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  • 1
    Description: Functional genomics uses system-wide approaches to generate genome-scale data and to describe gene functions. Recent genome-wide transcriptome studies have observed a great number of unexpected transcripts internal or antisense to known genes in bacteria and archaea, but the function of these unexpected transcripts is unclear. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the evolutionary conservation of unexpected transcriptional start sites (TSSs).In the first part of this thesis, we present the methodology to generate a set of high-confidence TSSs. Using high-resolution tiling microarrays and 5’-end RNA sequencing, combined with a semi-supervised machine learning approach, we identified 2,531 TSSs in S. oneidensis MR-1. We then classified them based on their relative positive compared with the current gene model. 18% of the identified TSSs were located inside coding sequences (CDSs).In the second part of this thesis, we present the conservation study of the high-confidence TSSs identified in MR-1. Comparative transcriptome analysis with seven additional Shewanella species revealed that the majority (76%) of the TSSs within the upstream regions of annotated genes (gTSSs) were conserved. 30% of the TSSs that were inside genes and on the sense strand (iTSSs) were also conserved. Sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are under purifying selection. Furthermore, conserved iTSSs are enriched for regulatory motifs, suggesting that they are regulated. Combining with the genome-wide mutagenesis data, we show that having internal promoters significantly eliminate polar effects which are expected if the internal promoters are not functional.In contrast, the transcription of antisense TSSs located inside CDSs (aTSSs) were significantly less likely to be conserved (22%). However, aTSSs whose transcription was conserved often have conserved promoter motifs and drive the expression of nearby genes. Overall, our findings demonstrate that some internal TSSs are conserved and drive protein expression despite their unusual locations, but the majority are not conserved and may reflect noisy initiation of transcription rather than a biological function.In the last part of the thesis, I present the development of a high-throughput assay, bacterial two-hybrid sequencing (B2H-seq), to construct protein interactome in bacteria. This technique, if successful, will complement the existing large-scale mutant fitness profiling method in Arkin lab, and improve the gene function annotation.
    Keywords: Biology; Genetics; Microbiology
    Source: eScholarship
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  • 2
    In: Nature Biotechnology, 2012, Vol.30(10), p.1002
    Description: Complex interactions among genetic components often result in variable systemic performance in designed multigene systems (l), (2). Using the bacterial clustered regularly interspaced short palindromic repeat (CRISPR) pathway (3), (4) we develop a synthetic RNA-processing platform, and show that efficient and specific cleavage of precursor mRNA enables reliable and predictable regulation of multigene operons. Physical separation of linked genetic elements by CRISPR-mediated cleavage is an effective strategy to achieve assembly of promoters, ribosome binding sites, cis-regulatory elements, and riboregulators into single- and multigene operons with predictable functions in bacteria. We also demonstrate that CRISPR-based RNA cleavage is effective for regulation in bacteria, archaea and eukaryotes. Programmable RNA processing using CRISPR offers a general approach for creating context-free genetic elements and can be readily used in the bottom-up construction of increasingly complex biological systems in a plug-and-play manner.
    Keywords: RNA Processing – Research ; Gene Expression – Research;
    ISSN: 1087-0156
    E-ISSN: 15461696
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  • 3
    In: PLoS ONE, 2017, Vol.12(2)
    Description: Genetic interaction mapping is useful for understanding the molecular basis of cellular decision making, but elucidating interactions genome-wide is challenging due to the massive number of gene combinations that must be tested. Here, we demonstrate a simple approach to thoroughly map genetic interactions in bacteria using microfluidic-based single cell sequencing. Using single cell PCR in droplets, we link distinct genetic information into single DNA sequences that can be decoded by next generation sequencing. Our approach is scalable and theoretically enables the pooling of entire interaction libraries to interrogate multiple pairwise genetic interactions in a single culture. The speed, ease, and low-cost of our approach makes genetic interaction mapping viable for routine characterization, allowing the interaction network to be used as a universal read out for a variety of biology experiments, and for the elucidation of interaction networks in non-model organisms.
