Reelin regulates neuronal positioning in cortical brain structures and neuronal migration via binding to the lipoprotein receptors Vldlr and Lrp8. Reeler mutant mice display severe brain morphological defects and behavioral abnormalities. Several reports have implicated reelin signaling in the etiology of neurodevelopmental and psychiatric disorders, including autism, schizophrenia, bipolar disorder, and depression. Moreover, it has been reported that VLDLR mRNA levels are increased in the post-mortem brain of autistic patients.
We generated transgenic (Tg) rats overexpressing Vldlr, and examined their histological and behavioral features.
Spontaneous locomotor activity was significantly increased in Tg rats, without detectable changes in brain histology. Additionally, Tg rats tended to show performance deficits in the radial maze task, suggesting that their spatial working memory was slightly impaired. Thus, Vldlr levels may be involved in determining locomotor activity and memory function.
Unlike reeler mice, patients with neurodevelopmental or psychiatric disorders do not show striking neuroanatomical aberrations. Therefore, it is notable, from a clinical point of view, that we observed behavioral phenotypes in Vldlr-Tg rats in the absence of neuroanatomical abnormalities.
Hyperactivity; Neurodevelopmental disorder; Psychiatric disorder; Reelin; Transgenic rat; Vldlr
The neurobiological basis of autism remains poorly understood. The diagnosis of autism is based solely on behavioural characteristics because there are currently no reliable biological markers. To test whether the anterior pituitary hormones and cortisol could be useful as biological markers for autism, we assessed the basal serum levels of these hormones in subjects with autism and normal controls.
Using a suspension array system, we determined the serum levels of six anterior pituitary hormones, including adrenocorticotropic hormone and growth hormone, in 32 drug-naive subjects (aged 6 to 18 years, all boys) with autism, and 34 healthy controls matched for age and gender. We also determined cortisol levels in these subjects by enzyme-linked immunosorbent assay. Serum levels of adrenocorticotropic hormone, growth hormone and cortisol were significantly higher in subjects with autism than in controls. In addition, there was a significantly positive correlation between cortisol and adrenocorticotropic hormone levels in autism.
Our results suggest that increased basal serum levels of adrenocorticotropic hormone accompanied by increased cortisol and growth hormone may be useful biological markers for autism.
Multiple lines of evidence suggest a serotoninergic dysfunction in autism. The role of LMX1B in the development and maintenance of serotoninergic neurons is well known. In order to examine the role, if any, of LMX1B with autism pathophysiology, a trio-based SNP association study using 252 family samples from the AGRE was performed. Using pair-wise tagging method, 24 SNPs were selected from the HapMap data, based on their location and minor allele frequency. Two SNPs (rs10732392 and rs12336217) showed moderate association with autism with p values 0.018 and 0.022 respectively in transmission disequilibrium test. The haplotype AGCGTG also showed significant association (p = 0.008). Further, LMX1B mRNA expressions were studied in the postmortem brain tissues of autism subjects and healthy controls samples. LMX1B transcripts was found to be significantly lower in the anterior cingulate gyrus region of autism patients compared with controls (p = 0.049). Our study suggests a possible role of LMX1B in the pathophysiology of autism. Based on previous reports, it is likely to be mediated through a seretoninergic mechanism. This is the first report on the association of LMX1B with autism, though it should be viewed with some caution considering the modest associations we report.
Axon-guidance proteins play a crucial role in brain development. As the dysfunction of axon-guidance signaling is thought to underlie the microstructural abnormalities of the brain in people with autism, we examined the postmortem brains of people with autism to identify any changes in the expression of axon-guidance proteins.
The mRNA and protein expression of axon-guidance proteins, including ephrin (EFN)A4, eEFNB3, plexin (PLXN)A4, roundabout 2 (ROBO)2 and ROBO3, were examined in the anterior cingulate cortex and primary motor cortex of autistic brains (n = 8 and n = 7, respectively) and control brains (n = 13 and n = 8, respectively) using real-time reverse-transcriptase PCR (RT-PCR) and western blotting. Real-time RT-PCR revealed that the relative expression levels of EFNB3, PLXNA4A and ROBO2 were significantly lower in the autistic group than in the control group. The protein levels of these three genes were further analyzed by western blotting, which showed that the immunoreactive values for PLXNA4 and ROBO2, but not for EFNB3, were significantly reduced in the ACC of the autistic brains compared with control brains.
