Divergence of the mRNA targets for the Ssb proteins of bacteriophages T4 and RB69

Background

Mortality rates have differed during distemper outbreaks among free-ranging raccoons (Procyon lotor) living around a large Chicago-area zoo, and appeared higher in year 2001 than in 1998 and 2000. We hypothesized that a more lethal variant of the local Canine distemper virus (CDV) lineage had emerged in 2001, and sought the genetic basis that led to increased virulence. However, a more complex model surfaced during preliminary analyses of CDV genomic sequences in infected tissues and of virus isolated in vitro from the raccoons.

Results

Phylogenetic analyses of subgenomic CDV fusion (F) -, phosphoprotein (P) -, and complete hemagglutinin (H) – gene sequences indicated that distinct American CDV lineages caused the distemper epizootics. The 1998 outbreak was caused by viruses that are likely from an old CDV lineage that includes CDV Snyder Hill and Lederle, which are CDV strains from the early 1950's. The 2000 and 2001 viruses appear to stem from the lineage of CDV A75/17, which was isolated in the mid 1970's. Only the 2001 viruses formed large syncytia in brain and/or lung tissue, and during primary isolation in-vitro in Vero cells, demonstrating at least one phenotypic property by which they differed from the other viruses.

Conclusions

Two different American CDV lineages caused the raccoon distemper outbreaks. The 1998 viruses are genetically distant to the 2000/2001 viruses. Since CDV does not cause persistent infections, the cycling of different CDV lineages within the same locale suggests multiple reintroductions of the virus to area raccoons. Our findings establish a precedent for determining whether the perceived differences in mortality rates are actual and attributable in part to inherent differences between CDV strains arising from different CDV lineages.     

Ecotoxicity impact assessment of laundry products: a comparison of USEtox and critical dilution volume approaches

Purpose  

There is an increasing interest in the assessment and comparison of the environmental impacts of consumer products. Schemes such as Grenelle de l’Environnement, currently under development in France, aim to assess and communicate the life cycle impacts of consumer products. Freshwater ecotoxicity is one of the impact categories under consideration. This paper presents the results of a comparison of USEtox and critical dilution volume (CDV) approaches for assessing laundry products.     

Critical scale of propagation influences dynamics of waves in a model of excitable medium

Background  

Duration and speed of propagation of the pulse are essential factors for stability of excitation waves. We explore the propagation of excitation waves resulting from periodic stimulation of an excitable cable to determine the minimal stable pulse duration in a rate-dependent modification of a Chernyak-Starobin-Cohen reaction-diffusion model.     

Transverse propagation of action potentials between parallel chains of cardiac muscle and smooth muscle cells in PSpice simulations

Background  

We previously examined transverse propagation of action potentials between 2 and 3 parallel chain of cardiac muscle cells (CMC) simulated using the PSpice program. The present study was done to examine transverse propagation between 5 parallel chains in an expanded model of CMC and smooth muscle cells (SMC).     

Propagation velocity profile in a cross-section of a cardiac muscle bundle from PSpice simulation

Background  

The effect of depth on propagation velocity within a bundle of cardiac muscle fibers is likely to be an important factor in the genesis of some heart arrhythmias.     

Effect of transverse gap-junction channels on transverse propagation in an enlarged PSpice model of cardiac muscle

Background  

In previous PSpice modeling studies of simulated action potentials (APs) in parallel chains of cardiac muscle, it was found that transverse propagation could occur between adjacent chains in the absence of gap-junction (gj) channels, presumably by the electric field (EF) generated in the narrow interstitial space between the chains. Transverse propagation was sometimes erratic, the more distal chains firing out of order.     

Large impact of the apoplast on somatic embryogenesis in <Emphasis Type="Italic">Cyclamen persicum</Emphasis> offers possibilities for improved developmental control <Emphasis Type="Italic">in vitro</Emphasis>

Background  

Clonal propagation is highly desired especially for valuable horticultural crops. The method with the potentially highest multiplication rate is regeneration via somatic embryogenesis. However, this mode of propagation is often hampered by the occurrence of developmental aberrations and non-embryogenic callus. Therefore, the developmental process of somatic embryogenesis was analysed in the ornamental crop Cyclamen persicum by expression profiling, comparing different developmental stages of embryogenic cell cultures, zygotic vs. somatic embryos and embryogenic vs. non-embryogenic cell cultures.     

