Tear staining in pigs: a potential tool for welfare assessment on commercial farms

Tear staining or chromodacryorrhea refers to a dark stain below the inner corner of the eye, caused by porphyrin-pigmented secretion from the Harderian gland. It has been shown to be a consistent indicator of stress in rats and to correlate with social stress and a barren environment in pigs. The current study was, to our knowledge, the first to test it on commercial pig farms as a potential welfare indicator. The study was carried out on three commercial farms in Finland, in connection to a larger study on the effects of different types of manipulable objects on tail and ear biting and other behavioural parameters. Farm A was a fattening farm, on which 768 growing-finishing pigs were studied in 73 pens. Farm B had a fattening unit, in which 656 growing-finishing pigs were studied in 44 pens, and a farrowing unit, in which 29 sows and their litters totalling 303 piglets were studied in 29 pens. Farm C was a piglet-producing farm, on which 167 breeder gilts were studied in 24 pens. Data collection included individual-level scoring of tear staining; scoring of tail and ear damage in the growing-finishing pigs and breeder gilts; a novel object test for the piglets; and a novel person test for the growing-finishing pigs on Farm B and the breeder gilts on Farm C. On Farm A, tear staining was found to correlate with tail damage scores (n=768, rs=0.14, P<0.001) and ear damage scores (n=768, rs=0.16, P<0.001). In the growing-finishing pigs on Farm B, tear staining of the left eye correlated with tail damage (n=656, rs=0.12, P<0.01) and that of the right eye correlated with ear damage (n=656, rs=0.10, P<0.01). On Farm A, tear-staining sores were lower in the treatment with three different types of manipulable objects as compared with controls (mean scores 3.3 and 3.9, respectively, n=31, F29=4.2, P<0.05). In the suckling piglets on Farm B, tear staining correlated with the latency to approach a novel object (n=29, rp=0.41, P<0.05). Although correlations with tail and ear damage were low, it was concluded that tear staining has promising potential as a new, additional welfare indicator for commercial pig farming. Further research is needed on the mechanisms of tear staining.

Multilayer Hydrophilic Poly(phenol-formaldehyde resin)-Coated Magnetic Graphene for Boronic Acid Immobilization as a Novel Matrix for Glycoproteome Analysis

Capturing glycopeptides selectively and efficiently from mixed biological samples has always been critical for comprehensive and in-depth glycoproteomics analysis, but the lack of materials with superior capture capacity and high specificity still makes it a challenge. In this work, we introduce a way first to synthesize a novel boronic-acid-functionalized magnetic graphene@phenolic-formaldehyde resin multilayer composites via a facile process. The as-prepared composites gathered excellent characters of large specific surface area and strong magnetic responsiveness of magnetic graphene, biocompatibility of resin, and enhanced affinity properties of boronic acid. Furthermore, the functional graphene composites were shown to have low detection limit (1 fmol) and good selectivity, even when the background nonglycopeptides has a concentration 100 fold higher. Additionally, enrichment efficiency of the composites was still retained after being used repeatedly (at least three times). Better yet, the practical applicability of this approach was evaluated by the enrichment of human serum with a low sample volume of 1 μL. All the results have illustrated that the magG@PF@APB has a great potential in glycoproteome analysis of complex biological samples.

High-Throughput Assessment of Cellular Mechanical Properties

Traditionally, cell analysis has focused on using molecular biomarkers for basic research, cell preparation, and clinical diagnostics; however, new microtechnologies are enabling evaluation of the mechanical properties of cells at throughputs that make them amenable to widespread use. We review the current understanding of how the mechanical characteristics of cells relate to underlying molecular and architectural changes, describe how these changes evolve with cell-state and disease processes, and propose promising biomedical applications that will be facilitated by the increased throughput of mechanical testing: from diagnosing cancer and monitoring immune states to preparing cells for regenerative medicine. We provide background about techniques that laid the groundwork for the quantitative understanding of cell mechanics and discuss current efforts to develop robust techniques for rapid analysis that aim to implement mechanophenotyping as a routine tool in biomedicine. Looking forward, we describe additional milestones that will facilitate broad adoption, as well as new directions not only in mechanically assessing cells but also in perturbing them to passively engineer cell state.

Gene expression patterns and environmental enrichment-induced effects in the hippocampi of mice suggest importance of Lsamp in plasticity

Limbic system associated membrane protein (Lsamp) gene is involved in behavioral adaptation in social and anxiogenic environments and has been associated with a broad spectrum of psychiatric diseases. Here we studied the activity of alternative promoters of Lsamp gene in mice in three rearing conditions (standard housing, environmental enrichment and social isolation) and in two different genetic backgrounds (129S6/SvEv and C57BL/6). Isolation had no effect on the expression levels of Lsamp. Environmental enrichment elevated the expression levels of Lsamp 1b transcript specifically in the hippocampus in B6 mice, and the same tendency existed across both mouse lines and both transcripts. Furthermore, we showed that the density of cells exhibiting 1b promoter activity is remarkably higher in the subgranular zone of the dentate gyrus in the hippocampal formation which is a specific area of enrichment-induced neurogenesis in adult rodents. On the contrary to 1b, 1a promoter is selectively active in the pyramidal and granule cell layers. We provide evidence that Lsamp modulates enrichment-induced activation of Bdnf as the enrichment-induced elevation of Bdnf in the hippocampus is significantly diminished in Lsamp-deficient mice; furthermore, a significant correlation was found between the expression levels of Lsamp and Bdnf transcripts in the hippocampus and frontal cortex. Significant strain differences in Lsamp expression were detected in the hippocampus, frontal cortex and thalamus that could be related to the different behavioral phenotype of B6 and 129Sv mice. Our data provides further evidence that LSAMP is implicated in the hippocampal connectivity and plasticity thereby modulating adaptability in changing environments.

High-throughput workflow for identification of phosphorylated peptides by LC-MALDI-TOF/TOF-MS coupled to in situ enrichment on MALDI plates functionalized by ion landing

We report an MS-based workflow for identification of phosphorylated peptides from trypsinized protein mixtures and cell lysates that is suitable for high-throughput sample analysis. The workflow is based on an in situ enrichment on matrix-assisted laser desorption/ionization (MALDI) plates that were functionalized by TiO2 using automated ion landing apparatus that can operate unsupervised. The MALDI plate can be functionalized by TiO2 into any array of predefined geometry (here, 96 positions for samples and 24 for mass calibration standards) made compatible with a standard MALDI spotter and coupled with high-performance liquid chromatography. The in situ MALDI plate enrichment was compared with a standard precolumn-based separation and achieved comparable or better results than the standard method. The performance of this new workflow was demonstrated on a model mixture of proteins as well as on Jurkat cells lysates. The method showed improved signal-to-noise ratio in a single MS spectrum, which resulted in better identification by MS/MS and a subsequent database search. Using the workflow, we also found specific phosphorylations in Jurkat cells that were nonspecifically activated by phorbol 12-myristate 13-acetate. These phosphorylations concerned the mitogen-activated protein kinase/extracellular signal-regulated kinase signaling pathway and its targets and were in agreement with the current knowledge of this signaling cascade. Control sample of non-activated cells was devoid of these phosphorylations. Overall, the presented analytical workflow is able to detect dynamic phosphorylation events in minimally processed mammalian cells while using only a short high-performance liquid chromatography gradient.

