Development of a Novel Bistable DNA Sensor for Anti-HIV Drug Discovery and Re-engineering of Recombinant Cyclin T1-Tat Protein with SUMO Fusion in Escherichia Coli

This dissertation focuses on the interaction of proteins and nucleic acids and their applications. It includes two projects: I: Development of a Novel Bistable DNA Sensor for Anti-HIV Drug Discovery and II. Re-engineering of Recombinant Cyclin T1-Tat Protein with SUMO Fusion in Escherichia Coli.I: Development of a Novel Bistable DNA Sensor for Anti-HIV Drug Discovery Screening drug compounds targeting HIV-1 NCp7 provide attractive candidates for new anti-retroviral therapeutics because of the highly conserved nature of the zinc fingers in NCp71 in selecting and packaging RNA in the HIV-1 life cycle. The unique 3-segment, reversible switch for high throughput screening (HTS) drug targets will be for the HIV-1 nucleocapsid (NC) protein. The Probe is a natural binding element for the NCp7 protein target or, in our case, an aptamer hairpin with loop sequence, TGTGGT, having a nano-molar affinity (Kd=16nM).2 Toggle is a damaged probe where the target-binding sequences are replaced with other bases. Cover is a mostly complementary strand for the probe and the toggle. A hairpin loop forms around the 5Me-dC-brancher in both the ON and OFF forms. Using Visual OMPTM simulation, the following two potential switch molecules (NM-1 and NM-2) were designed and successfully synthesized using a one-step ligation method with at least 90% purity as judged by mass spectrometry. Then fluorescence measurements using NM-1 and NM-2 with NCp7 protein were analyzed to demonstrate proof-of-principle for 3-segment nucleic acid switches. Increasing [NC] causes a dramatic decrease in CY3 fluorescence. The ON/OFF contrast ratio of NM-1 and NM-2 are 2.6 and 3.2 showing the feasibility of 3-segment switches being used to further modify the design of HTS switches for the HIV-1 NC. II. Re-engineering of Recombinant Cyclin T1-Tat Protein with SUMO Fusion in Escherichia Coli. Due to increasing drug resistance for current antiretroviral therapeutic (ART) treatments, it is important to add drugs targeting other aspects of HIV-1 infection to manage AIDS. Tat (trans-activator of transcription) protein up-regulates the transcription of viral-specific proteins by a factor of 1,0003, which makes Tat a very attractive drug target. High-level expression and purification of recombinant GST-CycT1(249-280)-linker(25aa)-Tat(1-101) fusion protein in Escherichia coli (E. coli) was challenging because CycT1-Tat forms inclusion bodies making it difficult to purify and obtain a high concentration of active CycT1-Tat. A commercially available pET-SUMO cloning vector was introduced for the high-level expression of four CycT1-Tat chimeras, F1-F4. The gene associated with the protein sequence was purchased from IDT and SUMO-CycT1-Tat (F1) fusion plasmid was prepared and transformed in E. coli BL21 (DE3). By inducing with IPTG, His6-SUMO-CycT1-Tat fusion protein was able to promote soluble expression making it more efficient to purify CycT1-Tat (F1) compared to GST fusion tag protein. The molecular weight of purified CycT1-Tat was confirmed with mass spectrometry (MALDI-TOF). For initial characterization of the TAR-CycT1-Tat complex, an Electrophoretic Mobility Shift Assay (EMSA) was carried out with partially purified CycT1-Tat protein using TAR-31 and truncated versions that altered the hairpin loop (TAR-H24) and deleted the bulge loop (TAR-B25). A TAR-CycT1-Tat complex was formed and a band shift was observed in the binding of CycT1-Tat to TAR-31 and a lower affinity complex with TAR-B25, but TAR-H24 did not bind

Semantic Based Information Retrieval System Using Modified Inverse Document Frequency

Today, Information Retrieval (IR) provides users with documents that will satisfy their information need. Word sense ambiguity is a cause of poor performance in IR system. IR performance will be increased if ambiguous words can be correctly disambiguated. Word Sense disambiguation (WSD) is the task to assign the correct meaning to such ambiguous words based on the surrounding context. Various senses provided by WSD process have been used as semantics for indexing the documents to aid the information retrieval system. K-Nearest Neighbour (KNN) is used for effective text classification in WSD process and the Vector Space Model (VSM) is used for IR process. The cosine similarity method is used in both KNN and VSM to calculate the similarity in which term frequency and inverse document frequency (TF-IDF) scheme is used to calculate the weight of each word. There is a challenge that the original TF-IDF scheme eliminates the related senses although there is a related sense. This paper thus proposes the modified TF-IDF method, so called TF-MIDF, to solve the no-relevant problem by modifying the IDF equation to improve the accuracy of IR performance. By comparing the performance between the original IDF scheme and the MIDF scheme, the average precision results of the original TF-IDF method is 71% and the average precision results of the TF-MIDF is 80%. Therefore, the proposed methodology is more precise than the original method while retrieving the relevant documents of the required information

Progress Report Integrated Seed Sector Development Myanmar: 2019

This report can also be downloaded from : http://www.d-portal.org

The Effects of Temperature Stress on the Quality and Yiel d of Soya Bean [ (Glycine max L.) Merrill. ]

