Genomic analyses and cloning of novel chicken natriuretic peptide genes reveal new insights into natriuretic peptide evolution

The natriuretic peptide (NP) family consists of multiple subtypes in teleosts, including atrial, B-type, ventricular, and C-type NPs (ANP, BNP, VNP, CNP-1–4, respectively), but only ANP, BNP, CNP-3, and CNP-4 have been identified in tetrapods. As part of understanding the molecular evolution of NPs in the tetrapod lineage, we identified NP genes in the chicken genome. Previously, only BNP and CNP-3 have been identified in birds, but we characterized two new chicken NP genes by cDNA cloning, synteny and phylogenetic analyses. One gene is an orthologue of CNP-1, which has only ever been reported in teleostei and bichir. The second gene could not be assigned to a particular NP subtype because of high sequence divergence and was named renal NP (RNP) due to its predominant expression in the kidney. CNP-1 mRNA was only detected in brain, while CNP-3 mRNA was expressed in kidney, heart, and brain. In the developing embryo, BNP and RNP transcripts were most abundant 24 h post-fertilization, while CNP mRNA increased in a stage-dependant manner. Synthetic chicken RNP stimulated an increase in cGMP production above basal level in chicken kidney membrane preparations and caused a potent dose-dependant vasodilation of pre-constricted dorsal aortic rings. From conserved chromosomal synteny, we propose that the CNP-4 and ANP genes have been lost in chicken, and that RNP may have evolved from a VNP-like gene. Furthermore, we have demonstrated for the first time that CNP-1 is retained in the tetrapod lineage.

Natriuretic peptide signalling in the gills of freshwater and seawater fishes

The gills are considered major targets for cardiac natriuretic peptides with studies confirming natriuretic peptide receptor presence on vascular and sometimes epithelial tissues. Natriuretic peptide intracellular signalling is via guanylyl cyclase receptors and the cGMP pathway, and via inhibitory G-proteins linked to cyclic AMP pathways. Natriuretic peptides in the gills alter branchial blood flow and may also alter ion transport in various salinities. We present an overview of natriuretic peptide cGMP and cAMP signalling in fishes and consider the implications of the recent discovery of several CNPs and BNP in bony fishes on natriuretic peptide receptor studies.

Molecular cloning of natriuretic peptides from the heart of reptiles : loss of ANP in diapsid reptiles and birds

Atrial natriuretic peptide (ANP) and B-type NP (BNP) are hormones involved in homeostatic control of body fluid and cardiovascular regulation. Both ANP and BNP have been cloned from the heart of mammals, amphibians, and teleost fishes, while an additional cardiac peptide, ventricular NP, has been found in selected species of teleost fish. However, in chicken, BNP is the primary cardiac peptide identified thus far. In contrast, the types of NP/s present in the reptilian heart are unknown, representing a considerable gap in our understanding of NP evolution. In the present study, we cloned and sequenced a BNP cDNA from the atria of representative species of reptile, including crocodile, lizard, snake, and tortoise. In addition, we cloned BNP from the pigeon atria. The reptilian and pigeon BNP cDNAs had ATTTA repeats in the 3′ untranslated region, as observed in all vertebrate BNP mRNAs. A high sequence homology was evident when comparing reptile and pigeon preproBNP with the previously identified chicken preproBNP. In particular, the predicted mature BNP-29 was identical between crocodile, tortoise, and chicken, with pigeon having a single amino acid substitution; lizard and snake BNP had seven and nine substitutions, respectively. Furthermore, an ANP cDNA could only be cloned from the tortoise atria. Since ANP was not isolated from the heart of any non-chelonian reptile and appears to be absent in birds, we propose that the ANP gene has been lost after branching of the turtles in the amniote line. This data provides new avenues for research on NP function in reptiles.

Does baiting influence the relative composition of the diet of foxes?

