Evolution of codon usage bias in Drosophila

We first review what is known about patterns of codon usage bias in Drosophila and make the following points: (i) Drosophila genes are as biased or more biased than those in microorganisms. (ii) The level of bias of genes and even the particular pattern of codon bias can remain phylogenetically invariant for very long periods of evolution. (iii) However, some genes, even very tightly linked genes, can change very greatly in codon bias across species. (iv) Generally G and especially C are favored at synonymous sites in biased genes. (v) With the exception of aspartic acid, all amino acids contribute significantly and about equally to the codon usage bias of a gene. (vi) While most individual amino acids that can use G or C at synonymous sites display a preference for C, there are exceptions: valine and leucine, which prefer G. (vii) Finally, smaller genes tend to be more biased than longer genes. We then examine possible causes of these patterns and discount mutation bias on three bases: there is little evidence of regional mutation bias in Drosophila, mutation bias is likely toward A+T (the opposite of codon usage bias), and not all amino acids display the preference for the same nucleotide in the wobble position. Two lines of evidence support a selection hypothesis based on tRNA pools: highly biased genes tend to be highly and/or rapidly expressed, and the preferred codons in highly biased genes optimally bind the most abundant isoaccepting tRNAs. Finally, we examine the effect of bias on DNA evolution and confirm that genes with high codon usage bias have lower rates of synonymous substitution between species than do genes with low codon usage bias. Surprisingly, we find that genes with higher codon usage bias display higher levels of intraspecific synonymous polymorphism. This may be due to opposing effects of recombination.

Quantitative trait loci and metabolic pathways

The interpretation of quantitative trait locus (QTL) studies is limited by the lack of information on metabolic pathways leading to most economic traits. Inferences about the roles of the underlying genes with a pathway or the nature of their interaction with other loci are generally not possible. An exception is resistance to the corn earworm Helicoverpa zea (Boddie) in maize (Zea mays L.) because of maysin, a C-glycosyl flavone synthesized in silks via a branch of the well characterized flavonoid pathway. Our results using flavone synthesis as a model QTL system indicate: (i) the importance of regulatory loci as QTLs, (ii) the importance of interconnecting biochemical pathways on product levels, (iii) evidence for “channeling” of intermediates, allowing independent synthesis of related compounds, (iv) the utility of QTL analysis in clarifying the role of specific genes in a biochemical pathway, and (v) identification of a previously unknown locus on chromosome 9S affecting flavone level. A greater understanding of the genetic basis of maysin synthesis and associated corn earworm resistance should lead to improved breeding strategies. More broadly, the insights gained in relating a defined genetic and biochemical pathway affecting a quantitative trait should enhance interpretation of the biological basis of variation for other quantitative traits.

World food trends and prospects to 2025

This paper reviews food (especially cereal) production trends and prospects for the world and its main regions. Despite fears to the contrary, in recent years we have seen continued progress toward better methods of feeding humanity. Sub-Saharan Africa is the sole major exception. Looking to the future, this paper argues that the continuation of recent cereal yield trends should be sufficient to cope with most of the demographically driven expansion of cereal demand that will occur until the year 2025. However, because of an increasing degree of mismatch between the expansion of regional demand and the potential for supply, there will be a major expansion of world cereal (and noncereal food) trade. Other consequences for global agriculture arising from demographic growth include the need to use water much more efficiently and an even greater dependence on nitrogen fertilizers (e.g., South Asia). Farming everywhere will depend more on information-intensive agricultural management procedures. Moreover, despite continued general progress, there still will be a significant number of undernourished people in 2025. Signs of heightened harvest variability, especially in North America, are of serious concern. Thus, although future general food trends are likely to be positive, in some respects we also could be entering a more volatile world.

Dynamic evolution of plant mitochondrial genomes: Mobile genes and introns and highly variable mutation rates

We summarize our recent studies showing that angiosperm mitochondrial (mt) genomes have experienced remarkably high rates of gene loss and concomitant transfer to the nucleus and of intron acquisition by horizontal transfer. Moreover, we find substantial lineage-specific variation in rates of these structural mutations and also point mutations. These findings mostly arise from a Southern blot survey of gene and intron distribution in 281 diverse angiosperms. These blots reveal numerous losses of mt ribosomal protein genes but, with one exception, only rare loss of respiratory genes. Some lineages of angiosperms have kept all of their mt ribosomal protein genes whereas others have lost most of them. These many losses appear to reflect remarkably high (and variable) rates of functional transfer of mt ribosomal protein genes to the nucleus in angiosperms. The recent transfer of cox2 to the nucleus in legumes provides both an example of interorganellar gene transfer in action and a starting point for discussion of the roles of mechanistic and selective forces in determining the distribution of genetic labor between organellar and nuclear genomes. Plant mt genomes also acquire sequences by horizontal transfer. A striking example of this is a homing group I intron in the mt cox1 gene. This extraordinarily invasive mobile element has probably been acquired over 1,000 times separately during angiosperm evolution via a recent wave of cross-species horizontal transfers. Finally, whereas all previously examined angiosperm mtDNAs have low rates of synonymous substitutions, mtDNAs of two distantly related angiosperms have highly accelerated substitution rates.

