Determination of volatile compounds of the first rose oil and the first rose water by HS-SPME/GC/MS techniques

Background: Rose water and rose oil are used in the perfume, cosmetic, pharmaceutical and food industries. The determination of volatile compounds in rose oil and rose water obtained from oil-bearing rose is highly important in terms of availability in the industry and in human health.Materials and Methods: Twenty four and twenty six volatile compounds were determined in the first rose oil and in the first rose water. Thus, in this study, volatile compounds in the first rose oil and first rose water have been determined by HS-SPME/GC/MS (Headspace-Solid Phase Micro Extraction/Gas Chromatography Mass Spectrometry) techniques which were not published previously for determining volatile compounds in rose oil and rose water.Results: Twenty four and twenty six volatile compounds were found in the first rose oil and in the first rose water, respectively. It was further discovered that both first rose oil and first rose water are rich in oxygenated monoterpenes and sesquiterpenes, with a third group of volatile compounds known as aliphatic hydrocarbons being found only in first rose oil. Citronellol contents of the first rose oil and rose water were found to be 43.40% and 40.13% respectively, whereas geraniol contents were 11.81% and 15.97%, respectively.Conclusion: These findings suggest that HS-SPME/GC/MS is a suitable technique for the determination of volatile compounds of rose oil and rose water.Keywords: Oil-bearing rose, Rosa damascena, HS-SPME/GC/MS, volatile compounds

Linking common human diseases to their phenotypes; development of a resource for human phenomics.

BackgroundIn recent years a large volume of clinical genomics data has become available due to rapid advances in sequencing technologies. Efficient exploitation of this genomics data requires linkage to patient phenotype profiles. Current resources providing disease-phenotype associations are not comprehensive, and they often do not have broad coverage of the disease terminologies, particularly ICD-10, which is still the primary terminology used in clinical settings.MethodsWe developed two approaches to gather disease-phenotype associations. First, we used a text mining method that utilizes semantic relations in phenotype ontologies, and applies statistical methods to extract associations between diseases in ICD-10 and phenotype ontology classes from the literature. Second, we developed a semi-automatic way to collect ICD-10-phenotype associations from existing resources containing known relationships.ResultsWe generated four datasets. Two of them are independent datasets linking diseases to their phenotypes based on text mining and semi-automatic strategies. The remaining two datasets are generated from these datasets and cover a subset of ICD-10 classes of common diseases contained in UK Biobank. We extensively validated our text mined and semi-automatically curated datasets by: comparing them against an expert-curated validation dataset containing disease-phenotype associations, measuring their similarity to disease-phenotype associations found in public databases, and assessing how well they could be used to recover gene-disease associations using phenotype similarity.ConclusionWe find that our text mining method can produce phenotype annotations of diseases that are correct but often too general to have significant information content, or too specific to accurately reflect the typical manifestations of the sporadic disease. On the other hand, the datasets generated from integrating multiple knowledgebases are more complete (i.e., cover more of the required phenotype annotations for a given disease). We make all data freely available at https://doi.org/10.5281/zenodo.4726713

PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research.

Understanding the relationship between the pathophysiology of infectious disease, the biology of the causative agent and the development of therapeutic and diagnostic approaches is dependent on the synthesis of a wide range of types of information. Provision of a comprehensive and integrated disease phenotype knowledgebase has the potential to provide novel and orthogonal sources of information for the understanding of infectious agent pathogenesis, and support for research on disease mechanisms. We have developed PathoPhenoDB, a database containing pathogen-to-phenotype associations. PathoPhenoDB relies on manual curation of pathogen-disease relations, on ontology-based text mining as well as manual curation to associate host disease phenotypes with infectious agents. Using Semantic Web technologies, PathoPhenoDB also links to knowledge about drug resistance mechanisms and drugs used in the treatment of infectious diseases. PathoPhenoDB is accessible at http://patho.phenomebrowser.net/ , and the data are freely available through a public SPARQL endpoint

DETERMINATION OF VOLATILE AROMA COMPOUNDS OF GANODERMA LUCIDUM BY GAS CHROMATOGRAPHY MASS SPECTROMETRY (HS-GC/MS)

This study was conducted at Horticulture Department of Cukurova University, Adana, Turkey during 2010-2011. Fresh sample of Ganoderma lucidum collected from Mersin province of Turkey was used as material. Volatile aroma compounds were performed by Headspace Gas Chromatography (HS-GC/MS). Alcohols, aldehydes, acids, phenol, L-Alanine, d-Alanine, 3-Methyl, 2-Butanamine, 2-Propanamine were determined. 1-Octen-3-ol (Alcohol) and 3-methyl butanal (Aldehyde) were identified as major aroma compounds

