The effect of heterochromatin changes with age in the reproductive system:

Aging affects all cells, but is prominent in the reproductive system. Oocytes age early, becoming aneuploid, thus limiting female reproductive age. Aged oocytes display phenotypes involving chromosome non-disjunction, causing genetic abnormalities such as Down’s syndrome. Spermatocytes age later than oocytes, but still show a reduction in fertility and an age-dependent rise in genetic diseases such as autism and schizophrenia. It has now become evident that age-related changes in heterochromatin contribute significantly to the etiology of aging. Using molecular biology tools together with microscopy, we decipher the effect of heterochromatin changes on the aging of gametes. We  determine which molecular pathways and players in heterochromatin are at play when gametes age, and if these pathways can be modified to delay the aging process in the reproductive system. We first aim to characterize the changes in heterochromatin during aging of spermatocytes and oocytes, using a myriad of genomic and microscopy tools for this aim, including cutting-edge technologies like single cell methylation sequencing. Second, we study the mechanism of age-related aging in the reproductive system in depth. We determine the causal relationship between heterochromatin dynamics and centromere binding proteins in oocytes and the levels of transposable elemnts in the genome which may cause DNA damage.  

Together, these experiments yield a comprehensive picture of how aging affects heterochromatin in oocytes and spermatocytes and whether molecular tools can prevent any ill effects. these experiments are mainly conducted in a mouse system, with addition of analysis of clinical samples.

The Link between Genomic instability, Abnormal Meiotic Gene Expression and Tumor Formation:

Cancer cells have a propensity to re-arrange their genome. Tumors tend to lose or gain whole chromosomes and re-arrange large genomic regions. When this process occurs continuously, the tumor becomes chromosome instable (CIN). CIN tumors are more aggressive and often harder to treat. In this project we aim to identify a new mechanism for CIN. It was previously shown that many tumors express high levels of genes which participate in meiosis. Meiosis is a process which occurs only in the reproductive system and is responsible for the reduction division which turns eggs and sperm into haploid cells (containing one copy of each chromosome). Since chromosome instability is built-in during meiosis (by the processes of homologous recombination and mono-orientation), the overexpression of meiosis-specific genes could in principle cause the tumor to become CIN.

We carry out  bioinformatics surveys of existing tumor data, together with an analysis of samples of cancer from the clinic in order to determine the correlation level between meiotic gene expression and CIN.

We  also mechanistically study the process, and overexpress single meiotic genes in cell lines, and measure the CIN in them.

This new mechanism could lead to the identification of markers and drug targets to diagnose and treat CIN tumors

Aging effects on the kinetics of periapical inflammation: ​

The kinetics and outcome of inflammation are affected by aging. Previous studies from many tissues and cell types show that cell proliferation capacity and rate are heavily affected by age. As a result, young tissues are more able to respond to stimuli and are generally more responsive to their environment. 

Apical periodontitis, an inflammatory process around the apex of a tooth root, is a remarkably widespread problem. Clinical experience shows that inadequate root canal treatments can remain healthy for many years, and that properly treated root canals can become infected. This leads to the conclusion that unidentified factors such as epigenetic aging may be critical for the success or failure of endodontic treatments. Up to date there are no clear recommendations for clinicians for the treatment of periapical lesions as a function of age. Our experiments establish a mouse model measuring the clinical and epigenetic parameters of a periapical inflammatory process in young vs. adult mice, working towards a tool to study the role of epigenetic aging in mouse periapical inflammation.

We use micro-CT, immunohistochemistry, FACS analysis and DNA methylation sequencing methods to characterize the immune response of mice to periapical lesion formation. 

GASP and prolonged starvation in eukaryotes:

The world around us is full of life, but its vast majority is found in a starved, stressed quiescent or dormant state, known as stationary phase cells, cells in G0, and spores. Despite its prevalence and obvious importance, our knowledge about population dynamics of cells during quiescence is poor. Most of our knowledge comes from experiments using bacteria, using long-term stationary phase (LTSP) cultures. Although bacteria in stationary phase seem static, some cell divisions do occur and eventually give rise to resistant mutants which take over the entire culture in these LTSP cultures. Interestingly, these cells eventually outcompete their parental strains in growth competition experiments. These mutants are termed growth advantage in stationary phase (GASP) phenotype. These cells use several strategies such as reduced growth rate to be able to transiently survive stressful conditions. Despite some work being done on these bacterial survivors, and some forms of persisters being found in eukaryotes, the extent to which GASP and persisters phenotype appear in LTSP cultures of eukaryotic organisms has not been studied. 

We aim to characterize the response of eukaryotic cells to long-term stress and apply lessons learned in the research of bacteria to this system. So far, we have managed to isolate yeast cells from a LTSP culture in the form of a 1.5 years old unfiltered beer bottle. These yeast cells show all the hallmark phenotypes of GASP mutants, namely being more resistant to various stress conditions than the parental strain, being a repeatable genetic phenomenon, showing stable phenotypes and being not transient as in persisters. 

We use genomic tools as well a phenotypic analysis in yeast and cancer cell lines to characterize GASP in eukaryotes

A taste from the past- yeast revival from ancient beer pots:

Beer is one of the oldest and basic consumed products in human culture. Recipes of beer brewing were found in Mesopotamian and Egyptian archeological sites. So far, attempts to reconstruct ancient beer were done using modern cultivated yeast.

We have recently succeeded, in a proof of concept experiment, to isolate a yeast strain which produced a flavorful beer from a 5000 years old Egyptian vessel found in Israel. Using many control samples, we found that this yeast is uniquely found in this vessel and most probably does not originate from the surrounding environment. Moreover, it was not found in vessels which did not contain beer from the same site or in modern pots, suggesting that it is not a natural clay inhabitant. Using modern genomic tools, we intend to characterize the genomic features of these yeast cells and what enabled them to survive for so long. 

This project is expected to yield knowledge about the evolution and the cultivation of beer yeast and about the production of one of the most important and common beverages among many cultures since the beginning of civilization, in a unique collaboration of archeologists, microbiologists, bioinformaticians and beer brewing experts. As a bonus, this project allows modern-time people to taste beer from the time of our ancestors.