The changes in the diet of foxes (Vulpes vulpes) in the Jervis Bay Region was assessed following a long-term baiting program by analysing the composition of fox faecal excreta (scats). In all, 470 fox scats were collected between April and August 2003 from two baited sites, Booderee National Park (BNP) and Beecroft Peninsula, and from two unbaited sites in the southern and northern parts of Jervis Bay National Park (SJBNP and NJBNP respectively). Diet was compared between these sites and mammalian diet was also compared from scats collected before baiting in 1996 and after baiting in 2000 at Beecroft Peninsula and in 2001 at Booderee National Park. In 2003, the most common species consumed by foxes was the common ringtail possum (Pseudocheirus peregrinus), except at unbaited NJBNP, where the swamp wallaby (Wallabia bicolor) was the most frequent dietary item. Significant dietary differences were found between unbaited and baited sites, with the long-nosed bandicoot (Perameles nasuta) and P. peregrinus featuring more in the diet of foxes from the baited sites. Marked increases in the frequency of occurrence of P. peregrinus and P. nasuta in fox scats occurred from before baiting through to after baiting. Relative fox abundance, as indexed by the number of scats collected per kilometre, was lowest in Booderee, followed by Beecroft, then SJBNP, with NJBNP having the highest relative abundance of foxes. We suggest that baiting did affect the diet of foxes on both peninsulas and that the dietary changes across baiting histories were intrinsically related to an increase in abundance in some taxa as a result of relaxed predator pressure following sustained fox control. However, the lack of unbaited control sites over the whole study precludes a definitive conclusion.

Natriuretic peptides and their receptors in the brain of the amphibian, Bufo marinus

The natriuretic peptides, atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP) and C-type natriuretic peptide (CNP) are members of a family of hormones that play an important role in mammalian fluid and electrolyte balance. In the periphery, natriuretic peptides reduce blood volume and subsequently blood pressure by increasing renal natriuresis and diuresis and relaxation of vascular smooth muscle. The actions of natriuretic peptides are mediated via two membrane-linked guanylate cyclase receptors (NPR-GC); natriuretic peptide receptor-A (NPR-A) which has a high affinity for ANP and BNP; and natriuretic peptide receptor-B (NPR-B)which has the greatest affinity for CNP. A third receptor not linked to guanylate cyclase, natriuretic peptide receptor-C (NPR-C) also exists, which binds to ANP, BNP and CNP with a relatively equal affinity, and is involved with clearance of the peptides from the circulation and tissues. The natriuretic peptides are present in the brain and are particularly predominant in cardiovascular and fluid and electrolyte regulating areas such as the anteroventral third ventricle (AV3V) region. This distribution has led to the suggestion natriuretic peptides play a neuromodulatory role in the central control of fluid homeostasis. Natriuretic peptides in the brain have been observed to inhibit the release of other fluid and electrolyte regulating hormones such as arginine vasopressin (AVP) and angiotensin II (AII). Natriuretic peptides have also been identified in the non-mammalian vertebrates although information regarding the distribution of the peptides and their receptors in the non-mammalian brain is limited. In amphibians, immunohistochemical studies have shown that natriuretic peptides are highly concentrated in the preoptic region of the brain, an area believed to be analogous to the A\T3\ region in mammals, which suggests that natriuretic peptides may also be involved in central fluid and electrolyte regulation in amphibians. To date, CNP is the only natriuretic peptide that has been isolated and cloned from the lower vertebrate brain, although studies on the distribution of CNP binding sites in the brain have only been performed in one fish species. Studies on the distribution of ANP binding sites in the lower vertebrate brain are similarly limited and have only been performed in one fish and two amphibian species. Moreover, the nature and distribution of the natriuretic peptide receptors has not been characterised. The current study therefore, used several approaches to investigate the distribution of natriuretic peptides and their receptors in the brain of the amphibian Bufo marinus. The topographical relationship of natriuretic peptides and the fluid and electrolyte regulating hormone arginine vasotocin was also investigated, in order to gain a greater understanding of the role of the natriuretic peptide system in the lower vertebrate brain. Immunohistochemical studies showed natriuretic peptides were distributed throughout the brain and were highly concentrated in the preoptic region and interpeduncular nucleus. No natriuretic peptide-like immunoreactivity (NP-IR) was observed in the pituitary gland. Arginine vasotocin-like immunoreactivity (AvT-IR) was confined to distinct regions, particularly in the preoptic/hypothalamic region and pituitary gland. Double labelling studies of NP-JR and AvT-IR showed the peptides are not colocalised in the same neural pathways. The distribution of natriuretic peptide binding sites using the ligands 125I-rat ANP (125I-rANP) and 125I-porcine CNP (125I-pCNP) showed different distributions in the brain of B. marinus. The specificity of binding was determined by displacement with unlabelled rat ANP, porcine CNP and C-ANF, an NPR-C specific ligand. 125I-rANP binding sites were broadly distributed throughout the brain with the highest concentration in pituitary gland, habenular, medial pallium and olfactory region. Minimal 125I-rANP binding was observed in the preoptic region. Residual 125I-rANP binding in the presence of C-ANF was observed in the olfactory region, habenular and pituitary gland indicating the presence of both NPR-GC and NPR-C in these regions. 125I-pCNP binding was limited to the olfactory region, pallium and posterior pituitary gland. All 125I-pCNP binding was displaced by C-ANF which suggests that CNP in the brain of B. marinus binds only to NPR-C. Affinity cross-linking and SDS-PAGB demonstrated two binding sites at 136 kDa and 65 kDa under reducing conditions. Guanylate cyclase assays showed 0.1 µM ANP increased cGMP levels 50% above basal whilst a 10-fold higher concentration of CNP was required to produce the same result. Molecular cloning studies revealed a 669 base pair fragment showing 91% homology with human and rat NPR-A and 89% homology with human, rat and eel NPR-B. A 432 base pair fragment showing 67% homology to the mammalian NPR-C and 58% homology with eel NPR-D was also obtained. The results show natriuretic peptides and their receptors are distributed throughout the brain of B. marinus which indicates that natriuretic peptides may participate in a range of regulatory functions throughout the brain. The potential for natriuretic peptides to regulate the release of the fluid and electrolyte regulating hormone AVT also exists due to the high number of natriuretic peptide binding sites in the posterior pituitary gland. At least two populations of natriuretic peptide receptors are present in the brain of B. marinus, one linked to guanylate cyclase and one resembling the mammalian clearance receptor. Furthermore, autoradiography and guanylate cyclase studies suggest ANP may be the major ligand in the brain of B. marinus, even though CNP is the only natriuretic peptide that has been isolated from the lower vertebrate brain to date.

