Genomic organization and promoter analysis of the bovine ADAM12 gene

A disintegrin and metalloprotease (ADAM) 12 is a member of the ADAM family possessing a putative role in a variety of biological processes such as modulation of proteolytic processing, cell adhesion, cell fusion, and signaling. Recently, it has been suggested that ADAM12 is involved in regulation of adipogenesis as well as myogenesis. In this study, we have determined the genomic structure of 5'- and 3'-regions in the bovine ADAM12 gene. We could obtain characteristics of lower homology of its exon 2 with human counterpart. Human exon S19 encodes for the sequence specific to a shorter secreted form of ADAM12S. The bovine ADAM12 gene had no canonical 3'-splice acceptor site at 5'-side of the putative exon S19, suggesting that the cattle could not produce a ADAM12S counterpart. To identify the regulatory elements, a 12 kb 5'-flanking region of the gene was cloned and luciferase reporter assay was carried out. Reporter plasmids with different length of proximal promoter region indicated the similar patterns of promoter activities between 3T3-L1 preadipose and Cos-1 nonadipose cells. However, 2.0 and 0.2 kb fragments located at - 8 and - 4.5 kb upstream of the putative transcription start site, respectively, increased the ADAM12 promoter activity about 1.5- to 2-fold in 3T3-L1, but not in Cos-1. These results suggested that the two distal regions might contribute to the preadipocyte-specific expression of ADAM12 gene.

Linkage disequilibrium structures in cattle and their application to breed identification testing

We examined the extent of linkage disequilibrium (LD) block lengths in four breed populations: Japanese Black, Angus, Hereford and Holstein. Three chromosomal regions in which QTL were previously mapped in Japanese Black populations were scanned with 84 microsatellite markers. The estimated LD lengths in these four purebred populations varied from 535 to 683 kb, which is much shorter than the values reported previously. Our findings suggest that QTL can be mapped in sub-centimorgan regions in these populations using an LD-mapping method. We also developed breed identification methods to distinguish Japanese Black from Angus, Hereford, Holstein and F(1) animals (Japanese Black x Holstein) respectively using the haplotypic frequencies of a pair of markers in the breed populations. After assessing the distributions of posterior probabilities to be Japanese Black, we obtained several pairs of markers that completely distinguished Japanese Black from the other breeds. We also obtained several combinations of six markers that completely distinguished Japanese Black animals from F(1) animals.

Linkage mapping of the locus responsible for forelimb-girdle muscular anomaly of Japanese black cattle on bovine chromosome 26

Forelimb-girdle muscular anomaly is an autosomal recessive disorder of Japanese black cattle characterized by tremor, astasia and abnormal shape of the shoulders. Pathological examination of affected animals reveals hypoplasia of forelimb-girdle muscles with reduced diameter of muscle fibres. To identify the gene responsible for this disorder, we performed linkage mapping of the disorder locus using an inbred pedigree including a great-grand sire, a grand sire, a sire and 26 affected calves obtained from a herd of Japanese black cattle. Two hundred and fifty-eight microsatellite markers distributed across the genome were genotyped across the pedigree. Four markers on the middle region of bovine chromosome 26 showed significant linkage with the disorder locus. Haplotype analysis using additional markers in this region refined the critical region of the disorder locus to a 3.5-Mb interval on BTA26 between BM4505 and MOK2602. Comparative mapping data revealed several potential candidate genes for the disorder, including NRAP, PDZD8 and HSPA12A, which are associated with muscular function.

FOXO transcription factor-dependent p15INK4b and p19INK4d expression

FOXO (Forkhead box O) transcription factors are involved in cell-cycle arrest or apoptosis induction by transcripting cell-cycle inhibitor p27(KIP1) or apoptosis-related genes, respectively. Akt/protein kinase B promotes cell proliferation and suppresses apoptosis, in part, by phosphorylating FOXOs. Phosphorylated FOXOs could not exhibit transcriptional activity because of their nuclear export. Here we show that p15(INK4b) and p19(INK4d) transcription is associated with FOXO-mediated G1 cell-cycle arrest. Inhibition of Akt signaling by PI3K inhibitors, a PDK1 inhibitor, or dominant-negative Akt transfection increased expression of p15(INK4b) and p19(INK4d) but not p16(INK4a) and p18(INK4c). Ectopic expression of wild type or active FOXO but not inactive form also increased p15(INK4b) and p19(INK4d) levels. FOXOs bound to promoter regions and induced transcription of these genes. No increase in the G1-arrested cell population, mediated by PI3K inhibitor LY294002, was observed in INK4b-/- or INK4d-/- murine embryonic fibroblasts. In summary, FOXOs are involved in G1 arrest caused by Akt inactivation via p15(INK4b) and p19(INK4d) transcription.

