Effect of overall feedback inhibition in unbranched biosynthetic pathways

We have determined the effects of control by overall feedback inhibition on the systemic behavior of unbranched metabolic pathways with an arbitrary pattern of other feedback inhibitions by using a recently developed numerical generalization of Mathematically Controlled Comparisons, a method for comparing the function of alternative molecular designs. This method allows the rigorous determination of the changes in systemic properties that can be exclusively attributed to overall feedback inhibition. Analytical results show that the unbranched pathway can achieve the same steady-state flux, concentrations, and logarithmic gains with respect to changes in substrate, with or without overall feedback inhibition. The analytical approach also shows that control by overall feedback inhibition amplifies the regulation of flux by the demand for end product while attenuating the sensitivity of the concentrations to the same demand. This approach does not provide a clear answer regarding the effect of overall feedback inhibition on the robustness, stability, and transient time of the pathway. However, the generalized numerical method we have used does clarify the answers to these questions. On average, an unbranched pathway with control by overall feedback inhibition is less sensitive to perturbations in the values of the parameters that define the system. The difference in robustness can range from a few percent to fifty percent or more, depending on the length of the pathway and on the metabolite one considers. On average, overall feedback inhibition decreases the stability margins by a minimal amount (typically less than 5%). Finally, and again on average, stable systems with overall feedback inhibition respond faster to fluctuations in the metabolite concentrations. Taken together, these results show that control by overall feedback inhibition confers several functional advantages upon unbranched pathways. These advantages provide a rationale for the prevalence of this control mechanism in unbranched metabolic pathways in vivo.     

Dynamic stability of steady states and static stabilization in unbranched metabolic pathways

The paper is concerned with the conditions of dynamic (asymptotic) stability of steady states in unbranched metabolic pathways. The stationary flux in such pathways is generally determined by the concentration of the end product due to the effector action of this product on the reactions proceeding in its synthetic pathway. The delay in feedback circuits causes violation of dynamic stability at large static stabilization factors. A method permitting analytic estimation of the critical stabilization factor is suggested. Sufficient and necessary conditions for asymptotic stability of the steady state in the general case of the pathway with a single feedback loop have been established. Mechanisms for maintenance of the steady state asymptotic stability at large static stabilization factors are studied. It has been shown that the range of dynamic stability can be widened greatly, if the pathway contains one or two reactions (but not more) of relatively small effective rate constants. Short strong negative feedback is also found to extend considerably the range of dynamic stability of the pathway. The feedback is more effective if it acts on the reaction with small effective rate constant.     

Landscape analysis of NTD diagnostics and considerations on the development of a strategy for regulatory pathways

Access to quality-assured, accurate diagnostics is critical to ensure that the 2021–2030 neglected tropical disease (NTD) road map targets can be achieved. Currently, however, there is limited regulatory oversight and few quality assurance mechanisms for NTD diagnostic tools. In attempting to address such challenges and the changing environment in regulatory requirements for diagnostics, a landscape analysis was conducted, to better understand the availability of NTD diagnostics and inform future regulatory frameworks. The list of commercially available diagnostics was compiled from various sources, including WHO guidance, national guidelines for case detection and management, diagnostic target product profiles and the published literature. The inventory was analyzed according to diagnostic type, intended use, regulatory status, and risk classification. To estimate the global need and size of the market for each type of diagnostic, annual procurement data were collected from WHO, procurement agencies, NGOs and international organizations, where available and global disease prevalence. Expert interviews were also conducted to ensure a better understanding of how diagnostics are procured and used. Of 125 diagnostic tools included in this analysis, rapid diagnostic tools accounted for 33% of diagnostics used for NTDs and very few diagnostics had been subjected to regulatory assessment. The number of tests needed for each disease was less than 1 million units per annum, except in the case of two diseases, suggesting limited commercial value. Despite the nature of the market, and presumed insufficient return on commercial investment, acceptable levels of assurance on performance, quality and safety of diagnostics are still required. Priority actions include setting up an agile, interim, stepwise risk assessment mechanism, in particular for diagnostics of lower risk, in order to support national NTD programmes and their partners with the selection and procurement of the diagnostics needed to control, eliminate and eradicate NTDs.     

Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways

MOTIVATION: Mathematical models are the only realistic method for representing the integrated dynamic behavior of complex biochemical networks. However, it is difficult to obtain a consistent set of values for the parameters that characterize such a model. Even when a set of parameter values exists, the accuracy of the individual values is questionable. Therefore, we were motivated to explore statistical techniques for analyzing the properties of a given model when knowledge of the actual parameter values is lacking. RESULTS: The graphical and statistical methods presented in the previous paper are applied here to simple unbranched biosynthetic pathways subject to control by feedback inhibition. We represent these pathways within a canonical nonlinear formalism that provides a regular structure that is convenient for randomly sampling the parameter space. After constructing a large ensemble of randomly generated sets of parameter values, the structural and behavioral properties of the model with these parameter sets are examined statistically and classified. The results of our analysis demonstrate that certain properties of these systems are strongly correlated, thereby revealing aspects of organization that are highly probable independent of selection. Finally, we show how specification of a given behavior affects the distribution of acceptable parameter values.     

Biosimilars: Key regulatory considerations and similarity assessment tools

A biosimilar drug is defined in the US Food and Drug Administration (FDA) guidance document as a biopharmaceutical that is highly similar to an already licensed biologic product (referred to as the reference product) notwithstanding minor differences in clinically inactive components and for which there are no clinically meaningful differences in purity, potency, and safety between the two products. The development of biosimilars is a challenging, multistep process. Typically, the assessment of similarity involves comprehensive structural and functional characterization throughout the development of the biosimilar in an iterative manner and, if required by the local regulatory authority, an in vivo nonclinical evaluation, all conducted with direct comparison to the reference product. In addition, comparative clinical pharmacology studies are conducted with the reference product. The approval of biosimilars is highly regulated although varied across the globe in terms of nomenclature and the precise criteria for demonstrating similarity. Despite varied regulatory requirements, differences between the proposed biosimilar and the reference product must be supported by strong scientific evidence that these differences are not clinically meaningful. This review discusses the challenges faced by pharmaceutical companies in the development of biosimilars.     

Studies of regulatory metabolism in Moniezia expansa: general considerations.

The activities of selected enzymes in the branched metabolic pathway to succinate or lactate were determined in cytosol and mitochondrial fractions. The enzymes of lowest activity in the cytosol, and thus possibly regulatory, are phosphofructokinase and pyruvate kinase. Malic enzyme activity could scarcely be detected in either compartment; phosphoenolpyruvate carboxykinase and malate dehydrogenase occur in both. The end products of metabolism are succinate and lactate; under anaerobic conditions lactate production increases whereas succinate production shows a small decrease. The presence of glucose in the medium does not influence the change, but causes an increase in total endproduct accumulation. Levels of metabolic intermediates in worms incubated aerobically and anaerobically are presented, and ‘cross-over’ plots and calculations of apparent equilibrium constants identify hexokinase, phosphofructokinase and pyruvate kinase as regulatory. Under aerobic conditions a large increase in the size of the malate pool is observed suggesting that the depression of lactate production is produced by its inhibitory effect on pyruvate kinase. Adenine nucleotide levels are maintained whether or not the worm is incubated under anaerobic conditions.     

MicroRNAs与疾病和发育

作为模式生物实验系统,线虫可用于研究控制动物发育和人类疾病遗传机制。研究发育缺陷的线虫突变体有助于在动物中发现对发育和生理过程有重要调控作用的基因。其中一些基因编码一类小RNA,如microRNA(miRNA),通过作用于特定基因信使RNA来调控其蛋白质表达。一些在线虫发育过程中有功能的miRNA在人体中也存在。它们参与调控与疾病相关的生物学过程,如癌症、糖尿病和神经退行性疾病。通过分析miRNA在临床样品、哺乳动物细胞和模式生物线虫中的表达,从而揭示miRNA调控途径在相关人类疾病中的功能。     

Scientific and regulatory considerations on the immunogenicity of biologics

Immune responses against non-vaccine biologics can affect their efficacy and safety, resulting in adverse events that could include administration reactions, hypersensitivity, deficiency syndromes and lack of a clinical response in treated patients. With the relatively recent development of numerous biologics, immunogenicity testing has become a key component in the demonstration of clinical safety and efficacy; in fact, it is highly unlikely that regulatory approval would be granted for a biologic without an assessment of its immunogenicity. However, recommendations from regulatory agencies regarding the requirements for when and how to carry out immunogenicity testing are dispersed among numerous guidance documents. To enable the evaluation of the effects of immunogenicity on safety and efficacy, the authors have consolidated recommendations from the regulatory guidelines, and present current approaches and future directions for the assessment of immunogenicity.     