Implementation of force distribution analysis for molecular dynamics simulations

Background  

The way mechanical stress is distributed inside and propagated by proteins and other biopolymers largely defines their function. Yet, determining the network of interactions propagating internal strain remains a challenge for both, experiment and theory. Based on molecular dynamics simulations, we developed force distribution analysis (FDA), a method that allows visualizing strain propagation in macromolecules.     

A Serological Survey of Infectious Disease in Yellowstone National Park’s Canid Community

Background

Gray wolves (Canis lupus) were reintroduced into Yellowstone National Park (YNP) after a >70 year absence, and as part of recovery efforts, the population has been closely monitored. In 1999 and 2005, pup survival was significantly reduced, suggestive of disease outbreaks.

Methodology/Principal Findings

We analyzed sympatric wolf, coyote (Canis latrans), and red fox (Vulpes vulpes) serologic data from YNP, spanning 1991–2007, to identify long-term patterns of pathogen exposure, identify associated risk factors, and examine evidence for disease-induced mortality among wolves for which there were survival data. We found high, constant exposure to canine parvovirus (wolf seroprevalence: 100%; coyote: 94%), canine adenovirus-1 (wolf pups [0.5–0.9 yr]: 91%, adults [≥1 yr]: 96%; coyote juveniles [0.5–1.5 yrs]: 18%, adults [≥1.6 yrs]: 83%), and canine herpesvirus (wolf: 87%; coyote juveniles: 23%, young adults [1.6–4.9 yrs]: 51%, old adults [≥5 yrs]: 87%) suggesting that these pathogens were enzootic within YNP wolves and coyotes. An average of 50% of wolves exhibited exposure to the protozoan parasite, Neospora caninum, although individuals’ odds of exposure tended to increase with age and was temporally variable. Wolf, coyote, and fox exposure to canine distemper virus (CDV) was temporally variable, with evidence for distinct multi-host outbreaks in 1999 and 2005, and perhaps a smaller, isolated outbreak among wolves in the interior of YNP in 2002. The years of high wolf-pup mortality in 1999 and 2005 in the northern region of the park were correlated with peaks in CDV seroprevalence, suggesting that CDV contributed to the observed mortality.

Conclusions/Significance

Of the pathogens we examined, none appear to jeopardize the long-term population of canids in YNP. However, CDV appears capable of causing short-term population declines. Additional information on how and where CDV is maintained and the frequency with which future epizootics might be expected might be useful for future management of the Northern Rocky Mountain wolf population.     

Is the development of falciparum malaria in the human host limited by the availability of uninfected erythrocytes?

Background  

The development and propagation of malaria parasites in their vertebrate host is a complex process in which various host and parasite factors are involved. Sometimes the evolution of parasitaemia seems to be quelled by parasite load. In order to understand the typical dynamics of evolution of parasitaemia, various mathematical models have been developed. The basic premise ingrained in most models is that the availability of uninfected red blood cells (RBC) in which the parasite develops is a limiting factor in the propagation of the parasite population.     

Characterization of extracellular matrix macromolecules in primary cultures of equine keratinocytes

Background  

Most research to date involving laminins and extracellular matrix protein function in both normal and pathological conditions involves in vitro culture of keratinocytes. Few methods are established to allow for prolonged propagation of keratinocytes from equine tissues, including the hoof lamellae. In this study we modified cell isolation and culture techniques to allow for proliferation and sub-culturing of equine lamellar keratinocytes. Additionally, the production and processing of extracellular matrix molecules by skin and lamellar keratinocytes were studied.     

