Multiple positive and negative regulators of signaling by the EGF-receptor

Signaling via the epidermal growth factor (EGF)-receptor family is subject to regulation and modulation by multiple ligands, effectors and negative regulators, as well as regulation by heterodimerization between family members and crosstalk between heterologous signaling pathways. Besides serving as a paradigm for receptor tyrosine kinases in general, this family is crucial for development and is often mutated or amplified in human tumors.     

Hepcidin非铁调控因子研究进展

铁调素（Hepcidin）是由肝细胞分泌的维持人体系统性铁平衡的核心因子,其通过改变细胞膜铁转运蛋白（ferroportin,Fpn）的表达量以调控肠黏膜细胞和巨噬细胞内铁的转出水平,从而决定机体循环铁水平并影响肝脏等主要储铁脏器的铁负荷程度。根据近年来的研究发现,影响Hepcidin表达的主要因素可以归纳为两个方面：一是机体本身对铁的需求,而由于铁本身又是Hb（hemoglobin,血红蛋白）的合成原料以及携氧成份,因此还应包括机体对Hb合成和缺氧的反应,介导因子主要包括携铁转铁蛋白（holo—transferrin,holo—Tf）、促红细胞生成素（erythropoietin,EPO）和缺氧诱导因子-1（hypoxia．inducible factor1,HIF．1）;另一则是源于疾病病理过程中相关致病因素、细胞因子、激素等非铁调控因子的改变对其表达调控机制产生的影响,并通过扰乱机体铁稳态加速疾病的发展或加重病情。随着研究资料的积累,糖尿病、部分心血管疾病、酒精性或非酒精性脂肪肝等慢性疾病存在铁过负荷已是不争的事实,多种hepcidin非铁调控因子在代谢紊乱型铁过负荷综合征（sysmetabolic iron overload syndrome）发生过程中的作用受到了广泛重视。对一些常见疾病中引起hepcidin表达变化异常和铁代谢紊乱的非铁因子及其作用机制的研究进展进行综述。     

Type IV collagens and Dpp positive and negative regulators of signaling

Decapentaplegic (Dpp) is an essential morphogen in the TGF-β/BMP superfamily which patterns fields of cells during multiple stages of Drosophila development, including the ovary and embryo. We have found that type IV collagens bind to Dpp and play essential roles in the regulation of its signaling during these two developmental stages. This article primarily focuses on type IV collagens and embryonic Dpp signaling to discuss aspects of the type IV collagen mutant phenotype in the context of additional data from the field. In addition, the restriction of Dpp signaling in the the ovary by type IV collagens is described, as the differences between the embryonic and ovarian Dpp sources result in distinct effects of collagen IV proteins in the two systems.     

A comparison of resonance tuning with positive versus negative sensory feedback

We used a computational model of rhythmic movement to analyze how the connectivity of sensory feedback affects the tuning of a closed-loop neuromechanical system to the mechanical resonant frequency (ω_r). Our model includes a Matsuoka half-center oscillator for a central pattern generator (CPG) and a linear, one-degree-of-freedom system for a mechanical component. Using both an open-loop frequency response analysis and closed-loop simulations, we compared resonance tuning with four different feedback configurations as the mechanical resonant frequency, feedback gain, and mechanical damping varied. The feedback configurations consisted of two negative and two positive feedback connectivity schemes. We found that with negative feedback, resonance tuning predominantly occurred when ω_r was higher than the CPG’s endogenous frequency (ω_CPG). In contrast, with the two positive feedback configurations, resonance tuning only occurred if ω_r was lower than ω_CPG. Moreover, the differences in resonance tuning between the two positive (negative) feedback configurations increased with increasing feedback gain and with decreasing mechanical damping. Our results indicate that resonance tuning can be achieved with positive feedback. Furthermore, we have shown that the feedback configuration affects the parameter space over which the endogenous frequency of the CPG or resonant frequency the mechanical dynamics dominates the frequency of a rhythmic movement.     

A perspective on mammalian caspases as positive and negative regulators of inflammation

Members of the caspase family of cysteine proteases coordinate the morphological and biochemical events that typify apoptosis. However, neutralization of caspase activity in mammals fails to block death in response to most proapoptotic stimuli. This is because many cell death triggers provoke mitochondrial dysfunction upstream of caspase activation as a consequence of BAX/BAK channel opening. Although genetic or pharmacological inactivation of caspases fails to block cell death in most instances, it does convert the phenotype from apoptosis to necrosis. This has important implications for how the immune system responds to such cells, as necrotic cells provoke inflammation whereas apoptotic cells typically do not. Here, we propose an alternative perspective on apoptosis-associated caspase function by suggesting that these proteases are activated, not to kill, but to extinguish the proinflammatory properties of dying cells. This perspective unifies the mammalian caspase family as either positive or negative regulators of inflammation.     