In this study, we found decreased expression of axon-guidance proteins such as PLXNA4 and ROBO2 in the brains of people with autism, and suggest that dysfunctional axon-guidance protein expression may play an important role in the pathophysiology of autism.
Accumulating evidence suggests that dysregulation of the immune system is
involved in the pathophysiology of autism spectrum disorders (ASD). The aim
of the study was to explore immunological markers in peripheral plasma
samples from non-medicated subjects with high-functioning ASD.
A multiplex assay for cytokines and chemokines was applied to plasma samples
from male subjects with high-functioning ASD (n = 28)
and matched controls (n = 28). Among a total of 48
analytes examined, the plasma concentrations of IL-1β, IL-1RA, IL-5,
IL-8, IL-12(p70), IL-13, IL-17 and GRO-α were significantly higher in
subjects with ASD compared with the corresponding values of matched controls
after correction for multiple comparisons.
The results suggest that abnormal immune responses as assessed by multiplex
analysis of cytokines may serve as one of the biological
trait markers for ASD.
Non-motor symptoms (e.g., depression, anxiety, and cognitive deficits) in patients with Parkinson disease (PD) precede the onset of the motor symptoms. Although these symptoms do not respond to pharmacological dopamine replacement therapy, their precise pathological mechanisms are currently unclear. The present study was undertaken to examine whether the unilateral 6-hydroxydopamine (6-OHDA) lesion to the substantia nigra pars compacta (SNc), which represents a model of long-term dopaminergic neurotoxicity, could affect cell proliferation in the adult rat brain. Furthermore, we examined the effects of the selective serotonin reuptake inhibitor (SSRI) fluoxetine and the selective noradrenaline reuptake inhibitor maprotiline on the reduction in cell proliferation in the subgranular zone (SGZ) by the unilateral 6-OHDA lesion.
A single unilateral injection of 6-OHDA into the rat SNc resulted in an almost complete loss of tyrosine hydroxylase (TH) immunoreactivity in the striatum and SNc, as well as in reductions of TH-positive cells and fibers in the ventral tegmental area (VTA). On the other hand, an injection of vehicle alone showed no overt change in TH immunoreactivity. A unilateral 6-OHDA lesion to SNc significantly decreased cell proliferation in the SGZ ipsilateral to the 6-OHDA lesion, but not in the contralateral SGZ or the subventricular zone (SVZ), of rats. Furthermore, subchronic (14 days) administration of fluoxetine (5 mg/kg/day), but not maprotiline significantly attenuated the reduction in cell proliferation in the SGZ by unilateral 6-OHDA lesion.
The present study suggests that cell proliferation in the SGZ of the dentate gyrus might be, in part, under dopaminergic control by SNc and VTA, and that subchronic administration of fluoxetine reversed the reduction in cell proliferation in the SGZ by 6-OHDA. Therefore, SSRIs such as fluoxetine might be potential therapeutic drugs for non-motor symptoms as well as motor symptoms in patients with PD, which might be associated with the reduction in cell proliferation in the SGZ.
Vacuolar-type ATPases (V-ATPases) exist in various cellular membranes of many organisms to regulate physiological processes by controlling the acidic environment. Here, we have determined the crystal structure of the A3B3 subcomplex of V-ATPase at 2.8 Å resolution. The overall construction of the A3B3 subcomplex is significantly different from that of the α3β3 sub-domain in FoF1-ATP synthase, because of the presence of a protruding ‘bulge' domain feature in the catalytic A subunits. The A3B3 subcomplex structure provides the first molecular insight at the catalytic and non-catalytic interfaces, which was not possible in the structures of the separate subunits alone. Specifically, in the non-catalytic interface, the B subunit seems to be incapable of binding ATP, which is a marked difference from the situation indicated by the structure of the FoF1-ATP synthase. In the catalytic interface, our mutational analysis, on the basis of the A3B3 structure, has highlighted the presence of a cluster composed of key hydrophobic residues, which are essential for ATP hydrolysis by V-ATPases.
crystal structure; FoF1; proton pump; rotary motor; V-ATPase
Obstetric complications have been regarded as a risk factor for schizophrenia later in life. One of the mechanisms underlying the association is postulated to be a hypoxic process in the brain in the offspring around the time of birth. Hippocampus is one of the brain regions implicated in the late-onset dopaminergic dysfunction associated with hypoxic obstetric complications.
