One novel and two uncommon MEFV mutations in Japanese patients with familial Mediterranean fever: a clinicogenetic study.

Familial Mediterranean fever (FMF) is an autoinflammatory disease caused by mutations in the MEFV gene and characterized by recurrent episodes of fever and polyserositis. To date, over 317 MEFV mutations have been reported, only nine of which account for almost all Japanese patients with FMF. Therefore, the prevalence of rare MEFV variants and their clinical characteristics remains unclear. This study identified MEFV mutations previously unreported in the Japanese population and described their clinical features. We performed MEFV genetic testing in 488 Japanese patients with clinically suspected FMF. Of these patients, we retrospectively analyzed three patients with novel or very uncommon MEFV mutations. In all patients, the clinical diagnosis of FMF was made according to Tel-Hashomer's criteria. One novel missense mutation (N679H) and two rare mutations (T681I and R410H) were identified in the MEFV gene. These mutations were found in compound heterozygous or complex genotypes with other known mutations in exons 1 or 2. According to clinical images, all three patients exhibited typical FMF symptoms. A number of patients with FMF caused by novel or uncommon MEFV variants might exist in the Japanese population; therefore, careful genetic testing is required for accurate diagnosis of this curable genetic disorder.

1H, 13C and 15N resonance assignment of the YTH domain of YTHDC2.

In humans, YTH (YT521-B homology) domain containing protein 2 (YTHDC2) plays a crucial role in the phase-shift from mitosis to meiosis. YTH domains bind to methylated adenosine nucleotides such as m6A. In a phylogenic tree, the YTH domain of YTHDC2 (YTH2) and that of the YTH containing protein YTHDC1 (YTH1) belong to the same sub-group. However, the binding affinity of m6A differs between these proteins. Here, we report 1H, 13C and 15N resonance assignment of YTH2 and its solution structure to examine the difference of the structural architecture and the dynamic properties of YTH1 and YTH2. YTH2 adopts a ß1-α1-ß2-α2-ß3-ß4-ß5-α3-ß6-α4 topology, which was also observed in YTH1. However, the ß4-ß5 loops of YTH1 and YTH2 are distinct in length and amino acid composition. Our data revealed that, unlike in YTH1, the structure of m6A-binding pocket of YTH2 formed by the ß4-ß5 loop is stabilized by electrostatic interaction. This assignment and the structural information for YTH2 will provide the insight on the further functional research of YTHDC2.

Direct and rapid genotyping of glutathione-S-transferase M1 and T1 from human blood specimens using the SmartAmp2 method.

Clinical studies have suggested that a defect in both glutathione S-transferase (GST) M1 and GSTT1 increases the risk of drug-induced hepatotoxicity. The present study developed the method that enables genotyping of GSTM1 and GSTT1 directly using a small aliquot of blood samples based on an isothermal Smart amplification process version 2 (SmartAmp-2). SmartAmp-2 reaction could complete the genotyping of GSTM1 and GSTT1 within 40 min. The frequency of wild-type, GSTM1 null, GSTT1 null, and double null was 24, 21, 35, and 19%, respectively, consistent with previous reports in the Japanese population. The genotypes of 94 human genomic DNA samples determined by SmartAmp-2 were identical to those determined by the conventional polymerase chain reaction method. SmartAmp-2 was able to determine the genotypes of GSTM1 and GSTT1 even when human blood specimens were used. The SmartAmp-2 method is a rapid and accurate means of identifying the GSTM1 and GSTT1 genotypes, making it less time and more labor efficient in clinical practice than conventional methods requiring preparation of genomic DNA and electrophoresis. This will contribute to evaluate the susceptibility of disease and adverse reactions to drugs caused by deletion of GSTM1 and GSTT1.

The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.