Unexpected signals in a system subject to kinetic proofreading

When multivalent ligands attach to IgEs bound to the receptors with high affinity for IgE on mast cells, the receptors aggregate, tyrosines on the receptors become phosphorylated, and a variety of cellular responses are stimulated. Prior studies, confirmed here, demonstrated that the efficiency with which later events are generated from earlier ones is inversely related to the dissociation rate of the aggregating ligand. This finding suggests that the cellular responses are constrained by a “kinetic proofreading” regimen. We have now observed an apparent exception to this rule. Doses of the rapidly or slowly dissociating ligands that generated equivalent levels of tyrosine-phosphorylated receptors comparably stimulated a putatively distal event: transcription of the gene for monocyte chemoattractant protein 1. Possible explanations of this apparent anomaly were explored.

Electronic reserves: copyright and permissions

Electronic reserves present a new service option for libraries to provide needed materials during hours that the library is not open and to user groups located some distance from library collections. Possible changes to current copyright law and publishers permissions policies have delayed the development of electronic reserves in many libraries. This paper reviews the current state of electronic reserves materials in the publishing and library communities and presents the results of a survey of publishers to determine permissions policies for electronic materials. Issues of concern to both libraries and publishers are discussed.

Exception or extension? : reorienting the Peacock Room among James McNeill Whistler's interior designs

"Although famous for his paintings and etchings today, James McNeill Whistler (1834-1903) was also an important interior designer in the nineteenth-century British Aesthetic movement. Whistler‘s most famous and only extant interior design is Harmony in Blue and Gold: The Peacock Room (1876-77). It is also his most puzzling interior. Long considered an exception to the rule of Whistler‘s other interiors, the Peacock Room has often been overlooked in the few studies of the artist‘s interior designs"

Copyright certificate for the Celestial Planisphere, [1806] July 11

Handwritten copy of a certificate acknowledging the deposit of the title of Croswell's celestial planisphere with the clerk of the District of Massachusetts.

THE DARK PERSONALITY AND JOB SUCCESS IN THE UNITED STATES ARMY: USE OF INTERPERSONAL MANIPULATION IN THE WORKPLACE

This dissertation relates job desires and outcomes to the Dark Personality (Psychopathy, Machiavellianism, Narcissism, Low Agreeableness, Low Honesty-Humility) in the United States Army. It purports that individuals high on the Dark Personality desire more power, money, and status, and that they obtain jobs that afford them these luxuries by using manipulation at work. Two pilot studies used samples of United States Army members to create and test index variables: Dark Personality, Total Manipulation in the workplace, Desire for Job Success, and Total Job Success in the Army. Individual personality traits, manipulation tactics, and job desires were examined in secondary analyses. Using a sample of 468 United States Army Members, central analyses indicated that Army members high on the Dark Personality desired Job Success. Likewise, army members higher on the Dark Personality used more Manipulation tactics at work, including the egregious tactics. Yet, using more Manipulation tactics at work predicted lower levels of Job Success in the Army. Most manipulation tactics had a negative impact on Job Success, with the exception of soft tactics like Reason and Responsibility Invocation. Together, these results indicate that selective use of soft manipulation predicted Job Success, but use of more manipulation tactics predicted less Job Success in the Army. Curvilinear results indicated that being either very low or very high on the Dark Personality predicted more Job Success in the Army, whereas having intermediate levels of the Dark Personality predicted less Job Success. Finally, possessing the Dark Personality and using more Manipulation tactics at work, together, predicted less Job Success in the Army. Collectively, the results indicate that army members with intermediate levels of the Dark Personality want more powerful and high paying jobs, yet their strategy of manipulating their coworkers to move up the job ladder does not result in higher ranking, higher paying Army positions. However, Army members highest on the Dark Personality achieved job success, defying the maladaptive influence that antisocial personality traits and manipulative behaviour had on job success for most Army members. Therefore, this dissertation indicates that successful corporate scoundrels exist in the Army, but there are few of them.

Copyright in the EU Digital Single Market. Report of the CEPS Digital Forum. June 2013

The scope and enforcement of copyright in the digital environment have been among the most complex and controversial subjects tackled by lawmakers all over the world for the last decade. Due to the ubiquitous use of digital technology, modern regulation of copyright inherently touches on numerous areas of law and social and economic policy, including communications privacy and Internet governance. Modernising the EU’s copyright framework is considered a key step towards achieving the goal of an EU Digital Single Market in the context of the ‘Digital Agenda for Europe’, an initiative launched by the European Commission in May 2010. How can the EU make copyright fit for purpose in the Internet age? What are the most suitable and realistic policy options to achieve the objective of a Digital Single Market in the creative content sectors? To give comprehensive answers to these questions, the CEPS Digital Forum formed a Task Force on Copyright in the EU Digital Single Market to foster a multi-stakeholder dialogue on the major challenges for copyright law in the online content sector today. Drawing on the discussions and input gathered by the Task Force, this report contains the conclusions and policy recommendations organised around three main themes: licensing rules and practices in the online music and film sectors, the definition and implementation of copyright exceptions in the digital environment and the present and future of online copyright enforcement in Europe.