In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling

Background Yarrowia lipolytica, an oleaginous yeast, is a promising platform strain for production of biofuels and oleochemicals as it can accumulate a high level of lipids in response to nitrogen limitation. Accordingly, many metabolic engineering efforts have been made to develop engineered strains of Y. lipolytica with higher lipid yields. Genome-scale model of metabolism (GEM) is a powerful tool for identifying novel genetic designs for metabolic engineering. Several GEMs for Y. lipolytica have recently been developed; however, not many applications of the GEMs have been reported for actual metabolic engineering of Y. lipolytica. The major obstacle impeding the application of Y. lipolytica GEMs is the lack of proper methods for predicting phenotypes of the cells in the nitrogen-limited condition, or more specifically in the stationary phase of a batch culture. Results In this study, we showed that environmental version of minimization of metabolic adjustment (eMOMA) can be used for predicting metabolic flux distribution of Y. lipolytica under the nitrogen-limited condition and identifying metabolic engineering strategies to improve lipid production in Y. lipolytica. Several well-characterized overexpression targets, such as diglyceride acyltransferase, acetyl-CoA carboxylase, and stearoyl-CoA desaturase, were successfully rediscovered by our eMOMA-based design method, showing the relevance of prediction results. Interestingly, the eMOMA-based design method also suggested non-intuitive knockout targets, and we experimentally validated the prediction with a mutant lacking YALI0F30745g, one of the predicted targets involved in one-carbon/methionine metabolism. The mutant accumulated 45% more lipids compared to the wild-type. Conclusion This study demonstrated that eMOMA is a powerful computational method for understanding and engineering the metabolism of Y. lipolytica and potentially other oleaginous microorganisms.This research was supported by the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning (NRF2017R1E1A1A01073523) and Industrial Strategic technology development program, 20002734 funded by the Ministry of Trade, Industry & Energy (MI, Korea

Classification of rice (oryza sativa l. japonica nipponbare) immunophilins (fkbps, cyps) and expression patterns under water stress

<p>Abstract</p> <p>Background</p> <p>FK506 binding proteins (FKBPs) and cyclophilins (CYPs) are abundant and ubiquitous proteins belonging to the peptidyl-prolyl <it>cis/trans </it>isomerase (PPIase) superfamily, which regulate much of metabolism through a chaperone or an isomerization of proline residues during protein folding. They are collectively referred to as immunophilin (IMM), being present in almost all cellular organs. In particular, a number of IMMs relate to environmental stresses.</p> <p>Results</p> <p>FKBP and CYP proteins in rice (<it>Oryza sativa </it>cv. Japonica) were identified and classified, and given the appropriate name for each IMM, considering the ortholog-relation with <it>Arabidopsis </it>and <it>Chlamydomonas </it>or molecular weight of the proteins. 29 FKBP and 27 CYP genes can putatively be identified in rice; among them, a number of genes can be putatively classified as orthologs of <it>Arabidopsis </it>IMMs. However, some genes were novel, did not match with those of <it>Arabidopsis </it>and <it>Chlamydomonas</it>, and several genes were paralogs by genetic duplication. Among 56 IMMs in rice, a significant number are regulated by salt and/or desiccation stress. In addition, their expression levels responding to the water-stress have been analyzed in different tissues, and some subcellular IMMs located by means of tagging with GFP protein.</p> <p>Conclusion</p> <p>Like other green photosynthetic organisms such as <it>Arabidopsis </it>(23 FKBPs and 29 CYPs) and <it>Chlamydomonas </it>(23 FKBs and 26 CYNs), rice has the highest number of IMM genes among organisms reported so far, suggesting that the numbers relate closely to photosynthesis. Classification of the putative FKBPs and CYPs in rice provides the information about their evolutional/functional significance when comparisons are drawn with the relatively well studied genera, <it>Arabidopsis </it>and <it>Chlamydomonas</it>. In addition, many of the genes upregulated by water stress offer the possibility of manipulating the stress responses in rice.</p

Are Portable Imaging Intraoperative Radiographs Helpful for Assessing Adequate Acetabular Cup Positioning in Total Hip Arthroplasty?

