Long-term operation of the pilot scale two-stage anaerobic digestion of municipal biowaste in Ho Chi Minh City.

A pilot-scale two-stage anaerobic digestion system, which includes a feed tank (0.4 m), a hydrolysis reactor (1.2 m) followed by a methane fermenter (4.

Low mitochondrial DNA diversity of Japanese Polled and Kuchinoshima feral cattle.

This study aims to estimate the mitochondrial genetic diversity and structure of Japanese Polled and Kuchinoshima feral cattle, which are maintained in small populations. We determined the mitochondrial DMA (mtDNA) displacement loop (D-loop) sequences for both cattle populations and analyzed these in conjunction with previously published data from Northeast Asian cattle populations. Our findings showed that Japanese native cattle have a predominant, Asian-specific mtDNA haplogroup T4 with high frequencies (0.

Genetic structure and relationships of 16 Asian and European cattle populations using DigiTag2 assay.

In this study, we genotyped 117 autosomal single nucleotide polymorphisms using a DigiTag2 assay to assess the genetic diversity, structure and relationships of 16 Eurasian cattle populations, including nine cattle breeds and seven native cattle. Phylogenetic and principal component analyses showed that Bos taurus and Bos indicus populations were clearly distinguished, whereas Japanese Shorthorn and Japanese Polled clustered with European populations. Furthermore, STRUCTURE analysis demonstrated the distinct separation between Bos taurus and Bos indicus (K=2), and between European and Asian populations (K=3).

Sampling method for estimating neutral allele frequency in a pedigreed population.

The estimated allele frequency at neutral DNA marker loci is a fundamental parameter for establishing a conservation scheme for a set of livestock breeds. In this study, we propose a novel 'minimum distance (MD) method' for estimating neutral allele frequencies, which minimizes the error by the use of pedigree information. Using computer simulation and actual microsatellite data for a pedigreed cattle population, the performance of the proposed method was compared with that of conventional random sampling (RND).

Heritabilities and genetic correlations of fatty acid compositions in longissimus muscle lipid with carcass traits in Japanese Black cattle.

Fatty acid composition and carcass traits of 2,275 Japanese Black steers and heifers were analyzed to estimate the heritabilities and genetic correlations using the REML procedure. Slices of LM at the 6th to 7th rib section were minced and homogenized, and total lipids were extracted for the analysis by a gas chromatograph. Oleic acid accounted for the majority (51.

Development of novel SNP system for individual and pedigree control in a Japanese Black cattle population using whole-genome genotyping assay.

Individual identification and parentage analysis using DNA markers are essential for assuring food identity and managing livestock population. The objective of this study was to develop a single nucleotide polymorphism (SNP) panel system for individual effective identification and parentage testing in a Japanese Black cattle population using BovineSNP50 BeadChip. On the basis of SNP frequencies, 60 unlinked informative SNPs were finally selected as candidate markers.

Development of SNP markers for individual identification and parentage test in a Japanese black cattle population.

This study describes the development of efficient single nucleotide polymorphism (SNP) markers for individual identification and parentage tests in a Japanese Black cattle population. An amplified fragment length polymorphism method was employed to detect informative candidate markers, and yielded 44 SNP markers from 220 primer combinations. 29 unlinked SNPs were finally selected as diagnostic markers.

Effect of SCD and SREBP genotypes on fatty acid composition in adipose tissue of Japanese Black cattle herds.

Fatty acid composition of beef adipose tissue is one of important traits because high proportions of monounsaturated fatty acid are related to favorable beef flavor and tenderness. In this study, we investigated effects of genetic factors such as stearoyl-CoA desaturase (SCD) and sterol regulatory element binding protein (SREBP) on beef carcass traits including fatty acid composition using two cattle populations. Sire effect was significantly related to almost all traits except BMS, suggesting that the trait examined in this study is highly controlled by genetic factors.

Association between fatty acid compositions and genotypes of FABP4 and LXR-alpha in Japanese black cattle.

