Digital Commons Network^™

Dfhic: A Dilated Full Convolution Model To Enhance The Resolution Of Hi-C Data, Bin Wang, Kun Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Hi-C technology has been the most widely used chromosome conformation capture(3C) experiment that measures the frequency of all paired interactions in the entire genome, which is a powerful tool for studying the 3D structure of the genome. The fineness of the constructed genome structure depends on the resolution of Hi-C data. However, due to the fact that high-resolution Hi-C data require deep sequencing and thus high experimental cost, most available Hi-C data are in low-resolution. Hence, it is essential to enhance the quality of Hi-C data by developing the effective computational methods.

Results: In this work, we propose …

Comparison Of Cone Mosaic Metrics From Images Acquired With The Spectralis High Magnification Module And Adaptive Optics Scanning Light Ophthalmoscopy, Niamh Wynne, Heather Heitkotter, Erica N. Woertz, Robert F. Cooper, Joseph Carroll

Biomedical Engineering Faculty Research and Publications

Purpose: To compare cone mosaic metrics derived from adaptive optics scanning light ophthalmoscopy (AOSLO) images with those derived from Heidelberg Engineering SPECTRALIS High Magnification Module (HMM) images.

Methods: Participants with contiguous cone mosaics had HMM imaging performed at locations superior and temporal to the fovea. These images were registered and averaged offline and then aligned to split-detection AOSLO images; 200 × 200-µm regions of interest were extracted from both modalities. Cones were semi-automatically identified by two graders to provide estimates of cone density and spacing.

Results: Thirty participants with contiguous cone mosaics were imaged (10 males, 20 females; age range, …

Tuning Between Quenching And Energy Transfer In Dna-Templated Heterodimer Aggregates, Azhad U. Chowdhury, Jonathan S. Huff, Matthew S. Barclay, Lance K. Patten, Aaron Sup, Natalya Hallstrom, Jeunghoon Lee, Paul H. Davis, Daniel B. Turner, Bernard Yurke, William B. Knowlton, Ryan D. Pensack

Materials Science and Engineering Faculty Publications and Presentations

Molecular excitons, which propagate spatially via electronic energy transfer, are central to numerous applications including light harvesting, organic optoelectronics, and nanoscale computing; they may also benefit applications such as photothermal therapy and photoacoustic imaging through the local generation of heat via rapid excited-state quenching. Here we show how to tune between energy transfer and quenching for heterodimers of the same pair of cyanine dyes by altering their spatial configuration on a DNA template. We assemble “transverse” and “adjacent” heterodimers of Cy5 and Cy5.5 using DNA Holliday junctions. We find that the transverse heterodimers exhibit optical properties consistent with excitonically interacting …

Influence Of Hydrophobicity On Excitonic Coupling In Dna-Templated Indolenine Squaraine Dye Aggregates, Olga A. Mass, Christopher K. Wilson, German Barcenas, Lan Li, Bernard Yurke, William B. Knowlton, Ryan D. Pensack, Jeunghoon Lee

Materials Science and Engineering Faculty Publications and Presentations

Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale. To further expand our ability to control photophysical properties of excitons, here, we investigated the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates covalently templated by DNA Holliday Junction (DNA …

The Low Abundance Of Cpg In The Sars-Cov-2 Genome Is Not An Evolutionarily Signature Of Zap, Ali Afrasiabi, Hamid Alinejad-Rokny, Azad Khosh, Mostafa Rahnama, Nigel Lovell, Zhenming Xu, Diako Ebrahimi

Plant Pathology Faculty Publications

The zinc finger antiviral protein (ZAP) is known to restrict viral replication by binding to the CpG rich regions of viral RNA, and subsequently inducing viral RNA degradation. This enzyme has recently been shown to be capable of restricting SARS-CoV-2. These data have led to the hypothesis that the low abundance of CpG in the SARS-CoV-2 genome is due to an evolutionary pressure exerted by the host ZAP. To investigate this hypothesis, we performed a detailed analysis of many coronavirus sequences and ZAP RNA binding preference data. Our analyses showed neither evidence for an evolutionary pressure acting specifically on CpG …

