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2021

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Articles 75481 - 75510 of 75623

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Host Variations In Sars-Cov-2 Infection, Doruk Altiok, Eli̇f Zeynep Savci, Büşra Özkara, Kami̇l Alkan, Di̇lara Sultan Namdar, Gi̇zem Tunçer, Buğrahan Regai̇p Kilinç, Evren Sui̇çmez, Güneysu Çeti̇n, Si̇nan Ünal, Beyza Dönmüş, Zeynep Yağmur Karagülleoğlu, Di̇lrüba Beyza Uncuoğlu, Cansu Tekeli̇, Hani̇fe Ayşegül Mendi̇ Jan 2021

Host Variations In Sars-Cov-2 Infection, Doruk Altiok, Eli̇f Zeynep Savci, Büşra Özkara, Kami̇l Alkan, Di̇lara Sultan Namdar, Gi̇zem Tunçer, Buğrahan Regai̇p Kilinç, Evren Sui̇çmez, Güneysu Çeti̇n, Si̇nan Ünal, Beyza Dönmüş, Zeynep Yağmur Karagülleoğlu, Di̇lrüba Beyza Uncuoğlu, Cansu Tekeli̇, Hani̇fe Ayşegül Mendi̇

Turkish Journal of Biology

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the zoonotic pathogen that causes the "Coronavirus Disease of 2019 (COVID-19)", and COVID-19 itself is yet to be thoroughly understood. Both the disease as well as the mechanisms by which the host interacts with the SARS-CoV-2 have not been fully enlightened. The epidemiological factors -e.g. age, sex, race-, the polymorphisms of the host proteins, the blood types and individual differences have all been in discussions about affecting the progression and the course of COVID-19 both individually and collectively, as their effects are mostly interwoven. We focused mainly on the effect of …

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Genomic Chronicle Of Sars-Cov-2: A Mutational Analysis With Over 1 Million Genome Sequences, Osman Mutluhan Uğurel, Oğuz Ata, Di̇lek Balik Jan 2021

Genomic Chronicle Of Sars-Cov-2: A Mutational Analysis With Over 1 Million Genome Sequences, Osman Mutluhan Uğurel, Oğuz Ata, Di̇lek Balik

Turkish Journal of Biology

Use of information technologies to analyse big data on SARS-CoV-2 genome provides an insight for tracking variations and examining the evolution of the virus. Nevertheless, storing, processing, alignment and analyses of these numerous genomes are still a challenge. In this study, over 1 million SARS-CoV-2 genomes have been analysed to show distribution and relationship of variations that could enlighten development and evolution of the virus. In all genomes analysed in this study, a total of over 215M SNVs have been detected and average number of SNV per isolate was found to be 21.83. Single nucleotide variant (SNV) average is observed …

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The Effect Of Weekend Curfews On Epidemics: A Monte Carlo Simulation, Hakan Kaygusuz, Ahmet Ni̇hat Berker Jan 2021

The Effect Of Weekend Curfews On Epidemics: A Monte Carlo Simulation, Hakan Kaygusuz, Ahmet Ni̇hat Berker

Turkish Journal of Biology

The ongoing COVID-19 pandemic is being responded with various methods, applying vaccines, experimental treatment options, total lockdowns or partial curfews. Weekend curfews are among the methods for reducing the number of infected persons, and this method is practically applied in some countries such as Turkey. In this study, the effect of weekend curfews on reducing the spread of a contagious disease, such as COVID-19, is modeled using a Monte Carlo algorithm with a hybrid lattice model. In the simulation setup, a fictional country with three towns and 26,610 citizens were used as a model. Results indicate that applying a weekend …

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The Current State Of Validated Small Molecules Inhibiting Sars-Cov-2 Non-Structural Proteins, Fati̇h Kocabaş, Merve Uslu Jan 2021

The Current State Of Validated Small Molecules Inhibiting Sars-Cov-2 Non-Structural Proteins, Fati̇h Kocabaş, Merve Uslu

Turkish Journal of Biology

The current COVID-19 outbreak has had a profound influence on public health and daily life. Despite all restrictions and vaccination programs, COVID-19 still can lead to fatality due to a lack of COVID-19-specific treatments. A number of studies have demonstrated the feasibility to develop therapeutics by targeting underlying components of the viral proteome. Here we reviewed recently developed and validated small molecule inhibitors of SARS-CoV-2's nonstructural proteins. We described the validation level of identified compounds specific for SARS-CoV-2 in the presence of in vitro and in vivo supporting data. The mechanisms of pharmacological activity, as well as approaches for developing …

