Super high resolution for single molecule-sequence-based typing of classical HLA loci at the 8-digit level using next generation sequencers.

Current human leukocyte antigen (HLA) DNA typing methods such as the sequence-based typing (SBT) and sequence-specific oligonucleotide (SSO) methods generally yield ambiguous typing results because of oligonucleotide probe design limitations or phase ambiguity for HLA allele assignment. Here we describe the development and application of the super high-resolution single-molecule sequence-based typing (SS-SBT) of HLA loci at the 8-digit level using next generation sequencing (NGS). NGS which can determine an HLA allele sequence derived from a single DNA molecule is expected to solve the phase ambiguity problem. Eight classical HLA loci-specific polymerase chain reaction (PCR) primers were designed to amplify the entire gene sequences from the enhancer-promoter region to the 3' untranslated region. Phase ambiguities of HLA-A, -B, -C, -DRB1 and -DQB1 were completely resolved and unequivocally assigned without ambiguity to single HLA alleles. Therefore, the SS-SBT method described here is a superior and effective HLA DNA typing method to efficiently detect new HLA alleles and null alleles without ambiguity.

Temporal association of serum progesterone concentrations and vaginal cytology in walruses (Odobenus rosmarus).

Concentrations of serum estradiol-17ß and progesterone were monitored in six female walruses using an enzyme immunoassay. Progesterone concentrations increased from March to May in females aged 6 y or older, and subsequently declined (October). No significant elevation of estradiol-17ß concentration was detected before an elevation of progesterone concentration. Vaginal smears from four females were examined with Papanicolaou staining. In all females, most epithelial cells were basophilic intermediate-superficial cells; no color change from basophilic to eosinophilic of the cells was detected. Meanwhile, the percentage of anucleate cells in vaginal smears reached its highest value before the elevation of progesterone concentration, followed by an increase in the percentage of leukocytes. We inferred that the change in populations of anucleate cells and leukocytes in vaginal smears reflected ovarian status and CL formation in female walruses.

Primary mucinous carcinoma of the skin: a case of metastasis after 10 years of disease-free interval.

Primary mucinous carcinoma of the skin (MCS) is a rare neoplasm. Clinically, it has a high local recurrence rate, but it is known to be a slow-growing benign tumor with a rare incidence of distant metastases. We present a case of primary MCS on the jaw that underwent tumor resection twice and was disease-free for 10 years after the second surgery. The patient had no evidence of local recurrence and distant metastasis until his 11th year follow-up. At that time, he was diagnosed with lung and bone metastasis and died 3 years after this. To our knowledge, this is the first case of MCS that presented with metastasis with more than 10-year disease-free interval. Since MCS is a slow-growing asymptomatic tumor, distant metastasis is difficult to diagnose without detailed radiological examination. We believe that computed tomography and resonance imaging should be performed for early diagnosis of metastasis even for cases with long-term disease-free interval, especially cases of local recurrence.

Activity of three-beta-hydroxysteroid dehydrogenase in granulosa cells treated in vitro with luteinizing hormone, follicle-stimulating hormone, prolactin, or a combination.