Double-walled carbon nanotube processing

Single-walled carbon nanotubes (SWCNTs) have been the focus of intense research, and the body of literature continues to grow exponentially, despite more than two decades having passed since the first reports. As well as extensive studies of the fundamental properties, this has seen SWCNTs used in a plethora of applications as far ranging as microelectronics, energy storage, solar cells, and sensors, to cancer treatment, drug delivery, and neuronal interfaces. On the other hand, the properties and applications of double-walled carbon nanotubes (DWCNTs) have remained relatively under-explored. This is despite DWCNTs not only sharing many of the same unique characteristics of their single-walled counterparts, but also possessing an additional suite of potentially advantageous properties arising due to the presence of the second wall and the often complex inter-wall interactions that arise. For example, it is envisaged that the outer wall can be selectively functionalized whilst still leaving the inner wall in its pristine state and available for signal transduction. A similar situation arises in DWCNT field effect transistors (FETs), where the outer wall can provide a convenient degree of chemical shielding of the inner wall from the external environment, allowing the excellent transconductance properties of the pristine nanotubes to be more fully exploited. Additionally, DWCNTs should also offer unique opportunities to further the fundamental understanding of the inter-wall interactions within and between carbon nanotubes. However, the realization of these goals has so far been limited by the same challenge experienced by the SWCNT field until recent years, namely, the inherent heterogeneity of raw, as-produced DWCNT material. As such, there is now an emerging field of research regarding DWCNT processing that focuses on the preparation of material of defined length, diameter and electronic type, and which is rapidly building upon the experience gained by the broader SWCNT community. This review describes the background of the field, summarizing some relevant theory and the available synthesis and purification routes; then provides a thorough synopsis of the current state-of-the-art in DWCNT sorting methodologies, outlines contemporary challenges in the field, and discusses the outlook for various potential applications of the resulting material.

Magnetite/Ceria-Codecorated Titanoniobate Nanosheet: A 2D Catalytic Nanoprobe for Efficient Enrichment and Programmed Dephosphorylation of Phosphopeptides

Global characterization and in-depth understanding of phosphoproteome based on mass spectrometry (MS) desperately needs a highly efficient affinity probe during sample preparation. In this work, a ternary nanocomposite of magnetite/ceria-codecorated titanoniobate nanosheet (MC-TiNbNS) was synthesized by the electrostatic assembly of Fe3O4 nanospheres and in situ growth of CeO 2 nanoparticles on pre-exfoliated titanoniobate and eventually utilized as the probe and catalyst for the enrichment and dephosphorylation of phosphopeptides. The two-dimensional (2D) structured titanoniobate nanosheet not only promoted the efficacy of capturing phosphopeptides with enlarged surface area, but also functioned as a substrate for embracing the magnetic anchor Fe3O4 to enable magnetic separation and mimic phosphatase CeO2 to produce identifying signatures of phosphopeptides. Compared to single-component TiNbNS or CeO2 nanoparticles, the ternary nanocomposite provided direct evidence of the number of phosphorylation sites while maintaining the enrichment efficiency. Moreover, by altering the on-sheet CeO2 coverage, the dephosphorylation activity could be fine-tuned, generating continuously adjustable signal intensities of both phosphopeptides and their dephosphorylated tags. Exhaustive detection of both mono- and multiphosphorylated peptides with precise counting of their phosphorylation sites was achieved in the primary mass spectra in the cases of digests of standard phosphoprotein and skim milk, as well as a more complex biological sample, human serum. With the resulting highly informative mass spectra, this multifunctional probe can be used as a promising tool for the fast and comprehensive characterization of phosphopeptides in MS-based phosphoproteomics.

Progress of Circulating Tumor Cells in Cancer Management

Circulating tumor cells are low-frequency cells that are shed into the peripheral bloodstream from a primary solid tumor and/or metastasis. Although these cells were recognized initially in 1869, it is only in the past 2 decades that they have been isolated for use as a surrogate biomarker to monitor response to therapy, evaluate prognosis, detect tumor mutations, assist in selecting personalized medicine, and enable earlier cancer diagnosis.

Tracing the trajectory of behavioral impairments and oxidative stress in an animal model of neonatal inflammation

Exposure to early-life inflammation results in time-of-challenge-dependent changes in both brain and behavior. The consequences of this neural and behavioral reprogramming are most often reported in adulthood. However, the trajectory for the expression of these various changes is not well delineated, particularly between the juvenile and adult phases of development. Moreover, interventions to protect against these neurodevelopmental disruptions are rarely evaluated. Here, female Sprague-Dawley rats were housed in either environmental enrichment (EE) or standard care (SC) and their male and female offspring were administered 50 μg/kg i.p. of lipopolysaccharide (LPS) or pyrogen-free saline in a dual-administration neonatal protocol. All animals maintained their respective housing assignments from breeding until the end of the study. LPS exposure on postnatal days (P) 3 and 5 of life resulted in differential expression of emotional and cognitive disruptions and evidence of oxidative stress across development. Specifically, social behavior was reduced in neonatal-treated (n)LPS animals at adolescence (P40), but not adulthood (P70). In contrast, male nLPS rats exhibited intact spatial memory as adolescents which was impaired in later life. Moreover, these males had decreased prefrontal cortex levels of glutathione at P40, which was normalized in adult animals. Notably, EE appeared to offer some protection against the consequences of inflammation on juvenile social behavior and fully prevented reduced glutathione levels in the juvenile prefrontal cortex. Combined, these time-dependent effects provide evidence that early-life inflammation interacts with other developmental variables, specifically puberty and EE, in the expression (and prevention) of select behavioral and molecular programs.

Development of the affinity materials for phosphorylated proteins/peptides enrichment in phosphoproteomics analysis

Reversible protein phosphorylation is a key event in numerous biological processes. Mass spectrometry (MS) is the most powerful analysis tool in modern phosphoproteomics. However, the direct MS analysis of phosphorylated proteins/peptides is still a big challenge because of the low abundance and insufficient ionization of phosphorylated proteins/peptides as well as the suppression effects of nontargets. Enrichment of phosphorylated proteins/peptides by affinity materials from complex biosamples is the most widely used strategy to enhance the MS detection. The demand of efficiently enriching phosphorylated proteins/peptides has spawned diverse affinity materials based on different enrichment principles (e.g., electronic attraction, chelating). In this review, we summarize the recent development of various affinity materials for phosphorylated proteins/peptides enrichment. We will highlight the design and fabrication of these affinity materials, discuss the enrichment mechanisms involved in different affinity materials, and suggest the future challenges and research directions in this field.

Clinical utility estimation for assay cutoffs in early phase oncology enrichment trials

Predictive enrichment strategies use biomarkers to selectively enroll oncology patients into clinical trials to more efficiently demonstrate therapeutic benefit. Because the enriched population differs from the patient population eligible for screening with the biomarker assay, there is potential for bias when estimating clinical utility for the screening eligible population if the selection process is ignored. We write estimators of clinical utility as integrals averaging regression model predictions over the conditional distribution of the biomarker scores defined by the assay cutoff and discuss the conditions under which consistent estimation can be achieved while accounting for some nuances that may arise as the biomarker assay progresses toward a companion diagnostic. We outline and implement a Bayesian approach in estimating these clinical utility measures and use simulations to illustrate performance and the potential biases when estimation naively ignores enrichment. Results suggest that the proposed integral representation of clinical utility in combination with Bayesian methods provide a practical strategy to facilitate cutoff decision-making in this setting.

Ultrasensitive protein concentration detection on a micro/nanofluidic enrichment chip using fluorescence quenching

A micro/nanofluidic enrichment device combined with the Förster resonance energy transfer (FRET) technique has been developed for sensitive detection of trace quantities of protein. In this approach, sample protein is first adsorbed on gold nanoparticles (AuNPs) to occupy part of the AuNP surface. Then, dye-labeled protein is added, which adsorbs to the residual active sites of the AuNP surface, saturating the AuNP surface with protein molecules. The unadsorbed dye-labeled protein remains in a free state in the system. Keeping a fixed amount of dye-labeled protein, a high concentration of sample protein leads to more free dye-labeled protein molecules remaining in the system, and thus a larger photoluminescence signal. Under the action of an electric field, the free dye-labeled protein molecules can be efficiently enriched in front of the nanochannel of a micro/nanofluidic chip, which greatly amplifies the magnitude of the photoluminescence and improves the detection sensitivity. As a demonstration, bovine serum albumin (BSA) and fluorescein isothiocyanate-labeled dog serum albumin (FITC-DSA) are used as sample and fluorescent proteins, respectively. Using the proposed strategy, a detection limit of BSA as low as 2.5 pg/mL can be achieved, which is more than 10(3) times lower than the reported minimums in most sensitive commercial protein quantification methods.

