the species tested. Additionally, our study revealed serious limitations of the Tokens task as it has been previously used. These results highlight the importance of controlling for confounding variables and of using multiple tasks to address inconsistencies present in the literature. PMID:25209941

Punishment and spite, the dark side of cooperation

PubMed Central

Jensen, Keith

2010-01-01

Causing harm to others would hardly seem to be relevant to cooperation, other than as a barrier to it. However, because selfish individuals will exploit cooperators, functional punishment is an effective mechanism for enforcing cooperation by deterring free-riding. Although functional punishment can shape the social behaviour of others by targeting non-cooperative behaviour, it can also intimidate others into doing almost anything. Second-party functional punishment is a self-serving behaviour at the disposal of dominant individuals who can coerce others into behaving cooperatively, but it need not do so. Third-party and altruistic functional punishment are less likely to be selfishly motivated and would seem more likely to maintain norms of cooperation in large groups. These forms of functional punishment may be an essential part of non-kin cooperation on a scale exhibited only by humans. While punitive sentiments might be the psychological force behind punitive behaviours, spiteful motives might also play an important role. Furthermore, functionally spiteful acts might not be maladaptive; reckoning gains relative to others rather than in absolute terms can lead to hyper-competitiveness, which might also be an important part of human cooperation, rather than just an ugly by-product. PMID:20679108

Outcrossed sex allows a selfish gene to invade yeast populations.

PubMed

Goddard, M R; Greig, D; Burt, A

2001-12-22

Homing endonuclease genes (HEGs) in eukaryotes are optional genes that have no obvious effect on host phenotype except for causing chromosomes not containing a copy of the gene to be cut, thus causing them to be inherited at a greater than Mendelian rate via gene conversion. These genes are therefore expected to increase in frequency in outcrossed populations, but not in obligately selfed populations. In order to test this idea, we compared the dynamics of the VDE HEG in six replicate outcrossed and inbred populations of yeast (Saccharomyces cerevisiae). VDE increased in frequency from 0.21 to 0.55 in four outcrossed generations, but showed no change in frequency in the inbred populations. The absence of change in the inbred populations indicates that any effect of VDE on mitotic replication rates is less than 1%. The data from the outcrossed populations best fit a model in which 82% of individuals are derived from outcrossing and VDE is inherited by 74% of the meiotic products from heterozygotes (as compared with 50% for Mendelian genes). These results empirically demonstrate how a host mating system plays a key role in determining the population dynamics of a selfish gene.

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.

A distributed incentive compatible pricing mechanism for P2P networks

NASA Astrophysics Data System (ADS)

Zhang, Jie; Zhao, Zheng; Xiong, Xiao; Shi, Qingwei

2007-09-01

Peer-to-Peer (P2P) systems are currently receiving considerable interest. However, as experience with P2P networks shows, the selfish behaviors of peers may lead to serious problems of P2P network, such as free-riding and white-washing. In order to solve these problems, there are increasing considerations on reputation system design in the study of P2P networks. Most of the existing works is concerning probabilistic estimation or social networks to evaluate the trustworthiness for a peer to others. However, these models can not be efficient all the time. In this paper, our aim is to provide a general mechanism that can maximize P2P networks social welfare in a way of Vickrey-Clarke-Groves family, while assuming every peer in P2P networks is rational and selfish, which means they only concern about their own outcome. This mechanism has some desirable properties using an O(n) algorithm: (1) incentive compatibility, every peer truly report its connection type; (2) individually rationality; and (3) fully decentralized, we design a multiple-principal multiple-agent model, concerning about the service provider and service requester individually.

Physical Activity Protects the Human Brain against Metabolic Stress Induced by a Postprandial and Chronic Inflammation.

PubMed

Pruimboom, Leo; Raison, Charles L; Muskiet, Frits A J

2015-01-01

In recent years, it has become clear that chronic systemic low-grade inflammation is at the root of many, if not all, typically Western diseases associated with the metabolic syndrome. While much focus has been given to sedentary lifestyle as a cause of chronic inflammation, it is less often appreciated that chronic inflammation may also promote a sedentary lifestyle, which in turn causes chronic inflammation. Given that even minor increases in chronic inflammation reduce brain volume in otherwise healthy individuals, the bidirectional relationship between inflammation and sedentary behaviour may explain why humans have lost brain volume in the last 30,000 years and also intelligence in the last 30 years. We review evidence that lack of physical activity induces chronic low-grade inflammation and, consequently, an energy conflict between the selfish immune system and the selfish brain. Although the notion that increased physical activity would improve health in the modern world is widespread, here we provide a novel perspective on this truism by providing evidence that recovery of normal human behaviour, such as spontaneous physical activity, would calm proinflammatory activity, thereby allocating more energy to the brain and other organs, and by doing so would improve human health.

Ant larvae as players in social conflict: relatedness and individual identity mediate cannibalism intensity.

PubMed

Schultner, Eva; Gardner, Andy; Karhunen, Markku; Helanterä, Heikki

2014-12-01

Conflict arises among social organisms when individuals differ in their inclusive-fitness interests. Ant societies are excellent models for understanding how genetic relatedness mediates conflict intensity. However, although conflicts within colonies typically arise over offspring production, the role of larvae as actors in social conflict has received little attention. We develop and empirically test kin-selection theory of larval egg cannibalism in ant societies. Specifically, we investigate how selection for cannibalism is mediated by nestmate relatedness and larval sex in a mathematical model and then test the model's predictions by measuring cannibalism levels in eight ant species with varying nestmate relatedness. In line with our theoretical predictions, cannibalism levels in larvae were significantly influenced by relatedness and sex. Increased relatedness was associated with reduced levels of cannibalism, indicating that larval behavior is mediated by inclusive-fitness considerations. Levels of cannibalism were significantly higher in male larvae, and our model suggests that this is due to sex differences in the benefits of cannibalism. By examining the selfish interests of larvae and the constraints they face in a social environment, our study presents a novel perspective on conflict in ants and on the evolution of selfish elements in social systems in general.

Outcrossed sex allows a selfish gene to invade yeast populations.

PubMed Central

Goddard, M. R.; Greig, D.; Burt, A.

2001-01-01

Homing endonuclease genes (HEGs) in eukaryotes are optional genes that have no obvious effect on host phenotype except for causing chromosomes not containing a copy of the gene to be cut, thus causing them to be inherited at a greater than Mendelian rate via gene conversion. These genes are therefore expected to increase in frequency in outcrossed populations, but not in obligately selfed populations. In order to test this idea, we compared the dynamics of the VDE HEG in six replicate outcrossed and inbred populations of yeast (Saccharomyces cerevisiae). VDE increased in frequency from 0.21 to 0.55 in four outcrossed generations, but showed no change in frequency in the inbred populations. The absence of change in the inbred populations indicates that any effect of VDE on mitotic replication rates is less than 1%. The data from the outcrossed populations best fit a model in which 82% of individuals are derived from outcrossing and VDE is inherited by 74% of the meiotic products from heterozygotes (as compared with 50% for Mendelian genes). These results empirically demonstrate how a host mating system plays a key role in determining the population dynamics of a selfish gene. PMID:11749707

Guilt about being born and debt concerning the gift of life.

PubMed

Lotterman, Andrew C

2003-01-01

A very powerful form of preoedipal guilt stems from a sense of having damaged the life-giving parent with one's most basic needs. A related phenomenon is the child's sense that another subjectivity has deliberately chosen to give and sustain the child's life. This experience gives rise to a compelling mixture of awe, reverence, and obligation, a sense of guilt about being born, of debt concerning the gift of life. This sense of guilt and debt are part of every child's development. Depending on how conflicts surrounding them are negotiated, the child can come to feel either an appetite for living or a crushing sense of selfishness and unworthiness. Such forms of guilt and debt may lead not only to masochism generally, but to a particularly pernicious form of negative therapeutic reaction that can sabotage psychoanalytic work. A patient may feel, for instance, that a successful psychoanalysis is a selfish indulgence and an immoral betrayal of a sacred duty to rescue his or her parents from their misery. Guilt about being born and the sense of debt concerning the gift of life are linked to various developmental, psychodynamic, interpersonal, and cultural phenomena.

Invasion and persistence of a selfish gene in the Cnidaria.

PubMed

Goddard, Matthew R; Leigh, Jessica; Roger, Andrew J; Pemberton, Andrew J

2006-12-20

Homing endonuclease genes (HEGs) are superfluous, but are capable of invading populations that mix alleles by biasing their inheritance patterns through gene conversion. One model suggests that their long-term persistence is achieved through recurrent invasion. This circumvents evolutionary degeneration, but requires reasonable rates of transfer between species to maintain purifying selection. Although HEGs are found in a variety of microbes, we found the previous discovery of this type of selfish genetic element in the mitochondria of a sea anemone surprising. We surveyed 29 species of Cnidaria for the presence of the COXI HEG. Statistical analyses provided evidence for HEG invasion. We also found that 96 individuals of Metridium senile, from five different locations in the UK, had identical HEG sequences. This lack of sequence divergence illustrates the stable nature of Anthozoan mitochondria. Our data suggests this HEG conforms to the recurrent invasion model of evolution. Ordinarily such low rates of HEG transfer would likely be insufficient to enable major invasion. However, the slow rate of Anthozoan mitochondrial change lengthens greatly the time to HEG degeneration: this significantly extends the periodicity of the HEG life-cycle. We suggest that a combination of very low substitution rates and rare transfers facilitated metazoan HEG invasion.

An invitation to die: initiators of sociality in a social amoeba become selfish spores

PubMed Central

Kuzdzal-Fick, Jennie J.; Queller, David C.; Strassmann, Joan E.

2010-01-01

Greater size and strength are common attributes of contest winners. Even in social insects with high cooperation, the right to reproduce falls to the well-fed queens rather than to poorly fed workers. In Dictyostelium discoideum, formerly solitary amoebae aggregate when faced with starvation, and some cells die to form a stalk which others ride up to reach a better location to sporulate. The first cells to starve have lower energy reserves than those that starve later, and previous studies have shown that the better-fed cells in a mix tend to form disproportionately more reproductive spores. Therefore, one might expect that the first cells to starve and initiate the social stage should act altruistically and form disproportionately more of the sterile stalk, thereby enticing other better-fed cells into joining the aggregate. This would resemble caste determination in social insects, where altruistic workers are typically fed less than reproductive queens. However, we show that the opposite result holds: the first cells to starve become reproductive spores, presumably by gearing up for competition and outcompeting late starvers to become prespore first. These findings pose the interesting question of why others would join selfish organizers. PMID:20504816

Development of DNA-Free Sediment for Ecological Assays with Genomic Endpoints

EPA Science Inventory

Recent advances in genomics are currently being exploited to discern ecological changes that have conventionally been measured using laborious counting techniques. For example, next generation sequencing technologies can be used to create DNA libraries from benthic community ass...

DNA-linked NanoParticle Lattices with Diamond Symmetry: Stability, Shape and Optical Properties

NASA Astrophysics Data System (ADS)

Emamy, Hamed; Tkachenko, Alexei; Gang, Oleg; Starr, Francis

The linking of nanoparticles (NP) by DNA has been proven to be an effective means to create NP lattices with specific order. Lattices with diamond symmetry are predicted to offer novel photonic properties, but self-assembly of such lattices has proven to be challenging due to the low packing fraction, sensitivity to bond orientation, and local heterogeneity. Recently, we reported an approach to create diamond NP lattices based on the association between anisotropic particles with well-defined tetravalent DNA binding topology and isotropically functionalized NP. Here, we use molecular dynamics simulations to evaluate the Gibbs free energy of these lattices, and thereby determine the stability of these lattices as a function of NP size and DNA stiffness. We also predict the equilibrium shape for the cubic diamond crystallite using the Wulff construction method. Specifically, we predict the equilibrium shape using the surface energy for different crystallographic planes. We evaluate surface energy directly form molecular dynamics simulation, which we correlate with theoretical estimates from the expected number of broken DNA bonds along a facet. Furthermore we study the optical properties of this structure, e.g optical bandgap.

DNA Micromanipulation Using Novel High-Force, In-Plane Magnetic Tweezer

NASA Astrophysics Data System (ADS)

McAndrew, Christopher; Mehl, Patrick; Sarkar, Abhijit

2010-03-01

We report the development of a magnetic force transducer that can apply piconewton forces on single DNA molecules in the focus plane allowing continuous high precision tethered-bead tracking. The DNA constructs, proteins, and buffer are introduced into a 200μL closed cell created using two glass slides separated by rigid spacers interspersed within a thin viscoelastic perimeter wall. This closed cell configuration isolates our sample and produces low-noise force-extension measurements. Specially-drawn micropipettes are used for capturing the polystyrene bead, pulling on the magnetic sphere, introducing proteins of interest, and maintaining flow. Various high-precision micromanipulators allow us to move pipettes and stage as required. The polystyrene bead is first grabbed, and held using suction; then the magnetic particle at the other end of the DNA is pulled by a force created by either two small (1mm x 2mm x 4mm) bar magnets or a micro magnet-tipped pipette. Changes in the end-to-end length of the DNA are observable in real time. We will present force extension data obtained using the magnetic tweezer.

Development of DNA-Free Sediment for Ecological Assays with Genomic Endpoints (NAC SETAC)

EPA Science Inventory

Recent advances in genomics are currently being exploited to discern ecological changes that have conventionally been measured using laborious counting techniques. For example, next generation sequencing technologies can be used to create DNA libraries from benthic community ass...

D1/D2 Domain of Large-Subunit Ribosomal DNA for Differentiation of Orpinomyces spp.▿

PubMed Central

Dagar, Sumit S.; Kumar, Sanjay; Mudgil, Priti; Singh, Rameshwar; Puniya, Anil K.

2011-01-01

This study presents the suitability of D1/D2 domain of large-subunit (LSU) ribosomal DNA (rDNA) for differentiation of Orpinomyces joyonii and Orpinomyces intercalaris based on PCR-restriction fragment length polymorphism (RFLP). A variation of G/T in O. intercalaris created an additional restriction site for AluI, which was used as an RFLP marker. The results demonstrate adequate heterogeneity in the LSU rDNA for species-level differentiation. PMID:21784906

Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes.

