GC/MS based metabolomics: development of a data mining system for metabolite identification by using soft independent modeling of class analogy (SIMCA)

<p>Abstract</p> <p>Background</p> <p>The goal of metabolomics analyses is a comprehensive and systematic understanding of all metabolites in biological samples. Many useful platforms have been developed to achieve this goal. Gas chromatography coupled to mass spectrometry (GC/MS) is a well-established analytical method in metabolomics study, and 200 to 500 peaks are routinely observed with one biological sample. However, only ~100 metabolites can be identified, and the remaining peaks are left as "unknowns".</p> <p>Result</p> <p>We present an algorithm that acquires more extensive metabolite information. Pearson's product-moment correlation coefficient and the Soft Independent Modeling of Class Analogy (SIMCA) method were combined to automatically identify and annotate unknown peaks, which tend to be missed in routine studies that employ manual processing.</p> <p>Conclusions</p> <p>Our data mining system can offer a wealth of metabolite information quickly and easily, and it provides new insights, particularly into food quality evaluation and prediction.</p

Study on Flow Characteristics Downstream of Annular Inlet Guide Vanes

ABSTRACT The main objectives of the present study are to identify the dominant parameters responsible for the generation of unsteady flow, determine the conditions under which flow oscillations are produced and the relation between the flow characteristics and the number of vanes with identical solidity. The flow instabilities downstream of inlet guide vanes (IGV) are clarified experimentally and by numerical simulation. The conditions for the onset of flow instability, including the number of cells and the oscillation characteristics of the unsteady flow, are discussed based on measured pressure fluctuations and the propagating angular velocity ratio of the instability for various radius ratios (r3/r2). The effectiveness of adjusting the number of vanes to control the flow instabilities is also discussed. INTRODUCTION Variable inlet guide vanes (IGV), which are a type of swirling flow generator, are installed at the inlet of centrifugal compressors to reduce the inlet mach number of the rotor blades. Under lower flow rates, the vane angle (β2) referring t

Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers

Background: The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses. Results: We generated de novo DNA and mRNA sequence information of L. racemosus and developed 110 polymorphic PCR-based markers from the data, and to complement the PCR markers, DArT-seq genotyping was applied to develop additional 9990 SNP markers. Approximately 52% of all the markers enabled us to clearly genotype 22 wheat-L. racemosus chromosome introgression lines, and L. racemosus chromosome-specific markers were highly efficient in detailed characterization of the translocation and recombination lines analyzed. A further analysis revealed remarkable transferability of the PCR markers to three other important Triticeae perennial species: L. mollis, Psathyrostachys huashanica and Elymus ciliaris, indicating their suitability for characterizing wheat-alien chromosome introgressions carrying chromosomes of these genomes. Conclusion: The efficiency of the markers in characterizing wheat-L. racemosus chromosome introgression lines proves their reliability, and their high transferability further broadens their scope of application. This is the first report on sequencing and development of markers from L. racemosus genome and the application of DArT-seq to develop markers from a perennial wild relative of wheat, marking a paradigm shift from the seeming concentration of the technology on cultivated species. Integration of these markers with appropriate cytogenetic methods would accelerate development and characterization of wheat-alien chromosome introgression lines

