Weak Intra-Ring Allosteric Communications of the Archaeal Chaperonin Thermosome Revealed by Normal Mode Analysis

Chaperonins are molecular machines that use ATP-driven cycles to assist misfolded substrate proteins to reach the native state. During the functional cycle, these machines adopt distinct nucleotide-dependent conformational states, which reflect large-scale allosteric changes in individual subunits. Distinct allosteric kinetics has been described for the two chaperonin classes. Bacterial (group I) chaperonins, such as GroEL, undergo concerted subunit motions within each ring, whereas archaeal and eukaryotic chaperonins (group II) undergo sequential subunit motions. We study these distinct mechanisms through a comparative normal mode analysis of monomer and double-ring structures of the archaeal chaperonin thermosome and GroEL. We find that thermosome monomers of each type exhibit common low-frequency behavior of normal modes. The observed distinct higher-frequency modes are attributed to functional specialization of these subunit types. The thermosome double-ring structure has larger contribution from higher-frequency modes, as it is found in the GroEL case. We find that long-range intersubunit correlation of amino-acid pairs is weaker in the thermosome ring than in GroEL. Overall, our results indicate that distinct allosteric behavior of the two chaperonin classes originates from different wiring of individual subunits as well as of the intersubunit communications.     

Analysis of human urine for fifteen phthalate metabolites using automated solid-phase extraction

We improved our previous analytical method to measure phthalate metabolites in urine as biomarkers for phthalate exposure by automating the solid-phase extraction (SPE) procedure and expanding the analytical capability to quantify four additional metabolites: phthalic acid, mono-3-carboxypropyl phthalate, mono-isobutyl phthalate (miBP), and monomethyl isophthalate. The method, which involves automated SPE followed by isotope dilution-high performance liquid chromatography (HPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS), allows for the quantitative measurement of 15 phthalate metabolites in urine with detection limits in the low ng/ml range. SPE automation allowed for the unattended sequential extraction of up to 100 samples at a time, and resulted in an increased sample throughput, lower solvent use, and better reproducibility than the manual SPE. Furthermore, the modified method permitted for the first time, the separation and quantification of mono-n-butyl phthalate (mBP) and its structural isomer miBP. The method was validated on spiked pooled urine samples and on pooled urine samples from persons with no known exposure to phthalates.     

Determination of total phthalates in urine by isotope-dilution liquid chromatography-tandem mass spectrometry

Diesters of 1,2-benzenedicarboxylic acid are a family of industrial compounds called "phthalates." The physical and chemical properties of these diesters, and therefore their potential uses, depend on the structure of the dialkyl or alkyl/aryl side chain. The urinary concentrations of phthalate monoesters, which are metabolites, have been used as biomarkers of human exposure to specific phthalates. However, several phthalates, particularly those with side chains of eight or more carbon atoms, are complex mixtures of isomers. For these, the phthalate metabolites to be used as biomarkers of exposure have not been unequivocally identified. We developed a method for assessing total exposure to phthalates, including the isomeric mixtures of high molecular weight phthalates, by measuring the concentration of phthalic acid (PA) in human urine after acid hydrolysis of the phthalate metabolites to PA. The present method accurately assesses total exposure to phthalates without noticeable contamination from the ubiquitous phthalates in the environment, but it gives no information about the parent phthalate.     

How many species of Paradoxurus civets are there? New insights from India and Sri Lanka