PubMed

Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2009-06-03

The prokaryotic toxin-antitoxin systems (TAS, also referred to as TA loci) are widespread, mobile two-gene modules that can be viewed as selfish genetic elements because they evolved mechanisms to become addictive for replicons and cells in which they reside, but also possess "normal" cellular functions in various forms of stress response and management of prokaryotic population. Several distinct TAS of type 1, where the toxin is a protein and the antitoxin is an antisense RNA, and numerous, unrelated TAS of type 2, in which both the toxin and the antitoxin are proteins, have been experimentally characterized, and it is suspected that many more remain to be identified. We report a comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems in prokaryotes. Using sensitive methods for distant sequence similarity search, genome context analysis and a new approach for the identification of mobile two-component systems, we identified numerous, previously unnoticed protein families that are homologous to toxins and antitoxins of known type 2 TAS. In addition, we predict 12 new families of toxins and 13 families of antitoxins, and also, predict a TAS or TAS-like activity for several gene modules that were not previously suspected to function in that capacity. In particular, we present indications that the two-gene module that encodes a minimal nucleotidyl transferase and the accompanying HEPN protein, and is extremely abundant in many archaea and bacteria, especially, thermophiles might comprise a novel TAS. We present a survey of previously known and newly predicted TAS in 750 complete genomes of archaea and bacteria, quantitatively demonstrate the exceptional mobility of the TAS, and explore the network of toxin-antitoxin pairings that combines plasticity with selectivity. The defining properties of the TAS, namely, the typically small size of the toxin and antitoxin genes, fast evolution, and extensive horizontal mobility, make the task of comprehensive identification of these systems particularly challenging. However, these same properties can be exploited to develop context-based computational approaches which, combined with exhaustive analysis of subtle sequence similarities were employed in this work to substantially expand the current collection of TAS by predicting both previously unnoticed, derived versions of known toxins and antitoxins, and putative novel TAS-like systems. In a broader context, the TAS belong to the resistome domain of the prokaryotic mobilome which includes partially selfish, addictive gene cassettes involved in various aspects of stress response and organized under the same general principles as the TAS. The "selfish altruism", or "responsible selfishness", of TAS-like systems appears to be a defining feature of the resistome and an important characteristic of the entire prokaryotic pan-genome given that in the prokaryotic world the mobilome and the "stable" chromosomes form a dynamic continuum. This paper was reviewed by Kenn Gerdes (nominated by Arcady Mushegian), Daniel Haft, Arcady Mushegian, and Andrei Osterman. For full reviews, go to the Reviewers' Reports section.

Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes

PubMed Central

Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2009-01-01

Background The prokaryotic toxin-antitoxin systems (TAS, also referred to as TA loci) are widespread, mobile two-gene modules that can be viewed as selfish genetic elements because they evolved mechanisms to become addictive for replicons and cells in which they reside, but also possess "normal" cellular functions in various forms of stress response and management of prokaryotic population. Several distinct TAS of type 1, where the toxin is a protein and the antitoxin is an antisense RNA, and numerous, unrelated TAS of type 2, in which both the toxin and the antitoxin are proteins, have been experimentally characterized, and it is suspected that many more remain to be identified. Results We report a comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems in prokaryotes. Using sensitive methods for distant sequence similarity search, genome context analysis and a new approach for the identification of mobile two-component systems, we identified numerous, previously unnoticed protein families that are homologous to toxins and antitoxins of known type 2 TAS. In addition, we predict 12 new families of toxins and 13 families of antitoxins, and also, predict a TAS or TAS-like activity for several gene modules that were not previously suspected to function in that capacity. In particular, we present indications that the two-gene module that encodes a minimal nucleotidyl transferase and the accompanying HEPN protein, and is extremely abundant in many archaea and bacteria, especially, thermophiles might comprise a novel TAS. We present a survey of previously known and newly predicted TAS in 750 complete genomes of archaea and bacteria, quantitatively demonstrate the exceptional mobility of the TAS, and explore the network of toxin-antitoxin pairings that combines plasticity with selectivity. Conclusion The defining properties of the TAS, namely, the typically small size of the toxin and antitoxin genes, fast evolution, and extensive horizontal mobility, make the task of comprehensive identification of these systems particularly challenging. However, these same properties can be exploited to develop context-based computational approaches which, combined with exhaustive analysis of subtle sequence similarities were employed in this work to substantially expand the current collection of TAS by predicting both previously unnoticed, derived versions of known toxins and antitoxins, and putative novel TAS-like systems. In a broader context, the TAS belong to the resistome domain of the prokaryotic mobilome which includes partially selfish, addictive gene cassettes involved in various aspects of stress response and organized under the same general principles as the TAS. The "selfish altruism", or "responsible selfishness", of TAS-like systems appears to be a defining feature of the resistome and an important characteristic of the entire prokaryotic pan-genome given that in the prokaryotic world the mobilome and the "stable" chromosomes form a dynamic continuum. Reviewers This paper was reviewed by Kenn Gerdes (nominated by Arcady Mushegian), Daniel Haft, Arcady Mushegian, and Andrei Osterman. For full reviews, go to the Reviewers' Reports section. PMID:19493340

Mechanism of chimera formation during the Multiple Displacement Amplification reaction.

PubMed

Lasken, Roger S; Stockwell, Timothy B

2007-04-12

Multiple Displacement Amplification (MDA) is a method used for amplifying limiting DNA sources. The high molecular weight amplified DNA is ideal for DNA library construction. While this has enabled genomic sequencing from one or a few cells of unculturable microorganisms, the process is complicated by the tendency of MDA to generate chimeric DNA rearrangements in the amplified DNA. Determining the source of the DNA rearrangements would be an important step towards reducing or eliminating them. Here, we characterize the major types of chimeras formed by carrying out an MDA whole genome amplification from a single E. coli cell and sequencing by the 454 Life Sciences method. Analysis of 475 chimeras revealed the predominant reaction mechanisms that create the DNA rearrangements. The highly branched DNA synthesized in MDA can assume many alternative secondary structures. DNA strands extended on an initial template can be displaced becoming available to prime on a second template creating the chimeras. Evidence supports a model in which branch migration can displace 3'-ends freeing them to prime on the new templates. More than 85% of the resulting DNA rearrangements were inverted sequences with intervening deletions that the model predicts. Intramolecular rearrangements were favored, with displaced 3'-ends reannealing to single stranded 5'-strands contained within the same branched DNA molecule. In over 70% of the chimeric junctions, the 3' termini had initiated priming at complimentary sequences of 2-21 nucleotides (nts) in the new templates. Formation of chimeras is an important limitation to the MDA method, particularly for whole genome sequencing. Identification of the mechanism for chimera formation provides new insight into the MDA reaction and suggests methods to reduce chimeras. The 454 sequencing approach used here will provide a rapid method to assess the utility of reaction modifications.

Basics of genome editing technology and its application in livestock species.

PubMed

Petersen, Bjoern

2017-08-01

In the last decade, the research community has witnessed a blooming of targeted genome editing tools and applications. Novel programmable DNA nucleases such as zinc finger nucleases (ZFNs), transcription activator-like endonucleases (TALENs) and the clustered regularly interspaced short palindromic repeats/Cas9 system (CRISPR/Cas9) possess long recognition sites and are capable of cutting DNA in a very specific manner. These DNA nucleases mediate targeted genetic alterations by enhancing the DNA mutation rate via induction of double-strand breaks at a predetermined genomic site. Compared to conventional homologous recombination-based gene targeting, DNA nucleases, also referred to as Genome Editors (GEs), can increase the targeting rate around 10,000- to 100,000-fold. The successful application of different GEs has been shown in a myriad of different organisms, including insects, amphibians, plants, nematodes and several mammalian species, including human cells and embryos. In contrast to all other DNA nucleases, that rely on protein-DNA binding, CRISPR/Cas9 uses RNA to establish a specific binding of its DNA nuclease. Besides its capability to facilitate multiplexed genomic modifications in one shot, the CRISPR/Cas is much easier to design compared to all other DNA nucleases. Current results indicate that any DNA nuclease can be successfully employed in a broad range of organisms which renders them useful for improving the understanding of complex physiological systems such as reproduction, producing transgenic animals, including creating large animal models for human diseases, creating specific cell lines, and plants, and even for treating human genetic diseases. This review provides an update on DNA nucleases, their underlying mechanism and focuses on their application to edit the genome of livestock species. © 2017 Blackwell Verlag GmbH.

Mechanism of chimera formation during the Multiple Displacement Amplification reaction

PubMed Central

Lasken, Roger S; Stockwell, Timothy B

2007-01-01

Background Multiple Displacement Amplification (MDA) is a method used for amplifying limiting DNA sources. The high molecular weight amplified DNA is ideal for DNA library construction. While this has enabled genomic sequencing from one or a few cells of unculturable microorganisms, the process is complicated by the tendency of MDA to generate chimeric DNA rearrangements in the amplified DNA. Determining the source of the DNA rearrangements would be an important step towards reducing or eliminating them. Results Here, we characterize the major types of chimeras formed by carrying out an MDA whole genome amplification from a single E. coli cell and sequencing by the 454 Life Sciences method. Analysis of 475 chimeras revealed the predominant reaction mechanisms that create the DNA rearrangements. The highly branched DNA synthesized in MDA can assume many alternative secondary structures. DNA strands extended on an initial template can be displaced becoming available to prime on a second template creating the chimeras. Evidence supports a model in which branch migration can displace 3'-ends freeing them to prime on the new templates. More than 85% of the resulting DNA rearrangements were inverted sequences with intervening deletions that the model predicts. Intramolecular rearrangements were favored, with displaced 3'-ends reannealing to single stranded 5'-strands contained within the same branched DNA molecule. In over 70% of the chimeric junctions, the 3' termini had initiated priming at complimentary sequences of 2–21 nucleotides (nts) in the new templates. Conclusion Formation of chimeras is an important limitation to the MDA method, particularly for whole genome sequencing. Identification of the mechanism for chimera formation provides new insight into the MDA reaction and suggests methods to reduce chimeras. The 454 sequencing approach used here will provide a rapid method to assess the utility of reaction modifications. PMID:17430586

Computer Center: 2 HyperCard Stacks for Biology.

ERIC Educational Resources Information Center

Duhrkopf, Richard, Ed.

1989-01-01

Two Hypercard stacks are reviewed including "Amino Acids," created to help students associate amino acid names with their structures, and "DNA Teacher," a tutorial on the structure and function of DNA. Availability, functions, hardware requirements, and general comments on these stacks are provided. (CW)

Writing DNA with GenoCAD.

PubMed

Czar, Michael J; Cai, Yizhi; Peccoud, Jean

2009-07-01

Chemical synthesis of custom DNA made to order calls for software streamlining the design of synthetic DNA sequences. GenoCAD (www.genocad.org) is a free web-based application to design protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks called genetic parts. By capturing design strategies in grammatical models of DNA sequences, GenoCAD guides the user through the design process. By successively clicking on icons representing structural features or actual genetic parts, complex constructs composed of dozens of functional blocks can be designed in a matter of minutes. GenoCAD automatically derives the construct sequence from its comprehensive libraries of genetic parts. Upon completion of the design process, users can download the sequence for synthesis or further analysis. Users who elect to create a personal account on the system can customize their workspace by creating their own parts libraries, adding new parts to the libraries, or reusing designs to quickly generate sets of related constructs.

Organization of supercoil domains and their reorganization by transcription

PubMed Central

Deng, Shuang; Stein, Richard A.; Higgins, N. Patrick

2006-01-01

Summary During a normal cell cycle, chromosomes are exposed to many biochemical reactions that require specific types of DNA movement. Separation forces move replicated chromosomes into separate sister cell compartments during cell division, and the contemporaneous acts of DNA replication, RNA transcription and cotranscriptional translation of membrane proteins cause specific regions of DNA to twist, writhe and expand or contract. Recent experiments indicate that a dynamic and stochastic mechanism creates supercoil DNA domains soon after DNA replication. Domain structure is subsequently reorganized by RNA transcription. Examples of transcription-dependent chromosome remodelling are also emerging from eukaryotic cell systems. PMID:16135220

Hegelians Axel Honneth and Robert Williams on the Development of Human Morality

ERIC Educational Resources Information Center

Huttunen, Rauno

2012-01-01

An individual is in the lowest phase of moral development if he thinks only of his own personal interest and has only his own selfish agenda in his mind as he encounters other humans. This lowest phase corresponds well with sixteenth century British moral egoism which reflects the rise of the new economic order. Adam Smith (1723-1790) wanted to…

Why acquiesce? Worker reproductive parasitism in the Eastern honeybee (Apis cerana).

PubMed

Holmes, M J; Tan, K; Wang, Z; Oldroyd, B P; Beekman, M

2014-05-01

Most societies are vulnerable to rogue individuals that pursue their own interests at the expense of the collective entity. Societies often protect themselves from selfish behaviour by 'policing', thereby enforcing the interests of the collective over those of individuals. In insect societies, for example, selfish workers can activate their ovaries and lay eggs, exploiting the collective brood rearing system for individual benefit. Policing, usually in the form of oophagy of worker-laid eggs, controls selfish behaviour. Importantly, once an effective system of policing has evolved, the incentive for personal reproduction is lost, and 'reproductive acquiescence' in which ovary activation is rare or absent is predicted to evolve. Studies of social Hymenoptera have largely supported the prediction of worker 'acquiescence'; workers of most species where policing is well developed have inactive ovaries. However, the eastern honeybee Apis cerana appears to be an exception. A. cerana colonies are characterized by highly efficient policing, yet about 5% of workers have active ovaries, even when a queen is present. This suggests that the evolution of acquiescence is incomplete in A. cerana. We regularly sampled male eggs and pupae from four A. cerana colonies. Workers had high levels of ovary activation overall (11.7%), and 3.8% of assignable male eggs and 1.1% of assignable male pupae were worker-laid. We conclude that workers with active ovaries lay their eggs, but these rarely survive to pupation because of intense policing. We then used our findings as well as previously published data on A. cerana and A. mellifera to redo the meta-analysis on which reproductive acquiescence theory is based. Including data on both species did not affect the relationship between effectiveness of policing and levels of worker reproduction. Their inclusion did, however, seriously weaken the relationship between relatedness among workers and levels of worker reproduction. Our work thus suggests that relatedness among workers does not affect the probability that workers will attempt to reproduce, but that it is coercion by peers that limits worker reproduction. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Comparative virology and AIDS (review).