Laser thermal therapy monitoring using complex differential variance in optical coherence tomography

Conventional thermal therapy monitoring techniques based on temperature are often invasive, limited by point sampling, and are indirect measures of tissue injury, while techniques such as magnetic resonance and ultrasound thermometry are limited by their spatial resolution.  The visualization of the thermal coagulation zone at high spatial resolution is particularly critical to the precise delivery of thermal energy to epithelial lesions. In this work, an integrated thulium laser thermal therapy monitoring system was developed based on complex differential variance (CDV), which enables the 2D visualization of the dynamics of the thermal coagulation process at high spatial and temporal resolution with an optical frequency domain imaging system. With proper calibration to correct for noise, the CDV‐based technique was shown to accurately delineate the thermal coagulation zone, which is marked by the transition from high CDV upon heating to a significantly reduced CDV once the tissue is coagulated, in 3 different tissue types ex vivo: skin, retina, and esophagus. The ability to delineate thermal lesions in multiple tissue types at high resolution opens up the possibility of performing microscopic image‐guided procedures in a vast array of epithelial applications ranging from dermatology, ophthalmology, to gastroenterology and beyond. 

     

Enzyme classification with peptide programs: a comparative study

Background  

Efficient and accurate prediction of protein function from sequence is one of the standing problems in Biology. The generalised use of sequence alignments for inferring function promotes the propagation of errors, and there are limits to its applicability. Several machine learning methods have been applied to predict protein function, but they lose much of the information encoded by protein sequences because they need to transform them to obtain data of fixed length.     

Observation of intermediate states of the human prion protein by high pressure NMR spectroscopy

Background  

Prions as causative agents of transmissible spongiform encephalopathies (TSEs) in humans and animals are composed of the infectious isomer, PrP^Sc, of the cellular prion protein, PrP^C. The conversion and thus the propensity of PrP^C to adopt alternative folds leads to the species-specific propagation of the disease. High pressure is a powerful tool to study the physico-chemical properties of proteins as well as the dynamics and structure of folding intermediates.     

Repolarization of the action potential enabled by Na<Superscript>+</Superscript> channel deactivation in PSpice simulation of cardiac muscle propagation

Background  

In previous studies on propagation of simulated action potentials (APs) in cardiac muscle using PSpice modeling, we reported that a second black-box (BB) could not be inserted into the K⁺ leg of the basic membrane unit because that caused the PSpice program to become very unstable. Therefore, only the rising phase of the APs could be simulated. This restriction was acceptable since only the mechanism of transmission of excitation from one cell to the next was being investigated.     

Sequencing of emerging canine distemper virus strain reveals new distinct genetic lineage in the United States associated with disease in wildlife and domestic canine populations

Background

Recent outbreaks of canine distemper have prompted examination of strains from clinical samples submitted to the University of Tennessee College of Veterinary Medicine (UTCVM) Clinical Virology Lab. We previously described a new strain of CDV that significantly diverged from all genotypes reported to date including America 2, the genotype proposed to be the main lineage currently circulating in the US. The aim of this study was to determine when this new strain appeared and how widespread it is in animal populations, given that it has also been detected in fully vaccinated adult dogs. Additionally, we sequenced complete viral genomes to characterize the strain and determine if variation is confined to known variable regions of the genome or if the changes are also present in more conserved regions.

Methods

Archived clinical samples were genotyped using real-time RT-PCR amplification and sequencing. The genomes of two unrelated viruses from a dog and fox each from a different state were sequenced and aligned with previously published genomes. Phylogenetic analysis was performed using coding, non-coding and genome-length sequences. Virus neutralization assays were used to evaluate potential antigenic differences between this strain and a vaccine strain and mixed ANOVA test was used to compare the titers.

Results

Genotyping revealed this strain first appeared in 2011 and was detected in dogs from multiple states in the Southeast region of the United States. It was the main strain detected among the clinical samples that were typed from 2011–2013, including wildlife submissions. Genome sequencing demonstrated that it is highly conserved within a new lineage and preliminary serologic testing showed significant differences in neutralizing antibody titers between this strain and the strain commonly used in vaccines.

Conclusion

This new strain represents an emerging CDV in domestic dogs in the US, may be associated with a stable reservoir in the wildlife population, and could facilitate vaccine escape.

