Local assembly and pre-mRNA splicing analyses by high-throughput sequencing data

Next generation sequencing (NGS) approaches have become one of the most widely used tools in biotechnology. With high throughput sequencing, people can analyze non-model species at an unprecedented high resolution. NGS provides fast, deep and cheap sequencing solutions, and it has been used to answer various biological questions. In this thesis, I have developed a set of tools and used them to study several interesting research topics. First, de novo whole-genome assembly is still a very challenging technical task. For eukaryotic genomes, de novo assembly typically requires computational resources with very large memory and fast processors. Instead of trying to assemble the whole genome as done in previous approaches, I focus on efficiently reconstructing the genomic regions related to the homologous protein or cDNA sequences. I have developed SRAssembler, a local assembly program using the iterative chromosome walking strategy to assemble the loci of interest directly. Second, I used high-throughput RNA sequencing (refered to as RNA-Seq) data to analyze different intron splicing models and their relative frequency of occurrence. The first mechanism I explored is the recursive splicing patterns in large introns. I have implemented a pipeline called RSSFinder, which can search for recursive sites confirmed by RNA-Seq data. My study suggests the prevalence of recursive splicing in different species. These predicted recursive sites can also be used to investigate certain diseases associated with abnormal splicing of transcripts. In addition, I have demonstrated the use of RNA-Seq data to decipher the detailed mechanisms involved in splicing and their relationship with transcription. Here I proposed mathematical models to estimate the distribution of mRNA splicing intermediates. I evaluated my models with simulated data and an Arabidopsis thaliana dataset. My results indicate that co-transcriptional splicing is widespread in Arabidopsis thaliana

Telecommunications Network Design: A Genetic Algorithm Approach

The network design to support a digital data service (DDS) is a major design issue for telecommunications organizations. Typically, the DDS network consists of three components - hubs, end-offices, and customer locations. The hubs are the primary nodes that form the backbone infrastructure. The customers are connected by leased lines to the local end-office and the end- offices are in turn connected to the hubs. Typically, the customers are always connected to one end-office and each end-office is connected to one hub or node, thereby creating a star topology in the local access network. There are costs involved in setting up and operating the hub, the links connecting the hubs, links from the end-office to hub, and links from the customer to the end- office. The network designer is primarily interested in designing a network infrastructure that meets the customers’requirements at minimum cost

A Novel Approach for Data Encryption Depending on User Location

The wide spread of WLAN and the popularity of mobile devices increases the frequency of data transmission between information system and mobile user. However, most of the data encryption technology is location-independent. An encrypted data can be decrypted anywhere. The encryption technology cannot restrict the location of data decryption. In order to meet the demand of data transmission in the future, a location-dependent approach, called location-dependent data encryption algorithm (LDEA), is proposed in this paper. A target latitude/longitude coordinate is determined firstly. The coordinate is incorporated with a random key for data encryption. The receiver can only decrypt the ciphertext when the coordinate acquired from GPS receiver match with the target coordinate. However, current GPS receiver is inaccuracy and inconsistent. The location of a mobile user is difficult to exactly match with the target coordinate. A toleration distance (TD) is also designed in LDEA to increase its practicality. The security analysis shows that the probability to break LDEA is almost impossible since the length of the random key is adjustable. A prototype is also implemented for experimental study. The results show that the ciphertext can only be decrypted under the restriction of TD. It illustrates that LDEA is effective and practical for data transmission to mobile users

Relationships between stress, coping and depressive symptoms among overseas university preparatory Chinese students: a cross-sectional study

<p>Abstract</p> <p>Background</p> <p>Mental health problems in young people are an important public health issue. Students leaving their hometown and family at a young age to pursue better educational opportunities overseas are confronted with life adjustment stress, which in turn affects their mental health and academic performance. This study aimed to examine the relationships among stress, coping strategies, and depressive symptoms using the stress coping framework in overseas Chinese university preparatory students in Taiwan.</p> <p>Methods</p> <p>A cross-sectional study was conducted at an overseas Chinese university preparatory institute in Taiwan. Of enrolled overseas Chinese university preparatory students at 2009, 756 completed a structured questionnaire measuring stress, strategies for coping with it, and the Center for Epidemiologic Studies Depression Scale.</p> <p>Results</p> <p>High levels of stress significantly predicted the adoption of active, problem-focused coping strategies (<it>R</it>²= 0.13<!-- entity --><it>, p </it>< .01) and passive, emotion-focused coping strategies (<it>R</it>²= 0.24<!-- entity --><it>, p </it>< .01). Acceptable CFI, SRMR, and RMSEA values from the structural equation modeling analysis demonstrated that the model satisfactorily fits the stress coping framework, after active coping strategies were eliminated from the model. Results from the Sobel test revealed that passive coping strategies mediated the relation between stress and depressive symptoms (<it>z </it>= 8.06, <it>p </it>< .001).</p> <p>Conclusion</p> <p>Our study results suggested that stress is associated with coping strategies and depressive symptoms and passive strategies mediate the relation between stress and depressive symptoms in overseas Chinese university preparatory students.</p

Observation of interlayer phonon modes in van der Waals heterostructures

We have investigated the vibrational properties of van der Waals heterostructures of monolayer transition metal dichalcogenides (TMDs), specifically MoS2/WSe2 and MoSe2/MoS2 heterobilayers as well as twisted MoS2 bilayers, by means of ultralow-frequency Raman spectroscopy. We discovered Raman features (at 30 ~ 40 cm-1) that arise from the layer-breathing mode (LBM) vibrations between the two incommensurate TMD monolayers in these structures. The LBM Raman intensity correlates strongly with the suppression of photoluminescence that arises from interlayer charge transfer. The LBM is generated only in bilayer areas with direct layer-layer contact and atomically clean interface. Its frequency also evolves systematically with the relative orientation between of the two layers. Our research demonstrates that LBM can serve as a sensitive probe to the interface environment and interlayer interactions in van der Waals materials

Observation of Interlayer Phonon Modes in van der Waals Heterostructures

We have investigated the vibrational properties of van der Waals heterostructures of monolayer transition metal dichalcogenides (TMDs), specifically MoS2/WSe2 and MoSe2/MoS2 heterobilayers and twisted MoS2 bilayers, by means of ultralow-frequency Raman spectroscopy. We discovered Raman features (at 30–40 cm−1) that arise from the layer-breathing mode (LBM) vibration between the two incommensurate TMD monolayers in these structures. The LBM Raman intensity correlates strongly with the suppression of photoluminescence that arises from interlayer charge transfer. The LBM is generated only in bilayer areas with direct layer-layer contact and an atomically clean interface. Its frequency also evolves systematically with the relative orientation between the two layers. Our research demonstrates that the LBM can serve as a sensitive probe to the interface environment and interlayer interactions in van der Waals materials

Immobilization of enzyme and antibody on ALD-HfO2-EIS structure by NH3 plasma treatment

Thin hafnium oxide layers deposited by an atomic layer deposition system were investigated as the sensing membrane of the electrolyte-insulator-semiconductor structure. Moreover, a post-remote NH3 plasma treatment was proposed to replace the complicated silanization procedure for enzyme immobilization. Compared to conventional methods using chemical procedures, remote NH3 plasma treatment reduces the processing steps and time. The results exhibited that urea and antigen can be successfully detected, which indicated that the immobilization process is correct