Not to be sniffed at: repurposing existing RNA-seq data to examine changes to human nasal microbiome composition in COVID-19 infection, compared to influenza and healthy controls

Objective: The human microbiome is essential in maintaining healthy physiology; compositional changes have been implicated in numerous physical and mental diseases. Thus far, COVID-19 microbiome research has focused primarily upon gut and lung bacterial communities. However, the early stages of COVID-19 infection and immune response occur in the nasal epithelium. Therefore, investigating nasal microbiome changes in early-stage COVID-19 may yield key insights into the immune system mechanisms involved in progression from mild/no symptoms to systemic organ failure/death, why this occurs in certain individuals, and how it may be prevented with early warning.Patients and Methods: Here we repurposed existing RNA-seq data to characterise the human nasal microbiome in COVID-19 infected samples and compared the taxonomic profile to healthy control and influenza-infected control samples, to identify COVID-19 specific nasal microbiome changes and attempt to rationalise these in the context of what is already known regarding mechanisms of the immune response to COVID-19.Results: We demonstrate that existing RNA-seq reads from human nasal swabs can be repurposed to characterize the human nasal microbiome robustly and accurately in health, early-stage COVID-19, and influenza. We observe that nasal microbiome composition (presence and abundance of phyla, genera, and species) significantly differs between health and disease, and between COVID-19 and influenza.Conclusions: Our observed healthy nasal microbial profiles match the findings of previous research, demonstrating that repurposing existing RNA-seq data is as accurate as targeted methods for taxonomic classification. We also observed many differential changes in the nasal microbiome profile to be disease specific. This will be key to enabling the potential for differential diagnosis based upon nasal microbiome profiles in the future

Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description

The role of a Mediterranean diet on the risk of oral and pharyngeal cancer.

BACKGROUND: The Mediterranean diet has a beneficial role on various neoplasms, but data are scanty on oral cavity and pharyngeal (OCP) cancer. METHODS: We analysed data from a case-control study carried out between 1997 and 2009 in Italy and Switzerland, including 768 incident, histologically confirmed OCP cancer cases and 2078 hospital controls. Adherence to the Mediterranean diet was measured using the Mediterranean Diet Score (MDS) based on the major characteristics of the Mediterranean diet, and two other scores, the Mediterranean Dietary Pattern Adherence Index (MDP) and the Mediterranean Adequacy Index (MAI). RESULTS: We estimated the odds ratios (ORs), and the corresponding 95% confidence intervals (CI), for increasing levels of the scores (i.e., increasing adherence) using multiple logistic regression models. We found a reduced risk of OCP cancer for increasing levels of the MDS, the ORs for subjects with six or more MDS components compared with two or less being 0.20 (95% CI 0.14-0.28, P-value for trend <0.0001). The ORs for the highest vs the lowest quintile were 0.20 (95% CI 0.14-0.28) for the MDP score (score 66.2 or more vs less than 57.9), and 0.48 (95% CI 0.33-0.69) for the MAI score (score value 2.1 or more vs value less 0.92), with significant trends of decreasing risk for both scores. The favourable effect of the Mediterranean diet was apparently stronger in younger subjects, in those with a higher level of education, and in ex-smokers, although it was observed in other strata as well. CONCLUSIONS: Our study provides strong evidence of a beneficial role of the Mediterranean diet on OCP cancer

Synthetic Biology Open Language (SBOL) Version 1.1.0

In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language (SBOL) Version 1.1.0 to enable the electronic exchange of information describing DNA components used in synthetic biology. We define: 1. the vocabulary, a set of preferred terms and 2. the core data model, a common computational representation

A research on phenolic and cyanogenic compounds in sweet and bitter kernelled apricot varieties

12th Symposium on Apricot Culture and Decline -- SEP 10-14, 2001 -- Avignon, FRANCEWOS: 000237601100025In this study, phenolic compounds situation were determined in sweet and bitter apricot varieties. For this purpose, sweet apricot varieties such as Kabaasi, Sam and Hasanbey and bitter varieties such as Adilcevaz-2, Adilcevaz-4 and X.1 Zerdali were used. Leaf and root samples were taken in May and September. Phenolics and cyanogenic glycosides were analysed by using thin layer chromatography and high performance liquid chromatography, respectively. Consequently, it was found that bitter kernelled apricots contain higher levels of phenolic and cyanogenic compounds in the leaves, roots and seeds than sweet kernelled ones. http://www.actahort.org/members/showpdf?booknrarnr=701_25Int Soc Hort Sci, INRA, Agri Obtent, Conseil Reg Provence Alpes Cotes Azur, Conseil Reg Languedoc Roussillon, Conseil Reg Rhone Alpes, CIHEAM, IAMZ, CIHEAM, IAMB, CEP, CTIFL, SERFEL, RMG Avignon, Coteaux Tricastin, GIE, PROMEGA FranceINCO-DC "APRIMED" [ICI 18 CT 98-0310]This research is supported by No: ICI 18 CT 98-0310 (INCO-DC "APRIMED"

Determination of phenolic compounds in male and female figs

1st International Symposium on Fig -- JUN 24-28, 1997 -- IZMIR, TURKEYWOS: 000079157300043In this trial, leaf extracts of some male and female cultivars and Sarilop clones were investigated by using thin layer chromatography. It was seen that tannin contents of male varieties were higher than those of the female varieties. Some spots that were determined in female figs did not appear in caprifigs.Int Soc Hort Sc

Determination of phenolic compounds in resistant and susceptible apricot hybrids to Sclerotinia laxa

XIth International Symposium on Apricot Culture -- MAY 25-30, 1997 -- VERIA MAKEDONIA, GREECEWOS: 000083017300114In this study, phenolic compounds of leaves in resistant and susceptible hybrids were investigated. It was seen that resistant hybrids contained more tannin and high number of phenolic components than the susceptibles.NAGREF, Int Soc Hort Sci, Greek Soc Hort Sci, Minist Agr, Geotech Chamber Greece, Minist Makedonia Thraki, Community Portaria Halkidiki, CRONOS, SA, CON VERI, SA, CONEX, SA, COPAIS, SA, DOW ELANCO, DRAGOUMANOS, ELVAK, SA, HARANTONIS, HELLAFARM, SA, Prefecture Imathia, Municipality Veria, Gen Secretariat Res & Techn, Agr Coop Union Messi, Imathia, Chem Ind NO Greece, Agr Bank Greece, INEMPOLIDIS, Ioannis, LAPAFARM, SA, PHILIPPOS, SA, Scientact Co, E & N Mamani, Venus, SA, Vitro Hellas, SA, Xiloyannis Bailis, SA, Zeneca Hella

Research on variation of female and male figs in terms of leaf properties and stomatal distribution

1st International Symposium on Fig -- JUN 24-28, 1997 -- IZMIR, TURKEYWOS: 000079157300021In the experiment, leaf and stomatal properties of some fig and caprifig varieties and Sarilop clones were investigated. It was found that mean stomata numbers in male and female cultivars varied according to the year.Int Soc Hort Sc