    Keywords: Research Article ; Biology And Life Sciences ; Research And Analysis Methods ; Biology And Life Sciences ; Biology And Life Sciences ; Research And Analysis Methods ; Biology And Life Sciences ; Research And Analysis Methods ; Biology And Life Sciences ; Research And Analysis Methods ; Engineering And Technology ; Biology And Life Sciences ; Biology And Life Sciences ; Research And Analysis Methods ; Biology And Life Sciences ; Biology And Life Sciences
    E-ISSN: 1932-6203
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  • 4
    Language: English
    In: Journal of bacteriology, 2014, Vol.196(20), pp.3643-3655
    Description: Mutant phenotypes provide strong clues to the functions of the underlying genes and could allow annotation of the millions of sequenced yet uncharacterized bacterial genes. However, it is not known how many genes have a phenotype under laboratory conditions, how many phenotypes are biologically interpretable for predicting gene function, and what experimental conditions are optimal to maximize the number of genes with a phenotype. To address these issues, we measured the mutant fitness of 1,586 genes of the ethanol-producing bacterium Zymomonas mobilis ZM4 across 492 diverse experiments and found statistically significant phenotypes for 89% of all assayed genes. Thus, in Z. mobilis, most genes have a functional consequence under laboratory conditions. We demonstrate that 41% of Z. mobilis genes have both a strong phenotype and a similar fitness pattern (cofitness) to another gene, and are therefore good candidates for functional annotation using mutant fitness. Among 502 poorly characterized Z. mobilis genes, we identified a significant cofitness relationship for 174. For 57 of these genes without a specific functional annotation, we found additional evidence to support the biological significance of these gene-gene associations, and in 33 instances, we were able to predict specific physiological or biochemical roles for the poorly characterized genes. Last, we identified a set of 79 diverse mutant fitness experiments in Z. mobilis that are nearly as biologically informative as the entire set of 492 experiments. Therefore, our work provides a blueprint for the functional annotation of diverse bacteria using mutant fitness. ; p. 3643-3655.
    Keywords: Genes ; Bacteria ; Prediction ; Phenotype ; Bacteriology ; Zymomonas Mobilis ; Mutants
    ISSN: 0021-9193
    Source: AGRIS (Food and Agriculture Organization of the United Nations)
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  • 5
    Language: English
    In: Psychiatric services (Washington, D.C.), 01 January 2017, Vol.68(1), pp.92-95
    Description: This study examined discharge planning practices by hospital providers for 17,053 psychiatric discharges in New York's statewide Medicaid program. Claims data were linked to information reported to New York State by managed behavioral health care organizations (MBHOs) conducting inpatient utilization reviews. MBHOs documented hospital providers' reports of the presence of three discharge planning practices for each discharge: communicating with an outpatient provider prior to discharge, scheduling an aftercare appointment, and forwarding a discharge summary. Hospital providers reported completing at least one of the three discharge planning practices for 85% of discharges. Individuals who received all three discharge planning practices had a higher likelihood of follow-up and kept their first outpatient follow-up visit at almost twice the speed compared with individuals who received none of the practices (hazard ratio=1.96, p〈.001). This study provided baseline information concerning routine discharge planning practices and their relationship to timeliness of care transitions.
    Keywords: Care Transitions ; Discharge Planning ; Engagement ; Hospitalization ; Inpatient Treatment ; Mental Health Systems/Hospitals ; Aftercare -- Statistics & Numerical Data ; Medicaid -- Statistics & Numerical Data ; Mental Disorders -- Therapy ; Mental Health Services -- Statistics & Numerical Data ; Patient Discharge -- Statistics & Numerical Data
    ISSN: 10752730
    E-ISSN: 1557-9700
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  • 6
    Language: English
    In: 2015 8th International Conference on Intelligent Computation Technology and Automation (ICICTA), June 2015, pp.360-363
    Description: In this paper, we propose an economic law education platform using computer and multimedia technology, and we aim to promote the teaching quality of the economic law course. Particularly, the contents of economic law course, three parts are included, that is, 1) Overview of economic law, 2) Market supervision law, and 3) Macro control law, and then 31 chapters are included in this course. Then, according to the main contents of economic law, we deisgn and implement a multimedia teaching resource sharing platform for economic law. Moreover, the proposed resource sharing platform is organized by three layers: 1) service layer, 2) management layer, and 3) resource layer. Next, we provide the flow char of the Multimedia teaching resource cloud sharing platform. Finally, to test the effectiveness of the proposed teaching resource sharing platform, we design a questionnaire. Experimental results verify that the proposed platform can effectively enhance the teaching quality of economic lar course.
