Bacterial genome mapper: A comparative bacterial genome mapping tool

Recently, next generation sequencing (NGS) technologies have led to a revolutionary increase in sequencing speed and costefficacy. Consequently, a vast number of contigs from many recently sequenced bacterial genomes remain to be accurately mapped and annotated, requiring the development of more convenient bioinformatics programs. In this paper, we present a newly developed web-based bioinformatics program, Bacterial Genome Mapper, which is suitable for mapping and annotating contigs that have been assembled from bacterial genome sequence raw data. By constructing a multiple alignment map between target contig sequences and two reference bacterial genome sequences, this program also provides very useful comparative genomics analysis of draft bacterial genomes. AVAILABILITY: The database is available for free at http://mbgm.kribb.re.kr.     

Combined analysis of the MspI and XbaI polymorphisms in intron 22 of the factor VIII gene for detection of hemophilia A in a Korean population

To determine the usefulness of MspI/int22h-1 (intron 22 homologous region-1) polymorphism of the factor VIII gene for molecular genetic diagnosis of hemophilia A in the Korean population, MspI/intron 22 and XbaI/intron 22 polymorphisms were analyzed in 101 unrelated Korean families with severe hemophilia A. The expected heterozygosity rates of MspI/int22h-1 and XbaI/int22h-1 polymorphisms were 49.5 and 43.6%, respectively; these polymorphisms were not in complete linkage disequilibrium. Combined analysis using both polymorphisms provided an informative rate of 66.3%. These results suggest that PCR analysis of the MspI/int22h-1 polymorphism of the factor VIII gene would be useful for carrier detection and prenatal diagnosis of hemophilia A in the Korean population.     

First record of the beetle family Biphyllidae (Coleoptera) in Korea

The Biphyllidae including four species, Biphyllus lewisi (Reitter), B. marmoratus (Reitter), B. rufopictus (Wollaston) and B. throscoides (Wollaston), are discovered for the first time in Korea. A key, habitus photographs and illustrations of diagnostic characters of the species are presented.     

Adaptive dynamic quadrature demodulation with autoregressive spectral estimation in ultrasound imaging

In medical ultrasound imaging, the frequency-dependent attenuation causes a downshift of the center frequency of transmitted ultrasound as it propagates through the body. The downshifting results in a considerable loss of signal-to-noise ratio (SNR) after quadrature demodulation (QDM) in which down-mixing and low pass filtering are involved. To overcome the problem, dynamic QDMs have been proposed, in which the change in the center frequency along the axial direction is obtained using autocorrelation-based spectral estimation and compensated in the QDM block. As an alternative, this paper proposes an adaptive dynamic QDM using the 2nd-order autoregressive model. The main advantage over the conventional dynamic QDMs is to use real radio-frequency (RF) data in the spectral estimation, while its counterparts require additional steps to obtain either complex RF signals or complex baseband signals. This allows the proposed method to be used with a minimal modification of signal processing blocks. The performances of the proposed method were evaluated through in vitro and in vivo experiments. The performances were also compared with those of the conventional dynamic QDM. From the experiments, it was learned that the proposed method improved SNR by maximally 7.8 dB in the near field compared with the conventional dynamic QDM. In the far field, however, its SNR improvement is similar to its counterpart. This may be explained by the fact that the signal loss mainly results from the amplitude attenuation and the diffraction rather than the frequency downshift in the far field. In addition, the proposed method improved contrast resolution (CR) by at least 6.8%, compared with that of the conventional dynamic QDM. The experimental results demonstrated that the proposed method can be used to improve SNR and CR of ultrasound images in an effective manner.     

FE65 as a link between VLDLR and APP to regulate their trafficking and processing

Background

Loss-of-function mutations in PTEN-induced kinase 1 (PINK1) have been linked to familial Parkinson??s disease, but the underlying pathogenic mechanism remains unclear. We previously reported that loss of PINK1 impairs mitochondrial respiratory activity in mouse brains.