Three-beta-hydroxysteroid dehydrogenase (3beta-HSD) is a key enzyme in the pathway that produces progesterone. Hy-Line hens (W36, W98, and Brown) were subjected to mild heat stress [36 degrees C for 24 h (acute heat stress, AHS) or 2 wk (chronic heat stress, CHS)] or maintained at 22 degrees C (thermoneutral, TN). Granulosa cells (GC) from the 3 largest follicles were isolated, dispersed, and incubated with luteinizing hormone (LH), follicle-stimulating hormone (FSH), prolactin (PRL), a combination, or no hormone (control), and then with pregnenolone nitro blue tetrazolium to determine 3beta-HSD activity. Treatment by LH (TN, P = 0.04; AHS, CHS, P < 0.0001) and by LH+FSH (TN, AHS, CHS, P < 0.0001) resulted in increased enzyme activity compared with the respective controls. In TN and CHS, LH+FSH increased the activity to a greater extent than LH alone (TN, P = 0.02; CHS, P = 0.0004); in AHS the increase was not significant (P = 0.29). Treatment with FSH, PRL, or LH+PRL decreased (TN, AHS) or had no effect (CHS) on 3beta-HSD activity. In TN and AHS cells, FSH and PRL reduced enzyme activity (P = 0.006 and 0.0580, respectively). When LH was added to PRL, suppression by PRL was mitigated somewhat. When LH and FSH were added to PRL, 3beta-HSD activity in AHS and CHS cells actually increased compared with the respective controls (P = 0.052 and 0.003) but remained below the activity of cells incubated with LH+FSH or LH alone. This suggests that gonadotropic actions of LH and LH+FSH are countered by the antigonadotropic action of PRL and, conversely, that PRL reduces the stimulatory action of LH and FSH. Strain differences in GC response to hormones were observed primarily in the CHS-treated birds; generally, W98 was highest; Browns showed the weakest response, and W36 was intermediate. In earlier studies, HS reduced circulating LH and GC progesterone and 3beta-HSD activity in vitro and increased circulating PRL. The results suggest a mechanism by which reduced activity of 3beta-HSD and progesterone by GC during HS might be explained, particularly with the differences in strains observed.

Menatetrenone (vitamin K2) acts directly on circulating human osteoclast precursors.

It is still not certain what the direct effect of menatetrenone is on osteoclast precursors. In the present study, we investigated whether menatetrenone has a direct effect on circulating osteoclast precursors to influence osteoclast differentiation. Monocytes isolated from human peripheral blood were cultured with receptor-activated NF-kappaB ligand (RANKL) and macrophage colony-stimulating factor (M-CSF). Menatetrenone or vitamin K1 was then added to the cultures. Geranylgeraniol or phytol (the respective side chain) was also added to the cultures instead of menatetrenone or vitamin K1, respectively. After 7 and 14 days incubation, cultures were evaluated for cytochemical and functional evidence of osteoclast formation. The number of tartrate-resistant acid phosphatase (TRAP)-positive multinucleated cells (MNCs) and the percentage area of lacunar resorption induced by RANKL and M-CSF were decreased when menatetrenone or geranylgeraniol was added to the cultures. Dose-dependent inhibition of osteoclast formation and lacunar resorption was seen when the cultures were treated with menatetrenone or geranylgeraniol. In contrast, vitamin K1 or phytol did not affect the number of TRAP-positive MNCs nor the percentage area of lacunar resorption. These results indicate that menatetrenone not only influences osteoclast formation via bone stromal cells but also acts directly on circulating osteoclast precursors to influence osteoclast differentiation. These findings also suggest that geranylgeraniol, the side chain of menatetrenone, plays an important role in this inhibitory effect.

3M integral bipolar cup system for dysplastic osteoarthritis. Clinical and radiographic review with five- to seven-year follow-up.

Between 1995 and 1997 we undertook 40 bipolar hip arthroplasties in 35 patients with dysplastic osteoarthritis. The steep and shallow acetabulum was excavated and the bipolar socket was placed high with an adjustment of leg-length. At follow-up of between five and seven years, there were 19 excellent, 16 good and five fair results according to the scoring system of Merle d'Aubigné and Postel. The mean radiographic superior migration of the bipolar socket was 2.1 mm (0 to 10). Osteolysis was noted in three hips within three years of the operation. Abduction on weight-bearing was recorded in 24 hips and the bipolar system was found to be functioning predominantly between the inner bearing and the metal femoral head in 20.

Development and characterization of microsatellite markers for Cryptomeria japonica D.Don.