Breast cancer resistance protein (BCRP) affected acquired resistance to gefitinib in a "never-smoked" female patient with advanced non-small cell lung cancer

Development of acquired resistance to gefitinib after an initial good response is common. Recently, it was reported that this acquired resistance is related to a secondary mutation associated with a substitution of threonine by methionine at codon 790 (T790M) of the epidermal growth factor receptor (EGFR) gene. In this report, we present a "never smoking" woman with advanced lung cancer who showed acquired resistance to gefitinib, and analysis of autopsy samples revealed no evidence of EGFR mutations in either exons 18-21 or codon 790, and positive immunostaining for breast cancer resistance protein (BCRP). We describe, for the first time, a case in which expression of BCRP was associated with acquired resistance to gefitinib, independent of EGFR mutations.

Clinical significance of dihydropyrimidine dehydrogenase (DPD), epidermal growth factor receptor (EGFR), and excision repair cross-complementing gene 1 (ERCC1) gene expression of tumor tissue in patients with advanced gastric cancer

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Background: Many methods for predicting the susceptibility of a gastric cancer(GC) to chemotherapy have been investigated. However, the clinical significance of biomarkers in GC cells remains unclear. There is a need for exploratory evaluations to understand the clinical implications of biomarkers. Methods: This study consisted of 151 patients (pts) who received chemotherapy for advanced GC. cDNA was derived from the laser-captured tumor cells of cancer specimens obtained by surgical resection or endoscopic biopsy and analyzed to determine mRNA expression relative to an internal reference gene (β-actin) using real-time RT-PCR method. Gene expression levels of thymidylate synthase (TS), DPD, orotate phosphoribosyl transferase, dihydrofolate reductase (DHFR), ERCC-1, EGFR and 22 other biomarkers related to anticancer drug sensitivity were measured. Results: DPD, EGFR, and ERCC1 gene expressions were significantly correlated with survival ( Table ). Multivariate analysis revealed that high DPD (p=0.0002, RR=2.67 [95% CI, 1.62–4.25]), low EGFR (p=0.0005, RR=0.29 [0.18–0.50]), and high ERCC1 (p<0.0001, RR=2.27 [1.45–3.47]) gene expressions were independently related to poor survival. As for first-line chemotherapy, an analysis of 60 pts treated with S-1 showed that low DHFR gene expression significantly correlated with a longer time to progression (TTP) (p=0.0017). An analysis of 54 pts who received cisplatin containing regimens ( + irinotecan or + S-1) as first-line therapy showed that low ERCC1 gene expression was slightly related to a better response (p=0.053). Conclusions: These results indicate that expression of DPD, ERCC1, and EGFR gene expressions in cancer specimens have predictive value for the outcome of advanced GC pts treated with chemotherapy. Low DHFR gene expression could be a predictor of a long TTP in patients receiving S-1 therapy.

[Table: see text]

No significant financial relationships to disclose.

Mapping of a Quantitative Trait Locus for Beef Marbling on Bovine Chromosome 9 in Purebred Japanese Black Cattle

The goal of this study is to detect quantitative trait loci (QTL) for carcass traits applicable for a DNA-based breeding system in a Japanese Black cattle population. A purebred paternal half-sib family from a commercial line composed of 65 steers was initially analyzed using 188 informative microsatellites giving a 16-cM average interval covering 29 autosomes. A significant QTL for marbling was detected in the centromeric portion of bovine chromosome (BTA) 9. After additional marker genotyping across a larger sample size composed of 169 individuals, this locus was refined to a 20-cM confidence interval between microsatellites BM1227 (24 cM) and DIK2741 (50 cM) at a 1% chromosome-wise threshold. The allele substitution effect between Q and q for a beef marbling standard score (1 to 12 range) on BTA9 was 1.0 (5.7% of total phenotypic variance in QTL contribution in this family). This result provides a primary platform for a marker-assisted selection system of the beef marbling trait within the Japanese Black (Wagyu) cattle population.

