The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

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Initial sequencing and analysis of the human genome.

Salt and drought stress signal transduction consists of ionic and osmotic homeostasis signaling pathways, detoxification (i.e., damage control and repair) response pathways, and pathways for growth regulation. The ionic aspect of salt stress is signaled via the SOS pathway where a calcium-responsive SOS3-SOS2 protein kinase complex controls the expression and activity of ion transporters such as SOS1. Osmotic stress activates several protein kinases including mitogen-activated kinases, which may mediate osmotic homeostasis and/or detoxification responses. A number of phospholipid systems are activated by osmotic stress, generating a diverse array of messenger molecules, some of which may function upstream of the osmotic stress-activated protein kinases. Abscisic acid biosynthesis is regulated by osmotic stress at multiple steps. Both ABA-dependent and -independent osmotic stress signaling first modify constitutively expressed transcription factors, leading to the expression of early response transcriptional activators, which then activate downstream stress tolerance effector genes.

/pdf/salt-and-drought-stress-signal-transduction-in-plants-4bj87ki2ww.pdf

Salt and drought stress signal transduction in plants

We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over time for almost every yeast gene, as cells responded to temperature shocks, hydrogen peroxide, the superoxide-generating drug menadione, the sulfhydryl-oxidizing agent diamide, the disulfide-reducing agent dithiothreitol, hyper- and hypo-osmotic shock, amino acid starvation, nitrogen source depletion, and progression into stationary phase. A large set of genes (approximately 900) showed a similar drastic response to almost all of these environmental changes. Additional features of the genomic responses were specialized for specific conditions. Promoter analysis and subsequent characterization of the responses of mutant strains implicated the transcription factors Yap1p, as well as Msn2p and Msn4p, in mediating specific features of the transcriptional response, while the identification of novel sequence elements provided clues to novel regulators. Physiological themes in the genomic responses to specific environmental stresses provided insights into the effects of those stresses on the cell.

/pdf/genomic-expression-programs-in-the-response-of-yeast-cells-4xrnicxf7t.pdf

Genomic expression programs in the response of yeast cells to environmental changes.

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

▪ Abstract Plant responses to salinity stress are reviewed with emphasis on molecular mechanisms of signal transduction and on the physiological consequences of altered gene expression that affect biochemical reactions downstream of stress sensing. We make extensive use of comparisons with model organisms, halophytic plants, and yeast, which provide a paradigm for many responses to salinity exhibited by stress-sensitive plants. Among biochemical responses, we emphasize osmolyte biosynthesis and function, water flux control, and membrane transport of ions for maintenance and re-establishment of homeostasis. The advances in understanding the effectiveness of stress responses, and distinctions between pathology and adaptive advantage, are increasingly based on transgenic plant and mutant analyses, in particular the analysis of Arabidopsis mutants defective in elements of stress signal transduction pathways. We summarize evidence for plant stress signaling systems, some of which have components analogous to t...

Plant cellular and molecular responses to high salinity.

Glucose-Induced Regulatory Defects intheSaccharomyces cerevisiae byplGrowthInitiation MutantandIdentification ofMIGJas a Partial Suppressor

In recent years there has been a growing interest in the use of optical manipulation techniques, such as optical 
tweezers, in biological research as the full potential of such applications are being realized. Biological research is 
developing towards the study of single entities to reveal new behaviors that cannot be discovered with more 
traditional ensemble techniques. To be able to study single cells we have developed a new method where a 
combination of micro-fluidics and optical tweezers was used. Micro-fluidic channels were fabricated using soft 
lithography. The channels consisted of a Y-shaped junction were two channels merged into one. By flowing 
different media in the two channels in laminar flow we were able to create a sharp concentration gradient at the 
junction. Single cells were trapped by the tweezers and the micro-fluidic system allowed fast environmental 
changes to be made for the cell in a reversible manner. The time required to change the surroundings of the cell 
was limited to how sharp mixing region the system could create, thus how far the cells had to be moved using 
the optical tweezers. With this new technique cellular response in single cells upon fast environmental changes 
could be investigated in real time. The cellular response was detected by monitoring variations in the cell by 
following the localization of fluorescently tagged proteins within the cell.

A microfluidic system for studies of stress response in single cells using optical tweezers

Transformierte Hefestämme mit Spannungsbeständigkeit und/oder verbesserten Gärungsverhalten

Access to competence in mathematical modelling may be a major hindrance for employing a systems biology approach in many research projects. Very commonly, the most successful systems biology studies are based on collaborations between experimentalists, contributing with the biological questions and experimental data and theoreticians, who contribute with skills in modelling, simulation and prediction. Collaboration across disciplines is not a trivial enterprise and very commonly requires skills to communicate across borders. This challenge, as well as the mere availability of matching theoreticians locally may prevent in many cases the integration of modelling and prediction into projects even if the interdisciplinary approaches offer great potential.”

Moving from Genetics to Systems Biology

We applied a novel genetic screening method, named “genetic tug-of-war” (gTOW) to estimate the upper limit of gene copy numbers in Saccharomyces cerevisiae. The study involved 29 HOG pathway related genes which included kinases, phosphatases and transcription factors to cover different set of players in the signal transduction system. In addition a phenotypic profiling was conducted in four different growth conditions with three outputs: lag phase, growth phase and efficiency of growth. A number of interesting hits were identified, including PBS2 which had low numbers of gene copies. It will be of interest to expand the study to encompass the entire known signal transduction system in yeast to search for sensitive nodes.

Stefan Hohmann

Papers

Glucose-Induced Regulatory Defects intheSaccharomyces cerevisiae byplGrowthInitiation MutantandIdentification ofMIGJas a Partial Suppressor

A microfluidic system for studies of stress response in single cells using optical tweezers

Transformierte Hefestämme mit Spannungsbeständigkeit und/oder verbesserten Gärungsverhalten

Moving from Genetics to Systems Biology

Robustness analysis of HOG pathway related genes in budding yeast