Inter- and intra-laboratory study to determine the reproducibility of toxicogenomics datasets

The application of toxicogenomics as a predictive tool for chemical risk assessment has been under evaluation by the toxicology community for more than a decade. However, it predominately remains a tool for investigative research rather than for regulatory risk assessment. In this study, we assessed whether the current generation of microarray technology in combination with an in vitro experimental design was capable of generating robust, reproducible data of sufficient quality to show promise as a tool for regulatory risk assessment. To this end, we designed a prospective collaborative study to determine the level of inter- and intra-laboratory reproducibility between three independent laboratories. All test centres (TCs) adopted the same protocols for all aspects of the toxicogenomic experiment including cell culture, chemical exposure, RNA extraction, microarray data generation and analysis. As a case study, the genotoxic carcinogen benzo[a]pyrene (B[a]P) and the human hepatoma cell line HepG2 were used to generate three comparable toxicogenomic data sets. High levels of technical reproducibility were demonstrated using a widely employed gene expression microarray platform. While differences at the global transcriptome level were observed between the TCs, a common subset of B[a]P responsive genes (n=400 gene probes) was identified at all TCs which included many genes previously reported in the literature as B[a]P responsive. These data show promise that the current generation of microarray technology, in combination with a standard in vitro experimental design, can produce robust data that can be generated reproducibly in independent laboratories. Future work will need to determine whether such reproducible in vitro model(s) can be predictive for a range of toxic chemicals with different mechanisms of action and thus be considered as part of future testing regimes for regulatory risk assessment.

Evaluation of the sporicidal activity of different chemical disinfectants used in hospitals against Clostridium difficile

Decontamination of surfaces and medical equipment is integral to the control of Clostridium difficile transmission, and many products claim to inactivate this bacterium effectively. Thirty-two disinfectants were tested against spores of C. difficile in a suspension test based on European Standard BS EN 13704:2002, with contact times of 1 and 60 min in simulations of clean (0.3% albumin) and dirty (3% albumin) conditions. The addition of a 1-min contact time was chosen as a more realistic simulation of probable real-life exposures in the situation being modelled than the 60 min specified by the Standard. The manufacturer's lowest recommended concentrations for use were tested. Sixteen products achieved >10(3) reduction in viability after 60 min (the pass criterion for the Standard) under both clean and dirty conditions. However, only eight products achieved >10(3) reduction in viability within 1 min under dirty conditions. Three products failed to reduce the viability of the C. difficile spores by a factor of 10(3) in any of the test conditions. This study highlights that the application of disinfectants claiming to be sporicidal is not, in itself, a panacea in the environmental control of C. difficile, but that carefully chosen environmental disinfectants could form part of a wider raft of control measures that include a range of selected cleaning strategies.

Patent data mining: a tool for accelerating HIV vaccine innovation

Global access to advanced vaccine technologies is challenged by the interrelated components of intellectual property (IP) management strategies, technology transfer (legal and technical) capabilities and the capacity necessary for accelerating R&D, commercialization and delivery of vaccines. Due to a negative association with the management of IP, patents are often overlooked as a vast resource of freely available, information akin to scientific journals as well as business and technological information and trends fundamental for formulating policies and IP management strategies. Therefore, a fundamental step towards facilitating global vaccine access will be the assembly, organization and analysis of patent landscapes, to identify the amount of patenting, ownership (assignees) and fields of technology covered. This is critical for making informed decisions (e.g., identifying licensees, building research and product development collaborations, and ascertaining freedom to operate). Such information is of particular interest to the HIV vaccine community where the HIV Vaccine Enterprise, have voiced concern that IP rights (particularly patents and trade secrets) may prevent data and materials sharing, delaying progress in research and development of a HIV vaccine. We have compiled and analyzed a representative HIV vaccine patent landscape for a prime-boost, DNA/adenoviral vaccine platform, as an example for identifying obstacles, maximizing opportunities and making informed IP management strategy decisions towards the development and deployment of an efficacious HIV vaccine.

PAF formation by human gastrointestinal mucosa/submucosa in-vitro: release by ricinoleic acid, and inhibition by 5-aminosalicylic acid

Human isolated gastrointestinal mucosa/submucosa incubated with ricinoleic acid (12·5–100 μg mL−1) or the calcium ionophore A23187 (10 μg mL−1) released platelet-activating factor (PAF) as determined by a scintillation proximity assay after extraction and purification. 5-Aminosalicylic acid (25–100 μg mL−1) inhibited PAF release by ricinoleic acid in a concentration-dependent manner, and 50 μg mL−1 reduced the effect of A23187. We suggest that PAF may play a role in the taxation and mucosal damage by ricinoleic acid released from castor oil.

Method for recording respiratory changes induced in guinea-pigs by aerosols of histamine or of specific antigen, and for assessing drugs which antagonise bronchoconstriction

A lightly-anaesthetised guinea-pig is made to breathe an aerosol of histamine or of specific antigen pumped into a breathing chamber. The guinea-pig’s respiration produces pressure changes which are recorded on a smoked drum. Isoprenaline and the antihistamine thenyldiamine, administered as aerosols or by injection, have been used to inhibit the reduction in “tidal volume” due to the bronchoconstrictor agents.

