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1.  Learned recognition of maternal signature odors mediates the first suckling episode in mice 
Current biology : CB  2012;22(21):1998-2007.
Summary
Background
Soon after birth all mammals must initiate milk suckling to survive. In rodents, this innate behavior is critically dependent on uncharacterized maternally-derived chemosensory ligands. Recently the first pheromone sufficient to initiate suckling was isolated from the rabbit. Identification of the olfactory cues that trigger first suckling in the mouse would provide the means to determine the neural mechanisms that generate innate behavior.
Results
Here we use behavioral analysis, metabolomics, and calcium imaging of primary sensory neurons and find no evidence of ligands with intrinsic bioactivity, such as pheromones, acting to promote first suckling in the mouse. Instead, we find that the initiation of suckling is dependent on variable blends of maternal ‘signature odors’ that are learned and recognized prior to first suckling.
Conclusions
As observed with pheromone-mediated behavior, the response to signature odors releases innate behavior. However, this mechanism tolerates variability in both the signaling ligands and sensory neurons which may maximize the probability that this first essential behavior is successfully initiated. These results suggest that mammalian species have evolved multiple strategies to ensure the onset of this critical behavior.
doi:10.1016/j.cub.2012.08.041
PMCID: PMC3494771  PMID: 23041191
3.  The genomic basis of vomeronasal-mediated behaviour 
Mammalian Genome  2013;25:75-86.
The vomeronasal organ (VNO) is a chemosensory subsystem found in the nose of most mammals. It is principally tasked with detecting pheromones and other chemical signals that initiate innate behavioural responses. The VNO expresses subfamilies of vomeronasal receptors (VRs) in a cell-specific manner: each sensory neuron expresses just one or two receptors and silences all the other receptor genes. VR genes vary greatly in number within mammalian genomes, from no functional genes in some primates to many hundreds in rodents. They bind semiochemicals, some of which are also encoded in gene families that are coexpanded in species with correspondingly large VR repertoires. Protein and peptide cues that activate the VNO tend to be expressed in exocrine tissues in sexually dimorphic, and sometimes individually variable, patterns. Few chemical ligand–VR–behaviour relationships have been fully elucidated to date, largely due to technical difficulties in working with large, homologous gene families with high sequence identity. However, analysis of mouse lines with mutations in genes involved in ligand–VR signal transduction has revealed that the VNO mediates a range of social behaviours, including male–male and maternal aggression, sexual attraction, lordosis, and selective pregnancy termination, as well as interspecific responses such as avoidance and defensive behaviours. The unusual logic of VR expression now offers an opportunity to map the specific neural circuits that drive these behaviours.
doi:10.1007/s00335-013-9463-1
PMCID: PMC3916702  PMID: 23884334
4.  Generation of the Sotos syndrome deletion in mice 
Mammalian Genome  2012;23(11-12):749-757.
Haploinsufficiency of the human 5q35 region spanning the NSD1 gene results in a rare genomic disorder known as Sotos syndrome (Sotos), with patients displaying a variety of clinical features, including pre- and postnatal overgrowth, intellectual disability, and urinary/renal abnormalities. We used chromosome engineering to generate a segmental monosomy, i.e., mice carrying a heterozygous 1.5-Mb deletion of 36 genes on mouse chromosome 13 (4732471D19Rik-B4galt7), syntenic with 5q35.2–q35.3 in humans (Df(13)Ms2Dja+/− mice). Surprisingly Df(13)Ms2Dja+/− mice were significantly smaller for their gestational age and also showed decreased postnatal growth, in contrast to Sotos patients. Df(13)Ms2Dja+/− mice did, however, display deficits in long-term memory retention and dilation of the pelvicalyceal system, which in part may model the learning difficulties and renal abnormalities observed in Sotos patients. Thus, haploinsufficiency of genes within the mouse 4732471D19Rik–B4galt7 deletion interval play important roles in growth, memory retention, and the development of the renal pelvicalyceal system.
