Usage and refactoring studies of python regular expressions

Though regular expressions provide a powerful search technique that is baked into every major language, is incorporated into a myriad of essential tools, and has been a fundamental aspect of Computer Science since the 1960\u27s, no one has ever formally studied how they are used in practice, or how to apply refactoring principals to improve understandability and conformance to community standards. This thesis presents the original work of studying a sample of regexes taken from Python projects mined from GitHub, determining what features are used most often, defining some categories that illuminate common use cases, and identifying areas of significance for language and tool designers. Furthermore, this thesis defines an equivalence class model used to explore comprehension of regexes, identifying the most common and most understandable representations of semantically identical regexes, suggesting several refactorings and preferred representations. Opportunities for future work include the novel and rich field of regex refactoring, semantic search of regexes, and further fundamental research into regex usage and understandability

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

Accurate variant calling in next generation sequencing (NGS) is critical to understand cancer genomes better. Here we present VarDict, a novel and versatile variant caller for both DNA- and RNA-sequencing data. VarDict simultaneously calls SNV, MNV, InDels, complex and structural variants, expanding the detected genetic driver landscape of tumors. It performs local realignments on the fly for more accurate allele frequency estimation. VarDict performance scales linearly to sequencing depth, enabling ultra-deep sequencing used to explore tumor evolution or detect tumor DNA circulating in blood. In addition, VarDict performs amplicon aware variant calling for polymerase chain reaction (PCR)-based targeted sequencing often used in diagnostic settings, and is able to detect PCR artifacts. Finally, VarDict also detects differences in somatic and loss of heterozygosity variants between paired samples. VarDict reprocessing of The Cancer Genome Atlas (TCGA) Lung Adenocarcinoma dataset called known driver mutations in KRAS, EGFR, BRAF, PIK3CA and MET in 16% more patients than previously published variant calls. We believe VarDict will greatly facilitate application of NGS in clinical cancer research

Structure-function analysis of the curli accessory protein CsgE defines surfaces essential for coordinating amyloid fiber formation

Curli amyloid fibers are produced as part of the extracellular biofilm matrix and are composed primarily of the major structural subunit CsgA. The CsgE chaperone facilitates the secretion of CsgA through CsgG by forming a cap at the base of the nonameric CsgG outer membrane pore. We elucidated a series of finely tuned nonpolar and charge-charge interactions that facilitate the oligomerization of CsgE and its ability to transport unfolded CsgA to CsgG for translocation. CsgE oligomerization in vitro is temperature dependent and is disrupted by mutations in the W48 and F79 residues. Using nuclear magnetic resonance (NMR), we identified two regions of CsgE involved in the CsgE-CsgA interaction: a head comprising a positively charged patch centered around R47 and a stem comprising a negatively charged patch containing E31 and E85. Negatively charged residues in the intrinsically disordered N- and C-terminal “tails” were not implicated in this interaction. Head and stem residues were mutated and interrogated using in vivo measurements of curli production and in vitro amyloid polymerization assays. The R47 head residue of CsgE is required for stabilization of CsgA- and CsgE-mediated curli fiber formation. Mutation of the E31 and E85 stem residues to positively charged side chains decreased CsgE-mediated curli fiber formation but increased CsgE-mediated stabilization of CsgA. No single-amino-acid substitutions in the head, stem, or tail regions affected the ability of CsgE to cap the CsgG pore as determined by a bile salt sensitivity assay. These mechanistic insights into the directed assembly of functional amyloids in extracellular biofilms elucidate possible targets for biofilm-associated bacterial infections.Curli represent a class of functional amyloid fibers produced by Escherichia coli and other Gram-negative bacteria that serve as protein scaffolds in the extracellular biofilm matrix. Despite the lack of sequence conservation among different amyloidogenic proteins, the structural and biophysical properties of functional amyloids such as curli closely resemble those of amyloids associated with several common neurodegenerative diseases. These parallels are underscored by the observation that certain proteins and chemicals can prevent amyloid formation by the major curli subunit CsgA and by alpha-synuclein, the amyloid-forming protein found in Lewy bodies during Parkinson’s disease. CsgA subunits are targeted to the CsgG outer membrane pore by CsgE prior to secretion and assembly into fibers. Here, we use biophysical, biochemical, and genetic approaches to elucidate a mechanistic understanding of CsgE function in curli biogenesis

Moving Beyond CHO: Alternative host systems may be the future of biotherapeutics

CHO cells are the primary expression system for recombinant proteins with significant investment over the last three decades resulting in robust cell lines and processes. The flexible nature of CHO has lent itself to multiple process formats, such as fed batch, perfusion and continuous cultures, and advances in omics technology has enabled customization of media formulations and targeted engineering of CHO cells. This knowledge has led to large gains in protein productivity that can be captured with culture duration and/or scale. Despite this, constant pressure exists to reduce cost of manufacturing and improve per batch productivity to meet the needs of increased patient populations and increase accessibility of these therapeutics. Biogen has partnered with MIT to take a holistic view of the potential future of biomanufacturing to identify technologies that can make step changes in productivity and cost reduction. This effort has identified the host system as the most important factor to enabling this vision. Specifically, a non-mammalian host could be the key to realizing the most significant gains in productivity and reduction in cost of manufacturing. Through this initiative, we sought to take a more comprehensive approach to investigate alternative hosts for recombinant antibody production. Eight non-mammalian hosts were selected based on several properties, including proven secretion of recombinant protein products, ability to glycosylate proteins, established genome or molecular biology toolkit, amongst others. The final panel of organisms included yeast, filamentous fungi, a diatom, and a trypanosome. In collaboration with Amyris, we evaluated these eight non-mammalian host cell lines to compare their suitability as a potential primary host for the biotechnology industry. Only non-engineered, wild-type strains were used as a starting point for this evaluation, which assessed the ability of each host to express the same IgG1 model antibody. The outcome of this comparative analysis demonstrated that several of the alternative hosts could express full length antibody with acceptable glycoforms. Additionally, the ease of culture, ability to engineer the genome, and flexibility of carbon source were assessed. As an output of this work, the most productive strains will be made available for use without restrictions to allow others in the community to freely work with these hosts. Based on this initial assessment, a strategy to further investigate the potential of the most promising hosts will be shared