Yazar "AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü" için PubMed İndeksli Yayınlar Koleksiyonu listeleme
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Alantolactone ameliorates graft versus host disease in mice
Odabas, Gul Pelin; Aslan, Kubra; Suna, Pinar Alisan; Kendirli, Perihan Kader; Erdem, Şerife; Çakır, Mustafa; Özcan, Alper; Yılmaz, Ebru; Karakukcu, Musa; Donmez-Altuntas, Hamiyet; Yay, Arzu Hanim; Deniz, Kemal; Altay, Derya; Arslan, Duran; Canatan, Halit; Eken, Ahmet; Unal, Ekrem (ELSEVIER, 2024)The anti-inflammatory and immunosuppressive drugs which are used in the treatment of Graft-versus-Host Disease (GVHD) have limited effects in controlling the severity of the disease. In this study, we aimed to investigate ... -
Analyzing the genetic diversity and biotechnological potential of Leuconostoc pseudomesenteroides by comparative genomics
Gumustop, Ismail; Ortakci, Fatih (Frontiers Media S.A., 2023)Leuconostoc pseudomesenteroides is a lactic acid bacteria species widely exist in fermented dairy foods, cane juice, sourdough, kimchi, apple dumpster, caecum, and human adenoid. In the dairy industry, Ln. pseudomesenteroides ... -
Berberine-containing natural-medicine with boiled peanut-OIT induces sustained peanut-tolerance associated with distinct microbiota signature
Srivastava, Kamal; Cao, Mingzhuo; Fidan, Ozkan; Shi, Yanmei; Yang, Nan; Nowak-Wegrzyn, Anna; Miao, Mingsan; Zhan, Jixun; Sampson, Hugh A.; Li, Xiu-Min (FRONTIERS MEDIA SA, 2023)BackgroundGut microbiota influence food allergy. We showed that the natural compound berberine reduces IgE and others reported that BBR alters gut microbiota implying a potential role for microbiota changes in BBR function. ... -
Biodiversity, drug discovery, and the future of global health: Introducing the biodiversity to biomedicine consortium, a call to action
Neergheen-Bhujun, Vidushi; Awan, Almas Taj; Baran, Yusuf; Bunnefeld, Nils; Chan, Kit; Edison Dela Cruz, Thomas; Egamberdieva, Dilfuza; Elsasser, Simon; Johnson, Mari-Vaughn V.; Komai, Shoji; Konevega, Andrey L.; Malone, John H.; Mason, Paul; Nguon, Rothsophal; Piper, Ross; Shrestha, Uttam Babu; Pesic, Milica; Kagansky, Alexander (UNIV EDINBURGH, GLOBAL HEALTH SOC, CENTRE POPULATION HEALTH SCIENCES, TEVIOT PL, EDINBURGH, EH8 9AG, SCOTLAND, 2017)[Özet Yok] -
Can mesenchymal stem/stromal cells and their secretomes combat bacterial persisters?
Bicer-Çalışkan, Mesude; Fidan, Ozkan (SPRINGER, 2023)The increasing number of life-threatening infections caused by persister bacteria is associated with various issues, including antimicrobial resistance and biofilm formation. Infections due to persister cells are often ... -
CiliaMiner: an integrated database for ciliopathy genes and ciliopathies
Turan, Merve Gül; Orhan, Mehmet Emin; Cevik, Sebiha; Kaptan, Oktay I. (OXFORD UNIV PRESS, 2023)Cilia are found in eukaryotic species ranging from single-celled organisms, such as Chlamydomonas reinhardtii, to humans, but not in plants. The ability to respond to repellents and/or attractants, regulate cell proliferation ... -
Circular RNA-MicroRNA-MRNA interaction predictions in SARS-CoV-2 infection
Demirci, Yilmaz Mehmet; Demirci, Muserref Duygu Sacar (WALTER DE GRUYTER GMBHGENTHINER STRASSE 13, D-10785 BERLIN, GERMANY, 2021)Different types of noncoding RNAs like microRNAs (miRNAs) and circular RNAs (circRNAs) have been shown to take part in various cellular processes including post-transcriptional gene regulation during infection. MiRNAs are ... -
Comparative Genomics of Lentilactobacillus parabuchneri isolated from dairy, KEM complex, Makgeolli, and Saliva Microbiomes
Gumustop, Ismail; Ortakci, Fatih (BMC, 2022)Background: Lentilactobacillus parabuchneri is of particular concern in fermented food bioprocessing due to causing unwanted gas formation, cracks, and off-flavor in fermented dairy foods. This species is also a known ... -
Comparative genomics of Leuconostoc lactis strains isolated from human gastrointestinal system and fermented foods microbiomes
Gümüştop, İsmail; Ortakçı, Fatih (BMCCAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND, 2022)Background: Leuconostoc lactis forms a crucial member of the genus Leuconostoc and has been widely used in the fermentation industry to convert raw material into acidified and flavored products in dairy and plant-based ... -
Comparative genomics of Loigolactobacillus coryniformis with an emphasis on L. coryniformis strain FOL-19 isolated from cheese
