Statistical methods for measuring interactions between protectors and sensitizers for freeze-thaw survival data

A statistical model is developed to generate the survival probabilities of cells subjected to freeze-thaw treatments using various sensitizing and/or protective agents. The purpose is to determine whether different freeze-thaw protective agents act independently or whether there is an interaction between the agents. The model permits a statistical analysis of the data to yield an objective quantitative assessment of the size and nature of the interaction.     

Analysis of cause of death: Competing risks or progressive illness‐death model?

The analysis of cause of death is increasingly becoming a topic in oncology. It is usually distinguished between disease‐related and disease‐unrelated death. A frequently used approach is to define death as disease‐related when a progression to advanced phases has occurred before, otherwise as disease‐unrelated. The data are often analyzed as competing risks, while a progressive illness‐death model might in fact describe the situation more precisely. In this study, we investigated under which circumstances this misspecification leads to biased estimations of the state occupation probabilities. We simulated data according to the progressive illness‐death model in various settings, analyzed them with a competing risks model and with a progressive illness‐death model and compared them to the true state occupation probabilities. Censoring was either added independently of the status or based on the patients' status. The simulations showed that the censoring mechanism was decisive for the bias while neither the progression hazard nor the Markov property was important. Further, we found a slightly increased standard deviation for the competing risk estimator when censoring was independent of the patients' status. For illustration, both methods were applied to two practical examples of chronic myeloid leukemia (CML): one randomized controlled trial and one registry data set. While in the first case both estimators yielded almost identical results, in the latter case, visible differences were found between both methods.     

Method used to establish a large animal model of drug-induced acute kidney injury

Acute kidney injury is a serious health hazard disease due to its complex etiology and lack of effective treatments, resulting in high medical costs and high mortality. At present, a large number of basic research studies on acute kidney injury have been carried out. However, acute kidney injury models established in rodents sometimes do not simulate the course of human disease well. Research in large animal models of acute kidney injury is relatively rare, and methods to build a mature model of acute kidney injury have failed. Because its kidney anatomy and morphology are very similar to those in humans, the mini pig is an ideal animal in which to model kidney disease. Nephrotoxic drug-induced acute kidney injury has a high incidence. In this study, we established models of acute kidney injury induced by two drugs (gentamicin and cisplatin). Finally, the model of cisplatin-induced acute kidney injury was developed successfully, but we found the model of gentamycin-induced acute kidney injury was not reproducible. Compared to other models, these models better represent acute kidney injury caused by antibiotics and chemotherapeutic drugs and provide a basis for the study of new treatments for acute kidney injury in a large animal model.     

Signalling by extracellular nucleotides in health and disease

Nucleotides are released from all cells through regulated pathways or as a result of plasma membrane damage or cell death. Outside the cell, nucleotides act as signalling molecules triggering multiple responses via specific plasma membrane receptors of the P2 family. In the nervous system, purinergic signalling has a key function in neurotransmission. Outside the nervous system, purinergic signalling is one of the major modulators of basal tissue homeostasis, while its dysregulation contributes to the pathogenesis of various disease, including inflammation and cancer. Pre-clinical and clinical evidence shows that selective P2 agonists or antagonists are effective treatments for many pathologies, thus highlighting the relevance of extracellular nucleotides and P2 receptors as therapeutic targets.     

Synphilin suppresses α-synuclein neurotoxicity in a Parkinson's disease Drosophila model

Parkinson's disease (PD) is the second most common neurodegenerative disorder in humans. It affects 1% of the population over 65-years old. Its causes are environmental and genetic. As the world population ages, there is an urgent need for better and more detailed animal models for this kind of disease. In this work we show that the use of transgenic Drosophila is comparable to more complicated and costly animal models such as mice. The Drosophila model behaves very similar to the equivalent transgenic mice model. We show that both Synphilin-1 and α-synuclein are toxic by themselves, but when co-expressed, they suppress their toxicity reciprocally. Importantly, the symptoms induced in the fly can be treated and partially reverted using standard PD pharmacological treatments. This work showcases Drosophila as a detailed and multifaceted model for Parkinson's disease, providing a convenient platform in which to study and find new genetic modifiers of PD. genesis 49:392-402, 2011.     