Food sensing: selection and characterization of DNA aptamers to Alicyclobacillus spores for trapping and detection from orange juice

The quality of the beverage industry's products has to be constantly monitored to fulfill consumers' high expectations. The thermo-acidophilic Gram-positive Alicyclobacillus spp. are not pathogenic, but their heat-resistant endospores can survive juice-processing conditions and have become a major economic concern for the fruit juice industry. Current detection methods rely on cultivation, isolation, and organism identification, which can take up to a week, resulting in economic loss. This work presents the selection and identification of DNA aptamers targeting Alicyclobacillus spores by spore-SELEX (systematic evolution of ligands by exponential enrichment) in orange-juice-simulating buffer. The selection process was verified by various techniques, including flow cytometric binding assays, radioactive binding assays, and agarose gel electrophoresis. The subsequent aptamer characterization included the determination of dissociations constants and selectivity by different techniques, such as surface plasmon resonance spectroscopy and fluorescence microscopy. In summary, 10 different aptamers with an affinity to Alicyclobacillus spp. have been developed, analyzed, and characterized in terms of affinity and specificity.

Judgments of Monkey's (Macaca mulatta) Facial Expressions by Humans: Does Housing Condition "Affect" Countenance?

The ability to interpret facial expressions of others is one of the more important abilities possessed by humans. However, is it possible for humans to accurately interpret the facial expressions of another species of primate, namely rhesus monkeys (Macaca mulatta)? We investigated this possibility by taking digital photos of four rhesus monkeys housed either singly or socially and allowing thirty-one participants to judge these photographs as representing either a happy, sad, or neutral monkey. Results indicated that the photographs of monkeys that were socially housed were more likely to be rated as happy or neutral than were photographs of singly housed monkeys. We suggest that these results imply important parallels between the perception of human and nonhuman primate facial expressions as well as introduce a potential new method for assessing nonhuman primate well-being.

The effect of moisture on the release and enrichment of heavy metals during pyrolysis of municipal solid waste

The investigation of the effect of moisture on the release and enrichment of heavy metals during pyrolysis of municipal solid waste is essential. This is important owing to: (i) the increasing amount of metals in the solid product of pyrolysis beyond the normalised level; (ii) the effect of moisture on the overall cost of pyrolysis process; and (iii) the utilisation of pyrolysis products. Seven metals were selected for evaluation: arsenic, cadmium, chromium, mercury, nickel, lead, and vanadium. Pyrolysis experiments were conducted in a steel retort at 650 °C. The municipal solid waste samples with moisture contents of 0, 30, and 65 wt% were investigated. The relative enrichment index and release of heavy metals were evaluated individually for liquid and solid fractions. A consistent trend was observed for the majority of metals investigated. Reductions of relative enrichment index and release, i.e. an increase of volatility, were observed for arsenic, chromium, cadmium, nickel, and vanadium, with an increase of municipal solid waste moisture. Whereas divergent results were obtained for lead and mercury. The effect of moisture on the relative enrichment index and release was greater at 65 wt% moisture than at 30 wt% for lead, and more remarkable at 30 wt% than at 65 wt% for mercury.

The effects of environmental enrichment and beak-trimming during the rearing period on subsequent feather damage due to feather-pecking in laying hens

This experiment investigated effects of environmental enrichment and beak-trimming during the rearing period on behavior in rearing and plumage damage later in life. Treatments were applied in a 2 × 2 factorial arrangement. Half of the birds were beak-trimmed at 1 d of age using an infra-red laser. A follow-up light-trim was performed at 11 wk of age with a hot blade. Environmental enrichment consisted of pecking strings, whole oats in the litter, and greater litter depth. Sixteen pens of 50 ISA Brown laying hens were used. Four pullets were selected from each pen as focal birds and observed in their home pens between 3 and 14 wk of age. Plumage damage was scored at the end of the experiment in wk 43. Beak-trimmed birds performed less ground-pecking (P = 0.003), less severe feather-pecking (P = 0.021) and more gentle feather-pecking (P = 0.018) than their non-trimmed counterparts during the rearing period. These birds also exhibited less feather damage in wk 43 (P < 0.001). The results indicate that gentle feather-pecking during rearing is not related to plumage damage when older. Additionally, higher rates of ground-pecking and severe feather-pecking during rearing may be predictive of plumage damage later in life. There was no effect of enrichment on plumage damage. It was concluded that while there was no effect on enrichment, beak-trimming appeared to be effective in reducing plumage damage in wk 43.

Phylogenomics and the dynamic genome evolution of the genus Streptococcus

The genus Streptococcus comprises important pathogens that have a severe impact on human health and are responsible for substantial economic losses to agriculture. Here, we utilize 46 Streptococcus genome sequences (44 species), including eight species sequenced here, to provide the first genomic level insight into the evolutionary history and genetic basis underlying the functional diversity of all major groups of this genus. Gene gain/loss analysis revealed a dynamic pattern of genome evolution characterized by an initial period of gene gain followed by a period of loss, as the major groups within the genus diversified. This was followed by a period of genome expansion associated with the origins of the present extant species. The pattern is concordant with an emerging view that genomes evolve through a dynamic process of expansion and streamlining. A large proportion of the pan-genome has experienced lateral gene transfer (LGT) with causative factors, such as relatedness and shared environment, operating over different evolutionary scales. Multiple gene ontology terms were significantly enriched for each group, and mapping terms onto the phylogeny showed that those corresponding to genes born on branches leading to the major groups represented approximately one-fifth of those enriched. Furthermore, despite the extensive LGT, several biochemical characteristics have been retained since group formation, suggesting genomic cohesiveness through time, and that these characteristics may be fundamental to each group. For example, proteolysis: mitis group; urea metabolism: salivarius group; carbohydrate metabolism: pyogenic group; and transcription regulation: bovis group.

Chemoautotrophic growth of ammonia-oxidizing Thaumarchaeota enriched from a pelagic redox gradient in the Baltic Sea

Ammonia-oxidizing archaea (AOA) are an important component of the planktonic community in aquatic habitats, linking nitrogen and carbon cycles through nitrification and carbon fixation. Therefore, measurements of these processes in culture-based experiments can provide insights into their contributions to energy conservation and biomass production by specific AOA. In this study, by enriching AOA from a brackish, oxygen-depleted water-column in the Landsort Deep, central Baltic Sea, we were able to investigate ammonium oxidation, chemoautotrophy, and growth in seawater batch experiments. The highly enriched culture consisted of up to 97% archaea, with maximal archaeal numbers of 2.9 × 10⁷ cells mL⁻¹. Phylogenetic analysis of the 16S rRNA and ammonia monooxygenase subunit A (amoA) gene sequences revealed an affiliation with assemblages from low-salinity and freshwater habitats, with Candidatus Nitrosoarchaeum limnia as the closest relative. Growth correlated significantly with nitrite production, ammonium consumption, and CO₂ fixation, which occurred at a ratio of 10 atoms N oxidized per 1 atom C fixed. According to the carbon balance, AOA biomass production can be entirely explained by chemoautotrophy. The cellular carbon content was estimated to be 9 fg C per cell. Single-cell-based ¹³C and ¹⁵N labeling experiments and analysis by nano-scale secondary ion mass spectrometry provided further evidence that cellular carbon was derived from bicarbonate and that ammonium was taken up by the cells. Our study therefore revealed that growth by an AOA belonging to the genus Nitrosoarchaeum can be sustained largely by chemoautotrophy.

Phosphoproteomics technologies and applications in plant biology research

Protein phosphorylation has long been recognized as an essential mechanism to regulate many important processes of plant life. However, studies on phosphorylation mediated signaling events in plants are challenged with low stoichiometry and dynamic nature of phosphorylated proteins. Significant advances in mass spectrometry based phosphoproteomics have taken place in recent decade, including phosphoprotein/phosphopeptide enrichment, detection and quantification, and phosphorylation site localization. This review describes a variety of separation and enrichment methods for phosphoproteins and phosphopeptides, the applications of technological innovations in plant phosphoproteomics, and highlights significant achievement of phosphoproteomics in the areas of plant signal transduction, growth and development.

