Critical Success Factors – a study of Project Management techniques using Pinto’s Model in the Malaysia housing construction companies perspective

Non-familiarity and not being well versed with project management knowledge areas and processes, the use of project management tools and techniques, standardizations, consistency and optimization of the project management processes implementation which lead to unnecessary schedule delays, cost overruns, poor quality, overlooked risks and scope creep are among the host of issues associated with Project Management over the project life cycle. Each housing construction company strives to achieve the most efficient and effective project management processes to achieve project success and each manages project management processes differently. This study investigates the importance placed by the respective stakeholders of the construction companies in managing project management processes in housing constructions projects based on the nine project management knowledge areas and ten elements of the “project implementation profile”. Data was collected through the questionnaires where the questionnaire used the Likert Scale to evaluate the data. Due to insufficient data, interviews with relevant personnel were conducted. Based on the questionnaires and interviews, there seem to be initiatives taken by the Company in attaining project success in constructions projects. The study finds that the stakeholders and Companies are practicing Project management processes in their construction projects. It is proposed that construction companies implement, standardize, institutionalize and optimize project management processes and usage in order to avoid financial losses, cost overruns, legal disputes and other problems to increase the probability of project success. (Abstract by author

Plus Ultra: Genome-Wide Spatial Transcriptomics with RNA seqFISH+

Visualizing single cells and their organization in intact tissue is crucial to understanding their governing biological function. Even though single cell RNA sequencing has provided many insights into the heterogeneity and gene expression profiles across many tissue types, the dissociation process which loses the spatial information is hindering our deeper understanding of how these transcriptional distinct cell types are organized and interacting in their native tissue environment. The thesis begins by giving a background on how single cell RNA sequencing has transformed biology and the emergence of spatial technology such as sequential fluorescence in situ hybridization (seqFISH). While spatial methods are useful for mapping the cell types identified from single cell RNA sequencing, the need for turning spatial technology such as seqFISH, which has high detection efficiency of the transcriptome with spatial information, into an in situ discovery tool is discussed as the scientific community’s goal heads towards building spatial atlases for every human tissues and organs such as the brain. While seqFISH has high detection efficiency, it is still limited in the number of genes capable of profiling at once. The major obstacle is the optical crowding problems when more RNA species are targeted and imaged using a fluorescence microscope. In Chapter 2, we first investigated, if the RNA molecules are instead captured on a coverslip and profiled with sequential barcoding strategy, the FISH-based method will reliably characterize the transcriptome when molecular crowding is not an issue. Finally, in Chapter 3, we demonstrate the barcoding strategy to break through the molecular crowding limit of multiplexed FISH. From being able to profile hundreds to a thousand genes by various multiplexed FISH methods at that time in the field, we succeeded in profiling 10,000 genes by RNA seqFISH+, an evolved version of seqFISH, in various intact tissue sections, turning seqFISH+ into a spatial discovery technology with its genome-wide coverage and high detection efficiency. The work described in this part of the thesis is highlighted in Nature Method’s Method of The Year 2020- Spatially-resolved Transcriptomic article.</p

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

Visualization of the transcriptome and the nuclear organization in situ has been challenging for single-cell analysis. Here, we demonstrate a multiplexed single-molecule in situ method, intron seqFISH, that allows imaging of 10,421 genes at their nascent transcription active sites in single cells, followed by mRNA and lncRNA seqFISH and immunofluorescence. This nascent transcriptome-profiling method can identify different cell types and states with mouse embryonic stem cells and fibroblasts. The nascent sites of RNA synthesis tend to be localized on the surfaces of chromosome territories, and their organization in individual cells is highly variable. Surprisingly, the global nascent transcription oscillated asynchronously in individual cells with a period of 2 hr in mouse embryonic stem cells, as well as in fibroblasts. Together, spatial genomics of the nascent transcriptome by intron seqFISH reveals nuclear organizational principles and fast dynamics in single cells that are otherwise obscured