Animal models of allergic bronchopulmonary aspergillosis

Among the allergic fungi, Aspergillus fumigatus, a saprophytic mold, distributed widely in the environment is a frequently recognized etiologic agent in a number of allergic conditions. Among the different allergic diseases caused by this fungus, allergic bronchopulmonary aspergillosis (ABPA) is by far the most significant one. The immunopathogenesis of this disease is not fully understood. Although several immunomodulatory treatments are available for allergic disease, none of them are applicable or relevant or useful in fungal induced allergy. It is essential to understand the pathogenesis of the disease including the antigen induced immunoregulation and the resulting factors, such as cytokine, chemokines, pathways activating factors, inflammatory and airway remodeling factors need to be understood for intervening with appropriate treatment. Animal models are essential in understanding these features of the disease. Several models of allergic aspergillosis have been developed in recent years in various animals. However, murine models have been studied more carefully and extensively. The exposure to antigen in mice leads to allergy very similar to ABPA with high IgE, elevated peripheral blood and lung eosinophils, pulmonary inflammation, and airway hyperreactivity. The role of various cytokines and chemokines and their receptors were also studied. In addition, immunotherapy and vaccination have been attempted in recent years using the murine model of ABPA. This review covers the murine model of Aspergillus induced allergy and asthma and presented critically our current understanding of the subject and the potential application of such a model in future for developing treatment modalities. This revised version was published online in June 2006 with corrections to the Cover Date.     

Interpreting interactions between treatments that slow aging

A major challenge in current research into aging using model organisms is to establish whether different treatments resulting in slowed aging involve common or distinct mechanisms. Such treatments include gene mutation, dietary restriction (DR), and manipulation of reproduction, gonadal signals and temperature. The principal method used to determine whether these treatments act through common mechanisms is to compare the magnitude of the effect on aging of each treatment separately with that when two are applied simultaneously. In this discussion we identify five types of methodological shortcomings that have marred such studies. These are (1) submaximal lifespan-extension by individual treatments, e.g. as a result of the use of hypomorphic rather than null alleles; (2) effects of a single treatment on survival through more than one mechanism, e.g. pleiotropic effects of lifespan mutants; (3) the difficulty of interpreting the magnitude of increases in lifespan in double treatments, and failure to measure and model age-specific mortality rates; (4) the non-specific effects of life extension suppressors; and (5) the possible occurrence of artefactual mutant interactions. When considered in the light of these problems, the conclusions of a number of recent lifespan interaction studies appear questionable. We suggest six rules for avoiding the pitfalls that can beset interaction studies.     

大麦种子对盐的发芽响应模型

为了明确盐对种子发芽影响的渗透效应和离子效应共同作用方式以及量化种子发芽对盐的响应, 以两个大麦(Hordeum vulgare)品种‘Cask’和‘County’为研究对象, 设置4个恒定温度(5、12、20和27 ℃)、5个等渗的NaCl和聚乙二醇(PEG)浓度梯度(-0.45、-0.88、-1.32、-1.76和-2.20 MPa, 蒸馏水作对照), 做常规发芽实验。结果显示: (1)两个品种在NaCl溶液中比在等渗的PEG溶液中发芽率高且发芽速度快; (2) NaCl和PEG分别作为渗透剂计算出的水势模型参数值差异很大, 说明水势模型不能用来描述种子发芽对盐的响应; (3)大麦种子在盐溶液中的发芽速率与盐浓度成显著的负相关直线关系, 因此我们修订了水势模型, 将修订后的模型命名为盐度模型, 用来量化盐对大麦种子发芽的影响。与水势模型计算出的发芽时间相比, 盐度模型计算出的50%种子发芽时间与大麦种子实际发芽时间更接近; (4)大麦种子在等渗的NaCl和PEG溶液中发芽速率差异随着水势降低, 先增加后降低。据此我们提出盐的渗透效应和离子效应共同作用于种子发芽的3种情况: 第一种在低盐条件下, 主要是渗透效应起负作用; 第二种情况在中盐条件下, 渗透效应和离子效应共同起作用, 离子效用的正作用强于渗透效应的负作用; 第三种情况在高盐条件下, 离子效应逐渐开始起离子毒害的负作用。     

