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Genome And Metabolome Mining Of Marine Obligate Salinispora Strains To Discover New Natural Products, Süleyman Özakin, Ebru İnce Bostanci
Genome And Metabolome Mining Of Marine Obligate Salinispora Strains To Discover New Natural Products, Süleyman Özakin, Ebru İnce Bostanci
Turkish Journal of Biology
Marine microorganisms are receiving more attention as a promising potential source of new natural products. In the present study, we performed genomic and metabolomic analyses to explore the metabolic potential of the obligate marine actinomycete genus Salinispora. The genomes of thirty Salinispora strains were prospected in search of biosynthetic gene clusters including polyketide synthase (PKS), nonribosomal peptide synthetase (NPRS), terpene, indole, lantibiotics, and siderophores. We determined considerable diversity of natural product biosynthetic gene clusters in their genome. There were a total of 1428 putative gene clusters involved in the biosynthesis of various bioactive natural products. Furthermore, 1509 ketosynthase (KS) and …
Protein Engineering Approaches For Antibody Fragments: Directed Evolution And Rational Design Approaches, Merve Arslan, Di̇lara Karadağ, Si̇bel Kalyoncu
Protein Engineering Approaches For Antibody Fragments: Directed Evolution And Rational Design Approaches, Merve Arslan, Di̇lara Karadağ, Si̇bel Kalyoncu
Turkish Journal of Biology
The number of therapeutic antibodies in preclinical, clinical, or approved phases has been increasing exponentially, mostly due to their known successes. Development of antibody engineering methods has substantially hastened the development of therapeutic antibodies. A variety of protein engineering techniques can be applied to antibodies to improve their affinity and/or biophysical properties such as solubility and stability. Antibody fragments (where all or some parts of constant regions are eliminated while the essential antigen binding region is preserved) are more suitable for protein engineering techniques because there are many in vitro screening technologies available for antibody fragments but not full-length antibodies. …
Transcriptome Analysis Reveals Differentially Expressed Genes Between Human Primary Bone Marrow Mesenchymal Stem Cells And Human Primary Dermal Fibroblasts, Eki̇m Z. Taşkiran, Beren Karaosmanoğlu
Transcriptome Analysis Reveals Differentially Expressed Genes Between Human Primary Bone Marrow Mesenchymal Stem Cells And Human Primary Dermal Fibroblasts, Eki̇m Z. Taşkiran, Beren Karaosmanoğlu
Turkish Journal of Biology
Stromal cells have been widely used in biomedical research and disease modeling studies in vitro. The most commonly used types of stromal cells are mesenchymal stem cells and fibroblasts. Their cellular phenotypes and differentiation capabilities are quite similar and there are no specific distinction criteria. In order to identify transcriptomic differences between these 2 cell types, we performed next-generation RNA sequencing. Using the global gene expression profile and pathway analysis, we showed that human primary bone marrow mesenchymal stem cells and human primary dermal fibroblasts have different molecular signatures. We also identified critical transcription factors that are differentially expressed between …
Complete Genome Sequence Analysis Of A Lytic Shigella Flexneri Vb_Sfls-Isf001 Bacteriophage, Khashayar Shahin, Majid Bouzari, Ran Wang
Complete Genome Sequence Analysis Of A Lytic Shigella Flexneri Vb_Sfls-Isf001 Bacteriophage, Khashayar Shahin, Majid Bouzari, Ran Wang
Turkish Journal of Biology
Shigellosis is one of the most important acute enteric infections caused by different species of Shigella, such as Shigella flexneri. Despite the use of antibiotic therapy to reduce disease duration, this approach is becoming less effective due to the emergence of antibiotic resistance among Shigella spp. Bacteriophages have been introduced as an alternative for controlling shigellosis. However, the bacteriophages must be without any lysogenic or virulence factors, toxin coding, or antibiotic-resistant genes. In this study, the whole genome sequence of vB_SflS-ISF001, a virulent Siphoviridae bacteriophage specific for Shigella flexneri, was obtained, and a comparative genomic analysis was carried out to …
Examining The Involvement Of Slx5 In The Apoptotic Response To Chronic Activation Of The Spindle Assembly Checkpoint, Pinar Buket Atalay, Eli̇f Ergi̇n Çavuşoğlu, Öykü Aşci, Duygu Aygüneş
Examining The Involvement Of Slx5 In The Apoptotic Response To Chronic Activation Of The Spindle Assembly Checkpoint, Pinar Buket Atalay, Eli̇f Ergi̇n Çavuşoğlu, Öykü Aşci, Duygu Aygüneş
Turkish Journal of Biology
Microtubule-targeting agents represent one of the most successful groups of anticancer drugs used in cancer therapy today. These drugs induce a prolonged mitotic arrest through chronic spindle assembly checkpoint (SAC) activation. Apoptosis, an outcome of the prolonged mitotic arrest, is the main mechanism by which these anticancer drugs kill cancer cells. However, not much is known about the mechanism that directs chronic SAC activation to apoptosis among other possible outcomes. The aim of this study is to investigate whether Slx5, a sumo-targeted ubiquitin E3 ligase, is involved in directing chronic SAC activation to apoptosis. We show that chronic SAC activation …
