Academic literature on the topic 'Primer designs'

A Primer for Students of Architecture in Sustainable Design, to be used as a part of design studios at the second or third year level. The Primer is written to students as individuals it can be used independent of any particular course assignments or requirements. the Primer is organized in three parts and around the five S.H.I.R.T. Principles, that introduce the student to a method of incorporating the new environmental constraints involved in the more sustainable design approaches.<br>Department of Architecture

Recombinant DNA technology has been commonly used in a number of fields to synthesize new products or generate products with a new pathway. Conventional cloning methods are expensive and require significant time and labor; λ-PCR, a new cloning method developed in the Senger lab, has a number of advantages compared to other cloning processes due to its employment of relatively inexpensive and widely available materials and time-efficiency. While the amount of lab work required for the cloning process is minimal, the importance of accurate primer design cannot be overstated. The target of this study was to create an effective procedure for λ-PCR primer design that ensures accurate cloning reactions. Additionally, synthetic ribosome binding sites (RBS) were included in the primer designs to test heterologous protein expression of the cyan fluorescent reporter with different RBS strengths. These RBS sequences were designed with an online tool, the RBS Calculator. A chimeric primer design procedure for λ-PCR was developed and shown to effectively create primers used for accurate cloning with λ-PCR; this method was used to design primers for CFP cloning in addition to two enzymes cloned in the Senger lab. A total of five strains of BL21(DE3) with pET28a + CFP were constructed, each with the same cyan fluorescent protein (CFP) reporter but different RBS sequences located directly upstream of the start codon of the CFP gene. Expression of the protein was measured using both whole-cell and cell-free systems to determine which system yields higher protein concentrations. A number of other factors were tested to optimize conditions for high protein expression, including: induction time, IPTG concentration, temperature, and media (for the cell-free experiments only). Additionally, expression for each synthetic RBS sequence was investigated to determine an accurate method for predicting protein translation. NUPACK and the Salis Lab RBS Calculator were both used to evaluate the effects of these different synthetic RBS sequences. The results of the plate reader experiments with the 5 CFP strains revealed a number of factors to be statistically significant when predicting protein expression, including: IPTG concentration, induction time, and in the cell-free experiments, type of media. The whole-cell system consistently produced higher amounts of protein than the cell-free system. Lastly, contrasts between the CFP strains showed each strain's performance did not match the predictions from the RBS Calculator. Consequently, a new method for improving protein expression with synthetic RBS sequences was developed using relationships between Gibbs free energy of the RBS-rRNA complex and expression levels obtained through experimentation. Additionally, secondary structure present at the RBS in the mRNA transcript was modeled with strain expression since these structures cause deviations in the relationship between Gibbs free energy of the mRNA-rRNA complex and CFP expression.<br>Master of Science<br>Recombinant DNA technology has been used to genetically enhance organisms to produce greater amounts of a product already made by the organism or to make an organism synthesize a new product. Genes are commonly modified in organisms using cloning practices which typically involves inserting a target gene into a plasmid and transforming the plasmid into the organism of interest. A new cloning process developed in the Senger lab, λ-PCR, improves the cloning process compared to other methods due to its use of relatively inexpensive materials and high efficiency. A primary goal of this study was to develop a procedure for λ-PCR primer design that allows for accurate use of the cloning method. Additionally, this study investigated the use of synthetic ribosome binding sites to control and improve expression of proteins cloned into an organism. Ribosome binding sites are sequences located upstream of the gene that increase the molecule’s affinity for the rRNA sequence on the ribosome, bind to the ribosome just upstream of the beginning of the gene, and initiate expression of the gene. Tools have been developed that create synthetic ribosome binding sites designed to produce specific amounts of protein. For example, the tools can increase or decrease expression of a gene depending on the application. These tools, the Salis Lab RBS Calculator and NUPACK, were used to design and evaluate the effects of the synthetic ribosome binding sites. Additionally, a new method was created to design synthetic ribosome binding sites since the methods used during the design process yielded inaccuracies. Each strain of E. coli contained the same gene, a cyan fluorescent protein (CFP), but had different RBS sequences located upstream of the gene. Expression of CFP was controlled via induction, meaning the addition of a particular molecule, IPTG in this system, triggered expression of CFP. Each of the CFP strains were tested with a variety of v conditions in order to find the conditions most suitable for protein expression; the variables tested include: induction time, IPTG (inducer) concentration, and temperature. Media was also tested for the cell-free systems, meaning the strains were grown overnight for 18 hours and lysed, a process where the cell membrane is broken in order to utilize the cell’s components for protein expression; the cell lysate was resuspended in new media for the experiments. ANOVA and multiple linear regression revealed IPTG concentration, induction time, and media to be significant factors impacting protein expression. This analysis also showed each CFP strain did not perform as the RBS Calculator predicted. Modeling each strain’s CFP expression using the RBS-rRNA binding strengths and secondary structures present in the RBS allowed for the creation of a new model for predicting and designing RBS sequences.