Despite advances in surgical techniques and instrumentation, current intra-operative estimations of acetabular version in total hip arthroplasty are of limited accuracy. In the present study, two experienced orthopedic surgeons compared intra-operatively measured (using portable imaging) anteversions and vertical inclinations of acetabular components with those measured using standardized radiographs post-operatively in 40 patients. Of the all vertical inclinations measured from intra-operative radiographs, 72.5% (n=29) were within ±2°, and 97.5% (n=39) were within ±5° of those determined using post-operative radiographs, and for anteversion, 52.5% (n=21) were within ±2°, and 97.5% (n=39) were within ±5°. Post-operative radiographs demonstrated that 90.0% (n=36) of vertical inclinations and anteversions were within the adequate zone. Obviously, our method has its limitations, but the authors conclude that the method described in this article better allows surgeons to verify acetabular version intra-operatively. In particular, the described method is suitable in cases with a deformed acetabular anatomy and difficult revision surgery

Comparative proteomic analysis of early salt stress-responsive proteins in roots of SnRK2 transgenic rice

<p>Abstract</p> <p>Background</p> <p>The rice roots are highly salt-sensitive organ and primary root growth is rapidly suppressed by salt stress. Sucrose nonfermenting 1-related protein kinase2 (SnRK2) family is one of the key regulator of hyper-osmotic stress signalling in various plant cells. To understand early salt response of rice roots and identify SnRK2 signaling components, proteome changes of transgenic rice roots over-expressing OSRK1, a rice SnRK2 kinase were investigated.</p> <p>Results</p> <p>Proteomes were analyzed by two-dimensional electrophoresis and protein spots were identified by LC-MS/MS from wild type and OSRK1 transgenic rice roots exposed to 150 mM NaCl for either 3 h or 7 h. Fifty two early salt -responsive protein spots were identified from wild type rice roots. The major up-regulated proteins were enzymes related to energy regulation, amino acid metabolism, methylglyoxal detoxification, redox regulation and protein turnover. It is noted that enzymes known to be involved in GA-induced root growth such as fructose bisphosphate aldolase and methylmalonate semialdehyde dehydrogenase were clearly down-regulated. In contrast to wild type rice roots, only a few proteins were changed by salt stress in OSRK1 transgenic rice roots. A comparative quantitative analysis of the proteome level indicated that forty three early salt-responsive proteins were magnified in transgenic rice roots at unstressed condition. These proteins contain single or multiple potential SnRK2 recognition motives. In vitro kinase assay revealed that one of the identified proteome, calreticulin is a good substrate of OSRK1.</p> <p>Conclusions</p> <p>Our present data implicate that rice roots rapidly changed broad spectrum of energy metabolism upon challenging salt stress, and suppression of GA signaling by salt stress may be responsible for the rapid arrest of root growth and development. The broad spectrum of functional categories of proteins affected by over-expression of OSRK1 indicates that OSRK1 is an upstream regulator of stress signaling in rice roots. Enzymes involved in glycolysis, branched amino acid catabolism, dnaK-type molecular chaperone, calcium binding protein, Sal T and glyoxalase are potential targets of OSRK1 in rice roots under salt stress that need to be further investigated.</p

Pulmonary Metastases of Alveolar Soft-Part Sarcoma: CT Findings in Three Patients

Alveolar soft-part sarcoma is a rare soft tissue sarcoma of young adults with unknown histogenesis, and the organ most frequently involved in metastasis is the lung. We report the CT findings of three patients of pulmonary metastases of alveolar soft-part sarcoma, which manifested as clearly enhanced pulmonary nodules or masses. On enhanced scans, some of the masses were seen to contain dilated and tortuous intratumoral vessels

A Case of Near Total Aortic Replacement in an Adolescent With Loeys-Dietz Syndrome

Loeys-Dietz syndrome is a recently described autosomal dominant disorder caused by mutations in the genes for transforming growth factor-beta receptor type 1 or 2 (TGF-ßR 1/2). The syndrome predisposes patients to aortic aneurysm and dissections, along with craniofacial and musculoskeletal abnormalities. Here we report the case of an adolescent who underwent serial near total aortic replacement, from the aortic valve to the descending aorta. Loeys-Dietz syndrome was confirmed in this case by the detection of a mutation in the TGF-ßR 2 gene

QT Prolongation and Life Threatening Ventricular Tachycardia in a Patient Injected With Intravenous Meperidine (Demerol®)

QT prolongation is a serious adverse drug effect, which is associated with an increased risk of Torsade de pointes and sudden death. Many drugs, including both cardiac and non-cardiac drugs, have been reported to cause prolongation of QT interval. Although meperidine has not been considered proarrhythmic, we present a unique case of a 16-year-old boy without an underlying cardiac disease, who developed polymorphic ventricular tachycardia, ventricular fibrillation and QT prolongation after an intravenous meperidine injection. He had no mutation in long QT syndrome genes (KCNQ1, KCNH2, and SCN5A), but single nucleotide polymorphisms were reported, including H558R in SCNA5A and K897T in KCNH2