Inheritance | EPFL Graph Search

Inheritance is the practice of receiving private property, titles, debts, entitlements, privileges, rights, and obligations upon the death of an individual. The rules of inheritance differ among societies and have changed over time. Officially bequeathing private property and/or debts can be performed by a testator via will, as attested by a notary or by other lawful means. Terminology In law, an "heir" ( heiress) is a person who is entitled to receive a share of the deceased's (the person who died) property, subject to the rules of inheritance in the jurisdiction of which the deceased was a citizen or where the deceased (decedent) died or owned property at the time of death. The inheritance may be either under the terms of a will or by intestate laws if the deceased had no will. However, the will must comply with the laws of the jurisdiction at the time it was created or it will be declared invalid (for example, some states do not recognise handwritt

Quantitative single-cell analysis of S. cerevisiae using a microfluidic live-cell imaging platform

Johannes Becker

Genome-wide manipulations and measurements have made huge progress over the last decades. In Saccharomyces cerevisiae, a well-studied eukaryotic model organism, homologous recombination allows for systematic deletion or alteration of a majority of its genes. Important products of these manipulation techniques are two libraries of modified strains: A deletion library consisting of all viable knockout mutants, and a GFP library in which 4159 proteins are successfully tagged with GFP. In addition, the development of a method that allows for the systematic construction of double mutants led to a virtually infinite number of potential strains of interest. These advancements in combinatorial biology need to be matched by methods of data measurement and analysis. In order to simultaneously observe the spatio-temporal dynamics of thousands of strains from the GFP library, Dénervaud et al. developed a microfluidic platform that allows for parallel imaging of 1152 strains in a single experiment. On this platform, strains can be grown and monitored in a controllable environment for several days, which results in the imaging of several millions of cells during one experiment. To objectively and quantitatively analyze this immense amount of information, we implemented an image analysis pipeline, which can extract experiment-wide information on single-cell protein abundance and subcellular localization. The construction of a supervised classifier to quantify localization information on a single cell level is a new approach and was invaluable to detect dynamic localization changes within the proteome. Using five different stress conditions, we gained insight into temporal changes of abundance and localization of multiple proteins. For example, we found that while localization changes can often be fast and transient, long-term response of a cell is usually enabled by changes in abundance. This shows a well-orchestrated response of a cell to external stimuli. To extend knowledge about cellular mechanisms, we used our microfluidic platform for two separate screens, combining GFP-reporter with additional deletion mutants. The advantage of our platform in comparison to more common approaches lies in its simultaneous measurement of fluorescence and phenotypic information on cell size and growth. For each deletion, we can quantify not only its influence onto the respective GFP-reporter under changing conditions, but also its effect on cell growth and size. We showed that it is advantageous to combine this information, as it allows pointing out possible underlying mechanisms of gene network regulations. In a first screen we investigated the behavior of several gene networks upon UV irradiation damage. We were able to show that four gene deletions influenced the localization of ribonucleotide-diphosphate reductase (Rnr4p). A second screen was designed to find genes that influence the induction of the galactose network. This screen uses more than 500 deletions of genes mostly related to chromatin in combination with two different reporter strains. A main focus of this study was the inheritance of memory during galactose reinduction. We found several previously unknown genes that potentially influence either induction or reinduction and were picked as candidates for further inheritance studies. Our microfluidic platform allows for unprecedented studies of proteomes in flux. [...]

EPFL2015

Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction Memory

Johannes Becker, Sebastian Maerkl

Transcriptional memory of gene expression enables adaptation to repeated stimuli across many organisms. However, the regulation and heritability of transcriptional memory in single cells and through divisions remains poorly understood. Here, we combined microfluidics with single-cell live imaging to monitor Saccharomyces cerevisiae galactokinase 1 (GAL1) expression over multiple generations. By applying pedigree analysis, we dissected and quantified the maintenance and inheritance of transcriptional reinduction memory in individual cells through multiple divisions. We systematically screened for loss- and gain-of-memory knockouts to identify memory regulators in thousands of single cells. We identified new loss-of-memory mutants, which affect memory inheritance into progeny. We also unveiled a gain-of-memory mutant, elp6 Delta, and suggest that this new phenotype can be mediated through decreased histone occupancy at the GAL1 promoter. Our work uncovers principles of maintenance and inheritance of gene expression states and their regulators at the single-cell level.

CELL PRESS2020

The Problematics of Testing Object-Oriented Software

Within object-oriented approaches, testing has almost been ignored in favor of analysis, design, and coding. However, object-orientedness does not solve the problem of testing by itself and may even induce new problems. Most work in testing has been done with "procedure-oriented" software in mind. Traditional methods, despite their efficiency, cannot be applied without adaptation to object-oriented systems. In an object-oriented system, the basic unit of testing is a class instead of a subprogram; testing should hence focus on classes and objects. Moreover, it is not possible to test the operations of a class in isolation, as they interact with each other by modifying the state of the object they are applied to. Sometimes testing object-oriented software can benefit from object-oriented technology, for instance, by capitalizing on the fact that a superclass has already been tested, and by decreasing the effort to test derived classes, which reduces the cost of testing in comparison with a flat class structure. The object-oriented paradigm can also be a hindrance to testing, due to the nature of some aspects of its very nature: encapsulation, inheritance and polymorphism. In the presence of encapsulation, the only way to observe the state of an object is through its operations; there is therefore a fundamental problem of observability. Inheritance opens the issue of re-testing. Should operations inherited from ancestor classes be re-tested in the context of the descendant class? A case analysis will show that there is no definite answer. Polymorphic calls are difficult to test. A test suite must ensure that all possible cases of bindings are covered. Moreover, when extending a software by a new derived class (programming by extension), calls with possible bindings to operations of this new derived class must be re-tested.

1994

Quantitative single-cell analysis of S. cerevisiae using a microfluidic live-cell imaging platform

Johannes Becker

EPFL2015