Three TNF α single nucleotide polymorphisms in the Japanese population

Background : Tumour necrosis factor-alpha (TNF &#102 ) is an essential regulator of immune responses and is implicated to relate to several types of disease susceptibilities. Population information on polymorphisms is essential for the study of genetic diseases. Aim : To obtain accurate information about single nucleotide polymorphisms (SNPs) in the TNF &#102 gene in the Japanese population. Subjects and Methods : The entire TNF &#102 gene was screened for SNPs by directly sequencing 48 chromosomes derived from 24 unrelated Japanese individuals. Allele frequencies of each polymorphism were determined and compared with those previously reported in other populations. Results : Three SNPs, -308G/A at nt -308, IVS1 + 125G/A at nt 492 and IVS3 + 104G/A at nt 1359 were observed, of which one (IVS3 + 104G/A at nt 1359) was novel. In addition, allele frequencies of -308G/A were remarkably different from those presented in the NCBI dbSNP, indicating a significant ethnic difference. Conclusions : The polymorphisms and allele frequencies obtained in this study will be useful for genetic studies of common diseases such as osteoporosis and rheumatoid arthritis in the Japanese population.     

Design and application research of nucleotide sequence analysis system software

INTRODUCTION　　From integrallevel and celllevel,the research of organism and diseasediagnosishave already entered molecular level.Molecular biology is the science to researchstructure and function of organism macromolecule.Based on differentgene code se-…     

Complete nucleotide sequence of the new potexvirus “Alstroemeria virus X”

Summary. A flexuous virus was isolated in Japan from an alstroemeria plant showing mosaic symptoms. The virus had a broad host range but had systemically latent infectivity in alstroemeria. The virus was assigned to the genus Potexvirus based on morphology and physical properties and on an analysis of the complete nucleotide sequence. The genomic RNA of the virus was 7,009 nucleotides in length, excluding the 3′-terminal poly (A) tail. It contained five open reading frames (ORFs), which was consistent with other members of the genus Potexvirus. Although nucleotide sequences of the ORFs differ from previously reported potexviruses, a phylogenetic analysis placed it phylogenetically close to Narcissus mosaic virus and Scallion virus X. Therefore, we propose that this virus should be designated as Alstroemeria virus X (AlsVX).     

Compartmentalization of cyclic nucleotide signaling: a question of when, where, and why?

Preciseness of cellular behavior depends upon how an extracellular cue mobilizes a correct orchestra of cellular messengers and effector proteins spatially and temporally. This concept, termed compartmentalization of cellular signaling, is now known to form the molecular basis of many aspects of cellular behavior in health and disease. The cyclic nucleotides cyclic adenosine monophosphate and cyclic guanosine monophosphate are ubiquitous cellular messengers that can be compartmentalized in three ways: first, by their physical containment; second, by formation of multiple protein signaling complexes; and third, by their selective depletion. Compartmentalized cyclic nucleotide signaling is a very prevalent response among all cell types. In order to understand how it becomes relevant to cellular behavior, it is important to know how it is executed in cells to regulate physiological responses and, also, how its execution or dysregulation can lead to a pathophysiological condition, which forms the scope of the presented review.     

Are single nucleotide polymorphisms of the immunoglobulin A Fc receptor gene associated with allergic asthma?

BACKGROUND: Eosinophils are important components of allergic inflammation. The immunoglobulin A (IgA) Fc receptor (FcalphaRI), encoded by the FCAR gene, is a possible candidate for eosinophil activation at mucosal surfaces, where IgA is abundant. Both elevated cell surface expression of FcalphaRI and increased avidity for IgA were described on eosinophils from allergic subjects. The aim of our study was to examine the possible association of FCAR gene polymorphisms with allergic asthma. METHODS: We screened three regions of the FCAR gene: (1) the promoter region, (2) exon 3, encoding the first extracellular domain (EC1), and (3) exon 5, coding for the transmembrane and cytoplasmic domain, for new and published polymorphisms using a sensitive temperature gradient gel electrophoresis technique and compared their frequencies in 112 patients diagnosed with allergic asthma and 100 healthy controls. RESULTS: Six polymorphisms, including two novel ones, were detected. No differences between patients and controls were found in the distribution of any of these polymorphisms. CONCLUSION: FcalphaRI polymorphism does not seem to be a risk factor in allergic asthma. Nevertheless, this is the first report on the distribution of 6 single nucleotide polymorphisms of the FCAR gene in a human population and the first study on FCAR polymorphism in allergic asthma.     