Keratin 14 Is A Novel Interaction Partner Of Keratinocyte Differentiation Regulator:Receptor-Interacting Protein Kinase 4, Ceren Sümer, Asi̇ye Büşra Boz Er, Tuba Di̇nçer
Keratin 14 Is A Novel Interaction Partner Of Keratinocyte Differentiation Regulator:Receptor-Interacting Protein Kinase 4, Ceren Sümer, Asi̇ye Büşra Boz Er, Tuba Di̇nçer
Turkish Journal of Biology
The epidermis, the outer layer of the skin, is formed by stratified keratinocyte layers. The self-renewal of the epidermis is provided by sustained proliferation and differentiation of the keratinocyte stem cells localized to the basal layer of the epidermis. Receptorinteracting protein kinase 4 (RIPK4) is an important regulator of keratinocyte differentiation, mutations of which are associated with congenital ectodermal malformations. In an attempt to identify the molecular basis of RIPK4's function, we applied yeast two-hybrid screen (Y2H) and found basal layer-specific keratin filament component keratin 14 (KRT14) as a novel RIPK4-interacting partner. During keratinocyte differentiation, layer-specific keratin composition is tightly …
Precipitation And Characterization Of Caco3 Of Bacillus Amyloliquefaciens U17 Strain Producing Urease And Carbonic Anhydrase, Merve Tepe, Şevki̇ Arslan, Tamer Koralay, Nazi̇me Mercan
Precipitation And Characterization Of Caco3 Of Bacillus Amyloliquefaciens U17 Strain Producing Urease And Carbonic Anhydrase, Merve Tepe, Şevki̇ Arslan, Tamer Koralay, Nazi̇me Mercan
Turkish Journal of Biology
In the present study, the properties of calcium carbonate mineralization and urease and carbonic anhydrase activities of Bacillus amyloliquefaciens U17 isolated from calcareous soil of Denizli (Turkey) were analyzed. CaCO3 was produced in all growth phases. Strain U17 showed 0.615 ± 0.092 μmol/min/mg urease enzyme activity in calcium mineralization medium and 1.315 ± 0.021 μmol/min/mg urease enzyme activity in Luria-Bertani medium supplemented with urea, whereas it showed 36.03 ± 5.48 nmol/min/ mg carbonic anhydrase enzyme activity in CaCO3 precipitation medium and 28.82 ± 3.31 nmol/min/mg carbonic anhydrase enzyme activity in Luria-Bertani medium supplemented with urea. The urease B protein expression …
Cytotoxic And Genotoxic Action Of Tagetes Patula Flower Methanol Extract And Patuletin Using The Allium Test, Mudassar Azhar, Ahsana Dar Farooq, Sayedul Haque, Samina Bano, Lubna Zaheer, Shaheen Faizi
Cytotoxic And Genotoxic Action Of Tagetes Patula Flower Methanol Extract And Patuletin Using The Allium Test, Mudassar Azhar, Ahsana Dar Farooq, Sayedul Haque, Samina Bano, Lubna Zaheer, Shaheen Faizi
Turkish Journal of Biology
Tagetes patula is used to treat cancer patients in alternative healthcare systems. However, its cytotoxic and genotoxic effects have not been reported. Therefore, the methanol extract of T. patula flower, the ethyl acetate fraction, and the pure compound patuletin were evaluated using the Allium test. The methanol extract and fraction contained ~3% and ~36% patuletin, respectively, with ~98% purity. The methanol extract caused inhibition of Allium root growth displaying an IC50 value of ~500 μg/mL, while the fraction and patuletin were more potent by ~2 and ~5 times, respectively. The Allium root tips demonstrated a decline in prophase, metaphase, anaphase, …
In Silico Approach To The Analysis Of Snps In The Human Apaf1 Gene, Tuğba Kaman, Ömer Faruk Karasakal, Ebru Özkan Oktay, Korkut Ulucan, Muhsi̇n Konuk
In Silico Approach To The Analysis Of Snps In The Human Apaf1 Gene, Tuğba Kaman, Ömer Faruk Karasakal, Ebru Özkan Oktay, Korkut Ulucan, Muhsi̇n Konuk
Turkish Journal of Biology
The apoptotic protease activating factor 1 (APAF1) gene encodes a cytoplasmic protein that initiates apoptosis and is a crucial factor in the mitochondria-dependent death pathway. APAF1 is implicated in many pathways such as apoptosis, neurodegenerative diseases, and cancer. The purpose of this study was to predict deleterious/damaging SNPs in the APAF1 gene via in silico analysis. To this end, APAF1 missense SNPs were obtained from the NCBI dbSNP database. In silico analysis of the missense SNPs was carried out by using publicly available online software tools. The stabilization and three-dimensional modeling of mutant proteins were also determined by using the …
Identification Of Streptomyces Strains Isolated From Humulus Lupulus Rhizosphere And Determination Of Plant Growth Promotion Potential Of Selected Strains, Fadi̇me Özdemi̇r Koçak
Identification Of Streptomyces Strains Isolated From Humulus Lupulus Rhizosphere And Determination Of Plant Growth Promotion Potential Of Selected Strains, Fadi̇me Özdemi̇r Koçak
Turkish Journal of Biology
In the present study it was aimed to obtain novel strains of actinomycetes that have the ability to promote plant growth. For this, seven soil samples from the rhizosphere of Humulus lupulus (Pazaryeri, Bilecik) were used and potential isolates were obtained. 16S rRNA genes of 30 isolates were amplified by PCR and sequenced. Eighteen isolates were found to be closely related to Streptomycetes spp. and they were tested for their proteolytic activity, cellulase activity, phosphate solubility, IAA production, biofilm formation, and growth in nitrogen-limited medium. Two isolates, HCI 12 and HCI 36, were selected according to the results of these …