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Determination Of The Interaction Between The Receptor Binding Domain Of 2019-Ncov Spike Protein, Tmprss2, Cathepsin B And Cathepsin L And Glycosidic And Aglycon Forms Of Some Flavonols, Erman Sali̇h İsti̇fli̇, Arzuhan Şihoğlu Tepe, Paulo Augusto Netz, Cengi̇z Sarikürkcü, İbrahi̇m Hali̇l Kiliç, Bektaş Tepe Jan 2021

Determination Of The Interaction Between The Receptor Binding Domain Of 2019-Ncov Spike Protein, Tmprss2, Cathepsin B And Cathepsin L And Glycosidic And Aglycon Forms Of Some Flavonols, Erman Sali̇h İsti̇fli̇, Arzuhan Şihoğlu Tepe, Paulo Augusto Netz, Cengi̇z Sarikürkcü, İbrahi̇m Hali̇l Kiliç, Bektaş Tepe

Turkish Journal of Biology

The novel coronavirus (COVID-19, SARS-CoV-2) is a rapidly spreading disease with a high mortality. In this research, the interactions between specific flavonols and the 2019-nCoV receptor binding domain (RBD), transmembrane protease, serine 2 (TMPRSS2), and cathepsins (CatB and CatL) were analyzed. According to the relative binding capacity index (RBCI) calculated based on the free energy of binding and calculated inhibition constants, it was determined that robinin (ROB) and gossypetin (GOS) were the most effective flavonols on all targets. While the binding free energy of ROB with the spike glycoprotein RBD, TMPRSS2, CatB, and CatL were -5.02, -7.57, -10.10, and -6.11 …

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Ss-Carboline Alkaloids Induce Structural Plasticity And Inhibition Of Sars-Cov-2 Nsp3 Macrodomain More Potently Than Remdesivir Metabolite Gs-441524: Computational Approach, Yusuf Oloruntoyin Ayipo, Sani Najib Yahaya, Halimah Funmilayo Babamale, Iqrar Ahmad, Harun Patel, Mohd Nizam Mordi Jan 2021

Ss-Carboline Alkaloids Induce Structural Plasticity And Inhibition Of Sars-Cov-2 Nsp3 Macrodomain More Potently Than Remdesivir Metabolite Gs-441524: Computational Approach, Yusuf Oloruntoyin Ayipo, Sani Najib Yahaya, Halimah Funmilayo Babamale, Iqrar Ahmad, Harun Patel, Mohd Nizam Mordi

Turkish Journal of Biology

The nsp3 macrodomain is implicated in the viral replication, pathogenesis and host immune responses through the removal of ADP-ribosylation sites during infections of coronaviruses including the SARS-CoV-2. It has ever been modulated by macromolecules including the ADP-ribose until Ni and co-workers recently reported its inhibition and plasticity enhancement unprecedentedly by remdesivir metabolite, GS-441524, creating an opportunity for investigating other biodiverse small molecules such as ß-Carboline (ßC) alkaloids. In this study, 1497 ßC analogues from the HiT2LEAD chemical database were screened, using computational approaches of Glide XP docking, molecular dynamics simulation and pk-CSM ADMET predictions. Selectively, ßC ligands, 129, 584, 1303 …

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Treatment Of Covid-19 Patients With Quercetin In Combination With Vitamin C And Bromelain: A Prospective, Single - Centre, Randomized, Controlled Trial, Hasan Önal, Bengü Arslan, Nurcan Üçüncü Ergun, Hani̇m Şeyma Topuz, Seda Yilmaz Semerci̇, Mehmet Eren Kurnaz, Yulet Mi̇ray Molu, Mehmet Abdussamet Bozkurt, Nuretti̇n Süner, Ali̇ Kocataş Jan 2021

Treatment Of Covid-19 Patients With Quercetin In Combination With Vitamin C And Bromelain: A Prospective, Single - Centre, Randomized, Controlled Trial, Hasan Önal, Bengü Arslan, Nurcan Üçüncü Ergun, Hani̇m Şeyma Topuz, Seda Yilmaz Semerci̇, Mehmet Eren Kurnaz, Yulet Mi̇ray Molu, Mehmet Abdussamet Bozkurt, Nuretti̇n Süner, Ali̇ Kocataş

