BBX16 mediates the repression of seedling photomorphogenesis downstream of the GUN1-GLK1 module during retrograde signaling

Plastid-to-nucleus retrograde signals (RS) initiated by dysfunctional chloroplasts impact photomorphogenic development. We previously showed that the transcription factor GLK1 acts downstream of the RS-regulator GUN1 in photodamaging conditions to regulate not only the well-established expression of photosynthesis-associated nuclear genes (PhANGs) but also to regulate seedling morphogenesis. Specifically, the GUN1/GLK1 module inhibits the light-induced PIF-repressed transcriptional network to suppress cotyledon development when chloroplast integrity is compromised, modulating the area exposed to potentially damaging high light. However, how the GUN1/GLK1 module inhibits photomorphogenesis upon chloroplast damage remained undefined. Here, we report the identification of BBX16 as a novel direct target of GLK1. BBX16 is induced and promotes photomorphogenesis in moderate light and it is repressed via GUN1/GLK1 after chloroplast damage. Additionally, we show that BBX16 represents a regulatory branching point downstream of GUN1/GLK1 in the regulation of PhANG expression and seedling development upon RS activation. The gun1 phenotype in lincomycin and the gun1-like phenotype of GLK1OX are markedly suppressed in gun1bbx16 and GLK1OXbbx16. This study identifies BBX16 as the first member of the BBX family involved in RS, and defines a molecular bifurcation mechanism operated by GLK1/BBX16 to optimize seedling deetiolation, and to ensure photoprotection in unfavorable light conditions.

On factorizable S-matrices, generalized TTbar, and the Hagedorn transition

We study solutions of the Thermodynamic Bethe Ansatz equations for relativistic theories defined by the factorizable S-matrix of an integrable QFT deformed by CDD factors. Such S-matrices appear under generalized TTbar deformations of integrable QFT by special irrelevant operators. The TBA equations, of course, determine the ground state energy E(R) of the finite-size system, with the spatial coordinate compactified on a circle of circumference R. We limit attention to theories involving just one kind of stable particles, and consider deformations of the trivial (free fermion or boson) S-matrix by CDD factors with two elementary poles and regular high energy asymptotics — the “2CDD model”. We find that for all values of the parameters (positions of the CDD poles) the TBA equations exhibit two real solutions at R greater than a certain parameter-dependent value R*, which we refer to as the primary and secondary branches. The primary branch is identified with the standard iterative solution, while the secondary one is unstable against iterations and needs to be accessed through an alternative numerical method known as pseudo-arc-length continuation. The two branches merge at the “turning point” R* (a square-root branching point). The singularity signals a Hagedorn behavior of the density of high energy states of the deformed theories, a feature incompatible with the Wilsonian notion of a local QFT originating from a UV fixed point, but typical for string theories. This behavior of E(R) is qualitatively the same as the one for standard TTbar deformations of local QFT.

Modeling the Multi-channel Section in the Supply Chain System using the Multiserver Queue Analogy

The industry generally consists of a supply chain system. The main constituents of any supply chain system are suppliers, manufacturers, distribution centers, and retailers. The system configuration can be straight chain, branched, cyclic, or a combination of all. An analytical model is needed to study system behavior as a result of the dynamics of its constituents. Modeling a multi-channel section becomes quite a challenging job in this regard. A method of modeling the multi-channel section will be discussed in this paper by adopting multi-server queues. As is well known, in a multi-server queue, there is a branching point at which the flow of entities begins to spread across several parallel servers. In the modeling perspective of this paper, the branching point is in the buffer (finished good warehouse in the factory, i.e., the focal echelon). That is the end of the waiting line from which the entity specifically moves to one of the servers, or in this context; it is called a channel. In this paper, the number of channels can be any, generalizable, can be more than two. Hence, the subsystem studied includes a factory, finished product warehouse, and several distribution centers. The factory produces by the mechanism of, where and r are stopping point and production restarting point, respectively. Production stops when the quantity of finished product in the warehouse reaches units and will restart the production when the quantity drops to the same or lower than units. The model is developed under Markovian assumptions by considering the quantities of production rates, the number of distribution centers (channels), travel time from factories to each distribution center, delivery lot size, and the time between the arrival of orders from distribution centers. The system under study is seen as a case of two echelons, namely factories and distribution channels. The numerical model obtained is applied to one case example with certain conditions. Comparisons with discrete simulation results give relatively small and acceptable differences. So, in the future, this model can complement the overall modeling of the supply chain system, a multi-echelon system with multi-channel distribution.

Ethanologenesis and respiration in a pyruvate decarboxylase-deficient Zymomonas mobilis

Objective Zymomonas mobilis is an alpha-proteobacterium with a rapid ethanologenic pathway, involving Entner–Doudoroff (E–D) glycolysis, pyruvate decarboxylase (Pdc) and two alcohol dehydrogenase (ADH) isoenzymes. Pyruvate is the end-product of the E–D pathway and the substrate for Pdc. Construction and study of Pdc-deficient strains is of key importance for Z. mobilis metabolic engineering, because the pyruvate node represents the central branching point, most novel pathways divert from ethanol synthesis. In the present work, we examined the aerobic metabolism of a strain with partly inactivated Pdc. Results Relative to its parent strain the mutant produced more pyruvate. Yet, it also yielded more acetaldehyde, the product of the Pdc reaction and the substrate for ADH, although the bulk ADH activity was similar in both strains, while the Pdc activity in the mutant was reduced by half. Simulations with the kinetic model of Z. mobilis E-D pathway indicated that, for the observed acetaldehyde to ethanol production ratio in the mutant, the ratio between its respiratory NADH oxidase and ADH activities should be significantly higher, than the measured values. Implications of this finding for the directionality of the ADH isoenzyme operation in vivo and interactions between ADH and Pdc are discussed.

