Crosstalk and the Dynamical Modularity of Feed-Forward Loops in Transcriptional Regulatory Networks

Network motifs, such as the feed-forward loop (FFL), introduce a range of complex behaviors to transcriptional regulatory networks, yet such properties are typically determined from their isolated study. We characterize the effects of crosstalk on FFL dynamics by modeling the cross regulation between two different FFLs and evaluate the extent to which these patterns occur in vivo. Analytical modeling suggests that crosstalk should overwhelmingly affect individual protein-expression dynamics. Counter to this expectation we find that entire FFLs are more likely than expected to resist the effects of crosstalk (approximate to 20% for one crosstalk interaction) and remain dynamically modular. The likelihood that cross-linked FFLs are dynamically correlated increases monotonically with additional crosstalk, but is independent of the specific regulation type or connectivity of the interactions. Just one additional regulatory interaction is sufficient to drive the FFL dynamics to a statistically different state. Despite the potential for modularity between sparsely connected network motifs, Escherichia coli (E. coli) appears to favor crosstalk wherein at least one of the cross-linked FFLs remains modular. A gene ontology analysis reveals that stress response processes are significantly overrepresented in the cross-linked motifs found within E. coli. Although the daunting complexity of biological networks affects the dynamical properties of individual network motifs, some resist and remain modular, seemingly insulated from extrinsic perturbations-an intriguing possibility for nature to consistently and reliably provide certain network functionalities wherever the need arise

Phosphatase Specificity and Pathway Insulation in Signaling Networks

AbstractPhosphatases play an important role in cellular signaling networks by regulating the phosphorylation state of proteins. Phosphatases are classically considered to be promiscuous, acting on tens to hundreds of different substrates. We recently demonstrated that a shared phosphatase can couple the responses of two proteins to incoming signals, even if those two substrates are from otherwise isolated areas of the network. This finding raises a potential paradox: if phosphatases are indeed highly promiscuous, how do cells insulate themselves against unwanted crosstalk? Here, we use mathematical models to explore three possible insulation mechanisms. One approach involves evolving phosphatase KM values that are large enough to prevent saturation by the phosphatase’s substrates. Although this is an effective method for generating isolation, the phosphatase becomes a highly inefficient enzyme, which prevents the system from achieving switch-like responses and can result in slow response kinetics. We also explore the idea that substrate degradation can serve as an effective phosphatase. Assuming that degradation is unsaturatable, this mechanism could insulate substrates from crosstalk, but it would also preclude ultrasensitive responses and would require very high substrate turnover to achieve rapid dephosphorylation kinetics. Finally, we show that adaptor subunits, such as those found on phosphatases like PP2A, can provide effective insulation against phosphatase crosstalk, but only if their binding to substrates is uncoupled from their binding to the catalytic core. Analysis of the interaction network of PP2A’s adaptor domains reveals that although its adaptors may isolate subsets of targets from one another, there is still a strong potential for phosphatase crosstalk within those subsets. Understanding how phosphatase crosstalk and the insulation mechanisms described here impact the function and evolution of signaling networks represents a major challenge for experimental and computational systems biology

Crosstalk, Network Dynamics, and the Evolution of Signaling

Cells have developed networks of interacting proteins to process information about their environment and respond appropriately to stimuli. Reversible post-translational modifications alter the functionality of these proteins, transmitting information through the cell. Bacteria primarily utilize Two-Component Signaling (TCS) networks, in which a sensor Histidine Kinase (HK) activates a Response Regulator (RR), which typically acts as a transcription factor. TCS pathways are insulated from one another, each responding to a unique stimulus. In contrast, metazoan signaling networks are extremely complex, to the point that individual pathways are no longer discernible from the web of interactions. Cellular decisions are no longer binary; the overall state of the network determines the response to inputs. In this work, we use mathematical modeling to explore the dynamics that give rise to the dichotomy in network complexity and the evolutionary pressures and benefits of crosstalk, or the lack thereof. We find that proteins can act as competitive inhibitors of each other when competing for a shared enzyme. For example, the phosphorylation of one protein would monopolize a phosphatase, decreasing the concentration of phosphatase available to competing substrates. Consequently, the other substrates would see an increase in their own phosphorylation, indicating the potential for crosstalk mediated by any shared enzyme. The shared competitive inhibition of enzymes by different substrates has a more drastic effect in bacterial TCS pathways. HKs are typically bifunctional, acting as both kinase and phosphatase for their RRs. These dynamics results in a situation in which the introduction of crosstalk to TCS networks would always decrease system efficiency. While the enzymes typical of metazoan networks do not have the same enzymatic constraints as TCS networks, the fact that they can evolve crosstalk does not explain the benefits that have driven such complexity. The extensive crosstalk present in metazoans has likely evolved due to the constraints multicellularity has placed on intracellular communication. Because of the complexity of the network, the expression of different signaling components in various cell types results in a high level of diversity in responses to stimuli. Ultimately, our work demonstrates that the cellular context must be considered in interpreting network connectivity

