Genetic Analyses in the Japanese Captive Population of Japanese Crested Ibis (Nipponia nippon) using Pedigree Information.

The Japanese captive population of Japanese crested ibis (Nipponia nippon) was established using 5 founders derived from the Chinese captive population. Its size has increased rapidly, and the maintenance phase is about to start. Thus, this study was designed to perform genetic analyses in this population with pedigree information, considering the adoption of mean kinship strategy as the breeding strategy suited to the maintenance phase. Because the relationships among the 5 founders were unknown, different assumptions were set up ranging from 0 to 0.25 of kinship coefficients between the 5 founders. Assuming that the 5 founders were non-inbred in all the assumptions, the results showed that the gene diversity and the mean inbreeding coefficient would fluctuate largely from ∼65% to ∼82% and from ∼0.07 to ∼0.29, respectively. Moreover, the genetic importance of individuals based on mean kinship shifted largely. This study suggested that the Japanese captive population had low gene diversity and high mean inbreeding coefficient even under the assumption that the 5 founders were unrelated and non-inbred. In addition, the study also suggested that it became more effective to analyze the genetic status and to introduce mean kinship strategy into this population with more credible molecular evaluation of the relationships among founders.

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.

Proteomic analysis of Nipponia nippon (ID#162).

We investigated the proteome of a female Crested Ibis (Nipponia nippon, ID#162) that died on March 10, 2010 at the Sado Japanese Crested Ibis Conservation Center. Protein preparations from the brain, trachea, liver, heart, lung, proventriculus, muscular stomach, small intestine, duodenum, ovary and neck muscle were subjected to in-solution shotgun mass spectrometry (MS)/MS analyses using an LTQ Orbitrap XL mass spectrometer. A search of the National Center for Biotechnology Information Gallus gallus databases revealed 4253 GI (GenInfo Identifier) numbers with the sum of the same 11 tissues examined in the Crested Ibis. To interpret the obtained proteomics data, it was verified in detail with the data obtained from the brain of the Crested Ibis. It has been reported that drebrin A is specifically expressed in adult chicken brain. In the shotgun proteomic analyses of the Crested Ibis, we identified drebrin A as a brain-specific protein. Furthermore, Western blotting analysis of the protein preparations from 10 tissues of the Crested Ibis and 150-day-old hens using anti-drebrin antibodies showed intensive expression of approximately 110 kDa polypeptides of drebrin in both brains. We believe firmly that the present data will contribute to initial and fundamental steps toward understanding the Crested Ibis proteome.

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.

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.

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.

Influence of essential trace minerals and micronutrient insufficiencies on harmful metal overload in a Mongolian patient with multiple sclerosis.

Parkinson's disease and other neurological disorders are prevalent in Mongolia. Our previous studies revealed a significant correlation of these diseases with high oxidative stress due to a high body burden of harmful metals, such as manganese, iron, lead, cadmium, and aluminum. This report describes a 37-year-old male Mongolian patient with multiple sclerosis and essential micronutrient deficiency. This patient demonstrated high oxidative stress, as shown by high urinary 8-hydroxy-2'-deoxyguanosine levels of 14.7 and 14.3 ng/mg creatinine (crea), although his hair levels of these toxic metals were markedly lower than other Mongolians. In addition, this patient was deficient not only in various essential minerals, including selenium, magnesium, copper, cobalt, vanadium, and nickel, but also in micronutrients such as vitamin B6, C, E, folic acid, niacin, and ß-carotene. Furthermore, after taking 2,3-dimercaptosuccinic acid, a chelating agent, urinary excretion of lead, cadmium, manganese, aluminum, iron, copper, and lithium were increased 156-, 8.4-, 7.6-, 4.3-, 3.3-, 2.1-, and 2.1-fold, respectively. These results suggest that this patient suffered from a deficiency in micronutrients such as essential minerals and vitamins, which resulted in a disturbance in the ability to excrete harmful metals into the urine and hair. It is possible that a deficiency of micronutrients and a high burden of heavy metals play a role in the pathogenesis of multiple sclerosis. Nutritional treatment may be an effective approach to this disease.

Associations between dietary n-6 and n-3 fatty acids and arachidonic acid compositions in plasma and erythrocytes in young and elderly Japanese volunteers.