血漿ADAMTSは肝硬変患者の予後をChild-PughスコアやMELDスコアと同様に生存率を予測できる可能性がある

Aim:  Decreased plasma ADAMTS13 activity (ADAMTS13:AC) results in accumulation of unusually large von Willebrand factor multimers and platelet thrombi formation. Our aim was to evaluate whether ADAMTS13:AC is a prognostic marker in patients with liver cirrhosis. Methods:  Plasma ADAMTS13:AC and its related parameters were examined in 108 cirrhotic patients. Results:  ADAMTS13:AC decreased as the severity of liver disease increased (means: controls 100%, Child A-cirrhotics 79%, Child B-cirrhotics 63%, and Child C-cirrhotics 31%). ADAMTS13:AC markedly decreased in the cirrhotics with hepatorenal syndrome, refractory ascites and hepatic encephalopathy. The cumulative survival time was the shortest (median: 4.5 months) in the cirrhotics with severe to moderate ADAMTS13:AC deficiency (50%). In contrast, based on the Child-Turcotte-Pugh (CTP) score, Child C-cirrhotics had the worst survival, but the survival probabilities did not differ between Child A and B cirrhotics. Based on the Model for End-Stage Liver Disease (MELD) score, the survival was the worst for the cirrhotics in the fourth quartile, but it was not different among cirrhotics in the first three quartiles. Cox proportional-hazards regression analysis showed that ADAMTS13:AC and serum albumin were independent factors affecting the survival. Conclusions:  ADAMTS13:AC concomitantly decreases as the functional liver capacity decreases. This activity may be a useful prognostic marker that is equal or superior to the CTP score and the MELD score to predict not only the short-term prognosis but also the long-term survival of the cirrhotic patients.博士（医学）・甲613号・平成26年3月17

First Detection of NaI D lines in High-Redshift Damped Lyman-alpha Systems

A Near-infrared (1.18-1.35 micron) high-resolution spectrum of the gravitationally-lensed QSO APM 08279+5255 was obtained with the IRCS mounted on the Subaru Telescope using the AO system. We detected strong NaI D 5891,5897 doublet absorption in high-redshift DLAs at z=1.062 and 1.181, confirming the presence of NaI, which was first reported for the rest-frame UV NaI 3303.3,3303.9 doublet by Petitjean et al. This is the first detection of NaI D absorption in a high-redshift (z>1) DLA. In addition, we detected a new NaI component in the z=1.062 DLA and four new components in the z=1.181 DLA. Using an empirical relationship between NaI and HI column density, we found that all "components" have large HI column density, so that each component is classified as DLA absorption. We also detected strong NaI D absorption associated with a MgII system at z=1.173. Because no other metal absorption lines were detected in this system at the velocity of the NaI absorption in previously reported optical spectra (observed 3.6 years ago), we interpret this NaI absorption cloud probably appeared in the line of sight toward the QSO after the optical observation. This newly found cloud is likely to be a DLA based upon its large estimated HI column density. We found that the N(NaI)/N(CaII) ratios in these DLAs are systematically smaller than those observed in the Galaxy; they are more consistent with the ratios seen in the Large Magellanic Cloud. This is consistent with dust depletion generally being smaller in lower metallicity environments. However, all five clouds of the z=1.181 system have a high N(NaI)/N(CaII) ratio, which is characteristic of cold dense gas. We tentatively suggest that the host galaxy of this system may be the most significant contributor to the gravitational-lens toward APM 08279+5255.Comment: 22 pages, 6 Postscript figures, 3 tables, ApJ in press (Vol.643, 2 June 2006

Erythropoietin Receptor Signaling Mitigates Renal Dysfunction-Associated Heart Failure by Mechanisms Unrelated to Relief of Anemia

ObjectivesWe examined the effect of asialoerythropoietin (asialoEPO), a nonerythrogenic derivative of erythropoietin (EPO), on renal dysfunction-associated heart failure.BackgroundAlthough EPO is known to exert beneficial effects on cardiac function, the clinical benefits in patients with chronic kidney disease are controversial. It remains to be addressed whether previously reported outcomes were the result of relief of the anemia, adverse effects of EPO, or direct cardiovascular effects.MethodsMice underwent 5/6 nephrectomy to cause renal dysfunction. Eight weeks later, when renal dysfunction was established, anemia and cardiac dysfunction and remodeling were apparent. Mice were then assigned to receive saline (control), recombinant human erythropoietin (rhEPO) at 5,000 IU (714 pmol)/kg, or asialoEPO at 714 pmol/kg, twice/week for 4 weeks.ResultsAlthough only rhEPO relieved the nephrectomy-induced anemia, both rhEPO and asialoEPO significantly and similarly mitigated left ventricular dilation and dysfunction. The hearts of rhEPO- or asialoEPO-treated mice showed less hypertrophy, reflecting decreases in cardiomyocyte hypertrophy and degenerative subcellular changes, as well as significant attenuation of fibrosis, leukocyte infiltration, and oxidative deoxyribonucleic acid damage. These phenotypes were accompanied by restored expression of GATA-4, sarcomeric proteins, and vascular endothelial growth factor and decreased inflammatory cytokines and lipid peroxidation. Finally, myocardial activation was observed of extracellular signal-regulated protein kinase and signal transducer and activator of transcription pathways in the treated mice.ConclusionsEPO receptor signaling exerts direct cardioprotection in an animal model of renal dysfunction-associated heart failure, probably by mitigating degenerative, pro-fibrosis, inflammatory, and oxidative processes but not through relief of anemia