Is the TAP2 single nucleotide polymorphism rs241447 truly associated with psoriasis in Poles?

Psoriasis vulgaris (PsV) is strongly associated with HLA-C*06:02. HLA class I molecules present antigenic peptides to CD8⁺ T lymphocytes. Peptide transport from cytosol to the endoplasmic reticulum is mediated by a transporter associated with antigen processing (TAP) composed of TAP1 and TAP2 polymorphic proteins. Here, we compared the distribution of three coding single nucleotide polymorphisms (SNPs), rs1057141 in TAP1 and rs1800454 and rs241447 in TAP2 as well as the HLA-C*06:02 allele in 438 patients diagnosed with PsV and 493 control individuals. In patients and controls non-stratified by HLA-C*06:02, TAP2 rs241447 was associated with PsV but other TAP1 and TAP2 SNPs were not. By contrast, stratification according to the Svejgaard and Ryder formula, as well as a logistic regression approach and haplotype analysis demonstrated that the effect of TAP2 rs241447 was entirely related to the presence of HLA-C*06:02. The secondary effect of TAP2 rs241447 in relation to primary effect of HLA-C*06:02 resulted from linkage disequilibrium (albeit not strong) between both markers. We conclude that joint coexistence of HLA-C*06:02 and the TAP2 rs241447C risk allele on the extended haplotype might explain the effect of TAP2 observed by us.     

Modulation of the hepatocyte rough endoplasmic reticulum single chloride channel by nucleotide–Mg2+ interaction

The effect of nucleotides on single chloride channels derived from rat hepatocyte rough endoplasmic reticulum vesicles incorporated into bilayer lipid membrane was investigated. The single chloride channel currents were measured in 200/50?mmol/l KCl cis/trans solutions. Adding 2.5?mM adenosine triphosphate (ATP) and adenosine diphosphate (ADP) did not influence channel activity. However, MgATP addition inhibited the chloride channels by decreasing the channel open probability (Po) and current amplitude, whereas mixture of Mg²⁺ and ADP activated the chloride channel by increasing the Po and unitary current amplitude. According to the results, there is a novel regulation mechanism for rough endoplasmic reticulum (RER) Cl^? channel activity by intracellular MgATP and mixture of Mg²⁺ and ADP that would result in significant inhibition by MgATP and activation by mixture of Mg²⁺ and ADP. These modulatory effects of nucleotide?CMg²⁺ complexes on chloride channels may be dependent on their chemical structure configuration. It seems that Mg?Cnucleotide?Cion channel interactions are involved to produce a regulatory response for RER chloride channels.     

Predicted stem-loop structures and variation in nucleotide sequence of 3′ noncoding regions among animal calicivirus genomes

Caliciviruses are nonenveloped with a polyadenylated genome of approximately 7.6 kb and a single capsid protein. The RNA Fold computer program was used to analyze 3-terminal noncoding sequences of five feline calicivirus (FCV), rabbit hemorrhagic disease virus (RHDV), and two San Miguel sea lion virus (SMSV) isolates. The FCV 3-terminal sequences are 40–46 nucleotides in length and 72–91% similar. The FCV sequences were predicted to contain two possible duplex structures and one stem-loop structure with free energies of –2.1 to –18.2 kcal/mole. The RHDV genomic 3-terminal RNA sequences are 54 nucleotides in length and share 49% sequence similarity to homologous regions of the FCV genome. The RHDV sequence was predicted to form two duplex structures in the 3-terminal noncoding region with a single stem-loop structure, resembling that of FCV. In contrast, the SMSV 1 and 4 genomic 3-terminal noncoding sequences were 185 and 182 nucleotides in length, respectively. Ten possible duplex structures were predicted with an average structural free energy of –35 kcal/mole. Sequence similarity between the two SMSV isolates was 75%. Furthermore, extensive cloverleaflike structures are predicted in the 3 noncoding region of the SMSV genome, in contrast to the predicted single stem-loop structures of FCV or RHDV.Disclaimer: No endorsements are herein implied. Brand names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standards of the products, and the use of the names by the USDA implies no approval of the products to the exclusion of others that may also be suitable.     

