127 research outputs found
Cellular Complexity in MAPK Signaling in Plants: Questions and Emerging Tools to Answer Them
Mitogen activated protein kinase (MAPK) cascades play an important role in many aspects of plant growth, development, and environmental response. Because of their central role in many important processes, MAPKs have been extensively studied using biochemical and genetic approaches. This work has allowed for the identification of the MAPK genes and proteins involved in a number of different signaling pathways. Less well developed, however, is our understanding of how MAPK cascades and their corresponding signaling pathways are organized at subcellular levels. In this review, we will provide an overview of plant MAPK signaling, including a discussion of what is known about cellular mechanisms for achieving signaling specificity. Then we will explore what is currently known about the subcellular localization of MAPK proteins in resting conditions and after pathway activation. Finally, we will discuss a number of new experimental methods that have not been widely deployed in plants that have the potential to provide a deeper understanding of the spatial and temporal dynamics of MAPK signaling
Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS
Vector Addition Systems with States (VASS) provide a well-known and
fundamental model for the analysis of concurrent processes, parameterized
systems, and are also used as abstract models of programs in resource bound
analysis. In this paper we study the problem of obtaining asymptotic bounds on
the termination time of a given VASS. In particular, we focus on the
practically important case of obtaining polynomial bounds on termination time.
Our main contributions are as follows: First, we present a polynomial-time
algorithm for deciding whether a given VASS has a linear asymptotic complexity.
We also show that if the complexity of a VASS is not linear, it is at least
quadratic. Second, we classify VASS according to quantitative properties of
their cycles. We show that certain singularities in these properties are the
key reason for non-polynomial asymptotic complexity of VASS. In absence of
singularities, we show that the asymptotic complexity is always polynomial and
of the form , for some integer , where is the
dimension of the VASS. We present a polynomial-time algorithm computing the
optimal . For general VASS, the same algorithm, which is based on a complete
technique for the construction of ranking functions in VASS, produces a valid
lower bound, i.e., a such that the termination complexity is .
Our results are based on new insights into the geometry of VASS dynamics, which
hold the potential for further applicability to VASS analysis.Comment: arXiv admin note: text overlap with arXiv:1708.0925
On Reachability Problems for Low-Dimensional Matrix Semigroup
We consider the Membership and the Half-Space Reachability problems for matrices in dimensions two and three. Our first main result is that the Membership Problem is decidable for finitely generated sub-semigroups of the Heisenberg group over rational numbers. Furthermore, we prove two decidability results for the Half-Space Reachability Problem. Namely, we show that this problem is decidable for sub-semigroups of GL(2,Z) and of the Heisenberg group over rational numbers
Recommended from our members
Containment and equivalence of weighted automata: Probabilistic and max-plus cases
This paper surveys some results regarding decision problems for probabilistic and max-plus automata, such as containment and equivalence. Probabilistic and max-plus automata are part of the general family of weighted automata, whose semantics are maps from words to real values. Given two weighted automata, the equivalence problem asks whether their semantics are the same, and the containment problem whether one is point-wise smaller than the other one. These problems have been studied intensively and this paper will review some techniques used to show (un)decidability and state a list of open questions that still remain
PPR proteins - orchestrators of organelle RNA metabolism.
Pentatricopeptide repeat (PPR) proteins are important RNA regulators in chloroplasts and mitochondria, aiding in RNA editing, maturation, stabilisation or intron splicing, and in transcription and translation of organellar genes. In this review, we summarise all PPR proteins documented so far in plants and the green alga Chlamydomonas. By further analysis of the known target RNAs from Arabidopsis thaliana PPR proteins, we find that all organellar-encoded complexes are regulated by these proteins, although to differing extents. In particular, the orthologous complexes of NADH dehydrogenase (Complex I) in the mitochondria and NADH dehydrogenase-like (NDH) complex in the chloroplast were the most regulated, with respectively 60 and 28% of all characterised A. thaliana PPR proteins targeting their genes
Arabidopsis CaM Binding Protein CBP60g Contributes to MAMP-Induced SA Accumulation and Is Involved in Disease Resistance against Pseudomonas syringae
Salicylic acid (SA)-induced defense responses are important factors during effector triggered immunity and microbe-associated molecular pattern (MAMP)-induced immunity in plants. This article presents evidence that a member of the Arabidopsis CBP60 gene family, CBP60g, contributes to MAMP-triggered SA accumulation. CBP60g is inducible by both pathogen and MAMP treatments. Pseudomonas syringae growth is enhanced in cbp60g mutants. Expression profiles of a cbp60g mutant after MAMP treatment are similar to those of sid2 and pad4, suggesting a defect in SA signaling. Accordingly, cbp60g mutants accumulate less SA when treated with the MAMP flg22 or a P. syringae hrcC strain that activates MAMP signaling. MAMP-induced production of reactive oxygen species and callose deposition are unaffected in cbp60g mutants. CBP60g is a calmodulin-binding protein with a calmodulin-binding domain located near the N-terminus. Calmodulin binding is dependent on Ca2+. Mutations in CBP60g that abolish calmodulin binding prevent complementation of the SA production and bacterial growth defects of cbp60g mutants, indicating that calmodulin binding is essential for the function of CBP60g in defense signaling. These studies show that CBP60g constitutes a Ca2+ link between MAMP recognition and SA accumulation that is important for resistance to P. syringae
Increased Anion Channel Activity Is an Unavoidable Event in Ozone-Induced Programmed Cell Death
Ozone is a major secondary air pollutant often reaching high concentrations
in urban areas under strong daylight, high temperature and stagnant
high-pressure systems. Ozone in the troposphere is a pollutant that is
harmful to the plant. generation by salicylic and abscisic acids.
Anion channel activation was also shown to promote the accumulation of
transcripts encoding vacuolar processing enzymes, a family of proteases
previously reported to contribute to the disruption of vacuole integrity
observed during programmed cell death.-induced
programmed cell death. Because ion channels and more specifically anion
channels assume a crucial position in cells, an understanding about the
underlying role(s) for ion channels in the signalling pathway leading to
programmed cell death is a subject that warrants future investigation
Tight polynomial bounds for Loop programs in polynomial space
We consider the following problem: given a program, find tight asymptotic
bounds on the values of some variables at the end of the computation (or at any given
program point) in terms of its input values. We focus on the case of polynomially-bounded
variables, and on a weak programming language for which we have recently shown that
tight bounds for polynomially-bounded variables are computable. These bounds are sets
of multivariate polynomials. While their computability has been settled, the complexity
of this program-analysis problem remained open. In this paper, we show the problem to
be PSPACE-complete. The main contribution is a new, space-efficient analysis algorithm.
This algorithm is obtained in a few steps. First, we develop an algorithm for univariate
bounds, a sub-problem which is already PSPACE-hard. Then, a decision procedure for
multivariate bounds is achieved by reducing this problem to the univariate case; this
reduction is orthogonal to the solution of the univariate problem and uses observations on
the geometry of a set of vectors that represent multivariate bounds. Finally, we transform
the univariate-bound algorithm to produce multivariate bounds
- β¦