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Browsing by Author "Zheng, Yi"

Now showing 1 - 3 of 3
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    Biological Agent Sensing Integrated Circuit (BASIC): A New Complementary Metal-oxide-semiconductor (CMOS) Magnetic Biosensor System
    Zheng, Yi (Virginia Tech, 2014-06-10)
    Fast and accurate diagnosis is always in demand by modern medical professionals and in the area of national defense. At present, limitations of testing speed, sample conditions, and levels of precision exist under current technologies, which are usually slow and involve testing the specimen under laboratory conditions. Typically, these methods also involve several biochemical processing steps and subsequent detection of low energy luminescence or electrical changes, all of which reduce the speed of the test as well as limit the precision. In order to solve these problems and improve the sensing performance, this project proposes an innovative CMOS magnetic biological sensor system for rapidly testing the presence of potential pathogens and bioterrorism agents (zoonotic microorganisms) both in specimens and especially in the environment. The sensor uses an electromagnetic detection mechanism to measure changes in the number of microorganisms--tagged by iron nanoparticles--that are placed on the surface of an integrated circuit (IC) chip. Measured magnetic effects are transformed into electronic signals that count the number and type of organisms present. This biosensor introduces a novel design of a conical-shaped inductor, which achieves ultra-accuracy of sensing biological pathogens. The whole system is integrated on a single chip based on the fabrication process of IBM 180 nm (CMOS_IBM_7RF), which makes the sensor small-sized, portable, high speed, and low cost. The results of designing, simulating, and fabricating the sensor are reported in this dissertation.
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    Electric Fields: A Metric for Molecular-level Understanding of Protein Mechanisms
    Zheng, Yi (Virginia Tech, 2024-05-07)
    Determining the molecular mechanisms at the origin of protein function remains a challenge due to the complex non-covalent interactions that shape their structure. Since the non-covalent interactions arise from charge fluctuations, electric fields can be used as a tool to quantify the interactions between a target and its environment. The contribution of each component of the system is reflected in the direction and strength of the electric field exerted on the target, which can be calculated from molecular dynamics simulations. The interactions experienced by ligands in enzymatic active sites determine the catalytic activity of the enzyme. Ligands in synthetic enzymes lack interactions with the protein scaffold, which limit their efficiency. To substitute for the role of non-effective protein scaffold, we introduced a polar DNA fragment to the enzyme vicinity, inducing electrostatic interactions that will facilitate the reaction. We found that the introduction of a DNA fragment enhanced the original interactions between the residues in the active site and the ligand, without creating new interaction hot spots. Using electric fields, we calculated a reduction in activation energy of 2.0 kcal/mol when introducing the DNA fragment, indicating a promising avenue for catalytic improvement. Inspired by the success in using electric fields to understand enzyme catalysis in the context of electrostatic preorganization theory, we generalized these fundamental concepts to another type of proteins: voltage-gated ion channels. Our results indicate that electric fields also report on channel activity. We find an asymmetry in the number of active residues for channel function between the four domains and between the two gating motifs of the permeation pathway, with domain I being the major contributor in both cases. The importance of residues for channel activity is not a simple linear correlation of their distance with the functional motif, but a relationship dominated by non-covalent interactions. Finally, we investigate the effects of loop dynamics on enzyme product inhibition. We modify the chemical nature of the unstructured loops that obstruct the active site of DszB by glycosylating serine and threonine residues. We monitor the corresponding variations in loop dynamics and their effect on the interaction between the enzyme and the product. Overall, promising results were found using electric fields in the investigation of protein mechanisms that are mainly dominated by non-covalent interactions and provide insight into the role of the individual components in the system.
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    Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types
    Guo, Shaogui; Zheng, Yi; Joung, Je-Gun; Liu, Shiqiang; Zhang, Zhonghua; Crasta, Oswald R.; Sobral, Bruno; Xu, Yong; Huang, Sanwen; Fei, Zhangjun (2010-06-17)
    Background Cucumber, Cucumis sativus L., is an economically and nutritionally important crop of the Cucurbitaceae family and has long served as a primary model system for sex determination studies. Recently, the sequencing of its whole genome has been completed. However, transcriptome information of this species is still scarce, with a total of around 8,000 Expressed Sequence Tag (EST) and mRNA sequences currently available in GenBank. In order to gain more insights into molecular mechanisms of plant sex determination and provide the community a functional genomics resource that will facilitate cucurbit research and breeding, we performed transcriptome sequencing of cucumber flower buds of two near-isogenic lines, WI1983G, a gynoecious plant which bears only pistillate flowers, and WI1983H, a hermaphroditic plant which bears only bisexual flowers. Result Using Roche-454 massive parallel pyrosequencing technology, we generated a total of 353,941 high quality EST sequences with an average length of 175bp, among which 188,255 were from gynoecious flowers and 165,686 from hermaphroditic flowers. These EST sequences, together with ~5,600 high quality cucumber EST and mRNA sequences available in GenBank, were clustered and assembled into 81,401 unigenes, of which 28,452 were contigs and 52,949 were singletons. The unigenes and ESTs were further mapped to the cucumber genome and more than 500 alternative splicing events were identified in 443 cucumber genes. The unigenes were further functionally annotated by comparing their sequences to different protein and functional domain databases and assigned with Gene Ontology (GO) terms. A biochemical pathway database containing 343 predicted pathways was also created based on the annotations of the unigenes. Digital expression analysis identified ~200 differentially expressed genes between flowers of WI1983G and WI1983H and provided novel insights into molecular mechanisms of plant sex determination process. Furthermore, a set of SSR motifs and high confidence SNPs between WI1983G and WI1983H were identified from the ESTs, which provided the material basis for future genetic linkage and QTL analysis. Conclusion A large set of EST sequences were generated from cucumber flower buds of two different sex types. Differentially expressed genes between these two different sex-type flowers, as well as putative SSR and SNP markers, were identified. These EST sequences provide valuable information to further understand molecular mechanisms of plant sex determination process and forms a rich resource for future functional genomics analysis, marker development and cucumber breeding.