Recent Statistical Contributions to Medical Device Development

Clinical trials in the development of new medical device products are in many ways analogous to clinical trials in the development of new drug or biologic products. However, the differences are important and not always intuitive to a statistician with only experience supporting development of drug and biologic products. In this paper we discuss some of the interesting differences with focus on the statistical innovation that is coming out of the medical device area. We discuss examples of the differences in clinical trial design and effects of these differences on clinical development programs.

The effect of long or chopped straw on pig behaviour

In the EU, pigs must have permanent access to manipulable materials such as straw, rope, wood, etc. Long straw can fulfil this function, but can increase labour requirements for cleaning pens, and result in problems with blocked slatted floors and slurry systems. Chopped straw might be more practical, but what is the effect on pigs' behaviour of using chopped straw instead of long straw? Commercial pigs in 1/3 slatted, 2/3 solid pens of 15 pigs were provided with either 100 g/pig per day of long straw (20 pens) or of chopped straw (19 pens). Behavioural observations were made of three focal pigs per pen (one from each of small, medium and large weight tertiles) for one full day between 0600 and 2300 h at each of ~40 and ~80 kg. The time spent rooting/investigating overall (709 s/pig per hour at 40 kg to 533 s/pig per hour at 80 kg), or directed to the straw/solid floor (497 s/pig per hour at 40 kg to 343 s/pig per hour at 80 kg), was not affected by straw length but reduced with age. Time spent investigating other pigs (83 s/pig per hour at 40 kg), the slatted floor (57 s/pig per hour) or pen fixtures (21 s/pig per hour) was not affected by age or straw length. Aggressive behaviour was infrequent, but lasted about twice as long in pens with chopped straw (2.3 s/pig per hour at 40 kg) compared with pens with long straw (1.0 s/pig per hour at 40 kg, P=0.060). There were no significant effects of straw length on tail or ear lesions, but shoulders were significantly more likely to have minor scratches with chopped straw (P=0.031), which may reflect the higher levels of aggression. Smaller pigs showed more rooting/investigatory behaviour, and in particular directed towards the straw/solid floor and the slatted floor than their larger pen-mates. Females exhibited more straw and pen fixture-directed behaviour than males. There were no effects of pig size or sex on behaviour directed towards other pigs. In summary, pigs spent similar amounts of time interacting with straw/solid floor when long and chopped straw were provided, and most aspects of pig-directed behaviour and injuries were not affected by straw length. There was an increase in pigs with minor shoulder lesions with chopped straw, perhaps because of increased aggression. The use of chopped straw as an enrichment material for pigs warrants further investigation in larger and more detailed studies.

Effect of Bungee-carcass enrichment on behavior and fecal glucocorticoid metabolites in two species of zoo-housed Felids

Enrichment can improve animal physiological and psychological well-being. This study sought to promote more natural felid behavior and prevent development or incidence of stereotypies through the use of a feeding enrichment. Our objectives are to use fecal glucocorticoid metabolites values and behavioral observations to quantify the effectiveness of the enrichment device for two species of large cats, Bengal tiger (Panthera tigris tigris; n = 2) and cougar (Felis concolor; n = 2). The feeding enrichment, a white-tailed deer carcass flank securely attached to an AussieDog Products(©) Felid 120-cm bungee, was implemented twice for each individual separated by 1 month. Fecal samples were obtained from each felid and analyzed for pre- and post-enrichment fecal glucocorticoid metabolites (FGM) concentrations using a cortisol enzyme immunoassay. An ethogram with 12 mutual exclusive behavioral categories was utilized to record behavioral responses to the enrichment. Results demonstrate that: 1) there were no differences (P > 0.05) in FGMs for either species between pre- and post-enrichment; 2) pacing decreased (P = 0.025) and walking increased (P = 0.017) after exposure to enrichment in both cougars; and 3) tigers reduced (P = 0.025) 'other' behavioral category after the first enrichment exposure and laid down more (P = 0.025) after the second enrichment exposure. The neutral hormonal impact on the animals coupled with the behavioral changes indicates that this enrichment is successful at altering the animals' behavior without adding physiological stress to their environments. These findings, combined with the low cost and versatility of the enrichment, promote the use of this enrichment to enhance large felid enclosures.

Development of multiplex PCR assay for simultaneous detection of Salmonella genus, Salmonella subspecies I, Salm. Enteritidis, Salm. Heidelberg and Salm. Typhimurium

AIMS

The aim of this research was to develop multiplex PCR assay that could simultaneously detect Salmonella genus, Salmonella subsp. I, Salm. Enteritidis, Heidelberg and Typhimurium because these Salmonella serovars are the most common isolates associated with poultry products.

METHODS AND RESULTS

Five primers were utilized to establish multiplex PCR and applied to Salmonella isolates from chickens and farm environments. These isolates were identified as Salmonella subsp. I and 16 of 66 isolates were classified as Salm. Enteritidis, while Heidelberg or Typhimurium was not detected. We also spiked three Salmonella strains on chicken breast meat to evaluate the specificity and sensitivity of multiplex PCR as well as qPCR to optimize quantification of Salmonella in these samples. The optimized multiplex PCR and qPCR could detect approx. 2·2 CFU of Salmonella per gram after 18 h enrichment.

CONCLUSIONS

The multiplex PCR and qPCR would provide rapid and consistent results. Also, these techniques would be useful for the detection and quantification of Salmonella in contaminated poultry, foods and environmental samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

The strategy for the rapid detection of Salmonella serovars in poultry is needed to further reduce the incidence of salmonellosis in humans. The optimized multiplex PCR will be useful to detect prevalent Salmonella serovars in poultry products.

Neuroinformatic analyses of common and distinct genetic components associated with major neuropsychiatric disorders

Major neuropsychiatric disorders are highly heritable, with mounting evidence suggesting that these disorders share overlapping sets of molecular and cellular underpinnings. In the current article we systematically test the degree of genetic commonality across six major neuropsychiatric disorders-attention deficit hyperactivity disorder (ADHD), anxiety disorders (Anx), autistic spectrum disorders (ASD), bipolar disorder (BD), major depressive disorder (MDD), and schizophrenia (SCZ). We curated a well-vetted list of genes based on large-scale human genetic studies based on the NHGRI catalog of published genome-wide association studies (GWAS). A total of 180 genes were accepted into the analysis on the basis of low but liberal GWAS p-values (<10(-5)). 22% of genes overlapped two or more disorders. The most widely shared subset of genes-common to five of six disorders-included ANK3, AS3MT, CACNA1C, CACNB2, CNNM2, CSMD1, DPCR1, ITIH3, NT5C2, PPP1R11, SYNE1, TCF4, TENM4, TRIM26, and ZNRD1. Using a suite of neuroinformatic resources, we showed that many of the shared genes are implicated in the postsynaptic density (PSD), expressed in immune tissues and co-expressed in developing human brain. Using a translational cross-species approach, we detected two distinct genetic components that were both shared by each of the six disorders; the 1st component is involved in CNS development, neural projections and synaptic transmission, while the 2nd is implicated in various cytoplasmic organelles and cellular processes. Combined, these genetic components account for 20-30% of the genetic load. The remaining risk is conferred by distinct, disorder-specific variants. Our systematic comparative analysis of shared and unique genetic factors highlights key gene sets and molecular processes that may ultimately translate into improved diagnosis and treatment of these debilitating disorders.