Oligogenic transmission of abnormal teat patterning phenotype (ATPP) in cattle

Abnormal teat patterning phenotype (ATPP) is characterized by one (moderate form) or two (severe form) absent teats in cattle. Using an allele-sharing non-parametric linkage strategy, significant associations with severe ATPP animals were detected on BTA17 (Z(max) = 7.3 at 21 cM), centromeric BTA1 (Z(max) = 3.7 at 8 cM) and telomeric BTA1 (Z(max) = 4.8 at 142 cM). The BTA17 region was also significantly associated in the analysis of the moderate ATPP animals (Z(max) = 5.3 at 0 cM). The transmission disequilibrium test in severe ATPP animals demonstrated significant over-transmission of paternal alleles in the BTA17 region (P = 2.2 x 10(-9)), the centromeric BTA1 region (P = 0.035) and the telomeric BTA1 region (P = 0.005). Significant over-transmission of the BTA17 region was also observed among the moderate ATPP animals (P = 2.3 x 10(-4)). These findings indicate that the BTA17 locus plays a key role in risk of the disease, and that the BTA17 locus contributes temporally in combination with the two other loci on BTA1 and/or possibly unknown modifier(s) in a probabilistic oligo- or polygenic manner of transmission. Haplotypes of these three loci can be used for marker-assisted animal breeding to control the recurrence of affected progeny with ATPP.

218 BREEDING TRIAL OF CONGENITAL HYDROCEPHALUS OF JAPANESE BLACK CATTLE USING EMBRYO TRANSFER

Hydrocephalus is a congenital defect of cattle. Births of Japanese Black calves with forehead doming were reported in Tohoku District from 1988 to 1989. The common finding on autopsy was the presence of excessive amounts of cerebrospinal fluid with expanding lateral ventricles without evidence of microbiologic infection. Breeding records for pedigree registration have been maintained by the Wagyu Registry Association in this area since 1960. A survey of the pedigrees suggested that an autosomal recessive gene might be responsible for the defect. The incidence of doming calves ceased by an advised mating system which excluded the suspected sires after 1990. Molecular genetics is useful for disclosing DNA sequences of a recessive gene and for detecting the carriers of the gene. This trial was conducted to produce congenital hydrocephalus calves for gene analysis using embryo transfer on a small number of the remaining cows that gave birth to affected calves over 10 years ago. One donor cow, 11 years old, was superovulated with 24 to 25 AU of FSH (Antrin; Kawasaki Mitaka K.K., Kawasaki, Japan) and inseminated with frozen semen of a suspected bull. Collected embryos were transferred on the day of the collection and the rest of them were frozen and transferred later. Superstimulation was repeated 4 times in this cow at an interval of 76-105 days during and 8-month period. A total of 4, 13, 17, and 18 embryos of good quality were collected. Eighteen fresh embryos were transferred into 7 (2 embryos each) and 4 (single embryo) recipients. Frozen embryos were transferred into 6 recipients (single embryo). Seven of 17 recipients became pregnant and gave birth to 8 calves. Three of 6 male calves born and one of 2 females showed symptoms of hydrocephalus. Clinically, 3 of the affected calves had a domed forehead and squint-eyes and were unable to stand. One calf underwent a fatal convulsion and ataxia 29 days after birth. Pathological findings of affected calves showed dilated bilateral ventricles with increased cerebrospinal fluid as typical lesions of hydrocephalus. Embryo transfer was demonstrated to be a useful tool for investigation of a potentially heritable disease. Gene scanning with microsatellite markers using the tissues from the calves and the related cattle was done. The suspected gene was found near the centromere of chromosome 3 (BTA3). It was possible to diagnose the mutant-carrier cattle using two DNA markers, INRA006 (17.0 cm) and BL41 (43.2 cm).