Reproductive development and growth by crops is especially important for human welfare because we depend on crop fruits and seeds, directly and indirectly, for most of our food. Seed production by crops depends on vegetative development and growth, development of pollen and egg, pollination, and fertilization. The final size of individual seeds generally hinges on cell division within the embryo, followed by seed filling and maturation process. Environmental conditions prior to the shift to reproductive development usually affect by influencing photosynthesis per unit of leaf area, canopy development and interception of solar radiation per unit of ground area, and initiation of potential fruiting site; a strong positive correlation between canopy photosynthesis per unit of ground area and seed number exists for most crops. For many crops where they are now grown, an increase of just a few °C significantly reduce yield. Dependence on soybeans for food and feed has increased rapidly in many countries during the last 30 years. Nutritionists believe that utilization of soybeans sh ould continue to increase in order to provide better nourishment for people throughout the world. For this goal to be realize, present produc tion areas must produce more soybeans and new production areas must be established

The Relationship between Teacher Empowerment and Organizational Commitment

The purpose of this study was to examine the relationship between teacher empowerment and organizational commitment in selected high schools and branch high schools. The subjects of this study consisted of all teachers who had at least one year of service at current schools. Quantitative descriptive research method was utilized for this study. As instruments, School Participant Empowerment Scale (SPES) developed by Short and Rinehart (1992, cited in Kirika, 2011), and Organizational Commitment Questionnaires (OCQ) developed by Mowday et al. (1979, cited in Kirika, 2011) were used. The Statistical Package for Social Sciences (SPSS Software) was used to analyze the obtained data. School Participant Empowerment Scale (SPES) was measured by six dimensions: decision making, professional growth, status, self-efficacy, autonomy and impact. Descriptive statistics revealed that teachers from all selected high schools and branch high schools possessed high levels of teacher empowerment. Descriptive statistics revealed that there were high levels of organizational commitment in selected schools. According to the results, all teachers from selected high schools and branch high schools perceived that they had high level of organizational commitment. Pearson correlation (r) described a statistically significant, positive relationship between teacher empowerment and organizational commitment

A STUDY ON SERVICE QUALITY OF SAKURA HOSPITAL IN YANGON

This paper aims to explore influencing service quality dimensions on customer satisfaction on Sakura Hospital and then to find out the effect of customer satisfaction on their loyalty on Sakura Hospital in Yangon. A sample of 120 respondents is chosen every five inpatients and outpatients at Saturdays and Sundays from first September to thirty September 2019 using systematic sampling method. Then analytical method and regression analysis were done in SPSS to analyze the data. The result of the study found that the Sakura Hospital get customer loyalty through their customer satisfaction on the service quality of the hospital. Among three types of service quality dimensions, customer get satisfaction through the staff conduct and staff’s problem solving of the interaction service quality, Cleanliness, availability of facility, information, ambient and design of the physical environment quality, valance and waiting time of the outcome quality. Among five types of customer satisfaction, Sakura Hospital get the customer loyalty from the customer satisfaction of reliability, responsiveness and empathy. Therefore, it is recommended the management team should give attention to the reliability, responsiveness and empathy of the doctors, nurses and staff of the hospital to improve the customer’s satisfaction that can get customer loyalty

Mining the Text using Association Rule Mining Technique

As the amount of text available in electronic form continues to increase at alarming rate, the tools to manage these textual resources effectively will become critical. Information Retrieval System tries to save the users access time by classifying the documents and clustering the documents because users spend a lot of time to find documents or information from texts. Therefore, text mining is the most popular and it is necessary to solve this problem. The largest amount of work in text mining has been in the areas of categorization, classification and clustering of documents. Text mining has many methods to find the useful information. Among these methods, association rule mining is very suitable for finding the most frequent words that occur in the document collection. Association rule analysis is the task of discovering association rules that occur frequently in a given text sets. Our proposed system had been developed by applying the preprocessing steps of text mining system and Apriori algorithm for finding the pairs of most frequent words. These frequent words are associated with each other and they can provide the trained texts for the document classification

Design of Six-phase Induction Motor

When the high current per phase for three-phase motors has been a problem, the use of six-phase induction motors is one of the alternatives in industry. The six-phase machine is a particular case of split-phase or dual-stator machine. It can be built by splitting a three-phase winding into two groups. These three-phase groups are shifted by 30 electrical degrees from each other. In this paper, the modified design of a six-phase induction motor was described. And then the performance testing of t-hp six-phase stator winding, squirrel-cage rotor induction motor was presented in details

Optimal Route Planning in Yangon Transportation Network

In recent year, the transportation networksare becoming more and more complex andnavigation services are increasingly necessaryfor the people living in the modern society. Oneof the requirements in the cities of Myanmar is tofulfill the effective transportation and navigationservice not only for the local people but also forthe foreigner who are not familiar withTransportation System in Myanmar. In thisproposed system, optimal path will berecommended for the person who will ride thebus from its location to nearest bus stop andsuggest the shortest path to the destination busstop. Modified Dijkstra Algorithm will be used tocalculate the optimal path by creating the graphdatabase for the Yangon transportation networkon the mobile device

A STUDY ON THE CAUSES OF FLUCTUATIONS IN BIRTH RATE AND DEATH RATE IN YANGON REGION

This thesis examines the causes of fluctuations in birth rate and death rate in Yangon Region. Descriptive method is used in this study. Both Primary and Secondary Data are collected. A sample of 200 households is asked from three townships which are Thakayta, Sangyoung and South Dagon by using face to face interviews via structured questionnaire. The sampling method applied in this study is two-step sampling. The cluster sampling is primarily used for selection of the townships in Yangon. Primary data is collected through the use of Personal Interview and questionnaire is with mothers of different age and level of education. What was found out in this study is that despite the population growth in Yangon Region, the primary reasons for having low birth and death rate were higher cost of living and higher cost of rearing babies, and married women having better education and better health knowledge. According to the result getting from focused group discussion, some married couples were worried about the divorce they might face in future while some said they were waiting until the time when they are ready to raise a child