On Ribosome Load, Codon Bias and Protein Abundance

Different codons encoding the same amino acid are not used equally in protein-coding sequences. In bacteria, there is a bias towards codons with high translation rates. This bias is most pronounced in highly expressed proteins, but a recent study of synthetic GFP-coding sequences did not find a correlation between codon usage and GFP expression, suggesting that such correlation in natural sequences is not a simple property of translational mechanisms. Here, we investigate the effect of evolutionary forces on codon usage. The relation between codon bias and protein abundance is quantitatively analyzed based on the hypothesis that codon bias evolved to ensure the efficient usage of ribosomes, a precious commodity for fast growing cells. An explicit fitness landscape is formulated based on bacterial growth laws to relate protein abundance and ribosomal load. The model leads to a quantitative relation between codon bias and protein abundance, which accounts for a substantial part of the observed bias for E. coli. Moreover, by providing an evolutionary link, the ribosome load model resolves the apparent conflict between the observed relation of protein abundance and codon bias in natural sequences and the lack of such dependence in a synthetic gfp library. Finally, we show that the relation between codon usage and protein abundance can be used to predict protein abundance from genomic sequence data alone without adjustable parameters.

On Ribosome Load, Codon Bias and Protein Abundance

Different codons encoding the same amino acid are not used equally in protein-coding sequences. In bacteria, there is a bias towards codons with high translation rates. This bias is most pronounced in highly expressed proteins, but a recent study of synthetic GFP-coding sequences did not find a correlation between codon usage and GFP expression, suggesting that such correlation in natural sequences is not a simple property of translational mechanisms. Here, we investigate the effect of evolutionary forces on codon usage. The relation between codon bias and protein abundance is quantitatively analyzed based on the hypothesis that codon bias evolved to ensure the efficient usage of ribosomes, a precious commodity for fast growing cells. An explicit fitness landscape is formulated based on bacterial growth laws to relate protein abundance and ribosomal load. The model leads to a quantitative relation between codon bias and protein abundance, which accounts for a substantial part of the observed bias for E. coli. Moreover, by providing an evolutionary link, the ribosome load model resolves the apparent conflict between the observed relation of protein abundance and codon bias in natural sequences and the lack of such dependence in a synthetic gfp library. Finally, we show that the relation between codon usage and protein abundance can be used to predict protein abundance from genomic sequence data alone without adjustable parameters.

Men's Modesty, Religion, and the State: Spaces of Collision

This article examines religious practices in the United States, which govern modesty and other dress norms for men. I focus both on the spaces within which they most collide with regulatory regimes of the state and the legal implications of these norms, particularly for observant Muslim men. Undergirding the research are those ‘‘gender equality’’ claims made by many religious adherents, that men are required to maintain proper modesty norms just as are women. Also undergirding the research is the extensive anti-Islam bias in American culture today. The spaces within which men’s religiously proscribed dress and grooming norms are most at issue—indicated by First Amendment legal challenges to rights of religious practice—are primarily those state-controlled, total institutions Goffman describes, such as in the military and prisons. The implications of gendered modesty norms are important, as state control over religious expression in prisons, for example, is much more difficult to contest than in other spaces, although this depends entirely on who is doing the contesting and within which religious context. In American society today—and particularly within the context of growing Islamaphobia following the 9/11 attacks—the implications are greatest for those men practicing ‘‘prison Islam.’’

Should Countries Engage in a Race to the Bottom? The Effect of Social Spending on FDI

This paper examines the effect of social spending in developing countries on foreign direct investment (FDI). Existing studies on the race to the bottom in social services attempt to discern the extent to which FDI affects social expenditure. However, it remains an open question whether FDI is actually attracted to lower spending levels. We find no indication that FDI is repelled by social spending; indeed there is strong evidence that investment is associated with greater programmatic emphases on health and education. These findings have important implications for leaders seeking to attract investment and for those attempting to expand social programs.

The Evolution of Media Coverage of Historical Sports Controversies

This thesis will cover sports controversies throughout the 20th Century in the context of the media’s newspaper coverage of the events. The 1919 Black Sox Scandal, the debate over American participation in the 1936 Olympics, and Muhammad Ali’s conversion to the Nation of Islam, standing as a notorious public figure, and conscientious objection to the Vietnam War will represent the three sports controversies. The media’s adherence to cultural norms is clear in all three cases. The consistent devotion to the cultural and racial atmosphere of their respective eras was constant and helped to perpetuate accepted, mainstream cultural attitudes. Cultural and racial norms were followed in the coverage of the three discussed controversies. The anti-Semitism and racially intolerant sentiments in America during great waves of immigration in the early 1900s allowed for journalists to freely vilify Jews as corrupters of baseball and the ballplayers who were rumored to have thrown the 1919 World Series. The white ballplayers were supported in the press, who protected their own and blamed outsiders. Jim Crow and the Americanization movement forced African American and Jewish newspapers to limit their journalistic bias on both sides of the debate over American participation in the 1936 Berlin Olympics. The white, mainstream press was void of bias as the spirit of isolationism in America triumphed over journalist’s leanings in the Olympic debate. The racial tension created by the Civil Rights movement of the 1960s created an atmosphere that allowed mainstream journalists to heap endless criticism on Muhammad Ali as he gained fame. By portraying him as a villain of society as both a religious radical and traitor to America, journalists created a common enemy in the minds of white America. In all three cases, a pattern of journalists expressing the state of cultural and racial norms of the era is present and significant.

Chinese Whiteness: The Discourse Of Race In Modern And Contemporary Chinese Culture

This thesis chronicles the development of western forms of race and racism in China. It then studies contemporary China using theories derived from whiteness studies in order to explain the unique position that whites (Caucasians) have in China today. In Chapter I, I break down the definition of race and introduce a foundation for a whiteness studies approach to research. In Chapter II, I analyze how Chinese classified themselves and other humans prior to the western system of race. In Chapter III, I chronicle the introduction of western forms of race and racism to China, and the appropriation of these concepts to suit Chinese goals. In Chapter IV, I approach cultural phenomenon in contemporary China by situating them in their historical traditions as well as by approaching them as displaying an internalized racism and white privilege. Finally in the Conclusion, I postulate on what China¿s contemporary racial system means for China.

Response Bias Using Two-Stage Data Collection: A study of elderly participants in a program.

Researchers examining the effects of programs, in this case a state-level pharmaceutical assistance program for the elderly, sometimes must rely on multiple methods of data collection. Two-stage data collection (e.g., a telephone interview followed by a mail questionnaire) was used to obtain a full range of information. Older age groups were found to participate less frequently in the telephone interview, while certain demographic factors characterized mail questionnaire nonparticipants, all of which supports past research. Results also show that those in the poorest health are less likely to participate in the mail survey. Combining the two methods did not result in high attrition, suggesting that innovation can be successfully employed. Knowledge of the bias associated with each method will aid in targeting special groups.