Exciton Delocalization And Scaffold Stability In Bridged Nucleotide-Substituted, Dna Duplex-Templated Cyanine Aggregates, Simon K. Roy, Olga A. Mass, Donald L. Kellis, Christopher K. Wilson, John A. Hall, Bernard Yurke, William B. Knowlton

Electrical and Computer Engineering Faculty Publications and Presentations

Molecular excitons play a foundational role in chromophore aggregates found in light-harvesting systems and offer potential applications in engineered excitonic systems. Controlled aggregation of chromophores to promote exciton delocalization has been achieved by covalently tethering chromophores to deoxyribonucleic acid (DNA) scaffolds. Although many studies have documented changes in the optical properties of chromophores upon aggregation using DNA scaffolds, more limited work has investigated how structural modifications of DNA via bridged nucleotides and chromophore covalent attachment impact scaffold stability as well as the configuration and optical behavior of attached aggregates. Here we investigated the impact of two types of bridged nucleotides, …

Customizable Aptamer Transducer Network Designed For Feed-Forward Coupling, Tim Hachigian, Drew Lysne, Elton Graugnard, Jeunghoon Lee

Materials Science and Engineering Faculty Publications and Presentations

Solution-based biosensors that utilize aptamers have been engineered in a variety of formats to detect a range of analytes for both medical and environmental applications. However, since aptamers have fixed base sequences, incorporation of aptamers into DNA strand displacement networks for feed-forward signal amplification and processing requires significant redesign of downstream DNA reaction networks. We designed a novel aptamer transduction network that releases customizable output domains, which can then be used to initiate downstream strand displacement reaction networks without any sequence redesign of the downstream reaction networks. In our aptamer transducer (AT), aptamer input domains are independent of output domains …

Excited-State Lifetimes Of Dna-Templated Cyanine Dimer, Trimer, And Tetramer Aggregates: The Role Of Exciton Delocalization, Dye Separation, And Dna Heterogeneity, Jonathan S. Huff, Daniel B. Turner, Olga A. Mass, Lance K. Patten, Christopher K. Wilson, Simon K. Roy, Matthew S. Barclay, Bernard Yurke, William B. Knowlton, Paul H. Davis, Ryan D. Pensack

Materials Science and Engineering Faculty Publications and Presentations

DNA-templated molecular (dye) aggregates are a novel class of materials that have garnered attention in a broad range of areas including light harvesting, sensing, and computing. Using DNA to template dye aggregation is attractive due to the relative ease with which DNA nanostructures can be assembled in solution, the diverse array of nanostructures that can be assembled, and the ability to precisely position dyes to within a few Angstroms of one another. These factors, combined with the programmability of DNA, raise the prospect of designer materials custom tailored for specific applications. Although considerable progress has been made in characterizing the …

Deep Neural Network Analysis Of Pathology Images With Integrated Molecular Data For Enhanced Glioma Classification And Grading, Linmin Pei, Karra A. Jones, Zeina A. Shboul, James Y. Chen, Khan M. Iftekharuddin

Electrical & Computer Engineering Faculty Publications

Gliomas are primary brain tumors that originate from glial cells. Classification and grading of these tumors is critical to prognosis and treatment planning. The current criteria for glioma classification in central nervous system (CNS) was introduced by World Health Organization (WHO) in 2016. This criteria for glioma classification requires the integration of histology with genomics. In 2017, the Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy (cIMPACT-NOW) was established to provide up-to-date recommendations for CNS tumor classification, which in turn the WHO is expected to adopt in its upcoming edition. In this work, we propose a novel …

Photoreceptor Inner Segment Morphology In Best Vitelliform Macular Dystrophy, Drew Scoles, Yusufu N. Sulai, Robert F. Cooper, Brian P. Higgins, Ryan D. Johnson, Joseph Carroll, Alfredo Dubra, Kimberly E. Stepien

Biomedical Engineering Faculty Research and Publications

PURPOSE

To characterize outer retina structure in best vitelliform macular dystrophy (BVMD) and to determine the effect of macular lesions on overlying and adjacent photoreceptors.