Electronic supplementary material
The online version of this article (doi:10.1007/s00335-012-9416-0) contains supplementary material, which is available to authorized users.
doi:10.1007/s00335-012-9416-0
PMCID: PMC3510424  PMID: 22926222
5.  Genomic variation in the vomeronasal receptor gene repertoires of inbred mice 
BMC Genomics  2012;13:415.
Background
Vomeronasal receptors (VRs), expressed in sensory neurons of the vomeronasal organ, are thought to bind pheromones and mediate innate behaviours. The mouse reference genome has over 360 functional VRs arranged in highly homologous clusters, but the vast majority are of unknown function. Differences in these receptors within and between closely related species of mice are likely to underpin a range of behavioural responses. To investigate these differences, we interrogated the VR gene repertoire from 17 inbred strains of mice using massively parallel sequencing.
Results
Approximately half of the 6222 VR genes that we investigated could be successfully resolved, and those that were unambiguously mapped resulted in an extremely accurate dataset. Collectively VRs have over twice the coding sequence variation of the genome average; but we identify striking non-random distribution of these variants within and between genes, clusters, clades and functional classes of VRs. We show that functional VR gene repertoires differ considerably between different Mus subspecies and species, suggesting these receptors may play a role in mediating behavioural adaptations. Finally, we provide evidence that widely-used, highly inbred laboratory-derived strains have a greatly reduced, but not entirely redundant capacity for differential pheromone-mediated behaviours.
Conclusions
Together our results suggest that the unusually variable VR repertoires of mice have a significant role in encoding differences in olfactory-mediated responses and behaviours. Our dataset has expanded over nine fold the known number of mouse VR alleles, and will enable mechanistic analyses into the genetics of innate behavioural differences in mice.
doi:10.1186/1471-2164-13-415
PMCID: PMC3460788  PMID: 22908939
Vomeronasal; Receptor; Olfaction; Pheromone; Behaviour; Genome sequencing; Single nucleotide polymorphism; Mouse
6.  Low budget analysis of Direct-To-Consumer genomic testing familial data 
F1000Research  2012;1:3.
Direct-to-consumer (DTC) genetic testing is a recent commercial endeavor that allows the general public to access personal genomic data. The growing availability of personal genomic data has in turn stimulated the development of non-commercial tools for DTC data analysis. Despite this new wealth of public resources, no systematic research has been carried out to assess these tools for interpretation of DTC data. Here, we provide an initial analysis benchmark in the context of a whole family, using single nucleotide polymorphism (SNP) data. Five blood-related DTC SNP chip data tests were analyzed in conjunction with one whole exome sequence. We report findings related to genomic similarity between individuals, genetic risks and an overall assessment of data quality; thus providing an evaluation of the current potential of public domain analysis tools for personal genomics. We envisage that as the use of personal genome tests spreads to the general population, publicly available tools will have a more prominent role in the interpretation of genomic data in the context of health risks and ancestry.
doi:10.12688/f1000research.1-3.v1
PMCID: PMC3941016  PMID: 24627758
7.  The mouse genetics toolkit: revealing function and mechanism 
Genome Biology  2011;12(6):224.
Large-scale projects are providing rapid global access to a wealth of mouse genetic resources to help discover disease genes and to manipulate their function.
doi:10.1186/gb-2011-12-6-224
PMCID: PMC3218837  PMID: 21722353
9.  Sexual dimorphism in olfactory signaling 
Current opinion in neurobiology  2010;20(6):770-775.
