[Spontaneous coronary artery dissection in a heart transplant patient. Report of one case]. / Disección coronaria espontánea en paciente trasplantada de corazón.

Spontaneous coronary artery dissection is an uncommon cause of acute coronary syndrome that predominantly affects women without cardiovascular risk factors. In transplant patients, spontaneous coronary artery dissection is an extremely rare condition, having been described in only three patients, in whom vascular damage secondary to the use of anticalcineurinics is postulated as a probable mechanism. We report a spontaneous coronary dissection in a female who received a heart transplant at 34 years of age. The diagnosis was made in a follow-up coronary angiography three years after transplantation, supplemented with optical coherence tomography. A percutaneous coronary revascularization of the involved artery was performed, with good immediate results and at one year of follow-up.

Revealing immune responses in the Mycobacterium avium subsp. paratuberculosis-infected THP-1 cells using single cell RNA-sequencing.

Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne's disease, which is a chronic and debilitating disease in ruminants. MAP is also considered to be a possible cause of Crohn's disease in humans. However, few studies have focused on the interactions between MAP and human macrophages to elucidate the pathogenesis of Crohn's disease. We sought to determine the initial responses of human THP-1 cells against MAP infection using single-cell RNA-seq analysis. Clustering analysis showed that THP-1 cells were divided into seven different clusters in response to phorbol-12-myristate-13-acetate (PMA) treatment. The characteristics of each cluster were investigated by identifying cluster-specific marker genes. From the results, we found that classically differentiated cells express CD14, CD36, and TLR2, and that this cell type showed the most active responses against MAP infection. The responses included the expression of proinflammatory cytokines and chemokines such as CCL4, CCL3, IL1B, IL8, and CCL20. In addition, the Mreg cell type, a novel cell type differentiated from THP-1 cells, was discovered. Thus, it is suggested that different cell types arise even when the same cell line is treated under the same conditions. Overall, analyzing gene expression patterns via scRNA-seq classification allows a more detailed observation of the response to infection by each cell type.

Disección coronaria espontánea en paciente trasplantada de corazón / Spontaneous coronary artery dissection in a heart transplant patient: report of one case

Spontaneous coronary artery dissection is an uncommon cause of acute coronary syndrome that predominantly affects women without cardiovascular risk factors. In transplant patients, spontaneous coronary artery dissection is an extremely rare condition, having been described in only three patients, in whom vascular damage secondary to the use of anticalcineurinics is postulated as a probable mechanism. We report a spontaneous coronary dissection in a female who received a heart transplant at 34 years of age. The diagnosis was made in a follow-up coronary angiography three years after transplantation, supplemented with optical coherence tomography. A percutaneous coronary revascularization of the involved artery was performed, with good immediate results and at one year of follow-up.

The genome of the Java medaka (Oryzias javanicus): Potential for its use in marine molecular ecotoxicology.

The Java medaka (Oryzias javanicus) is distributed in tropical brackish water and is considered as an ecotoxicological experimental organism for assessing diverse pollutions and global climate change effects in the ocean. In this study, we sequenced and assembled the genome of O. javanicus using the Oxford Nanopore technique and anchored the scaffolds to the 24 genetic linkage map of a sister species Oryzias melastigma. The assembled genome consisted of 773 scaffolds including 24 LG-based scaffolds, and the estimated genome length was 846.3 Mb (N50 = 19.3 Mb), containing 24,498 genes. As detoxification processes are crucial in aquatic organisms, antioxidant-related genes including glutathione S-transferases, superoxide dismutase, catalase, and glutathione peroxidase were identified in this study. In the genome of O. javanicus, a total of 21 GSTs, 4 SODs, 1 CAT, and 7 GPxs were identified and showed high similarities between sister species O. melastigma and Oryzias latipes. In addition, despite having 8 classes of cytosolic GSTs family, medaka showed no presence of GST pi and sigma classes, which are predominantly found in carp and salmon, but not in neoteleostei. This study adds another set to genome-library of Oryzias spp. and is a useful resource for better understanding of the molecular ecotoxicology.

The complete chloroplast genome of Hemerocallis Fulva.