Thirty four microsatellite markers for Cryptomeria japonica D. Don were developed by searching three types of library: a database of C. japonica cDNA sequences, a standard non-enriched genomic DNA library and a microsatellite-enriched library using magnetic particles. The enrichment of microsatellite sequences using magnetic particles is very efficient compared to the other two methods both in terms of the numbers of markers generated, and in the polymorphism they detect. The microsatellites developed from the genomic DNA library generally have longer repeat sequences and are more polymorphic than those from cDNA. All the developed microsatellite markers in this study showed polymorphism among 28 plus trees selected from locations scattered throughout Japan. The mean number of alleles per locus (MNA) detected in the 28 plus trees ranged from 2 to 21 with an average of 7.5. The Polymorphism Information Content (PIC) ranged from 0.160 to 0.936 with an average of 0.666. Co-dominant segregation of alleles in a three-generation pedigree of C. japonica was demonstrated at 34 microsatellite loci, and the segregation was not distorted from Mendelian expectation for all loci. In 12 out of 34 loci, a null allele was detected. Key relationships between polymorphic parameters, such as MNA and PIC, and the characteristics of microsatellite sequences, such as the longest repeat number, total repeat number and total number of nucleotides, were investigated using rank correlation coefficients, Kendall's tau. A positive correlation was found between repeat lengths and polymorphisms. The markers provide sufficient resolution for investigating gene flow within forests and seed orchards, and for genome mapping.

Correlation between renal blood flow and intrarenal Doppler measurements in canine autotransplanted kidney.

For proper interpretation of the changes in intrarenal Doppler ultrasound measurements, we evaluated the direct correlation between total renal blood flow and intrarenal Doppler parameters. Under progressive constriction of the renal artery in canine autotransplanted kidneys. we simultaneously measured blood flow at the main renal artery and Doppler parameters at the segmental artery. The changes in total renal blood flow were well correlated to changes in peak systolic velocity, end diastolic velocity and resistive index (RI) of the segmental artery (r = 0.964, 0.960 and 0.486, respectively). The acute reduction of total renal blood flow produces a linear decrease in Doppler parameters at intrarenal arteries. These results should be helpful for better understanding the changes in renal hemodynamics in various pathologic conditions as well as those induced by various vasoactive agents including angiotensin converting enzyme inhibitor.

Incorporation of nonnatural amino acids into proteins by using various four-base codons in an Escherichia coli in vitro translation system.

Incorporation of nonnatural amino acids into proteins is a powerful technique in protein research. Amber suppression has been used to this end, but this strategy does not allow multiple incorporation of nonnatural amino acids into single proteins. In this article, we developed an alternative strategy for nonnatural mutagenesis by using four-base codons. The four-base codons AGGU, CGGU, CCCU, CUCU, CUAU, and GGGU were successfully decoded by the nitrophenylalanyl-tRNA containing the complementary four-base anticodons in an Escherichia coli in vitro translation system. The most efficient four-base decoding was observed for the GGGU codon, which yielded 86% of the full-length protein containing nitrophenylalanine relative to the wild-type protein. Moreover, highly efficient incorporation of two different nonnatural amino acids was achieved by using a set of two four-base codons, CGGG and GGGU. This work shows that the four-base codon strategy is more advantageous than the amber suppression strategy in efficiency and versatility.

Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites.

Determination of the mRNA start site is the first step in identifying the promoter region, which is of key importance for transcriptional regulation of gene expression. The 'oligo-capping' method enabled us to introduce a sequence tag to the first base of an mRNA by replacing the cap structure of the mRNA. Using cDNA libraries made from oligo-capped mRNAs, we could identify the transcriptional start site of an individual mRNA just by sequencing the 5'-end of the cDNA. The fine mapping of transcriptional start sites was performed for 5880 mRNAs in 276 human genes. Contrary to our expectations, the majority of the genes showed a diverse distribution of transcriptional start sites. They were distributed over 61.7 bp with a standard deviation of 19.5. Our finding may reflect the dynamic nature of transcriptional initiation events of human genes in vivo.

Identification and characterization of the potential promoter regions of 1031 kinds of human genes.

To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumes of genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA libraries constructed by the "oligo-capping" method. We aligned the mRNA start sites with the genomic sequences and retrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences were searched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) contained TATA boxes, 872 (85%) contained initiators, 999 (97%) contained GC box, and 663 (64%) contained CAAT box. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced in TATA(+)/Inr(+) PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRA gene, and the TM30pl genes, which showed highly colon specific expression patterns, the consensus sequences of E boxes were commonly observed. The PPRs were also useful for exploring promoter SNPs.