What makes males and females behave differently? While genetic master-regulators commonly underlie physical differences, sexually dimorphic behavior is additionally influenced by sensory input such as olfactory cues. Olfaction requires both ligands for signaling and sensory neural circuits for detection. Specialized subsets of each interact to generate gender-dimorphic behavior. It has long been accepted that males and females emit sex-specific odor compounds that function as pheromones to promote stereotypic behavior. Significant advances have now been made in purifying and isolating several of these sex-specific olfactory ligands. In contrast, the neural mechanisms that enable a gender dimorphic response to these odors remain largely unknown. However, first progress has been made in identifying components of sexually dimorphic olfactory circuits in both Drosophila and the mouse.
doi:10.1016/j.conb.2010.08.015
PMCID: PMC3005963  PMID: 20833534
10.  Olfactory mechanisms of stereotyped behavior: on the scent of specialized circuits 
Current opinion in neurobiology  2010;20(3):274-280.
Summary
Investigation of how specialized olfactory cues, such as pheromones, are detected has primarily focused on the function of receptor neurons within a subsystem of the nasal cavity, the vomeronasal organ (VNO). Behavioral analyses have long indicated that additional, non-VNO olfactory neurons are similarly necessary for pheromone detection; however the identity of these neurons has been a mystery. Recent molecular, behavioral, and genomic approaches have led to the identification of multiple atypical sensory circuits that display characteristics suggestive of a specialized function. This review focuses on these non-VNO receptors and neurons, and evaluates their potential for mediating stereotyped olfactory behavior in mammals.
doi:10.1016/j.conb.2010.02.013
PMCID: PMC2883022  PMID: 20338743
11.  The vomeronasal organ mediates interspecies defensive behaviors through detection of protein pheromone homologs 
Cell  2010;141(4):692-703.
Summary
Potential predators emit uncharacterized chemosignals that warn receiving species of danger. Neurons that sense these stimuli remain unknown. Here we show that detection and processing of fear-evoking odors emitted from cat, rat, and snake require the function of sensory neurons in the vomeronasal organ. To investigate the molecular nature of the sensory cues emitted by predators, we isolated the salient ligands from two species using a combination of innate behavioral assays in naïve receiving animals, calcium imaging, and cFos induction. Surprisingly, the defensive behavior-promoting activity released by other animals is encoded by species-specific ligands belonging to the major urinary protein (Mup) family, homologs of aggression-promoting mouse pheromones. We show that recombinant Mup proteins are sufficient to activate sensory neurons and initiate defensive behavior similar to native odors. This co-option of existing sensory mechanisms provides a molecular solution to the difficult problem of evolving a variety of species-specific molecular detectors.
doi:10.1016/j.cell.2010.03.037
PMCID: PMC2873972  PMID: 20478258
12.  Ten Simple Rules for Editing Wikipedia 
PLoS Computational Biology  2010;6(9):e1000941.
doi:10.1371/journal.pcbi.1000941
PMCID: PMC2947980  PMID: 20941386
13.  Species Specificity in Major Urinary Proteins by Parallel Evolution 
PLoS ONE  2008;3(9):e3280.
Species-specific chemosignals, pheromones, regulate social behaviors such as aggression, mating, pup-suckling, territory establishment, and dominance. The identity of these cues remains mostly undetermined and few mammalian pheromones have been identified. Genetically-encoded pheromones are expected to exhibit several different mechanisms for coding 1) diversity, to enable the signaling of multiple behaviors, 2) dynamic regulation, to indicate age and dominance, and 3) species-specificity. Recently, the major urinary proteins (Mups) have been shown to function themselves as genetically-encoded pheromones to regulate species-specific behavior. Mups are multiple highly related proteins expressed in combinatorial patterns that differ between individuals, gender, and age; which are sufficient to fulfill the first two criteria. We have now characterized and fully annotated the mouse Mup gene content in detail. This has enabled us to further analyze the extent of Mup coding diversity and determine their potential to encode species-specific cues.
