A high confidence, manually validated human blood plasma protein reference set

<p>Abstract</p> <p>Background</p> <p>The immense diagnostic potential of human plasma has prompted great interest and effort in cataloging its contents, exemplified by the Human Proteome Organization (HUPO) Plasma Proteome Project (PPP) pilot project. Due to challenges in obtaining a reliable blood plasma protein list, HUPO later re-analysed their own original dataset with a more stringent statistical treatment that resulted in a much reduced list of high confidence (at least 95%) proteins compared with their original findings. In order to facilitate the discovery of novel biomarkers in the future and to realize the full diagnostic potential of blood plasma, we feel that there is still a need for an ultra-high confidence reference list (at least 99% confidence) of blood plasma proteins.</p> <p>Methods</p> <p>To address the complexity and dynamic protein concentration range of the plasma proteome, we employed a linear ion-trap-Fourier transform (LTQ-FT) and a linear ion trap-Orbitrap (LTQ-Orbitrap) for mass spectrometry (MS) analysis. Both instruments allow the measurement of peptide masses in the low ppm range. Furthermore, we employed a statistical score that allows database peptide identification searching using the products of two consecutive stages of tandem mass spectrometry (MS3). The combination of MS3 with very high mass accuracy in the parent peptide allows peptide identification with orders of magnitude more confidence than that typically achieved.</p> <p>Results</p> <p>Herein we established a high confidence set of 697 blood plasma proteins and achieved a high 'average sequence coverage' of more than 14 peptides per protein and a median of 6 peptides per protein. All proteins annotated as belonging to the immunoglobulin family as well as all hypothetical proteins whose peptides completely matched immunoglobulin sequences were excluded from this protein list. We also compared the results of using two high-end MS instruments as well as the use of various peptide and protein separation approaches. Furthermore, we characterized the plasma proteins using cellular localization information, as well as comparing our list of proteins to data from other sources, including the HUPO PPP dataset.</p> <p>Conclusion</p> <p>Superior instrumentation combined with rigorous validation criteria gave rise to a set of 697 plasma proteins in which we have very high confidence, demonstrated by an exceptionally low false peptide identification rate of 0.29%.</p

Fluorescent Labeling of SNAP-Tagged Proteins in Cells

One of the most prominent self-labeling tags is SNAP-tag. It is an in vitro evolution product of the human DNA repair protein O6 -alkylguanine-DNA alkyltransferase (hAGT) that reacts specifically with benzylguanine (BG) and benzylchloropyrimidine (CP) derivatives, leading to covalent labeling of SNAP-tag with a synthetic probe (Gronemeyer et al., Protein Eng Des Sel 19:309–316, 2006; Curr Opin Biotechnol 16:453–458, 2005; Keppler et al., Nat Biotechnol 21:86–89, 2003; Proc Natl Acad Sci U S A 101:9955– 9959, 2004). SNAP-tag is well suited for the analysis and quantification of fused target protein using fluorescence microscopy techniques. It provides a simple, robust, and versatile approach to the imaging of fusion proteins under a wide range of experimental conditions. © Springer Science+Business Media New York 2015

Association between alkaline phosphatase and hypertension in a rural Japanese population: The Nagasaki Islands study

Background: Although serum alkaline phosphatase (ALP) levels have been associated with hypertension, and ALP is known as an enzyme affected by alcohol consumption, no study has been published on the associations between ALP and the risk of hypertension in relation to drinking status.Methods: We conducted a cross-sectional study of 2,681 participants (837 men and 1,846 women) aged 30 to 89 years undergoing a general health check-up to investigate the associations between ALP and hypertension in relation to drinking status.Results: Of the 2,681 participants, 1,549 (514 men and 1,035 women) were diagnosed with hypertension. A sex difference was observed for the relationship between ALP and hypertension. While no significant association was observed for men, the association was significantly positive for women. The multivariable adjusted odds ratio and 95% coincidence interval (CI) of hypertension per increment of 1-log ALP were 0.95 (95% CI: 0.56 to 1.59) for men and 1.57 (95% CI: 1.07 to 2.33) for women. When this analysis was restricted to nondrinkers, a significantly elevated risk of hypertension was observed for men and remained significant for women; that is, 3.32 (95% CI: 1.38 to 8.02) for men and 1.68 (95% CI: 1.11 to 2.55) for women.Conclusion: ALP is associated with hypertension for both male and female nondrinkers, but not for drinkers. For analyses of associations between ALP and blood pressure, alcohol consumption should thus be considered a potential confounder