DDIEM: drug database for inborn errors of metabolism

Abstract: Background: Inborn errors of metabolism (IEM) represent a subclass of rare inherited diseases caused by a wide range of defects in metabolic enzymes or their regulation. Of over a thousand characterized IEMs, only about half are understood at the molecular level, and overall the development of treatment and management strategies has proved challenging. An overview of the changing landscape of therapeutic approaches is helpful in assessing strategic patterns in the approach to therapy, but the information is scattered throughout the literature and public data resources. Results: We gathered data on therapeutic strategies for 300 diseases into the Drug Database for Inborn Errors of Metabolism (DDIEM). Therapeutic approaches, including both successful and ineffective treatments, were manually classified by their mechanisms of action using a new ontology. Conclusions: We present a manually curated, ontologically formalized knowledgebase of drugs, therapeutic procedures, and mitigated phenotypes. DDIEM is freely available through a web interface and for download at http://ddiem.phenomebrowser.net

DDIEM: drug database for inborn errors of metabolism

Abstract: Background: Inborn errors of metabolism (IEM) represent a subclass of rare inherited diseases caused by a wide range of defects in metabolic enzymes or their regulation. Of over a thousand characterized IEMs, only about half are understood at the molecular level, and overall the development of treatment and management strategies has proved challenging. An overview of the changing landscape of therapeutic approaches is helpful in assessing strategic patterns in the approach to therapy, but the information is scattered throughout the literature and public data resources. Results: We gathered data on therapeutic strategies for 300 diseases into the Drug Database for Inborn Errors of Metabolism (DDIEM). Therapeutic approaches, including both successful and ineffective treatments, were manually classified by their mechanisms of action using a new ontology. Conclusions: We present a manually curated, ontologically formalized knowledgebase of drugs, therapeutic procedures, and mitigated phenotypes. DDIEM is freely available through a web interface and for download at http://ddiem.phenomebrowser.net

Reflexive Memory Authenticator: A Proposal for Effortless Renewable Biometrics

International audienceToday’s biometric authentication systems are still struggling with replay attacks and irrevocable stolen credentials. This paper introduces a biometric protocol that addresses such vulnerabilities. The approach prevents identity theft by being based on memory creation biometrics. It takes inspiration from two different authentication methods, eye biometrics and challenge systems, as well as a novel biometric feature: the pupil memory effect. The approach can be adjusted for arbitrary levels of security, and credentials can be revoked at any point with no loss to the user. The paper includes an analysis of its security and performance, and shows how it could be deployed and improved

Fruit characteristics of nine thornless blackberry genotypes

Fruit characteristics of nine semierect and trailing thornless blackberry genotypes were evaluated in Adana province, in the Mediterranean region of Turkey. Five cultivars ('Chester Thornless', 'Jumbo', 'Loch Ness' ('Nessy'), 'Navaho' and 'DirksenThornless') and four selections (Bursa-1, Bursa-2, Bursa-3 and Bartin) were characterized in 2001 and 2002. The genotypes were compared for yield, fruit weight, concentration of total soluble solid (TSS), fruit acidity, TSS / acidity ratio, pH, color and harvest periods. The highest TSS content was in 'Navaho'; the heaviest berries were in 'Jumbo'; the highest yield was in 'Chester Thornless;' and the longest harvesting period was in 'Jumbo' and 'Navaho' in both years

Inter- and intra-specific nursery characterization of three wild Pistacia species

Turkey has a huge wild Pistacia germplasm that mainly includes P. terebinthus, P. atlantica and P. eurycarpa species. In this study, seed and seedling behaviour of these species are characterized at intra- and inter-specific level. Seed and seedlings of 63 Pistacia genotypes: 10 P. terebinthus, 45 P. atlantica and eight P. eurycarpa genotypes from different parts of Turkey were evaluated as their characteristics of germination, seedling growth and budding success. Correlations between morphological traits of maternal trees and seed/seedling characteristics of their progeny were performed as well. There was a large variability for each of the evaluated character at the inter- and intra-specific level. However, in the average, P. eurycarpa had the highest germination percentage, whereas P. terebinthus had the lowest. The seedling growth of P. atlantica was better than P. terebinthus and P. eurycarpa. Budding success was not significant between species. Correlation coefficient values suggested that a few of the associations between morphological traits of maternal trees and seed germination and seedling characters of their progeny vary between those of three species

The effects of scarification, stratification and Ga-3 treatments on the germination of seeds and seedling growth in selected P-khinjuk types

2nd International Symposium on Pistachios and Almonds -- AUG 24-29, 1997 -- UNIV CALIF DAVIS, DAVIS, CAWOS: 000077152900063In this research, seeds from seven P. khinjuk types were selected from the Sanliurfa, Icel and Siirt provinces of Turkey. After testing the viability and germination percentages, the seeds of the selected P. khinjuk types were first scarified with H2SO4 and then sown directly, or sown after treatment with GA(3), or sown after stratification. Seedling growth and development, stem height and stem diameter were measured at 15 day intervals during the growth period. There were no significant differences among the selections in the viability of the seeds. Seed germination rate under the three treatments ranged between 40% (B-3382) and 96% (B-56A1). The highest germination rates were in the stratification treatment whereas the lowest germination rates were in the directly sown treatment. The highest stem diameter was obtained in the B-56A1 type in the stratification treatment. Since the stratification treatment gave the best results, it was assumed that GA(3) application could substitute for stratification. B-56A1 and B-5602 were found to have the highest germination and growth rates.Int Soc Hort Sc