Lightness of Being and the Burden of Gravity

The challenge of the human condition is to bear the loss that comes with every second, moving forward, breathing without thinking; moving forward, through moments that pass so uneventfully that we will not recall them, along with moments that we experience so profoundly that we begin to use them as landmarks in our personal histories. My view of time is of something that surrounds me and becomes a part of my identity. Yet, as I contemplate what it means to BE, I must face the constancy with which that being also changes. Regardless of the things that I remember, or that I forget, gravity perpetuates the movement of time. Thus, gravity becomes our greatest burden. Through my writing and research, I explore the dual nature of being, and the transient natures of both the intellectual and physical self. In my thesis exhibition, The Lightness of Being and The Burden of Gravity, I employed the medium of video installation in order to provide a space that evoked both the ephemeral and the physical sense of being. In my support paper, I discuss this exhibition in depth, as well as my conceptual connections to literary and artistic influences, such as the writings of Milan Kundera and Jorge Luis Borges, and the work of artists Masao Yamamoto, James Turrell, and Ann Hamilton

Gene Composer: database software for protein construct design, codon engineering, and gene synthesis

<p>Abstract</p> <p>Background</p> <p>To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering.</p> <p>Results</p> <p>An interactive <b>Alignment Viewer </b>allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The <b>Construct Design Module </b>enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned <it>in silico </it>into defined expression vectors. The <b>Gene Design Module </b>uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies.</p> <p>Conclusion</p> <p>We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease error correction in combination with PIPE cloning. In a sister manuscript we present data on how Gene Composer designed genes and protein constructs can result in improved protein production for structural studies.</p

Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer

<p>Abstract</p> <p>Background</p> <p>With the goal of improving yield and success rates of heterologous protein production for structural studies we have developed the database and algorithm software package Gene Composer. This freely available electronic tool facilitates the information-rich design of protein constructs and their engineered synthetic gene sequences, as detailed in the accompanying manuscript.</p> <p>Results</p> <p>In this report, we compare heterologous protein expression levels from native sequences to that of codon engineered synthetic gene constructs designed by Gene Composer. A test set of proteins including a human kinase (P38α), viral polymerase (HCV NS5B), and bacterial structural protein (FtsZ) were expressed in both <it>E. coli </it>and a cell-free wheat germ translation system. We also compare the protein expression levels in <it>E. coli </it>for a set of 11 different proteins with greatly varied G:C content and codon bias.</p> <p>Conclusion</p> <p>The results consistently demonstrate that protein yields from codon engineered Gene Composer designs are as good as or better than those achieved from the synonymous native genes. Moreover, structure guided N- and C-terminal deletion constructs designed with the aid of Gene Composer can lead to greater success in gene to structure work as exemplified by the X-ray crystallographic structure determination of FtsZ from <it>Bacillus subtilis</it>. These results validate the Gene Composer algorithms, and suggest that using a combination of synthetic gene and protein construct engineering tools can improve the economics of gene to structure research.</p

Gene Composer in a structural genomics environment

For structural biology applications, protein-construct engineering is guided by comparative sequence analysis and structural information, which allow the researcher to better define domain boundaries for terminal deletions and nonconserved regions for surface mutants. A database software application called Gene Composer has been developed to facilitate construct design

Technologies of the Self: Habitus and Capacities.

NoThis paper analyses Foucault's notion of technologies of the self, but does so through a non-Foucauldian style of analysis. It traces the use of the term technology back to the works of Aristotle and elaborates upon this definition. Here, technology is seen to be central not only in the production of works, but also in the production of selves. This idea is then developed through the work of other thinkers who have a similar technological view of the production of the self, particularly Marcel Mauss and John Dewey. Another important element emerges from their works, which is the production of self through the technology of habit or habitus. It is argued that habitus is not a socially determinate concept, because it allows for the development of both practical and critical reason, both of which permit the agent some freedom in their activities. However, it is possible to use the connotation of habitus with routine to understand something of the nature of social power. The concept of capacity is also introduced to extend the self-reflexive and knowing aspect of habitus, showing how this is an essential feature of the agential self. However, it is argued that although the development of practical and critical reason allows for reflexivity, the self is always grounded in technologies of the body and self, which constitute the aspect of the self reflected upon. Reflexivity, then, is a secondary and partial aspect of the self