TNF-α promoter single nucleotide polymorphisms and haplotypes associate with susceptibility of immune thrombocytopenia in Chinese adults

Objective

Tumor necrosis factor-alpha (TNF-α) participates as a candidate susceptibility factor for immune thrombocytopenia (ITP). This study attempted to investigate the association between five single nucleotide polymorphisms (SNPs) spanning the TNF-α promoter and the susceptibility of primary ITP in Chinese Han adults.

Methods

In 215 adult primary ITP patients and 206 healthy controls, SNPs were detected by PCR-RFLP and PCR-SSP. The χ² test or fisher’s exact test was used to compare frequencies of genotypes and alleles between patients and controls. Haplotypes were analyzed with the SHEsis online program. TNF-α, IFN-γ and Galectin-9 mRNA of 35 newly diagnosed adult ITP patients and 35 healthy controls were detected by qRT-PCR.

Results

The haplotype GGC (−238G/−308G/−857C) of TNF-α promoter was significantly associated with a decreased susceptibility of primary ITP, especially in males. The relative levels of mRNA expression of TNF-α, IFN-γ and Gal-9 in adult active primary ITP patients was significantly up-regulated compared with patients in remission and controls.

Conclusions

This study represented the first report that the haplotype GGC of TNF-α was differentially associated with the susceptibility of primary ITP in Chinese Han adults. The up-regulation of TNF-α, IFN-γ and Galectin-9 was significantly correlated with active primary ITP in adult patients.     

Association between single nucleotide polymorphism of vitamin D receptor start codon Fok Ⅰ and urinary calcium level

Objective To investigate the association between single nucleotide polymorphism (SNP) of Fok Ⅰ [the vitamin D receptor (VDR) start codon] and urinary calcium level. Methods Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to determine the Fok Ⅰ ploymorphism in peripheral blood samples from SO patients with (urinary stone group) and another 50 without urinary stones (control group). The genotype distribution and frequencies of Fok Ⅰ allele were compared between two groups. 24-h urinary calcium level was measured by routine urinalysis. Results The distribution of genotypes (urinary stone group vs controls) was 28% (14/50) vs 34% (17/50) for FF, 52% (26/50) vs 56% (28/50) for Ff, 20% (10/50) vs 10% (5/50) for ff, with the statistical differencs for FF and ff between two groups (P<0.05). The frequency of F allele was 54% (54/100) in urinary stone group vs 62% (62/100) in the controls (P>0.05) , and 46% (46/100) in urinary stone group vs 38% (38/100) in the controls, respectively (P<0.05). Level of 24-h urinary calcium level among FF, Ff and ff genetype- bearing subjects in urinary stone group was respectively (0.030±0.008) mmol/kg, (0.037±0.009) mmol/kg and (0.081±0.013) mmol/kg while (0.028±0.006) mmol/kg, (0.036±0.002) mmol/kg and (0.043±0.003) mmol/kg in control group, which was significantly different among ff genotype-bearing subjects (P<0.05) but not among FF or Ff genotype-bearing ones (P>0.05) of two groups. Conclusions The polymorphism of VDR start codon Fok I may be associared with increase of urinary calcium level in patients with urinary stones.     