The Effects of Various Peptides on Human Isolated Gut Muscle

The effects of eleven peptides of gastrointestinal origin have been studied on the contraction, relaxation and spontaneous activity of circular and longitudinal muscle strips from different regions of the human gastrointestinal tract. The effects varied with the peptides and sometimes with the region and muscle layer. There was either contraction, no effect, or relaxation and/or inhibition of an acetylcholine-induced contraction. Responses to some peptides are consistent with the possibility that they may contribute directly to the control of motility: galanin, neurotensin and substance P might be involved in contraction, and vasoactive intestinal peptide, peptide histidine isoleucine and peptide histidine methionine might be inhibitory transmitters.

Digestive challenges for vertebrate animals: microbial diversity, cardiorespiratory coupling, and dietary specialization

The digestive system is the interface between the supply of food for an animal and the demand for energy and nutrients to maintain the body, to grow, and to reproduce. Digestive systems are not morphologically static but rather dynamically respond to changes in the physical and chemical characteristics of the diet and the level of food intake. In this article, we discuss three themes that affect the ability of an animal to alter digestive function in relation to novel substrates and changing food supply: (1) the fermentative digestion in herbivores, (2) the integration of cardiopulmonary and digestive functions, and (3) the evolution of dietary specialization. Herbivores consume, digest, and detoxify complex diets by using a wide variety of enzymes expressed by bacteria, predominantly in the phyla Firmicutes and Bacteroidetes. Carnivores, such as snakes that feed intermittently, sometimes process very large meals that require compensatory adjustments in blood flow, acid secretion, and regulation of acid-base homeostasis. Snakes and birds that specialize in simple diets of prey or nectar retain their ability to digest a wider selection of prey. The digestive system continues to be of interest to comparative physiologists because of its plasticity, both phenotypic and evolutionary, and because of its widespread integration with other physiological systems, including thermoregulation, circulation, ventilation, homeostasis, immunity, and reproduction.

Measuring cortisol in hair and saliva from dogs: coat color and pigment differences

Cortisol concentrations are frequently measured from a variety of sources including blood, saliva, urine, and feces to quantify stress in dogs. However, a need still exists for less intrusive collection methods in domestic animals and for more efficient means of measuring basal cortisol. The objectives of the present study were to minimize restraint for saliva sampling, to validate hair for basal cortisol measurement in dogs, and to determine concentrations of cortisol within the hair shaft and in relation to hair color. Using food luring, 79% of dogs required no restraint for saliva collection. Salivary and hair cortisol concentrations were positively correlated (P = 0.001), thus validating hair as a medium for basal cortisol quantification. Black dogs had less cortisol than nonblack dogs (P = 0.039) in hair, but not saliva. Across dogs, the average amount of cortisol did not differ between proximal and distal hair sections (P = 0.348). However, for 7 of the 9 dogs, more cortisol was present in the distal portions of the hair. We observed a difference in cortisol concentrations among hairs of different colors from individual dogs (P = 0.001). From the same 7 x 7 cm ischiatic patch from the same dog, black (eumelanin) hairs were consistently lower in cortisol than yellow (pheomelanin) hairs, and cortisol concentrations of agouti hairs were intermediate. This is the first evidence that hair of different colors might sequester cortisol differently.

Conditioning of a free operant in Octupus cyaneus Gray

Operant conditioning was studied in six specimens of Octopus cyaneus Gray. An "arm-out-of-water" operant, in which the octopus inserted an arm up a feeding-tube breaking the water surface, proved susceptible to reinforcement schedules. An apparatus was developed that provided automated reinforcement and recording. Performance was studied under continuous reinforcement, fixed-ratio and variable-ratio schedules, and extinction conditions.

Behavioral and neurobiological characteristics influencing social hierarchy formation in female cynomolgus monkeys

Socially housed monkeys have been used as a model to study human diseases. The present study examined behavioral, physiological and neurochemical measures as predictors of social rank in 16 experimentally naïve, individually housed female cynomolgus monkeys (Macaca fascicularis). The two behavioral measures examined were novel object reactivity (NOR), as determined by latency to touch an opaque acrylic box placed in the home cage, and locomotor activity assessed in a novel open-field apparatus. Serum cortisol concentrations were evaluated three times per week for four consecutive weeks, and stress reactivity was assessed on one occasion by evaluating the cortisol response to adrenocorticotropic hormone (ACTH) following dexamethasone suppression. Measures of serotonin (5-HT) function included whole blood 5-HT (WBS) concentrations, cerebrospinal fluid (CSF) concentrations of the 5-HT metabolite 5-hydroxyindoleacetic acid (5-HIAA) and brain 5-HT transporter (SERT) availability obtained using positron emission tomography (PET). After baseline measures were obtained, monkeys were assigned to four social groups of four monkeys per group. The two measures that correlated with eventual social rank were CSF 5-HIAA concentrations, which were significantly higher in the animals who eventually became subordinate, and latency to touch the novel object, which was significantly lower in eventual subordinate monkeys. Measures of 5-HT function did not change as a consequence of social rank. These data suggest that levels of central 5-HIAA and measures of novel object reactivity may be trait markers that influence eventual social rank in female macaques.

Evaluation of an exclusion plot design for determining the impacts of native and exotic herbivores on forest understoreys

To study the effects of grazing and browsing by Sambar deer (Cervus unicolor), swamp wallaby (Wallabia bicolor) and wombats (Vombatus ursinus) exclosure plots measuring 10 m x 10 m were erected in the Upper Yarra and O'Shannassy water catchments near Melbourne, Victoria. Total exclusion fences and partial exclusion fences were erected. Design details and costs are provided. Operational problems are discussed.