BACKGROUND: We reported that the compositions of arachidonic acid (ARA) in erythrocytes and plasma phospholipids (PL) in the elderly were lower than those in the young, though the ARA intake was nearly identical. OBJECTIVE: We further analyzed data in four study groups with different ages and sexes, and determined that the blood ARA levels were affected by the kinds of dietary fatty acids ingested. METHODS: One hundred and four healthy young and elderly volunteers were recruited. Dietary records together with photographic records from 28 consecutive days were reviewed and the fatty acid composition in plasma lipid fractions and erythrocyte PL was analyzed. RESULTS: No correlations for ARA between dietary fatty acids and blood lipid fractions were observed. A significant negative correlation between eicosapentaenoic acid (EPA) + docosahexaenoic acid (DHA) intake and ARA composition in erythrocyte PL was observed. ARA composition in erythrocyte PL was significantly lower in elderly subjects than in young subjects, because EPA and DHA intake in elderly subjects was higher than in young subjects. However, after removing the effect of dietary EPA+DHA intake, the ARA composition in erythrocyte PL in elderly subjects was significantly lower than that in young subjects. CONCLUSIONS: Changes in physical conditions with aging influenced the low ARA composition of erythrocyte in elderly subjects in addition to the effects of dietary EPA and DHA.

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.

A high accumulation of hair minerals in Mongolian people: 2(nd) report; influence of manganese, iron, lead, cadmium and aluminum to oxidative stress, Parkinsonism and arthritis.

UNLABELLED: It was previously reported that the hair of Mongolian people showed very high accumulation of manganese (Mn), which may increase oxidative stress. This study (2(nd) report), indicated that not only Mn but other minerals had also accumulated at high levels in hair. It describes the influence of these minerals on oxidative stress, Parkinson's disease-like symptom (Parkinsonism) and arthritis, these diseases being prevalent in Mongolia. METHODS: 299 subjects were enrolled (including 21; Parkinsonism and 25; arthritis) from Ulaanbaatar and 5 other areas in Mongolia. Oxidative stress was evaluated by measuring the level of urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG). The minerals accumulated in scalp hair were measured by the inductively coupled plasma mass spectrometry method. As a control, 81 healthy Japanese subjects were enrolled. RESULTS: Mongolian subjects showed high accumulated levels of Mn, iron, lead, cadmium and aluminum accumulations in hair, as compared with Japanese subjects. These levels were correlated with urinary 8-OHdG levels. The subjects with Parkinsonism and arthritis demonstrated higher levels in these minerals than healthy subjects. CONCLUSION: High accumulations of these minerals may increase oxidative stress in Mongolian people, and induce Parkinsonism and arthritis through the high oxidative stress. The high accumulations of these minerals may be induced by eating large amounts of sheep meat. In addition, sandy wind pollution may also contribute to it.

Relationship of dietary habits and obesity to oxidative stress in Palauan people: compared with Japanese and Mongolian people.

The Republic of Palau belongs to Micronesia, and obese people and lifestyle-related diseases are prevalent there. We investigated the relationship of dietary habits and obesity to oxidative stress in Palauan people, as compared with those of Japanese and Mongolian people. A total of 126 healthy Palauan subjects were enrolled. Oxidative stress was evaluated by serum level of reactive oxygen metabolites (ROM). Antioxidant capacity was evaluated by serum level of biological antioxidant potential (BAP). In Palauan subjects, BMI> or =30 was observed in 45.0% of males and 59.1% of females (Japanese: males 1.3%, females 0.8%, Mongolian: males 6.3%, females 14.7%). Palauan subjects consumed 2553 kcal per day (Japanese 2121 kcal, Mongolians 2534 kcal). The ratios of carbohydrate energy to total energy were 59.8 % (Japanese 54.7 %, Mongolians 50.2%). The ratios of fat energy to total energy were 22.9% (Japanese 26.7%, Mongolians 34.5%). ROM levels in Palauan subjects showed higher than those in Japanese subjects, while BAP levels of Palauan subjects did not decrease compared to those of Japanese. ROM levels correlated with body fat ratio, and showed a reverse correlation with handgrip strength. Handgrip strength decreased in the subjects of more than forty years of age. These findings suggest that the obesity in Palauan people may have a connection with high intake of calories through carbohydrate eating rather than through fat eating. Their high oxidative stress may be induced by obesity, and contribute to an early decline of handgrip strength, ultimately in early aging.

