Genetic diversity and structure in the Sado captive population of the Japanese crested ibis.

The Japanese crested ibis Nipponia nippon is a critically threatened bird. We assessed genetic diversity and structure in the Sado captive population of the Japanese crested ibis based on 24 and 50 microsatellite markers developed respectively for the same and related species. Of a total of 74 loci, 19 showed polymorphisms in the five founder birds of the population, and therefore were useful for the analysis of genetic diversity and structure. Genetic diversity measures, A, ne, He, Hoand PIC, obtained by genotyping of the 138 descendants were similar to those of other species with population bottlenecks, and thus considerably low. The low level of genetic diversity resulting from such bottlenecks was consistent with the results of lower genetic diversity measures for the Sado captive relative to the Chinese population that is the source population for the Sado group as determined using previously reported data and heterozygosity excess by Hardy-Weinberg equilibrium tests. Further, individual clustering based on the allele-sharing distance and Bayesian model-based clustering revealed that the founder genomes were equally at population in total, and with various admixture patterns at individual levels inherited by the descendants. The clustering results, together with the result of inheritance of all alleles of the microsatellites from the founders to descendants, suggest that planned mating in captive-breeding programs for the population has succeeded in maintaining genetic diversity and minimizing kinship. In addition, the Bayesian model-based clustering assumed two different components of genomes in the Sado captive Japanese crested ibis, supporting a considerably low level of genetic diversity.

Dexmedetomidine and clonidine inhibit ventricular tachyarrhythmias in a rabbit model of acquired long QT syndrome.

BACKGROUND: Agents with α-2 adrenoreceptor (AR) agonistic action have reportedly suppressed tachyarrhythmias. METHODS AND RESULTS: We hypothesized that α-2 AR agonists would have an inhibitory effect on abnormal repolarization-related ventricular tachyarrhythmias (VTs). To test this hypothesis, the effects of 2 clinically available α-2 AR agonists (dexmedetomidine and clonidine) on the occurrence of VTs were assessed in a methoxamine-sensitized rabbit model of acquired long QT syndrome (Study 1: n=45). In control rabbits, administration of methoxamine and nifekalant almost invariably caused VTs (14/15). In contrast, incidence of VT significantly decreased during the treatment with dexmedetomidine (1µg·kg(-1)·min(-1): 5/12 [P<0.01 vs. control]) or with clonidine (33.3µg·kg(-1)·min(-1): 10/18 [P<0.01]). To verify that VTs in this animal model are triggered by early afterdepolarization (EAD), the monophasic action potential on the left ventricular surface was recorded in 28 open-chest rabbits (Study 2). EAD-like hump was less frequently detected during treatment with clonidine or dexmedetomidine (2/14) than in saline-treated rabbits (9/10, P<0.005). Presence of a hump was significantly related to the advent of VTs (P<0.05). CONCLUSIONS: Agents with α-2 AR agonistic action have an inhibitory effect on VTs in a rabbit model of long QT syndrome. Alpha-2 AR agonists, especially dexmedetomidine, may be a therapeutic choice for abnormal repolarization-related VTs that are resistant to conventional treatment.

Deep anesthesia suppresses ventricular tachyarrhythmias in rabbit model of the acquired long QT syndrome.

BACKGROUND: Anesthesia sometimes suppresses ventricular tachyarrhythmias (VT) resistant to conventional pharmacological treatment. METHODS AND RESULTS: To know (1) whether deep anesthesia inhibits abnormal repolarization-related VT and (2) if α2-adrenoreceptor (AR) agonistic action is associated with the antiarrhythmic effect of anesthetics, the incidence of VT in a rabbit model of acquired long QT syndrome using different anesthetic regimen was assessed. In Study 1 (n = 30), 15 rabbits were lightly anesthetized with ketamine (123 ± 46 mg/kg) and an α2-AR agonist, xylazine (9.4±3.0mg/kg), while combination of these anesthetics at high doses were used in the other 15 rabbits (343 ± 78 mg/kg and 38.9 ± 3.0 mg/kg). Administration of α1-AR stimulant, methoxamine and nifekalant (Ikr blocker) caused VT in all lightly anesthetized rabbits. In contrast, VT was observed only in 1 of the 15 deeply anesthetized rabbits (P < 0.01). In Study 2 (n = 15), 10 rabbits were anesthetized with high-dose ketamine and low-dose xylazine. In the other 5 rabbits, low-dose ketamine and high-dose xylazine were used. QTc interval in the latter was longer than that of the former (399 ± 56 ms vs. 494 ± 57 ms, P < 0.01). Although no VT appeared in high/low-rabbits, VT occurred in 3 out of 5 low/high-rabbits (P < 0.05). CONCLUSIONS: These results suggest that (1) deep anesthesia suppresses abnormal repolarization-related VT and (2) antiarrhythmic effect of anesthesia on this type of VT is not dependent on α2-AR agonistic action.