PubMed

Kodama, M; Kodama, T

1996-03-01

The scientific debate between pros and cons of the HIV criminal theory of AIDS still remains unsettled. The purpose of this review is to promote resolution of the problem by extracting a common principle of the host-virus relation using data resources for each of 4 viruses as follows: a) polyoma virus, b) Marek's disease virus, c) Ebola virus, d) Korean hemorrhagic fever virus. Conclusions drawn from this study are given as follows: i) Environment emerged as the cardinal factor to modify the process of virus infection in all of the 4 viruses studied. Above all, an accelerating effect of environmental stress on the progression of virus infection was noted in vivo in the majority of viral diseases. ii) Evidence is available to indicate that a healthy cell (or a healthy individual) may harbor virus genes of multiple species without manifesting any pathologic sign. iii) Evidence also suggests that the biological property as well as morphological structure of a virus may vary in reponse to a change of the bioenvironment. On the basis of the above information, we propose to renounce 2 assumptions of classical infection model: a) the hereditarily determined virulence of a microorganism (including virus) be the sole determinant of infection to the effect that its invasion into the host should automatically complete the programmed course of infection; b) virus, a quasi-living creature, should reserve its behavioral independence irrespective of a change of the bioenvironment. The new infection model was constructed on the basis of the selfish gene concept that had been invented by Richard Dawkins to explain the altruistic behavior of an individual. That is, the fate of an exogenous or endogenous virus is under the dual control of the host genome (selfish gene) and the outer environment. The progression of virus infection is conditioned by a crosstalk between them. The selfish gene may use virus (a lifeless substance) as a magic bullet to induce a designated host response. In that sense, virus is not allowed to retain behavioral independence in the practice of its task. The above new model of virus infection was tested for its validity in the recent data of AIDS epidemiology.

Automating gene library synthesis by structure-based combinatorial protein engineering: examples from plant sesquiterpene synthases.

PubMed

Dokarry, Melissa; Laurendon, Caroline; O'Maille, Paul E

2012-01-01

Structure-based combinatorial protein engineering (SCOPE) is a homology-independent recombination method to create multiple crossover gene libraries by assembling defined combinations of structural elements ranging from single mutations to domains of protein structure. SCOPE was originally inspired by DNA shuffling, which mimics recombination during meiosis, where mutations from parental genes are "shuffled" to create novel combinations in the resulting progeny. DNA shuffling utilizes sequence identity between parental genes to mediate template-switching events (the annealing and extension of one parental gene fragment on another) in PCR reassembly reactions to generate crossovers and hence recombination between parental genes. In light of the conservation of protein structure and degeneracy of sequence, SCOPE was developed to enable the "shuffling" of distantly related genes with no requirement for sequence identity. The central principle involves the use of oligonucleotides to encode for crossover regions to choreograph template-switching events during PCR assembly of gene fragments to create chimeric genes. This approach was initially developed to create libraries of hybrid DNA polymerases from distantly related parents, and later developed to create a combinatorial mutant library of sesquiterpene synthases to explore the catalytic landscapes underlying the functional divergence of related enzymes. This chapter presents a simplified protocol of SCOPE that can be integrated with different mutagenesis techniques and is suitable for automation by liquid-handling robots. Two examples are presented to illustrate the application of SCOPE to create gene libraries using plant sesquiterpene synthases as the model system. In the first example, we outline how to create an active-site library as a series of complex mixtures of diverse mutants. In the second example, we outline how to create a focused library as an array of individual clones to distil minimal combinations of functionally important mutations. Through these examples, the principles of the technique are illustrated and the suitability of automating various aspects of the procedure for given applications are discussed. Copyright © 2012 Elsevier Inc. All rights reserved.

DNA materials: bridging nanotechnology and biotechnology.

PubMed

Yang, Dayong; Hartman, Mark R; Derrien, Thomas L; Hamada, Shogo; An, Duo; Yancey, Kenneth G; Cheng, Ru; Ma, Minglin; Luo, Dan

2014-06-17

CONSPECTUS: In recent decades, DNA has taken on an assortment of diverse roles, not only as the central genetic molecule in biological systems but also as a generic material for nanoscale engineering. DNA possesses many exceptional properties, including its biological function, biocompatibility, molecular recognition ability, and nanoscale controllability. Taking advantage of these unique attributes, a variety of DNA materials have been created with properties derived both from the biological functions and from the structural characteristics of DNA molecules. These novel DNA materials provide a natural bridge between nanotechnology and biotechnology, leading to far-ranging real-world applications. In this Account, we describe our work on the design and construction of DNA materials. Based on the role of DNA in the construction, we categorize DNA materials into two classes: substrate and linker. As a substrate, DNA interfaces with enzymes in biochemical reactions, making use of molecular biology's "enzymatic toolkit". For example, employing DNA as a substrate, we utilized enzymatic ligation to prepare the first bulk hydrogel made entirely of DNA. Using this DNA hydrogel as a structural scaffold, we created a protein-producing DNA hydrogel via linking plasmid DNA onto the hydrogel matrix through enzymatic ligation. Furthermore, to fully make use of the advantages of both DNA materials and polymerase chain reaction (PCR), we prepared thermostable branched DNA that could remain intact even under denaturing conditions, allowing for their use as modular primers for PCR. Moreover, via enzymatic polymerization, we have recently constructed a physical DNA hydrogel with unique internal structure and mechanical properties. As a linker, we have used DNA to interface with other functional moieties, including gold nanoparticles, clay minerals, proteins, and lipids, allowing for hybrid materials with unique properties for desired applications. For example, we recently designed a DNA-protein conjugate as a universal adapter for protein detection. We further demonstrate a diverse assortment of applications for these DNA materials including diagnostics, protein production, controlled drug release systems, the exploration of life evolution, and plasmonics. Although DNA has shown great potential as both substrate and linker in the construction of DNA materials, it is still in the initial stages of becoming a well-established and widely used material. Important challenges include the ease of design and fabrication, scaling-up, and minimizing cost. We envision that DNA materials will continue to bridge the gap between nanotechnology and biotechnology and will ultimately be employed for many real-world applications.

Application of biomolecular recognition via magnetic nanoparticle in nanobiotechnology

NASA Astrophysics Data System (ADS)

Shen, Wei-Zheng; Cetinel, Sibel; Montemagno, Carlo

2018-05-01

The marriage of biomolecular recognition and magnetic nanoparticle creates tremendous opportunities in the development of advanced technology both in academic research and in industrial sectors. In this paper, we review current progress on the magnetic nanoparticle-biomolecule hybrid systems, particularly employing the recognition pairs of DNA-DNA, DNA-protein, protein-protein, and protein-inorganics in several nanobiotechnology application areas, including molecular biology, diagnostics, medical treatment, industrial biocatalysts, and environmental separations.

Creating Context for the Use of DNA Adduct Data in Risk Assessment

EPA Science Inventory

Assessments of human cancer risk require the integration of diverse types of data. Advancing technologies for quantitative measurements at the sub-cellular domain raise the critical issue of interpretation and use of DNA adduct data in context with current understanding of cancer...

DNA-Based Dynamic Reaction Networks.

PubMed

Fu, Ting; Lyu, Yifan; Liu, Hui; Peng, Ruizi; Zhang, Xiaobing; Ye, Mao; Tan, Weihong

2018-05-21

Deriving from logical and mechanical interactions between DNA strands and complexes, DNA-based artificial reaction networks (RNs) are attractive for their high programmability, as well as cascading and fan-out ability, which are similar to the basic principles of electronic logic gates. Arising from the dream of creating novel computing mechanisms, researchers have placed high hopes on the development of DNA-based dynamic RNs and have strived to establish the basic theories and operative strategies of these networks. This review starts by looking back on the evolution of DNA dynamic RNs; in particular' the most significant applications in biochemistry occurring in recent years. Finally, we discuss the perspectives of DNA dynamic RNs and give a possible direction for the development of DNA circuits. Copyright © 2018. Published by Elsevier Ltd.

Structural DNA Nanotechnology: State of the Art and Future Perspective

PubMed Central

2015-01-01

Over the past three decades DNA has emerged as an exceptional molecular building block for nanoconstruction due to its predictable conformation and programmable intra- and intermolecular Watson–Crick base-pairing interactions. A variety of convenient design rules and reliable assembly methods have been developed to engineer DNA nanostructures of increasing complexity. The ability to create designer DNA architectures with accurate spatial control has allowed researchers to explore novel applications in many directions, such as directed material assembly, structural biology, biocatalysis, DNA computing, nanorobotics, disease diagnosis, and drug delivery. This Perspective discusses the state of the art in the field of structural DNA nanotechnology and presents some of the challenges and opportunities that exist in DNA-based molecular design and programming. PMID:25029570

Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns.

PubMed

Tikhomirov, Grigory; Petersen, Philip; Qian, Lulu

2017-12-06

Self-assembled DNA nanostructures enable nanometre-precise patterning that can be used to create programmable molecular machines and arrays of functional materials. DNA origami is particularly versatile in this context because each DNA strand in the origami nanostructure occupies a unique position and can serve as a uniquely addressable pixel. However, the scale of such structures has been limited to about 0.05 square micrometres, hindering applications that demand a larger layout and integration with more conventional patterning methods. Hierarchical multistage assembly of simple sets of tiles can in principle overcome this limitation, but so far has not been sufficiently robust to enable successful implementation of larger structures using DNA origami tiles. Here we show that by using simple local assembly rules that are modified and applied recursively throughout a hierarchical, multistage assembly process, a small and constant set of unique DNA strands can be used to create DNA origami arrays of increasing size and with arbitrary patterns. We illustrate this method, which we term 'fractal assembly', by producing DNA origami arrays with sizes of up to 0.5 square micrometres and with up to 8,704 pixels, allowing us to render images such as the Mona Lisa and a rooster. We find that self-assembly of the tiles into arrays is unaffected by changes in surface patterns on the tiles, and that the yield of the fractal assembly process corresponds to about 0.95 m - 1 for arrays containing m tiles. When used in conjunction with a software tool that we developed that converts an arbitrary pattern into DNA sequences and experimental protocols, our assembly method is readily accessible and will facilitate the construction of sophisticated materials and devices with sizes similar to that of a bacterium using DNA nanostructures.

Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns

NASA Astrophysics Data System (ADS)

Tikhomirov, Grigory; Petersen, Philip; Qian, Lulu

2017-12-01

Self-assembled DNA nanostructures enable nanometre-precise patterning that can be used to create programmable molecular machines and arrays of functional materials. DNA origami is particularly versatile in this context because each DNA strand in the origami nanostructure occupies a unique position and can serve as a uniquely addressable pixel. However, the scale of such structures has been limited to about 0.05 square micrometres, hindering applications that demand a larger layout and integration with more conventional patterning methods. Hierarchical multistage assembly of simple sets of tiles can in principle overcome this limitation, but so far has not been sufficiently robust to enable successful implementation of larger structures using DNA origami tiles. Here we show that by using simple local assembly rules that are modified and applied recursively throughout a hierarchical, multistage assembly process, a small and constant set of unique DNA strands can be used to create DNA origami arrays of increasing size and with arbitrary patterns. We illustrate this method, which we term ‘fractal assembly’, by producing DNA origami arrays with sizes of up to 0.5 square micrometres and with up to 8,704 pixels, allowing us to render images such as the Mona Lisa and a rooster. We find that self-assembly of the tiles into arrays is unaffected by changes in surface patterns on the tiles, and that the yield of the fractal assembly process corresponds to about 0.95m - 1 for arrays containing m tiles. When used in conjunction with a software tool that we developed that converts an arbitrary pattern into DNA sequences and experimental protocols, our assembly method is readily accessible and will facilitate the construction of sophisticated materials and devices with sizes similar to that of a bacterium using DNA nanostructures.

DNA-carbon nano onion aggregate: triangle, hexagon, six-petal flower to dead-end network

NASA Astrophysics Data System (ADS)

Babar, Dipak Gorakh; Pakhira, Bholanath; Sarkar, Sabyasachi

2017-08-01

The interaction between calf-thymus (CT) dsDNA and water soluble carbon nano onion (wsCNO) in water follows denaturation of dsDNA (double stranded) to ssDNA (single stranded) as monitored by optical spectroscopy. The ssDNA concomitantly wraps the spiky surface of wsCNO to create triangular aggregate as the building block as observed by time-dependent SEM images. These triangles further aggregate leading to six-petal flower arrangement via hexagon and finally reach a dead end network as imaged by SEM and optical fluorescence microscopy. The dead-end network aggregate lost the intrinsic optical property of DNA suggesting complete loss of its activity.

Selfish DNA: a pharmaceutical perspective.

PubMed

Winckler, T

2013-07-01

Almost 25 years ago, Theo Dingermann published the discovery of a new mobile genetic element in the unicellular microbe Dictyostelium discoideum in the journal Science. An interesting property of this new molecular parasite, the Dictyostelium Repetitive Element (DRE), was that all integrations were found approximately 50 base pairs (bp) upstream of transfer RNA (tRNA) genes in the D. discoideum genome, thus implying an active targeting mechanism to avoid the disruption of host cell genes by the retrotransposition process. Since then, the facultative multicellular "social amoeba" D. discoideum has become a popular model for analyzing complex cellular functions such as cell movement, chemotaxis, phagocytosis, and cell differentiation, important areas of biomedical research that are often hard to investigate in cells from "higher organisms" including humans. Therefore, progress in the development of methods to study Dictyostelium biology has also provoked research on transposable elements in this organism. Early work on the DRE element suggested that studying its molecular mechanism of site-specific integration might promote human gene therapy technology through the design of integrating gene transfer vectors with low intrinsic genotoxic potential. In this review article, I will briefly review the original research performed on the DRE transposable element in the Dingermann lab and report on how the emergence of genomics technologies and the development of tools to analyze de novo retrotransposition events in D. discoideum cells will expand our knowledge of DRE biology in the future.

Chromosomes with a life of their own.

PubMed

Jones, R N; González-Sánchez, M; González-García, M; Vega, J M; Puertas, M J

2008-01-01

B chromosomes (Bs) can be described as 'passengers in the genome', a term that has been used for the repetitive DNA which comprises the bulk of the genome in large genome species, except that Bs have a life of their own as independent chromosomes. As with retrotransposons they can accumulate in number, but in this case by various processes of mitotic or meiotic drive, based on their own autonomous ways of using spindles, especially in the gametophyte phase of the life cycle of flowering plants. This selfish property of drive ensures their survival and spread in natural populations, even against a gradient of harmful effects on the host plant phenotype. Bs are inhabitants of the nucleus and they are subject to control by 'genes' in the A chromosome (As) complement. This interaction with the As, together with the balance between drive and harmful effects makes a dynamic system in the life of a B chromosome, notwithstanding the fact that we are only now beginning to unravel the story in a few favoured species. In this review we concentrate mainly on recent developments in the Bs of rye and maize, two of the species currently receiving most attention. We focus on their population dynamics and on the molecular basis of their structural organisation and mechanisms of drive, as well as on their mode of origin and potential applications in plant biotechnology. 2008 S. Karger AG, Basel

Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi.