METHODS

Five individuals with BVMD were followed prospectively with spectral domain optical coherence tomography and confocal and nonconfocal split-detector adaptive optics scanning light ophthalmoscopy (AOSLO). The AOSLO cone photoreceptor mosaic images were obtained within and around retinal lesions. Cone density was measured inside and outside lesions. In 2 subjects, densities were compared with published measurements acquired ∼2.5 years before. One subject was imaged 3 times over a 5-month period.

RESULTS

The AOSLO imaging demonstrated that …

Deletion Of Nfnab In Thermoanaerobacterium Saccharolyticum And Its Effect On Metabolism, Jonathan Lo, Tianyong Zheng, Daniel G. Olson, Natalie Ruppertsberger, Shital Tripathi, Adam Guss, Lee Lynd

Dartmouth Scholarship

NfnAB catalyzes the reversible transfer of electrons from reduced ferredoxin and NADH to 2 NADP⁺. The NfnAB complex has been hypothesized to be the main enzyme for ferredoxin oxidization in strains of Thermoanaerobacterium saccharolyticum engineered for increased ethanol production. NfnAB complex activity was detectable in crude cell extracts of T. saccharolyticum. Activity was also detected using activity staining of native PAGE gels. The nfnAB gene was deleted in different strains of T. saccharolyticum to determine its effect on end product formation. In wild-type T. saccharolyticum, deletion of nfnAB resulted in a 46% increase in H₂ formation but …

Cofactor Specificity Of The Bifunctional Alcohol And Aldehyde Dehydrogenase (Adhe) In Wild-Type And Mutant Clostridium Thermocellum And Thermoanaerobacterium Saccharolyticum, Tianyong Zheng, Daniel G. Olson, Liang Tian, Yannick J. Bomble, Michael Himmel, Jonathan Lo, Shuen Hon, A. Joe Shaw, Johannes P. Van Dijken, Lee Lynd

Dartmouth Scholarship

Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are thermophilic bacteria that have been engineered to produce ethanol from the cellulose and hemicellulose fractions of biomass, respectively. Although engineered strains of T. saccharolyticum produce ethanol with a yield of 90% of the theoretical maximum, engineered strains of C. thermocellum produce ethanol at lower yields (∼50% of the theoretical maximum). In the course of engineering these strains, a number of mutations have been discovered in their adhE genes, which encode both alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) enzymes. To understand the effects of these mutations, the adhE genes from six strains of C. …

Backfolding Of Wormlike Chains Confined In Nanochannels, Abhiram Muralidhar, Douglas R. Tree, Kevin D. Dorfman

Faculty Publications

Using pruned-enriched Rosenbluth method (PERM) simulations of a discrete wormlike chain model, we provide compelling evidence in support of Odijk’s prediction of two distinct Odijk regimes for a long wormlike chain confined in a nanochannel. In both cases, the chain of persistence length lp is renormalized into a series of deflection segments of characteristic length D2/3lp1/3, where D is the channel size. In the first (classic) Odijk regime, these deflection segments are linearly ordered. In the second Odijk regime, thin, long wormlike chains can backfold at a length scale quantified by the global persistence length. We …

Increase In Ethanol Yield Via Elimination Of Lactate Production In An Ethanol-Tolerant Mutant Of Clostridium Thermocellum, Ranjita Biswas, Sandeep Prabhu, Lee R. Lynd, Adam M. Guss

Dartmouth Scholarship

Large-scale production of lignocellulosic biofuel is a potential solution to sustainably meet global energy needs. One-step consolidated bioprocessing (CBP) is a potentially advantageous approach for the production of biofuels, but requires an organism capable of hydrolyzing biomass to sugars and fermenting the sugars to ethanol at commercially viable titers and yields. Clostridium thermocellum, a thermophilic anaerobe, can ferment cellulosic biomass to ethanol and organic acids, but low yield, low titer, and ethanol sensitivity remain barriers to industrial production. Here, we deleted the hypoxanthine phosphoribosyltransferase gene in ethanol tolerant strain of C. thermocellum adhE*(EA) in order to allow use …

Metastatic Tumor Evolution In Diuse Gastric Cancer And Cancer Organoid Modeling Implicate Tgfbr2 As A Potential Driver, Patrick Flaherty