Independent and competing disease risks: implications for host populations in variable environments

Disease models usually assume disease to act independently of other mortality- and morbidity-causing factors. Alternatively, disease may function as a competing risk factor, for example, killing already moribund hosts. Using tuberculosis (TB) in African buffalo as a model system, we explore consequences of competing or independent disease effects for host population dynamics. We include scenarios with density-dependent and density-independent effects of environmental variation, exemplified by variable food availability (driven by rainfall) and catastrophic droughts, respectively. Independent disease effects reduce population size linearly with prevalence, irrespective of the nature of environmental variation. Competing disease risks alter population size only if density-independent variation is present; then, disease reduces population size nonlinearly. Field data indicate that the net effect of TB on buffalo likely falls between the extremes of total independence and competition with other risk factors: TB increases mortality and decreases fecundity in some prime-aged buffalo, suggesting independent disease risks in these individuals, while similar disease effects in senescent buffalo may act as competing risks. Moreover, increased survival and fecundity of TB-negative buffalo may compensate for some disease-related losses. Model assumptions on independent or competing disease risks and environmental variability should be considered explicitly when assessing disease effects on wildlife populations.     

Staphylococcal protein A adsorption in neoplastic disease: analysis of physicochemical aspects

Staphylococcus aureus organisms and immobilized Staphylococcal protein A have been used as extracorporeal immunoadsorbents for the treatment of neoplastic disease. In a significant number of cases, a biologic response has been documented. This review analyzes the experimental results to date, correlates experimental design parameters with response to treatment, and discusses possible mechanisms of action. The evidence implicates protein A as the tumoricidal agent, although bacterial or complement components may act independently or synergistically. A more quantitative and fundamental approach is needed to exploit the potential for protein A immunoadsorption in treating neoplastic disease.     

Galanin transgenic mice with elevated circulating galanin levels alleviate demyelination in a cuprizone-induced MS mouse model

Multiple Sclerosis (MS) is a demyelinating autoimmune disease of the central nervous system (CNS) with a presumed autoimmune etiology. Approved treatments for MS are immunoregulatory and are able to reduce the inflammatory components of the disease. However, these treatments do not suppress progressive clinical disability. Approaches that directly protect myelin-producing oligodendrocytes and enhance remyelination are likely to improve long-term outcomes and reduce the rate of axonal damage. Galanin (GAL) is a bioactive neuropeptide that is widely distributed throughout the nervous system and has diverse neuromodulatory effects. In this study, using the cuprizone (CPZ) demyelination model of MS, we demonstrate that GAL has pronounced neuroprotective effects with respect to demyelination and remyelination. Using our GAL transgenic mouse (GAL-Tg), we identified a novel attenuation of OLs against CPZ induced demyelination, which was exerted independently of progenitor cells. Alleviation of myelin breakdown in the GAL-Tg mice was observed to be significant. Furthermore, we observed changes in the expression of the GAL receptor GalR1 during the demyelination and remyelination processes. Our data strongly indicate that GAL has the capacity to influence the outcome of primary insults that directly target OLs, as opposed to cases where immune activation is the primary pathogenic event. Taken together, these results suggest that GAL is a promising next-generation target for the treatment of MS.     

Effects of a disease affecting a predator on the dynamics of a predator-prey system

We study the effects of a disease affecting a predator on the dynamics of a predator-prey system. We couple an SIRS model applied to the predator population, to a Lotka-Volterra model. The SIRS model describes the spread of the disease in a predator population subdivided into susceptible, infected and removed individuals. The Lotka-Volterra model describes the predator-prey interactions. We consider two time scales, a fast one for the disease and a comparatively slow one for predator-prey interactions and for predator mortality. We use the classical “aggregation method” in order to obtain a reduced equivalent model. We show that there are two possible asymptotic behaviors: either the predator population dies out and the prey tends to its carrying capacity, or the predator and prey coexist. In this latter case, the predator population tends either to a “disease-free” or to a “disease-endemic” state. Moreover, the total predator density in the disease-endemic state is greater than the predator density in the “disease-free” equilibrium (DFE).     

