Andrew R Cossins

• BSc, PhD
• Managing Director at University of Liverpool

Postcopulatory interactions between the sexes in internally fertilizing species elicits both sexual conflict and sexual selection. Macroevolutionary and comparative studies have linked these processes to rapid transcriptomic evolution in sex‐specific tissues and substantial transcriptomic postmating responses in females, patterns of which are alter...

Mating causes substantial changes in females, altering male and female reproductive fitness. Some postmating effects are hypothesized to be at least partially mediated by gene expression changes, driven by postcopulatory sexual selection, which results in population divergence of reproductive proteins that could generate reproductive isolation. How...

The state of an animal prior to the application of a noxious stimulus can have a profound effect on their nociceptive threshold and subsequent behaviour. In mammals, the presence of acute stress preceding a painful event can have an analgesic effect whereas the presence of chronic stress can result in hyperalgesia. While considerable research has b...

Fish are used in a variety of experimental contexts often in high numbers. To maintain their welfare and ensure valid results during invasive procedures it is vital that we can detect subtle changes in behaviour that may allow us to intervene to provide pain-relief. Therefore, an automated method, the Fish Behaviour Index (FBI), was devised and use...

The ability to assess welfare is an important refinement that will ensure the good condition of animals used in experimentation. The present study investigated the impact of invasive procedures on the patterns of movement of zebrafish (Danio rerio). Recordings were made before and after fin clipping, PIT tagging and a standard pain test and these w...

Fish production is increasingly important to global food security. A major factor in maintaining health, productivity and welfare of farmed fish is the establishment and promotion of a stable and beneficial intestinal microbiota. Understanding the effects of factors such as host and environment on gut microbial community structure is essential for...

Sex differences in dioecious animals are pervasive and result from gene expression differences. Elevated sexual selection has been predicted to increase the number and expression of male-biased genes, and experimentally imposing monogamy on Drosophila melanogaster has led to a relative feminisation of the transcriptome. Here, we test this hypothesi...

After the publication of the article, the authors retrospectively noted that the name of Dr Dawn Jones, a postdoctoral researcher in the laboratory of Professor Christine Gosden, should have been added to the authors' list, whose contribution to the study greatly augmented the exploration of all the RNA products via adoption of the RNASeq (Illumina...

br/>Background Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene e...

Background Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expres...

In conjunction with the second International Environmental Omics Symposium (iEOS) conference, held at the University of Liverpool (UK) in September 2014, a workshop was held to bring together experts in toxicology and regulatory science from academia, government and industry. The purpose of the workshop was to review the specific roles that high-co...

Background In 2014, Western Africa experienced an unanticipated explosion of Ebola virus infections. What distinguishes fatal from non-fatal outcomes remains largely unknown, yet is key to optimising personalised treatment strategies. We used transcriptome data for peripheral blood taken from infected and convalescent recovering patients to identif...

Advances in genomic and transcriptome sequencing are revealing the massive scale of previously unrecognised alterations occurring during neoplastic transformation. Breast cancers are genetically and phenotypically heterogeneous. Each of the three major subtypes [ERBB2 amplified, estrogen receptor (ESR)-positive and triple-negative] poses diagnostic...

The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. T...

Crucian carp are unusual among vertebrates in surviving extended periods in the complete absence of molecular oxygen. During this time cardiac output is maintained though these mechanisms are not well understood. Using a high-density cDNA microarray, we have defined the genome-wide gene expression responses of cardiac tissue after exposing the fish...

The identification of nucleic acid aptamers would be advanced if they could be obtained after fewer rounds of selection and amplification. In this paper the identification of bivalent aptamers for thrombin by SELEX and single-step selection are compared using next generation sequencing and motif finding informatics. Results show that similar aptame...

Organismal development is the most dynamic period of the life cycle, yet we have only a rough understanding of the dynamics of gene expression during adolescent transition. Here we show that adolescence in Caenorhabditis elegans is characterized by a spectacular expression shift of conserved and highly polymorphic genes. Using a high resolution tim...

Chill and freeze represent very different components of low temperature stress. Whilst the principal mechanisms of tissue damage and of acquired protection from freeze-induced effects are reasonably well established, those for chill damage and protection are not. Non-freeze cold exposure (i.e. chill) can lead to serious disruption to normal life pr...

Ecological speciation occurs with the adaptation of populations to different environments and concurrent evolution of reproductive isolation. Phenotypic plasticity might influence both ecological adaptation and reproductive traits. We examined environment-specific gene expression and male mating success in cactophilic Drosophila mojavensis using tr...

Holding Your Breath Hemoglobin and myoglobin are widely responsible for oxygen transport and storage (see the Perspective by Rezende ). The ability of diving mammals to obtain enough oxygen to support extended dives and foraging is largely dependent on muscle myoglobin (Mb) content. Mirceta et al. (p. 1234192 ) found that in mammalian lineages with...

Nearly all aptamers identified so far for any given target molecule have been specific for the same binding site (epitope). The most notable exception to the 1 aptamer per target molecule rule is the pair of DNA aptamers that bind to different epitopes of thrombin. This communication refutes the suggestion that these aptamers exist because differen...

