467 research outputs found

    Digitalization and Development

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    This book examines the diffusion of digitalization and Industry 4.0 technologies in Malaysia by focusing on the ecosystem critical for its expansion. The chapters examine the digital proliferation in major sectors of agriculture, manufacturing, e-commerce and services, as well as the intermediary organizations essential for the orderly performance of socioeconomic agents. The book incisively reviews policy instruments critical for the effective and orderly development of the embedding organizations, and the regulatory framework needed to quicken the appropriation of socioeconomic synergies from digitalization and Industry 4.0 technologies. It highlights the importance of collaboration between government, academic and industry partners, as well as makes key recommendations on how to encourage adoption of IR4.0 technologies in the short- and long-term. This book bridges the concepts and applications of digitalization and Industry 4.0 and will be a must-read for policy makers seeking to quicken the adoption of its technologies

    A Multi-Omics Analysis of Transcription Control by BRD4

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    RNA polymerase II (Pol II) regulation during early elongation has emerged as a regulatory hub in the gene expression of multicellular organisms. Prior research links the BRD4 protein to this control point, regulating the release of paused Pol II into productive elongation. However, the exact roles and mechanisms by which BRD4 influences this and potentially other post-initiation regulatory processes remain unknown. This study combines rapid BRD4 protein degradation and multi-omics approaches, including nascent elongating transcript sequencing (NET-seq), to uncover BRD4’s direct protein functions. Applying NET-seq in comparative studies required experimental adaptations. First, analyses with spiked-in mouse cells proved essential for reliable normalization. Second, the study identified a disproportional enrichment of a chromatin-associated RNA class as NET-seq’s major limitation. Incorporating an additional enrichment step solved this problem and significantly increased Pol II coverage. The resulting high-sensitivity NET-seq method confirmed BRD4’s proposed role in early elongation by revealing a global defect in Pol II pause release upon BRD4 degradation. Observations from proteomics and chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments suggest that the failed recruitment of Pol II-associated factors (PAF) causes an assembly defect of a competent elongation complex. Interestingly, the elongation defect also affected transcribed enhancers. Pol II occupancy increased in a region proximal to the enhancer center, strikingly similar to the impaired Pol II pause release at genes. An integrated multi-omics analysis that included genome-wide 3D genome information revealed reduced interactions between these enhancers and other regulatory regions. Another unexpected result was the widespread Pol II readthrough transcription quantified by the developed readthrough index, revealing an apparent transcriptional termination defect. The implementation of long-read nascent RNA-sequencing (nascONT-seq) combined with a 3’-RNA cleavage efficiency test detected impaired 3’-RNA processing. Notably, those 3’-RNA cleavage defects correlated with the observed termination defects. A potential explanation is the BRD4-dependent recruitment of general 3’-RNA processing factors to the 5’-control region. These observations start to establish regulatory links between 5’ and 3’ control that require further validation. Overall, the results indicate a general BRD4-dependent 5’ elongation control point required for 3’-RNA processing and termination

    Understanding host-microbe interactions in maize kernel and sweetpotato leaf metagenomic profiles.

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    Functional and quantitative metagenomic profiling remains challenging and limits our understanding of host-microbe interactions. This body of work aims to mediate these challenges by using a novel quantitative reduced representation sequencing strategy (OmeSeq-qRRS), development of a fully automated software for quantitative metagenomic/microbiome profiling (Qmatey: quantitative metagenomic alignment and taxonomic identification using exact-matching) and implementing these tools for understanding plant-microbe-pathogen interactions in maize and sweetpotato. The next generation sequencing-based OmeSeq-qRRS leverages the strengths of shotgun whole genome sequencing and costs lower that the more affordable amplicon sequencing method. The novel FASTQ data compression/indexing and enhanced-multithreading of the MegaBLAST in Qmatey allows for computational speeds several thousand-folds faster than typical runs. Regardless of sample number, the analytical pipeline can be completed within days for genome-wide sequence data and provides broad-spectrum taxonomic profiling (virus to eukaryotes). As a proof of concept, these protocols and novel analytical pipelines were implemented to characterize the viruses within the leaf microbiome of a sweetpotato population that represents the global genetic diversity and the kernel microbiomes of genetically modified (GMO) and nonGMO maize hybrids. The metagenome profiles and high-density SNP data were integrated to identify host genetic factors (disease resistance and intracellular transport candidate genes) that underpin sweetpotato-virus interactions Additionally, microbial community dynamics were observed in the presence of pathogens, leading to the identification of multipartite interactions that modulate disease severity through co-infection and species competition. This study highlights a low-cost, quantitative and strain/species-level metagenomic profiling approach, new tools that complement the assay’s novel features and provide fast computation, and the potential for advancing functional metagenomic studies

    Mechanisms contributing to RNA localization and translation: study of neuronal zipcodes in primary cortical neurons, and translational changes in neurodegeneration

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    The regulation of gene expression in terms of space and time is governed by the distribution of RNA and proteins within a cell. This tightly controlled regulation is necessary for mediating cellular development and function. The localization of RNA is also a highly controlled process that is influenced by specific cis and trans-acting elements. In polarized cells, such as neurons, the localization of transcripts towards axons and dendrites (neurites) enables the immediate and efficient local synthesis of proteins in response to external stimuli. This thesis focuses on the examination of the cis-elements, or "zipcodes," that contribute to the localization of RNA towards the neurites and the translational defects that result in the peripheral neuropathy Charcot-Marie-Tooth (CMT) disease

    2023- The Twenty-seventh Annual Symposium of Student Scholars

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    The full program book from the Twenty-seventh Annual Symposium of Student Scholars, held on April 18-21, 2023. Includes abstracts from the presentations and posters.https://digitalcommons.kennesaw.edu/sssprograms/1027/thumbnail.jp

    Comparative gene prediction in human and mouse.

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    The completion of the sequencing of the mouse genome promises to help predict human genes with greater accuracy. While current ab initio gene prediction programs are remarkably sensitive (i.e., they predict at least a fragment of most genes), their specificity is often low, predicting a large number of false-positive genes in the human genome. Sequence conservation at the protein level with the mouse genome can help eliminate some of those false positives. Here we describe SGP2, a gene prediction program that combines ab initio gene prediction with TBLASTX searches between two genome sequences to provide both sensitive and specific gene predictions. The accuracy of SGP2 when used to predict genes by comparing the human and mouse genomes is assessed on a number of data sets, including single-gene data sets, the highly curated human chromosome 22 predictions, and entire genome predictions from ENSEMBL. Results indicate that SGP2 outperforms purely ab initio gene prediction methods. Results also indicate that SGP2 works about as well with 3x shotgun data as it does with fully assembled genomes. SGP2 provides a high enough specificity that its predictions can be experimentally verified at a reasonable cost. SGP2 was used to generate a complete set of gene predictions on both the human and mouse by comparing the genomes of these two species. Our results suggest that another few thousand human and mouse genes currently not in ENSEMBL are worth verifying experimentally

    General Course Catalog [2022/23 academic year]

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    General Course Catalog, 2022/23 academic yearhttps://repository.stcloudstate.edu/undergencat/1134/thumbnail.jp
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