We have sequenced the complete chloroplast genome of Hemerocallis fulva, a species of the Asphodelaceae family, through Illumina HiSeq paired-end sequencing. The total size of chloroplast genome of Hemerocallis fulva was 155,855 bp with a large single-copy (LSC) region of 84,607 bp, a small single-copy (SSC) region of 18,508 bp, and a pair of identical inverted repeat regions (IRs) of 26,370 bp. The genome contained a total of 112 genes, including 79 protein-coding genes, 29 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. The phylogenetic analysis of Hemerocallis fulva with 10 related species exhibited the closest taxonomical relationship with Aloe species in the Asphodelaceae family.

The complete chloroplast genome of Codonopsis lanceolata (Campanulaceae).

The complete chloroplast genome sequence of Codonopsis lanceolata was determined by next generation sequencing. The total length of chloroplast genome of C. lanceolata was 169,447 bp long, including a large single-copy (LSC) region of 85,253 bp, a small single-copy (SSC) region of 8060 bp, and a pair of identical inverted repeat regions (IRs) of 38,067 bp. A total of 110 genes was annotated, resulting in 79 protein-coding genes, 27 tRNA genes, and 4 rRNA genes. The phylogenetic analysis of C. lanceolata with related chloroplast genome sequences in this study provided the taxonomical relationship of C. lanceolata in the genus Campanula.

The complete chloroplast genomes of three Korean Echinochloa crus-galli accessions.

The complete chloroplast (cp) genomes of three Echinochloa crus-galli accessions (KR822684, KR822685, and KR822686) are reported in this work. The cp genome size is similar in three accessions, ranging from 139 846 bp to 139 860 bp. All three genomes have two inverted repeats (IR) of 22 748 bp per each IR with a large single copy (LSC) region of 81 833-81 844 bp and a small single copy (SSC) region of 12 517-12 520 bp. The total of 131 genes was identified in individual accession. Phylogenetic analysis revealed three Korean Echinochloa accessions belonged to E. crus-galli, and diverged less than 0.1 million years ago (Mya).

Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing.

Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF) in genetically modified rice cells. A total of 29.3 Gb (~72× coverage) was sequenced with a 2 × 150 bp paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR) amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites.

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing.

BACKGROUND: The honey bee is an important model system for increasing understanding of molecular and neural mechanisms underlying social behaviors relevant to the agricultural industry and basic science. The western honey bee, Apis mellifera, has served as a model species, and its genome sequence has been published. In contrast, the genome of the Asian honey bee, Apis cerana, has not yet been sequenced. A. cerana has been raised in Asian countries for thousands of years and has brought considerable economic benefits to the apicultural industry. A cerana has divergent biological traits compared to A. mellifera and it has played a key role in maintaining biodiversity in eastern and southern Asia. Here we report the first whole genome sequence of A. cerana. RESULTS: Using de novo assembly methods, we produced a 238 Mbp draft of the A. cerana genome and generated 10,651 genes. A.cerana-specific genes were analyzed to better understand the novel characteristics of this honey bee species. Seventy-two percent of the A. cerana-specific genes had more than one GO term, and 1,696 enzymes were categorized into 125 pathways. Genes involved in chemoreception and immunity were carefully identified and compared to those from other sequenced insect models. These included 10 gustatory receptors, 119 odorant receptors, 10 ionotropic receptors, and 160 immune-related genes. CONCLUSIONS: This first report of the whole genome sequence of A. cerana provides resources for comparative sociogenomics, especially in the field of social insect communication. These important tools will contribute to a better understanding of the complex behaviors and natural biology of the Asian honey bee and to anticipate its future evolutionary trajectory.

[First successful bridge to cardiac transplantation in Chile using the Heart Mate II device. Report of one case]. / Primer puente a trasplante cardiaco exitoso en Chile usando el dispositivo Heart Mate II.

