Kinetic analysis of local structure formations in protein folding

The protein folding process is described by a cluster model based on the assumption that local structures or clusters are formed at an early stage in different regions of the polypeptide chain. Possible local structural elements in a globular protein are helices, bends, and hydrophobic cores whose formation is presumably determined by the interaction with the environment. Thus the tendency of local structure formation is expressed by a surface free energy of the cluster, which is assigned to the interface between the cluster and its environment. The probability of finding the chain of N residues with k clusters and m residues in the cluster is represented by a cluster distribution map. The cluster model exhibits a distinct two-state-like equilibrium transition, which can be seen on this map as well-separated native and denatured populations at the midpoint of the transition. The native population is localized at k ≈ 1 and m ≈ N, while the position of the denatured population can vary significantly depending on the surface free energy of the cluster. If the surface free energy is strong, the denatured population is localized near k = 0 and m = 0. On the other hand, if the surface free energy is weak, the denatured population is localized at high k and m values. The dynamics of the cluster model are treated as a stochastic process involving the transition from a state (k,m) to one of its six neighbors. The transition probability for each transition is determined by the free energy difference between two states; thus no activation process is assumed. However, the conversion of the two macrostates, native and denatured populations, involves the free energy activation due to the cooperative interaction of the macrosystem. The dynamics are analyzed by following the time evolution of the population profile on the cluster distribution map. Kinetic schemes are proposed to describe the multistep mechanism of protein folding and unfolding.     

The lysyl oxidase like 2/3 enzymatic inhibitor,PXS‐5153A,reduces crosslinks and ameliorates fibrosis

Fibrosis is characterized by the excessive deposition of extracellular matrix and crosslinked proteins, in particular collagen and elastin, leading to tissue stiffening and disrupted organ function. Lysyl oxidases are key players during this process, as they initiate collagen crosslinking through the oxidation of the ε‐amino group of lysine or hydroxylysine on collagen side‐chains, which subsequently dimerize to form immature, or trimerize to form mature, collagen crosslinks. The role of LOXL2 in fibrosis and cancer is well documented, however the specific enzymatic function of LOXL2 and LOXL3 during disease is less clear. Herein, we describe the development of PXS‐5153A, a novel mechanism based, fast‐acting, dual LOXL2/LOXL3 inhibitor, which was used to interrogate the role of these enzymes in models of collagen crosslinking and fibrosis. PXS‐5153A dose‐dependently reduced LOXL2‐mediated collagen oxidation and collagen crosslinking in vitro. In two liver fibrosis models, carbon tetrachloride or streptozotocin/high fat diet‐induced, PXS‐5153A reduced disease severity and improved liver function by diminishing collagen content and collagen crosslinks. In myocardial infarction, PXS‐5153A improved cardiac output. Taken together these results demonstrate that, due to their crucial role in collagen crosslinking, inhibition of the enzymatic activities of LOXL2/LOXL3 represents an innovative therapeutic approach for the treatment of fibrosis.     

Co-operative Group Predation in a Sit-and-wait Cheyletid Mite

The Cheyletidae is a family of trombidiform mites with more than 100 predatory and parasitic species. The cheyletid Hemicheyletia morii Ehara is a predatory species occurring on leaves of tropical trees. Observations on the life history and behaviour of this species revealed a new type of sit-and-wait predacious tactic and a sociality previously unknown in Acari. In addition, nest cleaning by a member of the colony was observed. Our results show that this species possesses subsociality. These results are remarkable as group living, co-operative hunting and feeding are rare phenomena in this subclass. Furthermore, the occurrence of thelytoky observed suggests the importance of kin selection.     