Genetic diversity and phylogeny of the endangered Okinawa Rail, Gallirallus okinawae.

Genetic diversity of the wild population of the endangered Okinawa Rail, Gallirallus okinawae, was revealed by analyzing haplotypes in the mitochondrial control region for 177 individuals. We found 6 haplotypes with nucleotide differences at 6 sites. The four major haplotypes, Type 1 to Type 4, were present in 121 (68.4%), 21 (11.9%), 8 (4.5%) and 25 individuals (14.1%), respectively. Type 5 and Type 6 were each found in one individual. The gene diversity (h) and nucleotide diversity (pi) of Okinawa Rail were calculated to be 0.499 +/- 0.040 and 0.00146 +/- 0.00098, respectively. Gene diversity in Okinawa Rail is higher than that found in other endangered avian species, but the relative nucleotide diversity is lower due to few nucleotide differences among the haplotypes. Our sample of 177 individuals represents 20-25% of the total population, and thus allows a rigorous estimate of the population structure of Okinawa Rail, and makes it unlikely that more haplotypes would be found with additional sampling. The low nucleotide diversity in the control region may indicate that Okinawa Rail has gone through a recent bottleneck. The minimal span network of haplotypes, and the distribution pattern of sampled individuals, indicate that the number of birds with rare haplotypes, Type 5 and 6, decreased during the recent population decline caused by habitat loss and introduced predators. Our results are relevant to the current conservation program for the endangered Okinawa Rail, and perhaps for other species of flightless rails.

Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites.

The Palaeognathae comprise the flightless ratites and the volant tinamous, and together with the Neognathae constitute the extant members of class Aves. It is commonly believed that Palaeognathae originated in Gondwana since most of the living species are found in the Southern Hemisphere [1-3]. However, this hypothesis has been questioned because the fossil paleognaths are mostly from the Northern Hemisphere in their earliest time (Paleocene) and possessed many putative ancestral characters [4]. Uncertainties regarding the origin and evolution of Palaeognathae stem from the difficulty in estimating their divergence times [1, 2] and their remarkable morphological convergence. Here, we recovered nuclear genome fragments from extinct elephant birds, which enabled us to reconstruct a reliable phylogenomic time tree for the Palaeognathae. Based on the tree, we identified homoplasies in morphological traits of paleognaths and reconstructed their morphology-based phylogeny including fossil species without molecular data. In contrast to the prevailing theories, the fossil paleognaths from the Northern Hemisphere were placed as the basal lineages. Combined with our stable divergence time estimates that enabled a valid argument regarding the correlation with geological events, we propose a new evolutionary scenario that contradicts the traditional view. The ancestral Palaeognathae were volant, as estimated from their molecular evolutionary rates, and originated during the Late Cretaceous in the Northern Hemisphere. They migrated to the Southern Hemisphere and speciated explosively around the Cretaceous-Paleogene boundary. They then extended their distribution to the Gondwana-derived landmasses, such as New Zealand and Madagascar, by overseas dispersal. Gigantism subsequently occurred independently on each landmass.

Chemotherapy for advanced thymic carcinoma: clinical response to cisplatin, doxorubicin, vincristine, and cyclophosphamide (ADOC chemotherapy).

