PhD Cuong Nguyen

PhD Cuong Nguyen
The Vietnam Foundation
Quốc gia: Vietnamese
Tiểu sử:

OER Technology Manager - The Vietnam Foundation.

The Vietnam Foundation is dedicated to improving the lives of the Vietnamese people through education.

Despite rapid economic growth, Vietnam is constrained by a poor system of higher education.  Inadequately trained faculty, ineffective teaching methods, and the lack of access to modern technologies limit student learning in many ways.  Government sponsored educational reforms have not kept up with a rising educational need.

The Vietnam Foundation, through its work with the U.S. National Academies, brings the expertise of the U.S. academic community to assist Vietnam in the field of education.  We believe that by supporting educational training programs and integrating technology innovation we can improve tremendously the quality of higher education in Vietnam.

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Positional co-regulation of transcription factors in Saccharomyces cerevisiae

Recently there are several studies focused on the transcriptional regulation of gene expression in Saccharomyces cerevisiae. In this study, we investigate the regulation of gene expression by 106 transcription factors in S. cerevisiae based on genome wide location analysis data of Lee et al. (Science vol. 298, 2002). By computational methods, we analyze the position of genes regulated by 106 transcription factors on 16 chromosomes. The chromosome-wide distribution of regulated genes by 106 transcription factors is rather uniform over 16 chromosomes. However, detailed positional correlation analysis among target genes of transcription factors shows that nearby genes have more chances to be co-regulated by the transcription factor. As a consequence of positional co-regulation, we have identified the presence of 2-, 3-, 4-, 5- and 6-gene motif structure, called “operon-like motif structure,” in which n-genes are sequentially regulated by the same transcription factor. To understand functional role of the operon-like motif structure we investigate the correlation of the gene expression for these motif genes. The analysis shows high correlation among genes in the motifs compared to random gene pairs. This result indicates that genes in the operon-like motif structure are functionally correlated.

Positive feedback loops generate bistability

Positive feedback loops (PFLs) are basic elements of biological regulatory networks. They have been well studied theoretically, experimentally and also by simulation. It is said that PFLs have potential to exhibit bistability and irreversibility and play an important role: converting graded signal into discontinuous response. By interlocking them together, meaning that a product P is coordinately and positively regulated by both types, the possible dynamic scenarios are explored. By doing that, we are able to classify interlocking PFLs dynamical behaviors into 6 types: mono-stability, single bistability, non-overlapping, overlapping, nested and merged bistabilities. To be complete, we constructed a parameters phase plane of two feedback strength which shows irreversible regions of each types mentioned. Moreover, we found the rule of stability and asymptotic behavior of interlocked positive feedback loops.

Feedback controls in biological networks

In many biological systems the positive and negative feedbacks hook up and cooperate to work out the desired functions of the systems. For instance, the Mitotic trigger and regulation of the cell cycle of various organisms is regulated by interlocked PFL and dNFL related to the Mitotic Promoting Factor (MPF) and its friends and enemies (APC). The interlocked positive and delay negative feedback loops related to the CLOCK genes are also found in circadian regulation networks in broad range of species.

Cell cycle regulation in the budding yeast

Cell cycle is regulated cooperatively by several genes. The underlying regulatory mechanism of the cell cycle remains one of the hottest research topics of life science. In this talk, the cell cycle regulatory mechanism, especially the dynamic role of feedback loops will be presented taking the budding yeast as a target system. Based on the mathematical model developed by Chen et al. (MBC, 11, 369) the bifurcation diagram that shows the locations of stable and unstable solutions will be constructed at first. It is a kind of ‘dynamic load map’, attracted toward the stable solutions and repelled away from the unstable solutions on the map. The bifurcation diagram allows us to understand the regulatory mechanism of the ‘START’ transition, the initiation of a new round of a cell cycle, and the ‘FINISH’ transition, the completion of a cell cycle and returning back to the initial state. For example, the ‘start transition’ occurs at the point where the dynamics load map in fig 6. changes from a stable fixed point solution (blue line) to an oscillatory solution (green lines).

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