Identification of protein targets of nevirapine reactive metabolites using click chemistry and mass spectrometry-based differential proteomics

Abstract : Adverse drug reactions (ADRs) are undesirable effects caused after administration of a single dose or prolonged administration of drug or result from the combination of two or more drugs. Idiosyncratic drug reaction (IDR) is an adverse reaction that does not occur in most patients treated with a drug and does not involve the therapeutic effect of the drug. IDRs are unpredictable and often life-threatening. Idiosyncratic reaction is dependent on drug chemical characteristics or individual immunological response. IDRs are a major problem for drug development because they are usually not detected during clinical trials. In this study we focused on IDRs of Nevirapine (NVP), which is a non-nucleoside reverse transcriptase inhibitor used for the treatment of Human Immunodeficiency Virus (HIV) infections. The use of NVP is limited by a relatively high incidence of skin rash. NVP also causes a rash in female Brown Norway (BN) rats, which we use as animal model for this study. Our hypothesis is that idiosyncratic skin reactions associated with NVP treatment are due to post-translational modifications of proteins (e.g., glutathionylation) detectable by MS. The main objective of this study was to identify the proteins that are targeted by a reactive metabolite of Nevirapine in the skin. The specific objectives derived from the general objective were as follow: 1) To implement the click chemistry approach to detect proteins modified by a reactive NVP-Alkyne (NVP-ALK) metabolite. The purpose of using NVP-ALK was to couple it with Biotin using cycloaddition Click Chemistry reaction. 2) To detect protein modification using Western blotting and Mass Spectrometry techniques, which is important to understand the mechanism of NVP induced toxicity. 3) To identify the proteins using MASCOT search engine for protein identification, by comparing obtained spectrum from Mass Spectrometry with theoretical spectrum to find a matching peptide sequence. 4) To test if the drug or drug metabolites can cause harmful effects, as the induction of oxidative stress in cells (via protein glutathionylation). Oxidative stress causes cell damage that mediates signals, which likely induces the immune response. The results showed that Nevirapine is metabolized to a reactive metabolite, which causes protein modification. The extracted protein from the treated BN rats matched 10% of keratin, which implies that keratin was the protein targeted by the NVP-ALK.

Feeding–Danger Trade-Offs Underlie Stopover Site Selection by Migrants

To migrate successfully, birds need to store adequate fat reserves to fuel each leg of the journey. Migrants acquire their fuel reserves at stopover sites; this often entails exposure to predators. Therefore, the safety attributes of sites may be as important as the feeding opportunities. Furthermore, site choice might depend on fuel load, with lean birds more willing to accept danger to obtain good feeding. Here, we evaluate the factors underlying stopover-site usage by migrant Western Sandpipers (Calidris mauri) on a landscape scale. We measured the food and danger attributes of 17 potential stopover sites in the Strait of Georgia and Puget Sound region. We used logistic regression models to test whether food, safety, or both were best able to predict usage of these sites by Western Sandpipers. Eight of the 17 sites were used by sandpipers on migration. Generally, sites that were high in food and safety were used, whereas sites that were low in food and safety were not. However, dangerous sites were used if there was ample food abundance, and sites with low food abundance were used if they were safe. The model including both food and safety best-predicted site usage by sandpipers. Furthermore, lean sandpipers used the most dangerous sites, whereas heavier birds (which do not need to risk feeding in dangerous locations) used safer sites. This study demonstrates that both food and danger attributes are considered by migrant birds when selecting stopover sites, thus both these attributes should be considered to prioritize and manage stopover sites for conservation.

'Malicious Code Execution Detection and Response Immune System inspired by the Danger Theory'

The analysis of system calls is one method employed by anomaly detection systems to recognise malicious code execution. Similarities can be drawn between this process and the behaviour of certain cells belonging to the human immune system, and can be applied to construct an artificial immune system. A recently developed hypothesis in immunology, the Danger Theory, states that our immune system responds to the presence of intruders through sensing molecules belonging to those invaders, plus signals generated by the host indicating danger and damage. We propose the incorporation of this concept into a responsive intrusion detection system, where behavioural information of the system and running processes is combined with information regarding individual system calls.