     

Antibiotic-free selection in E. coli: new considerations for optimal design and improved production

Background  

The increasing regulatory requirements to which biological agents are subjected will have a great impact in the field of industrial protein expression and production. There is an expectation that in a near future, there may be "zero tolerance" towards antibiotic-based selection and production systems. Besides the antibiotic itself, the antibiotic resistance gene is an important consideration. The complete absence of antibiotic-resistance gene being the only way to ensure that there is no propagation in the environment or transfer of resistance to pathogenic strains.     

Comparing chemical environmental scores using USEtox<Superscript>™</Superscript> and CDV from the European Ecolabel

Purpose

USEtox^? (Rosenbaum et al. 2008) is a new model which can be used to calculate characterization factors for human and ecotoxicity impact categories used in life cycle assessment. The French ADEME-AFNOR (http://affichage-environnemental.afnor.org/) is currently considering this model to develop a new environmental labelling standard for consumer goods. The objective of this short study is to compare USEtox^? impact scores with critical dilution volume (CDV) scores from the European Ecolabel (http://ec.europa.eu/environment/ecolabel), a well-established tool widely used in Europe aiming at discriminating environmental friendly products.

Material and methods

The same range of chemicals (high scores to low scores) listed in both the USEtox^? database and the EU Ecolabel detergent ingredient database (DID-list) were used for the comparison. The DID-list is a reference list, which contains agreed and verified fate and ecotoxicity data. The ranking was made based on two different ranking parameters, one from each model: the environmental impact score from USEtox^? and the CDV from the EU Ecolabel. Additionally, a Spearman’s rank correlation (ρ) coefficient was calculated.

Results and discussion

Sixty-nine chemicals common in personal care and cleaning products were selected for the comparison between USEtox^? and EU Ecolabel methods. A “fair” agreement was found between the two models with a Spearman correlation coefficient ρ of 0.74, but a significant number of chemicals was ranked rather differently. The presence of outliers (i.e., different ranking) may be explained by several factors, which include the use of discrete versus continuous values to estimate the substance’s degradation constant. Another factor could be that the substances are grouped under classes in the DID-list, thus having average parameter values. The main factor though probably lays in the different sources of the physico-chemical, fate and ecotoxicity data within the two model databases and the different way they are used for the ranking parameter calculation.

Conclusions

Provided there is scientific consensus (and full transparency) on the raw data, both USEtox^? and EU Ecolabel methods are relevant for ranking chemicals based on their physico-chemical and toxicological properties, and therefore for calculating product environmental impact scores related to their hazard. However, the presence of a number of chemicals with different ranking scores creates the risk of inconsistent consumer product information when either the CDV (EU ecolabel) or USEtox^? (French “Affichage Environnemental”) is used for environmental labelling. To date, and for sake of consistency with an existing and used labelling scheme, the CDV appears much easier to implement with less uncertainty to calculate ecotoxicity impact score of products.

     

Threshold intensity factors as lower boundaries for crack propagation in ceramics

Background  

Slow crack growth can be described in a v (crack velocity) versus K_I (stress intensity factor) diagram. Slow crack growth in ceramics is attributed to corrosion assisted stress at the crack tip or at any pre-existing defect in the ceramic. The combined effect of high stresses at the crack tip and the presence of water or body fluid molecules (reducing surface energy at the crack tip) induces crack propagation, which eventually may result in fatigue. The presence of a threshold in the stress intensity factor, below which no crack propagation occurs, has been the subject of important research in the last years. The higher this threshold, the higher the reliability of the ceramic, and consequently the longer its lifetime.     

The crosstalk between EGF,IGF, and Insulin cell signaling pathways - computational and experimental analysis

Background  

Cellular response to external stimuli requires propagation of corresponding signals through molecular signaling pathways. However, signaling pathways are not isolated information highways, but rather interact in a number of ways forming sophisticated signaling networks. Since defects in signaling pathways are associated with many serious diseases, understanding of the crosstalk between them is fundamental for designing molecularly targeted therapy. Unfortunately, we still lack technology that would allow high throughput detailed measurement of activity of individual signaling molecules and their interactions. This necessitates developing methods to prioritize selection of the molecules such that measuring their activity would be most informative for understanding the crosstalk. Furthermore, absence of the reaction coefficients necessary for detailed modeling of signal propagation raises the question whether simple parameter-free models could provide useful information about such pathways.