Anthropogenic endocrine disruptors now contaminate all environments globally, with concomitant deleterious effects across diverse taxa. While most studies on endocrine disruption (ED) have focused on vertebrates, the superimposition of male sexual characteristics in the female dogwhelk, Nucella lapillus (imposex), caused by organotins, provides one...

Hypoxic vasodilation is a physiological response to low oxygen tension that increases blood supply to match metabolic demands. Although this response has been characterized for >100 years, the underlying hypoxic sensing and effector signaling mechanisms remain uncertain. We have shown that deoxygenated myoglobin in the heart can reduce nitrite to n...

Current aquatic chemical testing guidelines recognize that solvents can potentially interfere with the organism or environmental conditions of aquatic ecotoxicity tests and therefore recommend concentration limits for their use. These recommendations are based on evidence of adverse solvent effects in apical level tests. The growing importance of s...

Because of a recent whole genome duplication, the hypoxia-tolerant common carp and goldfish are the only vertebrates known to possess two myoglobin (Mb) paralogs. One of these, Mb1, occurs in oxidative muscle but also in several other tissues, including capillary endothelial cells, whereas the other, Mb2, is a unique isoform specific to brain neuro...

In 2000, fishermen reported the appearance of deformed reproductive organs in whitefish (Coregonus spp.) from Lake Thun, Switzerland. Despite intensive investigations, the causes of these abnormalities remain unknown. Using gene expression profiling, we sought to identify candidate genes and physiological processes possibly associated with the obse...

Western blotting of ependymin in stable rainbow trout dominance hierarchies. An example of the protein expression using western blots to demonstrate ependymin is upregulated in the subdominant (Subdom.) and less is expressed by the dominant (Dom.) followed by the subordinate (Subord.). A housekeeping protein β tubulin is unchanged in expression for...

Details of experimental protocols including the behavioural observations, intracerebroventricular injections, microarray analysis; RT-PCR and western blot. (DOC)

Changes in gene expression profile by manipulation of dominance status from subdominant to dominant. Removal of the dominant specimen from stable hierarchy led to the adoption of dominant status by the previously sub-dominant individuals (N) within a hierarchy. Figure A illustrates the changes in brain transcripts of the new dominant (N) at 2h, 48h...

List of genes that were differentially expressed between sub-dominant and either dominant or subordinate members of a stable social hierarchy. (DOCX)

Primers for RT-PCR analysis. (DOCX)

Theoretical and empirical studies have sought to explain the formation and maintenance of social relationships within groups. The resulting dominance hierarchies have significant fitness and survival consequences dependent upon social status. We hypothesised that each position or rank within a group has a distinctive brain gene expression profile t...

Historically, the majority of microarray work has been restricted to well-defined model organisms. This was primarily due to the limited availability of genomic or transcriptomic sequence data and the then high cost involved in developing microarrays. However, recent technological developments have greatly enhanced the speed of generating the under...

Coral bleaching has taken centre-stage in the debate over the likely biological effects of global environmental change. Central to any judgements on this issue is the ability of corals to display increased tolerance of debilitating or lethal conditions through phenotypic adaptations, such as heat-hardening, longer-term acclimatisation responses or...

Background Many vertebrates, including the goldfish, exhibit seasonal reproductive rhythms, which are a result of interactions between external environmental stimuli and internal endocrine systems in the hypothalamo-pituitary-gonadal axis. While it is long believed that differential expression of neuroendocrine genes contributes to establishing sea...

Historically, the majority of microarray work has been restricted to well-defined model organisms. This was primarily due to the limited availability of genomic or transcriptomic sequence data and the then high cost involved in developing microarrays. However, recent technological developments have greatly enhanced the speed of generating the under...

Large-scale toxicogenomic screening approaches offer great promise for generating a bias-free system-wide view of toxicological effects and modes-of-action of chemicals and ecotoxicants. However, early applications of microarray technology have identified relatively small groups of responding genes with which to define new targets for analysis by c...

Abstract Sesamin enhances the DHA content of tissue lipids in salmonid fish. We have examined whether this effect also occurs in common carp (Cyprinus carpio). Two-year-old common carps were fed a diet containing 5.8 g sesamin kg−1 feed for 69 days. No significant differences were found in the fish weight, specific growth rate, food conversion rati...

An understanding of the underpinning physiology and biochemistry of animals is essential to properly understand the impact of anthropogenic changes and natural catastrophes upon the conservation of endangered species. An observation on the tissue location of the key respiratory protein, myoglobin, now opens up new opportunities for understanding ho...

ExprAlign - the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles. This document contains supplementary material for the abovementioned paper. It includes the following Sections - Section A - ROC curves to optimise thresholds for correlation score. Section B - Figures S1-S3. Section C - List of ESTs who...

Sequence identification of ESTs from non-model species offers distinct challenges particularly when these species have duplicated genomes and when they are phylogenetically distant from sequenced model organisms. For the common carp, an environmental model of aquacultural interest, large numbers of ESTs remained unidentified using BLAST sequence al...