Addiction and reward-related genes show altered expression in the postpartum nucleus accumbens

Motherhood involves a switch in natural rewards, whereby offspring become highly rewarding. Nucleus accumbens (NAC) is a key CNS region for natural rewards and addictions, but to date no study has evaluated on a large scale the events in NAC that underlie the maternal change in natural rewards. In this study we utilized microarray and bioinformatics approaches to evaluate postpartum NAC gene expression changes in mice. Modular Single-set Enrichment Test (MSET) indicated that postpartum (relative to virgin) NAC gene expression profile was significantly enriched for genes related to addiction and reward in five of five independently curated databases (e.g., Malacards, Phenopedia). Over 100 addiction/reward related genes were identified and these included: Per1, Per2, Arc, Homer2, Creb1, Grm3, Fosb, Gabrb3, Adra2a, Ntrk2, Cry1, Penk, Cartpt, Adcy1, Npy1r, Htr1a, Drd1a, Gria1, and Pdyn. ToppCluster analysis found maternal NAC expression profile to be significantly enriched for genes related to the drug action of nicotine, ketamine, and dronabinol. Pathway analysis indicated postpartum NAC as enriched for RNA processing, CNS development/differentiation, and transcriptional regulation. Weighted Gene Coexpression Network Analysis (WGCNA) identified possible networks for transcription factors, including Nr1d1, Per2, Fosb, Egr1, and Nr4a1. The postpartum state involves increased risk for mental health disorders and MSET analysis indicated postpartum NAC to be enriched for genes related to depression, bipolar disorder (BPD), and schizophrenia. Mental health related genes included: Fabp7, Grm3, Penk, and Nr1d1. We confirmed via quantitative PCR Nr1d1, Per2, Grm3, Penk, Drd1a, and Pdyn. This study indicates for the first time that postpartum NAC involves large scale gene expression alterations linked to addiction and reward. Because the postpartum state also involves decreased response to drugs, the findings could provide insights into how to mitigate addictions.

Genome and metagenome sequencing: Using the human methyl-binding domain to partition genomic DNA derived from plant tissues

PREMISE OF THE STUDY

Variation in the distribution of methylated CpG (methyl-CpG) in genomic DNA (gDNA) across the tree of life is biologically interesting and useful in genomic studies. We illustrate the use of human methyl-CpG-binding domain (MBD2) to fractionate angiosperm DNA into eukaryotic nuclear (methyl-CpG-rich) vs. organellar and prokaryotic (methyl-CpG-poor) elements for genomic and metagenomic sequencing projects. •

METHODS

MBD2 has been used to enrich prokaryotic DNA in animal systems. Using gDNA from five model angiosperm species, we apply a similar approach to identify whether MBD2 can fractionate plant gDNA into methyl-CpG-depleted vs. enriched methyl-CpG elements. For each sample, three gDNA libraries were sequenced: (1) untreated gDNA, (2) a methyl-CpG-depleted fraction, and (3) a methyl-CpG-enriched fraction. •

RESULTS

Relative to untreated gDNA, the methyl-depleted libraries showed a 3.2-11.2-fold and 3.4-11.3-fold increase in chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA), respectively. Methyl-enriched fractions showed a 1.8-31.3-fold and 1.3-29.0-fold decrease in cpDNA and mtDNA, respectively. •

DISCUSSION

The application of MBD2 enabled fractionation of plant gDNA. The effectiveness was particularly striking for monocot gDNA (Poaceae). When sufficiently effective on a sample, this approach can increase the cost efficiency of sequencing plant genomes as well as prokaryotes living in or on plant tissues.

The functional response predicts the effect of resource distribution on the optimal movement rate of consumers

Understanding how often individuals should move when foraging over patchy habitats is a central question in ecology. By combining optimality and functional response theories, we show analytically how the optimal movement rate varies with the average resource level (enrichment) and resource distribution (patch heterogeneity). We find that the type of functional response predicts the effect of enrichment in homogeneous habitats: enrichment should decrease movement for decelerating functional responses, but increase movement for accelerating responses. An intermediate resource level thus maximises movement for type-III responses. Counterintuitively, greater movement costs favour an increase in movement. In heterogeneous habitats predictions further depend on how enrichment alters the variance of resource distribution. Greater patch variance always increases the optimal rate of movement, except for type-IV functional responses. While the functional response is well established as a fundamental determinant of consumer-resource dynamics, our results indicate its importance extends to the understanding of individual movement strategies.

Damaging biting behaviors in intensively kept rearing gilts: the effect of jute sacks and relations with production characteristics

Pigs may display biting behavior directed at pen mates, resulting in body damage such as tail wounds. We assessed the suitability of jute sacks (hung vertically at wall) to reduce biting behaviors and tail wounds in rearing gilts. Additionally, we assessed several characteristics of different types of tail biters. Tail docked rearing gilts originated from 72 litters, which were kept in partly slatted pens with jute sacks (J) or barren control pens (CON; 36 litters per treatment). Tail and ear damage were observed at weaning (4 wk) and during the weaner and rearing phase (17 J and 19 CON pens). Sow (dam) damage was also considered. Biting behaviors (tail, ear, and other) were observed during the weaner and rearing phase. Weight was recorded at birth, weaning, and end of the weaner phase and ADG was calculated from birth till weaning and from weaning till 9 wk. Furthermore, estimated breeding values for litter size, litter birth weight, back fat, and growth between birth and ∼ 105 kg, and ∼ 25 to 105 kg were determined. Jute sacks reduced tail and ear damage at weaning (both P < 0.001) and tended to reduce sow tail damage (P = 0.09). Jute sacks also reduced tail damage post-weaning (P < 0.001 to 0.03), with a 5-fold reduction of (mild) tail wounds at the age of 13 wk. Biting behaviors directed at pen mates were up to 50% lower in J pens (P < 0.001 to 0.04). Higher genotypic litter size, litter birth weight, growth, and lower back fat seemed associated with higher levels of ear or tail-biting behavior (P = 0.002 to 0.09), albeit dependent on treatment and phase. Higher phenotypic litter sizes were associated with higher levels of biting behaviors (P = 0.004-0.08). High-tail-biters and Medium-tail-biters (the latter less pronounced) stemmed from larger litters (P = 0.01 to 0.05), were heavier (P = 0.03 to 0.04), grew faster (P = 0.05 to 0.08), and displayed higher levels of all kinds of biting behavior directed to pen mates and the jute sack (P < 0.001 to 0.10) compared with non-tail-biters, the effect size dependent on treatment and phase of life. To conclude, jute sacks may profoundly reduce damaging behaviors and tail wounds in rearing gilts, probably because they partly meet the behavioral need of pigs for rooting and chewing. Furthermore, (tail) biting is associated with production level of the gilts (phenotypically and genetically), which suggests a role for breeding programs and additional research focusing on metabolic demands of (tail) biting pigs.

Label-free microfluidic enrichment of ring-stage Plasmodium falciparum-infected red blood cells using non-inertial hydrodynamic lift

BACKGROUND

Understanding of malaria pathogenesis caused by Plasmodium falciparum has been greatly deepened since the introduction of in vitro culture system, but the lack of a method to enrich ring-stage parasites remains a technical challenge. Here, a novel way to enrich red blood cells containing parasites in the early ring stage is described and demonstrated.

METHODS

A simple, straight polydimethylsiloxane microchannel connected to two syringe pumps for sample injection and two height reservoirs for sample collection is used to enrich red blood cells containing parasites in the early ring stage (8-10 h p.i.). The separation is based on the non-inertial hydrodynamic lift effect, a repulsive cell-wall interaction that enables continuous and label-free separation with deformability as intrinsic marker.

RESULTS

The possibility to enrich red blood cells containing P. falciparum parasites at ring stage with a throughput of ~12,000 cells per hour and an average enrichment factor of 4.3 ± 0.5 is demonstrated.

CONCLUSION

The method allows for the enrichment of red blood cells early after the invasion by P. falciparum parasites continuously and without any need to label the cells. The approach promises new possibilities to increase the sensitivity of downstream analyses like genomic- or diagnostic tests. The device can be produced as a cheap, disposable chip with mass production technologies and works without expensive peripheral equipment. This makes the approach interesting for the development of new devices for field use in resource poor settings and environments, e.g. with the aim to increase the sensitivity of microscope malaria diagnosis.

The effect of shelter on welfare of juvenile Atlantic salmon Salmo salar reared under a feed restriction regimen

This study investigated whether shelter (presence or absence) affected the frequency of fin damage in Atlantic salmon Salmo salar exposed to feed restrictions (0·73 or 0·33% of body mass day(-1) ). The presence of shelter had a positive effect on the pectoral fins at both feed ration levels and on the dorsal fin at the higher ration level but it had a negative effect on survival. The reduced feed rations resulted in fish of the same size and nutritional status as wild fish. The provision of shelter has potential to mitigate the negative effects of feed restrictions on fin quality, but the optimal shelter design requires some additional investigation.