PubMed

Ishikawa, Ken; Watanabe, Miki; Kuroita, Toshihiro; Uchiyama, Ikuo; Bujnicki, Janusz M; Kawakami, Bunsei; Tanokura, Masaru; Kobayashi, Ichizo

2005-07-21

To search for restriction endonucleases, we used a novel plant-based cell-free translation procedure that bypasses the toxicity of these enzymes. To identify candidate genes, the related genomes of the hyperthermophilic archaea Pyrococcus abyssi and Pyrococcus horikoshii were compared. In line with the selfish mobile gene hypothesis for restriction-modification systems, apparent genome rearrangement around putative restriction genes served as a selecting criterion. Several candidate restriction genes were identified and then amplified in such a way that they were removed from their own translation signal. During their cloning into a plasmid, the genes became connected with a plant translation signal. After in vitro transcription by T7 RNA polymerase, the mRNAs were separated from the template DNA and translated in a wheat-germ-based cell-free protein synthesis system. The resulting solution could be directly assayed for restriction activity. We identified two deoxyribonucleases. The novel enzyme was denoted as PabI, purified and found to recognize 5'-GTAC and leave a 3'-TA overhang (5'-GTA/C), a novel restriction enzyme-generated terminus. PabI is active up to 90 degrees C and optimally active at a pH of around 6 and in NaCl concentrations ranging from 100 to 200 mM. We predict that it has a novel 3D structure.

At the Bench: Helicobacter pylori, dysregulated host responses, DNA damage, and gastric cancer

PubMed Central

Hardbower, Dana M.; Peek, Richard M.; Wilson, Keith T.

2014-01-01

Helicobacter pylori infection is the strongest known risk factor for the development of gastric cancer. Given that ∼50% of the global population is infected with this pathogen, there is great impetus to elucidate underlying causes that mediate progression from infection to cancer. Recent evidence suggests that H. pylori-induced chronic inflammation and oxidative stress create an environment conducive to DNA damage and tissue injury. DNA damage leads to genetic instability and eventually, neoplastic transformation. Pathogen-encoded virulence factors induce a robust but futile immune response and alter host pathways that lower the threshold for carcinogenesis, including DNA damage repair, polyamine synthesis and catabolism, antioxidant responses, and cytokine production. Collectively, such dysregulation creates a protumorigenic microenvironment within the stomach. This review seeks to address each of these aspects of H. pylori infection and to call attention to areas of particular interest within this field of research. This review also seeks to prioritize areas of translational research related to H. pylori-induced gastric cancer based on insights garnered from basic research in this field. See related review by Dalal and Moss, At the Bedside: H. pylori, dysregulated host responses, DNA damage, and gastric cancer. PMID:24868089

Excitonic AND Logic Gates on DNA Brick Nanobreadboards.

PubMed

Cannon, Brittany L; Kellis, Donald L; Davis, Paul H; Lee, Jeunghoon; Kuang, Wan; Hughes, William L; Graugnard, Elton; Yurke, Bernard; Knowlton, William B

2015-03-18

A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, we have demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore density achievable via this brick-based approach provide a viable path toward developing information processing and storage systems.

Excitonic AND Logic Gates on DNA Brick Nanobreadboards

PubMed Central

2015-01-01

A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, we have demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore density achievable via this brick-based approach provide a viable path toward developing information processing and storage systems. PMID:25839049

An Optimal Seed Based Compression Algorithm for DNA Sequences

PubMed Central

Gopalakrishnan, Gopakumar; Karunakaran, Muralikrishnan

2016-01-01

This paper proposes a seed based lossless compression algorithm to compress a DNA sequence which uses a substitution method that is similar to the LempelZiv compression scheme. The proposed method exploits the repetition structures that are inherent in DNA sequences by creating an offline dictionary which contains all such repeats along with the details of mismatches. By ensuring that only promising mismatches are allowed, the method achieves a compression ratio that is at par or better than the existing lossless DNA sequence compression algorithms. PMID:27555868

Comparison of multiple gene assembly methods for metabolic engineering

Treesearch

Chenfeng Lu; Karen Mansoorabadi; Thomas Jeffries

2007-01-01

A universal, rapid DNA assembly method for efficient multigene plasmid construction is important for biological research and for optimizing gene expression in industrial microbes. Three different approaches to achieve this goal were evaluated. These included creating long complementary extensions using a uracil-DNA glycosylase technique, overlap extension polymerase...

Engaging with Molecular Form to Understand Function

ERIC Educational Resources Information Center

Barber, Nicola C.; Stark, Louisa A.

2014-01-01

Cells are bustling factories with diverse and prolific arrays of molecular machinery. Remarkably, this machinery self-organizes to carry out the complex biochemical activities characteristic of life. When Watson and Crick published the structure of DNA, they noted that DNA base pairing creates a double-stranded form that provides a means of…

Structure and Environment Influence in DNA Conduction

NASA Technical Reports Server (NTRS)

Adessi, C.; Walch, S.; Anantram, M. P.; Biegel, Bryan A. (Technical Monitor)

2002-01-01

Results for transmission through a poly(G) DNA molecule are presented. We show that a modification of the rise of a B-DNA form can induce a shift of the conduction channel toward the valence one. We clearly prove that deformation of the backbone of the molecule has a significant influence on hole transport. Finally, we observe that the presence of ionic species, such Na, near the molecule can create new conduction channels.

The aging enterprise: in whose interests?

PubMed

Estes, C L

1986-01-01

This paper revisits the aging enterprise in the context of the new competitive business ideology. Public policy has created an aging enterprise that assures that the needs of the aged will be processed and treated as a commodity. The medical-industrial complex, which comprises the most significant part of the aging enterprise, is a primary beneficiary of the recent reformulation of values and expectations vis-a-vis the state and the private sector. The new business ideology in health is aimed not only at controlling costs but, more importantly, at establishing health care as a market good like any other. Issues of access to needed services are raised for Medicare and Medicaid beneficiaries and for the uninsured. Budget cuts, medical cost control, and the market ideology are resulting in greater fragmentation, privatization, and corporatization of services, as indicated by the author's research on the private nonprofit health and social services sector in a sample of 8 states and 32 communities. In this paper, age-segregated politics and policies in the United States are challenged to utilize grass-roots political efforts that cross age and class barriers. Single-interest aging-based policies are criticized as a form of selfish separatism that could supplant an important and vitally needed intergenerational and coalition strategy.

Modeling Misbehavior in Cooperative Diversity: A Dynamic Game Approach

NASA Astrophysics Data System (ADS)

Dehnie, Sintayehu; Memon, Nasir

2009-12-01

Cooperative diversity protocols are designed with the assumption that terminals always help each other in a socially efficient manner. This assumption may not be valid in commercial wireless networks where terminals may misbehave for selfish or malicious intentions. The presence of misbehaving terminals creates a social-dilemma where terminals exhibit uncertainty about the cooperative behavior of other terminals in the network. Cooperation in social-dilemma is characterized by a suboptimal Nash equilibrium where wireless terminals opt out of cooperation. Hence, without establishing a mechanism to detect and mitigate effects of misbehavior, it is difficult to maintain a socially optimal cooperation. In this paper, we first examine effects of misbehavior assuming static game model and show that cooperation under existing cooperative protocols is characterized by a noncooperative Nash equilibrium. Using evolutionary game dynamics we show that a small number of mutants can successfully invade a population of cooperators, which indicates that misbehavior is an evolutionary stable strategy (ESS). Our main goal is to design a mechanism that would enable wireless terminals to select reliable partners in the presence of uncertainty. To this end, we formulate cooperative diversity as a dynamic game with incomplete information. We show that the proposed dynamic game formulation satisfied the conditions for the existence of perfect Bayesian equilibrium.

Effects of adaptive dynamical linking in networked games

NASA Astrophysics Data System (ADS)

Yang, Zhihu; Li, Zhi; Wu, Te; Wang, Long

2013-10-01

The role of dynamical topologies in the evolution of cooperation has received considerable attention, as some studies have demonstrated that dynamical networks are much better than static networks in terms of boosting cooperation. Here we study a dynamical model of evolution of cooperation on stochastic dynamical networks in which there are no permanent partners to each agent. Whenever a new link is created, its duration is randomly assigned without any bias or preference. We allow the agent to adaptively adjust the duration of each link during the evolution in accordance with the feedback from game interactions. By Monte Carlo simulations, we find that cooperation can be remarkably promoted by this adaptive dynamical linking mechanism both for the game of pairwise interactions, such as the Prisoner's Dilemma game (PDG), and for the game of group interactions, illustrated by the public goods game (PGG). And the faster the adjusting rate, the more successful the evolution of cooperation. We also show that in this context weak selection favors cooperation much more than strong selection does. What is particularly meaningful is that the prosperity of cooperation in this study indicates that the rationality and selfishness of a single agent in adjusting social ties can lead to the progress of altruism of the whole population.

Transfusion-free treatment of Jehovah's Witnesses: respecting the autonomous patient's motives.

PubMed Central

Malyon, D

1998-01-01

What makes Jehovah's Witnesses tick? What motivates practitioners of medicine? How is benevolent human behaviour to be interpreted? The explanation that fear of censure, mind-control techniques or enlightened self-interest are the real motivators of human conduct is questioned. Those who believe that man was created in "God's image", hold that humanity has the potential to rise above selfishly driven attitudes and actions, and reflect the qualities of love, kindness and justice that separate us from the beasts. A comparison of general medical ethics and disciplines, and those of the Jehovah's Witness community, is made in this context. The easy charge that frequent deaths result from refusal of blood transfusions is examined. The central source of antipathy towards Jehovah's Witnesses, namely the alleged imposition of extreme and even harmful refusal of blood therapy on our children is addressed. Of course, "...few dilemmas are likely to be resolved wisely or satisfactorily by a blinkered adherence to abstract principles alone. Solutions to most cases will be dictated by a combination of factors. The support of medical ethics by Jehovah's Witnesses, and their willingness to share in reasoned and ethical debate, while at the same time holding firm to their religious and conscientious principles are emphasised. PMID:9873976

Escalation and Resolution of Border Disputes and Interstate Conflicts in Africa: The Malawi-Tanzania Case

DTIC Science & Technology

2011-06-01

struggle in the region. They cause relentless strife, including refugee problems, environmental degradation, deforestation , small arms proliferation...human and natural resources, extreme poverty and hunger abound on the continent.”42 Furthermore, a snapshot of Africa reveals deforestation , fast...Malawi, while Tanzania is disadvantaged . Since players selfishly attempt to maximize their outcomes, via ‘maximin theorem,’ the outcome is BD that

Myth, Metaphor, and Imagination: Framing Homeland Security as Art and Archetype

DTIC Science & Technology

2013-03-01

repeatable, patterned, and consequential, science reveals stability and balance. As creative, emergent, mutant, and selfish, art is a self -styled...broader applications. Soft vigilance is open to novelty and takes in more information, while hyper vigilance locks in on an object of attention and...deficiency requirements of physiological needs, safety needs, love and belonging, and esteem, but also the being requirements of self -actualization and

Freedom and the State: Kant on Revolution and International Interface

DTIC Science & Technology

1999-11-11

physical and psychological nature and many of them make us selfish and disagreeable beings. In fact, Kant contends that human beings are naturally...circumstances include a "defective education, bad company,... the viciousness of a natural disposition insensitive to shame,... levity and thoughtlessness...possibility of ethical action. Unless we are capable of choosing duty over inclinations, we cannot be held responsible for our actions (GMM 49). This

A Game Theory Based Solution for Security Challenges in CRNs

NASA Astrophysics Data System (ADS)

Poonam; Nagpal, Chander Kumar

2018-03-01

Cognitive radio networks (CRNs) are being envisioned to drive the next generation Ad hoc wireless networks due to their ability to provide communications resilience in continuously changing environments through the use of dynamic spectrum access. Conventionally CRNs are dependent upon the information gathered by other secondary users to ensure the accuracy of spectrum sensing making them vulnerable to security attacks leading to the need of security mechanisms like cryptography and trust. However, a typical cryptography based solution is not a viable security solution for CRNs owing to their limited resources. Effectiveness of trust based approaches has always been, in question, due to credibility of secondary trust resources. Game theory with its ability to optimize in an environment of conflicting interests can be quite a suitable tool to manage an ad hoc network in the presence of autonomous selfish/malevolent/malicious and attacker nodes. The literature contains several theoretical proposals for augmenting game theory in the ad hoc networks without explicit/detailed implementation. This paper implements a game theory based solution in MATLAB-2015 to secure the CRN environment and compares the obtained results with the traditional approaches of trust and cryptography. The simulation result indicates that as the time progresses the game theory performs much better with higher throughput, lower jitter and better identification of selfish/malicious nodes.

Truthful Channel Sharing for Self Coexistence of Overlapping Medical Body Area Networks

PubMed Central

Dutkiewicz, Eryk; Zheng, Guanglou

2016-01-01

As defined by IEEE 802.15.6 standard, channel sharing is a potential method to coordinate inter-network interference among Medical Body Area Networks (MBANs) that are close to one another. However, channel sharing opens up new vulnerabilities as selfish MBANs may manipulate their online channel requests to gain unfair advantage over others. In this paper, we address this issue by proposing a truthful online channel sharing algorithm and a companion protocol that allocates channel efficiently and truthfully by punishing MBANs for misreporting their channel request parameters such as time, duration and bid for the channel. We first present an online channel sharing scheme for unit-length channel requests and prove that it is truthful. We then generalize our model to settings with variable-length channel requests, where we propose a critical value based channel pricing and preemption scheme. A bid adjustment procedure prevents unbeneficial preemption by artificially raising the ongoing winner’s bid controlled by a penalty factor λ. Our scheme can efficiently detect selfish behaviors by monitoring a trust parameter α of each MBAN and punish MBANs from cheating by suspending their requests. Our extensive simulation results show our scheme can achieve a total profit that is more than 85% of the offline optimum method in the typical MBAN settings. PMID:26844888

No costly prosociality among related long-tailed macaques (Macaca fascicularis).