Identification of quantitative trait loci affecting corpora lutea and number of teats in a Meishan x Duroc F2 resource population

Understanding of the genetic control of female reproductive performance in pigs would offer the opportunity to utilize natural variation and improve selective breeding programs through marker-assisted selection. The Chinese Meishan is one of the most prolific pig breeds known, farrowing 3 to 5 more viable piglets per litter than Western breeds. This difference in prolificacy is attributed to the Meishan's superior prenatal survival. Our study utilized a 3-generation resource population, in which the founder grandparental animals were purebred Meishan and Duroc pigs, in a genome scan for QTL. Grandparent, F1, and F2 animals were genotyped for 180 microsatellite markers. Reproductive traits, including number of corpora lutea (number of animals = 234), number of fetuses per animal (n = 226), number of teats (n = 801), and total number born (n = 288), were recorded for F2 females. Genome-wide significance level thresholds of 1, 5, and 10% were calculated using a permutation approach. We identified 9 QTL for 3 traits at a 10% genome-wise significance level. Parametric interval mapping analysis indicated evidence of a 1% genome-wise significant QTL for corpora lutea on SSC 3. Nonparametric interval mapping for number of teats found 4 significant QTL on chromosomes SSC3 (P < 0.01), SSC7 (P < 0.01), SSC8 (P < 0.01), and SSC12 (P < 0.05). Partial imprinting of a QTL affecting teat number (P < 0.10) was detected on SSC8. Using the likelihood-ratio test for a categorical trait, 2 QTL for pin nipples were detected on SSC2 and SSC16 (P < 0.01). Fine mapping of the QTL regions will be required for their application to introgression programs and gene cloning.

Mapping of quantitative trait loci for carcass traits in a Japanese Black (Wagyu) cattle population

To detect quantitative trait loci (QTL) that influence economically important traits in a purebred Japanese Black cattle population, we performed a preliminary genome-wide scan using 187 microsatellite markers across a paternal half-sib family composed of 258 offspring. We located six QTL at the 1% chromosome-wise level on bovine chromosomes (BTA) 4, 6, 13, 14 and 21. A second screen of these six QTL regions using 138 additional paternal offspring half-sib from the same sire, provided further support for five QTL: carcass weight on BTA14 (22-39 cM), one for rib thickness on BTA6 (27-58 cM) and three for beef marbling score (BMS) on BTA4 (59-67 cM), BTA6 (68-89 cM) and BTA21 (75-84 cM). The location of QTL for subcutaneous fat thickness on BTA13 was not supported by the second screen (P > 0.05). We determined that the combined contribution of the three QTLs for BMS was 10.1% of the total variance. The combined phenotypic average of these three Q was significantly different (P < 0.001) from those of other allele combinations. Analysis of additional half-sib families will be necessary to confirm these QTL.

An integrated radiation hybrid map of bovine chromosome 18 that refines a critical region associated with multiple ocular defects in cattle

Congenital multiple ocular defects (MOD) of Japanese black cattle is a hereditary ocular disorder with an autosomal recessive mode of inheritance showing developmental defects of the lens, retina and iris, persistent embryonic eye vascularization and microphthalmia. The MOD locus has been mapped by linkage analysis to a 6.6-cM interval on the proximal end of bovine chromosome 18, which corresponds to human chromosome 16q and mouse chromosome 8. To refine the MOD region in cattle, we constructed an integrated radiation hybrid (RH) map of the proximal region of bovine chromosome 18, which consisted of 17 genes and 10 microsatellite markers, using the SUNbRH7000 panel. Strong conservation of gene order was found among the corresponding chromosomal regions in cattle, human and mouse. The MOD-critical region was fine mapped to a 59.5-cR region that corresponds to a 6.3-Mb segment of human chromosome 16 and a 4.8-Mb segment of mouse chromosome 8. Several positional candidate genes, including FOXC2 and USP10, were identified in this region.

