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Öğe Construction and characterization of a de novo draft genome of garden cress (Lepidium sativum L.)(Springer Heidelberg, 2022) Patat, Aysenur Soyturk; Sen, Fatima; Erdogdu, Behic Selman; Uncu, Ali Tevfik; Uncu, Ayse OzgurGarden cress (Lepidium sativum L.) is a Brassicaceae crop recognized as a healthy vegetable and a medicinal plant. Lepidium is one of the largest genera in Brassicaceae, yet, the genus has not been a focus of extensive genomic research. In the present work, garden cress genome was sequenced using the long read high-fidelity sequencing technology. A de novo, draft genome assembly that spans 336.5 Mb was produced, corresponding to 88.6% of the estimated genome size and representing 90% of the evolutionarily expected orthologous gene content. Protein coding gene content was structurally predicted and functionally annotated, resulting in the identification of 25,668 putative genes. A total of 599 candidate disease resistance genes were identified by predicting resistance gene domains in gene structures, and 37 genes were detected as orthologs of heavy metal associated protein coding genes. In addition, 4289 genes were assigned as transcription factor coding. Six different machine learning algorithms were trained and tested for their performance in classifying miRNA coding genomic sequences. Logistic regression proved the best performing trained algorithm, thus utilized for pre-miRNA coding loci identification in the assembly. Repetitive DNA analysis involved the characterization of transposable element and microsatellite contents. L. sativum chloroplast genome was also assembled and functionally annotated. Data produced in the present work is expected to constitute a foundation for genomic research in garden cress and contribute to genomics-assisted crop improvement and genome evolution studies in the Brassicaceae family.Öğe SERUM LEVELS OF OXIDATIVE STRESS MARKERS IN SUBCLINICAL AND OVERT HYPOTHYROIDISM VERSUS CONTROL GROUP IN POPULATION OF KUTAHYA CITY, TURKEY(Gomal Medical Coll, 2021) Yontem, Mustafa; Arslan, Serap; Erdogdu, Behic Selman; Kocak, Fatma EmelBackground: Overproduction of oxygen-related free radicals and inadequate antioxidant defense are critical in hypothyroidism, as they might lead to future life-threatening diseases. The objectives of this study were to compare serum levels of oxidative stress markers; total oxidant status (TOS), total antioxidant status (TAS), oxidative stress index (OSI), paraoxonase-1 (PON-1), and arylesterase (ARYL) in patients with subclinical hypothyroidism (SH) and overt hypothyroidism (OH) versus healthy controls in population of Kutahya city, Turkey. Materials & Methods: This cross-sectional study was conducted at Department of Biochemistry, Faculty of Medicine, Kutahya University of Health Sciences, Kutahya, Turkey, from July to December, 2016. Three study groups of 45 each were formed as healthy controls, patients with SH and OH. Serum levels of TOS, TAS, OSI, PON-1, and ARYL were five research variables with ratio scale, but skewed, so described by median and IQR with 95% Cl. Kruskal-Wallis and multiple comparison tests were used for hypotheses testing. Results: Serum levels of TOS and OSI were higher in SH group (p-values 0.032; <.0001; respectively) and OH group (p-values <.0001; <.0001, respectively) than healthy controls, while serum levels of TAS, PON-1 and ARYL were lower in SH group (p-values <.0001; <.0001; <.0001, respectively) and OH group (p-values <.0001; <.0001; <.0001, respectively) than control group. Conclusion: Our study showed that serum levels of TOS and OSI were higher in subclinical and overt hypothyroidism than in healthy controls; while serum levels of TAS, PON-1, and ARYL were lower in subclinical and overt hypothyroidism than in healthy controls.Öğe SERUM LEVELS OF OXIDATIVE STRESS PARAMETERS IN POSTMENOPAUSAL VERSUS FERTILE WOMEN OF KUTAHYA CITY, TURKEY(Gomal Medical Coll, 2021) Erdogdu, Behic Selman; Yontem, Mustafa; Kocak, Fatma Emel; Yazar, HayrullahBackground: Decreased concentration of both oestrogen hormone and vitamin D in postmenopausal period may lead to oxidative stress, lipid peroxidation, dyslipidaemia, osteoporosis, and cardiovascular diseases. The objectives of this study were to determine and compare the serum levels of oxidative stress parameters; TOS, TAS, OSI, PON-1, ARYL in postmenopausal and fertile women of Kutahya city, Turkey. Materials & Methods: This cross-sectional study was conducted at Department of Biochemistry, Faculty of Medicine, Kutahya University of Health Sciences, Kutahya, Turkey from July, 2016 to December, 2016. Kutahya is a city in western Turkey, with population of 237,804 as per 2011 estimates. Two samples were drawn from this population with consecutive technique. Study group included 40 menopausal women, while control group included 40 healthy fertile women. After overnight fasting, venous blood samples were collected, centrifuged, aliquoted into a polystyrene tube, and aliquots were stored at -80 degrees C until measurement for total oxidant status (TOS), total antioxidant status (TAS), paraoxonase-1 (PON-1), and arylesterase (ARYL) measurements were made. Levels of TOS, TAS, OSI, PON-1, ARYL were five research variables on ratio scale. `Normal' data were described by mean, range and SD and skewed data by median, Q1, Q3 and IQR with 95% confidence intervals. For normal data, independent-samples t-test and for skewed data Mann-Whitney U test was used for hypotheses testing. Results: Serum total oxidant status (TOS) and oxidative stress index (OSI) levels were significantly higher (p-value.015 &.003 respectively), and serum paraoxonase-1 (PON-1) and arylesterase (ARYL) levels were significantly lower in postmenopausal than fertile women (p-value <.0001 &.0005 respectively), with no statistical difference for serum total antioxidant status (TAS) levels between the two groups (p-value.186). Conclusion: Postmenopausal period is associated with oxidative stress and decreased antioxidant defence. HDL-c-dependent PON-1 and ARYL activities are also reducing due to a decrease of HDL-c with menopause. Elevated levels of TOS and OSI, decreased levels of PON-1 and ARYL may lead to various life-threatening diseases such as cardiovascular disorders or cancer.