Evaluation of different enrichment methods for pathogenic Yersinia species detection by real time PCR

BACKGROUND

Yersiniosis is a zoonotic disease reported worldwide. Culture and PCR based protocols are the most common used methods for detection of pathogenic Yersinia species in animal samples. PCR sensitivity could be increased by an initial enrichment step. This step is particularly useful in surveillance programs, where PCR is applied to samples from asymptomatic animals. The aim of this study was to evaluate the improvement in pathogenic Yersinia species detection using a suitable enrichment method prior to the real time PCR (rtPCR). Nine different enrichment protocols were evaluated including six different broth mediums (CASO, ITC, PSB, PBS, PBSMSB and PBSSSB).

RESULTS

The analysis of variance showed significant differences in Yersinia detection by rtPCR according to the enrichment protocol used. These differences were higher for Y. pseudotuberculosis than for Y. enterocolitica. In general, samples incubated at lower temperatures yielded the highest detection rates. The best results were obtained with PBSMSB and PBS2. Application of PBSMSB protocol to free-ranging wild board samples improved the detection of Y. enterocolitica by 21.2% when compared with direct rtPCR. Y. pseudotuberculosis detection was improved by 10.6% when results obtained by direct rtPCR and by PBSMSB enrichment before rtPCR were analyzed in combination.

CONCLUSIONS

The data obtained in the present study indicate a difference in Yersinia detection by rtPCR related to the enrichment protocol used, being PBSMSB enrichment during 15 days at 4°C and PBS during 7 days at 4°C the most efficient. The use of direct rtPCR in combination with PBSMSB enrichment prior to rtPCR resulted in an improvement in the detection rates of pathogenic Yersinia in wild boar and could be useful for application in other animal samples.

BDNF contributes to the facilitation of hippocampal synaptic plasticity and learning enabled by environmental enrichment

Sensory, motor, and cognitive stimuli, resulting from interactions with the environment, play a key role in optimizing and modifying the neuronal circuitry required for normal brain function. An experimental animal model for this phenomenon comprises environmental enrichment (EE) in rodents. EE causes profound changes in neuronal and signaling levels of excitation and plasticity throughout the entire central nervous system and the hippocampus is particularly affected. The mechanisms underlying these changes are not yet fully understood. As brain-derived neurotrophic factor (BDNF) supports hippocampal long-term potentiation (LTP), we explored whether it participates in the facilitation of synaptic plasticity and hippocampus-dependent learning that occurs following EE. In the absence of EE, LTP elicited by high-frequency stimulation was equivalent in wildtype mice and heterozygous BDNF(+/-) siblings. LTP elicited by theta-burst stimulation in BDNF(+/-) mice was less than in wildtypes. Long-term depression (LTD) was also impaired. EE for three weeks, beginning after weaning, improved hippocampal LTP in both wildtype and transgenic animals, with LTP in transgenics achieving levels seen in wildtypes in the absence of EE. Object recognition memory was evident in wildtypes 24 h and 7 days after initial object exposure. EE improved memory performance in wildtypes 24 h but not 7 days after initial exposure. BDNF(+/-) mice in the absence of EE showed impaired memory 7 days after initial object exposure that was restored by EE. Western blotting revealed increased levels of BDNF, but not proBDNF, among both EE cohorts. These data support that BDNF plays an intrinsic role in improvements of synaptic plasticity and cognition that occur in EE.

Enrichment options for African painted dogs (Lycaon pictus)

Best practices for carnivore enrichment encourage the diversity of species-typical behaviors, increased activity, and reduced stereotypic behavior; ideally considering the life-history and behavior of each species. African wild dogs (Lycaon pictus), or painted dogs, are social carnivores that have large home ranges and complex pack dynamics (e.g., variation in group size, relatedness, etc.). As there are relatively few studies on painted dog enrichment, the goal of this study was to compile a list of enrichment options used by institutions participating in the species survival plan (SSP). Representatives were asked to describe social groups (n = 45), enclosures (n = 21), enrichment practices (options, delivery frequency, perceived success), and overall best practices. Respondents (61%, n = 23) reported using options for all six enrichment categories recommended by the Canid Taxon Advisory Group: environmental enrichment devices, habitat, sensory, food, behavioral, and social. Perceived success was significantly higher for the food category, followed by the sensory and behavioral categories. All respondents reported delivering enrichment at least multiple times a month, and most reported multiple times per week. Enclosure size did not differ significantly for mixed-sex groups (n = 28) compared to single-sex groups (n = 17). We discuss respondents' suggestions for best practices and the need to record data to compare perceived success with actual behavioral effects, controlling for variation in group size and composition. Overall, respondents recommended a flexible approach, since not all painted dogs and groups respond in the same way to the enrichment options.

Facile synthesis of magnetic mesoporous hollow carbon microspheres for rapid capture of low-concentration peptides

Mesoporous and hollow carbon microspheres embedded with magnetic nanoparticles (denoted as MHM) were prepared via a facile self-sacrificial method for rapid capture of low-abundant peptides from complex biological samples. The morphology, structure, surface property, and magnetism were well-characterized. The hollow magnetic carbon microspheres have a saturation magnetization value of 130.2 emu g(-1) at room temperature and a Brunauer-Emmett-Teller specific surface area of 48.8 m(2) g(-1) with an average pore size of 9.2 nm for the mesoporous carbon shell. The effectiveness of these MHM affinity microspheres for capture of low-concentration peptides was evaluated by standard peptides, complex protein digests, and real biological samples. These multifunctional hollow carbon microspheres can realize rapid capture and convenient separation of low-concentration peptides. They were validated to have better performance than magnetic mesoporous silica and commercial peptide-enrichment products. In addition, they can be easily recycled and present excellent reusability. Therefore, it is expected that this work may provide a promising tool for high-throughput discovery of peptide biomarkers from biological samples for disease diagnosis and other biomedical applications.

Enrichment of spermatogonial stem cells from long-term cultured human testicular cells

OBJECTIVE

To evaluate the degree of enrichment of spermatogonial stem cells (SSCs) from human testicular cell cultures by ITGA6+, HLA-/ITGA6+, GPR125+, and HLA-/GPR125+ magnetic-assisted cell sorting (MACS).

DESIGN

Experimental basic science study.

SETTING

Reproductive biology laboratory.

PATIENT(S)

Multiple samples of cryopreserved human testicular cells from two prostate cancer patients with normal spermatogenesis.

INTERVENTION(S)

Cultured human testicular cells subjected to four sorting strategies based on MACS and xenotransplanted to the testes of mice to determine the enrichment for SSCs.

MAIN OUTCOME MEASURE(S)

Enrichment for human spermatogonia and SSCs tested by expression analysis of spermatogonial markers ITGA6, GPR125, ZBTB16, UCHL1, and ID4 using quantitative real-time polymerase chain reaction (qPCR) and by xenotransplantation into the testes of mice, respectively.

RESULT(S)

Compared with the nonsorted cultured testicular cells, only the ITGA6+ and HLA-/GPR125+ sorted cells showed enrichment for ID4. No difference in expression of ZBTB16 and UCHL1 was observed. Xenotransplantation of the sorted cell fractions showed a 7.1-fold enrichment of SSCs with ITGA6+.

CONCLUSION(S)

Magnetic-assisted cell sorting of cultured human testicular cells using ITGA6 allows for enrichment of SSCs, which aids in further molecular characterization of cultured human SSCs and enhances testicular colonization upon transplantation in future clinical settings.