Mathematics and Statistics Department Faculty Publication Series

Background: Gastric cancer is the second-leading cause of global cancer deaths, with metastatic disease representing the primary cause of mortality. To identify candidate drivers involved in oncogenesis and tumor evolution, we conduct an extensive genome sequencing analysis of metastatic progression in a diffuse gastric cancer. This involves a comparison between a primary tumor from a hereditary diffuse gastric cancer syndrome proband and its recurrence as an ovarian metastasis. Results: Both the primary tumor and ovarian metastasis have common biallelic loss-of-function of both the CDH1 and TP53 tumor suppressors, indicating a common genetic origin. While the primary tumor exhibits amplification of …

Overexpression Of Dcf1 Inhibits Glioma Through Destruction Of Mitochondria And Activation Of Apoptosis Pathway, Yuqiong Xie, Qang Li, Qingbo Yang

Electrical and Computer Engineering Faculty Research & Creative Works

Gliomas are the most common brain tumors affecting the central nervous system and are associated with a high mortality rate. DCF1 is a membrane protein that was previously found to play a role in neural stem cell differentiation. In the present study, we found that overexpression of dcf1 significantly inhibited cell proliferation, migration, and invasion and dramatically promoted apoptosis in the glioblastoma U251 cell line. DCF1 deletion mutations in the functional region showed that the complete structure of DCF1 was necessary for apoptosis. Furthermore, significantly lower tumorigenicity was observed in athymic nude mice by transplanting U251 cells overexpressing dcf1. To …

Is Dna A Good Model Polymer?, Douglas R. Tree, Abhiram Muralidhar, Patrick S. Doyle, Kevin D. Dorfman

Faculty Publications

The details surrounding the crossover from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy, and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the pruned-enriched Rosenbluth method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike …

Creating A Package In R, Brit Schneiders, Eric Archer

STAR Program Research Presentations

In a time of increasingly efficient technology and data production, scientists are producing data faster than it can be analyzed. Therefore, user accessibility to data analysis is becoming more and more critical. In general, researchers have a set of raw data and want an efficient means to their final analysis. A package serves as that means by creating a set of functions and making them accessible to the user. Often, a user has a small piece of code to run (a single R script, for example), and that script requires the use of certain functions, which are contained in a …

Atypical Glycolysis In Clostridium Thermocellum, Jilai Zhou, Daniel G. Olson, D. Aaron Argyros, Yu Deng, Walter M. Van Gulik, Johannes P. Van Dijken, Lee R. Lynd

Dartmouth Scholarship

Cofactor specificities of glycolytic enzymes in Clostridium thermocellum were studied with cellobiose-grown cells from batch cultures. Intracellular glucose was phosphorylated by glucokinase using GTP rather than ATP. Although phosphofructokinase typically uses ATP as a phosphoryl donor, we found only pyrophosphate (PPi)-linked activity. Phosphoglycerate kinase used both GDP and ADP as phosphoryl acceptors. In agreement with the absence of a pyruvate kinase sequence in the C. thermocellum genome, no activity of this enzyme could be detected. Also, the annotated pyruvate phosphate dikinase (ppdk) is not crucial for the generation of pyruvate from phosphoenolpyruvate (PEP), as deletion of the ppdk gene did …

Molecular Diversity Of Bacteroidales In Fecal And Environmental Samples And Swine-Associated Subpopulations, Regina Lamendella, Kent C. Li, Daniel B. Oerther, Jorge W. Santo Domingo

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

Several swine-specific microbial source tracking methods are based on PCR assays targeting Bacteroidales 16S rRNA gene sequences. The limited application of these assays can be explained by the poor understanding of their molecular diversity in fecal sources and environmental waters. In order to address this, we studied the diversity of 9,340 partial (>600bp in length) Bacteroidales 16S rRNA gene sequences from 13 fecal sources and nine feces-contaminated watersheds. The compositions of major Bacteroidales populations were analyzed to determine which host and environmental sequences were contributing to each group. This information allowed us to identify populations which were both exclusive …

Systematic Genomic Identification Of Colorectal Cancer Genes Delineating Advanced From Early Clinical Stage, Hojoon Lee, Patrick Flaherty, Hanlee P. Ji

