Glucose Signaling Pathway and Growth Conditions Regulate Gene Expression in Retrotransposon Ty2

Gene expression in the yeast retrotransposon Ty2 is regulated at transcriptional and translational levels. In this study, we have shown that the transcription of Ty2 is partially dependent on the membrane-bound glucose sensors Gpr1p and Mth1p in Saccharomyces cerevisiae. Transcription of Ty2 decreased approx. 3-fold in the gpr1, mth1 yeast mutant. Moreover, our results revealed that the transcription of Ty2 fl uctuates during the growth stages of S. cerevisae. Both transcription and the frameshift rate of Ty2 rapidly dropped when the stationary stage yeast cells were inoculated into fresh medium. There was an instant activation of Ty2 transcription and a high level expression during the entire logarithmic stage of yeast growth. However, the transcription of Ty2 decreased 2-fold when the yeast cultures entered the stationary stage. The frameshift rate in Ty2 also varied depending on the growth conditions. The highest frameshift level was observed during the mid-logarithmic stage. It decreased up to 2-fold during the stationary stage. Furthermore, we have found that the frameshift rate of Ty2 diminished at least 5-fold in slowly growing yeasts. These results indicate that the transcription and the frameshift effi ciency are coordinately regulated in the retrotransposon Ty2 depending on the growth conditions of S. cerevisiae

Reactions of anthocyanin rich in maize genotypes to low temperature treatments according to photosynthesis, gas exchange properties, and bio-active compounds

Low temperatures during the early growing stages limit the productivity of maize considerably. Investigating responses of different coloured corns (Zea mays L.) to chilling may reveal alternative genotypes which can be preferred under early sowing conditions of water-shortage farming areas. The aim of this study is determining whether the color factor affects the tolerance to chilling in maize and which properties are effective on the low temperature tolerance. We exposed corns with different colours (white, yellow, red, purple) to different temperatures [8°C, 12°C, 16°C, 25°C (control)] and analysed the effects of temperature on morphological, physiological, bio-active properties and stress indicators. Using 14-day old seedlings, we noted that purple corn had the highest seedling length, seedling weight, chlorophyll content, stomatal conductance, chlorophyll B and total phenolic content in the 8°C and followed by white (photosynthesis rate, chlorophyll fluorescence, chlorophyll A and carotenoids), yellow (transpiration rate, sub stomatal CO2, and total antioxidant activity) and red corns (water use efficiency, total anthocyanin content and proline). On the other hand, white corn maintained its superiority in other treatments, receiving the highest values in 9 of 17 characteristics at 12°C, in 8 of 17 at 16°C and in 10 of 17 in the control. Performance of purple corn in the 8°C was the most remarkable one in all genotypes and treatments. Based on our results, it has been concluded that white and purple corns are more chilling tolerant genotypes and may be alternative for early sowing conditions in drought farming areas

Libraries in the Ancient World

Lionel Casson was an academician at the New York University. His book “Libraries in the Ancient World” was published by Yale University in 2002 with renewed edition. The first edition of the book was published in 2001. The book has not been translated into Turkish yet. The author, who has studies on antiquity and maritime history, gives information about libraries from Antiquity to the Middle Ages in his book. He reviewed the libraries in terms of what they looked like, how their internal processes are, their collections, methods of acquisition and what services they offered.New York Üniversitesinde öğretim üyeliği yapmış olan Lionel Casson’un “Libraries in the Ancient World” başlıklı kitabı, yenilenmiş baskısıyla, 2002 yılında orijinal dilinde Yale Üniversitesi tarafından yayımlanmıştır. Kitabın ilk baskısı 2001 yılında yapılmış olmakla birlikte; Türkçe çevirisi henüz bulunmamaktadır. Antik Çağ ve denizcilik tarihi üzerine çalışmaları bulunan yazar, Antik Çağ’dan Orta Çağ’a kadar olan kütüphaneler hakkında bilgiler verdiği kitabında; kütüphanelerin nasıl göründüğünü ve işlediğini, koleksiyonlarını, kaynak edinme yöntemlerini, hangi hizmetleri sunduklarını incelemiştir

Mask Combination of Multi-layer Graphs for Global Structure Inference

Structure inference is an important task for network data processing and analysis in data science. In recent years, quite a few approaches have been developed to learn the graph structure underlying a set of observations captured in a data space. Although real-world data is often acquired in settings where relationships are influenced by a priori known rules, such domain knowledge is still not well exploited in structure inference problems. In this paper, we identify the structure of signals defined in a data space whose inner relationships are encoded by multi-layer graphs. We aim at properly exploiting the information originating from each layer to infer the global structure underlying the signals. We thus present a novel method for combining the multiple graphs into a global graph using mask matrices, which are estimated through an optimization problem that accommodates the multi-layer graph information and a signal representation model. The proposed mask combination method also estimates the contribution of each graph layer in the structure of signals. The experiments conducted both on synthetic and real-world data suggest that integrating the multi-layer graph representation of the data in the structure inference framework enhances the learning procedure considerably by adapting to the quality and the quantity of the input data

