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The warfare between bacteria and phages - viruses that infect bacteria - has been raging for billions of years. During this time both sides have evolved various attack and defense systems. In this talk I will describe 3 related projects: 1. Is there an optimal number of such defense or anti-defense systems? 2. How can different phages which prey on the same bacteria co-exist, in contradiction with the expected competitive exclusion? 3. Some phages have developed the ability to garner environmental information, enabling them to make more "intelligent" decisions. How much is such intelligence worth, in terms of other resources?
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Promiscuous binding of Janus kinases (JAKs) to class I/II cytokine receptors has been
reported, yet its role in signaling is unclear. To systematically explore JAK pairing in type
I interferon (IFN-I) signaling, we generated an artificial IFN-I receptor (AIR) by replacing
the extracellular domains of IFNAR1 and IFNAR2 with anti-mEGFP and mCherry
nanobodies. The heterodimeric AIR restored near-native IFN-I activity, while the
homomeric variant of IFNAR2 (AIR-dR2) initiated much weaker signaling despite
harboring docking sites for STAT proteins. To further investigate the roles of JAKs on the
receptors, knockout (KO) JAK1, JAK2, TYK2, and JAK2/TYK2 were generated. JAK1
KO led to a complete loss of IFN-I signaling, partially restored by TYK2 overexpression.
TYK2 KO cells retained partial activity, which was elevated by JAK1 overexpression,
suggesting both JAKs partially substitute each other.
Conversely, JAK2 KO only moderately impacted the biological activity of IFN-Is, even in
JAK2/TYK2 KO cells. Live cell micropatterning confirmed promiscuous binding of JAK1,
JAK2, and TYK2 to IFNAR1 and IFNAR2. Moreover, the identities of recruitment of
different JAKs on the ICDs were related to their respective concentrations in the cell, which
varies between cell lines. Yet, the efficiency of JAK cross-phosphorylation and
downstream signaling also depend on their identity. Promiscuity of JAK binding was also
observed for IFNL1, IL-10-Rbβ, TPOR, and GHR but not for EPOR, accompanied by
different downstream signaling activities. The competitive binding of JAKs to cytokine
receptors and the highly diverse absolute and relative JAK expression levels in different
cell types can account for cell type-dependent signaling pleiotropy observed for cytokine
receptors.

Circadian clocks in unicellular phototrophic organisms are known to display remarkable reliability. In contrast, not much is known about how circadian clocks perform in a multicellular setting. Are clocks in multicellular cyanobacteria coupled and synchronized with one another? Are clocks entrained only by external cues? What is the spatial extent of synchronization? What is the role of cell-cell variations in copy numbers of molecules comprising the core clock (demographic noise) in setting the temporal pattern and its robustness? To tackle quantitatively these and other questions, we studied the dynamics of a circadian clock-controlled gene in Anabaena sp. PCC 7120, a multicellular cyanobacterium in which cells are arranged one after the other and coupled by protein channels, in a one-dimensional structure. Our real-time, single-cell level measurements showed significant synchronization and spatial coherence along filaments, and clock coupling mediated by cell-cell communication. Furthermore, we found significant variability in expression between different cells along filaments. A stochastic one-dimensional toy model of coupled clocks and their phosphorylation states shows that demographic noise can seed stochastic oscillations outside the region where deterministic limit cycles with circadian periods occur. The model reproduces the observed spatio-temporal coherence along filaments and provides a robust description of coupled circadian clocks in a multicellular organism, despite significant stochasticity in biomolecular reactions. Lastly, we carried out experiments in which developmental processes were induced. Our experiments showed that gene expression in different vegetative intervals along a developed filament was discoordinated, and that differentiation took place preferentially within a limited interval of the circadian clock cycle. The transition to multicellularity demanded coordination between clocks via cell-cell communication, to optimize fitness in the presence of significant demographic noise.

A group is cubulated if it acts freely and cocompactly on a CAT(0) cube complex, a high-dimensional generalization of a tree. Cubulating hyperbolic groups has proven to be a fruitful endeavor over the past couple decades, as cubulation implies strong subgroup separability and linearity properties. Generalizing property FA, we consider the n-dimensional cubical fixed point property. A group has property FW_n if every action on an n-dimensional CAT(0) cube complex has a global fixed-point. We will show how to produce many examples of FW_n groups and prove that random groups have FW_n for every n.