PubMed

Sterck, Elisabeth H M; Olesen, Caroline U; Massen, Jorg J M

2015-08-01

Altruism, benefiting another at a cost to the donor, may be achieved through prosocial behavior. Studies of nonhuman animals typically investigate prosocial behavior with paradigms in which the donor can choose to give a recipient a food item, and the choice does not affect the donor's reward (which is either present or absent). In such tasks, long-tailed macaques (Macaca fascicularis) show prosocial behavior, especially toward kin. Here, we tested captive long-tailed macaques with related recipients in an alternative task, in which the donor had to give up a preferred reward to benefit the recipient; that is, they had to choose a lower valued reward for themselves to provide food to their kin. Overall, the macaques did not provide their kin with food. The task forced the donor to balance its prosocial behavior with its selfish choice for a higher value reward, a balance that turned out to favor selfish motives. Consequently, our study shows that a prosocial tendency is not sufficient to elicit costly prosocial behavior in long-tailed macaques. Subsequently, we feel that tasks in which the donor must choose a lower value reward to benefit another individual may allow the titration of the strength of prosocial behavior, and thus provides interesting possibilities for future comparative studies. (c) 2015 APA, all rights reserved).

A game-theoretic approach to optimize ad hoc networks inspired by small-world network topology

NASA Astrophysics Data System (ADS)

Tan, Mian; Yang, Tinghong; Chen, Xing; Yang, Gang; Zhu, Guoqing; Holme, Petter; Zhao, Jing

2018-03-01

Nodes in ad hoc networks are connected in a self-organized manner. Limited communication radius makes information transmit in multi-hop mode, and each forwarding needs to consume the energy of nodes. Insufficient communication radius or exhaustion of energy may cause the absence of some relay nodes and links, further breaking network connectivity. On the other hand, nodes in the network may refuse to cooperate due to objective faulty or personal selfish, hindering regular communication in the network. This paper proposes a model called Repeated Game in Small World Networks (RGSWN). In this model, we first construct ad hoc networks with small-world feature by forming "communication shortcuts" between multiple-radio nodes. Small characteristic path length reduces average forwarding times in networks; meanwhile high clustering coefficient enhances network robustness. Such networks still maintain relative low global power consumption, which is beneficial to extend the network survival time. Then we use MTTFT strategy (Mend-Tolerance Tit-for-Tat) for repeated game as a rule for the interactions between neighbors in the small-world networks. Compared with other five strategies of repeated game, this strategy not only punishes the nodes' selfishness more reasonably, but also has the best tolerance to the network failure. This work is insightful for designing an efficient and robust ad hoc network.

The dynamic relationship between polyandry and selfish genetic elements

PubMed Central

Wedell, Nina

2013-01-01

Selfish genetic elements (SGEs) are ubiquitous in eukaryotes and bacteria, and make up a large part of the genome. They frequently target sperm to increase their transmission success, but these manipulations are often associated with reduced male fertility. Low fertility of SGE-carrying males is suggested to promote polyandry as a female strategy to bias paternity against male carriers. Support for this hypothesis is found in several taxa, where SGE-carrying males have reduced sperm competitive ability. In contrast, when SGEs give rise to reproductive incompatibilities between SGE-carrying males and females, polyandry is not necessarily favoured, irrespective of the detrimental impact on male fertility. This is due to the frequency-dependent nature of these incompatibilities, because they will decrease in the population as the frequency of SGEs increases. However, reduced fertility of SGE-carrying males can prevent the successful population invasion of SGEs. In addition, SGEs can directly influence male and female mating behaviour, mating rates and reproductive traits (e.g. female reproductive tract length and male sperm). This reveals a potent and dynamic interaction between SGEs and polyandry highlighting the potential to generate sexual selection and conflict, but also indicates that polyandry can promote harmony within the genome by undermining the spread of SGEs. PMID:23339240

Properties and natural occurrence of maternal-effect selfish genes ('Medea' factors) in the red flour beetle, tribolium castaneum

PubMed

Beeman; Friesen

1999-05-01

Maternally acting selfish genes, termed 'Medea' factors, were found to be widespread in wild populations of Tribolium castaneum collected in Europe, North and South America, Africa and south-east Asia, but were rare or absent in populations from Australia and the Indian subcontinent. We detected at least four distinct genetic loci in at least two different linkage groups that exhibit the Medea pattern of differential mortality of genotypes within maternal families. Although each M factor tested had similar properties of maternal lethality to larvae and zygotic self-rescue, M factors representing distinct loci did not show cross-rescue. Alleles at two of these loci, M1 and M4, were by far the most prevalent, M4 being the predominant type. M2 and M3 were each found only once, in Pakistan and Japan, respectively. Although M1 could be genetically segregated from M4 and maintained as a purified stock, the M1 factor invariably co-occurred with M4 in field populations, whereas M4 usually occurred in the absence of other Medea factors. The dominant maternal lethal action of M1 could be selectively inactivated (reverted) by gene-knockout gamma irradiation with retention of zygotic rescue activity.

Detrimental effects of an autosomal selfish genetic element on sperm competitiveness in house mice

PubMed Central

Sutter, Andreas; Lindholm, Anna K.

2015-01-01

Female multiple mating (polyandry) is widespread across many animal taxa and indirect genetic benefits are a major evolutionary force favouring polyandry. An incentive for polyandry arises when multiple mating leads to sperm competition that disadvantages sperm from genetically inferior mates. A reduction in genetic quality is associated with costly selfish genetic elements (SGEs), and studies in invertebrates have shown that males bearing sex ratio distorting SGEs are worse sperm competitors than wild-type males. We used a vertebrate model species to test whether females can avoid an autosomal SGE, the t haplotype, through polyandry. The t haplotype in house mice exhibits strong drive in t heterozygous males by affecting spermatogenesis and is associated with homozygous in utero lethality. We used controlled matings to test the effect of the t haplotype on sperm competitiveness. Regardless of mating order, t heterozygous males sired only 11% of zygotes when competing against wild-type males, suggesting a very strong effect of the t haplotype on sperm quality. We provide, to our knowledge, the first substantial evidence that polyandry ameliorates the harmful effects of an autosomal SGE arising through genetic incompatibility. We discuss potential mechanisms in our study species and the broader implications for the benefits of polyandry. PMID:26136452

'Morals can not be drawn from facts but guidance may be': the early life of W.D. Hamilton's theory of inclusive fitness.

PubMed

Swenson, Sarah A

2015-12-01

W.D. Hamilton's theory of inclusive fitness saw the evolution of altruism from the point of view of the gene. It was at heart a theory of limits, redefining altruistic behaviours as ultimately selfish. This theory inspired two controversial texts published almost in tandem, E.O. Wilson's Sociobiology: The New Synthesis (1975) and Richard Dawkins's The Selfish Gene (1976). When Wilson and Dawkins were attacked for their evolutionary interpretations of human societies, they claimed a distinction between reporting what is and declaring what ought to be. Can the history of sociobiological theories be so easily separated from its sociopolitical context? This paper draws upon unpublished materials from the 1960s and early 1970s and documents some of the ways in which Hamilton saw his research as contributing to contemporary concerns. It pays special attention to the 1969 Man and Beast Smithsonian Institution symposium in order to explore the extent to which Hamilton intended his theory to be merely descriptive versus prescriptive. From this, we may see that Hamilton was deeply concerned about the political chaos he perceived in the world around him, and hoped to arrive at a level of self-understanding through science that could inform a new social order.

Physical Activity Protects the Human Brain against Metabolic Stress Induced by a Postprandial and Chronic Inflammation

PubMed Central

Pruimboom, Leo; Raison, Charles L.; Muskiet, Frits A. J.

2015-01-01

In recent years, it has become clear that chronic systemic low-grade inflammation is at the root of many, if not all, typically Western diseases associated with the metabolic syndrome. While much focus has been given to sedentary lifestyle as a cause of chronic inflammation, it is less often appreciated that chronic inflammation may also promote a sedentary lifestyle, which in turn causes chronic inflammation. Given that even minor increases in chronic inflammation reduce brain volume in otherwise healthy individuals, the bidirectional relationship between inflammation and sedentary behaviour may explain why humans have lost brain volume in the last 30,000 years and also intelligence in the last 30 years. We review evidence that lack of physical activity induces chronic low-grade inflammation and, consequently, an energy conflict between the selfish immune system and the selfish brain. Although the notion that increased physical activity would improve health in the modern world is widespread, here we provide a novel perspective on this truism by providing evidence that recovery of normal human behaviour, such as spontaneous physical activity, would calm proinflammatory activity, thereby allocating more energy to the brain and other organs, and by doing so would improve human health. PMID:26074674

Diverging effects of clean versus dirty money on attitudes, values, and interpersonal behavior.

PubMed

Yang, Qing; Wu, Xiaochang; Zhou, Xinyue; Mead, Nicole L; Vohs, Kathleen D; Baumeister, Roy F

2013-03-01

Does the cue of money lead to selfish, greedy, exploitative behaviors or to fairness, exchange, and reciprocity? We found evidence for both, suggesting that people have both sets of meaningful associations, which can be differentially activated by exposure to clean versus dirty money. In a field experiment at a farmers' market, vendors who handled dirty money subsequently cheated customers, whereas those who handled clean money gave fair value (Experiment 1). In laboratory studies with economic games, participants who had previously handled and counted dirty money tended toward selfish, unfair practices-unlike those who had counted clean money or dirty paper, both of which led to fairness and reciprocity. These patterns were found with the trust game (Experiment 2), the prisoner's dilemma (Experiment 4), the ultimatum game (Experiment 5), and the dictator game (Experiment 6). Cognitive measures indicated that exposure to dirty money lowered moral standards (Experiment 3) and reduced positive attitudes toward fairness and reciprocity (Experiments 6-7), whereas exposure to clean money had the opposite effects. Thus, people apparently have 2 contradictory sets of associations (including behavioral tendencies) to money, which is a complex, powerful, and ubiquitous aspect of human social life and cultural organization. PsycINFO Database Record (c) 2013 APA, all rights reserved

Children are sensitive to norms of giving.

PubMed

McAuliffe, Katherine; Raihani, Nichola J; Dunham, Yarrow

2017-10-01

People across societies engage in costly sharing, but the extent of such sharing shows striking cultural variation, highlighting the importance of local norms in shaping generosity. Despite this acknowledged role for norms, it is unclear when they begin to exert their influence in development. Here we use a Dictator Game to investigate the extent to which 4- to 9-year-old children are sensitive to selfish (give 20%) and generous (give 80%) norms. Additionally, we varied whether children were told how much other children give (descriptive norm) or what they should give according to an adult (injunctive norm). Results showed that children generally gave more when they were exposed to a generous norm. However, patterns of compliance varied with age. Younger children were more likely to comply with the selfish norm, suggesting a licensing effect. By contrast, older children were more influenced by the generous norm, yet capped their donations at 50%, perhaps adhering to a pre-existing norm of equality. Children were not differentially influenced by descriptive or injunctive norms, suggesting a primacy of norm content over norm format. Together, our findings indicate that while generosity is malleable in children, normative information does not completely override pre-existing biases. Copyright © 2017 Elsevier B.V. All rights reserved.

Genome size variation affects song attractiveness in grasshoppers: evidence for sexual selection against large genomes.

PubMed

Schielzeth, Holger; Streitner, Corinna; Lampe, Ulrike; Franzke, Alexandra; Reinhold, Klaus

2014-12-01

Genome size is largely uncorrelated to organismal complexity and adaptive scenarios. Genetic drift as well as intragenomic conflict have been put forward to explain this observation. We here study the impact of genome size on sexual attractiveness in the bow-winged grasshopper Chorthippus biguttulus. Grasshoppers show particularly large variation in genome size due to the high prevalence of supernumerary chromosomes that are considered (mildly) selfish, as evidenced by non-Mendelian inheritance and fitness costs if present in high numbers. We ranked male grasshoppers by song characteristics that are known to affect female preferences in this species and scored genome sizes of attractive and unattractive individuals from the extremes of this distribution. We find that attractive singers have significantly smaller genomes, demonstrating that genome size is reflected in male courtship songs and that females prefer songs of males with small genomes. Such a genome size dependent mate preference effectively selects against selfish genetic elements that tend to increase genome size. The data therefore provide a novel example of how sexual selection can reinforce natural selection and can act as an agent in an intragenomic arms race. Furthermore, our findings indicate an underappreciated route of how choosy females could gain indirect benefits. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Why did eukaryotes evolve only once? Genetic and energetic aspects of conflict and conflict mediation

PubMed Central

Blackstone, Neil W.

2013-01-01

According to multi-level theory, evolutionary transitions require mediating conflicts between lower-level units in favour of the higher-level unit. By this view, the origin of eukaryotes and the origin of multicellularity would seem largely equivalent. Yet, eukaryotes evolved only once in the history of life, whereas multicellular eukaryotes have evolved many times. Examining conflicts between evolutionary units and mechanisms that mediate these conflicts can illuminate these differences. Energy-converting endosymbionts that allow eukaryotes to transcend surface-to-volume constraints also can allocate energy into their own selfish replication. This principal conflict in the origin of eukaryotes can be mediated by genetic or energetic mechanisms. Genome transfer diminishes the heritable variation of the symbiont, but requires the de novo evolution of the protein-import apparatus and was opposed by selection for selfish symbionts. By contrast, metabolic signalling is a shared primitive feature of all cells. Redox state of the cytosol is an emergent feature that cannot be subverted by an individual symbiont. Hypothetical scenarios illustrate how metabolic regulation may have mediated the conflicts inherent at different stages in the origin of eukaryotes. Aspects of metabolic regulation may have subsequently been coopted from within-cell to between-cell pathways, allowing multicellularity to emerge repeatedly. PMID:23754817

Why did eukaryotes evolve only once? Genetic and energetic aspects of conflict and conflict mediation.

PubMed

Blackstone, Neil W

2013-07-19

According to multi-level theory, evolutionary transitions require mediating conflicts between lower-level units in favour of the higher-level unit. By this view, the origin of eukaryotes and the origin of multicellularity would seem largely equivalent. Yet, eukaryotes evolved only once in the history of life, whereas multicellular eukaryotes have evolved many times. Examining conflicts between evolutionary units and mechanisms that mediate these conflicts can illuminate these differences. Energy-converting endosymbionts that allow eukaryotes to transcend surface-to-volume constraints also can allocate energy into their own selfish replication. This principal conflict in the origin of eukaryotes can be mediated by genetic or energetic mechanisms. Genome transfer diminishes the heritable variation of the symbiont, but requires the de novo evolution of the protein-import apparatus and was opposed by selection for selfish symbionts. By contrast, metabolic signalling is a shared primitive feature of all cells. Redox state of the cytosol is an emergent feature that cannot be subverted by an individual symbiont. Hypothetical scenarios illustrate how metabolic regulation may have mediated the conflicts inherent at different stages in the origin of eukaryotes. Aspects of metabolic regulation may have subsequently been coopted from within-cell to between-cell pathways, allowing multicellularity to emerge repeatedly.