Individualized significance of the −251 A/T single nucleotide polymorphism of interleukin-8 in severe infections

Based on the concept of the individualized nature of sepsis, we investigated the significance of the ?251 A/T (rs4073) single nucleotide polymorphism (SNP) of interleukin (IL)-8 in relation to the underlying infection. Genotyping was performed in 479 patients with severe acute pyelonephritis (UTI, n?=?146), community-acquired pneumonia (CAP, n?=?109), intra-abdominal infections (IAI, n?=?119), and primary bacteremia (BSI, n?=?105) by restriction fragment length polymorphism of the polymerase chain reaction (PCR) product and compared with 104 healthy volunteers. Circulating IL-8 was measured within the first 24 h of diagnosis by an immunosorbent assay. Carriage of the AA genotype was protective from the development of UTI (odds ratio 0.38, p: 0.007) and CAP (odds ratio 0.30, p: 0.004), but not from IAI and BSI. Protection from the development of severe sepsis/septic shock was provided for carriers of the AA genotype among patients with UTI (odds ratio 0.15, p: 0.015). This was accompanied by greater concentrations of circulating IL-8 among patients with the AA genotype. It is concluded that carriage of rs4073 modifies susceptibility for severe infection in an individualized way. This is associated with a modulation of circulating IL-8.     

The nucleotide sequence of the 5′ non-coding and capsid coding genome regions of two bovine enterovirus strains

Summary The sequence of cDNA clones representing the 5 non-coding regions (NCR) and capsid regions of two bovine enteroviruses (strains PS-87 and RM-2; serotype two viruses) have been determined and compared with that obtained from a serotype one strain (VG-5-27). All three strains showed a longer 5 NCR compared to human enteroviruses and rhinoviruses due in part to a hundred residue insertion approximately at a hundred residues in from the 5 end. However, another domain occurring at nucleotide 187–222 in poliovirus is absent in each bovine enterovirus. Comparisons of the predicted structural protein amino acid sequences indicate that PS-87 shares most sequence identity with RM-2 and then with VG-5-27 in that order. The VP1 protein of PS-87 and RM-2 are shorter than the equivalent VP1 of VG-5-27 due in part to a truncation at their C-terminii. VP3 is only slightly smaller than VP2 in each virus.The nucleotide sequences have been submitted to the EMBL database under the accession numbers X79368 and X79369 for PS-87 and RM-2 respectively     

Functional characterization of nonsynonymous single nucleotide polymorphisms in the electrogenic Na+�CHCO 3 ? cotransporter NBCe1A

The electrogenic Na(+)-HCO(3)(-) cotransporter NBCe1 encoded by SLC4A4 plays essential roles in the regulation of intracellular/extracellular pH. Homozygous mutations in NBCe1 cause proximal renal tubular acidosis associated with ocular abnormalities. In the present study, we tried to perform functional characterization of the four nonsynonymous single nucleotide polymorphisms (SNPs), E122G, S356Y, K558R, and N640I in NBCe1A. Functional analysis in Xenopus oocytes revealed that while the K558R variant had a significantly reduced transport activity corresponding to 47% of the wild-type activity, the remaining variants E122G, S356Y, and N640I did not change the NBCe1A activity. Apparent Na(+) affinity of K558R was not different from that of wild-type NBCe1A. Immunohistological analyses in HEK293 cells and MDCK cells indicated that none of these SNPs changed the trafficking behaviors of NBCe1A. Functional analysis in HEK293 cells also revealed that only the K558R variant had a reduced transport activity, corresponding to 41-47% of the wild-type activity. From these results, we conclude that among four SNPs, only the K558R variant, which is predicted to lie in transmembrane segment 5, significantly reduces the NBCe1A activity without changing the trafficking behavior or the apparent extracellular Na(+) affinity.     

Complete nucleotide sequence of a new potexvirus, “Phaius virus X”, isolated from Phaius flavus Lindl.

A flexuous virus was isolated from cultivated Phaius flavus Lindl. plants in Japan with a latent infection. The virus was assigned to the genus Potexvirus based on morphology and analysis of its complete nucleotide sequence. The genome is 5,816 nucleotides in length, excluding the 3′-terminal poly (A) tail, and contains five open reading frames (ORFs), which is consistent with other members of the genus Potexvirus. The ORF nucleotide sequences differ from those of previously reported potexviruses, but the newly isolated virus is closely related to lily virus X and mint virus X. We propose that this virus should be designated as Phaius virus X (PhaVX).     