Effect of maternal care on hearing onset induced by developmental changes in the auditory periphery

Handling (H) and cross-fostering (CF) rodent pups during postnatal development triggers changes in maternal behavior which in turn trigger long-term physiological changes in the offspring. However, less is known about the short-term effects of H and CF on infant development. In this study we hypothesized that manipulations of maternal care affect the onset of hearing in Wistar rats. To test this hypothesis we obtained auditory brainstem responses (ABRs) and micro-CT x-ray scans to measure changes in the development of the auditory periphery in H and CF pups manipulated at postnatal day (P)1, P5, or P9. We found evidence of changes in hearing development in H and CF pups compared with naive pups, including changes in the percentage of animals with ABRs during development, a decrease in ABR thresholds between P13 and P15, and anatomical results consistent with an accelerated formation of the middle ear cavity and opening of the ear canal. Biochemical measurements showed elevated levels of thyroid hormone in plasma from naive and CF pups. These results provide evidence that manipulations of maternal care accelerate hearing onset in Wistar rats. Understanding the mechanisms by which maternal care affects hearing onset opens new opportunities to study experience-dependent development of mammalian hearing.

Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat

Sandy coastal sediments are global hotspots for microbial mineralization of organic matter and denitrification. These sediments are characterized by advective porewater flow, tidal cycling and an active and complex microbial community. Metagenomic sequencing of microbial communities sampled from such sediments showed that potential sulfur oxidizing Gammaproteobacteria and members of the enigmatic BD1-5/SN-2 candidate phylum were abundant in situ (>10% and ~2% respectively). By mimicking the dynamic oxic/anoxic environmental conditions of the sediment in a laboratory chemostat, a simplified microbial community was selected from the more complex inoculum. Metagenomics, proteomics and fluorescence in situ hybridization showed that this simplified community contained both a potential sulfur oxidizing Gammaproteobacteria (at 24 ± 2% abundance) and a member of the BD1-5/SN-2 candidate phylum (at 7 ± 6% abundance). Despite the abundant supply of organic substrates to the chemostat, proteomic analysis suggested that the selected gammaproteobacterium grew partially autotrophically and performed hydrogen/formate oxidation. The enrichment of a member of the BD1-5/SN-2 candidate phylum enabled, for the first time, direct microscopic observation by fluorescent in situ hybridization and the experimental validation of the previously predicted translation of the stop codon UGA into glycine.

Genus-specific PCR assay for screening Arcobacter spp. in chicken meat

BACKGROUND

The number of emerging pathogenic species described within the genus Arcobacter has increased rapidly during the last few years. In this work a genus-specific polymerase chain reaction (PCR) assay was developed for detection of the species of Arcobacter most commonly associated with foods. The assay uses primers designed to amplify an 85 bp DNA fragment on the 16S rRNA gene and was applied to the detection of Arcobacter spp. in retail chicken meat.

RESULTS

Primer specificity was tested against a panel of Arcobacter spp., related Campylobacter and Helicobacter spp. and other food bacteria. Arcobacter primers consistently and selectively amplified the expected DNA fragment in all tested Arcobacter spp. Bacterial control primers confirmed the presence of amplifiable DNA in the samples. The applicability of the PCR assay to food was validated through screening of fresh retail chicken samples for the presence of Arcobacter spp., with a result of 45% (23 out of 51) positive samples.

CONCLUSION

The genus-specific PCR assay developed has the potential to be used as a quick and sensitive alternative method for the survey of Arcobacter contamination in meats.

The effects of prenatal cocaine, post-weaning housing and sex on conditioned place preference in adolescent rats

RATIONALE

Gestational exposure to cocaine now affects several million people including adolescents and young adults. Whether prenatal drug exposures alter an individual's tendency to take and/or abuse drugs is still a matter of debate.

OBJECTIVES

This study sought to answer the question "Does prenatal exposure to cocaine, in a dose-response fashion, alter the rewarding effects of cocaine using a conditioned place preference (CPP) procedure during adolescence in the rat?" Further, we wanted to assess the possible sex differences and the role of being raised in an enriched versus impoverished environment.

METHODS

Virgin female Sprague-Dawley rats were dosed daily with cocaine at 30 mg/kg (C30), 60 mg/kg (C60), or vehicle intragastrically prior to mating and throughout gestation. Pups were culled, fostered and, on postnatal day (PND) 23, placed into isolation cages or enriched cages with three same-sex littermates and stimulus objects. On PND43-47, CPP was determined across a range of cocaine doses.

RESULTS

C30 exposure increased sensitivity to the rewarding effects of cocaine in adolescent males, and being raised in an enriched environment further enhanced this effect. Rats exposed to C60 resembled the controls in cocaine CPP. Overall, females were modestly affected by prenatal cocaine and enrichment.

CONCLUSIONS

These data support the unique sensitivity of males to the effects of gestational cocaine, that moderate prenatal cocaine doses produce greater effects on developing reward circuits than high doses and that housing condition interacts with prenatal treatment and sex such that enrichment increases cocaine CPP mostly in adolescent males prenatally exposed to moderate cocaine doses.

Biosensors for the detection of circulating tumour cells

Metastasis is the cause of most cancer deaths. Circulating tumour cells (CTCs) are cells released from the primary tumour into the bloodstream that are considered the main promoters of metastasis. Therefore, these cells are targets for understanding tumour biology and improving clinical management of the disease. Several techniques have emerged in recent years to isolate, detect, and characterise CTCs. As CTCs are a rare event, their study requires multidisciplinary considerations of both biological and physical properties. In addition, as isolation of viable cells may give further insights into metastatic development, cell recovery must be done with minimal cell damage. The ideal system for CTCs analysis must include maximum efficiency of detection in real time. In this sense, new approaches used to enrich CTCs from clinical samples have provided an important improvement in cell recovery. However, this progress should be accompanied by more efficient strategies of cell quantification. A range of biosensor platforms are being introduced into the technology for CTCs quantification with promising results. This review provides an update on recent progress in CTCs identification using different approaches based on sensor signaling.

Testing for efficacy in adaptive clinical trials with enrichment

Adaptive design of clinical trials has attracted considerable interest because of its potential of reducing costs and saving time in the clinical development process. In this paper, we consider the problem of assessing the effectiveness of a test treatment over a control by a two-arm randomized clinical trial in a potentially heterogenous patient population. In particular, we study enrichment designs that use accumulating data from a clinical trial to adaptively determine patient subpopulation in which the treatment effect is eventually assessed. A hypothesis testing procedure and a lower confidence limit are presented for the treatment effect in the selected patient subgroups. The performances of the new methods are compared with existing approaches through a simulation study.

Protein-protein interaction and pathway analyses of top schizophrenia genes reveal schizophrenia susceptibility genes converge on common molecular networks and enrichment of nucleosome (chromatin) assembly genes in schizophrenia susceptibility loci

Recent genome-wide association studies have identified many promising schizophrenia candidate genes and demonstrated that common polygenic variation contributes to schizophrenia risk. However, whether these genes represent perturbations to a common but limited set of underlying molecular processes (pathways) that modulate risk to schizophrenia remains elusive, and it is not known whether these genes converge on common biological pathways (networks) or represent different pathways. In addition, the theoretical and genetic mechanisms underlying the strong genetic heterogeneity of schizophrenia remain largely unknown. Using 4 well-defined data sets that contain top schizophrenia susceptibility genes and applying protein-protein interaction (PPI) network analysis, we investigated the interactions among proteins encoded by top schizophrenia susceptibility genes. We found proteins encoded by top schizophrenia susceptibility genes formed a highly significant interconnected network, and, compared with random networks, these PPI networks are statistically highly significant for both direct connectivity and indirect connectivity. We further validated these results using empirical functional data (transcriptome data from a clinical sample). These highly significant findings indicate that top schizophrenia susceptibility genes encode proteins that significantly directly interacted and formed a densely interconnected network, suggesting perturbations of common underlying molecular processes or pathways that modulate risk to schizophrenia. Our findings that schizophrenia susceptibility genes encode a highly interconnected protein network may also provide a novel explanation for the observed genetic heterogeneity of schizophrenia, ie, mutation in any member of this molecular network will lead to same functional consequences that eventually contribute to risk of schizophrenia.