Gumustop, Ismail; Ortakci, Fatih (ELSEVIER, 2023)Loigolactobacillus coryniformis is a member of lactic acid bacteria isolated from various ecological niches. We isolated a novel L. coryniformis strain FOL-19 from artisanal Tulum cheese and performed the whole-genome ... -
Computational prediction of microRNAs in Histoplasma capsulatum
Demirci, Mueserref Duygu Sagar (ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 24-28 OVAL RD, LONDON NW1 7DX, ENGLAND, 2020)MicroRNAs (miRNAs) are small and non-coding RNAs that regulate gene expression through post-transcriptional regulation. Although, the standard miRNA repository, MiRBase, lists more than 200 organisms having miRNA mediated ... -
A decision support system for the prediction of mortality in patients with acute kidney injury admitted in intensive care unit
Kayaalti, Selda; Kayaalti, Omer; Aksebzeci, Bekir Hakan (UNIV SOUTH BOHEMIA, FAC HEALTH & SOCIAL STUD, JIROVCOVA, CESKA BUDEJOVICE, 370 04, CZECH REPUBLIC, 2020)Intensive care unit (ICU) is a very special unit of a hospital, where healthcare professionals provide treatment and, later, close followup to the patients. It is crucial to estimate mortality in ICU patients from many ... -
Discovery of adapalene and dihydrotachysterol as antiviral agents for the Omicron variant of SARS‑CoV‑2 through computational drug repurposing
Fidan, Özkan; Mujwar, Somdutt; Kciuk, Mateusz (SPRINGER, VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS, 2022)Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been signifcantly paralyzing the societies, economies and health care systems around the globe. The mutations on the genome of SARS-CoV-2 led to the emergence ... -
Editorial: Microbial production of medicinally important agents
Zeng, Jia; Zhan, Jixun; Qiao, Xue; Fidan, Ozkan (FRONTIERS MEDIA SA, 2023)Harnessing microbial systems as bio-factories for the production of medically significant agents presents a thriving avenue in pharmaceutical research. From manufacturing natural products, including potent secondary ... -
Environmental responsiveness of tubulin glutamylation in sensory cilia is regulated by the p38 MAPK pathway
Kimura, Yoshishige; Tsutsumi, Koji; Konno, Alu; Ikegami, Koji; Hameed, Saira; Kaneko, Tomomi; Kaplan, Oktay Ismail; Teramoto, Takayuki; Fujiwara, Manabi; Ishihara, Takeshi; Blacque, Oliver E.; Setou, Mitsutoshi (NATURE PUBLISHING GROUP, MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND, 2018)Glutamylation is a post-translational modification found on tubulin that can alter the interaction between microtubules (MTs) and associated proteins. The molecular mechanisms regulating tubulin glutamylation in response ... -
Ethacrynic acid and cinnamic acid combination exhibits selective anticancer effects on K562 chronic myeloid leukemia cells
Yenigul, Munevver; Akcok, Ismail; Gencer Akcok, Emel Basak (SPRINGER, 2022)Background Despite the recent advances in chemotherapy, the outcomes and the success of these treatments still remain insufficient. Novel combination treatments and treatment strategies need to be developed in order to ... -
Exploring the binding capacity of lactic acid bacteria derived bacteriocins against RBD of SARS-CoV-2 Omicron variant by molecular simulations
The changes in the SARS-CoV-2 genome have resulted in the emergence of new variants. Some of the variants have been classified as variants of concern (VOC). These strains have higher transmission rate and improved fitness. ... -
Exploring therapeutic avenues: mesenchymal stem/stromal cells and exosomes in confronting enigmatic biofilm-producing fungi
Bicer, Mesude (SPRINGER, 2024)Fungal infections concomitant with bioflms can demonstrate an elevated capacity to withstand substantially higher concentrations of antifungal agents, contrasted with infectious diseases caused by planktonic cells. This ... -
Genomic, probiotic, and metabolic potentials of Liquorilactobacillus nagelii AGA58, a novel bacteriocinogenic motile strain isolated from lactic acid-fermented shalgam
Yetiman, Ahmet Evren; Ortakci, Fatih (ELSEVIER, 2023)This study aimed to perform genomic, probiotic, and metabolic characterization of a novel Liquorilactobacillus nagelii AGA58 isolated from a lactic acid-fermented shalgam beverage to understand its metabolic potentials and ... -
Histopathology image classification: highlighting the gap between manual analysis and AI automation
Doğan, Refika Sultan; Yılmaz, Bülent (FRONTIERS MEDIA SA, 2023)The field of histopathological image analysis has evolved significantly with the advent of digital pathology, leading to the development of automated models capable of classifying tissues and structures within diverse ...