A Bayesian platform trial design to simultaneously evaluate multiple drugs in multiple indications with mixed endpoints

In the era of targeted therapies and immunotherapies, the traditional drug development paradigm of testing one drug at a time in one indication has become increasingly inefficient. Motivated by a real-world application, we propose a master-protocol–based Bayesian platform trial design with mixed endpoints (PDME) to simultaneously evaluate multiple drugs in multiple indications, where different subsets of efficacy measures (eg, objective response and landmark progression-free survival) may be used by different indications as single or multiple endpoints. We propose a Bayesian hierarchical model to accommodate mixed endpoints and reflect the trial structure of indications that are nested within treatments. We develop a two-stage approach that first clusters the indications into homogeneous subgroups and then applies the Bayesian hierarchical model to each subgroup to achieve precision information borrowing. Patients are enrolled in a group-sequential way and adaptively assigned to treatments according to their efficacy estimates. At each interim analysis, the posterior probabilities that the treatment effect exceeds prespecified clinically relevant thresholds are used to drop ineffective treatments and “graduate” effective treatments. Simulations show that the PDME design has desirable operating characteristics compared to existing method.     

Which Call Parameters Signal Threat to Conspecifics in White‐Throated Magpie‐Jay Mobbing Calls?

Abstract Variation in signals often encodes additional information beyond that provided by the main signal. Many species communicate degree of threat using such signal variation. However, multiple signal parameters often covary with threat level, and it is unclear whether receivers are using variation along one or more parameters when assessing threat level. White-throated magpie-jays ( Calocitta formosa ) vary several call parameters when mobbing, and here I report on an experiment testing whether such variation contains information used by conspecific receivers, and which parameters are salient to receivers. I collected data on natural mobbing sequences in two threat contexts and found that mobbing calls were highly variable in both length and inter-call interval, but on average, both parameters were shorter in high threat contexts, while call frequency did not differ. To determine how jays respond to such between-context variation, I conducted a playback experiment in which call length and inter-call interval were independently varied in a factorial design. This is one of the first studies to my knowledge to deconstruct and independently test covarying signal parameters in an anti-predator signaling system. Magpie-jays responded more often to treatments with either short call lengths or short inter-call intervals, in concordance with the natural calling data. However, the two parameters did not appear to act independently; responses were not additive, and short calls at short inter-call intervals elicited no stronger of a response than short calls at long intervals or long calls at short intervals. Receivers can use either parameter when assessing threat level. These data demonstrate that mobbing can signal threat level, that call length and call rate are redundant, and that receivers need not use both to determine whether to approach.     

Expression and site-directed mutagenesis of human protein disulfide isomerase in Escherichia coli. This multifunctional polypeptide has two independently acting catalytic sites for the isomerase activity.

Protein disulfide isomerase (PDI, EC 5.3.4.1) is a highly unusual multifunctional polypeptide, being identical to the beta subunit of prolyl 4-hydroxylase, a cellular thyroid hormone binding protein and a component of the microsomal triglyceride transfer protein complex, and highly similar to a polypeptide acting in vitro as a glycosylation site binding protein. It has two -Cys-Gly-His-Cys- sequences which, it has been proposed, act as catalytic sites for the isomerase activity, but few data have been available to indicate whether one or both of them do indeed act as catalytic sites and whether the two presumed catalytic sites act independently or cooperatively. We report here on the expression of human PDI in Escherichia coli with three different signal sequences. All three polypeptide variants were secreted into the periplasmic space as fully active enzymes. Oligonucleotide-directed mutagenesis was used to convert either one or both of the -Cys-Gly-His-Cys- sequences to -Ser-Gly-His-Cys-. The PDI activity of both polypeptides containing a single modified sequence was about 50% of that of the wild-type polypeptide, whereas the polypeptide with two modified sequences had no isomerase activity. It is thus concluded that both -Cys-Gly-His-Cys- sequences act as catalytic sites for the isomerase activity, and the two catalytic sites appear to operate independently of one another.     