Turkish Journal of Biology

Scientific research continues on new preventive and therapeutic strategies against severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2). So far, there is no proven curative treatment, and a valid alternative therapeutic approach needs to be developed. This study is designed to evaluate the effect of quercetin in COVID-19 treatment. This was a single-centre, prospective randomized controlled cohort study. Routine care versus QCB (quercetin, vitamin C, bromelain) supplementation was compared between 429 patients with at least one chronic disease and moderate-to-severe respiratory symptoms. Demographic features, signs, laboratory results and drug administration data of patients were recorded. The endpoint was that QCB supplementation was …

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Targeting Cov-2 Spike Rbd And Ace-2 Interaction With Flavonoids Of Anatolian Propolis By In Silico And In Vitro Studies In Terms Of Possible Covid-19 Therapeutics, Hali̇l İbrahi̇m Güler, Fulya Ay Şal, Zehra Can, Yakup Kara, Oktay Yildiz, Ali̇ Osman Beldüz, Sabri̇ye Çanakçi, Sevgi̇ Kolayli Jan 2021

Targeting Cov-2 Spike Rbd And Ace-2 Interaction With Flavonoids Of Anatolian Propolis By In Silico And In Vitro Studies In Terms Of Possible Covid-19 Therapeutics, Hali̇l İbrahi̇m Güler, Fulya Ay Şal, Zehra Can, Yakup Kara, Oktay Yildiz, Ali̇ Osman Beldüz, Sabri̇ye Çanakçi, Sevgi̇ Kolayli

Turkish Journal of Biology

Propolis is a multi-functional bee product rich in polyphenols. In this study, the inhibitory effect of Anatolian propolis against SARS-coronavirus-2 (SARS-CoV-2) was investigated in vitro and in silico. Raw and commercial propolis samples were used, and both samples were found to be rich in caffeic acid, p-coumaric acid, ferulic acid, t-cinnamic acid, hesperetin, chrysin, pinocembrin, and caffeic acid phenethyl ester (CAPE) at HPLC-UV analysis. Ethanolic propolis extracts (EPE) were used in the ELISA screening test against the spike S1 protein (SARS-CoV-2): ACE-2 interaction for in vitro study. The binding energy values of these polyphenols to the SARS-CoV-2 spike and ACE-2 …

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Coronavac (Sinovac) Covid-19 Vaccine-Induced Molecular Changes In Healthy Human Serum By Infrared Spectroscopy Coupled With Chemometrics, Ayça Doğan Mollaoğlu, Rafi̇g Gurbanov, Mete Severcan, Feri̇de Severcan Jan 2021

Coronavac (Sinovac) Covid-19 Vaccine-Induced Molecular Changes In Healthy Human Serum By Infrared Spectroscopy Coupled With Chemometrics, Ayça Doğan Mollaoğlu, Rafi̇g Gurbanov, Mete Severcan, Feri̇de Severcan

Turkish Journal of Biology

From the beginning of the COVID-19 coronavirus pandemic in December of 2019, the disease has infected millions of people worldwide and caused hundreds of thousands of deaths. Since then, several vaccines have been developed. One of those vaccines is inactivated CoronaVac-Sinovac COVID-19 vaccine. In this proof of concept study, we first aimed to determine CoronaVac-induced biomolecular changes in healthy human serum using infrared spectroscopy. Our second aim was to see whether the vaccinated group can be separated or not from the non-vaccinated group by applying chemometric techniques to spectral data. The results revealed that the vaccine administration induced significant changes …

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The Potential Use Of Drosophila As An In Vivo Model Organism For Covid-19-Related Research: A Review, Eşref Demi̇r Jan 2021

The Potential Use Of Drosophila As An In Vivo Model Organism For Covid-19-Related Research: A Review, Eşref Demi̇r