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

Visualization of the transcriptome and the nuclear organization in situ has been challenging for single-cell analysis. Here, we demonstrate a multiplexed single-molecule in situ method, intron seqFISH, that allows imaging of 10,421 genes at their nascent transcription active sites in single cells, followed by mRNA and lncRNA seqFISH and immunofluorescence. This nascent transcriptome-profiling method can identify different cell types and states with mouse embryonic stem cells and fibroblasts. The nascent sites of RNA synthesis tend to be localized on the surfaces of chromosome territories, and their organization in individual cells is highly variable. Surprisingly, the global nascent transcription oscillated asynchronously in individual cells with a period of 2 hr in mouse embryonic stem cells, as well as in fibroblasts. Together, spatial genomics of the nascent transcriptome by intron seqFISH reveals nuclear organizational principles and fast dynamics in single cells that are otherwise obscured

Integrated spatial genomics reveals global architecture of single nuclei

Identifying the relationships between chromosome structures, nuclear bodies, chromatin states and gene expression is an overarching goal of nuclear-organization studies. Because individual cells appear to be highly variable at all these levels, it is essential to map different modalities in the same cells. Here we report the imaging of 3,660 chromosomal loci in single mouse embryonic stem (ES) cells using DNA seqFISH+, along with 17 chromatin marks and subnuclear structures by sequential immunofluorescence and the expression profile of 70 RNAs. Many loci were invariably associated with immunofluorescence marks in single mouse ES cells. These loci form ‘fixed points’ in the nuclear organizations of single cells and often appear on the surfaces of nuclear bodies and zones defined by combinatorial chromatin marks. Furthermore, highly expressed genes appear to be pre-positioned to active nuclear zones, independent of bursting dynamics in single cells. Our analysis also uncovered several distinct mouse ES cell subpopulations with characteristic combinatorial chromatin states. Using clonal analysis, we show that the global levels of some chromatin marks, such as H3 trimethylation at lysine 27 (H3K27me3) and macroH2A1 (mH2A1), are heritable over at least 3–4 generations, whereas other marks fluctuate on a faster time scale. This seqFISH+-based spatial multimodal approach can be used to explore nuclear organization and cell states in diverse biological systems

Integrated spatial genomics reveals global architecture of single nuclei

Identifying the relationships between chromosome structures, nuclear bodies, chromatin states and gene expression is an overarching goal of nuclear-organization studies. Because individual cells appear to be highly variable at all these levels, it is essential to map different modalities in the same cells. Here we report the imaging of 3,660 chromosomal loci in single mouse embryonic stem (ES) cells using DNA seqFISH+, along with 17 chromatin marks and subnuclear structures by sequential immunofluorescence and the expression profile of 70 RNAs. Many loci were invariably associated with immunofluorescence marks in single mouse ES cells. These loci form ‘fixed points’ in the nuclear organizations of single cells and often appear on the surfaces of nuclear bodies and zones defined by combinatorial chromatin marks. Furthermore, highly expressed genes appear to be pre-positioned to active nuclear zones, independent of bursting dynamics in single cells. Our analysis also uncovered several distinct mouse ES cell subpopulations with characteristic combinatorial chromatin states. Using clonal analysis, we show that the global levels of some chromatin marks, such as H3 trimethylation at lysine 27 (H3K27me3) and macroH2A1 (mH2A1), are heritable over at least 3–4 generations, whereas other marks fluctuate on a faster time scale. This seqFISH+-based spatial multimodal approach can be used to explore nuclear organization and cell states in diverse biological systems

First high-quality draft genome sequence of Pasteurella multocida sequence type 128 isolated from infected bone

We report here the first high-quality draft genome sequence of Pasteurella multocida sequence type 128, which was isolated from the infected finger bone of an adult female who was bitten by a domestic dog. The draft genome will be a valuable addition to the scarce genomic resources available for P. multocida

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

Imaging the transcriptome in situ with high accuracy has been a major challenge in single-cell biology, which is particularly hindered by the limits of optical resolution and the density of transcripts in single cells. Here we demonstrate an evolution of sequential fluorescence in situ hybridization (seqFISH+). We show that seqFISH+ can image mRNAs for 10,000 genes in single cells—with high accuracy and sub-diffraction-limit resolution—in the cortex, subventricular zone and olfactory bulb of mouse brain, using a standard confocal microscope. The transcriptome-level profiling of seqFISH+ allows unbiased identification of cell classes and their spatial organization in tissues. In addition, seqFISH+ reveals subcellular mRNA localization patterns in cells and ligand–receptor pairs across neighbouring cells. This technology demonstrates the ability to generate spatial cell atlases and to perform discovery-driven studies of biological processes in situ