Genetic Tracing of Jatropha

Jatropha curcas L. (Jatropha), a shrub species of the family Euphorbiaceae, has been recognized as a promising biofuel plant for reducing greenhouse gas emissions. However, recent attempts at commercial cultivation in Africa and Asia have failed because of low productivity. It is important to elucidate genetic diversity and relationship in worldwide Jatropha genetic resources for breeding of better commercial cultivars. Here, genetic diversity was analyzed by using 246 accessions from Mesoamerica, Africa and Asia, based on 59 simple sequence repeat markers and eight retrotransposon-based insertion polymorphism markers. We found that central Chiapas of Mexico possesses the most diverse genetic resources, and the Chiapas Central Depression could be the center of origin. We identified three genetic groups in Mesoamerica, whose distribution revealed a distinct geographic cline. One of them consists mainly of accessions from central Chiapas. This suggests that it represents the original genetic group. We found two Veracruz accessions in another group, whose ancestors might be shipped from Port of Veracruz to the Old World, to be the source of all African and Asian Jatropha. Our results suggest the human selection that caused low productivity in Africa and Asia, and also breeding strategies to improve African and Asian Jatropha. Cultivars improved in the productivity will contribute to expand mass commercial cultivation of Jatropha in Africa and Asia to increase biofuel production, and finally will support in the battle against the climate change

Genetic tracing of Jatropha curcas L. From its mesoamerican origin to the world

Jatropha curcas L. (Jatropha), a shrub species of the family Euphorbiaceae, has been recognized as a promising biofuel plant for reducing greenhouse gas emissions. However, recent attempts at commercial cultivation in Africa and Asia have failed because of low productivity. It is important to elucidate genetic diversity and relationship in worldwide Jatropha genetic resources for breeding of better commercial cultivars. Here, genetic diversity was analyzed by using 246 accessions from Mesoamerica, Africa and Asia, based on 59 simple sequence repeat markers and eight retrotransposonbased insertion polymorphism markers. We found that central Chiapas of Mexico possesses the most diverse genetic resources, and the Chiapas Central Depression could be the center of origin. We identified three genetic groups in Mesoamerica, whose distribution revealed a distinct geographic cline. One of them consists mainly of accessions from central Chiapas. This suggests that it represents the original genetic group. We found two Veracruz accessions in another group, whose ancestors might be shipped from Port of Veracruz to the Old World, to be the source of all African and Asian Jatropha. Our results suggest the human selection that caused low productivity in Africa and Asia, and also breeding strategies to improve African and Asian Jatropha. Cultivars improved in the productivity will contribute to expand mass commercial cultivation of Jatropha in Africa and Asia to increase biofuel production, and finally will support in the battle against the climate change.Li H, Tsuchimoto S, Harada K, Yamasaki M, Sakai H, Wada N, Alipour A, Sasai T, Tsunekawa A,Tsujimoto H, Ando T, Tomemori H, Sato S, Hirakawa H, Quintero VP, Zamarripa A, Santos P, Hegazy A, Ali AM and Fukui K (2017) GeneticTracing of Jatropha curcas L. from Its Mesoamerican Origin to the World. Front. Plant Sci. 8:1539.doi: 10.3389/fpls.2017.01539