Diversity in genes responsible for lifestyle-related diseases in Asia-Pacific region.

In Asia-Pacific countries, both environmental modernization and hereditary traits of Mongoloid reported to cause rapid increase in lifestyle-related diseases (LRD). However, reproducibility of reported responsive-factors is low. To examine this, a decision-tree method of complexity-model was applied to select LRD-responsive-factors. Genomic DNA was collected from Asia-Pacific regions. Single nucleotide polymorphisms (SNPs) on genomic DNA were determined as hereditary-trait-factor. Three indices of LRD (BMI, body fat, and serum leptin levels) were classified according to published criteria. WEKA Machine-learning system was used as decision-tree software. Age was added as a factor with different dimension. Selected factors were validated by other statistical methods. In Thai-males, GLUT) (glucose-transporter 1)-SNP was most-responsive to body fat, followed by USF1-SNP (transcription-factor for lipid metabolism). Differences between genotypes were validated (P = .002 for GLUT1 by Levene's, P = .071 for USF1 by ANOVA). Responsive-factors of Thai-females, Palau-males and Palau-females, were consisted with SNPs and age, and varied by groups. Convincing responsive-factors were not selected from mixed-data. Decision-tree-analysis successfully selected the convincing results. Responsive-factors differed by ethnic group and gender.

Dietary habits of Mongolian people, and their influence on lifestyle-related diseases and early aging.

Mongolians are known to have relatively short life expectancy. In order to examine the role of dietary habits in the early aging of Mongolians, the food intake inquiry, anthropometric measurements and blood clinical tests were performed for 365 healthy inhabitants in Murun, a northern Mongolia city, and compared to those of Japanese. Murun inhibitants were found to have a characteristic dietary habit of taking large amounts of meat, milk, dairy products and wheat flour products, in contrast little vegetables, fruits and fishes. The daily calorie intake of the adults was estimated to be 2,525 kcal, and the fat/total calorie ratio was calculated 33.7%, about 1.3-fold higher than that of Japanese. The intake ratio of fatty acid from the Mongolian foods, saturated : mono-unsaturated : poly-unsaturated fatty acids (PUFA) ratio, was 10.3 : 7.8 : 3.0. Results of blood clinical tests showed significantly higher levels of serum triglycerides, low-density lipoprotein cholesterol (LDL) and homocysteine, and lower levels of high-density lipoprotein cholesterol (HDL), n-3 PUFA, folic acid and adiponectin, in comparison with those of Japanese. In addition, the Mongolians were also found to have significantly high levels of oxidative stress markers, such as serum malondialdehyde-modified LDL (MDA-LDL), urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG) and serum reactive oxygen metabolites (ROM). The serum ROM level in the Mongolians seemed to associate with their body fat ratio (p<0.05), and was significantly inverse-correlated to handgrip strength (p<0.001). Obesity was observed at a high incidence in the subjects over 30-year old, and over 40-year old their handgrip ability was markedly decreased. These findings suggest that in the Mongolians the dietary habits associate with their lifestyle-related diseases and early aging, and the improvement of dietary habits is an effective strategy for health promotion of the inhabitants.

Investigation of oxidative stress and dietary habits in Mongolian people, compared to Japanese people.

BACKGROUND: The average life span of Mongolians is 62 years for males and 69 years for females. This life span is about 16 years shorter than that of Japanese. Mongolian people generally eat meat, fat and diary products but less vegetables or fruit. Thus, we investigated the state of oxidative stress and dietary habits of Mongolians. METHODS: The investigation was performed in Murun city in the northwest area of Mongolia. A total of 164 healthy subjects (24-66 y) were enrolled. As a marker of reactive oxygen species, the levels of reactive oxygen metabolites (ROM) were measured using the d-ROM test. Interviews about dietary habits were performed using the Food Frequency Questionnaire established by the Kagawa Nutrition University. RESULTS: ROM levels were 429.7 +/- 95.2 Carr U for Murun subjects, whereas Japanese people (n = 220, 21-98 y) showed 335.3 +/- 59.8 (p < 0.001). The levels of serum malondialdehyde-modified low-density lipoprotein-cholesterol and urinary 8-hydroxydeoxyguanosine were also high. ROM levels correlated with body fat ratio and inversely correlated with handgrip strength. Handgrip strength in the subjects over 45 years decreased more rapidly than that of age-matched Japanese. Murun subjects ate larger amounts of meat, fat, milk and flour and dairy products than Japanese, but less vegetables or fruit. Serum vitamin A and E levels were the same as Japanese references, but vitamin C levels were lower. CONCLUSION: Murun subjects may be in high oxidative stress, which may have a relationship with early ageing and several diseases, ultimately resulting in their short life span. In order to increase antioxidant capacity and suppress overproduction of ROM, antioxidant food intake is recommended.

