Metabolic Engineering of oleaginous yeast for the production of biofuels

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2012.Cataloged from PDF version of thesis.Includes bibliographical references.The past few years have introduced a flurry of interest over renewable energy sources. Biofuels have gained attention as renewable alternatives to liquid transportation fuels. Microbial platforms for biofuel production have become an attractive option for this purpose, mitigating numerous challenges found in crop-based production. Towards this end, metabolic engineering has established itself as an enabling technology for biofuels development. In this work we investigate the strategies of metabolic engineering for developing a biodiesel production platform, utilizing the oleaginous yeast Yarrowia lipolytica as the host organism. We establish new genetic tools for engineering Y. lipolytica beginning with an expression vector utilizing the genetic features from translation elongation factor 1-a (TEF). Additionally, a complementary plasmid was developed allowing for multiple plasmid integration. Bioinformatics analysis of intronic genes in hemiascomycetous yeast also identified relationships between functional pathways and intron enrichment, chronicling the evolutionary journey of yeast species. Next gene targets were examined within the lipid synthesis pathway: acetyl-coA carboxylase (ACC), delta9-desaturase (D9), ATP citrate lyase (ACL), and diacylglycerol acyltransferase (DGA). A combinatorial investigation revealed the order of contribution to lipid overproduction (from strongest to weakest): DGA, ACC, D9, ACL. Scale-up batch fermentation of selected strains revealed exceptionally high lipid accumulation and yield. These results demonstrate the balance between cellular growth and lipid production which is being modified through these genetic manipulations. We next explored utilization of alternative substrates to expand the capabilities and utility of Y. lipolytica. For xylose, a prevalent substrate in cellulosic feedstocks, expression of the redox pathway from Scheffersomyces stipitis and adaptation led to successful substrate utilization. Through the use of cofermentation, growth and productivity on xylose was improved dramatically with xylose-to-lipids conversion successfully demonstrated. For acetate, a potentially useful substrate for electrofuel production, lipid production using our strongest performing strain resulted in high lipid accumulation and yield. From this study, metabolic engineering of Y. lipolytica was successfully used to achieve exceptional lipid overproduction from a variety of substrates. Our genetic tools and recombinant strains establish a strong platform for the study and development of microbial processes for the production of biofuels.by Mitchell Tai.Ph.D

Controlling Locomotion of a Robotic Leg

Dr. Xing and Professor Refvem are working to research and develop a quadruped robot that is capable of basic movements including walking, running, and jumping. As senior project group F-11, we are joining a team of engineers to assist in the development of the quadruped. Our team was tasked with creating a mathematical model, designing a control method, and implementing that control method for the quadruped\u27s legs in Simulink. This will allow both current and future students to understand the response of the system and provide a building point for future researchers to create working quadrupedal robots. This report documents our research and cumulative work to reach our goals. The report highlights our final design for the controller loop, our implementation process for each controller component, and our design verification tests to justify our work

Evidence of Self-Directed Learning on a High School Robotics Team

Self-directed learning is described as an individual taking the initiative to engage in a learning experience while assuming responsibility to follow through to its conclusion. Robotics competitions are examples of informal environments that can facilitate self-directed learning. This study examined how mentor involvement, student behavior, and physical workspace contributed to self-directed learning on one robotics competition team. How did mentors transfer responsibility to students? How did students respond to managing a team? Are the physical attributes of a workspace important? The mentor, student, and workplace factors captured in the research showed mentors wanting students to do the work, students assuming leadership roles, and the limited workspace having a positive effect on student productivity

Obesity and the microvasculature

Overweight and obesity are thought to significantly influence a person's risk of cardiovascular disease, possibly via its effect on the microvasculature. Retinal vascular caliber is a surrogate marker of microvascular disease and a predictor of cardiovascular events. The aim of this systematic review and meta-analysis was to determine the association between body mass index (BMI) and retinal vascular caliber. Relevant studies were identified by searches of the MEDLINE and EMBASE databases from 1966 to August 2011. Standardized forms were used for data extraction. Among over 44,000 individuals, obese subjects had narrower arteriolar and wider venular calibers when compared with normal weight subjects, independent of conventional cardiovascular risk factors. In adults, a 1 kg/m(2) increase in BMI was associated with a difference of 0.07 μm [95% CI: -0.08; -0.06] in arteriolar caliber and 0.22 μm [95% CI: 0.21; 0.23] in venular caliber. Similar results were found for children. Higher BMI is associated with narrower retinal arteriolar and wider venular calibers. Further prospective studies are needed to examine whether a causative relationship between BMI and retinal microcirculation exists

How instructions modify perception: An fMRI study investigating brain areas involved in attributing human agency

Behavioural studies suggest that the processing of movement stimuli is influenced by beliefs about the agency behind these actions. The current study examined how activity in social and action related brain areas differs when participants were instructed that identicalmovement stimuli were either human or computer generated.Participants viewed a series of point-light animation figures derived frommotion-capture recordings of amoving actor, while functional magnetic resonance imaging (fMRI) was used to monitor patterns of neural activity. The stimuli were scrambled to produce a range of stimulus realism categories; furthermore, before each trial participants were told that they were about to view either a recording of human movement or a computersimulated pattern of movement. Behavioural results suggested that agency instructions influenced participants' perceptions of the stimuli. The fMRI analysis indicated different functions within the paracingulate cortex: ventral paracingulate cortex was more active for human compared to computer agency instructed trials across all stimulus types, whereas dorsal paracingulate cortex was activated more highly in conflicting conditions (human instruction, lowrealismor vice versa). These findings support the hypothesis that ventral paracingulate encodes stimuli deemed to be of human origin,whereas dorsal paracingulate cortex is involvedmore in the ascertainment of human or intentional agency during the observation of ambiguous stimuli. Our results highlight the importance of prior instructions or beliefs on movement processing and the role of the paracingulate cortex in integrating prior knowledge with bottom-up stimuli