Exploiting side information in Bayesian nonparametric models and their applications

 My research is to exploit side information into advanced Bayesian nonparametric models. We have developed some novel models for data clustering and medical data analysis and also have made our methods scalable for large-scale data. I have published my research in several journal and conference papers.

Bayesian nonparametric approaches to abnormality detection in video surveillance

In data science, anomaly detection is the process of identifying the items, events or observations which do not conform to expected patterns in a dataset. As widely acknowledged in the computer vision community and security management, discovering suspicious events is the key issue for abnormal detection in video surveil-lance. The important steps in identifying such events include stream data segmentation and hidden patterns discovery. However, the crucial challenge in stream data segmenta-tion and hidden patterns discovery are the number of coherent segments in surveillance stream and the number of traffic patterns are unknown and hard to specify. Therefore, in this paper we revisit the abnormality detection problem through the lens of Bayesian nonparametric (BNP) and develop a novel usage of BNP methods for this problem. In particular, we employ the Infinite Hidden Markov Model and Bayesian Nonparamet-ric Factor Analysis for stream data segmentation and pattern discovery. In addition, we introduce an interactive system allowing users to inspect and browse suspicious events.

Small-variance asymptotics for bayesian nonparametric models with constraints

The users often have additional knowledge when Bayesian nonparametric models (BNP) are employed, e.g. for clustering there may be prior knowledge that some of the data instances should be in the same cluster (must-link constraint) or in different clusters (cannot-link constraint), and similarly for topic modeling some words should be grouped together or separately because of an underlying semantic. This can be achieved by imposing appropriate sampling probabilities based on such constraints. However, the traditional inference technique of BNP models via Gibbs sampling is time consuming and is not scalable for large data. Variational approximations are faster but many times they do not offer good solutions. Addressing this we present a small-variance asymptotic analysis of the MAP estimates of BNP models with constraints. We derive the objective function for Dirichlet process mixture model with constraints and devise a simple and efficient K-means type algorithm. We further extend the small-variance analysis to hierarchical BNP models with constraints and devise a similar simple objective function. Experiments on synthetic and real data sets demonstrate the efficiency and effectiveness of our algorithms.