Quality control of biotechnology-derived vaccines: technical and regulatory considerations

Vaccines for human use have been produced for decades using classical manufacturing methods including culture of viruses and bacteria followed by various concentration-, inactivation-, detoxification-, conjugation production processes. Availability of techniques for molecular biology and for the complete chemical synthesis of genes provides prospects of genetic engineering of microorganisms so as to generate novel biotechnological/biological-derived vaccines. The potential large-scale availability of biotechnology-derived vaccines makes feasible their evaluation in the prevention and/or treatment of various infectious, chronic, degenerative and cancer human diseases. There are potential safety concerns that arise from the novel manufacturing processes and from the complex structural and biological characteristics of the products. These products have distinguishing characteristics to which consideration should be given in a well-defined quality control testing programme. The evaluation of their quality, safety, efficacy and stability necessitate complex analytical methods and appropriate physicochemical, biochemical and immunochemical methods for the analysis of the molecular entity. A flexible approach to the control of these novel products is being developed by regulatory authorities so that recommendations can be modified in the light of experience of research and development in vaccinology, production and use of biotechnology products and with the further development of new technologies.     

泛素化修饰对维甲酸诱导基因I样受体家族(RLRs)信号通路分子调控作用的研究进展

维甲酸诱导基因I样受体家族(retinoid acid-inducible gene-I-like receptors, RLRs)信号通路作为众多抗感染免疫信号通路之一，在诱导促炎细胞因子、趋化因子和I型干扰素产生等方面发挥重要的调控作用。作为蛋白质翻译后修饰之一的泛素化(ubiquitination)，是由泛素蛋白(ubiquitin)与目标蛋白上不同的氨基酸位点产生结合来调控蛋白的命运，如启动蛋白酶体途径降解蛋白或激活转运等功能。而RLRs信号通路分子的泛素化修饰既是调控多种效应因子的方式之一，也是病毒经此诱发动物重要疾病以及自身免疫病、慢性炎症的经典路径之一。本文主要综述RLRs信号通路中重要的效应器分子的典型结构特征、泛素化修饰类型和功能，探讨泛素化修饰调控RLRs信号通路关键分子的作用，为相关疾病的干预或治疗提供参考。     

Modulating modulation: crosstalk between regulatory pathways of presynaptic calcium channels

The activity of some voltage-gated calcium channels (VGCCs) can be inhibited by specific G protein beta subunits. Conversely, in the case of N-type VGCCs, protein kinase C can relieve Gbeta-dependent inhibition by phosphorylating at least one specific site on the calcium channel. A recent publication describes a newly identified method of intracellular regulation of specific VGCCs. Wu et al. have uncovered that VGCC activity can be regulated by phosphatidylinositol-4',5'-bisphosphate (PIP2). Whereas PIP2 is important for maintaining the activity (open state) of Cav2.1 (N-type) and Cav2.2 (P/Q-type) channels, the enzymatic breakdown of PIP2 leads to the inactivation of these channels. Additionally, PIP2 can cause changes in voltage-dependent activation of Cav2.2 (P/Q-type) channels that make it more difficult for these channels to open (from the closed state). Furthermore, protein kinase A activity can circumvent PIP2-mediated inhibition. Thus, the PIP2-mediated regulation of VGCCs is tightly controlled by the functions of kinases (and phosphatases), as well as phospholipases. Wu et al. stress that because PIP2 can be found at synapses, PIP2-dependent control of VGCCs "could have profound consequences on synaptic transmission and plasticity."     

Rapid speciation via parallel, directional selection on regulatory genetic pathways

Regulatory genetic pathways are ubiquitous in organisms and play a central role in the realization of the phenotype during development. We explored the proposition that these pathways can provide a plausible source of the epistatic variation that has been implicated in the evolution of postzygotic reproductive isolation. We modeled gene regulation as a matching function between the product of one locus and the promoter site of the next locus in the pathway, with binding strength determining the amount of product. When the phenotype is subject to parallel selection in a pair of independent populations, we find that the fitnesses of F(1)and F(2)hybrids often drop to very low values as the populations respond in genetically different and incompatible ways. The simulations support the predictions of the analytical models. Hybrid fitness reduction occurs more often as the number of loci in the pathway increases, and as the binding site interactions become more complex. Less hybrid fitness reduction is seen when the populations start with imperfect binding in the pathway. In contrast, when we constructed the phenotype without gene regulation using multiplicative rules, isomorphic to the additive phenotype commonly assumed in evolutionary models, we found no appreciable F(1)fitness reduction and only slight F(2)fitness reduction. The interaction of genetic drift and mutation, even at very high rates, did not reduce hybrid fitness at all on the time-scales we considered. Clearly, the evolution of regulatory genetic pathways can play an important role in speciation, but much more empirical information is needed on the effect of allelic variability in regulatory site interactions before this role is fully understood.