Activation of nucleotide receptors inhibits M-type K current [I K(M)] in neuroblastoma × glioma hybrid cells

A phospholipase-C-linked nucleotide receptor, sensitive to both uridine and adenosine triphosphate (UTP and ATP) has been cloned from NG108-15 neuroblastoma × glioma hybrid cells. We have tested whether activation of this receptor could inhibit the voltage-dependent K⁺ current [I _K(M) or M-current] in NG108-15 cells recorded using whole-cell patch-clamp methods. Both UTP and ATP inhibited I _K(M) by 44% and 42%, respectively, at 100 M. Mean IC₅₀ values were: UTP, 0.77±0.27 M; ATP, 1.81±0.82 M. The order of nucleotide and nucleoside activity at 100 M was: UTP = ATP > ATP[S] = ITP > 2 MeSATP > ADP = GTP AMP-CPP, adenosine, where ATP[S] is adenosine 5-O-(3-thiotriphosphate), ITP is inosine 5-triphosphate, 2-MeSATP is 2-methylthio ATP and AMP-CPP is , methylene ATP. This rank order accords with their activities at the cloned P_2U receptor. Effects were not inhibited by suramin (up to 500 M) or by pre-incubation for 12 h in 500 ng·ml^–1 Pertussis toxin. Inhibition of I_K(M) was frequently preceded by a transient outward current, probably a Ca²⁺-activated K⁺ current, responding to Ca²⁺ mobilization. No effect on the delayed rectifier K⁺ current was observed. These observations match those expected from stimulating other phospholipase-C-linked receptors in NG108-15 cells.Shemyakin Institute of Bio-organic Chemistry, on leave from the Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia     

Determination of the nucleotide sequences at the extreme 5′ and 3′ ends of swine hepatitis E virus genome

Summary.  The nucleotide sequences at the extreme 5′ and 3′ ends of swine hepatitis E virus (swine HEV) genome were determined, and genomic sequence of swine HEV is now complete. Sequence analysis revealed that the 3′ and 5′ non-coding regions (NCRs) of swine HEV are closely related to that of the US-1 and US-2 strains of human HEV. Like the two U.S. strains of human HEV, an extra G residue immediately proceeding the poly(A) tail was identified in swine HEV. The 5′ NCR of swine HEV also differed from many HEV strains: it lacks an A residue at its 5′ very end, and the extra 9 nucleotides in the US-2 strain. In the 3′ NCR, swine HEV shared 90–91% nucleotide sequence identities with the US-1 and US-2 strains but only about 58–65% identities with other HEV strains. This study further suggests that the US-1 and US-2 strains of human HEV may be of swine origin. The availability of the complete sequence of swine HEV should facilitate the construction of an infectious cDNA clone of swine HEV. Received April 20, 2001 Accepted July 10, 2001     

eIF2B promotes eIF5 dissociation from eIF2?GDP to facilitate guanine nucleotide exchange for translation initiation

Protein synthesis factor eIF2 delivers initiator tRNA to the ribosome. Two proteins regulate its G-protein cycle: eIF5 has both GTPase-accelerating protein (GAP) and GDP dissociation inhibitor (GDI) functions, and eIF2B is the guanine nucleotide exchange factor (GEF). In this study, we used protein–protein interaction and nucleotide exchange assays to monitor the kinetics of eIF2 release from the eIF2•GDP/eIF5 GDI complex and determine the effect of eIF2B on this release. We demonstrate that eIF2B has a second activity as a GDI displacement factor (GDF) that can recruit eIF2 from the eIF2•GDP/eIF5 GDI complex prior to GEF action. We found that GDF function is dependent on the eIF2Bɛ and eIF2Bγ subunits and identified a novel eIF2–eIF2Bγ interaction. Furthermore, GDF and GEF activities are shown to be independent. First, eIF2B GDF is insensitive to eIF2α phosphorylation, unlike GEF. Second, we found that eIF2Bγ mutations known to disrupt GCN4 translational control significantly impair GDF activity but not GEF function. Our data therefore define an additional step in the protein synthesis initiation pathway that is important for its proper control. We propose a new model to place eIF2B GDF function in the context of efficient eIF2 recycling and its regulation by eIF2 phosphorylation.