Obesity, bone status and dietary intake of Palauan elderly congregating in a Senior Citizen's Center.

A health survey of obesity and bone density measured by an Achilles Ultrasound bone densitometer (Lunar, USA) and nutritional intake was carried out for 15 male and 30 female Palauan elderly persons congregating in a Senior Citizens' Center. The subjects had high obesity values with mean BMI of 27.0 in males and 28.9 in females, and with mean body fat % of 22.3 in males and 39.8 in females (p < 0.01). The females showed a great decline in bone density from 60 to 70 years of age, with mean Stiffness index of 65.0 compared with that of 80.0 for males of the same age group. The subjects have all undergone a certain acculturation in their dietary habits, influenced by traditional Palauan, East-Asian, and Western food and dietary patterns. While all subjects had high carbohydrate intakes, and males had significantly greater intakes of energy, protein, calcium, phosphorus, iron, vitamin B1 and niacin than females. To determine the association of nutritional intake with obesity and Stiffness index, principal component analysis was carried out for amounts of intake of each food group. Correlation analysis between the scores of each principal food component and the body fat %, the BMI and the stiffness index was done. The score of the fourth principal component named "greater variety of food intake" was found to have significant positive correlation with body fat %. However, between the nutritional intake and body fat %, only a relationship could be identified. The findings indicate a need develop appropriate nutrition education and, particularly to address the problem of obesity.

Comparison of electrocardiogram findings and lifestyles between urbanized people and ger-living people in Ulaanbaatar, Mongolia.

In Ulaanbaatar, lifestyles differ between urbanized people (group A) and ger (tent)-living people (group B). Group A earn high annual incomes and live in houses or apartments. Group B (who had moved to Ulaanbaatar from nomadic areas) earn low incomes and live in narrow gers. In 2002, we investigated daily food intake, health status, and electrocardiogram (ECG) in these groups. In total, 256 subjects (group A, 142; group B, 114) were enrolled. Group A ate meat, vegetables, and fruits high enough by a Western style. Group B consumed meat but ate only small amounts of vegetables and fruits. They took a lot of fat, however, the serum lipid levels of them were not so high. The fat source as energy was plant oil for cooking rather than meat. Several abnormal ECG findings including left ventricular hypertrophy (LVH) were found in 32 (22.5%) of group A and 50 (43.9%) of group B (P < 0.001). LVH was also found more in group B than in group A. LVH in group A males was accompanied by high body weight (BW), hypertension, and high LDL-cholesterol, whereas LVH in group B males seemed to be related to an unbalanced diet, high salt intake, smoking, and some low socio-economic problems. In order to promote health condition, such risk factors should securely be eliminated from the lifestyles.

Prevalence of diego blood group Dia antigen in Mongolians: comparison with that in Japanese.

The Diego blood group is composed of Di(a) and Di(b) antigens. Prevalence of the Di(a) antigen is known to be different among races. The Di(a) antigen is generally found in Oriental people. Thus, it is called a Mongoloid factor. In Japanese, the prevalence of this antigen is 8.78%. However, the prevalence in Mongolians had not previously been examined. In September of 2002, we determined this antigen among inhabitants of Ulaanbaatar. It was found in 24 of 242 subjects (9.92%). This prevalence approximates that in Japanese. The Rh blood group phenotypes also showed patterns similar to those in Japanese. These results are not contrary to the presumption that Mongolians and Japanese may have a common racial background.

A survey of life-style diseases of inhabitants of Thailand.

To elucidate the way to prevent lifestyle-related diseases, such as diabetes mellitus and hypertension, in Asian countries, a comparative study between Mongoloids was conducted at Palau, in Oceania, the Republic of China, Thailand, Mongolia and Japan, from 1998 to October 2002. The survey comprised a social survey, nutrition survey, physical and medical examinations, biomedical analyses, urinalyses, and DNA analyses. This is an interim report for Thailand.