Our results show that the mouse Mup gene cluster is composed of two subgroups: an older, more divergent class of genes and pseudogenes, and a second class with high sequence identity formed by recent sequential duplications of a single gene/pseudogene pair. Previous work suggests that truncated Mup pseudogenes may encode a family of functional hexapeptides with the potential for pheromone activity. Sequence comparison, however, reveals that they have limited coding potential. Similar analyses of nine other completed genomes find Mup gene expansions in divergent lineages, including those of rat, horse and grey mouse lemur, occurring independently from a single ancestral Mup present in other placental mammals. Our findings illustrate that increasing genomic complexity of the Mup gene family is not evolutionarily isolated, but is instead a recurring mechanism of generating coding diversity consistent with a species-specific function in mammals.
doi:10.1371/journal.pone.0003280
PMCID: PMC2533699  PMID: 18815613
14.  Olfactory mucosa-expressed organic anion transporter, Oat6, manifests high affinity interactions with odorant organic anions 
We have characterized the expression of organic anion transporter 6, Oat6 (slc22a20), in olfactory mucosa, as well as its interaction with several odorant organic anions. In situ hybridization reveals diffuse Oat6 expression throughout olfactory epithelium, yet olfactory neurons laser-capture microdissected from either the main olfactory epithelium (MOE) or the vomeronasal organ (VNO) did not express Oat6 mRNA. These data suggest that Oat6 is expressed in non-neuronal cells of olfactory tissue, such as epithelial and/or other supporting cells. We next investigated interaction of Oat6 with several small organic anions that have previously been identified as odortype components in mouse urine. We find that each of these compounds, propionate, 2- and 3-methylbutyrate, benzoate, heptanoate and 2-ethylhexanoate, inhibits Oat6-mediated uptake of a labeled tracer, estrone sulfate, consistent with their being Oat6 substrates. Previously, we noted defects in the renal elimination of odortype and odortype-like molecules in Oat1 knockout mice. The finding that such molecules interact with Oat6 raises the possibility that odorants secreted into the urine through one OAT-mediated mechanism are transported through the olfactory mucosa through another OAT-mediated mechanism. Oat6 might play a direct or indirect role in olfaction, such as modulation of the availability of odorant organic anions at the mucosal surface for presentation to olfactory neurons or facilitation of delivery to a distal site of chemosensation, among other possibilities that we discuss.
doi:10.1016/j.bbrc.2006.10.136
PMCID: PMC1810587  PMID: 17094945
Organic Anion Transporter; Oat; Slc22a20; olfactory mucosa; volatile organic acid; odorant
15.  Genome-wide Generation and Systematic Phenotyping of Knockout Mice Reveals New Roles for Many Genes 
Cell  2013;154(2):452-464.
Summary
Mutations in whole organisms are powerful ways of interrogating gene function in a realistic context. We describe a program, the Sanger Institute Mouse Genetics Project, that provides a step toward the aim of knocking out all genes and screening each line for a broad range of traits. We found that hitherto unpublished genes were as likely to reveal phenotypes as known genes, suggesting that novel genes represent a rich resource for investigating the molecular basis of disease. We found many unexpected phenotypes detected only because we screened for them, emphasizing the value of screening all mutants for a wide range of traits. Haploinsufficiency and pleiotropy were both surprisingly common. Forty-two percent of genes were essential for viability, and these were less likely to have a paralog and more likely to contribute to a protein complex than other genes. Phenotypic data and more than 900 mutants are openly available for further analysis.
PaperClip
Graphical Abstract
Highlights
•Large openly available resource of targeted mouse mutants and phenotypic data•Screen for broad range of disease features and traits•Many novel phenotypes suggest functions for both studied and unstudied genes•Haploinsufficiency and pleiotropy are common
More than 900 new mutant mice lines and a multifaceted phenotypic screening platform reveal unanticipated pleiotropies, widespread effects of haploinsufficiency, potential disease models, and functions for unstudied genes.
doi:10.1016/j.cell.2013.06.022
PMCID: PMC3717207  PMID: 23870131
16.  Disruption of Mouse Cenpj, a Regulator of Centriole Biogenesis, Phenocopies Seckel Syndrome 
PLoS Genetics  2012;8(11):e1003022.