Turkish Journal of Biology

The world urgently needs effective antiviral approaches against emerging viruses, as shown by the coronavirus disease 2019 (COVID-19) pandemic, which has become an exponentially growing health crisis. Scientists from diverse backgrounds have directed their efforts towards identifying key features of SARS-CoV-2 and clinical manifestations of COVID-19 infection. Reports of more transmissible variants of SARS-CoV-2 also raise concerns over the possibility of an explosive trajectory of the pandemic, so scientific attention should focus on developing new weapons to help win the fight against coronaviruses that may undergo further mutations in the future. Drosophila melanogaster offers a powerful and potential in vivo …

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Cannabinoids For Sars-Cov-2 And Is There Evidence Of Their Therapeutic Efficacy?, Ahmet Onay, Abdulselam Ertaş, Veysel Süzerer, İsmai̇l Yener, Mustafa Abdullah Yilmaz, Emi̇ne Ayaz Ti̇lkat, Remzi̇ Eki̇nci̇, Nesri̇n Bozhan, Sevgi̇ İrtegün Jan 2021

Cannabinoids For Sars-Cov-2 And Is There Evidence Of Their Therapeutic Efficacy?, Ahmet Onay, Abdulselam Ertaş, Veysel Süzerer, İsmai̇l Yener, Mustafa Abdullah Yilmaz, Emi̇ne Ayaz Ti̇lkat, Remzi̇ Eki̇nci̇, Nesri̇n Bozhan, Sevgi̇ İrtegün

Turkish Journal of Biology

To combat the coronaviruses and their novel variants, therapeutic drugs and the development of vaccines that are to be effective throughout human life are urgently needed. The endocannabinoid system (ECS) acts as a modulator in the activation of the microcirculation, immune system, and autonomic nervous system, along with controlling pharmacological functions such as emotional responses, homeostasis, motor functions, cognition, and motivation. The ECS contains endogenous cannabinoids, cannabinoid receptor (CBRs), and enzymes that regulate their biosynthesis, transport, and degradation. Moreover, phytocannabinoids and synthetic cannabinoids that mimic the action of endocannabinoids also play an essential role in the modulation of the ECS. …

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Cover And Contents Jan 2021

Cover And Contents

Turkish Journal of Biology

No abstract provided.

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Endoplasmic Reticulum Stress And Oncomir-Associated Chemotherapeutic Drug Resistance Mechanisms In Breast Cancer Tumors, Leila Mehdizadehtapeh, Pinar Obakan Yerli̇kaya Jan 2021

Endoplasmic Reticulum Stress And Oncomir-Associated Chemotherapeutic Drug Resistance Mechanisms In Breast Cancer Tumors, Leila Mehdizadehtapeh, Pinar Obakan Yerli̇kaya

Turkish Journal of Biology

Breast cancer, as a heterogenous malign disease among the top five leading causes of cancer death worldwide, is defined as by far the most common malignancy in women. It contributes to 25% of all cancer-associated deaths after menopause. Breast cancer is categorized based on the expression levels of cell surface and intracellular steroid receptors [estrogen, progesterone receptors, and human epidermal growth factor receptor (HER2)], and the treatment approaches frequently include antiestrogen, aromatase inhibitors, and Herceptin. However, the management and prevention strategies due to adverse side effects stress the patients. The unsuccessful treatments cause to raise the drug levels, leading to …

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Effects Of Bradykinin On Proliferation, Apoptosis, And Cycle Of Glomerular Mesangial Cells Via The Tgf-Ss1/Smad Signaling Pathway, Ji Dong, Li Ding, Liuwei Wang, Zijun Yang, Yulin Wang, Ying Zang, Xuexia Cao, Lin Tang Jan 2021

Effects Of Bradykinin On Proliferation, Apoptosis, And Cycle Of Glomerular Mesangial Cells Via The Tgf-Ss1/Smad Signaling Pathway, Ji Dong, Li Ding, Liuwei Wang, Zijun Yang, Yulin Wang, Ying Zang, Xuexia Cao, Lin Tang

Turkish Journal of Biology

We aimed to assess the effects of bradykinin (BK) on the proliferation, apoptosis, and cycle of glomerular mesangial cells via the transforming growth factor-ß 1 (TGF-ß1)/Smad signaling pathway. Rat glomerular mesangial cells, HBZY-1, were divided into normal group (untreated), model group (5 ng/L TGF-ß1), BK group (5 ng/L TGF-ß1 + 1 ng/L BK), and inhibitor group [5 ng/L TGF-ß1 + 1 ng/L LY2109761 (TGF-ß1-specific inhibitor)]. The cell proliferation, cycle, apoptosis, expression of type I collagen (Col-1), and protein expressions of Col-1, TGF-ß1, and phosphorylated Smad2 (p-Smad2) were detected by EdU labeling, flow cytometry, acridine orange/ethidium bromide (AO/EB) dual staining, immunofluorescence …