Invasion and Persistence of a Selfish Gene in the Cnidaria

PubMed Central

Goddard, Matthew R.; Leigh, Jessica; Roger, Andrew J; Pemberton, Andrew J

2006-01-01

Background Homing endonuclease genes (HEGs) are superfluous, but are capable of invading populations that mix alleles by biasing their inheritance patterns through gene conversion. One model suggests that their long-term persistence is achieved through recurrent invasion. This circumvents evolutionary degeneration, but requires reasonable rates of transfer between species to maintain purifying selection. Although HEGs are found in a variety of microbes, we found the previous discovery of this type of selfish genetic element in the mitochondria of a sea anemone surprising. Methods/Principal Findings We surveyed 29 species of Cnidaria for the presence of the COXI HEG. Statistical analyses provided evidence for HEG invasion. We also found that 96 individuals of Metridium senile, from five different locations in the UK, had identical HEG sequences. This lack of sequence divergence illustrates the stable nature of Anthozoan mitochondria. Our data suggests this HEG conforms to the recurrent invasion model of evolution. Conclusions Ordinarily such low rates of HEG transfer would likely be insufficient to enable major invasion. However, the slow rate of Anthozoan mitochondrial change lengthens greatly the time to HEG degeneration: this significantly extends the periodicity of the HEG life-cycle. We suggest that a combination of very low substitution rates and rare transfers facilitated metazoan HEG invasion. PMID:17183657

Does polyandry control population sex ratio via regulation of a selfish gene?

PubMed

Price, Tom A R; Bretman, Amanda; Gradilla, Ana C; Reger, Julia; Taylor, Michelle L; Giraldo-Perez, Paulina; Campbell, Amy; Hurst, Gregory D D; Wedell, Nina

2014-05-22

The extent of female multiple mating (polyandry) can strongly impact on the intensity of sexual selection, sexual conflict, and the evolution of cooperation and sociality. More subtly, polyandry may protect populations against intragenomic conflicts that result from the invasion of deleterious selfish genetic elements (SGEs). SGEs commonly impair sperm production, and so are likely to be unsuccessful in sperm competition, potentially reducing their transmission in polyandrous populations. Here, we test this prediction in nature. We demonstrate a heritable latitudinal cline in the degree of polyandry in the fruitfly Drosophila pseudoobscura across the USA, with northern population females remating more frequently in both the field and the laboratory. High remating was associated with low frequency of a sex-ratio-distorting meiotic driver in natural populations. In the laboratory, polyandry directly controls the frequency of the driver by undermining its transmission. Hence we suggest that the cline in polyandry represents an important contributor to the cline in sex ratio in nature. Furthermore, as the meiotic driver causes sex ratio bias, variation in polyandry may ultimately determine population sex ratio across the USA, a dramatic impact of female mating decisions. As SGEs are ubiquitous it is likely that the reduction of intragenomic conflict by polyandry is widespread.

Global adaptation in networks of selfish components: emergent associative memory at the system scale.

PubMed

Watson, Richard A; Mills, Rob; Buckley, C L

2011-01-01

In some circumstances complex adaptive systems composed of numerous self-interested agents can self-organize into structures that enhance global adaptation, efficiency, or function. However, the general conditions for such an outcome are poorly understood and present a fundamental open question for domains as varied as ecology, sociology, economics, organismic biology, and technological infrastructure design. In contrast, sufficient conditions for artificial neural networks to form structures that perform collective computational processes such as associative memory/recall, classification, generalization, and optimization are well understood. Such global functions within a single agent or organism are not wholly surprising, since the mechanisms (e.g., Hebbian learning) that create these neural organizations may be selected for this purpose; but agents in a multi-agent system have no obvious reason to adhere to such a structuring protocol or produce such global behaviors when acting from individual self-interest. However, Hebbian learning is actually a very simple and fully distributed habituation or positive feedback principle. Here we show that when self-interested agents can modify how they are affected by other agents (e.g., when they can influence which other agents they interact with), then, in adapting these inter-agent relationships to maximize their own utility, they will necessarily alter them in a manner homologous with Hebbian learning. Multi-agent systems with adaptable relationships will thereby exhibit the same system-level behaviors as neural networks under Hebbian learning. For example, improved global efficiency in multi-agent systems can be explained by the inherent ability of associative memory to generalize by idealizing stored patterns and/or creating new combinations of subpatterns. Thus distributed multi-agent systems can spontaneously exhibit adaptive global behaviors in the same sense, and by the same mechanism, as with the organizational principles familiar in connectionist models of organismic learning.

Sperm DNA fragmentation affects epigenetic feature in human male pronucleus.

PubMed

Rajabi, H; Mohseni-Kouchesfehani, H; Eslami-Arshaghi, T; Salehi, M

2018-02-01

To evaluate whether the sperm DNA fragmentation affects male pronucleus epigenetic factors, semen analysis was performed and DNA fragmentation was assessed by the method of sperm chromatin structure assay (SCSA). Human-mouse interspecies fertilisation was used to create human male pronucleus. Male pronucleus DNA methylation and H4K12 acetylation were evaluated by immunostaining. Results showed a significant positive correlation between the level of sperm DNA fragmentation and DNA methylation in male pronuclei. In other words, an increase in DNA damage caused an upsurge in DNA methylation. In the case of H4K12 acetylation, no correlation was detected between DNA damage and the level of histone acetylation in the normal group, but results for the group in which male pronuclei were derived from sperm cells with DNA fragmentation, increased DNA damage led to a decreased acetylation level. Sperm DNA fragmentation interferes with the active demethylation process and disrupts the insertion of histones into the male chromatin in the male pronucleus, following fertilisation. © 2017 Blackwell Verlag GmbH.

TALE nickase mediates high efficient targeted transgene integration at the human multi-copy ribosomal DNA locus.

PubMed

Wu, Yong; Gao, Tieli; Wang, Xiaolin; Hu, Youjin; Hu, Xuyun; Hu, Zhiqing; Pang, Jialun; Li, Zhuo; Xue, Jinfeng; Feng, Mai; Wu, Lingqian; Liang, Desheng

2014-03-28

Although targeted gene addition could be stimulated strikingly by a DNA double strand break (DSB) created by either zinc finger nucleases (ZFNs) or TALE nucleases (TALENs), the DSBs are really mutagenic and toxic to human cells. As a compromised solution, DNA single-strand break (SSB) or nick has been reported to mediate high efficient gene addition but with marked reduction of random mutagenesis. We previously demonstrated effective targeted gene addition at the human multicopy ribosomal DNA (rDNA) locus, a genomic safe harbor for the transgene with therapeutic potential. To improve the transgene integration efficiency by using TALENs while lowering the cytotoxicity of DSBs, we created both TALENs and TALE nickases (TALENickases) targeting this multicopy locus. A targeting vector which could integrate a GFP cassette at the rDNA locus was constructed and co-transfected with TALENs or TALENickases. Although the fraction of GFP positive cells using TALENs was greater than that using TALENickases during the first few days after transfection, it reduced to a level less than that using TALENickases after continuous culture. Our findings showed that the TALENickases were more effective than their TALEN counterparts at the multi-copy rDNA locus, though earlier studies using ZFNs and ZFNickases targeting the single-copy loci showed the reverse. Besides, TALENickases mediated the targeted integration of a 5.4 kb fragment at a frequency of up to 0.62% in HT1080 cells after drug selection, suggesting their potential application in targeted gene modification not being limited at the rDNA locus. Copyright © 2014 Elsevier Inc. All rights reserved.

Heat-resistant DNA tile arrays constructed by template-directed photoligation through 5-carboxyvinyl-2′-deoxyuridine

PubMed Central

Tagawa, Miho; Shohda, Koh-ichiroh; Fujimoto, Kenzo; Sugawara, Tadashi; Suyama, Akira

2007-01-01

Template-directed DNA photoligation has been applied to a method to construct heat-resistant two-dimensional (2D) DNA arrays that can work as scaffolds in bottom-up assembly of functional biomolecules and nano-electronic components. DNA double-crossover AB-staggered (DXAB) tiles were covalently connected by enzyme-free template-directed photoligation, which enables a specific ligation reaction in an extremely tight space and under buffer conditions where no enzymes work efficiently. DNA nanostructures created by self-assembly of the DXAB tiles before and after photoligation have been visualized by high-resolution, tapping mode atomic force microscopy in buffer. The improvement of the heat tolerance of 2D DNA arrays was confirmed by heating and visualizing the DNA nanostructures. The heat-resistant DNA arrays may expand the potential of DNA as functional materials in biotechnology and nanotechnology. PMID:17982178

Barcode extension for analysis and reconstruction of structures

NASA Astrophysics Data System (ADS)

Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L.; Gootenberg, Jonathan S.; Yin, Peng

2017-03-01

Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.

Barcode extension for analysis and reconstruction of structures.

PubMed

Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L; Gootenberg, Jonathan S; Yin, Peng

2017-03-13

Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.

Barcode extension for analysis and reconstruction of structures

PubMed Central

Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L; Gootenberg, Jonathan S; Yin, Peng

2017-01-01

Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures. PMID:28287117

The Self-Assembly of DNA Nanostructures for use as Organizing Templates

NASA Astrophysics Data System (ADS)

Samec, Timothy; Cholewinski, Mitchell; Reamer, Nickalas; Reardon, Michael; Ford, Arlene

There is growing interest in the self-assembling capabilities of DNA to create functional nanodevices for use in cancer detection and treatment. One important reason for this interest is that DNA nanostructures are highly programmable molecules. This means that these structures allow for increased stability and control when designing biomacromolecules via adhesion of plasmonic nanoparticles and other similar materials. Our current work reports on the procedure and construction of hexagonal two-dimensional DNA lattice structures using three specific DNA single strands. We also reflect on several barriers that were presented during fabrication as well as the adaptations made to overcome the aforementioned barriers by improving the quality, reproducibility, and yield of the hexagonal two-dimensional DNA lattice as organizing templates.

Transformable Rhodobacter strains, method for producing transformable Rhodobacter strains

DOEpatents

Laible, Philip D.; Hanson, Deborah K.

2018-05-08

The invention provides an organism for expressing foreign DNA, the organism engineered to accept standard DNA carriers. The genome of the organism codes for intracytoplasmic membranes and features an interruption in at least one of the genes coding for restriction enzymes. Further provided is a system for producing biological materials comprising: selecting a vehicle to carry DNA which codes for the biological materials; determining sites on the vehicle's DNA sequence susceptible to restriction enzyme cleavage; choosing an organism to accept the vehicle based on that organism not acting upon at least one of said vehicle's sites; engineering said vehicle to contain said DNA; thereby creating a synthetic vector; and causing the synthetic vector to enter the organism so as cause expression of said DNA.

DNA-Assembled Advanced Plasmonic Architectures.

PubMed

Liu, Na; Liedl, Tim

2018-03-28

The interaction between light and matter can be controlled efficiently by structuring materials at a length scale shorter than the wavelength of interest. With the goal to build optical devices that operate at the nanoscale, plasmonics has established itself as a discipline, where near-field effects of electromagnetic waves created in the vicinity of metallic surfaces can give rise to a variety of novel phenomena and fascinating applications. As research on plasmonics has emerged from the optics and solid-state communities, most laboratories employ top-down lithography to implement their nanophotonic designs. In this review, we discuss the recent, successful efforts of employing self-assembled DNA nanostructures as scaffolds for creating advanced plasmonic architectures. DNA self-assembly exploits the base-pairing specificity of nucleic acid sequences and allows for the nanometer-precise organization of organic molecules but also for the arrangement of inorganic particles in space. Bottom-up self-assembly thus bypasses many of the limitations of conventional fabrication methods. As a consequence, powerful tools such as DNA origami have pushed the boundaries of nanophotonics and new ways of thinking about plasmonic designs are on the rise.

Fluorescence Resonance Energy Transfer-Based Photonic Circuits Using Single-Stranded Tile Self-Assembly and DNA Strand Displacement.

PubMed

Zhang, Xuncai; Ying, Niu; Shen, Chaonan; Cui, Guangzhao

2017-02-01

Structural DNA nanotechnology has great potential in the fabrication of complicated nanostructures and devices capable of bio-sensing and logic function. A variety of nanostructures with desired shapes have been created in the past few decades. But the application of nanostructures remains to be fully studied. Here, we present a novel biological information processing system constructed on a self-assembled, spatially addressable single-stranded tile (SST) nanostructure as DNA nano-manipulation platform that created by SST self-assembly technology. Utilizing DNA strand displacement technology, the fluorescent dye that is pre-assembled in the nano-manipulation platform is transferred from the original position to the destination, which can achieve photonic logic circuits by FRET signal cascades, including logic AND, OR, and NOT gates. And this transfer process is successfully validated by visual DSD software. The transfer process proposed in this study may provide a novel method to design complicated biological information processing system constructed on a SST nanostructure, and can be further used to develop intelligent delivery of drug molecules in vivo.

New redox-active layer create via epoxy-amine reaction - The base of genosensor for the detection of specific DNA and RNA sequences of avian influenza virus H5N1.

PubMed

Malecka, Kamila; Stachyra, Anna; Góra-Sochacka, Anna; Sirko, Agnieszka; Zagórski-Ostoja, Włodzimierz; Dehaen, Wim; Radecka, Hanna; Radecki, Jerzy

2015-03-15

This paper concerns the development of a redox-active monolayer and its application for the construction of an electrochemical genosensor designed for the detection of specific DNA and RNA oligonucleotide sequences related to the avian influenza virus (AIV) type H5N1. This new redox layer was created on a gold electrode surface step by step. Cyclic Voltammetry, Osteryoung Square-Wave Voltammetry and Differential Pulse Voltammetry were used for its characterization. This new redox-active layer was applied for the construction of the DNA biosensor. The NH2-NC3 probe (20-mer) was covalently attached to the gold electrode surface via a "click" reaction between the amine and an epoxide group. The hybridization process was monitored using the Osteryoung Square-Wave Voltammetry. The 20-mer DNA and ca. 280-mer RNA oligonucleotides were used as the targets. The constructed genosensor was capable to determine complementary oligonucleotide sequences with a detection limit in the pM range. It is able to distinguish the different position of the part RNA complementary to the DNA probe. The genosensor was very selective. The 20-mer DNA as well as the 280-mer RNA oligonucleotides without a complementary sequence generated a weak signal. Copyright © 2014 Elsevier B.V. All rights reserved.