The role of systemic chemotherapy and optimal regimen in thymic carcinoma remains uncertain. We evaluated the clinical responsiveness of ADOC (cisplatin, doxorubicin, vincristine, and cyclophosphamide) chemotherapy for advanced thymic carcinoma that have distant metastatic or unresectable lesions. From 1996 to 2000, we treated eight cases of thymic carcinoma. According to the classification by Masaoka et al., the clinical stage in one case was IVa, whereas the others were IVb. Histologic subtypes were as follows: four cases were squamous cell carcinoma, two cases were undifferentiated, and two were small-cell carcinoma. All patients received 50 mg/m2 of cisplatin and 40 mg/m2 of doxorubicin intravenously on day 1, 0.6 mg/m2 of vincristine intravenously on day 3, and 700 mg/m2 of cyclophosphamide intravenously on day 4, ADOC regimen, respectively, at 3- to 4-week intervals. Six patients obtained a partial response after ADOC chemotherapy and the overall clinical response rate was 75%. There were no life-threatening side effects noted. Cisplatin plus VP-16 chemotherapy (PVP) was performed in three cases before the ADOC regimen, but PVP chemotherapy did not show beneficial effects in two patients. Median survival time was 19 months. ADOC chemotherapy appears to have significant activity against thymic carcinoma.

Structure and polymorphism of the major histocompatibility complex class II region in the Japanese Crested Ibis, Nipponia nippon.

The major histocompatibility complex (MHC) is a highly polymorphic genomic region that plays a central role in the immune system. Despite its functional consistency, the genomic structure of the MHC differs substantially among organisms. In birds, the MHC-B structures of Galliformes, including chickens, have been well characterized, but information about other avian MHCs remains sparse. The Japanese Crested Ibis (Nipponia nippon, Pelecaniformes) is an internationally conserved, critically threatened species. The current Japanese population of N. nippon originates from only five founders; thus, understanding the genetic diversity among these founders is critical for effective population management. Because of its high polymorphism and importance for disease resistance and other functions, the MHC has been an important focus in the conservation of endangered species. Here, we report the structure and polymorphism of the Japanese Crested Ibis MHC class II region. Screening of genomic libraries allowed the construction of three contigs representing different haplotypes of MHC class II regions. Characterization of genomic clones revealed that the MHC class II genomic structure of N. nippon was largely different from that of chicken. A pair of MHC-IIA and -IIB genes was arranged head-to-head between the COL11A2 and BRD2 genes. Gene order in N. nippon was more similar to that in humans than to that in chicken. The three haplotypes contained one to three copies of MHC-IIA/IIB gene pairs. Genotyping of the MHC class II region detected only three haplotypes among the five founders, suggesting that the genetic diversity of the current Japanese Crested Ibis population is extremely low. The structure of the MHC class II region presented here provides valuable insight for future studies on the evolution of the avian MHC and for conservation of the Japanese Crested Ibis.

Identification of novel genetic markers and evaluation of genetic structure in a population of Japanese crested ibis.

Japanese population of the Japanese crested ibis Nipponia nippon was founded by five individuals gifted from the People's Republic of China. In order to exactly evaluate genetic structure, we first performed development of novel genetic makers using 89 microsatellite primer pairs of related species for cross-amplification. Of these, only three primer pairs were useful for the genetic markers. Additionally, we sequenced allelic PCR products of these three markers together with 10 markers previously identified. Most markers showed typical microsatellite repeat units, but two markers were not simple microsatellites. Moreover, over half of the markers did not have the same repeat units as those of the original species. These results suggested that development of novel genetic markers in this population by cross-amplification is not efficient, partly because of low genetic diversity. Furthermore, the cluster analysis by STRUCTURE program using 17 markers showed that the five founders were divided into two clusters. However, the genetic relationships among the founders indicated by the clustering seemed to be questionable, because the analysis relied largely on a small number of triallelic markers, in spite of the addition of the three useful markers. Therefore, more efficient methods for identifying large numbers of single nucleotide polymorphisms are desirable.

Genome-wide SNP and STR discovery in the Japanese crested ibis and genetic diversity among founders of the Japanese population.