A buccal cell model comet assay: development and evaluation for human biomonitoring and nutritional studies

The comet assay is a widely used biomonitoring tool for DNA damage. The most commonly used cells in human studies are lymphocytes. There is an urgent need to find an alternative target human cell that can be collected from normal subjects with minimal invasion. There are some reports of buccal cells, collected easily from the inside of the mouth, being used in studies of DNA damage and repair, and these were of interest. However, our preliminary studies following the published protocol showed that buccal cells sustained massive damage and disintegrated at the high pH [O. Ostling, K.J. Johanson. Microelectrophoretic study of radiation-induced DNA damages in individual mammalian cells. Biochem. Biophys. Res. Commun. 123 (1984) 291-298] used, but that at lower pH were extremely resistant to lysis, an essential step in the comet assay. Therefore, the aims of this study were to develop a protocol than enabled buccal cell lysis and DNA damage testing in the comet assay, and to use the model to evaluate the potential use of the buccal cell model in human biomonitoring and nutritional study. Specifically, we aimed to investigate intra- and inter-individual differences in buccal cell DNA damage (as strand breaks), the effect of in vitro exposure to both a standard oxidant challenge and antioxidant treatment, as well as in situ exposure to an antioxidant-rich beverage and supplementation-related effects using a carotenoid-rich food. Successful lysis was achieved using 0.25% trypsin for 30 min followed by proteinase K (1mg/ml) treatment for 60 min. When this procedure was performed on cells pre-embedded in agarose on a microscope slide, followed by electrophoresis (in 0.01 M NaOH, 1mM EDTA, pH 9.1, 18 min at 12 V), a satisfactory comet image was obtained, though inter-individual variation was quite wide. Pre-lysis exposure of cells to a standard oxidant challenge (induced by H2O2) increased DNA strand breaks in a dose related manner, and incubation of cells in Trolox (a water soluble Vitamin E analogue) conferred significant protection (P<0.05) against subsequent oxidant challenge. Exposure of buccal cell in situ (i.e. in the mouth) to antioxidant-rich green tea led to an acute decrease in basal DNA strand breaks. In a controlled human intervention trial, buccal cells from 14 subjects after 28 days' supplementation with a carotenoid-rich berry (Fructus barbarum L.) showed a small but statistically significant (P<0.05) decrease in DNA strand breaks. These data indicate that this buccal cell comet assay is a feasible and potentially useful alternative tool to the usual lymphocyte model in human biomonitoring and nutritional work.     

Distinct lipidomic profiles in models of physiological and pathological cardiac remodeling,and potential therapeutic strategies

Cardiac myocyte membranes contain lipids which remodel dramatically in response to heart growth and remodeling. Lipid species have both structural and functional roles. Physiological and pathological cardiac remodeling have very distinct phenotypes, and the identification of molecular differences represent avenues for therapeutic interventions. Whether the abundance of specific lipid classes is different in physiological and pathological models was largely unknown. The aim of this study was to determine whether distinct lipids are regulated in settings of physiological and pathological remodeling, and if so, whether modulation of differentially regulated lipids could modulate heart size and function. Lipidomic profiling was performed on cardiac-specific transgenic mice with 1) physiological cardiac hypertrophy due to increased Insulin-like Growth Factor 1 (IGF1) receptor or Phosphoinositide 3-Kinase (PI3K) signaling, 2) small hearts due to depressed PI3K signaling (dnPI3K), and 3) failing hearts due to dilated cardiomyopathy (DCM). In hearts of dnPI3K and DCM mice, several phospholipids (plasmalogens) were decreased and sphingolipids increased compared to mice with physiological hypertrophy. To assess whether restoration of plasmalogens could restore heart size or cardiac function, dnPI3K and DCM mice were administered batyl alcohol (BA; precursor to plasmalogen biosynthesis) in the diet for 16 weeks. BA supplementation increased a major plasmalogen species (p18:0) in the heart but had no effect on heart size or function. This may be due to the concurrent reduction in other plasmalogen species (p16:0 and p18:1) with BA. Here we show that lipid species are differentially regulated in settings of physiological and pathological remodeling. Restoration of lipid species in the failing heart warrants further examination.     

