METAMODELS AND PHYLOGENETIC REPLICATION: A SYSTEMATIC APPROACH TO THE EVOLUTION OF DEVELOPMENTAL PATHWAYS

Molecular genetic analysis of phenotypic variation has revealed many examples of evolutionary change in the developmental pathways that control plant and animal morphology. A major challenge is to integrate the information from diverse organisms and traits to understand the general patterns of developmental evolution. This integration can be facilitated by evolutionary metamodels—traits that have undergone multiple independent changes in different species and whose development is controlled by well-studied regulatory pathways. The metamodel approach provides the comparative equivalent of experimental replication, allowing us to test whether the evolution of each developmental pathway follows a consistent pattern, and whether different pathways are predisposed to different modes of evolution by their intrinsic organization. A review of several metamodels suggests that the structure of developmental pathways may bias the genetic basis of phenotypic evolution, and highlights phylogenetic replication as a value-added approach that produces deeper insights into the mechanisms of evolution than single-species analyses.     

Mediators,Genes and Signaling in Adventitious Rooting

Adventitious roots are a post-embryonic root which arise from the stem and leaves and from non-pericycle tissues in old roots and it is one of the most important ways of vegetative propagation in plants. Many exogenous and endogenous factors regulate the formation of adventitious roots, such as Ca²⁺, sugars, auxin, polyamines, ethylene, nitric oxide, hydrogen peroxide, carbon monoxide, cGMP, MAPKs and peroxidase, etc. These mediators are thought to function as signaling and mediate auxin signal transduction during the formation of adventitious roots. To date, only a few genes have been identified that are associated with the general process of adventitious rooting, such as ARL1, VvPRP1, VvPRP2, HRGPnt3, LRP1 and RML, etc. Auxin has been shown to be intimately involved in the process of adventitious rooting and function as crucial role in adventitious rooting. Great progress has been made in elucidating the auxin-induced genes and auxin signaling pathway, especially in auxin response Aux/IAA and ARF genes family and the auxin receptor TIR1. Although, some of important aspects of adventitious rooting signaling have been revealed, the intricate signaling network remains poorly understood.     

Quantitative modeling perspectives on the ErbB system of cell regulatory processes

The complexities of the processes involved in ErbB-mediated regulation of cellular phenotype are broadly appreciated, so much so that it might be reasonably argued that this highly studied system provided significant impetus for the systems perspective on cell signaling processes in general. Recent years have seen major advances in the level of characterization of the ErbB system as well as our ability to make measurements of the system. This new data provides significant new insight, while at the same time creating new challenges for making quantitative statements and predictions with certainty. Here, we discuss recent advances in each of these directions and the interplay between them, with a particular focus on quantitative modeling approaches to interpret data and provide predictive power. Our discussion follows the sequential order of ErbB pathway activation, beginning with considerations of receptor/ligand interactions and dynamics, proceeding to the generation of intracellular signals, and ending with determination of cellular phenotype. As discussed herein, these processes become increasingly difficult to describe or interpret in terms of traditional models, and we review emerging methodologies to address this complexity.     

Hypothermia attenuates ischemia/reperfusion-induced endothelial cell apoptosis via alterations in apoptotic pathways and JNK signaling

Hypothermia is the most effective means of protecting the brain, heart and other organs during ischemia/reperfusion (I/R) injury. However, the precise mechanisms for hypothermia to inhibit I/R-induced endothelial cell apoptosis are not fully understood. In the present study, human umbilical endothelial cells (HUVECs) were exposed to ischemia followed by reperfusion under normothermia (37 °C) or hypothermia (33 °C). Our results showed that hypothermia markedly reduced I/R-induced endothelial cell apoptosis, the expression of cleaved caspase-3 and PARP. Moreover, hypothermia markedly reversed I/R-induced activation of Fas/caspase-8, the increase of Bax and decrease of Bcl-2. Furthermore, hypothermia inhibited JNK1/2 activation via MKP-1 induction. Together, these data demonstrate that hypothermia represses I/R-induced endothelial cell apoptosis by inhibiting both extrinsic- and intrinsic-dependent apoptotic pathways and activation of JNK1/2.     