The Place of Histochemical Stains for Differential Diagnosis in Duodenal Biopsies

The biopsy is the primary examination method in diagnosing duodenal pathologies and Gluten enteropathy that can cause symptoms such as gas, diarrhea, weight loss, anemia, osteoporosis. Allows monitoring of response to therapy. Histochemical studies are inevitable in specific findings such as reactive changes, giardia, subepithelial collagen thickening, fibrosis, and gastric metaplasia. We aimed to understand the contribution of histochemical applications to differential diagnosis and to show their superiority compared to hematoxylin-eosin sections in routine use by simultaneously making histomorphological evaluations on hematoxylin and eosin sections. This research is a retrospective study conducted in 2011, using the archives of Yüzüncü Yıl University, Faculty of Medicine, Department of Pathology, between 2001-2010. Ten normal, 50 Gluten enteropathy and 50 duodenitis samples; Along with histopathological examinations, we applied Masson Trichrome, Periodic acid-Schiff, Periodic acid-Schiff with diastasis, Periodic acid Schiff-Alcian Blue, High Iron Diamine-Alcian Blue. Chi-square, likelihood ratio tests, and SPSS (ver: 13) statistical package program used. We detected microscopic findings parallel to diagnostic criteria. While the number of goblet cells and intraepithelial neutrophils did not differ in the groups (P =0.176 and P=0.096), there was a significant variation in the intraepithelial lymphocyte count (P=0.010). The frequency of flattening and blunting of the villi, crypt hyperplasia, and Brunner gland hyperplasia were significant in gluten enteropathies (P=0.000). Conclusion We could not find any difference in specific pathologies associated with histochemical studies in our group, so hematoxylin-eosin sections are more valuable in the differential diagnosis

Line × Tester Analysis of Stomatal Conductance, Chlorophyll Content, Photosynthetic Efficiency, and Transpiration Rate Traits in Maize

This study evaluated seven inbred lines of maize (Zea mays L.), three testers and 21 hybrids produced by line ×tester mating design. Stomatal conductance, chlorophyll content, photosynthetic efficiency, and transpirationrate traits of parents and progenies were observed. The study was conducted in Konya, in the mid-Anatolianregion of Turkey. The mean values of the stomatal conductance, chlorophyll content, photosynthetic efficiency,and transpiration rate measurements were evaluated using Duncan’s multiple range test for grouping parent andoffspring groups. The variance for general combining ability, the variance for specific combining ability, the relativevariance, additive variance, dominance variance, √D / A, narrow-sense heritability and broad-sense heritabilityparameters of the population, along with the heterosis rates of the progenies, were calculated for each trait.The parental general combining abilities and specific combining abilities of the progenies were determined. Weobserved parents with significant and positive general combining abilities [3.4 (stomatal conductance, transpirationrate); 14.20 (photosynthetic efficiency, transpiration rate)] and their progenies with significant and positivespecific combining abilities [3.4 × FRMo 17 (stomatal conductance, transpiration rate); 3.4 × ADK 451 (transpirationrate); 14.20 × FRMo 17 (transpiration rate)]. Results of the study showed the possibility of using physiologicalproperties as selection criteria

Molecular etiology of arthrogryposis in multiple families of mostly Turkish origin