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The Effects Of Pikfyve Inhibitor Ym201636 On Claudins And Malignancy Potential Of Nonsmall Cell Cancer Cells, Eda Doğan, Zekeri̇ya Düzgün, Zafer Yildirim, Berri̇n Özdi̇l Bay, Hüseyi̇n Aktuğ, Vi̇ldan Bozok Çeti̇ntaş Jan 2021

The Effects Of Pikfyve Inhibitor Ym201636 On Claudins And Malignancy Potential Of Nonsmall Cell Cancer Cells, Eda Doğan, Zekeri̇ya Düzgün, Zafer Yildirim, Berri̇n Özdi̇l Bay, Hüseyi̇n Aktuğ, Vi̇ldan Bozok Çeti̇ntaş

Turkish Journal of Biology

PIKfyve is an evolutionarily conserved lipid and protein kinase enzyme that has pleiotropic cellular functions. The aim of the present study was to investigate the effects of phosphatidylinositol-3-phosphate 5-kinase (PIKfyve) inhibitor, YM201636, on nonsmall cell lung cancer (NSCLC) cells growth, tumorigenicity, and claudin (CLDN) expressions. Three NSCLC cell lines (Calu-1, H1299 and HCC827) were used to compare the effects of YM201636. Cytotoxic effects of YM201636 were analysed using XTT assay. Malignancy potential of cells assesses with wound healing and soft agar colony-forming assays. mRNA and protein expressions of claudins were analysed by qRT-PCR and immunofluorescence staining. Our results revealed that …

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A Novel Rock Inhibitor: Off-Target Effects Of Metformin, Aysun Özdemi̇r, Mustafa Ark Jan 2021

A Novel Rock Inhibitor: Off-Target Effects Of Metformin, Aysun Özdemi̇r, Mustafa Ark

Turkish Journal of Biology

In drug discovery, most small molecules cannot cross many stages, only a few can become drug candidates. Once the drug molecule is approved and marketed, nontarget effects that are not easily distinguishable from the actual target of the drugs might be evaluated. This situation restricts the treatment. Thus, the discovery of new drugs is a very long and expensive process. In recent years, without developing new drugs, the approach of using different and new target molecules in new indications apart from the indications of licensed drug molecules has gained importance. In this study, using the connectivity map program, it was …

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Cellular Iron Storage And Trafficking Are Affected By Gtn Stimulation In Primary Glial And Meningeal Cell Culture, Lati̇fe Arzu Aral, Mehmet Ali̇ Ergün, Hayrunni̇sa Bolay Belen Jan 2021

Cellular Iron Storage And Trafficking Are Affected By Gtn Stimulation In Primary Glial And Meningeal Cell Culture, Lati̇fe Arzu Aral, Mehmet Ali̇ Ergün, Hayrunni̇sa Bolay Belen

Turkish Journal of Biology

A well-balanced intracellular iron trafficking in glial cells plays a role in homeostatic processes. Elevated intracellular iron triggers oxidative stress and cell damage in many neurological disorders, including migraine. This study aimed to investigate the effects of glyceryl trinitrate (GTN), on cellular iron homeostasis, matrixmetalloproteinase (MMP)-9, and calcitonin gene related peptide (CGRP) receptor (CRLR/CGRPR1) production in microglia, astrocyte, and meningeal cell cultures. Primary glial and meningeal cells in culture were exposed to GTN for 24 h. Messenger RNA expression was assessed using qPCR. Iron accumulation was visualized via modified Perl?s histochemistry. MMP-9 levels in cell culture supernatants were measured using …

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Arid4b Alters Cell Cycle And Cell Death Dynamics During Mouse Embryonic Stem Cell Differentiation, Gözde Güven, Nihal Terzi Çizmeci̇oğlu Jan 2021

Arid4b Alters Cell Cycle And Cell Death Dynamics During Mouse Embryonic Stem Cell Differentiation, Gözde Güven, Nihal Terzi Çizmeci̇oğlu

