Translation efficiency is a determinant of the magnitude of miRNA-mediated repression

Abstract MicroRNAs are well known regulators of mRNA stability and translation. However, the magnitude of both translational repression and mRNA decay induced by miRNA binding varies greatly between miRNA targets. This can be the result of cis and trans factors that affect miRNA binding or action. We set out to address this issue by studying how various mRNA characteristics affect miRNA-mediated repression. Using a dual luciferase reporter system, we systematically analyzed the ability of selected mRNA elements to modulate miRNA-mediated repression. We found that changing the 3′UTR of a miRNA-targeted reporter modulates translational repression by affecting the translation efficiency. This 3′UTR dependent modulation can be further altered by changing the codon-optimality or 5′UTR of the luciferase reporter. We observed maximal repression with intermediate codon optimality and weak repression with very high or low codon optimality. Analysis of ribosome profiling and RNA-seq data for endogenous miRNA targets revealed translation efficiency as a key determinant of the magnitude of miRNA-mediated translational repression. Messages with high translation efficiency were more robustly repressed. Together our results reveal modulation of miRNA-mediated repression by characteristics and features of the 5′UTR, CDS and 3′UTR

A Tale of Two Tragedies: Catharsis of Hero and City in Milton’s Samson Agonistes and Shakespeare’s Coriolanus

In his prologue to Samson Agonistes, Milton champions the conventions of Greek tragedy over those followed by Elizabethan dramatists. Great tragedy, he contends, purges fear and pity out of audiences, facilitating a more sober, moral, rational life. Based on his argument and on the content of the poem, the most important difference between classical and Elizabethan tragedy is the Chorus. The Chorus represents a poetic, monolithic, communal voice that interacts dialectically with a strong, independent hero. The Elizabethans eschewed the unified Chorus in favor of realistic and comedic imitation of the various members of the British masses, which, according to Milton, dilutes the dialectical conflict of heroic independence with community morals and weakens the potential of tragedy to produce a cathartic synthesis in the audience. In order to further understand and test Milton’s conception of the Chorus, this dissertation compares Samson Agonistes with Shakespeare’s Coriolanus. Coriolanus was selected because many critics have contended that it is the closest Shakespearean tragedy comes to imitating the unified structure and aims of classical tragedy while still retaining many Elizabethan conventions. Coriolanus is a model of the Aristotelian tragic hero who is superior in virtue but falls because of an error. His aristocratic, military values are depicted in sharp contrast with the increasingly republican values of the Roman citizens. Those citizens are depicted in typical, Elizabethan fashion, making their conflict with Coriolanus an ideal contrast with the Chorus’s conflict with Samson. Further, there are many fascinating parallels between the experiences of Samson and Coriolanus and in the structure of both plays. This dissertation will argue that while Shakespeare’s more realistic and entertaining imitation of complex political interactions does produce tragic emotions, especially in the final confrontation between Coriolanus, Volumnia, and Virgilia, Coriolanus dies rejected by Romans, Volscians, and often by audiences. On the other hand, Milton’s tightly constructed dialectic between Samson and the Chorus, including the conflicts with Manoa and Dalila, tends to produce a more meditative experience and to mediate a clearer cathartic resolution. Samson dies celebrated by the Danite Chorus, and audiences, with some important exceptions, have accepted him as a hero

When does cyclic dominance lead to stable spiral waves?

Species diversity in ecosystems is often accompanied by characteristic spatio-temporal patterns. Here, we consider a generic two-dimensional population model and study the spiraling patterns arising from the combined effects of cyclic dominance of three species, mutation, pair-exchange and individual hopping. The dynamics is characterized by nonlinear mobility and a Hopf bifurcation around which the system's four-phase state diagram is inferred from a complex Ginzburg-Landau equation derived using a perturbative multiscale expansion. While the dynamics is generally characterized by spiraling patterns, we show that spiral waves are stable in only one of the four phases. Furthermore, we characterize a phase where nonlinearity leads to the annihilation of spirals and to the spatially uniform dominance of each species in turn. Away from the Hopf bifurcation, when the coexistence fixed point is unstable, the spiraling patterns are also affected by the nonlinear diffusion