We used an animal model of perinatal asphyxia, in which rat pups were exposed to 15 min of intrauterine anoxia during Cesarean section birth. At 6 and 12 weeks after birth, the behavior of the pups was assessed using a methamphetamine-induced locomotion test. In addition, the histopathology of the hippocampus was examined by means of stereology. At 6 weeks, there was no change in the methamphetamine-induced locomotion. However, at 12 weeks of age, we found an elevation in methamphetamine-induced locomotor activity, which was associated with an increase of dopamine release in the nucleus accumbens. At the same age, we also found a reduction of the dentate granule cells of the hippocampus.
These results suggest that the dopaminergic dysregulation after perinatal asphyxia is associated with a reduction in hippocampal dentate granule cells, and this may partly contribute to the pathogenesis of schizophrenia.
Accumulation of amyloid-β peptide (Aβ) in the brain is closely associated with cognitive decline in Alzheimer's disease (AD). Stereotaxic infusion of neprilysin-encoding viral vectors into the hippocampus has been shown to decrease Aβ in AD-model mice, but more efficient and global delivery is necessary to treat the broadly distributed burden in AD. Here we developed an adeno-associated virus (AAV) vector capable of providing neuronal gene expression throughout the brains after peripheral administration. A single intracardiac administration of the vector carrying neprilysin gene in AD-model mice elevated neprilysin activity broadly in the brain, and reduced Aβ oligomers, with concurrent alleviation of abnormal learning and memory function and improvement of amyloid burden. The exogenous neprilysin was localized mainly in endosomes, thereby effectively excluding Aβ oligomers from the brain. AAV vector-mediated gene transfer may provide a therapeutic strategy for neurodegenerative diseases, where global transduction of a therapeutic gene into the brain is necessary.
Embryonic and fetal myocardial growth is characterized by a dramatic increase in myocyte number, but whether the expansion of the myocyte compartment is dictated by activation and commitment of resident cardiac stem cells (CSCs), division of immature myocytes or both is currently unknown.
In this study, we tested whether prenatal cardiac development is controlled by activation and differentiation of CSCs and whether division of c-kit-positive CSCs in the mouse heart is triggered by spontaneous Ca2+ oscillations.
We report that embryonic-fetal c-kit-positive CSCs are self-renewing, clonogenic and multipotent in vitro and in vivo. The growth and commitment of c-kit-positive CSCs is responsible for the generation of the myocyte progeny of the developing heart. The close correspondence between values computed by mathematical modeling and direct measurements of myocyte number at E9, E14, E19 and one day after birth strongly suggests that the organogenesis of the embryonic heart is dependent on a hierarchical model of cell differentiation regulated by resident CSCs. The growth promoting effects of c-kit-positive CSCs are triggered by spontaneous oscillations in intracellular Ca2+, mediated by IP3 receptor activation, which condition asymmetric stem cell division and myocyte lineage specification.
Myocyte formation derived from CSC differentiation is the major determinant of cardiac growth during development. Division of c-kit-positive CSCs in the mouse is promoted by spontaneous Ca2+ spikes, which dictate the pattern of stem cell replication and the generation of a myocyte progeny at all phases of prenatal life and up to one day after birth.
Cardiac stem cells; cardiac development; calcium waves; asymmetric cell division
Endomitosis and endoreplication are atypical modes of cell cycle that results in genome duplication in single nucleus. Because the cell size of given cell type is generally proportional to the nuclear DNA content, endoreplication and endomitosis are effective strategy of cell growth, which are widespread in multicellular organisms, especially those in plant kingdom. We found that these processes might be differently regulated by GIGAS CELL1 (GIG1) and its paralog UV-INSENSITIVE4 (UVI4) in Arabidopsis thaliana. GIG1 and UVI4 may negatively regulate activities of anaphase-promoting complex or cyclosome (APC/C) ubiquitin ligase that acts as an important mitotic regulator. The gig1 mutation induced ectopic occurrence of endomitosis during somatic cell division, while it has been reported that uvi4 mutation resulted in premature occurrence of endoreplication during organ development. Overexpression of GIG1 and UVI4 dramatically increased the amount of mitotic cyclin, CYCB1;1, a well-known substrate of APC/C. Ectopic endomitosis in gig1 was enhanced by mutation in CYCB2;2 and suppressed by downregulation of APC10 encoding a core subunit of APC/C. Overexpression of CDC20.1, an activator protein of APC/C, further promoted the ectopic endomitosis in gig1. These findings suggest that endomitosis and endoreplication are regulated by similar molecular mechanisms, in which two related proteins, GIG1 and UVI4, may inhibit APC/C in different ways.