Fine tuning of cell signals by glycosylation

Carbohydrates on the glycoproteins and glycosphingolipids expressed on the cell surface membrane play crucial roles in the determination of cell fates by being involved in the fine tuning of cell signalling as reaction molecules in the front line to various extrinsic stimulants. In glycoproteins, modification of proteins is performed by substitution of sugar chains to one or multiple sites of individual proteins, leading to quantitative and qualitative changes of receptor functions in the cell membrane. As for glycosphingolipids, majority of them consist of two moieties, i.e. carbohydrates and ceramides, and are localized in the microdomains such as lipid rafts or detergent-resistant microdomains. They generate and/or modulate cell signals to determine the cell fates by interacting with various carbohydrate-recognizing proteins. Modes of glycosylation and mechanisms by which glycosylation is involved in the regulation of cell signals are now hot subjects in glycobiology.     

Fine tuning of TCR signaling by CD5

Current data indicate that CD5 functions as an inhibitor of TCR signal transduction. Consistent with this role, thymocyte selection in TCR transgenic/CD5(-/-) mice is altered in a manner suggestive of enhanced TCR signaling. However, the impact of CD5 deletion on thymocyte selection varies depending on the transgenic TCR analyzed, ranging from a slight to a marked shift from positive toward negative selection. An explanation for the variable effect of CD5 on selection is suggested by the observation that CD5 surface expression is regulated by TCR signal intensity during development and CD5 surface levels on mature thymocytes and T cells parallel the avidity of the positively selecting TCR/MHC/ligand interaction. In this study, we generated mice that overexpress CD5 during thymocyte development (CD5-tg), and then examined the effect of CD5 overexpression or CD5 deletion (CD5(-/-)) on selection of thymocytes that express the same TCR transgenes. The results demonstrate that the effect on thymocyte selection of altering CD5 expression depends on the avidity of the selecting interaction and, consequently, the level of basal (endogenous) CD5 surface expression. Substitution of endogenous CD5 with a transgene encoding a truncated form of the protein failed to rescue the CD5(-/-) phenotype, demonstrating that the cytoplasmic domain of CD5 is required for its inhibitory function. Together, these results indicate that inducible regulation of CD5 surface expression during thymocyte selection functions to fine tune the TCR signaling response.     

Immunomodulatory mast cells: negative, as well as positive, regulators of immunity

Mast cells can promote inflammation and other tissue changes in IgE-associated allergic disorders, as well as in certain innate and adaptive immune responses that are thought to be independent of IgE. However, mast cells can also have anti-inflammatory and immunosuppressive functions. Here, we review the evidence that mast cells can have negative, as well as positive, immunomodulatory roles in vivo, and we propose that mast cells can both enhance and later suppress certain features of an immune response.     

Fine tuning PDK1 activity by phosphorylation at Ser163

3-Phosphoinositide-dependent protein kinase-1 (PDK1) mediates phosphorylation and activation of members of the AGC protein kinase family and plays an essential role in insulin signaling and action. However, whether and how PDK1 activity is regulated in cells remains largely uncharacterized. In the present study, we show that PDK1 undergoes insulin-stimulated and phosphatidylinositol 3-kinase-dependent phosphorylation at Ser244 in the activation loop and at a novel site: Ser163 in the hinge region between the two lobes of the kinase domain. Sequence alignment studies revealed that the residue corresponding to Ser163 of PDK1 in all other AGC kinases is glutamate, suggesting that a negative charge at this site may be important for PDK1 function. Replacing Ser163 with a negatively charged residue, glutamate, led to a 2-fold increase in PDK1 activity. Molecular modeling studies suggested that phosphorylated Ser163 may form additional hydrogen bonds with Tyr149 and Gln223. In support of this, mutation of Tyr149 to Ala is sufficient to reduce PDK1 activity. Taken together, our results suggest that PDK1 phosphorylation of Ser163 may provide a mechanism to fine-tune PDK1 activity and function in cells.     

Mining gene expression data for positive and negative co-regulated gene clusters

MOTIVATION: Analysis of gene expression data can provide insights into the positive and negative co-regulation of genes. However, existing methods such as association rule mining are computationally expensive and the quality and quantities of the rules are sensitive to the support and confidence values. In this paper, we introduce the concept of positive and negative co-regulated gene cluster (PNCGC) that more accurately reflects the co-regulation of genes, and propose an efficient algorithm to extract PNCGCs. RESULTS: We experimented with the Yeast dataset and compared our resulting PNCGCs with the association rules generated by the Apriori mining algorithm. Our results show that our PNCGCs identify some missing co-regulations of association rules, and our algorithm greatly reduces the large number of rules involving uncorrelated genes generated by the Apriori scheme. AVAILABILITY: The software is available upon request.