Implantable ventricular assist devices are an effective treatment option for end-stage heart failure patients as a bridge to cardiac transplantation, to improve the clinical condition and organ function allowing discharge from the hospital to await for transplantation. The second alternative is to use the device as destination therapy for patients with contraindications for cardiac transplantation, in whom it is maintained indefinitely. We report a 43-year-old patient, with a dilated cardiomyopathy, severe left ventricular dysfunction and advanced heart failure. A ventricular assist device Heart Mate II©, as a bridge to transplantation, was implanted to the patient in the United States. It was explanted for the first time in Chile at the National Thorax Institute. Heart transplantation was performed using the bicaval technique. Induction of immunosuppression was done with basiliximab. Generic immunosuppression was carried out with cyclosporine, mycophenolate mofetil and prednisone. Postoperatively the patient evolved with right femoral vein thrombosis in the femoral cannulation site, phlegmasia alba dolens, rhabdomyolysis, oliguric acute renal failure, which required renal replacement therapy, severe shock, with high requirements of vasoactive drugs and need for mechanical ventilation. He required a reoperation for hemothorax and had an Enterobacter pneumonia. After a period of serious illness, he began a gradual recovery and was discharged from the hospital after 58 days. After two years, he remains in functional class I, with a normal graft function.

Understanding pathogenic Burkholderia glumae metabolic and signaling pathways within rice tissues through in vivo transcriptome analyses.

Burkholderia glumae is a causal agent of rice grain and sheath rot. Similar to other phytopathogens, B. glumae adapts well to the host environment and controls its biology to induce diseases in the host plant; however, its molecular mechanisms are not yet fully understood. To gain a better understating of the actual physiological changes that occur in B. glumae during infection, we analyzed B. glumae transcriptome from infected rice tissues using an RNA-seq technique. To accomplish this, we analyzed differentially expressed genes (DEGs) and identified 2653 transcripts that were significantly altered. We then performed KEGG pathway and module enrichment of the DEGs. Interestingly, most genes involved bacterial chemotaxis-mediated motility, ascorbate and trehalose metabolisms, and sugar transporters including l-arabinose and d-xylose were found to be highly enriched. The in vivo transcriptional profiling of pathogenic B. glumae will facilitate elucidation of unknown plant-pathogenic bacteria interactions, as well as the overall infection processes.

Primer puente a trasplante cardiaco exitoso en Chile usando el dispositivo Heart Mate II / First successful bridge to cardiac transplantation in Chile using the Heart Mate II device. Report of one case

Implantable ventricular assist devices are an effective treatment option for end-stage heart failure patients as a bridge to cardiac transplantation, to improve the clinical condition and organ function allowing discharge from the hospital to await for transplantation. The second alternative is to use the device as destination therapy for patients with contraindications for cardiac transplantation, in whom it is maintained indefinitely. We report a 43-year-old patient, with a dilated cardiomyopathy, severe left ventricular dysfunction and advanced heart failure. A ventricular assist device Heart Mate II©, as a bridge to transplantation, was implanted to the patient in the United States. It was explanted for the first time in Chile at the National Thorax Institute. Heart transplantation was performed using the bicaval technique. Induction of immunosuppression was done with basiliximab. Generic immunosuppression was carried out with cyclosporine, mycophenolate mofetil and prednisone. Postoperatively the patient evolved with right femoral vein thrombosis in the femoral cannulation site, phlegmasia alba dolens, rhabdomyolysis, oliguric acute renal failure, which required renal replacement therapy, severe shock, with high requirements of vasoactive drugs and need for mechanical ventilation. He required a reoperation for hemothorax and had an Enterobacter pneumonia. After a period of serious illness, he began a gradual recovery and was discharged from the hospital after 58 days. After two years, he remains in functional class I, with a normal graft function.

Complete Genome Sequence of Mycobacterium bovis BCG Korea, the Korean Vaccine Strain for Substantial Production.

Mycobacterium bovis bacillus Calmette-Guérin (BCG) is the only vaccine available against tuberculosis, and the strains used worldwide represent a family of daughter strains with distinct genotypic characteristics. Here, we report the complete genome sequence of M. bovis BCG Korea, the strain that will be actually used in Korea for vaccine production.

Widespread occurrence of the tfd-II genes in soil bacteria revealed by nucleotide sequence analysis of 2,4-dichlorophenoxyacetic acid degradative plasmids pDB1 and p712.