Transmission of the PabI family of restriction DNA glycosylase genes: mobility and long-term inheritance.

PubMed

Kojima, Kenji K; Kobayashi, Ichizo

2015-10-19

R.PabI is an exceptional restriction enzyme that functions as a DNA glycosylase. The enzyme excises an unmethylated base from its recognition sequence to generate apurinic/apyrimidinic (AP) sites, and also displays AP lyase activity, cleaving the DNA backbone at the AP site to generate the 3'-phospho alpha, beta-unsaturated aldehyde end in addition to the 5'-phosphate end. The resulting ends are difficult to religate with DNA ligase. The enzyme was originally isolated in Pyrococcus, a hyperthermophilic archaeon, and additional homologs subsequently identified in the epsilon class of the Gram-negative bacterial phylum Proteobacteria, such as Helicobacter pylori. Systematic analysis of R.PabI homologs and their neighboring genes in sequenced genomes revealed co-occurrence of R.PabI with M.PabI homolog methyltransferase genes. R.PabI and M.PabI homolog genes are occasionally found at corresponding (orthologous) loci in different species, such as Helicobacter pylori, Helicobacter acinonychis and Helicobacter cetorum, indicating long-term maintenance of the gene pair. One R.PabI and M.PabI homolog gene pair is observed immediately after the GMP synthase gene in both Campylobacter and Helicobacter, representing orthologs beyond genera. The mobility of the PabI family of restriction-modification (RM) system between genomes is evident upon comparison of genomes of sibling strains/species. Analysis of R.PabI and M.PabI homologs in H. pylori revealed an insertion of integrative and conjugative elements (ICE), and replacement with a gene of unknown function that may specify a membrane-associated toxin (hrgC). In view of the similarity of HrgC with toxins in type I toxin-antitoxin systems, we addressed the biological significance of this substitution. Our data indicate that replacement with hrgC occurred in the common ancestor of hspAmerind and hspEAsia. Subsequently, H. pylori with and without hrgC were intermixed at this locus, leading to complex distribution of hrgC in East Asia and the Americas. In Malaysia, hrgC was horizontally transferred from hspEAsia to hpAsia2 strains. The PabI family of RM system behaves as a mobile, selfish genetic element, similar to the other families of Type II RM systems. Our analysis additionally revealed some cases of long-term inheritance. The distribution of the hrgC gene replacing the PabI family in the subpopulations of H. pylori, hspAmerind, hspEAsia and hpAsia2, corresponds to the two human migration events, one from East Asia to Americas and the other from China to Malaysia.

Replicative DNA Polymerase δ but Not ε Proofreads Errors in Cis and in Trans

PubMed Central

Flood, Carrie L.; Rodriguez, Gina P.; Bao, Gaobin; Shockley, Arthur H.; Kow, Yoke Wah; Crouse, Gray F.

2015-01-01

It is now well established that in yeast, and likely most eukaryotic organisms, initial DNA replication of the leading strand is by DNA polymerase ε and of the lagging strand by DNA polymerase δ. However, the role of Pol δ in replication of the leading strand is uncertain. In this work, we use a reporter system in Saccharomyces cerevisiae to measure mutation rates at specific base pairs in order to determine the effect of heterozygous or homozygous proofreading-defective mutants of either Pol ε or Pol δ in diploid strains. We find that wild-type Pol ε molecules cannot proofread errors created by proofreading-defective Pol ε molecules, whereas Pol δ can not only proofread errors created by proofreading-defective Pol δ molecules, but can also proofread errors created by Pol ε-defective molecules. These results suggest that any interruption in DNA synthesis on the leading strand is likely to result in completion by Pol δ and also explain the higher mutation rates observed in Pol δ-proofreading mutants compared to Pol ε-proofreading defective mutants. For strains reverting via AT→GC, TA→GC, CG→AT, and GC→AT mutations, we find in addition a strong effect of gene orientation on mutation rate in proofreading-defective strains and demonstrate that much of this orientation dependence is due to differential efficiencies of mispair elongation. We also find that a 3′-terminal 8 oxoG, unlike a 3′-terminal G, is efficiently extended opposite an A and is not subject to proofreading. Proofreading mutations have been shown to result in tumor formation in both mice and humans; the results presented here can help explain the properties exhibited by those proofreading mutants. PMID:25742645

Nanomechanical molecular devices made of DNA origami.

PubMed

Kuzuya, Akinori; Ohya, Yuichi

2014-06-17

CONSPECTUS: Eight years have passed since the striking debut of the DNA origami technique ( Rothemund, P. W. K. Nature 2006 , 440 , 297 - 302 ), in which long single-stranded DNA is folded into a designed nanostructure, in either 2D or 3D, with the aid of many short staple strands. The number of proposals for new design principles for DNA origami structures seems to have already reached a peak. It is apparent that DNA origami study is now entering the second phase of creating practical applications. The development of functional nanomechanical molecular devices using the DNA origami technique is one such application attracting significant interest from researchers in the field. Nanomechanical DNA origami devices, which maintain the characteristics of DNA origami structures, have various advantages over conventional DNA nanomachines. Comparatively high assembly yield, relatively large size visible via atomic force microscopy (AFM) or transmission electron microscopy (TEM), and the capability to assemble multiple functional groups with precision using multiple staple strands are some of the advantages of the DNA origami technique for constructing sophisticated molecular devices. This Account describes the recent developments of such nanomechanical DNA origami devices and reviews the emerging target of DNA origami studies. First, simple "dynamic" DNA origami structures with transformation capability, such as DNA origami boxes and a DNA origami hatch with structure control, are briefly summarized. More elaborate nanomechanical DNA origami devices are then reviewed. The first example describes DNA origami pinching devices that can be used as "single-molecule" beacons to detect a variety of biorelated molecules, from metal ions at the size of a few tens of atomic mass number units to relatively gigantic proteins with a molecular mass greater than a hundred kilodaltons, all on a single platform. Clamshell-like DNA nanorobots equipped with logic gates can discriminate different cell lines, open their shell, and bind to their target. An intelligent DNA origami "sheath" can mimic the function of suppressors in a transcription regulation system to control the expression of a loaded gene. DNA origami "rolls" are created to construct precisely arranged plasmonic devices with metal nanoparticles. All of their functions are derived from their nanomechanical movement, which is programmable by designing the DNA sequence or by using the significant repository of technical achievements in nucleic acid chemistry. Finally, some studies on detailed structural parameters of DNA origami or their mechanical properties in nanoscale are discussed, which may be useful and inspiring for readers who intend to design new nanomechanical DNA origami devices.

Building block synthesis using the polymerase chain assembly method.

PubMed

Marchand, Julie A; Peccoud, Jean

2012-01-01

De novo gene synthesis allows the creation of custom DNA molecules without the typical constraints of traditional cloning assembly: scars, restriction site incompatibility, and the quest to find all the desired parts to name a few. Moreover, with the help of computer-assisted design, the perfect DNA molecule can be created along with its matching sequence ready to download. The challenge is to build the physical DNA molecules that have been designed with the software. Although there are several DNA assembly methods, this section presents and describes a method using the polymerase chain assembly (PCA).

Bioinformatics Approaches for Fetal DNA Fraction Estimation in Noninvasive Prenatal Testing

PubMed Central

Peng, Xianlu Laura; Jiang, Peiyong

2017-01-01

The discovery of cell-free fetal DNA molecules in plasma of pregnant women has created a paradigm shift in noninvasive prenatal testing (NIPT). Circulating cell-free DNA in maternal plasma has been increasingly recognized as an important proxy to detect fetal abnormalities in a noninvasive manner. A variety of approaches for NIPT using next-generation sequencing have been developed, which have been rapidly transforming clinical practices nowadays. In such approaches, the fetal DNA fraction is a pivotal parameter governing the overall performance and guaranteeing the proper clinical interpretation of testing results. In this review, we describe the current bioinformatics approaches developed for estimating the fetal DNA fraction and discuss their pros and cons. PMID:28230760

Bioinformatics Approaches for Fetal DNA Fraction Estimation in Noninvasive Prenatal Testing.

PubMed

Peng, Xianlu Laura; Jiang, Peiyong

2017-02-20

The discovery of cell-free fetal DNA molecules in plasma of pregnant women has created a paradigm shift in noninvasive prenatal testing (NIPT). Circulating cell-free DNA in maternal plasma has been increasingly recognized as an important proxy to detect fetal abnormalities in a noninvasive manner. A variety of approaches for NIPT using next-generation sequencing have been developed, which have been rapidly transforming clinical practices nowadays. In such approaches, the fetal DNA fraction is a pivotal parameter governing the overall performance and guaranteeing the proper clinical interpretation of testing results. In this review, we describe the current bioinformatics approaches developed for estimating the fetal DNA fraction and discuss their pros and cons.

From Cognition To Language: The Modeling Field Theory Approach

DTIC Science & Technology

2006-10-02

emergence of cells, it is still not clear how such an assemblage could be formed and maintained starting from selfish genes (see [46] for a review). In...have been struggling with for more than three decades [39]. For example, although the coordinated work of distinct genes is germane to the...290, 2005. [19] D. K. Lewis, Convention: a Philosophical Study. Harvard University Press, Cambridge, MA, 1969. [20] R. Dawkins , J. R. Krebs, “Animal

Appreciating the World: A Framework for Doing Socio-Political Analysis

DTIC Science & Technology

2012-06-08

intuitively understand the structure will result in some individuals poaching elephants for personal gain and know that selfish interest can drive...ivory poaching in Africa. The group is focused on improving a condition they view negatively, thus progressing to a better state of affairs. They...The soldier provides a unique opportunity to explore the impact of interests on individual decision making. The soldier’s split identity meant he had a

The Web-Based DNA Vaccine Database DNAVaxDB and Its Usage for Rational DNA Vaccine Design.

PubMed

Racz, Rebecca; He, Yongqun

2016-01-01

A DNA vaccine is a vaccine that uses a mammalian expression vector to express one or more protein antigens and is administered in vivo to induce an adaptive immune response. Since the 1990s, a significant amount of research has been performed on DNA vaccines and the mechanisms behind them. To meet the needs of the DNA vaccine research community, we created DNAVaxDB ( http://www.violinet.org/dnavaxdb ), the first Web-based database and analysis resource of experimentally verified DNA vaccines. All the data in DNAVaxDB, which includes plasmids, antigens, vaccines, and sources, is manually curated and experimentally verified. This chapter goes over the detail of DNAVaxDB system and shows how the DNA vaccine database, combined with the Vaxign vaccine design tool, can be used for rational design of a DNA vaccine against a pathogen, such as Mycobacterium bovis.

Molecular Precision at Micrometer Length Scales: Hierarchical Assembly of DNA-Protein Nanostructures.

PubMed

Schiffels, Daniel; Szalai, Veronika A; Liddle, J Alexander

2017-07-25

Robust self-assembly across length scales is a ubiquitous feature of biological systems but remains challenging for synthetic structures. Taking a cue from biology-where disparate molecules work together to produce large, functional assemblies-we demonstrate how to engineer microscale structures with nanoscale features: Our self-assembly approach begins by using DNA polymerase to controllably create double-stranded DNA (dsDNA) sections on a single-stranded template. The single-stranded DNA (ssDNA) sections are then folded into a mechanically flexible skeleton by the origami method. This process simultaneously shapes the structure at the nanoscale and directs the large-scale geometry. The DNA skeleton guides the assembly of RecA protein filaments, which provides rigidity at the micrometer scale. We use our modular design strategy to assemble tetrahedral, rectangular, and linear shapes of defined dimensions. This method enables the robust construction of complex assemblies, greatly extending the range of DNA-based self-assembly methods.

Double-stranded DNA translocase activity of transcription factor TFIIH and the mechanism of RNA polymerase II open complex formation.

PubMed

Fishburn, James; Tomko, Eric; Galburt, Eric; Hahn, Steven

2015-03-31

Formation of the RNA polymerase II (Pol II) open complex (OC) requires DNA unwinding mediated by the transcription factor TFIIH helicase-related subunit XPB/Ssl2. Because XPB/Ssl2 binds DNA downstream from the location of DNA unwinding, it cannot function using a conventional helicase mechanism. Here we show that yeast TFIIH contains an Ssl2-dependent double-stranded DNA translocase activity. Ssl2 tracks along one DNA strand in the 5' → 3' direction, implying it uses the nontemplate promoter strand to reel downstream DNA into the Pol II cleft, creating torsional strain and leading to DNA unwinding. Analysis of the Ssl2 and DNA-dependent ATPase activity of TFIIH suggests that Ssl2 has a processivity of approximately one DNA turn, consistent with the length of DNA unwound during transcription initiation. Our results can explain why maintaining the OC requires continuous ATP hydrolysis and the function of TFIIH in promoter escape. Our results also suggest that XPB/Ssl2 uses this translocase mechanism during DNA repair rather than physically wedging open damaged DNA.

DNA origami based Au–Ag-core–shell nanoparticle dimers with single-molecule SERS sensitivity† †Electronic supplementary information (ESI) available: Additional information about materials and methods, designs of DNA origami templates, height profiles, additional SERS spectra, assignment of DNA bands, SEM images, additional AFM images, FDTD simulations, additional reference spectra for Cy3 and detailed description of EF estimation, simulated absorption and scattering spectra. See DOI: 10.1039/c5nr08674d Click here for additional data file.

PubMed Central

Prinz, J.; Heck, C.; Ellerik, L.; Merk, V.

2016-01-01

DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 1010, which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled. PMID:26892770

A new model for ancient DNA decay based on paleogenomic meta-analysis

PubMed Central

Ware, Roselyn; Smith, Oliver; Collins, Matthew

2017-01-01

Abstract The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics. PMID:28486705

Automatic image analysis and spot classification for detection of pathogenic Escherichia coli on glass slide DNA microarrays

USDA-ARS?s Scientific Manuscript database

A computer algorithm was created to inspect scanned images from DNA microarray slides developed to rapidly detect and genotype E. Coli O157 virulent strains. The algorithm computes centroid locations for signal and background pixels in RGB space and defines a plane perpendicular to the line connect...

A Linked Series of Laboratory Exercises in Molecular Biology Utilizing Bioinformatics and GFP

ERIC Educational Resources Information Center

Medin, Carey L.; Nolin, Katie L.