The degradation of the poly(A) tail is crucial for posttranscriptional gene regulation and for quality control of mRNA. Poly(A)-specific ribonuclease (PARN) is one of the major mammalian 3' specific exo-ribonucleases involved in the degradation of the mRNA poly(A) tail, and it is also involved in the regulation of translation in early embryonic development. The interaction between PARN and the m(7)GpppG cap of mRNA plays a key role in stimulating the rate of deadenylation. Here we report the solution structures of the cap-binding domain of mouse PARN with and without the m(7)GpppG cap analog. The structure of the cap-binding domain adopts the RNA recognition motif (RRM) with a characteristic alpha-helical extension at its C-terminus, which covers the beta-sheet surface (hereafter referred to as PARN RRM). In the complex structure of PARN RRM with the cap analog, the base of the N(7)-methyl guanosine (m(7)G) of the cap analog stacks with the solvent-exposed aromatic side chain of the distinctive tryptophan residue 468, located at the C-terminal end of the second beta-strand. These unique structural features in PARN RRM reveal a novel cap-binding mode, which is distinct from the nucleotide recognition mode of the canonical RRM domains.

One-step detection of the 2009 pandemic influenza A(H1N1) virus by the RT-SmartAmp assay and its clinical validation.

BACKGROUND: In 2009, a pandemic (pdm) influenza A(H1N1) virus infection quickly circulated globally resulting in about 18,000 deaths around the world. In Japan, infected patients accounted for 16% of the total population. The possibility of human-to-human transmission of highly pathogenic novel influenza viruses is becoming a fear for human health and society. METHODOLOGY: To address the clinical need for rapid diagnosis, we have developed a new method, the "RT-SmartAmp assay", to rapidly detect the 2009 pandemic influenza A(H1N1) virus from patient swab samples. The RT-SmartAmp assay comprises both reverse transcriptase (RT) and isothermal DNA amplification reactions in one step, where RNA extraction and PCR reaction are not required. We used an exciton-controlled hybridization-sensitive fluorescent primer to specifically detect the HA segment of the 2009 pdm influenza A(H1N1) virus within 40 minutes without cross-reacting with the seasonal A(H1N1), A(H3N2), or B-type (Victoria) viruses. RESULTS AND CONCLUSIONS: We evaluated the RT-SmartAmp method in clinical research carried out in Japan during a pandemic period of October 2009 to January 2010. A total of 255 swab samples were collected from outpatients with influenza-like illness at three hospitals and eleven clinics located in the Tokyo and Chiba areas in Japan. The 2009 pdm influenza A(H1N1) virus was detected by the RT-SmartAmp assay, and the detection results were subsequently compared with data of current influenza diagnostic tests (lateral flow immuno-chromatographic tests) and viral genome sequence analysis. In conclusion, by the RT-SmartAmp assay we could detect the 2009 pdm influenza A(H1N1) virus in patients' swab samples even in early stages after the initial onset of influenza symptoms. Thus, the RT-SmartAmp assay is considered to provide a simple and practical tool to rapidly detect the 2009 pdm influenza A(H1N1) virus.

Isothermal single nucleotide polymorphism genotyping and direct PCR from whole blood using a novel whole-blood lysis buffer.

Cell lysis and subsequent release of genomic DNA is an ongoing dilemma for molecular biological techniques. In most cases, technologies such as PCR and other amplification techniques require DNA extraction and purification steps. The Smart Amplification Process Version 2 (SmartAmp2) is an isothermal and integrated amplification technology that eliminates the need for time-consuming sample preparation for the rapid detection of nucleic acids, including single nucleotide polymorphisms (SNPs), mutations, and other targets. In addition, DNA amplification directly from whole blood is beneficial and lessens the risk of cross-contamination. Traditional SmartAmp2 assays entail two steps and require an alkali pretreatment step at 98 degrees C prior to the 60 degrees C run. To make SmartAmp2 truly isothermal and to simplify DNA amplification, we hereby introduce the SmartAmp Isothermal Lysis Buffer (SIL-B), a newly developed chaotropic lysis buffer that enables the simultaneous recovery and denaturation of genomic material directly from whole blood at a uniform 60 degrees C. The improved method for isolating nucleic acids from whole blood is a critical milestone in making SmartAmp2 truly isothermal from start to finish at one temperature, increasing its potential to be routinely used in field point-of-care testing. Furthermore, pretreatment with SIL-B enables the PCR amplification of genomic material directly from whole blood.