The Japanese crested ibis is an internationally conserved, critically threatened bird. Captive-breeding programs have been established to conserve this species in Japan. Since the current Japanese population of crested ibis originates only from 5 founders donated by the Chinese government, understanding the genetic diversity between them is critical for an effective population management. To discover genome-wide single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) while obtaining genotype data of these polymorphic markers in each founder, reduced representation libraries were independently prepared from each of the founder genomes and sequenced on an Illumina HiSeq2000. This yielded 316 million 101-bp reads. Consensus sequences were created by clustering sequence reads, and then sequence reads from each founder were mapped to the consensus sequences, resulting in the detection of 52,512 putative SNPs and 162 putative STRs. The numbers of haplotypes and STR alleles and the investigation of genetic similarities suggested that the total genetic diversity between the founders was lower, although we could not identify a pair with closely related genome sequences. This study provided important insight into protocols for genetic management of the captive breeding population of Japanese crested ibis in Japan and towards the national project for reintroduction of captive-bred individuals into the wild. We proposed a simple, efficient, and cost-effective approach for simultaneous detection of genome-wide polymorphic markers and their genotypes for species currently lacking a reference genome sequence.

The W- and Z-linked EE0.6 sequences used for molecular sexing of captive Japanese crested ibis on Sado Island.

The Japanese crested ibis Nipponia nippon is a critically threatened bird. Accurate sexing is necessary to perform effective management of captive breeding toward a national project for a tentative release of the Japanese crested ibis on Sado Island. A PCR-based sexing method targeting a 0.6 kb EcoRI fragment (EE0.6) sequence on W chromosome with AWS03 and USP3 primers has been developed for the Japanese crested ibis. However, the primers were selected from the EE0.6 sequences from bird species other than the Japanese crested ibis. In this study, we determined the W- and Z-linked EE0.6 sequences in the Japanese crested ibis, and clarified Japanese crested ibis sequence mismatch in the binding sites of the primers. Further, we found no polymorphism in the primer binding sites among five founder birds for the Sado captive Japanese crested ibis population. These findings validated the PCR-based sexing method with the AWS03 and USP3 as accurate molecular sexing methods of captive Japanese crested ibis on the Sado Island. Additionally, we designed a primer set for a novel PCR-based sexing, based on the EE0.6 sequences obtained in this study. This novel sexing method may be useful for future ecological research following the release of Japanese crested ibis on Sado Island. This is the first report to show the EE0.6 sequences in Japanese crested ibis.

Non-invasive sampling technique for DNA extraction from captive Japanese Crested Ibis on Sado Island.

The Japanese Crested Ibis Nipponia nippon is a critically threatened bird. The post-hatch eggs of the current captive population of this species on Sado Island have been stored at room temperature for the long-term. In this study, we investigated the suitability of the vascularized chorioallantois membrane from the eggs as a non-invasive DNA source. Using microsatellite loci developed for the Japanese Crested Ibis, we performed three experiments for comparison of genotypes obtained among DNA. First, DNA from five different sites of the identical membrane showed the same genotypes at either of two loci examined. Second, DNA from the membrane of each full-sibling birds and blood of their parents showed the genotypes that were consistent with Mendelian parent-offspring relationships at any of eight loci examined. Third, DNA from the membrane and blood of the same bird showed the matched genotypes at any of eight loci examined. These results indicate that the vascularized chorioallantois membrane from post-hatch eggs stored at room temperature for the long- term can be used as a reliable DNA source of offspring that had hatched from the egg. This study will promote a molecular genetics study on genetic diversity of the current captive Japanese Crested Ibis population on Sado Island.

Human atrial natriuretic peptide suppresses torsades de pointes in rabbits.

BACKGROUND: The increase in inward current, primarily L-type Ca2+ current, facilitates torsades de pointes (TdP). Because human atrial natriuretic peptide (ANP) moderates the L-type Ca2+ current, in our study it was hypothesized that ANP counteracts TdP. METHODS AND RESULTS: We tested the effect of ANP, guanosine 3', 5'-cyclic monophosphate analogue (8-bromo cGMP) and hydralazine on the occurrence of TdP in a rabbit model. In control rabbits, administration of methoxamine and nifekalant almost invariably caused TdP (14/15). In contrast, ANP (10 microg . kg(-1) . min(-1)) markedly abolished TdP (2/15), whereas hydralazine failed to show a comparable anti-arrhythmic action (10/15). TdP occurred only in 1 of 15 rabbits treated with 8-bromo cGMP. Presence of early afterdepolarization-like hump in the ventricular monophasic action potential was associated with the occurrence of TdP. CONCLUSION: Results suggest that ANP affects TdP in the rabbit model, and that this anti-arrhythmic effect of ANP is not necessarily shared by other vasodilating agents.