Araştırma Çıktıları

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Author: search.filters.author.Ozcan, OrhanHas files: Yes

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    A global metagenomic map of urban microbiomes and antimicrobial resistance
    (CELL PRESS, 2021-01-01) Danko, David; Bezdan, Daniela; Afshin, Evan E.; Ahsanuddin, Sofia; Bhattacharya, Chandrima; Butler, Daniel J.; Chng, Kern Rei; Donnellan, Daisy; Hecht, Jochen; Jackson, Katelyn; Kuchin, Katerina; Karasikov, Mikhail; Lyons, Abigail; Mak, Lauren; Meleshko, Dmitry; Mustafa, Harun; Mutai, Beth; Neches, Russell Y.; Ng, Amanda; Nikolayeva, Olga; Nikolayeva, Tatyana; Png, Eileen; Ryon, Krista A.; Sanchez, Jorge L.; Shaaban, Heba; Sierra, Maria A.; Thomas, Dominique; Young, Ben; Abudayyeh, Omar O.; Alicea, Josue; Bhattacharyya, Malay; Blekhman, Ran; Castro-Nallar, Eduardo; Canas, Ana M.; Chatziefthimiou, Aspassia D.; Crawford, Robert W.; De Filippis, Francesca; Deng, Youping; Desnues, Christelle; Dias-Neto, Emmanuel; Dybwad, Marius; Elhaik, Eran; Ercolini, Danilo; Frolova, Alina; Gankin, Dennis; Gootenberg, Jonathan S.; Graf, Alexandra B.; Green, David C.; Hajirasouliha, Iman; Hastings, Jaden J. A.; Hernandez, Mark; Iraola, Gregorio; Jang, Soojin; Kahles, Andre; Kelly, Frank J.; Knights, Kaymisha; Kyrpides, Nikos C.; Labaj, Pawel P.; Lee, Patrick K. H.; Leung, Marcus H. Y.; Ljungdahl, Per O.; Mason-Buck, Gabriella; McGrath, Ken; Meydan, Cem; Mongodin, Emmanuel F.; Moraes, Milton Ozorio; Nagarajan, Niranjan; Nieto-Caballero, Marina; Noushmehr, Houtan; Oliveira, Manuela; Ossowski, Stephan; Osuolale, Olayinka O.; Ozcan, Orhan; Paez-Espino, David; Rascovan, Nicolas; Richard, Hugues; Ratsch, Gunnar; Schriml, Lynn M.; Semmler, Torsten; Sezerman, Osman U.; Shi, Leming; Shi, Tieliu; Siam, Rania; Song, Le Huu; Suzuki, Haruo; Court, Denise Syndercombe; Tighe, Scott W.; Tong, Xinzhao; Udekwu I, Klas; Ugalde, Juan A.; Valentine, Brandon; Vassilev I, Dimitar; Vayndorf, Elena M.; Velavan, Thirumalaisamy P.; Wu, Jun; Zambrano, Maria M.; Zhu, Jifeng; Zhu, Sibo; Mason, Christopher E.; Consortium, Int MetaSU. B.
    We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97\% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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    Expression Profile of Glossina pallidipes MicroRNAs During Symptomatic and Asymptomatic Infection With Glossina pallidipes Salivary Gland Hypertrophy Virus (Hytrosavirus)
    (FRONTIERS MEDIA SA, 2018-01-01) Meki, Irene K.; Ince, Ikbal A.; Kariithi, Henry M.; Boucias, Drion G.; Ozcan, Orhan; Parker, Andrew G.; Viak, Just M.; van Oers, Monique M.; Abd-Alla, Adly M. M.
    The Glossina pallidipes salivary gland hypertrophy virus (GpSGHV) infects tsetse flies predominantly asymptomatically and occasionally symptomatically. Symptomatic infections are characterized by overt salivary gland hypertrophy (SGH) in mass reared tsetse flies, which causes reproductive dysfunctions and colony collapse, thus hindering tsetse control via sterile insect technique (SIT). Asymptomatic infections have no apparent cost to the fly's fitness. Here, small RNAs were sequenced and profiles in asymptomatically and symptomatically infected G. pallidipes flies determined. Thirty-eight host-encoded microRNAs (miRNAs) were present in both the asymptomatic and symptomatic fly profiles, while nine host miRNAs were expressed specifically in asymptomatic flies versus 10 in symptomatic flies. Of the shared 38 miRNAs, 15 were differentially expressed when comparing asymptomatic with symptomatic flies. The most up-regulated host miRNAs in symptomatic flies was predicted to target immune-related mRNAs of the host. Six GpSGHV-encoded miRNAs were identified, of which five of them were only in symptomatic flies. These virus-encoded miRNAs may not only target host immune genes but may also participate in viral immune evasion. This evidence of differential host miRNA profile in Glossina in symptomatic flies advances our understanding of the GpSGHV-Glossina interactions and provides potential new avenues, for instance by utilization of particular miRNA inhibitors or mimics to better manage GpSGHV infections in tsetse mass-rearing facilities, a prerequisite for successful SIT implementation.