Using molecular data and morphological features, we investigated the species limits and genetic diversity among populations of the Asian palm civets of the genus Paradoxurus. Our main objectives were to determine the number of species within Paradoxurus hermaphroditus and to test the validity of the newly proposed species within Paradoxurus zeylonensis. Fragments of two mitochondrial (Cytochrome b, Control Region) and one nuclear (intron 7 of the beta fibrinogen) markers were sequenced from 128 individuals of P. hermaphroditus, P. zeylonensis and Paradoxurus jerdoni. DNA sequences were analysed using phylogenetic and haplotype network methods. Our analyses confirmed that P. hermaphroditus comprises three major clades, which should be recognized as separate species: P. hermaphroditus (Indian and Indochinese regions), Paradoxurus musangus (mainland Southeast Asia, Sumatra, Java and other small Indonesian islands) and Paradoxurus philippinensis (Mentawai Islands, Borneo and the Philippines). Furthermore, we have proposed that there are two subspecies within both P. musangus and P. philippinensis, and there might be at least two or three subspecies within P. hermaphroditus. We found a very low genetic diversity and no geographical structure within P. zeylonensis and did not find any support for splitting P. zeylonensis into several species nor subspecies. Finally, we confirmed that P. jerdoni and P. zeylonensis are sister species.     

Quantification of 22 phthalate metabolites in human urine

Phthalates are ubiquitous industrial chemicals with high potential for human exposure. Validated analytical methods to measure trace concentrations of phthalate metabolites in humans are essential for assessing exposure to phthalates. Previously, we developed a sensitive and accurate automated analytical method for measuring up to 16 phthalate metabolites in human urine by using on-line solid phase extraction coupled with isotope dilution-high performance liquid chromatography (HPLC)-electrospray ionization-tandem mass spectrometry. To include the measurement of seven additional analytes, including oxidative metabolites of diisononyl and diisodecyl phthalates, two chemicals used extensively in numerous consumer products, we used a novel nontraditional HPLC solvent gradient program. With this approach, we achieved adequate resolution and sensitivity for all 22 analytes with limits of detection in the low ng/mL range, without increasing the analytical run time. The method also has high accuracy with automatic recovery correction, high precision, and excellent sample throughput with minimal matrix effects. Although it is possible to measure these 22 phthalate metabolites with adequate precision and accuracy at sub-parts-per-billion levels, additional information, including toxicokinetic data, is needed to demonstrate the usefulness of these phthalate metabolites for exposure assessment purposes.     

Improved quantitative detection of 11 urinary phthalate metabolites in humans using liquid chromatography-atmospheric pressure chemical ionization tandem mass spectrometry

Phthalates are widely used as industrial solvents and plasticizers, with global use exceeding four million tons per year. We improved our previously developed high-performance liquid chromatography-atmospheric pressure chemical ionization-tandem mass spectrometric (HPLC-APCI-MS/MS) method to measure urinary phthalate metabolites by increasing the selectivity and the sensitivity by better resolving them from the solvent front, adding three more phthalate metabolites, monomethyl phthalate (mMP), mono-(2-ethyl-5-oxohexyl)phthalate (mEOHP) and mono-(2-ethyl-5-hydroxyhexyl)phthalate (mEHHP); increasing the sample throughput; and reducing the solvent usage. Furthermore, this improved method enabled us to analyze free un-conjugated mono-2-ethylhexyl phthalate (mEHP) by eliminating interferences derived from coelution of the glucuronide-bound, or conjugated form, of the mEHP on measurements of the free mEHP. This method for measuring phthalate metabolites in urine involves solid-phase extraction followed by reversed-phase HPLC-APCI-MS/MS using isotope dilution with (13)C(4) internal standards. We further evaluated the ruggedness and the reliability of the method by comparing measurements made by multiple analysts at different extraction settings on multiple instruments. We observed mMP, monoethyl phthalate (mEP), mono-n-butyl phthalate (mBP), monobenzyl phthalate (mBzP), mEHP, mEHHP and mEOHP in the majority of urine specimens analyzed with DEHP-metabolites mEHHP and mEOHP present in significantly higher amounts than mEHP.     

