Evaluation of three high abundance protein depletion kits for umbilical cord serum proteomics

<p>Abstract</p> <p>Background</p> <p>High abundance protein depletion is a major challenge in the study of serum/plasma proteomics. Prior to this study, most commercially available kits for depletion of highly abundant proteins had only been tested and evaluated in adult serum/plasma, while the depletion efficiency on umbilical cord serum/plasma had not been clarified. Structural differences between some adult and fetal proteins (such as albumin) make it likely that depletion approaches for adult and umbilical cord serum/plasma will be variable. Therefore, the primary purposes of the present study are to investigate the efficiencies of several commonly-used commercial kits during high abundance protein depletion from umbilical cord serum and to determine which kit yields the most effective and reproducible results for further proteomics research on umbilical cord serum.</p> <p>Results</p> <p>The immunoaffinity based kits (PROTIA-Sigma and 5185-Agilent) displayed higher depletion efficiency than the immobilized dye based kit (PROTBA-Sigma) in umbilical cord serum samples. Both the PROTIA-Sigma and 5185-Agilent kit maintained high depletion efficiency when used three consecutive times. Depletion by the PROTIA-Sigma Kit improved 2DE gel quality by reducing smeared bands produced by the presence of high abundance proteins and increasing the intensity of other protein spots. During image analysis using the identical detection parameters, 411 ± 18 spots were detected in crude serum gels, while 757 ± 43 spots were detected in depleted serum gels. Eight spots unique to depleted serum gels were identified by MALDI- TOF/TOF MS, seven of which were low abundance proteins.</p> <p>Conclusions</p> <p>The immunoaffinity based kits exceeded the immobilized dye based kit in high abundance protein depletion of umbilical cord serum samples and dramatically improved 2DE gel quality for detection of trace biomarkers.</p

Integrative species delimitation in the morphologically conservative Stegana subgen. Orthostegana (Diptera, Drosophilidae)

With the increasing number of cryptic species discovered in major branches of the subfamily Steganinae, accurate species identification is becoming challenging. Possible evolutionary stasis often gives rise to the formation of morphological conservatism and cryptic species, as is the case for the members of the Stegana (subgen. Orthostegana). In this study, the species boundaries of all Asian Orthostegana were accessed based on two mitochondrial genes [cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 2 (ND2)] using different species delimitation methods and evolutionary models. By integrating morphological and molecular evidence, we clearly validated the evolutionary independence of all five known species and identified nine new species from Southwest China: Stegana (Orthostegana) aini Peng &amp;amp; Chen sp. nov., S. (O.) brevivittata Peng &amp;amp; Chen sp. nov., S. (O.) cuodi Peng &amp;amp; Chen sp. nov., S. (O.) fuscofemorata Peng &amp;amp; Chen sp. nov., S. (O.) latipalpula Peng &amp;amp; Chen sp. nov., S. (O.) macrostephana Peng &amp;amp; Chen sp. nov., S. (O.) mohnihei Peng &amp;amp; Chen sp. nov., S. (O.) obscurala Peng &amp;amp; Chen sp. nov., and S. (O.) pinguitia Peng &amp;amp; Chen sp. nov. Moreover, we discussed the relationship between the Asian Orthostegana lineage and the subgen. Oxyphortica, and the necessity of taxonomic re-evaluation for the Neotropical species with molecular data. The high morphological conservatism within Orthostegana is largely the outcome of in situ diversification for adapting to the ecological environment

Gene Responses to Oxygen Availability in Kluyveromyces lactis: an Insight on the Evolution of the Oxygen-Responding System in Yeast

The whole-genome duplication (WGD) may provide a basis for the emergence of the very characteristic life style of Saccharomyces cerevisiae—its fermentation-oriented physiology and its capacity of growing in anaerobiosis. Indeed, we found an over-representation of oxygen-responding genes in the ohnologs of S. cerevisiae. Many of these duplicated genes are present as aerobic/hypoxic(anaerobic) pairs and form a specialized system responding to changing oxygen availability. HYP2/ANB1 and COX5A/COX5B are such gene pairs, and their unique orthologs in the ‘non-WGD’ Kluyveromyces lactis genome behaved like the aerobic versions of S. cerevisiae. ROX1 encodes a major oxygen-responding regulator in S. cerevisiae. The synteny, structural features and molecular function of putative KlROX1 were shown to be different from that of ROX1. The transition from the K. lactis-type ROX1 to the S. cerevisiae-type ROX1 could link up with the development of anaerobes in the yeast evolution. Bioinformatics and stochastic analyses of the Rox1p-binding site (YYYATTGTTCTC) in the upstream sequences of the S. cerevisiae Rox1p-mediated genes and of the K. lactis orthologs also indicated that K. lactis lacks the specific gene system responding to oxygen limiting environment, which is present in the ‘post-WGD’ genome of S. cerevisiae. These data suggested that the oxygen-responding system was born for the specialized physiology of S. cerevisiae

Kidney Protection Effect of Ginsenoside Re and Its Underlying Mechanisms on Cisplatin-Induced Kidney Injury