cell division; cyclin; endomitosis; endoreplication; ubiquitin ligase
We conducted 2 studies to determine whether dense and thin NCR schedules exert different influences over behavior and whether these influences change as dense schedules are thinned. In Study 1, we observed that thin as well as dense NCR schedules effectively decreased problem behavior exhibited by 3 individuals. In Study 2, we compared the effects of 2 NCR schedules in multielement designs, one with and the other without an extinction (EXT) component, while both schedules were thinned. Problem behavior remained low as the NCR schedule with EXT was thinned, but either (a) did not decrease initially or (b) subsequently increased as the NCR schedule without EXT was thinned. These results suggest that dense schedules of NCR decrease behavior by altering its motivating operation but that extinction occurs as the NCR schedule is thinned. The benefits and limitations of using dense or thin NCR schedules are discussed.
functional analysis; noncontingent reinforcement; self-injurious behavior; aggression; schedule effects; motivating operation; extinction
Some individuals with intellectual disabilities do not respond to praise as a reinforcer, which may limit their ability to learn. We evaluated 2 procedures (stimulus pairing and response–stimulus pairing), both of which involved pairing previously neutral praise statements with preferred edible items, to determine their usefulness in establishing praise as a reinforcer. Results of Study 1 indicated that stimulus pairing was not effective in conditioning praise as a reinforcer for 3 of 4 subjects; results were inconclusive for the 4th subject. Results of Study 2 indicated that response–stimulus pairing was effective in conditioning praise as a reinforcer for 4 of 8 subjects. After conditioning, praise also increased the occurrence of additional target responses for these 4 subjects.
conditioned reinforcement; praise; social reinforcement
We examined the effects of several variations in response rate on the calculation of total, interval, exact-agreement, and proportional reliability indices. Trained observers recorded computer-generated data that appeared on a computer screen. In Study 1, target responses occurred at low, moderate, and high rates during separate sessions so that reliability results based on the four calculations could be compared across a range of values. Total reliability was uniformly high, interval reliability was spuriously high for high-rate responding, proportional reliability was somewhat lower for high-rate responding, and exact-agreement reliability was the lowest of the measures, especially for high-rate responding. In Study 2, we examined the separate effects of response rate per se, bursting, and end-of-interval responding. Response rate and bursting had little effect on reliability scores; however, the distribution of some responses at the end of intervals decreased interval reliability somewhat, proportional reliability noticeably, and exact-agreement reliability markedly.
interobserver agreement; reliability; response rate; response distribution
We evaluated an inexpensive, efficient, and noninvasive technique for measuring tissue damage produced by self-injurious behavior (SIB). The technique involved computerized measurement of wound surface area (WSA) based on digital photographs. In Study 1, we compared photographic measurement to a more commonly used procedure, transparency measurement, in estimating WSA of 20 wound models. Results showed that both methods were reliable and that there was a high degree of correspondence between the 2 sets of measures. In Study 2, we compared photographic WSA measures to direct-observation measures in documenting changes over time in the SIB exhibited by a woman with Prader-Willi syndrome. Results showed that increases and decreases in observed SIB during baseline and treatment conditions corresponded with changes in WSA measures, indicating that the computer-assisted photographic technique may be useful as a corroborative measure or as a primary measure when direct observation of SIB is not feasible.
differential reinforcement; functional analysis; injury measurement; self-injurious behavior
We compared the effects of 2 observer-training procedures. In vivo training involved practice during actual treatment sessions. Video training involved practice while watching progressively more complex simulations. Fifty-nine undergraduate students entered 1 of the 2 training conditions sequentially according to an ABABAB design. Results showed that the 2 training methods produced almost identical scores on a posttraining observational test; however, the video method required fewer training sessions to complete.
observer training; measurement; reliability; video instruction
We conducted 2 studies on reinforcer preference in patients with dementia. Results of preference assessments yielded differential selections by 14 participants. Unlike prior studies with individuals with intellectual disabilities, all participants showed a noticeable preference for leisure items over edible items. Results of a subsequent analysis with 3 participants showed reinforcement effects when highly preferred items were delivered as consequences.