Mathematics and Statistics Department Faculty Publication Series

Background: Colorectal cancer is the third leading cause of cancer deaths in the United States. The initial assessment of colorectal cancer involves clinical staging that takes into account the extent of primary tumor invasion, determining the number of lymph nodes with metastatic cancer and the identification of metastatic sites in other organs. Advanced clinical stage indicates metastatic cancer, either in regional lymph nodes or in distant organs. While the genomic and genetic basis of colorectal cancer has been elucidated to some degree, less is known about the identity of specific cancer genes that are associated with advanced clinical stage and …

Rvd: A Command-Line Program For Ultrasensitive Rare Single Nucleotide Variant Detection Using Targeted Next-Generation Dna Resequencing, Anna Cushing, Patrick Flaherty, Erik Hopmans, John M. Bell, Hanlee P. Ji

Mathematics and Statistics Department Faculty Publication Series

Background: Rare single nucleotide variants play an important role in genetic diversity and heterogeneity of specific human disease. For example, an individual clinical sample can harbor rare mutations at minor frequencies. Genetic diversity within an individual clinical sample is oftentimes reflected in rare mutations. Therefore, detecting rare variants prior to treatment may prove to be a useful predictor for therapeutic response. Current rare variant detection algorithms using next generation DNA sequencing are limited by inherent sequencing error rate and platform availability. Findings: Here we describe an optimized implementation of a rare variant detection algorithm called RVD for use in targeted …

Beyond Gel Electrophoresis: Microfluidic Separations, Fluorescence Burst Analysis, And Dna Stretching, Kevin D. Dorfman, Scott B. King, Daniel W. Olson, Joel D. P. Thomas, Douglas R. Tree

Faculty Publications

This review addresses methods for obtaining sequence information directly from unamplified genomic length DNA. Our generic starting point is a large piece of DNA that contains many thousands of base pairs (kilobase pairs, kbp) or even millions of base pairs (megabase pairs, Mbp). We would like to determine the genomic distance between two repeats of a given sequence, indicated by the red dots on the coiled DNA molecule in Figure 1. Let us consider the case where these sequences are restriction sites, which can be selectively cut using proteins known as restriction enzymes. For decades, gel electrophoresis served as the …

High Ethanol Titers From Cellulose By Using Metabolically Engineered Thermophilic, Anaerobic Microbes, D. Aaron Argyros, Shital A. Tripathi, Trisha F. Barrett, Stephen R. Rogers, Lawrence F. Feinberg, Daniel G. Olson, Justin M. Foden, Bethany B. Miller, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza

Dartmouth Scholarship

This work describes novel genetic tools for use in Clostridium thermocellum that allow creation of unmarked mutations while using a replicating plasmid. The strategy employed counter-selections developed from the native C. thermocellum hpt gene and the Thermoanaerobacterium saccharolyticum tdk gene and was used to delete the genes for both lactate dehydrogenase (Ldh) and phosphotransacetylase (Pta). The Δldh Δpta mutant was evolved for 2,000 h, resulting in a stable strain with 40:1 ethanol selectivity and a 4.2-fold increase in ethanol yield over the wild-type strain. Ethanol production from cellulose was investigated with an engineered coculture of organic acid-deficient engineered strains of …

Mutant Alcohol Dehydrogenase Leads To Improved Ethanol Tolerance In Clostridium Thermocellum, Steven D. Brown, Adam M. Guss, Tatiana V. Karpinets, Jerry M. Parks

Dartmouth Scholarship

Clostridium thermocellum is a thermophilic, obligately anaerobic, Gram-positive bacterium that is a candidate microorganism for converting cellulosic biomass into ethanol through consolidated bioprocessing. Ethanol intolerance is an important metric in terms of process economics, and tolerance has often been described as a complex and likely multigenic trait for which complex gene interactions come into play. Here, we resequence the genome of an ethanol-tolerant mutant, show that the tolerant phenotype is primarily due to a mutated bifunctional acetaldehyde-CoA/alcohol dehydrogenase gene (adhE), hypothesize based on structural analysis that cofactor specificity may be affected, and confirm this hypothesis using enzyme assays. …