Variation in capsaicin contents of different Capsicum species and lines by varying drying parameters

Capsaicin is a pungent capsaicinoid and is the main therapeutic and flavoring compound of Capsicum pepper species. Capsicum species have an important place in world spice production and markets. They are adapted to warm climates and are widely grown in China and Turkey. Besides food purposes, they have renowned therapeutic properties for a number of illnesses. In the present study, various Capsicum species and lines were studied for their capsaicin contents according to different harvest time and drying parameters. In this concept, some local lines and introduced Capsicum species (Capsicum frutescens 26, Aci{dotless} Çiçek 52 and Capsicum chinense 38) from different countries were cultivated under the ecological conditions of the Çukurova region of Turkey in 2003-2004. Plants were harvested at two different times and three phases in each harvest time and drying parameters, related to ripening, and dried by various techniques (sun, solar tunnel dryer and cabinet dryer at varying drying temperatures such as 40°, 60° and 80°). The capsaicin contents of different Capsicum species and lines were affected by harvest time and drying parameters. Capsaicin contents were within the range 0.50-4.20%. The highest capsaicin content was obtained from the solar tunnel drying at the second harvest in the local Capsicum line Aci{dotless} Çiçek 52. © 2010

Variation in capsaicin contents of different Capsicum species and lines by varying drying parameters

Capsaicin is a pungent capsaicinoid and is the main therapeutic and flavoring compound of Capsicum pepper species. Capsicum species have an important place in world spice production and markets. They are adapted to warm climates and are widely grown in China and Turkey. Besides food purposes, they have renowned therapeutic properties for a number of illnesses. In the present study, various Capsicum species and lines were studied for their capsaicin contents according to different harvest time and drying parameters. In this concept, some local lines and introduced Capsicum species (Capsicum frutescens 26, Aci{dotless} Çiçek 52 and Capsicum chinense 38) from different countries were cultivated under the ecological conditions of the Çukurova region of Turkey in 2003-2004. Plants were harvested at two different times and three phases in each harvest time and drying parameters, related to ripening, and dried by various techniques (sun, solar tunnel dryer and cabinet dryer at varying drying temperatures such as 40°, 60° and 80°). The capsaicin contents of different Capsicum species and lines were affected by harvest time and drying parameters. Capsaicin contents were within the range 0.50-4.20%. The highest capsaicin content was obtained from the solar tunnel drying at the second harvest in the local Capsicum line Aci{dotless} Çiçek 52. © 2010

Seasonal and diurnal variability of essential oil and its components in Origanum onites L. grown in the ecological conditions of Cukurova

WOS: 000235933500002Turkish Oregano (Origanum onites L.) is one of the most commonly collected from nature as well as cultivated Origanum species in Turkey. In addition, Turkish Oregano is the most exported Origanum species from Turkey to the entire World. In this study, the seasonal and diurnal variability of the essential oil content in Origanum onites L. grown in the ecological conditions of Cukurova was studied from September 2000-August 2001. Monthly variability of the essential oil composition was also studied. The plant cuttings collected from the region were rooted in the greenhouse and transferred to the field in a split plot design with three replications. One year later from transplanting,fresh leaves from the top shoots were collected every week three times a day on Monday (at 08.(00), 12.(00) and 16.(00) o'clock) throughout the year. The content and composition of the essential oil were analysed in fresh leaf samples by hydrodistillation. The essential oil content changed according to the seasons and the hour of day. The highest essential oil content (% 1.92) was found in the post-flowering -at the beginning of the seed formation period in the afternoon harvests during the second half of June (40(th) week). The essential oil composition varied monthly and the highest value (% 73.65) of carvacrol, the main component of the essential oil, was obtained from the flowering period in May

Fibroblast adhesion on unidirectional polymeric nanofilms

Nanotextured polymeric surfaces with inclined rods reveal highly anisotropic properties concerning wetting and adhesion. In this work, we report on the interaction of fibroblast cells with these highly anisotropic materials. The authors quantified removal of adherent cells from such surfaces by a laminar flow. The critical shear force needed for cell removal from the surface depends on the inclination direction. Based on electron microscopy cross sections we deduce that interactions of cellular filopodia extending into the nanotextured surface are causing the direction depending removal