'Malicious Code Execution Detection and Response Immune System inspired by the Danger Theory'

The analysis of system calls is one method employed by anomaly detection systems to recognise malicious code execution. Similarities can be drawn between this process and the behaviour of certain cells belonging to the human immune system, and can be applied to construct an artificial immune system. A recently developed hypothesis in immunology, the Danger Theory, states that our immune system responds to the presence of intruders through sensing molecules belonging to those invaders, plus signals generated by the host indicating danger and damage. We propose the incorporation of this concept into a responsive intrusion detection system, where behavioural information of the system and running processes is combined with information regarding individual system calls.

Obstacle Crossing With Dual Tasking Is A Danger For Individuals With Alzheimer's Disease And For Healthy Older People.

The aim of this study was to analyze the effects of dual tasking on obstacle crossing during walking by individuals with Alzheimer's disease (AD) and by healthy older people. Thirty four elderly individuals (16 healthy subjects and 18 individuals with AD) were recruited to participate in this study. Three AD individuals and one control participant were excluded due to exclusion criteria. The participants were instructed to walk barefoot at their own speed along an 8 m long pathway. Each participant performed five trials for each condition (unobstructed walking, unobstructed walking with dual tasking, and obstacle crossing during walking with dual tasking). The trials were completely randomized for each participant. The mid-pathway stride was measured in the unobstructed walking trials and the stride that occurred during the obstacle avoidance was measured in the trials that involved obstacle crossing. The behavior of the healthy elderly subjects and individuals with AD was similar for obstacle crossing during walking with dual tasking. Both groups used the posture first strategy to prioritize stability and showed decreased attention to executive tasking while walking. Additionally, AD had a strong influence on the modifications that are made by the elderly while walking under different walking conditions.

A new genus and two new species of Stevardiinae (Characiformes: Characidae) with a hypothesis on their relationships based on morphological and histological data

Lepidocharax, new genus, and Lepidocharax diamantina and L. burnsi new species from eastern Brazil are described herein. Lepidocharax is considered a monophyletic genus of the Stevardiinae and can be distinguished from the other members of this subfamily except Planaltina, Pseudocorynopoma, and Xenurobrycon by having the dorsal-fin origin vertically aligned with the anal-fin origin, vs. dorsal fin origin anterior or posterior to anal-fin origin. Additionally the new genus can be distinguished from those three genera by not having the scales extending over the ventral caudal-fin lobe modified to form the dorsal border of the pheromone pouch organ or to represent a pouch scale in sexually mature males. In this paper, we describe these two recently discovered species and the ultrastructure of their spermatozoa.

Beyond the Fragmentation Threshold Hypothesis: Regime Shifts in Biodiversity Across Fragmented Landscapes

Ecological systems are vulnerable to irreversible change when key system properties are pushed over thresholds, resulting in the loss of resilience and the precipitation of a regime shift. Perhaps the most important of such properties in human-modified landscapes is the total amount of remnant native vegetation. In a seminal study Andren proposed the existence of a fragmentation threshold in the total amount of remnant vegetation, below which landscape-scale connectivity is eroded and local species richness and abundance become dependent on patch size. Despite the fact that species patch-area effects have been a mainstay of conservation science there has yet to be a robust empirical evaluation of this hypothesis. Here we present and test a new conceptual model describing the mechanisms and consequences of biodiversity change in fragmented landscapes, identifying the fragmentation threshold as a first step in a positive feedback mechanism that has the capacity to impair ecological resilience, and drive a regime shift in biodiversity. The model considers that local extinction risk is defined by patch size, and immigration rates by landscape vegetation cover, and that the recovery from local species losses depends upon the landscape species pool. Using a unique dataset on the distribution of non-volant small mammals across replicate landscapes in the Atlantic forest of Brazil, we found strong evidence for our model predictions - that patch-area effects are evident only at intermediate levels of total forest cover, where landscape diversity is still high and opportunities for enhancing biodiversity through local management are greatest. Furthermore, high levels of forest loss can push native biota through an extinction filter, and result in the abrupt, landscape-wide loss of forest-specialist taxa, ecological resilience and management effectiveness. The proposed model links hitherto distinct theoretical approaches within a single framework, providing a powerful tool for analysing the potential effectiveness of management interventions.