Results

In this study, we investigate how loss of PINK1 impairs mitochondrial respiration using cultured primary fibroblasts and neurons. We found that intact mitochondria in PINK1?/? cells recapitulate the respiratory defect in isolated mitochondria from PINK1?/? mouse brains, suggesting that these PINK1?/? cells are a valid experimental system to study the underlying mechanisms. Enzymatic activities of the electron transport system complexes are normal in PINK1?/? cells, but mitochondrial transmembrane potential is reduced. Interestingly, the opening of the mitochondrial permeability transition pore (mPTP) is increased in PINK1?/? cells, and this genotypic difference between PINK1?/? and control cells is eliminated by agonists or inhibitors of the mPTP. Furthermore, inhibition of mPTP opening rescues the defects in transmembrane potential and respiration in PINK1?/? cells. Consistent with our earlier findings in mouse brains, mitochondrial morphology is similar between PINK1?/? and wild-type cells, indicating that the observed mitochondrial functional defects are not due to morphological changes. Following FCCP treatment, calcium increases in the cytosol are higher in PINK1?/? compared to wild-type cells, suggesting that intra-mitochondrial calcium concentration is higher in the absence of PINK1.

Conclusions

Our findings show that loss of PINK1 causes selective increases in mPTP opening and mitochondrial calcium, and that the excessive mPTP opening may underlie the mitochondrial functional defects observed in PINK1?/? cells.     

Effect of propofol on oxidative stress status in erythrocytes from dogs under general anaesthesia

Background

Piglets are born with eight sharp teeth that during nursing can cause facial lesions on littermates and teat lesions on the sow. Teeth grinding in piglets is therefore often practiced to reduce these lesions. The aim of this study was to assess the consequences of grinding piglet teeth in regard to the occurrence of lesions. In this study the piglets' teeth were grinded in 28 litters, and in 36 litters the piglets' teeth were kept intact. Twice, one time during the first week and one time during the second week after birth facial lesions of the piglets were scored and the teats of the sows were examined for lesions. The facial lesion score accounted for the amount and severity of lesions. The individual observations on piglets in the litter were synthesized in a litter facial lesion score.

Findings

69.8% and 43.5% of the piglets had facial lesions in week 1 and week 2 respectively. The effect of treatment was not significant on litter facial lesion score. The litter facial lesion score was higher in week 1 than in week 2 (p < 0.001) and higher in large litters (p = 0.003) than in small litters. Mortality between week 1 and week 2 was higher in litters with intact teeth (p = 0.02). Sow teat lesions only occurred if litters had intact teeth.

Conclusions

According to our results teeth grinding is only justifiable in large litters.     

Highly Pure and Expandable PSA-NCAM-Positive Neural Precursors from Human ESC and iPSC-Derived Neural Rosettes

Homogeneous culture of neural precursor cells (NPCs) derived from human pluripotent stem cells (hPSCs) would provide a powerful tool for biomedical applications. However, previous efforts to expand mechanically dissected neural rosettes for cultivation of NPCs remain concerns regarding non-neural cell contamination. In addition, several attempts to purify NPCs using cell surface markers have not demonstrated the expansion capability of the sorted cells. In the present study, we show that polysialic acid-neural cell adhesion molecule (PSA-NCAM) is detected in neural rosette cells derived from hPSCs, and employ PSA-NCAM as a marker for purifying expandable primitive NPCs from the neural rosettes. PSA-NCAM-positive NPCs (termed hNPC(PSA-NCAM+)) were isolated from the heterogeneous cell population of mechanically harvested neural rosettes using magnetic-based cell sorting. The hNPC(PSA-NCAM+) extensively expressed neural markers such as Sox1, Sox2, Nestin, and Musashi-1 (80～98% of the total cells) and were propagated for multiple passages while retaining their primitive characteristics in our culture condition. Interestingly, PSA-NCAM-negative cells largely exhibited characteristics of neural crest cells. The hNPC(PSA-NCAM+) showed multipotency and responsiveness to instructive cues towards region-specific neuronal subtypes in vitro. When transplanted into the rat striatum, hNPC(PSA-NCAM+) differentiated into neurons, astrocytes, and oligodendrocytes without particular signs of tumorigenesis. Furthermore, Ki67-positive proliferating cells and non-neural lineage cells were rarely detected in the grafts of hNPC(PSA-NCAM+) compared to those of neural rosette cells. Our results suggest that PSA-NCAM-mediated cell isolation provides a highly expandable population of pure primitive NPCs from hPSCs that will lend themselves as a promising strategy for drug screening and cell therapy for neurodegenerative disorders.     