Turkish Journal of Biology

Cell division and death play an important role in embryonic development. Cell specialization is accompanied with slow proliferation and quiescence. Cell death is important for morphogenesis. Gene expression changes during differentiation is coordinated by lineage-specific transcription factors and chromatin factors. It is not yet fully understood how alterations in gene expression and cell cycle/death mechanisms are connected. We previously identified a chromatin protein Arid4b as a critical factor for meso/ endoderm differentiation of mouse embryonic stem cells (mESCs). The differentiation defect of Arid4b-deficient mESCs might be due to misregulation of cell proliferation or death. Here, we identified a role for …

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Detection Of Grain Yield Qtls In The Durum Population Lahn/Cham1 Tested Incontrasting Environments, Issame Farouk, Ahmad Alsaleh, Jihan Motowaj, Fatima Gaboun, Bouchra Belkadi, Abdelkarim Filali Maltouf, Zakaria Kehel, Ismahane Elouafi, Nasserelhaq Nsarellah, M. Miloudi Nachit Jan 2021

Detection Of Grain Yield Qtls In The Durum Population Lahn/Cham1 Tested Incontrasting Environments, Issame Farouk, Ahmad Alsaleh, Jihan Motowaj, Fatima Gaboun, Bouchra Belkadi, Abdelkarim Filali Maltouf, Zakaria Kehel, Ismahane Elouafi, Nasserelhaq Nsarellah, M. Miloudi Nachit

Turkish Journal of Biology

Durum wheat (Triticum turgidum L. var durum) is tetraploid wheat (AABB); it is the main source of semolina and other pasta products. Grain yield in wheat is quantitatively inherited and influenced by the environment. The genetic map construction constitutes the essential step in identifying quantitative trait loci (QTLs) linked to complex traits, such as grain yield. The study aimed to construct a genetic linkage map of two parents that are widely grown durum cultivars (Lahn and Cham1) in the Mediterranean basin, which is characterized by varying climate changes. The genetic linkage map of Lahn/Cham1 population consisted of 112 recombinant inbred …

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Expression Profiles Of Interferon-Related Genes In Cells Infected With Influenza A Viruses Or Transiently Transfected With Plasmids Encoding Viral Rna Polymerase, Eli̇f Çağlayan, Kadi̇r Turan Jan 2021

Expression Profiles Of Interferon-Related Genes In Cells Infected With Influenza A Viruses Or Transiently Transfected With Plasmids Encoding Viral Rna Polymerase, Eli̇f Çağlayan, Kadi̇r Turan

Turkish Journal of Biology

Influenza A viruses frequently change their genetic characteristics, which leads to the emergence of new viruses. Consequently, elucidation of the relationship between influenza A virus and host cells has a great importance to cope with viral infections. In this study, it was aimed to determine expression profiles of interferon response genes in human embryonic kidney 293 (HEK293) cells infected with human (A/WSN-H1N1) and avian influenza A viruses (duck/Pennsylvania/10218/84/H5N2) or transfected with plasmids encoding viral RdRP subunits and, to obtain clues about the genes that may be important for the viral pathogenesis. The HEK293 cells cultured in a 12-well plate were …

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Current Mutatome Of Sars-Cov-2 In Turkey Reveals Mutations Of Interest, Doğa Eski̇er, Evren Akalp, Özlem Dalan, Gökhan Karakülah, Yavuz Oktay Jan 2021

Current Mutatome Of Sars-Cov-2 In Turkey Reveals Mutations Of Interest, Doğa Eski̇er, Evren Akalp, Özlem Dalan, Gökhan Karakülah, Yavuz Oktay

Turkish Journal of Biology

As the underlying pathogen for the COVID-19 pandemic that has affected tens of millions of lives worldwide, SARS-CoV-2 and its mutations are among the most urgent research topics worldwide. Mutations in the virus genome can complicate attempts at accurate testing or developing a working treatment for the disease. Furthermore, because the virus uses its own proteins to replicate its genome, rather than host proteins, mutations in the replication proteins can have cascading effects on the mutation load of the virus genome. Due to the global, rapidly developing nature of the COVID-19 pandemic, local demographics of the virus can be difficult …

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Cover And Contents Jan 2021

Cover And Contents

Turkish Journal of Biology

No abstract provided.