Impact of dihydrofolate reductase (DHFR) and thymidylate synthase (TS) on outcomes of postoperative patients with gastric cancer

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Background: The clinical significance of biomarkers in resected gastric cancer (GC) remains unclear. Detailed exploratory evaluations are required to better understand the clinical implications of biomarkers. Methods: The study group comprised 87 patients who received chemotherapy for recurrent or residual GC after resection of their primary tumors at National Cancer Center Hospital. The patients received 1 to 5 regimens of chemotherapy (median: 2). Total RNA was isolated from laser-captured tumor cells of the resected cancer specimens, and the gene expressions of TS, DPD, DHFR, ERCC1, MRP1, and 22 other biomarkers related to anticancer drug sensitivity were quantitatively evaluated by a real-time RT-PCR assay. Results: The gene expressions of TS, DHFR, MTHFD, RRM1, and ERCC1 were significantly related to survival ( Table ). Multivariate analysis revealed that high DHFR (p < 0.001, RR = 1.70 [95% CI, 1.28–2.29]) and high TS (p = 0.004, RR = 1.53 [1.15–2.06]) gene expressions were independently related to poor survival. As compared with intestinal type tumors, diffuse type tumors had higher DPD (p < 0.001) and lower Her2 (p < 0.001) gene expressions. As for first line chemotherapy, an analysis of 29 patients treated with S-1, an oral DPD inhibitory fluoropyrimidine, showed that patients with diffuse type tumors tended to respond better (p = 0.13) than those with intestinal type tumors. An analysis of 29 patients treated with cisplatin plus irinotecan as first line therapy showed that low ERCC1 gene expression was slightly but not significantly related to a better response (p = 0.087). Analyses of patients treated with other first line regimens revealed no significant correlation of any biomarker with response. Conclusions: Increased gene expressions of DHFR and TS in surgical specimens are significantly predictors of poor outcomes in postoperative patients with GC.

[Table: see text]

[Table: see text]

Effect of paroxetine on marble-burying behavior in mice

The present study was undertaken to investigate the effect of paroxetine, a selective serotonin reuptake inhibitor (SSRI), on marble-burying behavior in mice in comparison with those of fluvoxamine and clomipramine. Marble-burying test is extensively used as an animal model for obsessive/compulsive disorder. A significant inhibition in marble-burying behavior was observed with paroxetine, at a dose of 10 mg/kg. The earlier SSRI, fluvoxamine, also significantly inhibited marble-burying behavior at a dose of 30 mg/kg. Although clomipramine, a tricyclic antidepressant, caused an inhibition in marble-burying behavior, a high dose of 100 mg/kg was needed to show a significant effect. On the other hand, all the drugs used in the present study showed no significant changes in spontaneous locomotor activity at doses inhibiting marble-burying behavior. In conclusion, it was confirmed that paroxetine has a potent inhibitory effect on marble-burying behavior in mice, and could have a similar antiobsessive/anticompulsive activity in human beings.

Genome-wide linkage disequilibrium in two Japanese beef cattle breeds

There is little knowledge about the degree of linkage disequilibrium (LD) in beef cattle. This study aims to perform a genome-wide search for LD in Japanese Black and Japanese Brown beef cattle and to compare the level of LD between these two breeds. Parameter D' (the LD coefficient) was used as a measure of LD, and LD was tested for significance of allelic associations between syntenic and between non-syntenic marker pairs. Effects of breed, chromosome, genetic map distance and their interactions with D' were tested based on least squares analyses. Both breeds showed high levels of LD, which ranged over several tens of cM and declined as the marker distance increased for syntenic marker pairs. A rapid decline of the D' value was observed between markers that were spaced 5 and 20 cM apart. LD was significant in most cases for marker pairs <40 cM apart but was not significant between non-syntenic loci. The pattern of LD found in these two breeds was similar to that previously published for dairy cattle. The D' value between breeds was not significantly different (P > 0.05), but the interaction between breed and chromosome was highly significant (P < 0.001). Genetic selection seems to have caused the heterogeneity of the D' values among chromosomes within breed. These results indicate that LD mapping is a useful tool for fine-mapping quantitative trait loci of economically important traits in Japanese beef cattle.