Crosstalk and the evolvability of intracellular communication

Metazoan signalling networks are complex, with extensive crosstalk between pathways. It is unclear what pressures drove the evolution of this architecture. We explore the hypothesis that crosstalk allows different cell types, each expressing a specific subset of signalling proteins, to activate different outputs when faced with the same inputs, responding differently to the same environment. We find that the pressure to generate diversity leads to the evolution of networks with extensive crosstalk. Using available data, we find that human tissues exhibit higher levels of diversity between cell types than networks with random expression patterns or networks with no crosstalk. We also find that crosstalk and differential expression can influence drug activity: no protein has the same impact on two tissues when inhibited. In addition to providing a possible explanation for the evolution of crosstalk, our work indicates that consideration of cellular context will likely be crucial for targeting signalling networks

Orbitally excited and hybrid mesons from the lattice

We discuss in general the construction of gauge-invariant non-local meson operators on the lattice. We use such operators to study the $P$- and $D$-wave mesons as well as hybrid mesons in quenched QCD, with quark masses near the strange quark mass. The resulting spectra are compared with experiment for the orbital excitations. For the states produced by gluonic excitations (hybrid mesons) we find evidence of mixing for non-exotic quantum numbers. We give predictions for masses of the spin-exotic hybrid mesons with $J^{PC}=1^{-+},\ 0^{+-}$, and$2^{+-}$.Comment: 31 pages, LATEX, 8 postscript figures. Reference adde

Maturation of the proteasome core particle induces an affinity switch that controls regulatory particle association

Proteasome assembly is a complex process, requiring 66 subunits distributed over several subcomplexes to associate in a coordinated fashion. Ten proteasome-specific chaperones have been identified that assist in this process. For two of these, the Pba1-Pba2 dimer, it is well established that they only bind immature core particles (CPs) in vivo. In contrast, the regulatory particle (RP) utilizes the same binding surface but only interacts with the mature CP in vivo. It is unclear how these binding events are regulated. Here, we show that Pba1-Pba2 binds tightly to the immature CP, preventing RP binding. Changes in the CP that occur on maturation significantly reduce its affinity for Pba1-Pba2, enabling the RP to displace the chaperone. Mathematical modelling indicates that this ‘affinity switch’ mechanism has likely evolved to improve assembly efficiency by preventing the accumulation of stable, non-productive intermediates. Our work thus provides mechanistic insights into a crucial step in proteasome biogenesis

Distinct roles of parvalbumin and somatostatin interneurons in gating the synchronization of spike-times in the neocortex

Synchronization of precise spike times across multiple neurons carries information about sensory stimuli. Inhibitory interneurons are suggested to promote this synchronization, but it is unclear whether distinct interneuron subtypes provide different contributions. To test this, we examined single-unit recordings from barrel cortex in vivo and used optogenetics to determine the contribution of parvalbumin (PV)– and somatostatin (SST)–positive interneurons to the synchronization of spike times across cortical layers. We found that PV interneurons preferentially promote the synchronization of spike times when instantaneous firing rates are low (<12 Hz), whereas SST interneurons preferentially promote the synchronization of spike times when instantaneous firing rates are high (>12 Hz). Furthermore, using a computational model, we demonstrate that these effects can be explained by PV and SST interneurons having preferential contributions to feedforward and feedback inhibition, respectively. Our findings demonstrate that distinct subtypes of inhibitory interneurons have frequency-selective roles in the spatiotemporal synchronization of precise spike times

Skeletonized internal thoracic artery harvesting reduces chest wall dysesthesia after coronary bypass surgery

ObjectiveA pain syndrome related to intercostal nerve injury during internal thoracic artery harvesting causes significant morbidity after coronary bypass surgery. We hypothesized that its incidence and severity might be reduced by using skeletonized internal thoracic artery harvesting rather than pedicled harvesting.MethodsIn a prospective double-blind clinical trial, 41 patients undergoing coronary bypass were randomized to receive either unilateral pedicled or skeletonized internal thoracic artery harvesting. Patients were assessed 7 (early) and 21 (late) weeks postoperatively with reproducible sensory stimuli used to detect chest wall sensory deficits (dysesthesia) and with a pain questionnaire used to assess neuropathic pain.ResultsAt 7 weeks postoperatively, the area of harvest dysesthesia (percentage of the chest) in the skeletonized group (n = 21) was less (median, 0%; interquartile range, 0–0) than in the pedicled group (n = 20) (2.8% [0–13], P = .005). The incidence of harvest dysesthesia at 7 weeks was 14% in the skeletonized group versus 50% in the pedicled group (P = .02). These differences were not sustained at 21 weeks, as the median area of harvest dysesthesia in both groups was 0% (P = .89) and the incidence was 24% and 25% in the skeletonized and pedicled groups, respectively (P = 1.0). The incidence of neuropathic pain in the skeletonized group compared with the pedicled group was 5% versus 10% (P = .6) at 7 weeks and 0% versus 0% (P = 1.0) at 21 weeks.ConclusionsCompared with pedicled harvesting, skeletonized harvesting of the internal thoracic artery provides a short-term reduction in the extent and incidence of chest wall dysesthesia after coronary bypass, consistent with reduced intercostal nerve injury and therefore the reduced potential for neuropathic chest pain