Thesis (M.S. in Engineering Acoustics) Naval Postgraduate School, June 1995.<br>Thesis advisor(s): Anthony A. Atchley, Thomas J. Hofler. "June 1995." Includes bibliographical references. Also available online.

To date, there is a scant amount of research on the long-term benefits of exercise training for individuals with moderate to severe chronic obstructive pulmonary disease. The purpose of this study was to evaluate standardized outcomes of a six-month maintenance pulmonary rehabilitation program to determine maintenance of functional capacity. Twenty-three subjects (sixteen men, seven women) diagnosed with clinical COPD ages 30-82 (65 + 12 years) participated in the retrospective study. The subjects were referred to an eight-week comprehensive pulmonary rehabilitation program after which upon twelve subjects continued onto a maintenance program. Eleven subjects chose not to participate in the maintenance program and were given a home exercise program and were encouraged to remain active. Hemodynamic, functional, and educational measures were taken prior to entry, upon completion of the hospital program, and again six-months post-program. Outcome tests were standardized using the Indiana Society of Cardiovascular and Pulmonary Rehabilitation Outcomes Manual. Significantdifferences were found between the maintenance and non-maintenance groups for systolic blood pressure in resting, exercise, and recovery measures at six months reevaluation. Differences in oxygen saturation were also found to reach significance between the two groups during recovery from the six-minute walk test. Interestingly, duration of exercise was found to be statistically significant between the two groups as well as emergency room visits and physician visits within the last six months. The maintenance group tended to have fewer emergency room and physician visits in addition to having self-reported higher durations of exercise. In conclusion, maintenance pulmonary rehabilitation programs have been shown to maintain physical activity levels for COPD patients and as a result, fewer quality of life consequences specifically the number of hospital admissions and emergency room visits.<br>Department of Biology

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.<br>Includes bibliographical references (leaves 93-96).<br>The future of synthetic biology research hinges upon the development of accurate and inexpensive whole gene synthesis technologies. Recent advances in the purification of solid-phase manufactured oligonucleotides make it possible to manufacture whole genes by polymerase chain reaction methods. Yet, despite the improvement in laboratory methods, whole gene synthesis is not rapidly progressing because most gene design software takes an excessively naive approach to the complex problem of designing component oligonucleotides for whole gene synthesis. The synthetic biology community needs a flexible, robust and optimal primer design tool. We present the software design for a tool which designs oligonucleotides that are compatible with a wide variety of oligo purification and whole gene assembly protocols. Our design strategy uses physical sequence feature identification, optimal artificial intelligence search techniques, and sequence optimisation via intelligent codon substitution to produce near-optimal oligonucleotide arrays. We address all aspects of the oligonucleotide design problem, from physical constraints to the computational overhead involved in searching for an optimal solution, and provide an extensive set of data structures and algorithms.<br>by Amanda Victrix Allen Wozniak.<br>M.Eng.

Genes homologous to a set of known, aligned, genes can be found by screening DNA libraries with PCR. PCR primers for such screens are commonly designed via a method described by Sells and Chernoff (1995). This standard design method does not make use of information about the evolutionary relationship between the known genes. The present study investigated the efficacy of using information about evolutionary relationships (inferred from the sequence data) in the design of PCR primers. This study compares the standard primer design method (represented herein by a modified multinomial distribution) with evolutionary model based primer design methods. The primer design method that, given an alignment of known sequences with one sequence left out, assigned a higher probability, on average, to the left-out sequence, was defined as the better method. By this measure of relative performance, an evolutionary model based primer design method sensitive to states correlated across sites of a sequence, outperformed the standard method, on the alignments studied.