High-resolution physical mapping and construction of a porcine contig spanning the intramuscular fat content QTL

We previously mapped a locus for porcine intramuscular fat content (IMF) by linkage analysis to a 17.1-cM chromosome interval on Sus scrofa chromosome 7 (SSC7) flanked by microsatellite markers SW1083 and SW581. In this study, we identified 34 microsatellite markers and 14 STSs from the 17.1-cM IMF quantitative trait loci (QTL) region corresponding to HSA14q and aligned those loci using the INRA-University of Minnesota porcine radiation hybrid (IMpRH) panel. We then constructed a 5.2-Mb porcine bacterial artificial chromosome (BAC) contig of this region that was aligned using the RH panel. Finally, the IMF QTL was fine-mapped to 12.6 cM between SJ169 and MM70 at the 0.1% chromosome-wise significance level by genotyping the previously studied F2 resource family with 17 additional microsatellites. We also demonstrated that the SJ169-MM70 interval spans approximately 3.0 Mb and contains at least 12 genes: GALC, GPR65, KCNK10, SPATA7, PTPN21, FLJ11806, EML5, TTC8, CHES1, CAP2P1, CHORDC2P and C14orf143.

The effect of higher-order dispersion on slow light propagation in photonic crystal waveguides

We have studied the dispersion of ultrafast pulses in a photonic crystal waveguide as a function of optical frequency, in both experiment and theory. With phase-sensitive and time-resolved near-field microscopy, the light was probed inside the waveguide in a non-invasive manner. The effect of dispersion on the shape of the pulses was determined. As the optical frequency decreased, the group velocity decreased. Simultaneously, the measured pulses were broadened during propagation, due to an increase in group velocity dispersion. On top of that, the pulses exhibited a strong asymmetric distortion as the propagation distance increased. The asymmetry increased as the group velocity decreased. The asymmetry of the pulses is caused by a strong increase of higher order dispersion. As the group velocity was reduced to 0.116(9) .c, we found group velocity dispersion of -1.1(3) .10(6) ps(2)/km and third order dispersion of up to 1.1(4) .10(5) ps(3)/km. We have modelled our interferometric measurements and included the full dispersion of the photonic crystal waveguide. Our mathematical model and the experimental findings showed a good correspondence. Our findings show that if the most commonly used slow light regime in photonic crystals is to be exploited, great care has to be taken about higher-order dispersion.

Characterization and RH mapping of bovine microsatellites generated from a microdissected BTA20-specific DNA library

Bovine chromosome 20 (BTA20) is associated with several quantitative trait loci (QTL) for meat tenderness, birth weight, milk yield and composition. Fine mapping of these QTL requires the development of additional informative markers to increase the resolution of the BTA20 genetic and physical maps. A BTA20-specific library was constructed by means of microdissection and microcloning, and screened for dinucleotide repeats with (CA)16 and (GT)16 oligos. A total of 60 new microsatellites (MS) were developed and characterized for polymorphism using the U.S. Department of Agriculture (USDA)/Meat Animal Research Center (MARC) bovine reference family, of which 53 markers were informative in this family. The number of alleles for these loci varied from 1 to 14, with an average of 6.5. Thirty-three of these MSs, together with 105 markers previously mapped to BTA20, were scored on a 7000-rad cattle-hamster whole-genome radiation hybrid panel (SUNbRH), resulting in a high-resolution RH7000 rad map for BTA20.

Linkage analysis reveals two independent loci for ocular disorders in a local Japanese Black cattle population

A vision-impairing ocular disorder was observed in a local Japanese Black cattle population, and assumed to be an autosomal recessive disease based on the presence of a founder cow. A genome scan using seven affected half-sib pairs revealed a linkage to BTA5 (Z(max) = 7.0, LOD(max) = 2.0), designated the bovine ocular disorder 1 (bod1) locus. Of the seven animals, three were heterozygous at the bod1 locus. Analysis in these three animals revealed linkage to markers on BTA18, and this locus was designated bod2. Detailed haplotype inspection of 16 affected animals indicated linkage to BTA5 in 12 animals, BTA18 in three animals, and linkage to both BTA5 and BTA18 in one animal. The bod1 locus was mapped to a 25 cM interval between DIK5237 and DIK5210 on BTA5 (Z(max) = 17.0, LOD(max) = 11.8), and bod2 was mapped to a 7 cM interval between DIK5411 and INRA038 on BTA18 (Z(max) = 13.0, LOD(max) = 4.0). This study demonstrated that the independent involvement of loss of function mutations in two loci is likely responsible for this genetic heterogeneity.