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Targeting The Tumor Stroma: Integrative Analysis Reveal Gata2 And Toryaip1 As Novel Prognostic Targets In Breast And Ovarian Cancer, Ömer Faruk Erceylan, Ayşe Savaş, Esra Göv Jan 2021

Targeting The Tumor Stroma: Integrative Analysis Reveal Gata2 And Toryaip1 As Novel Prognostic Targets In Breast And Ovarian Cancer, Ömer Faruk Erceylan, Ayşe Savaş, Esra Göv

Turkish Journal of Biology

Tumor stroma interaction is known to take a crucial role in cancer growth and progression. In the present study, it was performed gene expression analysis of stroma samples with ovarian and breast cancer through an integrative analysis framework to identify common critical biomolecules at multiomics levels. Gene expression datasets were statistically analyzed to identify common differentially expressed genes (DEGs) by comparing tumor stroma and normal stroma samples. The integrative analyses of DEGs indicated that there were 59 common core genes, which might be feasible to be potential marks for cancer stroma targeted strategies. Reporter molecules (i.e. receptor, transcription factors and …

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Prediction Of Host-Pathogen Protein Interactions By Extended Network Model, İrfan Kösesoy, Murat Gök, Tamer Kahveci̇ Jan 2021

Prediction Of Host-Pathogen Protein Interactions By Extended Network Model, İrfan Kösesoy, Murat Gök, Tamer Kahveci̇

Turkish Journal of Biology

Knowledge of the pathogen-host interactions between the species is essentialin order to develop a solution strategy against infectious diseases. In vitro methods take extended periods of time to detect interactions and provide very few of the possible interaction pairs. Hence, modelling interactions between proteins has necessitated the development of computational methods. The main scope of this paper is integrating the known protein interactions between thehost and pathogen organisms to improve the prediction success rate of unknown pathogen-host interactions. Thus, the truepositive rate of the predictions was expected to increase.In order to perform this study extensively, encoding methods and learning algorithms …

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Transcriptome Profiles Associated With Selenium-Deficiency-Dependent Oxidative Stress Identify Potential Diagnostic And Therapeutic Targets In Liver Cancer Cells, Damla Gözen, Deni̇z Cansen Kahraman, Kübra Narci, Huma Shehwana, Özlen Konu, Rengül Çeti̇n Atalay Jan 2021

Transcriptome Profiles Associated With Selenium-Deficiency-Dependent Oxidative Stress Identify Potential Diagnostic And Therapeutic Targets In Liver Cancer Cells, Damla Gözen, Deni̇z Cansen Kahraman, Kübra Narci, Huma Shehwana, Özlen Konu, Rengül Çeti̇n Atalay

Turkish Journal of Biology

Hepatocellular carcinoma (HCC) is one of the most common cancer types with high mortality rates and displays increased resistance to various stress conditions such as oxidative stress. Conventional therapies have low efficacies due to resistance and off-target effects in HCC. Here we aimed to analyze oxidative stress-related gene expression profiles of HCC cells and identify genes that could be crucial for novel diagnostic and therapeutic strategies. To identify important genes that cause resistance to reactive oxygen species (ROS), a model of oxidative stress upon selenium (Se) deficiency was utilized. The results of transcriptome-wide gene expression data were analyzed in which …

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Arid4b Physically Interacts With Tfap2c In Mouse Embryonic Stem Cells, Ezgi̇ Gül Keski̇n, Jialiang Huang, Ni̇hal Terzi̇ Çi̇zmeci̇oğlu Jan 2021

Arid4b Physically Interacts With Tfap2c In Mouse Embryonic Stem Cells, Ezgi̇ Gül Keski̇n, Jialiang Huang, Ni̇hal Terzi̇ Çi̇zmeci̇oğlu

Turkish Journal of Biology

Precise regulation of gene expression is required for embryonic stem cell (ESC) differentiation. Transcription factor (TF) networks coordinate the balance of pluripotency and differentiation in response to extracellular and intracellular signals. Chromatin factors work alongside TFs to achieve timely regulation of gene expression for differentiation process. Our previous studies showed that a member of the Sin3a corepressor complex, Arid4b, is critical for proper mouse ESC differentiation into mesoderm and endoderm. We found elevated histone 3 lysine 27 acetylation (H3K27Ac) in a subset of genomic loci in meso/endoderm directed arid4b? cells, coincident with their derepression. We reasoned that Sin3a complex may …