Profiling of T‐cell receptor signaling complex assembly in human CD4 T‐lymphocytes using RP protein arrays

The RP protein (RPP) array approach immobilizes minute amounts of cell lysates or tissue protein extracts as distinct microspots on NC‐coated slide. Subsequent detection with specific antibodies allows multiplexed quantification of proteins and their modifications at a scale that is beyond what traditional techniques can achieve. Cellular functions are the result of the coordinated action of signaling proteins assembled in macromolecular complexes. These signaling complexes are highly dynamic structures that change their composition with time and space to adapt to cell environment. Their comprehensive analysis requires until now relatively large amounts of cells (>5×10⁷) due to their low abundance and breakdown during isolation procedure. In this study, we combined small scale affinity capture of the T‐cell receptor (TCR) and RPP arrays to follow TCR signaling complex assembly in human ex vivo isolated CD4 T‐cells. Using this strategy, we report specific recruitment of signaling components to the TCR complex upon T‐cell activation in as few as 0.5 million of cells. Second‐ to fourth‐order TCR interacting proteins were accurately quantified, making this strategy specially well‐suited to the analysis of membrane‐associated signaling complexes in limited amounts of cells or tissues, e.g., ex vivo isolated cells or clinical specimens.     

多功能的钙／钙调素依赖的蛋白激酶II介导的细胞信号传导

钙调素（Calmodulin,CaM）是一个特别的对钙敏感的蛋白,在钙信号传导通路中扮演重要角色钙／钙调素依赖性蛋白激酶（Calcium／calmodulin-dependent kinases（CaMKs））与荷尔蒙、神经迷质及其他信号引起的细胞反应相关、作为重要的第二信使,钙／钙调素依赖的蛋白激酶Ⅱ（CaM—KⅡ）是一类在细咆中无所不在的表达的蛋白激酶,能维持细胞内的钙浓度在很低的水平,再增加后续的特定的钙激动刺激。钙／钙调素依赖的簧白激酶Ⅱ独特的全酶结构和自我调节的性质使其对短暂的钙信号和胞内钙的变化能做出延长反应：本文从结构、合成、细胞分布、反应底物、生理功能等方面介绍了钙／钙调素依赖的蛋白激酶Ⅱ的激活对细胞信号传导的作用。     

Emergence and transmission of visual awareness through optical coding in the brain: A redox molecular hypothesis on visual mental imagery

Does the primary visual cortex mediate consciousness for higher-level stages of information processing by providing an outlet for mental imagery? Evidence based on neural electrical activity is inconclusive as reflected in the “imagery debate” in cognitive science. Neural information and activity, however, also depend on regulated biophoton (optical) signaling. During encoding and retrieval of visual information, regulated electrical (redox) signals of neurons are converted into synchronized biophoton signals by bioluminescent radical processes. That is, visual information may be represented by regulated biophotons of mitochondrial networks in retinotopically organized cytochrome oxidase-rich neural networks within early visual areas. Therefore, we hypothesize that regulated biophotons can generate intrinsic optical representations in the primary visual cortex and then propagate variably degraded versions along cytochrome oxidase pathways during both perception and imagery. Testing this hypothesis requires to establish a methodology for measurement of in vivo and/or in vitro increases of biophoton emission in humans' brain during phosphene inductions by transcranial magnetic stimulation and to compare the decrease in phosphene thresholds during transcranial magnetic stimulation and imagery. Our hypothesis provides a molecular mechanism for the visual buffer and for imagery as the prevalent communication mode (through optical signaling) within the brain. If confirmed empirically, this hypothesis could resolve the imagery debate and the underlying issue of continuity between perception and abstract thought.     

Eph/ephrin recognition and the role of Eph/ephrin clusters in signaling initiation

The Eph receptors and their ephrin ligands play crucial roles in a large number of cell–cell interaction events, including those associated with axon pathfinding, neuronal cell migration and vasculogenesis. They are also involved in the patterning of most tissues and overall cell positioning in the development of the vertebrate body plan. The Eph/ephrin signaling system manifests several unique features that differentiate it from other receptor tyrosine kinases, including initiation of bi-directional signaling cascades and the existence of ligand and receptor subclasses displaying promiscuous intra-subclass interactions, but very rare inter-subclass interactions. In this review we briefly discuss these features and focus on recent studies of the unique and expansive high-affinity Eph/ephrin assemblies that form at the sites of cell–cell contact and are required for Eph signaling initiation. This article is part of a Special Issue entitled: Emerging recognition and activation mechanisms of receptor tyrosine kinases.     

Plant secretome — From cellular process to biological activity

Recent studies suggest that plants secrete a large number of proteins and peptides into the extracellular space. Secreted proteins play a crucial role in stress response, communication and development of organisms. Here we review the current knowledge of the secretome of more than ten plant species, studied in natural conditions or during (a)biotic stress. This review not only deals with the classical secretory route via endoplasmic reticulum and Golgi followed by proteins containing a known N-terminal signal peptide, but also covers new findings about unconventional secretion of leaderless proteins. We describe alternative secretion pathways and the involved compartments like the recently discovered EXPO. The well characterized secreted peptides that function as ligands of receptor proteins exemplify the biological significance and activity of the secretome. This article is part of a Special Issue entitled: An Updated Secretome.