Variovorax sp. strain DB1 and Pseudomonas pickettii strain 712 are 2,4-dicholorophenoxy-acetic acid (2,4-D)-degrading bacteria, which were isolated from agricultural soils in Republic of Korea and USA, respectively. Each strain harbors a 2,4-D degradative plasmid and is able to utilize 2,4-D as the sole source of carbon for its growth. The 2,4-D degradative plasmid pDB1 of strain DB1 consisted of a 65,269-bp circular molecule with a G+C content of 66.23% and had 68 ORFs. The 2,4-D degradative plasmid p712 of strain 712 was composed of a 62,798-bp circular molecule with a 62.11% G+C content and had 62 ORFs. The plasmids pDB1 and p712 share significantly homologous 2,4-D degradative genes with high similarity to the tfdR, tfdB-II, tfdC-II, tfdD-II, tfdE-II, tfdF-II, tfdK and tfdA genes of plasmid pJP4 of Alcaligenes eutrophus isolated from Australia. In a phylogenetic analysis with trfA, traL, and trbA genes, pDB1 belonged to IncP-1ß with pJP4, while p712 belonged to IncP-1ε with pKJK5 and pEMT3. The results indicated that, in spite of the differences in their backbone regions, the 2,4-D catabolic genes of the two plasmids were closely related and also related to the well-known 2,4-D degradative plasmid pJP4 even though all were isolated from different geographic regions. Other similarities in the genetic organization and the presence of IS1071 suggested that these catabolic genes may be on a transposable element, leading to widespread occurrence in soil bacteria.

Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling.

Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the next-generation DNA sequencer (NGS) Roche/454 and Illumina/Solexa systems, along with bioinformation analysis technologies of whole-genome de novo assembly, expression profiling, DNA variation discovery, and genotyping. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing de novo assembly of novel genome sequencing data. It is necessary to have DNA sequence information from a multiplatform NGS with at least 2× and 30× depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly. Massive short-length reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a whole-genome transcriptome, depending on the tissue samples. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through de novo assembly in any whole-genome sequenced species. The 20× and 50× coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average 30× coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence.

Complete genome sequence of Mycobacterium intracellulare clinical strain MOTT-64, belonging to the INT1 genotype.

Here, we report the complete genome sequence of the Mycobacterium intracellulare clinical strain MOTT-64, previously grouped into the INT1 genotype among five genotypes of M. intracellulare. This genome sequence will serve as a valuable reference for understanding the disparity in the virulence and epidemiologic traits among M. intracellulare genotypes.

Complete genome sequence of Mycobacterium intracellulare strain ATCC 13950(T).

Here we report the first complete genome sequence of Mycobacterium intracellulare ATCC 13950(T), a Mycobacterium avium complex (MAC) strain. This genome sequence will serve as a valuable reference for understanding the epidemiologic, biological, and pathogenic aspects of the disparity between MAC members.

Complete genome sequence of Mycobacterium intracellulare clinical strain MOTT-02.

Here, we report the first complete genome sequence of the Mycobacterium intracellulare clinical strain MOTT-02, which was previously grouped in the INT2 genotype of M. intracellulare. This genome sequence will serve as a valuable reference for improving the understanding of the disparity in the virulence and epidemiologic traits between M. intracellulare genotypes.

Comparison of analytical methods and residue patterns of pymetrozine in Aster scaber.

Residues of the polar pesticide pymetrozine were compared using two methods: hydromatrix and liquid-liquid extraction (LLE). The biological half-life and the final residue level were investigated using Aster scaber over a 10-days cultivation period. The respective biological half-lives of the pesticide were 4.2 and 3.5 days at the recommended and double dose. The final residue levels were 1.28 and 1.98 mg kg(-1), respectively, at the same application rate of pymetrozine according to the GAP standard of the United Kingdom. Average recovery was higher with LLE than with the hydromatrix method. Dissipation curves of pymetrozine were influenced by the application amount and growth rate of A. scaber. The final residue level of pymetrozine could be predicted to be lower than the UK maximum residue limit for lettuce applying the GAP standard.

Genome sequence of Lactobacillus johnsonii PF01, isolated from piglet feces.

Lactobacillus johnsonii PF01, an autochthonous bacterium of the gastrointestinal tract, was isolated from a fecal sample from a piglet. The strain adhered specifically to the duodenal and jejunal epithelial cells of the piglet and had high bile resistance activity. Here we report the genomic sequence of L. johnsonii PF01.