Na,K-ATPase as A Brownian Motor: Electric Field-InducedConformational Fluctuation Leads to Uphill Pumping of Cation inthe Absence of ATP

Na,K-ATPase uses chemical bond energy of ATP to pump K⁺ into, andNa⁺ out of a cell. Both are uphill transports. During the catalyticcycle the enzyme alternates between two conformational states, E₁ andE₂. This communication describes an experiment, which employs electricfield to drive oscillation or fluctuation of enzyme conformation betweenthe E₁ and the E₂ states. It is shown that the field-inducedconformational oscillation or fluctuation leads to uphill pumping of thecation by the enzyme without consumption of ATP. Biochemical specificityof the catalysis is preserved. Data indicate that Na,K-ATPase can harvestenergy from the applied electric field to perform chemical work, and aratchet mechanism is inherent in this energy transduction process. ATheory of Electroconformational Coupling (TEC) that embodies essentialfeatures of the Brownian Ratchet successfully simulates the field-frequencyand field-amplitude optima and other features of the ion pumping activity.A four-state TEC motor can achieve high efficiency of the energytransduction, asymptotically reaching 100% under the optimal condition.Pumping by ion rectification fails to reach high efficiency. The TECconcept is also mused to understand other biological motors and engines.     

Seed depredation negates the benefits of midstory hardwood removal on longleaf pine seedling establishment

Midstory hardwoods are traditionally removed to restore longleaf pine on fire‐excluded savannas. However, recent evidence demonstrating midstory hardwood facilitation on longleaf pine seedling survival has brought this practice into question on xeric sites. Also, midstory hardwoods could facilitate longleaf pine seedling establishment, as hardwood litter may conceal seeds from seed predators or improve micro‐environmental conditions for seedling establishment. However, little is known about these potential mechanisms. In this study, we tracked longleaf pine seed depredation and germination in artificially seeded plots (11 seeds/m²) in a factorial design fully crossing hardwood retention or removal with vertebrate seed predator access or exclusion in the Sandhills Ecoregion of North Carolina, U.S.A. Seed depredation averaged 78% across treatments and was greatest in unexcluded plots. Hardwood retention did not affect seed depredation. Longleaf pine averaged 3.6 germinants/4 m² across treatments, and was six times more abundant where vertebrates had been excluded. Hardwood removal had a strong positive effect on seedling germination, likely due to the removal of litter, but only when vertebrates were excluded. Our results indicated midstory hardwoods are not facilitating longleaf pine seedling establishment. Nevertheless, our results indicated that hardwood removal may not increase longleaf pine seedling establishment, as seed depredation diminished the effectiveness of hardwood removal under mast seed availability. Collectively, these results demonstrate the underlying complexity of the longleaf pine ecosystem, and suggest that planting may need to be part of the restoration strategy on sites where seed depredation limits longleaf pine natural regeneration.     

Effects of an anti-inflammatory VAP-1/SSAO inhibitor,PXS-4728A,on pulmonary neutrophil migration

Background and purpose

The persistent influx of neutrophils into the lung and subsequent tissue damage are characteristics of COPD, cystic fibrosis and acute lung inflammation. VAP-1/SSAO is an endothelial bound adhesion molecule with amine oxidase activity that is reported to be involved in neutrophil egress from the microvasculature during inflammation. This study explored the role of VAP-1/SSAO in neutrophilic lung mediated diseases and examined the therapeutic potential of the selective inhibitor PXS-4728A.

Methods

Mice treated with PXS-4728A underwent intra-vital microscopy visualization of the cremaster muscle upon CXCL1/KC stimulation. LPS inflammation, Klebsiella pneumoniae infection, cecal ligation and puncture as well as rhinovirus exacerbated asthma models were also assessed using PXS-4728A.

Results

Selective VAP-1/SSAO inhibition by PXS-4728A diminished leukocyte rolling and adherence induced by CXCL1/KC. Inhibition of VAP-1/SSAO also dampened the migration of neutrophils to the lungs in response to LPS, Klebsiella pneumoniae lung infection and CLP induced sepsis; whilst still allowing for normal neutrophil defense function, resulting in increased survival. The functional effects of this inhibition were demonstrated in the RV exacerbated asthma model, with a reduction in cellular infiltrate correlating with a reduction in airways hyperractivity.