The Van Gogh-like 2 (vangl2) gene is typically associated with planar cell polarity pathways, which is essential for correct orientation of epithelial cells during development. The encoded protein of this gene is a transmembrane protein and is highly conserved through evolution. Van Gogh-like 2 was selected for further study on the basis of consist...

A full list of differentially expressed genes between seasons. (0.65 MB XLS)

Two-dimensional PCA plot for transcriptomes from Hyp slides in three seasonal time points (May, August, and December). (0.08 MB PPT)

Gene ontolgy (GO) term enrichment analysis for the genes with H-L-L pattern. (0.28 MB PPT)

Oligonucleotide primers used for real-time RT-PCR assays. (0.03 MB DOC)

Detailed information about the experimental design, brain tissue, sampling seasonal time and other information. (0.04 MB DOC)

Eigenvalues of PCA for Figure 3. (2.07 MB TIF)

MI-3 is a consortium of 11 universities and research laboratories whose mission is to develop complementary metal-oxide semiconductor (CMOS) active pixel sensors (APS) and to apply these sensors to a range of imaging challenges. A range of sensors has been developed: On-Pixel Intelligent CMOS (OPIC)—designed for in-pixel intelligence; FPN—designed...

Myoglobin (Mb) is famous as a muscle-specific protein--yet the common carp expresses the gene (cMb1) encoding this protein in a range of non-muscle tissues and also expresses a novel isoform (cMb2) in the brain. Using a homologous antibody and riboprobes, we have established the relative amounts and cellular sites of non-muscle Mb expression in dif...

The mechanical properties of the axial muscles vary along the length of a fish's body. This variation in performance correlates with the expression of certain muscle proteins. Parvalbumin (PARV) is an important calcium binding protein that helps modulate intracellular calcium levels which set the size and shape of the muscle calcium transient. It t...

Microarray analyses provide information on the relative expression levels of large numbers of gene products (transcripts). As such they have been widely used to examine differences in gene expression across a variety of samples such as tissues and life-cycle stages. Due to a previous lack of sequence data, microarray analyses have typically centred...

Many vertebrates, including the goldfish, exhibit seasonal reproductive rhythms, which are a result of interactions between external environmental stimuli and internal endocrine systems in the hypothalamo-pituitary-gonadal axis. While it is long believed that differential expression of neuroendocrine genes contributes to establishing seasonal repro...

Nociception is the sensory mechanism by which potentially harmful stimuli are detected in animals and humans. The behavioural responses to noxious stimulation have been studied in two fish species thus far. However, since species-specific differences are seen in mammals, more species need to be examined to determine whether nociceptive responses ar...

Goldfish (Carassius auratus) are excellent model organisms for the neuroendocrine signaling and the regulation of reproduction in vertebrates. Goldfish also serve as useful model organisms in numerous other fields. In contrast to mammals, teleost fish do not have a median eminence; the anterior pituitary is innervated by numerous neuronal cell type...

We investigated the effects of fluoxetine, a selective serotonin reuptake inhibitor, on neuroendocrine function and the reproductive axis in female goldfish. Fish were given intraperitoneal injections of fluoxetine twice a week for 14 days, resulting in five injections of 5 microg fluoxetine/g body wt. We measured the monoamine neurotransmitters se...

Stearoyl-CoA desaturases (SCDs) are key enzymes of fatty acid biosynthesis whose regulation underpins responses to dietary, thermal, and hormonal treatment. Although two isoforms are known to exist in the common carp and human and four in mouse, there is no coherent view on how this gene family evolved to generate functionally diverse members. Here...

Nitric oxide generated from the nitrite ion limits the tissue damage caused by restricted blood flow. Gene knockout experiments in mice now reveal that myoglobin is the mediator of this effect.

The breadth of mechanistic analyses of environmental stress responses is greatly enhanced by the use of contemporary post-genomic screening technologies, notably including massively parallel transcript analysis by microarray. These genome-wide investigations are entirely dependent upon the creation of a suite of resources that are directed against...

Recent studies have demonstrated that teleost fish possess nociceptors that detect potentially painful stimuli and that the physiological properties of these fibres are markedly similar to those found in mammals. This finding led to suggestions of possible pain perception in fish, contrary to the view that the sensory response in these animals is l...

The common carp is an important fish species satisfying ornamental, food and recreational fisheries’ needs worldwide, but in common with other cyprinid fishes, it is particularly renowned for its environmental tolerance. Investigating the mechanistic basis of growth, disease and environmental tolerance is greatly enhanced by access to a comprehensi...

Specific PCR products are detected with an antibody-free lateral-flow device by sandwiching them between reporter oligonucleotides covalently attached to gold nanoparticles (GNPs) and capture oligonucleotides covalently attached to a nitrocellulose chromatographic strip.

The common carp (Cyprinus carpio) has a well-developed capacity to modify muscle properties in response to changes in temperature. Understanding the mechanisms underpinning this phenotypic response at the protein level may provide fundamental insights into the molecular basis of adaptive processes in skeletal muscle. In this study, common carp were...