Background: Fatty acid composition has become an important trait in the beef industry in terms of beef flavor and decreasing the circulating concentration of LDL cholesterol. In this study, we examined the association between polymorphisms of six genes, adipocytes-type fatty acid binding protein (FABP4), liver X receptor alpha (LXRalpha), cytochrome b5 (Cyt b5), long-chain acyl-CoA synthetase (ACSL) 1, ACSL4 and diacylglycerol acyltransferase 2 (DGAT2) and fatty acid composition.

Results: Sequence comparisons revealed 14 single nucleotide polymorphisms in six genes.

The ubiquitin ligase gene (WWP1) is responsible for the chicken muscular dystrophy.

Chicken muscular dystrophy with abnormal muscle (AM) has been studied for more than 50 years, but the gene responsible for it remains unclear. Our previous studies narrowed down the AM candidate region to approximately 1Mbp of chicken chromosome 2q containing seven genes. In this study, we performed sequence comparison and gene expression analysis to elucidate the responsible gene.

Genotype of bovine sterol regulatory element binding protein-1 (SREBP-1) is associated with fatty acid composition in Japanese Black cattle.

To investigate genetic factors that affect fatty acid composition in beef carcass, we previously investigated genetic profiles of stearoyl-CoA desaturase (SCD) and their effect on fatty acid composition in fat tissue of cattle. It has been known that sterol regulatory element binding protein (SREBP) is a transcription factor that regulates gene expression levels of SCD and other genes relevant to lipid and fatty acid metabolism in tissue. Therefore, we determined the full-length sequence of bovine SREBP-1 cDNA and then surveyed polymorphisms in whole exons and introns in the bovine genome.

Stearoyl-CoA desaturase mRNA expression during bovine adipocyte differentiation in primary culture derived from Japanese Black and Holstein cattle.

Stearoyl-CoA desaturase (SCD) catalyzes the synthesis of monounsaturated fatty acids (MUFAs). In cattle, the MUFAs are related to softness and flavor of meat. In order to investigate gene expression profile during bovine preadipocyte differentiation, we isolated stromal-vascular cells from perirenal adipose tissues of Japanese Black and Holstein steers.

[Dipylidium caninum infection in an infant].

Dipylidium caninum, the dog tapeworm, is a common intestinal cestode of domestic dogs and cats, but few cases have been reported of human infection by this parasite in Japan. We repot a case of D. caninum infection in a 17 month-old girl, who sometimes had symptoms of abdominal pain, diarrhea, and dysphoria at night.

Effect of sire mating patterns on future genetic merit and inbreeding in a closed beef cattle population.

Alternative breeding strategies were simulated based on the population structure of the Tajima strain of Japanese Black cattle. An analysis of the population structure revealed that some sires up to 20 years of age have been used in Tajima. In addition, 95% of newborn calves were the progeny of only 20 sires, and their mating frequencies were significantly skewed.

Genetic analysis of calf market weight and carcass traits in Japanese Black cattle.

Heritabilities of and genetic correlations between additive direct and maternal genetic effects for calf market weight, and additive direct genetic effects for carcass traits, were estimated for Japanese Black cattle by REML procedures under 2-trait animal models. Data were collected from calf and carcass markets in Hyogo and Tottori prefectures and analyzed separately by prefecture. Calf market weight was measured on 42,745 and 23,566 calves in Hyogo and Tottori, respectively.

Evaluation of genetic diversity in Japanese Brown cattle population by pedigree analysis.

The Japanese Brown is the second most common domestic beef breed in Japan. However, nowadays this breed is facing reduction in numbers because of pressure from a profitable domestic breed. This breed is uniformly characterized by its brown coat colour, but is comprised of two isolated sub-breeds, Kumamoto and Kouchi, each possessing a different gene pool.

Prediction of inbreeding in commercial females maintained by rotational mating with partially isolated sire lines.

The solution to the inbreeding problem for livestock breeds in commercial use is often complicated by hierarchical population structure, in which favourable genes are accumulated in the upper level of the hierarchy (breeding population) by artificial selection and the genetic progress achieved is transferred to the lower level through migration of males. When the breeding population is subdivided into several isolated lines, rotational mating with the lines has been shown to be quite an effective system to reduce the short- and long-term inbreeding of commercial females in the lower level. In practice, however, some amount of migration should be allowed among the lines to reduce the rate of inbreeding in each line.