2011-01-01

Molecular biologists commonly use bioinformatics to map and analyze DNA and protein sequences and to align different DNA and protein sequences for comparison. Additionally, biologists can create and view 3D models of protein structures to further understand intramolecular interactions. The primary goal of this 10-week laboratory was to introduce…

Creating context for the use of DNA adduct data in cancer risk assessment: I. Proposed framework for data organization *

EPA Science Inventory

The assessment of human cancer risk from chemical exposure requires the integration of diverse types of data. Such data involve effects at the cell and tissue levels. This report focuses on the specific utility of one type of data, namely DNA adducts. Emphasis is placed on the ap...

DNA-Based Enzyme Reactors and Systems

PubMed Central

Linko, Veikko; Nummelin, Sami; Aarnos, Laura; Tapio, Kosti; Toppari, J. Jussi; Kostiainen, Mauri A.

2016-01-01

During recent years, the possibility to create custom biocompatible nanoshapes using DNA as a building material has rapidly emerged. Further, these rationally designed DNA structures could be exploited in positioning pivotal molecules, such as enzymes, with nanometer-level precision. This feature could be used in the fabrication of artificial biochemical machinery that is able to mimic the complex reactions found in living cells. Currently, DNA-enzyme hybrids can be used to control (multi-enzyme) cascade reactions and to regulate the enzyme functions and the reaction pathways. Moreover, sophisticated DNA structures can be utilized in encapsulating active enzymes and delivering the molecular cargo into cells. In this review, we focus on the latest enzyme systems based on novel DNA nanostructures: enzyme reactors, regulatory devices and carriers that can find uses in various biotechnological and nanomedical applications. PMID:28335267

RiboSketch: Versatile Visualization of Multi-stranded RNA and DNA Secondary Structure.

PubMed

Lu, Jacob S; Bindewald, Eckart; Kasprzak, Wojciech; Shapiro, Bruce A

2018-06-15

Creating clear, visually pleasing 2D depictions of RNA and DNA strands and their interactions is important to facilitate and communicate insights related to nucleic acid structure. Here we present RiboSketch, a secondary structure image production application that enables the visualization of multistranded structures via layout algorithms, comprehensive editing capabilities, and a multitude of simulation modes. These interactive features allow RiboSketch to create publication quality diagrams for structures with a wide range of composition, size, and complexity. The program may be run in any web browser without the need for installation, or as a standalone Java application. https://binkley2.ncifcrf.gov/users/bindewae/ribosketch_web.

Electrophoretic and field-effect graphene for all-electrical DNA array technology.

PubMed

Xu, Guangyu; Abbott, Jeffrey; Qin, Ling; Yeung, Kitty Y M; Song, Yi; Yoon, Hosang; Kong, Jing; Ham, Donhee

2014-09-05

Field-effect transistor biomolecular sensors based on low-dimensional nanomaterials boast sensitivity, label-free operation and chip-scale construction. Chemical vapour deposition graphene is especially well suited for multiplexed electronic DNA array applications, since its large two-dimensional morphology readily lends itself to top-down fabrication of transistor arrays. Nonetheless, graphene field-effect transistor DNA sensors have been studied mainly at single-device level. Here we create, from chemical vapour deposition graphene, field-effect transistor arrays with two features representing steps towards multiplexed DNA arrays. First, a robust array yield--seven out of eight transistors--is achieved with a 100-fM sensitivity, on par with optical DNA microarrays and at least 10 times higher than prior chemical vapour deposition graphene transistor DNA sensors. Second, each graphene acts as an electrophoretic electrode for site-specific probe DNA immobilization, and performs subsequent site-specific detection of target DNA as a field-effect transistor. The use of graphene as both electrode and transistor suggests a path towards all-electrical multiplexed graphene DNA arrays.

Complementation between polymerase- and exonuclease-deficient mitochondrial DNA polymerase mutants in genomically engineered flies

PubMed Central

Bratic, Ana; Kauppila, Timo E. S.; Macao, Bertil; Grönke, Sebastian; Siibak, Triinu; Stewart, James B.; Baggio, Francesca; Dols, Jacqueline; Partridge, Linda; Falkenberg, Maria; Wredenberg, Anna; Larsson, Nils-Göran

2015-01-01

Replication errors are the main cause of mitochondrial DNA (mtDNA) mutations and a compelling approach to decrease mutation levels would therefore be to increase the fidelity of the catalytic subunit (POLγA) of the mtDNA polymerase. Here we genomically engineer the tamas locus, encoding fly POLγA, and introduce alleles expressing exonuclease- (exo−) and polymerase-deficient (pol−) POLγA versions. The exo− mutant leads to accumulation of point mutations and linear deletions of mtDNA, whereas pol− mutants cause mtDNA depletion. The mutant tamas alleles are developmentally lethal but can complement each other in trans resulting in viable flies with clonally expanded mtDNA mutations. Reconstitution of human mtDNA replication in vitro confirms that replication is a highly dynamic process where POLγA goes on and off the template to allow complementation during proofreading and elongation. The created fly models are valuable tools to study germ line transmission of mtDNA and the pathophysiology of POLγA mutation disease. PMID:26554610

DNA-Templated Introduction of an Aldehyde Handle in Proteins.

PubMed

Kodal, Anne Louise B; Rosen, Christian B; Mortensen, Michael R; Tørring, Thomas; Gothelf, Kurt V

2016-07-15

Many medical and biotechnological applications rely on protein labeling, but a key challenge is the production of homogeneous and site-specific conjugates. This can rarely be achieved by simple residue-specific random labeling, but generally requires genetic engineering. Using site-selective DNA-templated reductive amination, we created DNA-protein conjugates with control over labeling stoichiometry and without genetic engineering. A guiding DNA strand with a metal-binding functionality facilitates site-selectivity by directing the coupling of a second reactive DNA strand in the vicinity of a protein metal-binding site. We demonstrate DNA-templated reductive amination for His6 -tagged proteins and metal-binding proteins, including IgG1 antibodies. We also used a cleavable linker between the DNA and the protein to remove the DNA and introduce a single aldehyde on the protein. This functions as a handle for further modifications with desired labels. In addition to directing the aldehyde positioning, the DNA provides a straightforward route for purification between reaction steps. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Positive regulation of meiotic DNA double-strand break formation by activation of the DNA damage checkpoint kinase Mec1(ATR).

PubMed

Gray, Stephen; Allison, Rachal M; Garcia, Valerie; Goldman, Alastair S H; Neale, Matthew J

2013-07-31

During meiosis, formation and repair of programmed DNA double-strand breaks (DSBs) create genetic exchange between homologous chromosomes-a process that is critical for reductional meiotic chromosome segregation and the production of genetically diverse sexually reproducing populations. Meiotic DSB formation is a complex process, requiring numerous proteins, of which Spo11 is the evolutionarily conserved catalytic subunit. Precisely how Spo11 and its accessory proteins function or are regulated is unclear. Here, we use Saccharomyces cerevisiae to reveal that meiotic DSB formation is modulated by the Mec1(ATR) branch of the DNA damage signalling cascade, promoting DSB formation when Spo11-mediated catalysis is compromised. Activation of the positive feedback pathway correlates with the formation of single-stranded DNA (ssDNA) recombination intermediates and activation of the downstream kinase, Mek1. We show that the requirement for checkpoint activation can be rescued by prolonging meiotic prophase by deleting the NDT80 transcription factor, and that even transient prophase arrest caused by Ndt80 depletion is sufficient to restore meiotic spore viability in checkpoint mutants. Our observations are unexpected given recent reports that the complementary kinase pathway Tel1(ATM) acts to inhibit DSB formation. We propose that such antagonistic regulation of DSB formation by Mec1 and Tel1 creates a regulatory mechanism, where the absolute frequency of DSBs is maintained at a level optimal for genetic exchange and efficient chromosome segregation.

DNA cytoskeleton for stabilizing artificial cells.

PubMed

Kurokawa, Chikako; Fujiwara, Kei; Morita, Masamune; Kawamata, Ibuki; Kawagishi, Yui; Sakai, Atsushi; Murayama, Yoshihiro; Nomura, Shin-Ichiro M; Murata, Satoshi; Takinoue, Masahiro; Yanagisawa, Miho

2017-07-11

Cell-sized liposomes and droplets coated with lipid layers have been used as platforms for understanding live cells, constructing artificial cells, and implementing functional biomedical tools such as biosensing platforms and drug delivery systems. However, these systems are very fragile, which results from the absence of cytoskeletons in these systems. Here, we construct an artificial cytoskeleton using DNA nanostructures. The designed DNA oligomers form a Y-shaped nanostructure and connect to each other with their complementary sticky ends to form networks. To undercoat lipid membranes with this DNA network, we used cationic lipids that attract negatively charged DNA. By encapsulating the DNA into the droplets, we successfully created a DNA shell underneath the membrane. The DNA shells increased interfacial tension, elastic modulus, and shear modulus of the droplet surface, consequently stabilizing the lipid droplets. Such drastic changes in stability were detected only when the DNA shell was in the gel phase. Furthermore, we demonstrate that liposomes with the DNA gel shell are substantially tolerant against outer osmotic shock. These results clearly show the DNA gel shell is a stabilizer of the lipid membrane akin to the cytoskeleton in live cells.

Paranemic Crossover DNA: There and Back Again.

PubMed

Wang, Xing; Chandrasekaran, Arun Richard; Shen, Zhiyong; Ohayon, Yoel P; Wang, Tong; Kizer, Megan E; Sha, Ruojie; Mao, Chengde; Yan, Hao; Zhang, Xiaoping; Liao, Shiping; Ding, Baoquan; Chakraborty, Banani; Jonoska, Natasha; Niu, Dong; Gu, Hongzhou; Chao, Jie; Gao, Xiang; Li, Yuhang; Ciengshin, Tanashaya; Seeman, Nadrian C

2018-06-18

Over the past 35 years, DNA has been used to produce various nanometer-scale constructs, nanomechanical devices, and walkers. Construction of complex DNA nanostructures relies on the creation of rigid DNA motifs. Paranemic crossover (PX) DNA is one such motif that has played many roles in DNA nanotechnology. Specifically, PX cohesion has been used to connect topologically closed molecules, to assemble a three-dimensional object, and to create two-dimensional DNA crystals. Additionally, a sequence-dependent nanodevice based on conformational change between PX and its topoisomer, JX 2 , has been used in robust nanoscale assembly lines, as a key component in a DNA transducer, and to dictate polymer assembly. Furthermore, the PX motif has recently found a new role directly in basic biology, by possibly serving as the molecular structure for double-stranded DNA homology recognition, a prominent feature of molecular biology and essential for many crucial biological processes. This review discusses the many attributes and usages of PX-DNA-its design, characteristics, applications, and potential biological relevance-and aims to accelerate the understanding of PX-DNA motif in its many roles and manifestations.

Exonuclease of human DNA polymerase gamma disengages its strand displacement function.

PubMed

He, Quan; Shumate, Christie K; White, Mark A; Molineux, Ian J; Yin, Y Whitney

2013-11-01

Pol γ, the only DNA polymerase found in human mitochondria, functions in both mtDNA repair and replication. During mtDNA base-excision repair, gaps are created after damaged base excision. Here we show that Pol γ efficiently gap-fills except when the gap is only a single nucleotide. Although wild-type Pol γ has very limited ability for strand displacement DNA synthesis, exo(-) (3'-5' exonuclease-deficient) Pol γ has significantly high activity and rapidly unwinds downstream DNA, synthesizing DNA at a rate comparable to that of the wild-type enzyme on a primer-template. The catalytic subunit Pol γA alone, even when exo(-), is unable to synthesize by strand displacement, making this the only known reaction of Pol γ holoenzyme that has an absolute requirement for the accessory subunit Pol γB. © 2013. Published by Elsevier B.V.

Recent Advances in the Structural Mechanisms of DNA Glycosylases

PubMed Central

Brooks, Sonja C.; Adhikary, Suraj; Rubinson, Emily H.; Eichman, Brandt F.

2012-01-01

DNA glycosylases safeguard the genome by locating and excising a diverse array of aberrant nucleobases created from oxidation, alkylation, and deamination of DNA. Since the discovery 28 years ago that these enzymes employ a base flipping mechanism to trap their substrates, six different protein architectures have been identified to perform the same basic task. Work over the past several years has unraveled details for how the various DNA glycosylases survey DNA, detect damage within the duplex, select for the correct modification, and catalyze base excision. Here, we provide a broad overview of these latest advances in glycosylase mechanisms gleaned from structural enzymology, highlighting features common to all glycosylases as well as key differences that define their particular substrate specificities. PMID:23076011

A DNA sequence analysis package for the IBM personal computer.

PubMed Central

Lagrimini, L M; Brentano, S T; Donelson, J E

1984-01-01

We present here a collection of DNA sequence analysis programs, called "PC Sequence" (PCS), which are designed to run on the IBM Personal Computer (PC). These programs are written in IBM PC compiled BASIC and take full advantage of the IBM PC's speed, error handling, and graphics capabilities. For a modest initial expense in hardware any laboratory can use these programs to quickly perform computer analysis on DNA sequences. They are written with the novice user in mind and require very little training or previous experience with computers. Also provided are a text editing program for creating and modifying DNA sequence files and a communications program which enables the PC to communicate with and collect information from mainframe computers and DNA sequence databases. PMID:6546433

Bio Computing and Information Systems: A Quest

DTIC Science & Technology

2003-06-01

on Security and Privacy, 1996 4) Dawkins , R. The Selfish Gene . Oxford University Press, 1989 5) Dumpert, K. The Social Biology of Ants...mechanisms of genetic control, which switch genes on and off. The archetypal example of genetic regulation in bacteria is the lac operon of E. coli...first studied in the 1950s by Jacques Monod and François Jacob. The lac operon is a set of genes and regulatory sequences involved in the metabolism of

Emergence and Influence of the Zapatista Social Netwar

DTIC Science & Technology

2001-01-01

Dawkins , Richard, The Selfish Gene , New York: Oxford University Press, 1989. Diaz del Castillo, Bernal, The Conquest of New Spain [1568], Balti- more...as biological bodies are based on units of “self-replicating patterns of information” (p. 329). In his view (p. 192), Just as genes propagate...themselves in the gene pool by leaping from body to body via sperm or eggs, so memes propagate themselves in the meme pool by leaping from brain to brain via

Catching the ’Network Science’ Bug: Insight and Opportunity for the Operations Researcher

DTIC Science & Technology

2008-01-21

publication: Operations Research agents often interface in a decentralized and asynchronous manner, and where the interaction of “ selfish ” agents...interaction of the two. For example, in a metabolic network, the activation of a gene may alter the biochemical pathways that in turn can alter other genes , and...people, computers, vehicles, cells, or genes . In these systems, all configurations are not feasible, simply because survival for these systems means