Alzheimer's disease; dementia; preference assessment
To evaluate the involvement of the mitogen-activated protein kinase (MAPK) cascade in orofacial neuropathic pain mechanisms, this study assessed nocifensive behavior evoked by mechanical or thermal stimulation of the whisker pad skin, phosphorylation of extracellular signal-regulated kinase (ERK) in trigeminal spinal subnucleus caudalis (Vc) neurons, and Vc neuronal responses to mechanical or thermal stimulation of the whisker pad skin in rats with the chronic constriction nerve injury of the infraorbital nerve (ION-CCI). The mechanical and thermal nocifensive behavior was significantly enhanced on the side ipsilateral to the ION-CCI compared to the contralateral whisker pad or sham rats. ION-CCI rats had an increased number of phosphorylated ERK immunoreactive (pERK-IR) cells which also manifested NeuN-IR but not GFAP-IR and Iba1-IR, and were significantly more in ION-CCI rats compared with sham rats following noxious but not non-noxious mechanical stimulation. After intrathecal administration of the MEK1 inhibitor PD98059 in ION-CCI rats, the number of pERK-IR cells after noxious stimulation and the enhanced thermal nocifensive behavior but not the mechanical nocifensive behavior were significantly reduced in ION-CCI rats. The enhanced background activities, afterdischarges and responses of wide dynamic range neurons to noxious mechanical and thermal stimulation in ION-CCI rats were significantly depressed following i.t. administration of PD98059, whereas responses to non-noxious mechanical and thermal stimulation were not altered. The present findings suggest that pERK-IR neurons in the Vc play a pivotal role in the development of thermal hypersensitivity in the face following trigeminal nerve injury.
Campylobacter jejuni is the most common bacterium that causes diarrhea worldwide, and chickens are considered the main reservoir of this pathogen. This study investigated the effects of serial truncation of lipooligosaccharide (LOS), a major component of the outer membrane of C. jejuni, on its bile resistance and intestinal colonization ability in chickens. Genes encoding manno-heptose synthetases or glycosyltransferases were inactivated to generate isogenic mutants. Serial truncation of the LOS core oligosaccharide caused a stepwise increase in susceptibilities of two C. jejuni strains, NCTC 11168 and 81-176, to bile acids. Inactivation of hldE, hldD, or waaC caused severe truncation of the core oligosaccharide, which greatly increased the susceptibility to bile acids. Both wild-type strains grew normally in chicken intestinal extracts, whereas the mutants with severe oligosaccharide truncation were not detected 12 h after inoculation. These mutants attained viable bacterial counts in the bile acid-free extracts 24 h after inoculation. The wild-type strain 11-164 was present in the cecal contents at >107 CFU/g on 5 days after challenge infection and after this time period, whereas its hldD mutant was present at <103 CFU/g throughout the experimental period. Trans-complementation of the hldD mutant with the wild-type hldD allele completely restored the in vivo colonization level to that of the wild-type strain. Mutants with a shorter LOS had higher hydrophobicities. Thus, the length of the LOS core oligosaccharide affected the surface hydrophobicity and bile resistance of C. jejuni as well as its ability to colonize chicken intestines.