Effect of single base insertion into anticodon loop of frameshift suppressor tRNA.

Frameshift suppressor tRNAs containing an additional nucleotide at anticodon loop were prepared and their translational activity was evaluated in an E. coli in vitro translation system. The mutated tRNA(CCCG) was chemically aminoacylated with nitrophenylalanine, and added to the in vitro translation system together with a streptavidin mRNA containing CGGG codon. Western blot analysis indicates that the mutated tRNAs can decode the four-base codon, except 32.1C and 33.1G mutants.

A covariant change of the two highly conserved bases in the GTPase-associated center of 28 S rRNA in silkworms and other moths.

The GTPase-associated center in 23/28 S rRNA is one of the most conserved functional domains throughout all organisms. We detected a unique sequence of this domain in Bombyx mori species in which the bases at positions 1094 and 1098 (numbering from Escherichia coli 23 S rRNA) are C and G instead of the otherwise universally conserved bases U and A, respectively. These changes were also observed in four other species of moths, but not in organisms other than the moths. Characteristics of the B. mori rRNA domain were investigated by native polyacrylamide gel electrophoresis using RNA fragments containing residues 1030-1128. Although two bands of protein-free RNA appeared on gel, they shifted to a single band when bound to Bombyx ribosomal proteins Bm-L12 and Bm-P complex, equivalent to E. coli L11 and L8, respectively. Bombyx RNA showed lower binding capacity than rat RNA for the ribosomal proteins and anti-28 S autoantibody, specific for a folded structure of the eukaryotic GTPase-associated domain. When the C(1094)/G(1098) bases in Bombyx RNA were replaced by the conserved U/A bases, the protein-free RNA migrated as a single band, and the complex formation with Bm-L12, Bm-P complex, and anti-28 S autoantibody was comparable to that of rat RNA. The results suggest that the GTPase-associated domain of moth-type insects has a labile structural feature that is caused by an unusual covariant change of the U(1094)/A(1098) bases to C/G.

Substrate specificity analysis of microbial transglutaminase using proteinaceous protease inhibitors as natural model substrates.

The substrate specificity of microbial transglutaminase (MTG) from Streptomyces mobaraensis (formerly categorized Streptoverticillium) was studied using a Streptomyces proteinaceous protease inhibitor, STI2, as a model amine-donor substrate. Chemical modification and mutational analysis to address the substrate requirements for MTG were carried out around the putative reactive site region of STI2 on the basis of the highly refined tertiary structure and the solvent accessibility index of Streptomyces subtilisin inhibitor, SSI, a homolog of STI2. The results suggest that the P1 reactive center site (position 70 of STI2) for protease subtilisin BPN' or trypsin may be the prime Lys residue that can be recognized by MTG, when succinylated beta-casein was used as a partner Gln-substrate. It is characteristic in that the same primary enzyme contact region of STI2 is shared by both enzymes, MTG and proteases. For quantitative analysis of the TG reaction, we established an ELISA-based monitoring assay system using an anti-SSI polyclonal antibody highly cross-reactive with STI2. Site-specific STI2 mutants were prepared by an Escherichia coli expression-secretion vector system and subjected to the assay system. We reached several conclusions concerning the nature of the flanking amino acid residues affecting the MTG reactivity of the substrate Lys residue: (i) site-specific mutations from Asn to Lys or Arg at position 69 preceding the amine-donor 70Lys, led to enhanced substrate reactivity; (ii) amino acid replacement at 67Ile with Ser led to higher substrate reactivity, (iii) additive effects were obtained by a combination of the positive mutations at positions 67 and 69 as described above, and (iv) Gly at position 65 might be essential for MTG reaction. Moreover, the substrate specificity of guinea pig liver tissue transglutaminase (GTG) was compared with that of MTG using STI2 and its mutants. In contrast to MTG, replacement of Gly by Asp at position 65 was the most favorable for substrate reactivity. Also, 70Lys appeared not to be a prime amine-donor site for GTG-mediated cross-linking, suggesting a difference in substrate recognition between MTG and GTG.