Background/Aims: Cisplatin (CDDP) was the first platinum-containing anti-cancer drug. However, CDDP causes nephrotoxicity as a side effect, which limits its clinic application. The aim of this study was to investigate the renoprotective effect of ginsenoside Re (G-Re) in a murine model of CDDP-induced acute kidney injury. Methods: Male ICR mice were divided into 4 groups. G-Re was administered to the mice by oral gavage once a day at a dose of 25 mg/kg for 10 days. On the 7th day, a single injection of CDDP (25 mg/kg) was given at 1 h after G-Re treatment. Results: CDDP administration resulted in renal dysfunction, as evidenced by an increase in the serum levels of creatinine and urea nitrogen. Oxidative stress in the CDDP group was reflected by an increase of malondialdehyde and a depletion of reduced glutathione and catalase in renal tissue. These findings were supported by increased 4-hydroxynonenal expression, which was significantly reduced by G-Re. Simultaneously, the overexpression of cytochrome P450 E1 was inhibited. G-Re inhibited the inflammatory response by the reduction of the protein expression of cyclooxygenase-2 and inducible nitric oxide synthase. Furthermore, CDDP increased the expression of Bax and decreased Bcl-2 expression in renal tissue. Hematoxylin and eosin, Hoechst 33258, and TUNEL staining also confirmed the presence of acute tubular necrosis and apoptosis. G-Re significantly decreased the levels of indicators of renal dysfunction, inflammatory cytokines, apoptosis, and malondialdehyde in the kidney and also significantly attenuated the histopathological changes associated with acute renal failure. Conclusions: Collectively, the results of this study suggest that the nephroprotective potential of G-Re may, in part, be related to its anti-oxidant, anti-inflammatory, and anti-apoptotic effects

Climate services for addressing climate change: Iindication of a climate livable city in China

China, like many countries, is under great pressure to reduce climate change and adapt to current situations while simultaneously undertaking economic development and transformation. This study takes advantage of climate opportunities and provides a new concept and mode of urban climate services in order to address climate change. Eighteen indicators based on climate and climate-related variables were used to provide an assessment, in the form of an index, of how livable a city is depending on prevailing climatic conditions. The resulting index can also be used to investigate how recent and future changes in the climatic conditions could affect livability. All Chinese cities and regions share the common goals of promoting low-carbon development, improving resilience against climate change, and integrating economic growth with climate actions. Climate services have been developed in China to provide decision-makers this measure of livability. Such a move facilitates sustainable development alongside economic growth by aiding government efforts in climate adaptation and low-carbon development. Our approach represents multidisciplinary and demand-driven research on adaptation to and the impacts of regional climate change, thereby transforming climate science into a climate service and ensuring that climate information can be provided in a scientific, practical, and customized way for policy-makers. The outputs can be used locally to take concrete climate actions and integrate climate services into decision-making processes

The Litsea genome and the evolution of the laurel family

The laurel family within the Magnoliids has attracted attentions owing to its scents, variable inflorescences, and controversial phylogenetic position. Here, we present a chromosome-level assembly of the Litsea cubeba genome, together with low-coverage genomic and transcriptomic data for many other Lauraceae. Phylogenomic analyses show phylogenetic discordance at the position of Magnoliids, suggesting incomplete lineage sorting during the divergence of monocots, eudicots, and Magnoliids. An ancient whole-genome duplication (WGD) event occurred just before the divergence of Laurales and Magnoliales; subsequently, independent WGDs occurred almost simultaneously in the three Lauralean lineages. The phylogenetic relationships within Lauraceae correspond to the divergence of inflorescences, as evidenced by the phylogeny of FUWA, a conserved gene involved in determining panicle architecture in Lauraceae. Monoterpene synthases responsible for production of specific volatile compounds in Lauraceae are functionally verified. Our work sheds light on the evolution of the Lauraceae, the genetic basis for floral evolution and specific scents

Acute Iloprost Inhalation Improves Right Ventricle Function in Pulmonary Artery Hypertension: A Cardiac Magnetic Resonance Study

Background: Right ventricle (RV) function is among the most important prognostic factors for pulmonary arterial hypertension (PAH) patients. Inhaled iloprost, an inhaled member of the prostacyclin family, is effective for the treatment of severe PAH and acute RV failure. However, the acute effects of iloprost on RV physiology have not been thoroughly explored in the past.Materials and Methods: This prospective study involved 69 incident PAH patients, including 23 idiopathic PAH (IPAH) patients, 26 patients with PAH associated with connective tissue disease (CTD-PAH) and 20 with PAH associated with congenital heart disease (CHD-PAH). All patients underwent both right heart catheterization and cardiac magnetic resonance imaging at baseline and 20 min after 5 μg iloprost inhalation.Results: Acute iloprost inhalation reduced PVR from 13 ± 7 to 10 ± 6 Wood U (P &lt; 0.001), increased RV ejection fraction (RVEF) from 31 ± 11 to 35 ± 12 % (P &lt; 0.001), increased RV stroke volume from 53 ± 21 to 57 ± 22 ml (P &lt; 0.001) and decreased RV end-diastolic volume from 179 ± 67 to 172 ± 69 ml (P &lt; 0.001). Acute iloprost inhalation-induced RVEF improvement was correlated with the degree of PVR reduction (P &lt; 0.001) in IPAH patients, but not in CTD-PAH or CHD-PAH patients.Conclusion: Acute iloprost inhalation improved RVEF, RV stroke volume and decreased RV volume in IPAH and CTD-PAH patients. Iloprost-induced RVEF increase was proportional to PVR reduction in IPAH patients, but not in CTD-PAH or CHD-PAH patients