Investigating and modeling the combined effects of pH and osmotic pressure on seed germination for use in phytoactivity and allelopathic research

Phytoactivity and allelopathic studies are heavily dependent on germination bioassays of water solutions of allelochemical(s), which necessarily imply that pH and osmotic pressure vary among treatments and between treatments and controls and are therefore a confounding factor in the assessment of seed germination responses to allelochemical(s). When the contribution of pH and osmotic pressure to seed germination responses is considered in experimental designs their effects are almost without exceptions examined separately being assumed, without any evidences, that pH and osmotic pressure act independently on seed germination responses. The objectives of this work were to examine experimentally such assumption using wheat, lettuce, and subterranean clover cultivars to evaluate and model the combined effects on germination of pH and osmotic pressure in the range between 3.0–6.0 and 0–100 mOsmol kg^?1, respectively. Empirical equations are fitted, discussed, and the need to consider the simultaneous effects of pH and osmotic pressure firmly established. Finally, the use of the equations fitted and its impact on conclusions is exemplified in a dose-response bioassay of water extracts of Cistus ladanifer on seed germination using subterranean clover as target species where hormesis was found before allelochemical effects were corrected for pH and osmotic pressure values of control and extracts.     

Theory of transport noise in membrane channels with open-closed kinetics

A theoretical approach to transport noise in kinetic systems, which has recently been developed, is applied to electric fluctuations around steady-states in membrane channels with different conductance states. The channel kinetics may be simple two state (open-closed) kinetics or more complicated. The membrane channel is considered as a sequence of binding sites separated by energy barriers over which the ions have to jump according to the usual single-file diffusion model. For simplicity the channels are assumed to act independently. In the special case of ionic movement fast compared with the channel open-closed kinetics the results agree with those derived from the usual Master equation approach to electric fluctuations in nerve membrane channels.For the simple model of channels with one binding site and two energy barries the coupling between the fluctuations coming from the open-closed kinetics and from the jump diffusion is investigated.     

Orthotopic Implantation and Peripheral Immune Cell Monitoring in the II-45 Syngeneic Rat Mesothelioma Model

The enormous upsurge of interest in immune-based treatments for cancer such as vaccines and immune checkpoint inhibitors, and increased understanding of the role of the tumor microenvironment in treatment response, collectively point to the need for immune-competent orthotopic models for pre-clinical testing of these new therapies. This paper demonstrates how to establish an orthotopic immune-competent rat model of pleural malignant mesothelioma. Monitoring disease progression in orthotopic models is confounded by the internal location of the tumors. To longitudinally monitor disease progression and its effect on circulating immune cells in this and other rat models of cancer, a single tube flow cytometry assay requiring only 25 µl whole blood is described. This provides accurate quantification of seven immune parameters: total lymphocytes, monocytes and neutrophils, as well as the T-cell subsets CD4 and CD8, B-cells and Natural Killer cells. Different subsets of these parameters are useful in different circumstances and models, with the neutrophil to lymphocyte ratio having the greatest utility for monitoring disease progression in the mesothelioma model. Analyzing circulating immune cell levels using this single tube method may also assist in monitoring the response to immune-based treatments and understanding the underlying mechanisms leading to success or failure of treatment.     

Quantifying the relative importance of variation in predation and the environment for species coexistence

Coexistence and food web theory are two cornerstones of the long‐standing effort to understand how species coexist. Although competition and predation are known to act simultaneously in communities, theory and empirical study of these processes continue to be developed largely independently. Here, we integrate modern coexistence theory and food web theory to simultaneously quantify the relative importance of predation and environmental fluctuations for species coexistence. We first examine coexistence in a theoretical, multitrophic model, adding complexity to the food web using machine learning approaches. We then apply our framework to a stochastic model of the rocky intertidal food web, partitioning empirical coexistence dynamics. We find the main effects of both environmental fluctuations and variation in predator abundances contribute substantially to species coexistence. Unexpectedly, their interaction tends to destabilise coexistence, leading to new insights about the role of bottom‐up vs. top‐down forces in both theory and the rocky intertidal ecosystem.