    Keywords: Economics ; Education ; Multimedia Communication ; Resource Management ; Law ; Computers ; Economic Law ; Computer Science ; Multimedia Technology ; Cloud Sharing Platform ; Education ; Computer Science ; Law ; Economics
    Source: IEEE Conference Publications
    Source: IEEE Xplore
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  • 7
    Language: English
    In: Physical Review A, 3/2017, Vol.95(3)
    Description: James' effective Hamiltonian method has been extensively adopted to investigate largely detuned interacting quantum systems. This method is just corresponding to the second-order perturbation theory, and cannot be exploited to treat the problems which should be solved by using the third or higher-order perturbation theory. In this paper, we generalize James' effective Hamiltonian method to the higher-order case. Using the method developed here, we reexamine two examples published recently [Phys. Rev.Lett. 117, 043601 (2016), Phys. Rev A 92, 023842 (2015)], our results turn out to be the same as the original ones derived from the third-order perturbation theory and adiabatic elimination method respectively. For some specific problems, this method can simplify the calculating procedure, and the resultant effective Hamiltonian is more general. Comment: 5 pages, no figure, submitted to Phys. Rev. A
    Keywords: Quantum Physics;
    ISSN: 2469-9926
    E-ISSN: 2469-9934
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  • 8
    Language: English
    In: The International Journal of Advanced Manufacturing Technology, 2017, Vol.93(9), pp.3955-3966
    Description: A piston is an important part of an engine. Its shape is designed into middle-convex and varying ellipse (MCVE) to adapt to the complex working environment. The main requirements of MCVE piston machining are high frequency response, small range tool motion, and high precision. In this article, an MCVE data model is established for the piston profile design, and the turning principle and control procedure are discussed to develop a fast tool servo (FTS) system for piston turning. In the end, back propagation neural network (BPNN) and genetic algorithm (GA) are combined to optimize the process parameters in the MCVE piston machining, which includes general turning parameters and special MCVE turning parameters. Through the experiments and BPNN-GA optimization, the ellipticity error ( E ) and surface roughness ( Ra ) of all pistons met the design requirements. According to verification experiments, the optimization results of E and Ra are 3.04 and 1.204 μm, respectively, and their relative errors are 10.13 and 4.27%, respectively. It has been proved that the MCVE data model and the control design of FTS are feasible and can effectively produce MCVE piston; the BPNN-GA optimization method is obviously effective and can improve processing effect and machining efficiency.
    Keywords: MCVE ; FTS ; BPNN ; GA ; Piston machining
    ISSN: 0268-3768
    E-ISSN: 1433-3015
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  • 9
    Language: English
    In: PLoS ONE, 01 January 2013, Vol.8(12), p.e83517
    Description: BACKGROUND:Candida albicans (C. albicans), the most common human fungal pathogen, can cause fatal systemic infections under certain circumstances. Mannan-binding lectin (MBL),a member of the collectin family in the C-type lectin superfamily, is an important serum component associated with innate immunity. Toll-like receptors (TLRs) are expressed extensively, and have been shown to be involved in C. albicans-induced cellular responses. We first examined whether MBL modulated heat-killed (HK) C. albicans-induced cellular responses in phorbol 12-myristate 13-acetate (PMA)-activated human THP-1 macrophages. We then investigated the possible mechanisms of its inhibitory effect. METHODOLOGY/PRINCIPAL FINDING:Enzyme-linked immunosorbent assay (ELISA) and reverse transcriptasepolymerase chain reaction (RT-PCR) analysis showed that MBL at higher concentrations (10-20 µg/ml) significantly attenuated C. albicans-induced chemokine (e.g., IL-8) and proinflammatory cytokine (e.g., TNF-α) production from PMA-activated THP-1 cells at both protein and mRNA levels. Electrophoretic mobility shift assay (EMSA) and Western blot (WB) analysis showed that MBL could inhibit C. albicans-induced nuclear factor-κB (NF-κB) DNA binding and its translocation in PMA-activated THP-1 cells. MBL could directly bind to PMA-activated THP-1 cells in the presence of Ca(2+), and this binding decreased TLR2 and TLR4 expressions in C. albicans-induced THP-1 macrophages. Furthermore, the binding could be partially inhibited by both anti-TLR2 monoclonal antibody (clone TL2.1) and anti-TLR4 monoclonal antibody (clone HTA125). In addition, co-immunoprecipitation experiments and microtiter wells assay showed that MBL could directly bind to the recombinant soluble form of extracellular TLR2 domain (sTLR2) and sTLR4. CONCLUSIONS/SIGNIFICANCE:Our study demonstrates that MBL can affect proinflammatory cytokine and chemokine expressions by modifying C. albicans-/TLR-signaling pathways. This study supports an important role for MBL on the regulation of C. albicans-induced cellular responses.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 10
    Language: English
    In: The International Journal of Advanced Manufacturing Technology, 2017, Vol.91(1), pp.751-761
    Description: Laser welding technology for skin-stringer joints is widely used in aircraft manufacturing. Double-sided laser beam welding of skin-stringer joints is an approved method for producing defect-free welds. The main drawback for the use of single-sided welding method for T-joints is the occurrence of weld defects. To achieve dual-beam laser-welded T-joint, a dual-beam laser welding platform based on multi-axis CNC machine is set up in this paper. A novel control method of double-sided seam tracking and error compensation based on vision sensor is proposed. The weld seams on both sides of the T-joint are detected simultaneously by two vision sensors. At the same time, the welding deviation on both sides of the T-joint are compensated at real time by an independent error compensation control method based on self-adaptive fuzzy-PID controller. The result shows that the dual-beam laser welding system can achieve high precision dynamic deviation compensation in the double-sided welding process at a high speed.
    Keywords: T-joint ; Seam tracking ; Double-sided welding ; Dual laser beam ; Vision sensor ; Structure light ; Fuzzy-PID
    ISSN: 0268-3768
    E-ISSN: 1433-3015
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