Functional analysis of the individual oligosaccharide chains of sendai virus fusion protein.

The roles of N-linked glycosylation in the intracellular transport and fusion activity of the Sendai virus fusion (F) protein were studied. Each of three potential glycosylation motifs (designated g1, g2, and g3) in the F protein was mutated separately or in combination with the other sites. When the mutant F proteins were transiently expressed in COS cells, they showed significant changes in electrophoretic mobility, indicating that all three motifs in the F protein are glycosylated. Glycosylation-defective mutants which lacked the g2-oligosaccharide chain showed decreased immunoreactivity with a monoclonal antibody specific for the native conformation and were inefficiently transported to the cell surface. Such mutants, with the exception of a double mutant lacking g1 and g2-oligosaccharide chains, were also not able to induce syncytia formation when cells expressing them plus the hemagglutinin-neuraminidase protein were treated with trypsin. Mutations at the other glycosylation sites did not significantly affect the immunoreactivity with the monoclonal antibody or the efficiency of intracellular transport of the F protein. These results indicate that the N-linked oligosaccharide chain attached at g2 is important for efficient intracellular transport and for the fusion activity of the F protein.

Properties of tofus and soy milks prepared from soybeans having different subunits of glycinin.

The contribution of soybean protein to the physical properties of tofu, a product manufactured by curdling soy milk with coagulants such as calcium or magnesium chloride, was studied by comparing the properties of soy milk prepared from soybeans with different subunits (I, IIa, and IIb) of glycinin with amino acid residues deleted. The breaking stress value of the tofu curds prepared from soybeans having group I was higher than those without group I. The soy milks having group I contained more protein particles and showed more sensitivity to calcium and magnesium ions than those without group I. The amounts of glycinin and protein particles were higher in the soy milks having group I than those in the soy milks without group I. To elucidate the influence of each group on the breaking stress, the glycinin content was adjusted to an identical level in soy milks having each group. Among the tofu curds from three groups, their order of hardness according to their breaking stress was IIa, IIb, and I. The order of particle content among these soy milks was also IIa, IIb, and I. Therefore, the results suggested that the breaking stress value of the tofu curd is dependent upon the number of protein particles in the soy milk and that the number of the particles is determined by the proportion and structure of glycinin in the soybean.

Identification and characterization of cell lines with a defect in a post-adsorption stage of Sendai virus-mediated membrane fusion.

In the early stage of infection, Sendai virus delivers its genome into the cytoplasm by fusing the viral envelope with the cell membrane. Although the adsorption of virus particles to cell surface receptors has been characterized in detail, the ensuing complex process that leads to the fusion between the lipid bilayers remains mostly obscure. In the present study, we identified and characterized cell lines with a defect in the Sendai virus-mediated membrane fusion, using fusion-mediated delivery of fragment A of diphtheria toxin as an index. These cells, persistently infected with the temperature-sensitive variant Sendai virus, had primary viral receptors indistinguishable in number and affinity from those of parental susceptible cells. However, they proved to be thoroughly defective in the Sendai virus-mediated membrane fusion. We also found that viral HN protein expressed in the defective cells was responsible for the interference with membrane fusion. These results suggested the presence of a previously uncharacterized, HN-dependent intermediate stage in the Sendai virus-mediated membrane fusion.

MR appearance of paraganglioma of the cauda equina. Case reports.

PURPOSE: To investigate the value of MR imaging for preoperative diagnosis of paraganglioma of the cauda equina. MATERIAL AND METHODS: A retrospective review of 2 cases of paraganglioma of the cauda equina examined with MR imaging was undertaken. Features assessed included the homogeneity of the lesions, presence or absence of serpiginous flow void and thin hypointense margins. RESULTS: In case 1, the tumor was hyperintense on the postcontrast examination and serpiginous flow void suggested vessels in the upper pole of the tumor. In case 2, the tumor was encapsulated by a thin hypointense margin on both T1- and T2-weighted images, which suggested hemosiderin. CONCLUSION: The MR appearance may be of great value in the preoperative diagnosis of paraganglioma of the cauda equina.