Disruption of the centromere protein J gene, CENPJ (CPAP, MCPH6, SCKL4), which is a highly conserved and ubiquitiously expressed centrosomal protein, has been associated with primary microcephaly and the microcephalic primordial dwarfism disorder Seckel syndrome. The mechanism by which disruption of CENPJ causes the proportionate, primordial growth failure that is characteristic of Seckel syndrome is unknown. By generating a hypomorphic allele of Cenpj, we have developed a mouse (Cenpjtm/tm) that recapitulates many of the clinical features of Seckel syndrome, including intrauterine dwarfism, microcephaly with memory impairment, ossification defects, and ocular and skeletal abnormalities, thus providing clear confirmation that specific mutations of CENPJ can cause Seckel syndrome. Immunohistochemistry revealed increased levels of DNA damage and apoptosis throughout Cenpjtm/tm embryos and adult mice showed an elevated frequency of micronucleus induction, suggesting that Cenpj-deficiency results in genomic instability. Notably, however, genomic instability was not the result of defective ATR-dependent DNA damage signaling, as is the case for the majority of genes associated with Seckel syndrome. Instead, Cenpjtm/tm embryonic fibroblasts exhibited irregular centriole and centrosome numbers and mono- and multipolar spindles, and many were near-tetraploid with numerical and structural chromosomal abnormalities when compared to passage-matched wild-type cells. Increased cell death due to mitotic failure during embryonic development is likely to contribute to the proportionate dwarfism that is associated with CENPJ-Seckel syndrome.
Author Summary
Mutation of the gene CENPJ has been found to cause primary microcephaly, an inherited disorder that is characterised by severely reduced brain size. More recently, mutation of CENPJ has been associated with Seckel syndrome, a disorder that is characterised by a severe reduction in both brain and body size that is apparent at birth, mental retardation, and skeletal abnormalities, in addition to a number of other clinical manifestations. Here, we have generated a mouse that expresses only low levels of mouse Cenpj protein and find that it recapitulates many of the key features of Seckel syndrome. Moreover, we find that errors during the proliferation of Cenpjtm/tm cells frequently lead to abnormal numbers of chromosomes or damaged chromosomes, which is likely to be the cause of increased cell death during embryonic development and to contribute to the proportionate dwarfism that is characteristic of Seckel syndrome.
doi:10.1371/journal.pgen.1003022
PMCID: PMC3499256  PMID: 23166506
17.  Modeling Partial Monosomy for Human Chromosome 21q11.2-q21.1 Reveals Haploinsufficient Genes Influencing Behavior and Fat Deposition 
PLoS ONE  2012;7(1):e29681.
Haploinsufficiency of part of human chromosome 21 results in a rare condition known as Monosomy 21. This disease displays a variety of clinical phenotypes, including intellectual disability, craniofacial dysmorphology, skeletal and cardiac abnormalities, and respiratory complications. To search for dosage-sensitive genes involved in this disorder, we used chromosome engineering to generate a mouse model carrying a deletion of the Lipi–Usp25 interval, syntenic with 21q11.2-q21.1 in humans. Haploinsufficiency for the 6 genes in this interval resulted in no gross morphological defects and behavioral analysis performed using an open field test, a test of anxiety, and tests for social interaction were normal in monosomic mice. Monosomic mice did, however, display impaired memory retention compared to control animals. Moreover, when fed a high-fat diet (HFD) monosomic mice exhibited a significant increase in fat mass/fat percentage estimate compared with controls, severe fatty changes in their livers, and thickened subcutaneous fat. Thus, genes within the Lipi–Usp25 interval may participate in memory retention and in the regulation of fat deposition.
doi:10.1371/journal.pone.0029681
PMCID: PMC3262805  PMID: 22276124

Results 1-17 (17)