Focus on Ethylene: Disruption of Ethylene Responses by Turnip mosaic virus Mediates Suppression of Plant Defense against the Green Peach Aphid Vector

Plants employ diverse responses mediated by phytohormones to defend themselves against pathogens and herbivores. Adapted pathogens and herbivores often manipulate these responses to their benefit. Previously, we demonstrated that Turnip mosaic virus (TuMV) infection suppresses callose deposition, an important plant defense induced in response to feeding by its aphid vector, the green peach aphid (Myzus persicae), and increases aphid fecundity compared with uninfected control plants. Further, we determined that production of a single TuMV protein, Nuclear Inclusion a-Protease (NIa-Pro) domain, was responsible for changes in host plant physiology and increased green peach aphid reproduction. To characterize the underlying molecular mechanisms of this phenomenon, we examined the role of three phytohormone signaling pathways, jasmonic acid, salicylic acid, and ethylene (ET), in TuMV-infected Arabidopsis (Arabidopsis thaliana), with or without aphid herbivory. Experiments with Arabidopsis mutants ethylene insensitive2 and ethylene response1, and chemical inhibitors of ET synthesis and perception (aminoethoxyvinyl-glycine and 1-methylcyclopropene, respectively), show that the ET signaling pathway is required for TuMV-mediated suppression of Arabidopsis resistance to the green peach aphid. Additionally, transgenic expression of NIa-Pro in Arabidopsis alters ET responses and suppresses aphid-induced callose formation in an ET-dependent manner. Thus, disruption of ET responses in plants is an additional function of NIa-Pro, a highly conserved potyvirus protein. Virus-induced changes in ET responses may mediate vector-plant interactions more broadly and thus represent a conserved mechanism for increasing transmission by insect vectors across generations.Plants suffer from numerous pathogen and herbivore challenges in both natural and agricultural environments, often facing multiple simultaneous threats (Casteel and Hansen, 2014). For example, many plant pathogens depend on insect vectors for transmission, including over 75% of all described plant viruses (Nault, 1997). Thus, plants must recognize, prioritize, and mount the most appropriate response to both the insect that is feeding and the pathogen being transmitted. Despite constant attack, plants persist, largely due to a sophisticated surveillance system. Plants respond with an arsenal of defenses that may be morphological, biochemical, or molecular in nature (Jones and Dangl, 2006; Jander and Howe, 2008). Nevertheless, pathogens and insects successfully colonize plants by actively compromising plant perception and/or defense responses.Recent studies show that synergisms exist between challengers, where both parties benefit during dual attack. For example, some virus infections can decrease plant defenses against insects, increasing plant palatability and vector fitness. Consequently, improved insect performance will increase the number of viruliferous vectors, promoting virus transmission to new hosts (Mauck et al., 2010; Casteel and Jander, 2013; Casteel et al., 2014; Li et al., 2014). Thus, vector-plant interactions represent a critical and synergistic relationship, ultimately determining survival and host range. Although numerous studies have examined virus-plant interactions, few have examined the molecular and genetic mechanisms mediating plant-virus-vector interactions and alterations in plant defenses (Li et al., 2014; Mauck et al., 2014).While defenses vary widely across plant species, the phytohormones that regulate their production are somewhat conserved. Modulation of hormone composition, timing, and concentration specifies plant responses to an attack (Mur et al., 2006; Verhage et al., 2010) and represents an excellent target for compromising defenses. Numerous studies have demonstrated that at least three phytohormones, jasmonic acid (JA), salicylic acid (SA), and ethylene (ET), have major roles in orchestrating plant defense responses (Bari and Jones, 2009; Erb et al., 2012; Pieterse et al., 2012). In general, SA signaling is critical for defense responses against a wide range of pathogens, including viruses (Glazebrook, 2005; Carr et al., 2010). Production of JA and ET, meanwhile, are involved in regulation of plant response to herbivores, necrotrophic pathogens, and nonpathogenic microbes (Glazebrook, 2005; Howe and Jander, 2008; Van der Ent et al., 2009). Virus infection can also alter JA and ET signaling (Carr et al., 2010; Lewsey et al., 2010; Wei et al., 2010; Mauck et al., 2014).Together, Arabidopsis (Arabidopsis thaliana), the green peach aphid (Myzus persicae), and Turnip mosaic virus (TuMV) constitute an excellent model system for investigating the molecular and biochemical mechanisms that underlie plant-aphid-virus interactions. As a well-studied model plant, Arabidopsis provides numerous genetic resources that can be used to investigate responses to aphid feeding and virus infection. The green peach aphid is a broad-host-range aphid and the world’s most prolific plant virus vector, transmitting more than 100 different viral species (Kennedy et al., 1962). The green peach aphid is the most common aphid pest on Arabidopsis in greenhouses and growth chambers (Bush et al., 2006), and we also have observed it feeding from Arabidopsis growing in nature. Due to the agricultural relevance of the green peach aphid, there is a large body of literature about the biology of this insect and its interactions with host plants, going back more than 100 years. More recently, several research groups have initiated projects to study plant defense against aphids using Arabidopsis and the green peach aphid as a model system (de Vos et al., 2007; Louis and Shah, 2013). TuMV is a positive-strand RNA virus that infects not only Arabidopsis but also hundreds of other species in more than 40 plant families (Walsh and Jenner, 2002). It is considered to be one of the most damaging viruses for vegetable crops worldwide (Tomlinson, 1987; Nguyen et al., 2013; Yasaka et al., 2015) and is transmitted by the green peach aphid and many other aphid species in both natural and agricultural settings (Shattuck, 1992). Largely due to its ability to systemically infect Arabidopsis (Sánchez et al., 1998; Martín Martín et al., 1999), TuMV has become a model for potyvirus-host interactions (Walsh and Jenner, 2002).In this study, we investigate the role of phytohormone signals in TuMV’s ability to suppress plant defense and enhance aphid fecundity during infection of host plants. First, we show that TuMV infection induces SA and ET accumulation in Arabidopsis. Next, using genetic and pharmacological analyses, we demonstrate that ET signaling is necessary for TuMV-initiated suppression of plant defense responses and enhanced aphid reproduction in plants. Further, we show that expression of the viral protein Nuclear Inclusion a-Protease (NIa-Pro) alters ET responses and that ET is also required for NIa-Pro’s role in suppressing aphid-induced defense in virus-infected plants. This molecular, biochemical, and genetic evidence reveals that TuMV may modulate ET responses not only to increase plant susceptibility to infection but also to increase vector performance.     