BACKGROUND. Arthrogryposis, defined as congenital, joint contractures in 2 or more body areas, is a clinical sign rather than a specific disease diagnosis. To date, more than 400 different disorders have been described that present with arthrogryposis, and variants of more than 220 genes have been associated with these disorders; however, the underlying molecular etiology remains unknown in the considerable majority of these cases. METHODS. We performed whole exome sequencing (WES) of 52 patients with clinical presentation of arthrogryposis from 48 different families. RESULTS. Affected individuals from 17 families (35.4%) had variants in known arthrogryposis-associated genes, including homozygous variants of cholinergic gamma nicotinic receptor (CHRNG, 6 subjects) and endothelin converting enzyme-like 1 (ECELI, 4 subjects). Deleterious variants in candidate arthrogryposis-causing genes (fibrillin 3 [FBN3], myosin IXA [MY09A], and pleckstrin and Sec7 domain containing 3 [PSD3]) were identified in 3 families (6.2%). Moreover, in 8 families with a homozygous mutation in an arthrogryposis-associated gene, we identified a second locus with either a homozygous or compound heterozygous variant in a candidate gene (myosin binding protein C, fast type (MYBPC2] and vacuolar protein sorting 8 [VPS8], 2 families, 4.2%) or in another disease-associated genes (6 families, 12.5%), indicating a potential mutational burden contributing to disease expression. CONCLUSION. In 58.3% of families, the arthrogryposis manifestation could be explained by a molecular diagnosis; however, the molecular etiology in subjects from 20 families remained unsolved by WES. Only 5 of these 20 unrelated subjects had a clinical presentation consistent with amyoplasia; a phenotype not thought to be of genetic origin. Our results indicate that increased use of genome-wide technologies will provide opportunities to better understand genetic models for diseases and molecular mechanisms of genetically heterogeneous disorders, such as arthrogryposis. FUNDING. This work was supported in part by US National Human Genome Research Institute (NHGRI)/National Heart, Lung, and Blood Institute (NHLBI) grant U54HG006542 to the Baylor-Hopkins Center for Mendelian Genomics, and US National Institute of Neurological Disorders and Stroke (NINDS) grant RO1NS058529 to J.R. Lupski.US NHGRI/NHLBI [U54HG006542]; US NINDSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Neurological Disorders & Stroke (NINDS) [R01NS058529]; CPRIT training Program [RP140102]; Medical Genetics Research Fellowship Program [T32 GM07526]; NATIONAL HUMAN GENOME RESEARCH INSTITUTEUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Human Genome Research Institute (NHGRI) [U54HG006542] Funding Source: NIH RePORTER; NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCESUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [T32GM007526] Funding Source: NIH RePORTER; NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKEUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Neurological Disorders & Stroke (NINDS) [R01NS058529] Funding Source: NIH RePORTERWe thank the patients and their families who participated in this study. This work was supported in part by US NHGRI/NHLBI grant U54HG006542 to the Baylor-Hopkins Center for Mendelian Genomics and US NINDS grant R01NS058529 to J.R. Lupski. W.L. Charng is supported by CPRIT training Program RP140102, and T. Harel is supported by the T32 GM07526 Medical Genetics Research Fellowship Program

Etiopathogenesis of Sheehan’s Syndrome: Roles of Coagulation Factors and TNF-Alpha

Sheehan’s Syndrome (SS) is defined as pituitary hormone deficiency due to ischemic infarction of the pituitary gland as a result of massive postpartum uterine hemorrhage. Herein, we aimed to investigate the roles of Factor II (G20210A), Factor V (G1691A), MTHFR (C677T and A1298C), PAI-1 4G/5G, and TNF-α (-308  G>A) gene polymorphisms in the etiopathogenesis of SS. Venous blood samples were obtained from 53 cases with SS and 43 healthy women. Standard methods were used to extract the genomic DNAs. Factor II (G20210A), Factor V (G1691A), and MTHFR (C677T and A1298C) polymorphisms were identified by real-time PCR. PAI-1 4G/5G and TNF-α (-308  G>A) gene polymorphisms were detected with polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) methods. According to statistical analysis, none of the polymorphisms were found to be significantly higher in the SS group compared to the control group. Hence, we suggest that genetic factors other than Factor II, Factor V, MTHFR, PAI-1, and TNF-α gene polymorphisms should be researched in the etiopathogenesis of SS

Role of serum organic solute transporter alpha/beta and sodium taurocholate cotransporting polypeptide in intrahepatic cholestasis of pregnancy

Objectives: This study aimed to assess the role of OST-α, OST-β and NTCP in patients with ICP, with a view to determine patients with severe prognosis and to minimize adverse fetal outcomes. Material and methods: Sixty-nine pregnant women diagnosed with ICP and 50 healthy women were included the study. Serum OST-α, OST-β and NTCP were measured using ELISA kits. Results: The median OST-α levels were 176.3 pg/mL in women with ICP and 201 pg/mL in healthy subjects (p = 0.205). The median OST-β levels were found to be 51.17 pg/mL in patients with ICP and 40.9 pg/mL in controls (p = 0.033). Median NTCP levels were 519.7 ng/mL in the ICP group and 483.3 ng/mL in healthy women (p = 0.051). Conclusions: This is the first study to evaluate serum levels of OST-α, OST-β and NTCP in patients with ICP. It is likely that OST-α, OST-β and NTCP contribute to the etiopathogenesis of ICP. Serum OST-α and OST-β levels can be used as diagnostic and monitoring markers of ICP, and the inhibition of these molecules could provide therapeutic benefit in ICP by reducing the circulation of enterohepatic bile acids