Fe-phyllosilicate redox cycling organisms from a redox transition zone in Hanford 300 Area sediments

Microorganisms capable of reducing or oxidizing structural iron (Fe) in Fe-bearing phyllosilicate minerals were enriched and isolated from a subsurface redox transition zone at the Hanford 300 Area site in eastern Washington, USA. Both conventional and in situ “i-chip” enrichment strategies were employed. One Fe(III)-reducing Geobacter (G. bremensis strain R1, Deltaproteobacteria) and six Fe(II) phyllosilicate-oxidizing isolates from the Alphaproteobacteria (Bradyrhizobium japonicum strains 22, is5, and in8p8), Betaproteobacteria (Cupriavidus necator strain A5-1, Dechloromonas agitata strain is5), and Actinobacteria (Nocardioides sp. strain in31) were recovered. The G. bremensis isolate grew by oxidizing acetate with the oxidized form of NAu-2 smectite as the electron acceptor. The Fe(II)-oxidizers grew by oxidation of chemically reduced smectite as the energy source with nitrate as the electron acceptor. The Bradyrhizobium isolates could also carry out aerobic oxidation of biotite. This is the first report of the recovery of a Fe(II)-oxidizing Nocardioides, and to date only one other Fe(II)-oxidizing Bradyrhizobium is known. The 16S rRNA gene sequences of the isolates were similar to ones found in clone libraries from Hanford 300 sediments and groundwater, suggesting that such organisms may be present and active in situ. Whole genome sequencing of the isolates is underway, the results of which will enable comparative genomic analysis of mechanisms of extracellular phyllosilicate Fe redox metabolism, and facilitate development of techniques to detect the presence and expression of genes associated with microbial phyllosilicate Fe redox cycling in sediments.

Improving structural similarity based virtual screening using background knowledge

BACKGROUND

Virtual screening in the form of similarity rankings is often applied in the early drug discovery process to rank and prioritize compounds from a database. This similarity ranking can be achieved with structural similarity measures. However, their general nature can lead to insufficient performance in some application cases. In this paper, we provide a link between ranking-based virtual screening and fragment-based data mining methods. The inclusion of binding-relevant background knowledge into a structural similarity measure improves the quality of the similarity rankings. This background knowledge in the form of binding relevant substructures can either be derived by hand selection or by automated fragment-based data mining methods.

RESULTS

In virtual screening experiments we show that our approach clearly improves enrichment factors with both applied variants of our approach: the extension of the structural similarity measure with background knowledge in the form of a hand-selected relevant substructure or the extension of the similarity measure with background knowledge derived with data mining methods.

CONCLUSION

Our study shows that adding binding relevant background knowledge can lead to significantly improved similarity rankings in virtual screening and that even basic data mining approaches can lead to competitive results making hand-selection of the background knowledge less crucial. This is especially important in drug discovery and development projects where no receptor structure is available or more frequently no verified binding mode is known and mostly ligand based approaches can be applied to generate hit compounds.

Hybridization-based antibody cDNA recovery for the production of recombinant antibodies identified by repertoire sequencing

High-throughput sequencing of the antibody repertoire is enabling a thorough analysis of B cell diversity and clonal selection, which may improve the novel antibody discovery process. Theoretically, an adequate bioinformatic analysis could allow identification of candidate antigen-specific antibodies, requiring their recombinant production for experimental validation of their specificity. Gene synthesis is commonly used for the generation of recombinant antibodies identified in silico. Novel strategies that bypass gene synthesis could offer more accessible antibody identification and validation alternatives. We developed a hybridization-based recovery strategy that targets the complementarity-determining region 3 (CDRH3) for the enrichment of cDNA of candidate antigen-specific antibody sequences. Ten clonal groups of interest were identified through bioinformatic analysis of the heavy chain antibody repertoire of mice immunized with hen egg white lysozyme (HEL). cDNA from eight of the targeted clonal groups was recovered efficiently, leading to the generation of recombinant antibodies. One representative heavy chain sequence from each clonal group recovered was paired with previously reported anti-HEL light chains to generate full antibodies, later tested for HEL-binding capacity. The recovery process proposed represents a simple and scalable molecular strategy that could enhance antibody identification and specificity assessment, enabling a more cost-efficient generation of recombinant antibodies.

Circulating tumor cell enrichment based on physical properties

The metastatic dissemination and spread of malignant circulating tumor cells (CTCs) accounts for more than 90% of cancer-related deaths. CTCs detach from a primary tumor, travel through the circulatory system, and then invade and proliferate in distant organs. The detection of CTCs from blood has been established for prognostic monitoring and is predictive of patient outcome. Analysis of CTCs could enable the means for early detection and screening in cancer, as well as provide diagnostic access to tumor tissues in a minimally invasive way. The fundamental challenge with analyzing CTCs is the fact that they occur at extremely low concentrations in blood, on the order of one out of a billion cells. Various technologies have been proposed to isolate CTCs for enrichment. Here we focus on antigen-independent approaches that are not limited by specific capture antibodies. Intrinsic physical properties of CTCs, including cell size, deformability, and electrical properties, are reviewed, and technologies developed to exploit them for enrichment from blood are summarized. Physical enrichment technologies are of particular interest as they have the potential to increase yield and enable the analysis of rare CTC phenotypes that may not be otherwise obtained.

Development and evaluation of a novel combinatorial selective enrichment and multiplex PCR technique for molecular detection of major virulence-associated genes of enterotoxigenic Staphylococcus aureus in food samples

AIMS

To develop a multiplex PCR assay coupled with selective enrichment step to detect major virulence-associated genes of enterotoxigenic Staphylococcus aureus and evaluate the same directly on contaminated food samples.

METHODS AND RESULTS

The most important virulence-associated genes of Staph. aureus, which are commonly related to food safety issues, are targeted in this study. They include five major enterotoxigenic genes-sea, seb, sec, seg and sei, tst-which encodes TSST-1, mecA-which confer methicillin resistance and coa-for the enzyme coagulase along with an internal amplification control (IAC) to rule out false-negative result. A modified mannitol salt broth (MSB) supplemented with sodium pyruvate was used for selective enrichment of Staph. aureus from food samples prior to PCR. Evaluation of efficiency of different media revealed that enrichment of samples in modified MSB followed by PCR resulted in specific, sensitive and effective amplification of the targeted genes in comparison with other enrichment media. Incorporation of bovine serum albumin (BSA) as PCR enhancer improved the intensity of amplicons. The standardized multiplex PCR (mPCR) format was able to detect all the target genes at a bacterial load of 10(6) CFU ml(-1) in any sample. The PCR results were unequivocally correlated with the conventional methods when the mPCR format was assessed on a total of 91 Staph. aureus isolates. The entire assay was found to be effectual when evaluated on naturally contaminated food samples.

CONCLUSIONS

The combinatorial approach involving selective enrichment followed by mPCR developed in this study was found to be effective for the detection of toxigenic Staph. aureus directly from various food sources.

SIGNIFICANCE AND IMPACT OF THE STUDY

The developed format would find a promising application in early detection of food contaminations as well as in the diagnosis of food poisoning due to Staph. aureus.

Cultivation of planktonic anaerobic ammonium oxidation (anammox) bacteria using membrane bioreactor

Enrichment cultures of anaerobic ammonium oxidation (anammox) bacteria as planktonic cell suspensions are essential for studying their ecophysiology and biochemistry, while their cultivation is still laborious. The present study aimed to cultivate two phylogenetically distinct anammox bacteria, "Candidatus Brocadia sinica" and "Ca. Scalindua sp." in the form of planktonic cells using membrane bioreactors (MBRs). The MBRs were continuously operated for more than 250 d with nitrogen loading rates of 0.48-1.02 and 0.004-0.09 kgN m(-3) d(-1) for "Ca. Brocadia sinica" and "Ca. Scalindua sp.", respectively. Planktonic anammox bacterial cells were successfully enriched (>90%) in the MBRs, which was confirmed by fluorescence in-situ hybridization and 16S rRNA gene sequencing analysis. The decay rate and half-saturation constant for NO2(-) of "Ca. Brocadia sinica" were determined to be 0.0029-0.0081 d(-1) and 0.47 mgN L(-1), respectively, using enriched planktonic cells. The present study demonstrated that MBR enables the culture of planktonic anammox bacterial cells, which are suitable for studying their ecophysiology and biochemistry.