Epigenome-wide analysis of neonatal CD4+ T-cell DNA methylation sites potentially affected by maternal fish oil supplementation

Supplementation of fish oil rich in omega-3 polyunsaturated fatty acids (n-3 PUFA) during pregnancy has been shown to confer favorable health outcomes in the offspring. In a randomized controlled trial, we have previously shown that n-3 PUFA supplementation in pregnancy was associated with modified immune responses and some markers of immune maturation. However, the molecular mechanisms underlying these heritable effects are unclear. To determine whether the biological effects of maternal n-3 PUFA supplementation are mediated through DNA methylation, we analyzed CD4⁺ T-cells purified from cryo-banked cord blood samples from a previously conducted clinical trial. Of the 80 mother-infant pairs that completed the initial trial, cord blood samples of 70 neonates were available for genome-wide DNA methylation profiling. Comparison of purified total CD4⁺ T-cell DNA methylation profiles between the supplement and control groups did not reveal any statistically significant differences in CpG methylation, at the single-CpG or regional level. Effect sizes among top-ranked probes were lower than 5% and did not warrant further validation. Tests for association between methylation levels and key n-3 PUFA parameters, docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), or total n-3 PUFAs were suggestive of dose-dependent effects, but these did not reach genome-wide significance. Our analysis of the microarray data did not suggest strong modifying effects of in utero n-3 PUFA exposure on CD4⁺ T-cell methylation profiles, and no probes on the array met our criteria for further validation. Other epigenetic mechanisms may be more relevant mediators of functional effects induced by n-3 PUFA in early life.