Conclusions and implications

This study demonstrates that the endothelial cell ligand VAP-1/SSAO contributes to the migration of neutrophils during acute lung inflammation, pulmonary infection and airway hyperractivity. These results highlight the potential of inhibiting of VAP-1/SSAO enzymatic function, by PXS-4728A, as a novel therapeutic approach in lung diseases that are characterized by neutrophilic pattern of inflammation.     

Asthma and Maternal Body Mass Index Are Related to Pediatric Body Mass Index and Obesity: Results from the Third National Health and Nutrition Examination Survey

Objective: Clinical research has shown an increased prevalence of obesity in children with asthma. This study was designed to assess the relationship between asthma and pediatric body mass index (BMI) in a national database and to examine factors that may modify this relationship. Design: The cross‐sectional relationship between asthma and pediatric BMI and obesity (BMI ≥ 85th percentile) was studied. Variables that may influence the relationship between asthma and pediatric BMI, such as race/ethnicity and television watching were included in the model for the total sample. A smaller sample of 3009 white and African American youth were studied in regression models including maternal BMI. Study Population: A nationally representative crosssectional sample of 5154 children and adolescents of 6 to 16 years of age from the Third National Health And Nutrition Examination Survey. Results: In the full sample, asthma and television watching were related to BMI, accounting for 3% of the variance in BMI. When maternal BMI was included in the nonHispanic sample, television watching, maternal BMI, and the interaction of maternal BMI and asthma were related to youth BMI, accounting for 15% of the variance. The standardized BMI z‐score for those youth without asthma and no maternal obesity was 0.06, which increased to 0.33 if the youth had asthma, to 0.70 if the youth did not have asthma but the mother was obese, and to 1.71 if the youth had asthma and the mother was obese. Asthma, television watching, and maternal BMI were independent predictors of youth obesity. Conclusions: BMI and prevalence of obesity is higher in youth with asthma. Pediatric BMI, but not obesity, is also related to the interaction of asthma and maternal BMI in white and African American youth. Comorbidity of asthma and obesity may complicate treatment of either condition, and prevention of obesity should be encouraged for asthmatic children.     

Assessing the use of mitochondrial cox1 gene and cox2-3 spacer for genetic diversity study of Malaysian Gracilaria changii (Gracilariaceae, Rhodophyta) from Peninsular Malaysia

Advances in DNA-based genetic markers provide the essential tools in measurement of genetic diversity relating to the evolution, biogeography, and systematics of red algae by exploiting genetic variation in the entire genome of organisms. The understanding of genetic diversity in Gracilaria changii (Gracilariaceae, Rhodophyta) will provide valuable information for conservation, plant breeding management, and strain selection for cultivation. However, information of intraspecific genetic variation is still rudimentary. In this study, two mitochondrial encoded markers, cytochrome oxidase subunit 1 (cox1) and intergenic spacer between the cytochrome oxidase subunits 2 and 3 (cox2-3 spacer) were used to investigate genetic diversity in 40 individuals of G. changii collected from 11 different geographically distinct populations from Peninsular Malaysia. Seven distinct mitochondrial haplotypes were identified with the cox1 gene and three mitochondrial haplotypes with the cox2-3 spacer. Intraspecific nucleotide differences ranged from 0 to 6 bp for the cox1 and 0–4 bp for the cox2-3 spacer, respectively. This is the first report comparing the suitability of mitochondrial markers of the cox1 gene and the cox2-3 spacer for genetic diversity studies on G. changii. The present study showed that the cox1 gene is a potential molecular marker to infer intraspecific genetic variation in red macroalgae. The cox1 marker is more variable compared to the cox2-3 spacer and revealed genetic variation and phylogeographic structure for this ecologically and economically important species.