Modeled 3D-Structures of Proteobacterial Transglycosylases from Glycoside Hydrolase Family 17 Give Insight in Ligand Interactions Explaining Differences in Transglycosylation Products

The structures of glycoside hydrolase family 17 (GH17) catalytic modules from modular proteins in the ndvB loci in Pseudomonas aeruginosa (Glt1), P. putida (Glt3) and Bradyrhizobium diazoefficiens (previously B. japonicum) (Glt20) were modeled to shed light on reported differences between these homologous transglycosylases concerning substrate size, preferred cleavage site (from reducing end (Glt20: DP2 product) or non-reducing end (Glt1, Glt3: DP4 products)), branching (Glt20) and linkage formed (1,3-linkage in Glt1, Glt3 and 1,6-linkage in Glt20). Hybrid models were built and stability of the resulting TIM-barrel structures was supported by molecular dynamics simulations. Catalytic amino acids were identified by superimposition of GH17 structures, and function was verified by mutagenesis using Glt20 as template (i.e., E120 and E209). Ligand docking revealed six putative subsites (−4, −3, −2, −1, +1 and +2), and the conserved interacting residues suggest substrate binding in the same orientation in all three transglycosylases, despite release of the donor oligosaccharide product from either the reducing (Glt20) or non-reducing end (Glt1, Gl3). Subsites +1 and +2 are most conserved and the difference in release is likely due to changes in loop structures, leading to loss of hydrogen bonds in Glt20. Substrate docking in Glt20 indicate that presence of covalently bound donor in glycone subsites −4 to −1 creates space to accommodate acceptor oligosaccharide in alternative subsites in the catalytic cleft, promoting a branching point and formation of a 1,6-linkage. The minimum donor size of DP5, can be explained assuming preferred binding of DP4 substrates in subsite −4 to −1, preventing catalysis.

On the importance of evolving phenotype distributions on evolutionary diversification

Evolutionary branching occurs when a population with a unimodal phenotype distribution diversifies into a multimodally distributed population consisting of two or more strains. Branching results from frequency-dependent selection, which is caused by interactions between individuals. For example, a population performing a social task may diversify into a cooperator strain and a defector strain. Branching can also occur in multi-dimensional phenotype spaces, such as when two tasks are performed simultaneously. In such cases, the strains may diverge in different directions: possible outcomes include division of labor (with each population performing one of the tasks) or the diversification into a strain that performs both tasks and another that performs neither. Here we show that the shape of the population’s phenotypic distribution plays a role in determining the direction of branching. Furthermore, we show that the shape of the distribution is, in turn, contingent on the direction of approach to the evolutionary branching point. This results in a distribution–selection feedback that is not captured in analytical models of evolutionary branching, which assume monomorphic populations. Finally, we show that this feedback can influence long-term evolutionary dynamics and promote the evolution of division of labor.

Superinfection and the evolution of an initial asymptomatic stage

Pathogens have evolved a variety of life-history strategies. An important strategy consists of successful transmission by an infected host before the appearance of symptoms, that is, while the host is still partially or fully asymptomatic. During this initial stage of infection, it is possible for another pathogen to superinfect an already infected host and replace the previously infecting pathogen. Here, we study the effect of superinfection during the first stage of an infection on the evolutionary dynamics of the degree to which the host is asymptomatic (host latency) in that same stage. We find that superinfection can lead to major differences in evolutionary behaviour. Most strikingly, the duration of immunity following infection can significantly influence pathogen evolutionary dynamics, whereas without superinfection the outcomes are independent of host immunity. For example, changes in host immunity can drive evolutionary transitions from a fully symptomatic to a fully asymptomatic first infection stage. Additionally, if superinfection relative to susceptible infection is strong enough, evolution can lead to a unique strategy of latency that corresponds to a local fitness minimum, and is therefore invasible by nearby mutants. Thus, this strategy is a branching point, and can lead to coexistence of pathogens with different latencies. Furthermore, in this new framework with superinfection, we also find that there can exist two interior singular strategies. Overall, new evolutionary outcomes can cascade from superinfection.

Minimal set of periods for continuous self-maps of the eight space

Let $G_{k}$ G k be a bouquet of circles, i.e., the quotient space of the interval $[0,k]$ [ 0 , k ] obtained by identifying all points of integer coordinates to a single point, called the branching point of $G_{k}$ G k . Thus, $G_{1}$ G 1 is the circle, $G_{2}$ G 2 is the eight space, and $G_{3}$ G 3 is the trefoil. Let $f: G_{k} \to G_{k}$ f : G k → G k be a continuous map such that, for $k>1$ k > 1 , the branching point is fixed.If $\operatorname{Per}(f)$ Per ( f ) denotes the set of periods of f, the minimal set of periods of f, denoted by $\operatorname{MPer}(f)$ MPer ( f ) , is defined as $\bigcap_{g\simeq f} \operatorname{Per}(g)$ ⋂ g ≃ f Per ( g ) where $g:G_{k}\to G_{k}$ g : G k → G k is homological to f.The sets $\operatorname{MPer}(f)$ MPer ( f ) are well known for circle maps. Here, we classify all the sets $\operatorname{MPer}(f)$ MPer ( f ) for self-maps of the eight space.