Archaeosine (G+) is found at position 15 of many archaeal tRNAs. In Euryarchaeota, the G+ precursor, 7-cyano-7-deazaguanine (preQ0), is inserted into tRNA by tRNA-guanine transglycosylase (arcTGT) before conversion into G+ by ARChaeosine Synthase (ArcS). However, many Crenarchaeota known to harbor G+ lack ArcS homologs. Using comparative genomics approaches, two families that could functionally replace ArcS in these organisms were identified: 1) GAT-QueC, a two-domain family with an N-terminal glutamine amidotransferase class-II domain fused to a domain homologous to QueC, the enzyme that produces preQ0; 2) QueF-like, a family homologous to the bacterial enzyme catalyzing the reduction of preQ0 to 7-aminomethyl-7-deazaguanine. Here we show that these two protein families are able to catalyze the formation of G+ in a heterologous system. Structure and sequence comparisons of crenarchaeal and euryarchaeal arcTGTs suggest the crenarchaeal enzymes have broader substrate specificity. These results led to a new model for the synthesis and salvage of G+ in Crenarchaeota.
Peripheral stalk subunits of eukaryotic or mammalian vacuolar ATPases (V-ATPases) play key roles in regulating its assembly and disassembly. In a previous study, we purified several subunits and their isoforms of the peripheral stalk region of Homo sapiens (human) V-ATPase; such as C1, E1G1, H, and the N-terminal cytoplasmic region of Vo, a1. Here, we investigated the in vitro binding interactions of the subunits at the stalk region and measured their specific affinities. Surface plasmon resonance experiments revealed that the subunit C1 binds the E1G1 heterodimer with both high and low affinities (2.8 nM and 1.9 µM, respectively). In addition, an E1G1-H complex can be formed with high affinity (48 nM), whereas affinities of other subunit pairs appeared to be low (∼0.21−3.0 µM). The putative ternary complex of C1-H-E1G1 was not much strong on co-incubation of these subunits, indicating that the two strong complexes of C1-E1G1 and H-E1G1 in cooperation with many other weak interactions may be sufficiently strong enough to withstand the torque of rotation during catalysis. We observed a partially stable quaternary complex (consisting of E1G1, C1, a1NT, and H subunits) resulting from discrete peripheral subunit interactions stabilizing the complex through their intrinsic affinities. No binding was observed in the absence of E1G1 (using only H, C1, and a1NT); therefore, it is likely that, in vivo, the E1G1 heterodimer has a significant role in the initiation of subunit assembly. Multiple interactions of variable affinity in the stalk region may be important to the mechanism of reversible dissociation of the intact V-ATPase.
Targeted gene deletion is now available for molecular genetic research of dermatophytes, and the physiological roles of several genes have been elucidated. However, this method cannot be applied to essential genes, which can be potential drug targets. To overcome this limitation, we have developed a conditional gene knockdown system using a copper-responsive promoter. The promoter sequence of the copper transporter gene CTR4 (PCTR4) and that of the copper efflux pump gene CRP1 (PCRP1) derived from Trichophyton rubrum were examined for their response to copper in Arthroderma vanbreuseghemii. PCTR4 was demonstrated to repress expression of a reporter gene in the presence of copper, while the activity of PCRP1 was induced by addition of copper. Importantly, PCTR4 regulated the gene expression more tightly. Furthermore, when PCTR4 was applied to regulate the expression of the endogenous genes ERG1 and TRP5, their conditional mutants exhibited decreased growth activity under the repressive conditions. These results suggest that the PCTR4-based gene regulation system represents a powerful tool for identification and characterization of a broad range of genes, including essential genes, in dermatophytes.
The usefulness of endoscope-assisted microsurgical removal of vestibular schwannomas in the internal auditory canal (IAC) was evaluated. Microsurgical removal using the endoscope was done in 28 procedures and microsurgical removal without an endoscope was done in 43 procedures. A retrosigmoid approach was used. The tumor location in the IAC was classified as grade 1 (located up to the mid-portion), 2, 3, or 4 (located up to the fundus with bony destruction) according to the tumor extent, and residual tumor in the IAC was evaluated as grade A (remnant tumor was not observed), B, C, or D (remnant tumor was observed over the mid-portion) according to the extent of remnant tumor. The residual tumor in the IAC was less in the endoscope-assisted group than in the microsurgery group. There was a significant difference only in grade 2, that is, tumor located beyond the mid-portion of the IAC. There was no significant difference in the results of preservation of useful hearing, facial nerve function, and tumor recurrence between the two groups. The benefit of endoscope-assistance microsurgery was shown for those patients whose tumors extended beyond the mid-portion of the IAC but did not reach the fundus.