Simulation Of Dna Extension In Nanochannels, Yanwei Wang, Douglas R. Tree, Kevin D. Dorfman

Faculty Publications

We have used a realistic model for double-stranded DNA and Monte Carlo simulations to compute the extension (mean span) of a DNA molecule confined in a nanochannel over the full range of confinement in a high ionic strength buffer. The simulation data for square nanochannels resolve the apparent contradiction between prior simulation studies and the predictions from Flory theory, demonstrating the existence of two transition regimes between weak confinement (the de Gennes regime) and strong confinement (the Odijk regime). The simulation data for rectangular nanochannels support the use of the geometric mean for mapping data obtained in rectangular channels onto …

Comparative Fecal Metagenomics Unveils Unique Functional Capacity Of The Swine Gut, Regina Lamendella, Jorge W. Santo Domingo, Shreya Ghosh, John Martinson, Daniel B. Oerther

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

Background: Uncovering the taxonomic composition and functional capacity within the swine gut microbial consortia is of great importance to animal physiology and health as well as to food and water safety due to the presence of human pathogens in pig feces. Nonetheless, limited information on the functional diversity of the swine gut microbiome is available. Results: Analysis of 637, 722 pyrosequencing reads (130 megabases) generated from Yorkshire pig fecal DNA extracts was performed to help better understand the microbial diversity and largely unknown functional capacity of the swine gut microbiome. Swine fecal metagenomic sequences were annotated using both MG-RAST and …

Ultrasensitive Detection Of Rare Mutations Using Next-Generation Targeted Resequencing, Patrick Flaherty, Georges Natsoulis, Omkar Muralidharan, Mark Winters, Jason Buenrostro, John Bell, Sheldon Brown, Mark Holodniy, Nancy Zhang, Hanlee P. Ji

Mathematics and Statistics Department Faculty Publication Series

With next-generation DNA sequencing technologies, one can interrogate a specific genomic region of interest at very high depth of coverage and identify less prevalent, rare mutations in heterogeneous clinical samples. However, the mutation detection levels are limited by the error rate of the sequencing technology as well as by the availability of variant-calling algorithms with high statistical power and low false positive rates. We demonstrate that we can robustly detect mutations at 0.1% fractional representation. This represents accurate detection of one mutant per every 1000 wild-type alleles. To achieve this sensitive level of mutation detection, we integrate a high accuracy …

Development Of Pyrf-Based Genetic System For Targeted Gene Deletion In Clostridium Thermocellum And Creation Of A Pta Mutant, Shital A. Tripathi, Daniel G. Olson, D. Aaron Argyros, Bethany B. Miller, Trisha F. Barrett, Daniel M. Murphy, Jesse D. Mccool, Anne K. Warner, Vineet B. Rajgarhia, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza

Dartmouth Scholarship

We report development of a genetic system for making targeted gene knockouts in Clostridium thermocellum, a thermophilic anaerobic bacterium that rapidly solubilizes cellulose. A toxic uracil analog, 5-fluoroorotic acid (5-FOA), was used to select for deletion of the pyrF gene. The ΔpyrF strain is a uracil auxotroph that could be restored to a prototroph via ectopic expression of pyrF from a plasmid, providing a positive genetic selection. Furthermore, 5-FOA was used to select against plasmid-expressed pyrF, creating a negative selection for plasmid loss. This technology was used to delete a gene involved in organic acid production, namely pta, which encodes …

Quantifying And Resolving Multiple Vector Transformants In S. Cerevisiae Plasmid Libraries, Thomas C. Scanlon, Elizabeth C. Gray, Karl E. Griswold

Dartmouth Scholarship

In addition to providing the molecular machinery for transcription and translation, recombinant microbial expression hosts maintain the critical genotype-phenotype link that is essential for high throughput screening and recovery of proteins encoded by plasmid libraries. It is known that Escherichia coli cells can be simultaneously transformed with multiple unique plasmids and thusly complicate recombinant library screening experiments. As a result of their potential to yield misleading results, bacterial multiple vector transformants have been thoroughly characterized in previous model studies. In contrast to bacterial systems, there is little quantitative information available regarding multiple vector transformants in yeast. Saccharomyces cerevisiae is the …