Feynman graphs, rooted trees, and Ringel-Hall algebras

We construct symmetric monoidal categories \LRF, \FD of rooted forests and Feynman graphs. These categories closely resemble finitary abelian categories, and in particular, the notion of Ringel-Hall algebra applies. The Ringel-Hall Hopf algebras of \LRF, \FD, \HH_{\LRF}, \HH_{\FD} are dual to the corresponding Connes-Kreimer Hopf algebras on rooted trees and Feynman graphs. We thus obtain an interpretation of the Connes-Kreimer Lie algebras on rooted trees and Feynman graphs as Ringel-Hall Lie algebras

On the structure and representations of the insertion-elimination Lie algebra

We examine the structure of the insertion-elimination Lie algebra on rooted trees introduced in \cite{CK}. It possesses a triangular structure \g = \n_+ \oplus \mathbb{C}.d \oplus \n_-, like the Heisenberg, Virasoro, and affine algebras. We show in particular that it is simple, which in turn implies that it has no finite-dimensional representations. We consider a category of lowest-weight representations, and show that irreducible representations are uniquely determined by a "lowest weight" $\lambda \in \mathbb{C}$. We show that each irreducible representation is a quotient of a Verma-type object, which is generically irreducible

Dna2 is a structure-specific nuclease, with affinity for 5'-flap intermediates

Dna2 is a nuclease/helicase with proposed roles in DNA replication, double-strand break repair and telomere maintenance. For each role Dna2 is proposed to process DNA substrates with a 5'-flap. To date, however, Dna2 has not revealed a preference for binding or cleavage of flaps over single-stranded DNA. Using DNA binding competition assays we found that Dna2 has substrate structure specificity. The nuclease displayed a strong preference for binding substrates with a 5'-flap or some variations of flap structure. Further analysis revealed that Dna2 recognized and bound both the single-stranded flap and portions of the duplex region immediately downstream of the flap. A model is proposed in which Dna2 first binds to a flap base, and then the flap threads through the protein with periodic cleavage, to a terminal flap length of ~5 nt. This resembles the mechanism of flap endonuclease 1, consistent with cooperation of these two proteins in flap processing

Spirals and heteroclinic cycles in a spatially extended Rock-Paper-Scissors model of cyclic dominance

Spatially extended versions of the cyclic-dominance Rock-Paper-Scissors model have traveling wave (in one dimension) and spiral (in two dimensions) behaviour. The far field of the spirals behave like traveling waves, which themselves have profiles reminiscent of heteroclinic cycles. We compute numerically a nonlinear dispersion relation between the wavelength and wavespeed of the traveling waves, and, together with insight from heteroclinic bifurcation theory and further numerical results from 2D simulations, we are able to make predictions about the overall structure and stability of spiral waves in 2D cyclic dominance models

Production and characterization of recombinant protein preparations of Endonuclease G-homologs from yeast, C. elegans and humans

Nuc1p, CPS-6, EndoG and EXOG are evolutionary conserved mitochondrial nucleases from yeast, Caenorhabditis elegans and humans, respectively. These enzymes play an important role in programmed cell death as well as mitochondrial DNA-repair and recombination. Whereas a significant interest has been given to the cell biology of these proteins, in particular their recruitment during caspase-independent apoptosis, determination of their biochemical properties has lagged behind. In part, biochemical as well as structural analysis of mitochondrial nucleases has been hampered by the fact that upon cloning and overexpression in Escherichia coli these enzymes can exert considerable toxicity and tend to aggregate and form inclusion bodies. We have, therefore, established a uniform E. coli expression system allowing us to obtain these four evolutionary related nucleases in active form from the soluble as well as insoluble fractions of E. coli cell lysates. Using preparations of recombinant Nuc1p, CPS-6, EndoG and EXOG we have compared biochemical properties and the substrate specificities of these related nucleases on selected substrates in parallel. Whereas Nuc1p and EXOG in addition to their endonuclease activity exert 5'-3'- exonuclease activity, CPS-6 and EndoG predominantly are endonucleases. These findings allow speculating that the mechanisms of action of these related nucleases in cell death as well as DNA-repair and recombination differ according to their enzyme activities and substrate specificities. © 2010 Elsevier Inc. All rights reserved

Gepner-like models and Landau-Ginzburg/sigma-model correspondence

The Gepner-like models of $k^{K}$-type is considered. When $k+2$ is multiple of $K$ the elliptic genus and the Euler characteristic is calculated. Using free-field representation we relate these models with $\sigma$-models on hypersurfaces in the total space of anticanonical bundle over the projective space $\mathbb{P}^{K-1}$