TESTING STATISTICAL HYPOTHESIS ON RANDOM TREES AND APPLICATIONS TO THE PROTEIN CLASSIFICATION PROBLEM

Efficient automatic protein classification is of central importance in genomic annotation. As an independent way to check the reliability of the classification, we propose a statistical approach to test if two sets of protein domain sequences coming from two families of the Pfam database are significantly different. We model protein sequences as realizations of Variable Length Markov Chains (VLMC) and we use the context trees as a signature of each protein family. Our approach is based on a Kolmogorov-Smirnov-type goodness-of-fit test proposed by Balding et at. [Limit theorems for sequences of random trees (2008), DOI: 10.1007/s11749-008-0092-z]. The test statistic is a supremum over the space of trees of a function of the two samples; its computation grows, in principle, exponentially fast with the maximal number of nodes of the potential trees. We show how to transform this problem into a max-flow over a related graph which can be solved using a Ford-Fulkerson algorithm in polynomial time on that number. We apply the test to 10 randomly chosen protein domain families from the seed of Pfam-A database (high quality, manually curated families). The test shows that the distributions of context trees coming from different families are significantly different. We emphasize that this is a novel mathematical approach to validate the automatic clustering of sequences in any context. We also study the performance of the test via simulations on Galton-Watson related processes.

Acquisition of the English article system in SLA and the Missing Surface Inflection Hypothesis

This paper examines the article system in interlanguage grammar focusing on Japanese learners of English, whose native language lacks articles. It will be demonstrated that for the acquisition of the English article system, count/mass distinctions and definiteness are the crucial factors. Although Japanese does not employ the article system to encode these aspects, it will be argued that they are nevertheless syntactically encoded through its classifier system. Hence, the problem for these learners must be to map these features onto the appropriate surface forms as the Missing Surface Inflection Hypothesis predicts (Prévost & White 2000). This suggestion will further be supported empirically by a fill-in-the article task. It will be concluded that these Japanese learners understand the English article system fairly well, possibly due to their native language, yet have problems with realizing the relevant features (i.e. count/mass distinctions and definiteness) in the target language.

Regulation of photosynthetic pigments in micro-algae by multiple environmental factors: a dynamic balance hypothesis

Environmental effects on the concentration of photosynthetic pigments in micro-algae can be explained by dynamics of photosystem synthesis and deactivation. A model that couples photosystem losses to the relative cellular rates of energy harvesting (light absorption) and assimilation predicts optimal concentrations of light-harvesting pigments and balanced energy flow under environmental conditions that affect light availability and metabolic rates. Effects of light intensity, nutrient supply and temperature on growth rate and pigment levels were similar to general patterns observed across diverse micro-algal taxa. Results imply that dynamic behaviour associated with photophysical stress, and independent of gene regulation, might constitute one mechanism for photo-acclimation of photosynthesis.

Patient matching in treatment for alcohol dependence: is the null hypothesis still alive and well?

In the light of Project MATCH, is it reasonable to accept the null hypothesis that there are no clinically signi® cant matching effects between patient characteristics and cognitive± behaviour therapy (CBT), motivational enhancement therapy (MET) and Twelve-Step facilitation therapy (TSF)? The Project MATCH investigators considered the null hypothesis but preferred the alternative hypothesis that further analysis may reveal combinations of patient and therapist characteristics that show more substantial matching effects than any of the variables that they have examined to date.1

The glass ceiling hypothesis - A comparative study of the United States, Sweden, and Australia

The general-care glass ceiling hypothesis states that not only is it more difficult for women than for men to be promoted up levels of authority hierarchies within workplaces but also that the obstacles women face relative to men become greater as they move rtp the hierarchy. Gender-based discrimination in promotions is not simply present across levels of hierarchy but is more intense at higher levels. Empirically, this implies that the relative rates of women being promoted to higher levels compared to men should decline with the level of the hierarchy. This article explores this hypothesis with data from three countries: the United States, Australia, and Sweden. The basic conclusion is that while there is strong evidence for a general gender gap in authority-the odds of women having authority are less than those of men-there is no evidence for systematic glass ceiling effects in the United States and only weak evidence for such effects in the other two countries.