微生物学技术

Building a dynamic model of a complete biological cell is one of the great challenges of the 21st century. While this objective could appear unrealistic until recently, considerable improvements in high-throughput data collection techniques, computational performance, data in ...

Genetic regulatory circuits are often regarded as precise machines that accurately determine the level of expression of each protein. Most experimental technologies used to measure gene expression levels are incapable of testing and challenging this notion, as they often measure l ...

This chapter presents a discussion of metabolic modeling from graph theory and logical modeling perspectives. These perspectives are closely related and focus on the coarse structure of metabolism, rather than the finer details of system behavior. The models have been used as backgrou ...

Systematic analysis of Saccharomyces cerevisiae metabolic functions and pathways has been the subject of extensive studies and established in many aspects. With the reconstruction of the yeast genome-scale metabolic (GSM) network and in silico simulation of the GSM model, the nature ...

Metabolomics involves the investigation of the intracellular (endometabolome) and extracellular (exometabolome) pools of metabolites in biological systems. Methods to sample the exometabolome and to quench metabolism and extract intracellular metabolites for the mo ...

Phenotypic variations of an organism may arise from alterations of cellular networks, ranging from the complete loss of a gene product to the specific perturbation of a single molecular interaction. In interactome networks that are modeled as nodes (macromolecules) connected by edges ...

Early achievements in proteomics were qualitative, typified by the identification of very small quantities of proteins. However, as the subject has developed, there has been a pressure to develop approaches to define the amounts of each protein – whether in a relative or an absolute sense. A fur ...

Whilst the study of yeast genomes and transcriptomes is in an advanced state, there is still much to learn about the resulting proteins in terms of cataloging, characterization of post-translational modifications, turnover, and the dynamics of sub-cellular localization and interac ...

In this chapter, we present an up-to-date view of the optimal characteristics of the yeast Saccharomyces cerevisiae as a model eukaryote for systems biology studies, with main molecular mechanisms, biological networks, and sub-cellular organization essentially conserved in all e ...

The automated cell, compound and environment screening system (ACCESS) was developed as an automated platform for chemogenomic research. In the yeast Saccharomyces cerevisiae, a number of genomic screens rely on the modulation of gene dose to determine the mode of action of bioactive com ...

Competition experiments are an effective way to provide a measurement of the fitness of yeast strains. The availability of the Saccharomyces cerevisiae yeast knock-out (YKO) deletion collection allows scientists to retrieve fitness data for the ~6,000 S. cerevisiae genes at the same ti ...

Cell growth is highly regulated and its deregulation is related to many human diseases such as cancer. Nutritional cues stimulate cell growth through modulation of TOR (target of rapamycin) signaling pathway. At the center of this pathway is a large serine/threonine protein kinase TOR, whi ...

Protein interactions are inherently dynamic. In no system is this more true and important than in signaling pathways, where spatial and temporal control of specific protein interactions is key to signaling specificity and timing. While genetic and biochemical interactions form a nec ...

In the early days of the yeast genome sequencing project, gene annotation was in its infancy and suffered the problem of many false positive annotations as well as missed genes. The lack of other sequences for comparison also prevented the annotation of conserved, functional sequences that we ...

Chromatin plays critical roles in processes governed in different timescales – responses to environmental changes require rapid plasticity, while long-term stability through multiple cell generations requires epigenetically heritable chromatin. Understanding the ...

The genomes of eukaryotic organisms are packaged into nuclei by wrapping DNA around proteins in a structure known as chromatin. The most basic unit of chromatin, the nucleosome, consists of approximately 146bp of DNA wrapped around an octamer of histone proteins. The placement of nucleosom ...

In this protocol, we describe a pipeline for transcript analysis in yeast via the quantification of mRNA expression levels. In the first section, we consider the well-established, proprietary Affymetrix GeneChip� approach to generating transcriptomics data. In the next section, we co ...

In the last decade, it became clear that transcription goes far beyond that of protein-coding genes. Most RNA molecules are transcribed from intergenic regions or introns and exhibit much variability in size, expression level, secondary structure, and evolutionary conservation. Wh ...

Cryptic unstable transcripts (CUTs) have been recently described as a major class of non-coding RNAs. These transcripts are, however, extremely unstable in normal cells and their analyzes pose specific technical problems. In this chapter, after a brief introduction discussing gene ...

Nearly all eukaryotic mRNAs terminate in a poly(A) tail that serves important roles in mRNA utilization. In the cytoplasm, the poly(A) tail promotes both mRNA stability and translation, and these functions are frequently regulated through changes in tail length. To identify the scope of poly ...