vestibular schwannoma; endoscopy; retrosigmoid approach; internal auditory canal
Cytochrome P450 CYP2 family enzymes are important in a variety of physiological and toxicological processes. CYP2 genes are highly diverse and orthologous relationships remain clouded among CYP2s in different taxa. Sequence and expression analyses of CYP2 genes in diapsids including birds and reptiles may improve understanding of this CYP family. We sought CYP2 genes in a liver cDNA library of the common cormorant (Phalacrocorax carbo), and in the genomes of other diapsids, chicken (Gallus gallus), zebra finch (Taeniopygia guttata), and anole lizard (Anolis carolinensis), for phylogenetic and/or syntenic analyses. Screening of the cDNA library yielded four CYP2 cDNA clones that were phylogenetically classified as CYP2C45, CYP2J25, CYP2AC1, and CYP2AF1. There are numerous newly identified diapsid CYP2 genes that include genes related to the human CYP2Cs, CYP2D6, CYP2G2P, CYP2J2, CYP2R1, CYP2U1, CYP2W1, CYP2AB1P, and CYP2AC1P. Syntenic relationships show that avian CYP2Hs are orthologous to CYP2C62P in humans, CYP2C23 in rats, and Cyp2c44 in mice, and suggest that avian CYP2Hs, along with human CYP2C62P and mouse Cyp2c44, could be renamed as CYP2C23, based upon the nomenclature rules. Analysis of sequence and synteny identifies cormorant and finch CYPs that are apparent orthologs of phenobarbital-inducible chicken CYP2C45. Transcripts of all four cormorant CYP2 genes were detected in the liver of birds from Lake Biwa, Japan. The transcript levels bore no significant relationship to levels of chlorinated organic pollutants in the liver, including polychlorinated biphenyls and dichlorodiphenyltrichloroethane and its metabolites. In contrast, concentrations of perfluorooctane sulfonate and perfluorononanoic acid were negatively correlated with levels of CYP2C45 and/or CYP2J25, suggesting down-regulation of expression by these environmental pollutants. This study expands our view of the phylogeny and evolution of CYP2s, and provides evolutionary insight into the chemical regulation of CYP2 gene expression in diapsids including birds.
Anole lizard; Chicken; Common (great) cormorant; CYP2; Cytochrome P450; Diapsid; Zebra finch
Genomic selection is an effective tool for animal and plant breeding, allowing effective individual selection without phenotypic records through the prediction of genomic breeding value (GBV). To date, genomic selection has focused on a single trait. However, actual breeding often targets multiple correlated traits, and, therefore, joint analysis taking into consideration the correlation between traits, which might result in more accurate GBV prediction than analyzing each trait separately, is suitable for multi-trait genomic selection. This would require an extension of the prediction model for single-trait GBV to multi-trait case. As the computational burden of multi-trait analysis is even higher than that of single-trait analysis, an effective computational method for constructing a multi-trait prediction model is also needed.
We described a Bayesian regression model incorporating variable selection for jointly predicting GBVs of multiple traits and devised both an MCMC iteration and variational approximation for Bayesian estimation of parameters in this multi-trait model. The proposed Bayesian procedures with MCMC iteration and variational approximation were referred to as MCBayes and varBayes, respectively. Using simulated datasets of SNP genotypes and phenotypes for three traits with high and low heritabilities, we compared the accuracy in predicting GBVs between multi-trait and single-trait analyses as well as between MCBayes and varBayes. The results showed that, compared to single-trait analysis, multi-trait analysis enabled much more accurate GBV prediction for low-heritability traits correlated with high-heritability traits, by utilizing the correlation structure between traits, while the prediction accuracy for uncorrelated low-heritability traits was comparable or less with multi-trait analysis in comparison with single-trait analysis depending on the setting for prior probability that a SNP has zero effect. Although the prediction accuracy with varBayes was generally lower than with MCBayes, the loss in accuracy was slight. The computational time was greatly reduced with varBayes.
In genomic selection for multiple correlated traits, multi-trait analysis was more beneficial than single-trait analysis and varBayes was much advantageous over MCBayes in computational time, which would outweigh the loss of prediction accuracy caused by the approximation procedure, and is thus considered a practical method of choice.
Genomic selection; Multiple traits; Bayesian regression; MCMC iteration; Variational approximation