Overcoming controllability problems in distributed testing from an input output transition system

This is the Pre-print version of the Article. The official published version can be accessed from the link below - Copyright @ 2012 Springer VerlagThis paper concerns the testing of a system with physically distributed interfaces, called ports, at which it interacts with its environment. We place a tester at each port and the tester at port p observes events at p only. This can lead to controllability problems, where the observations made by the tester at a port p are not sufficient for it to be able to know when to send an input. It is known that there are test objectives, such as executing a particular transition, that cannot be achieved if we restrict attention to test cases that have no controllability problems. This has led to interest in schemes where the testers at the individual ports send coordination messages to one another through an external communications network in order to overcome controllability problems. However, such approaches have largely been studied in the context of testing from a deterministic finite state machine. This paper investigates the use of coordination messages to overcome controllability problems when testing from an input output transition system and gives an algorithm for introducing sufficient messages. It also proves that the problem of minimising the number of coordination messages used is NP-hard

Enclosing a pen reduced time to response to questionnaire mailings

OBJECTIVES: To assess the effectiveness of including a pen in postal questionnaires on response rate, necessity of reminders, time to response, and completeness of response to the primary outcome question (POQ).   STUDY DESIGN AND SETTING: A two-arm randomized controlled trial (RCT) embedded within the screening of older women for prevention of fracture trial (SCOOP). Women, aged 70-75 years, were randomized to receive a pen with their questionnaire (n = 3,826) or to receive the questionnaire alone (n = 3,829). The results were combined with another embedded RCT in a meta-analysis.   RESULTS: A response rate of 92.4% was observed in the pen group compared with 91.3% in the control group (odds ratio [OR] = 1.16; 95% confidence interval [CI]: 0.98, 1.37; P = 0.08). There was a difference in reminders required (OR = 0.88; 95% CI: 0.79, 0.98; P = 0.02), time to response (hazard ratio = 1.06; 95% CI: 1.01, 1.11; P = 0.01) and some difference in the completeness of response to the POQ (OR = 1.18; 95% CI: 1.00, 1.39; P = 0.05). The pooled OR from the meta-analysis for response rate was 1.21 (95% CI: 1.05, 1.39; P = 0.01).   CONCLUSION: Inclusion of a pen with postal questionnaires potentially has a positive impact on response rates and the number of reminders required. There may be some reduction in time to response. Studies of different participant groups are needed to test the effectiveness over more diverse populations

Diffusing an Innovation: Clinician Perceptions of Continuous Predictive Analytics Monitoring in Intensive Care

Background The purpose of this article is to describe neonatal intensive care unit clinician perceptions of a continuous predictive analytics technology and how those perceptions influenced clinician adoption. Adopting and integrating new technology into care is notoriously slow and difficult; realizing expected gains remain a challenge. Methods Semistructured interviews from a cross-section of neonatal physicians (n ¼ 14) and nurses (n ¼ 8) from a single U.S. medical center were collected 18 months following the conclusion of the predictive monitoring technology randomized control trial. Following qualitative descriptive analysis, innovation attributes from Diffusion of Innovation Theory-guided thematic development. Results Results suggest that the combination of physical location as well as lack of integration into work flow or methods of using data in care decisionmaking may have delayed clinicians from routinely paying attention to the data. Once data were routinely collected, documented, and reported during patient rounds and patient handoffs, clinicians came to view data as another vital sign. Through clinicians’ observation of senior physicians and nurses, and ongoing dialogue about data trends and patient status, clinicians learned how to integrate these data in care decision making (e.g., differential diagnosis) and came to value the technology as beneficial to care delivery. Discussion The use of newly created predictive technologies that provide early warning of illness may require implementation strategies that acknowledge the risk–benefit of treatment cliniciansmust balance and take advantage of existing clinician trainingmethods

Levels of acute phase proteins remain stable after ischemic stroke

Background: Inflammation and inflammatory biomarkers play an important role in atherosclerosis and cardiovascular disease. Little information is available, however, on time course of serum markers of inflammation after stroke. Methods: First ischemic stroke patients ≥40 years old had levels of high-sensitivity C-reactive protein (hsCRP), serum amyloid A (SAA), and fibrinogen measured in plasma samples drawn at 1, 2, 3, 7, 14, 21 and 28 days after stroke. Levels were log-transformed as needed, and parametric and non-parametric statistical tests were used to test for evidence of a trend in levels over time. Levels of hsCRP and SAA were also compared with levels in a comparable population of stroke-free participants. Results: Mean age of participants with repeated measures (n = 21) was 65.6 ± 11.6 years, and 13 (61.9%) were men, and 15 (71.4%) were Hispanic. Approximately 75% of patients (n = 15) had mild strokes (NIH Stroke Scale score 0–5). There was no evidence of a time trend in levels of hsCRP, SAA, or fibrinogen for any of the markers during the 28 days of follow-up. Mean log(hsCRP) was 1.67 ± 1.07 mg/L (median hsCRP 6.48 mg/L) among stroke participants and 1.00 ± 1.18 mg/L (median 2.82 mg/L) in a group of 1176 randomly selected stroke-free participants from the same community (p = 0.0252). Conclusion: Levels of hsCRP are higher in stroke patients than in stroke-free subjects. Levels of inflammatory biomarkers associated with atherosclerosis, including hsCRP, appear to be stable for at least 28 days after first ischemic stroke