Inducing Apical Periodontitis in Mice

The mechanisms involved in local induced inflammation can be studied using several available animal models. One of these is the induction of apical ...

Hebrew University of Jerusalem

Quantitative traits are conditioned by several genetic determinants. Since such genes influence many important complex traits in various organisms, the identification of quantitative trait loci (QTLs) is of major interest, but still encounters serious difficulties. We detected four linked genes within one QTL, which participate in controlling sporulation efficiency in Saccharomyces cerevisiae. Following the identification of single nucleotide polymorphisms by comparing the sequences of 145 genes between the parental strains SK1 and S288c, we analyzed the segregating progeny of the cross between them. Through reciprocal hemizygosity analysis, four genes, RAS2, PMS1, SWS2, and FKH2, located in a region of 60 kilobases on Chromosome 14, were found to be associated with sporulation efficiency. Three of the four "high" sporulation alleles are derived from the "low" sporulating strain. Two of these sporulation-related genes were verified through allele replacements. For RAS2, the causative variation was suggested to be a single nucleotide difference in the upstream region of the gene. This quantitative trait nucleotide accounts for sporulation variability among a set of ten closely related winery yeast strains. Our results provide a detailed view of genetic complexity in one "QTL region" that controls a quantitative trait and reports a single nucleotide polymorphism-trait association in wild strains. Moreover, these findings have implications on QTL identification in higher eukaryotes.

Four linked genes participate in controlling sporulation efficiency in budding yeast.

Recently, it was suggested that tissue variation in cancer risk originates from differences in the number of stem-cell divisions underlying each tissue, leading to different mutation loads. We show that this variation is also correlated with the degree of aberrant CpG island DNA methylation in normal cells. Methylation accumulates during aging in a subset of molecules, suggesting that the epigenetic landscape within a founder-cell population may contribute to tumor formation.

Contribution of epigenetic mechanisms to variation in cancer risk among tissues.

In experimental evolution, scientists evolve organisms in the lab, typically by challenging them to new environmental conditions. How best to evolve a desired trait? Should the challenge be applied abruptly, gradually, periodically, sporadically? Should one apply chemical mutagenesis, and do strains with high innate mutation rate evolve faster? What are ideal population sizes of evolving populations? There are endless strategies, beyond those that can be exposed by individual labs. We therefore arranged a community challenge, Evolthon, in which students and scientists from different labs were asked to evolve Escherichia coli or Saccharomyces cerevisiae for an abiotic stress-low temperature. About 30 participants from around the world explored diverse environmental and genetic regimes of evolution. After a period of evolution in each lab, all strains of each species were competed with one another. In yeast, the most successful strategies were those that used mating, underscoring the importance of sex in evolution. In bacteria, the fittest strain used a strategy based on exploration of different mutation rates. Different strategies displayed variable levels of performance and stability across additional challenges and conditions. This study therefore uncovers principles of effective experimental evolutionary regimens and might prove useful also for biotechnological developments of new strains and for understanding natural strategies in evolutionary arms races between species. Evolthon constitutes a model for community-based scientific exploration that encourages creativity and cooperation.

Evolthon: A community endeavor to evolve lab evolution.

The ability to reproduce is a major trait of living organisms. This ability is carried out by specialized reproductive cells-gametes. In mammals, gametes develop through a unique developmental pathway. Extensive changes in the epigenome of gametes occur during embryonic development. With birth, gametes continue to mature and develop until puberty. This growth process is accompanied by further epigenetic changes. When gametes mature, they reside within specialized organs-the gonads-and are exposed to both internal and external signals. The gametes' epigenome reacts to these signals, and epigenetic changes which occur can alter gene expression and the ability of the cells to go through the cell cycle. The epigenome also ages and may be one of the key players in gamete aging, which, at least for females, occurs relatively early in life. The journey gametes undertake throughout the life of the organism is thus full of epigenetic changes. In this review, we depict these changes and the mechanisms involved in them. We focus on four stages of gamete development: gametes in embryonic development, during puberty and until sexual maturity, in adulthood, and during the process of aging. In each stage, we focus on one aspect of epigenetic changes and discuss it in more detail. These four stages include many different molecular players, lots of enzymatic activity, and abrupt changes. By this, these stages resemble the four seasons of the year. Thus, we describe epigenetic changes in gametes as changes throughout four seasons of life.

Epigenetic changes in mammalian gametes throughout their lifetime: the four seasons metaphor.

Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research. So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms-yeast in this case-from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio- and experimental archaeology that aim to reconstruct ancient artifacts and products.

Article	Year
Four linked genes participate in controlling sporulation efficiency in budding yeast. PLoS genetics\| PubMed ID: 17112318	2006
Contribution of epigenetic mechanisms to variation in cancer risk among tissues. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 28193856	2017
Evolthon: A community endeavor to evolve lab evolution. PLoS biology\| PubMed ID: 30925180	2019
Epigenetic changes in mammalian gametes throughout their lifetime: the four seasons metaphor. Chromosoma\| PubMed ID: 31030260	2019
Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology. mBio\| PubMed ID: 31040238	2019

Michael Klutstein

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