Made available in DSpace on 2014-12-17T14:56:06Z (GMT). No. of bitstreams: 1 KligerKFR.pdf: 1442515 bytes, checksum: b8c82b51681c5740727addb5f0eed20a (MD5) Previous issue date: 2005-04-04<br>Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior<br>It proposes a established computational solution in the development of a software to construct species-specific primers, used to improve the diagnosis of virus of plant for PCR. Primers are indispensable to PCR reaction, besides providing the specificity of the diagnosis. Primer is a synthetic, short, single stranded piece of DNA, used as a starter in PCR technique. It flanks the sequence desired to amplify. Species-specific primers indicate the well known region of beginning and ending where the polymerase enzyme is going to amplify on a certain species, i.e. it is specific for only a species. Thus, the main objective of this work is to automatize the process of choice of primers, optimizing the specificity of chosen primers by the traditional method<br>Prop?e-se uma solu??o computacional baseada no desenvolvimento de um software para construir primers esp?cie-espec?ficos, usados para melhorar o diagn?stico de viroses de planta por PCR. Primers s?o indispens?veis ? rea??o PCR, al?m de proporcionar a especificidade do diagn?stico. Um primer ? um fragmento de DNA sint?tico, curto e de fita simples, utilizado como um iniciador na t?cnica PCR que flanqueia a seq??ncia que se deseja amplificar. Primers esp?cie-espec?ficos s?o primers que s? indicam a regi?o bem conhecida de in?cio e t?rmino onde a enzima polimerase vai amplificar, de uma determinada esp?cie, ou seja, ? espec?fica para somente uma esp?cie. Assim, o objetivo principal deste trabalho ? automatizar o processo de escolha de primers, otimizando a especificidade dos primers escolhidos pelo m?todo tradicional

Thesis (S.M.)--Massachusetts Institute of Technology, Computation for Design and Optimization Program, 2007.<br>Includes bibliographical references (p. 97-99).<br>In this thesis, we study primal solutions for general optimization problems. In particular, we employ the subgradient method to solve the Lagrangian dual of a convex constrained problem, and use a primal-averaging scheme to obtain near-optimal and near-feasible primal solutions. We numerically evaluate the performance of the scheme in the framework of Network Utility Maximization (NUM), which has recently drawn great research interest. Specifically for the NUM problems, which can have concave or nonconcave utility functions and linear constraints, we apply the dual-based decentralized subgradient method with averaging to estimate the rate allocation for individual users in a distributed manner, due to its decomposability structure. Unlike the existing literature on primal recovery schemes, we use a constant step-size rule in view of its simplicity and practical significance. Under the Slater condition, we develop a way to effectively reduce the amount of feasibility violation at the approximate primal solutions, namely, by increasing the value initial dual iterate; moreover, we extend the established convergence results in the convex case to the more general and realistic situation where the objective function is convex. In particular, we explore the asymptotical convergence properties of the averaging sequence, the tradeoffs involved in the selection of parameter values, the estimation of duality gap for particular functions, and the bounds for the amount of constraint violation and value of primal cost per iteration. Numerical experiments performed on NUM problems with both concave and nonconcave utility functions show that, the averaging scheme is more robust in providing near-optimal and near-feasible primal solutions, and it has consistently better performance than other schemes in most of the test instances.<br>by Jing Ma.<br>S.M.

Thesis: S.M. in Engineering and Management, Massachusetts Institute of Technology, Engineering Systems Division, 2015.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (pages 138-148).<br>About 5 million cases of skin cancer will be diagnosed in the United States in 2015, making skin cancer the most common cancer diagnosis in the United States. About 13,000 Americans will die from skin cancer in 2015. Often skin cancers are diagnosed at later stages, are expensive to treat, and result in fatalities. For melanoma, responsible for 75% of skin cancer deaths, the overall 5-year survival rate is 98% for skin lesions detected in their early stages, and this survival rate drops to 16% after the disease has spread to other organs. If these fatal skin cancers were detected earlier they would cost less to treat and result in better patient outcomes. There is no single resource available that maps the full state of the skin cancer care delivery, and most current views are colored by a stakeholder's perspective. We connected with stakeholders at different levels of the skin cancer care delivery system to create an overall picture of the system's current state and to identify gaps in care. We interviewed 9 skin cancer patients, 8 primary care physicians, and 9 dermatologists. Through this research, we discovered that the structure of how skin cancer care is delivered promotes opportunities to miss skin cancers and includes many barriers between initial cancer suspicion and disease diagnosis. Frequently patients do not evaluate themselves for skin cancer, primary care physicians have low accuracy in identifying skin cancers, and dermatologists manage a very small portion of the population who develop skin cancers. At a higher level, feedback between patients and physicians is frequently lost in the system, physicians are not accountable for patient outcomes, and patient health is not supported by the system until the patient identifies a health issue and acts to remedy the issue. To close these system gaps, we identified technologies, including micro-biopsies and electrical impedance spectrometry, which could be used to improve rates of skin cancer identification and promote better patient health outcomes. Additionally, we recommend physicians find a way to collaborate on cases, identify their own weaknesses in assessment, and capture patient outcomes to relay incorrect assessments to other physicians to improve future patient care.<br>by Susan Conover.<br>S.M. in Engineering and Management