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Positive Regulation Of Tnfr1 Signaling Via Sh3 Recognition Motif, Fatma Ece Çopuroğlu, Fatma Zehra Hapi̇l Zevkli̇ler, Şükran Burçak Yoldaş, Osman Ni̇dai̇ Özeş Jan 2021

Positive Regulation Of Tnfr1 Signaling Via Sh3 Recognition Motif, Fatma Ece Çopuroğlu, Fatma Zehra Hapi̇l Zevkli̇ler, Şükran Burçak Yoldaş, Osman Ni̇dai̇ Özeş

Turkish Journal of Biology

TNF is a pleiotropic cytokine and shows its biological function by binding to its receptors called TNFR1 and TNFR2. While TNFR1 induces apoptosis by activation of caspase-8 via the "death domain", it also activates IKKα/β, MKK3/6, MKK4/7 by activation of TAK1. Although the TNFR1 signaling pathway is known by in large, it is not known how AKT and MAPKs p38, ERK1/2, and JNK1/2 are activated. The presence of a proline-rich PPAP region, (P448PAP451, a binding site for the SH3 domain-containing proteins) very close to the C-terminus promoted us to determine whether this region has any role in the TNFR1 signal …

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Negative Regulation Of Diminutive Cancer Regulator Through Differentiation And Microrna Pathway Components In Drosophila Cells, Sumira Malik Jan 2021

Negative Regulation Of Diminutive Cancer Regulator Through Differentiation And Microrna Pathway Components In Drosophila Cells, Sumira Malik

Turkish Journal of Biology

Drosophila model is intensively studied for the development of cancer. The diminutive (dMyc), a homolog of the human MYC gene, is responsible for cell- apoptosis and its upregulation is responsible for determining the fate of cancerous growth in humans and Drosophila model. This work implores the requirement of dMyc and its expression as one of the major regulator of cancer with other proteins and repression of dMyc mRNA in Drosophila S2 cells. Here we report protein complex of Argonaute 1 (AGO1), Bag of marbles (Bam), and Brain tumor (Brat) proteins and not the individual factor of this complex repression of …

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Compensatory Expression Regulation Of Highly Homologous Proteins Hnrnpa1 Andhnrnpa2, Yan Chang, Xiao Feng Lu, Jia Ying Qiu Jan 2021

Compensatory Expression Regulation Of Highly Homologous Proteins Hnrnpa1 Andhnrnpa2, Yan Chang, Xiao Feng Lu, Jia Ying Qiu

Turkish Journal of Biology

Heterogeneous nuclear ribonucleoprotein (HNRNP) A1 and A2 are the most abundant HNRNPs with nearly identical functions, and play important roles in regulating gene expression at multiple levels (i.e. transcription, posttranscription, and translation). However, the expression and regulation mechanism of HNRNPA1 and A2 themselves remain unclear. In this study, the amino acid sequences of HNRNPA1 and HNRNPA2 were compared and found to have 78% and 86% homology in key functional domains. Transfection of HEK293 cells with small interfering RNA and overexpression vectors of HNRNPA1 and HNRNPA2 demonstrated that HNRNPA1 and HNRNPA2 paralogs regulate each other?s expression in a compensatory manner at …

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Synthesis Of Intracellular And Extracellular Gold Nanoparticles With A Green Machine And Its Antifungal Activity, Nurbanu Gürsoy, Betül Yilmaz Öztürk, İlknur Dağ Jan 2021

Synthesis Of Intracellular And Extracellular Gold Nanoparticles With A Green Machine And Its Antifungal Activity, Nurbanu Gürsoy, Betül Yilmaz Öztürk, İlknur Dağ

Turkish Journal of Biology

Green synthesis method is being increasingly used in the development of safe, stable, and eco-friendly nanostructures with biological resources. In this study, extracellular and intracellular synthesis of gold nanoparticles (AuNPs) was carried out using green algae Chlorella sorokiniana Shihira & R.W. Fresh algae were isolated and identified from Musaözü Pond located in the province of Eskişehir and then extraction process were performed. Optimization studies were studied using pH value, metal salt concentration, and time parameters for extracellular synthesis and using only time parameter for intrasellular synthesis. Since more controlled and optimum conditions can be achieved in the production of AuNPs …

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