Using graph theory to analyze biological networks

Understanding complex systems often requires a bottom-up analysis towards a systems biology approach. The need to investigate a system, not only as individual components but as a whole, emerges. This can be done by examining the elementary constituents individually and then how these are connected. The myriad components of a system and their interactions are best characterized as networks and they are mainly represented as graphs where thousands of nodes are connected with thousands of vertices. In this article we demonstrate approaches, models and methods from the graph theory universe and we discuss ways in which they can be used to reveal hidden properties and features of a network. This network profiling combined with knowledge extraction will help us to better understand the biological significance of the system

Massive contamination of Exophiala dermatitidis and E. phaeomuriformis in railway stations in subtropical Turkey

In order to reveal the source of contamination of opportunistic fungi, their natural habitat has to be understood. Black yeast-like fungi are abundant in man-made environments, particularly in those that are rich in toxic hydrocarbons such as railway ties. In this study, we investigated the presence of black fungi on creosote-treated oak railway ties and concrete sleepers stained with petroleum oil. Samples were collected at two central stations in Turkish cities, Mersin and Adana, and from Tarsus town station located between these two. The sample locations had subtropical climates. A total of 570 railway samples, including 320 from oak and 250 from concrete, were collected. Cotton swabs moistened with sterile physiological saline were applied to the ties and inoculated onto malt extract agar followed by incubation at 37 degrees C. Overall, we recovered 97 black yeast-like fungi (17.0 % positive). Sixty-three fungi (19.7 %) were collected from creosote-treated oak, whereas 34 isolates (13.6 %) were derived from concrete; the difference was significant (P = 0.05). Identification using rDNA internal transcribed spacer revealed Exophiala dermatitidis (57.7 %) and Exophiala phaeomuriformis (42.3 %). This study suggested that hydrocarbons enrich these opportunistic black yeasts. An eventual health risk is discussed

Isolation of Cryptococcus neoformans from a chestnut tree (Castanea sativa), Denizli, Turkey

WOS: 000459548000007PubMed ID: 30683040Cryptococcus neoformans is a basidiomycetous encapsulated yeast that can cause life-threatening infections in immunosuppressed humans and animals. C. neoformans/Cryptococcus gattii infections are considered to be acquired via inhalation of aerosolized particles from the environment. Avian guano, decaying tree hollows and soil are known as environmental niches. In recent years, colonization of the woody structures of different trees such as Eucalyptus camaldulensis, Tamarix hispida, Platanus orientalis and Punica granatum has been reported in the environmental study of the western Anatolian region. Based on the results of previous studies, our country may have intensive Cryptococcus colonization niches in the western regions. The aim of this study was to investigate the presence of the colonization of C.neoformans niche in chestnut (Castanea spp.) trees on higher altitudes.. In the study, the colonization of C.neoformans was screened on chestnut trees (Castanea spp.) in Aydin-Odemis-Denizli geographical area. This area consists of mountainous terrain between the fertile plain formed by two major rivers.This region is one of the widespreading areas of chestnut farming in Anatolia. Two hundred and fourteen chestnut trees that had deep fissures or trunk hollows were screened during mid-summer 2017. A swabbing technique was used, and all samples were cultured on Staib agar medium containing biphenyl and antibiotics. Cultures were checked for ten days for suspicious brown colonies. Suspicious yeast colonies were tested for the identification of pathogenic Cryptococcus by conventional methods and canavanine-glycine-bromothymol agar reactions. ITS 1-4 primers were used for strain PCR tests. We determined the mating type and serotypes by PCR analysis of the STE20 genes using STE20 (Aa), STE20 (A alpha), STE20 (Da), and STE20 (D alpha) primers. V8 agar medium was used for mating cultivation. Only one (0.47%) strain of C. neoformans was isolated from 214 screened trees. This strain was confirmed by ITS 1-4 sequencing. The serotype A MAT alpha mating type was observed. Basidium, basidiospores and clamp connections in hyphal structure were noted with MAT alpha mating on V8 agar medium. In this study, the first C.neoformans isolate from a chestnut tree (Castanea sativa) was determined from Denizli region. Further studies of distribution of human pathogenic Cryptococcus will be helpful to determine the risk areas for the living organisms in our region

ATR-FTIR Spectroscopy Highlights the Problem of Distinguishing Between Exophiala dermatitidis and E-phaeomuriformis Using MALDI-TOF MS

WOS: 000369061400008PubMed ID: 26373644The present study compared two chemical-based methods, namely, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, to understand the misidentification of Exophiala dermatitidis and Exophiala phaeomuriformis. The study utilized 44 E. dermatitidis and 26 E. phaeomuriformis strains, which were partially treated with strong acids and bases for further evaluation. MALDI-TOF MS and ATR-FTIR spectroscopy data of the two Exophiala species were compared. Data groupings were observed for the chromic acid- and nitric acid-treated species when the black yeast sources were categorized as creosoted-oak sleepers, concrete sleepers, or dishwasher isolates. The MALDI-TOF MS data for the metalloenzyme-containing regions were consistent with the ATR-FTIR spectroscopy data. These results indicated that environmental isolates might contain metals not found in human isolates and might interfere with chemical-based identification methods. Therefore, MALDI-TOF MS reference libraries should be created for clinical strains and should exclude petroleum-associated environmental isolates