Genotype patterns and characteristics of PRNP in the Korean population

Creutzfeldt-Jakob disease (CJD), included in the human transmissible spongiform encephalopathies (TSE), is widely known to be caused by an abnormal accumulation of misfolding prion protein in the brain. Human prion protein gene (PRNP) is mapped in chromosome 20p13 and many single nucleotide polymorphisms (SNPs) in PRNP have been discovered. However, the functionality of SNPs in PRNP is yet unclear, though several SNPs have been known as important mutation related with susceptibility human prion diseases. Our aim is to identify specific genotype patterns and characteristics in the PRNP genomic region and to understand susceptibility among Korean discriminated prion disease patients, suspected CJD patients and the KARE data group. Here, we have researched genotypes and SNPs allele frequencies in PRNP in discriminated prion disease patients group (n = 22), suspected prion diseases patients group (n = 163) and the Korea Association REsource (KARE) data group (n = 296) in Korea. The sequencing regions were promoter region, exon1 and exon2 with their junction parts among 481 samples. A total of 25 SNPs were shown in this study. Nucleotide frequencies of all SNPs are exceedingly tended to bias toward dominant homozygote types except in rs2756271. Genotype frequencies at codon 129 and 219 coding region were similar with previous studies in Korea and Japan. Pathogenic mutations such as 102P/L, 200E/K and 203V/I were observed in discriminated CJD patients group, and 180V/I and 232M/R were shown in suspected prion disease patients group and the KARE data group. A total of 10 SNPs were newly identified, six in the promoter region, one in exon 2 and three in the 3′ UTR. The strong and unique linkage disequilibrium (D' = 0.94, r² = 0.89) was observed between rs57633656 and rs1800014 which is located in codon 219 coding region. We expect that these data can be provided to determine specific susceptibility and a protective factor of prion diseases not only in Koreans but also in East Asians.     

Immunoevasive property of a polydnaviral product, CpBV-lectin, protects the parasitoid egg from hemocytic encapsulation of Plutella xylostella (Lepidoptera: Yponomeutidae)

Immunosuppression is the main pathological symptom of the diamondback moth, Plutella xylostella (Lepidoptera: Yponomeutidae), parasitized by an endoparasitoid wasp, Cotesia plutellae (vestalis, Hymenoptera: Braconidae). C. plutellae bracovirus (CpBV), which is a symbiotic virus of C. plutellae, has been known to be the main parasitic factor in the host-parasitoid interaction. CpBV-lectin, encoded in the viral genome and expressed in P. xylostella during early parasitization stage, was suspected to play a role in immunoevasion of defense response. Here we expressed CpBV-lectin in Sf9 cells using a recombinant baculovirus for subsequent functional assays. The recombinant CpBV-lectin exhibited hemagglutination against vertebrate erythrocytes. Its hemagglutinating activity increased with calcium, but inhibited by adding EDTA, indicating its C-type lectin property. CpBV-lectin showed specific carbohydrate-binding affinity against N-acetyl glucosamine and N-acetyl neuraminic acid. The role of this CpBV-lectin in immunosuppression was analyzed by exposing hemocytes of nonparasitized P. xylostella to rat erythrocytes or FITC-labeled bacteria pretreated with recombinant CpBV-lectin, which resulted in significant reduction in adhesion or phagocytosis, respectively. The immunosuppressive activity of CpBV-lectin was further analyzed under in vitro encapsulation response of hemocytes against parasitoid eggs collected at 1- or 24-h post-parasitization. Hemocytic encapsulation was observed against 1-h eggs but not against 24-h eggs. When the 1-h eggs were pretreated with the recombinant CpBV-lectin, encapsulation response was completely inhibited, where CpBV-lectin bound to the parasitoid eggs, but not to hemocytes. These results suggest that CpBV-lectin interferes with hemocyte recognition by masking hemocyte-binding sites on the parasitoid eggs.     

Naturally acquired IgM antibody response to the C-terminal region of the merozoite surface protein 1 of Plasmodium vivax in Korea: use for serodiagnosis of vivax malaria

The antibody levels against the C-terminal region of the merozoite surface protein 1 of Plasmodium vivax (PvMSP1c) were measured in 276 patients with P. vivax malaria (patient group), 320 malaria-na?ve healthy individuals (control group 1), and 70 malaria-na?ve individuals with various disorders (control group 2) using the immunoglobulin M (IgM) capture enzyme-linked immunosorbent assay (ELISA) and the direct sandwich ELISA. To evaluate the antibody response during relapse, 5 relapsed patients were tested using the IgM capture ELISA. The IgM antibodies were negative in 99.7% of control group 1 and in 100% of control group 2; they were positive in 90.6% of the patient group. The total antibody levels were positive in 88.4% of the patient group with the direct sandwich ELISA. The sera from the second malaria episode, i.e., relapsed patients, were 100% positive on the IgM capture ELISA. The results of this study suggest that the IgM capture ELISA may be a useful diagnostic method for P. vivax malaria for both primary infection and relapse.