Association between type 2 diabetes mellitus and body composition based on MRI fat fraction mapping

PurposeTo explore the association between type 2 diabetes mellitus (T2DM) and body composition based on magnetic resonance fat fraction (FF) mapping.MethodsA total of 341 subjects, who underwent abdominal MRI examination with FF mapping were enrolled in this study, including 68 T2DM patients and 273 non-T2DM patients. The FFs and areas of visceral adipose tissue (VAT), subcutaneous adipose tissue (SAT) and abdominal muscle (AM) were measured at the level of the L1-L2 vertebral. The FF of bone marrow adipose tissue (BMAT) was determined by the averaged FF values measured at the level of T12 and L1 vertebral, respectively. The whole hepatic fat fraction (HFF) and pancreatic fat fraction (PFF) were measured based on 3D semi-automatic segmentation on the FF mapping. All data were analyzed by GraphPad Prism and MedCalc.ResultsVAT area, VAT FF, HFF, PFF of T2DM group were higher than those of non-T2DM group after adjusting for age and sex (P &lt; 0.05). However, there was no differences in SAT area, SAT FF, BMAT FF, AM area and AM FF between the two groups (P &gt; 0.05). VAT area and PFF were independent risk factors of T2DM (all P &lt; 0.05). The area under the curve (AUC) of the receiver operating characteristic (ROC) for VAT area and PFF in differentiating between T2DM and non-T2DM were 0.685 and 0.787, respectively, and the AUC of PFF was higher than VAT area (P &lt; 0.05). Additionally, in seemingly healthy individuals, the SAT area, VAT area, and AM area were found to be significantly associated with being overweight and/or obese (BMI ≥ 25) (all P &lt; 0.05).ConclusionsIn this study, it was found that there were significant associations between T2DM and VAT area, VAT FF, HFF and PFF. In addition, VAT area and PFF were the independent risk factors of T2DM. Especially, PFF showed a high diagnostic performance in discrimination between T2DM and non-T2DM. These findings may highlight the crucial role of PFF in the pathophysiology of T2DM, and it might be served as a potential imaging biomarker of the prevention and treatment of T2DM. Additionally, in individuals without diabetes, focusing on SAT area, VAT area and AM area may help identify potential health risks and provide a basis for targeted weight management and prevention measures

Gold(I)-Catalyzed Cycloisomerizations and Alkoxycyclizations of ortho-(Alkynyl)styrenes

Indenes and related polycyclic structures have been efficiently synthesized by gold(I)-catalyzed cycloisomerizations of appropriate ortho-(alkynyl)styrenes. Disubstitution at the terminal position of the olefin was demonstrated to be essential to obtain products originating from a formal 5-endo-dig cyclization. Interestingly, a complete switch in the selectivity of the cyclization of o-(alkynyl)-α-methylstyrenes from 6-endo to 5-endo was observed by adding an alcohol to the reaction media. This allowed the synthesis of interesting indenes bearing an all-carbon quaternary center at C1. Moreover, dihydrobenzo[a]fluorenes can be obtained from substrates bearing a secondary alkyl group at the β-position of the styrene moiety by a tandem cycloisomerization/1,2-hydride migration process. In addition, diverse polycyclic compounds were obtained by an intramolecular gold-catalyzed alkoxycyclization of o-(alkynyl)styrenes bearing a nucleophile in their structure. Finally, the use of a chiral gold complex allowed access to elusive chiral 1H-indenes in good enantioselectivitiesMinisterio de Economia y Competitividad (MINECO) and FEDER (CTQ2010-15358 and CTQ2013-48937-C2-1-P) and Junta de Castilla y Leon (BU237U13) for financial support. A.M.S. thanks the Junta de Castilla y Leon (Consejeria de Educacion) and the Fondo Social Europeo for a PIRTU contract. M.A.R. and P.G.-G. thank MEC for a "Young Foreign Researchers" (SB2009-0186) contract and MINECO for "Juan de la Cierva" contract, respectivelyThis is the peer reviewed version of the following article: Sanjuán, A. M., Rashid, M. A., García-García, P., Martínez-Cuezva, A., Fernández-Rodríguez, M. A., Rodríguez, F. and Sanz, R. (2015), Gold(I)-Catalyzed Cycloisomerizations and Alkoxycyclizations of ortho-(Alkynyl)styrenes. Chem. Eur. J., 21: 3042–3052. doi: 10.1002/chem.201405789, which has been published in final form at 10.1002/chem.201405789. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archivin