Conservation of genetic diversity in the Japanese Black cattle population by the construction of partially isolated lines.

In the Japanese Black cattle population, five genetically divergent sub-populations have played important roles as suppliers of breeding stocks to the entire breed. We supposed a situation where five lines were constructed from each of the five subpopulations, and applied to this set of lines a management plan to conserve genetic diversity. Assuming that the male migration pattern among the lines followed the island model, we assessed the optimum male migration rate and required male numbers in each line, satisfying the following three conditions simultaneously: (i) the rate of inbreeding in each line was below 0.

Trace of native cattle in Japanese Holstein assessed by mitochondrial DNA sequence polymorphism.

On the basis of sequence variation in the displacement loop region of mtDNA, 588 Japanese and North American Holstein cows were classified into 5 mitochondrial haplotypes, which were found in Japanese Black cattle. One of the haplotypes (named type 1), which was present at the highest frequency in Japanese Black cattle, was not observed in either European or African cattle. This haplotype is characterized by 2 single-nucleotide polymorphisms.

Reduction of inbreeding in commercial females by rotational mating with several sire lines.

A mating system to reduce the inbreeding of commercial females in the lower level was examined theoretically, assuming a hierarchical breed structure, in which favorable genes are accumulated in the upper level by artificial selection and the achieved genetic progress is transferred to the lower level through migration of males. The mating system examined was rotational mating with several closed sire lines in the upper level. Using the group coancestry theory, we derived recurrence equations for the inbreeding coefficient of the commercial females.

An association study using AFLP markers and application to a beef cattle breeding population.

Using amplified fragment length polymorphism (AFLP) fingerprinting, selective genotyping was performed to determine if this method was effective for selecting superior breeding stock. Forty-eight cows with extreme genetic merit for beef marbling score (BMS) were selected from a population of Japanese Black cattle (n = 4462), including 25 with the highest for predicted breeding value (PBV) and 23 with the lowest. Sixteen AFLP fragments were selected for further analysis based on fragment frequency differences between the high and low groups.

Identification of mitochondrial DNA substitutions related to meat quality in Japanese Black cattle.

Complete sequences of mitochondrial (mt) genomes of eight Japanese Black cattle were determined to investigate the relationships between mt deoxyribonucleic acid (DNA) displacement loop (D-loop) types and other mtDNA regions and to identify the variation in the coding region that may influence the economic traits. The survey of mitochondrial sequences in the encoding region revealed 14 substitutions including six antonymous substitutions and one in 16S ribosomal ribonucleic acid (rRNA). Three methods of polymorphic DNA analyses (polymerase chain reaction [PCR]-restriction fragment length polymorphism [RFLP], mismatch PCR-RFLP, PCR-single-strand conformation polymorphism [SSCP]) were performed on these seven candidate substitutions (base pair [bp] 2,232, 12,158, 12,908, 13,310, 14,122, 14,140, and 14,565) for 202 Japanese Black cattle.

Alternative splicing isoform of tau protein kinase I/glycogen synthase kinase 3beta.

Glycogen synthase kinase 3 (GSK3) plays important roles in Wnt and insulin signaling, cell fate determination, and Alzheimer-like tau phosphorylation. We discovered an isoform of tau protein kinase I (TPKI)/GSK3beta with a 13 amino acid insert in the catalytic domain owing to alternative splicing. The alternative transcripts were found in the brains of the mouse, rat and human, with highly conserved sequences.

Inbreeding and effective population size of Japanese Black cattle.

The objective of this research was to estimate the amount of inbreeding and effective population size of the Japanese Black breed using pedigree records from bulls and heifers registered between 1985 and 1997. Inbreeding was quantified by three F-statistics: actual inbreeding, inbreeding expected under random mating, and inbreeding due to population subdivision. During the period of 1985 to 1997, the inbreeding expected under random mating increased from 2.

Highly sensitive urine-based enzyme-linked immunosorbent assay for detection of antibody to Helicobacter pylori.

Background: Enzyme-linked immunosorbent assay (ELISA) has been widely used for detection of Helicobacter pylori (H. pylori), but sample collection is often invasive, complicated, and expensive. Urine samples can be obtained noninvasively and are easier and safer to handle than serum samples.