Identification of transcription factor binding sites in promoter databases

Transcription factors (TFs) are the proteins which regulates the expression of their target genes either in a positive or negative manner. TFs realize this task by binding to a specific DNA sequence contained in promoter regions, via their DNA binding motifs. Among ETS family TFs, Pea3 proteins are involved in the regulation of expression of genes, which are important for cell growth, development, differentiation, oncogenic transformation and apoptosis. In silico studies should be done to find out the novel target genes for this TF. Even though a few bioinformatics tools are available for this purpose, the user needs to go back and forth between different tools, and to repeat these steps for each of their candidate gene. Here we combined these tools and constituted a new tool which examines the affinity of any TF towards the selected target genes’ promoter sequences. The tool is tested on several genes, which are predicted to be regulated by Pea3 TF

Architectural And Structural System Design of Precast Concrete Structures In Earthquake Zones

Precast concrete systems, which are the result of industrialization in the field of construction, are faced with the prejudice of insufficient earthquake resistance despite their many advantages and their use is limited in Turkey. These systems, which have proven earthquake resistance if they are designed properly, can be used safely in low-rise or multi-storey buildings with different functions in earthquake zones. The aim of this study is to determine the architectural design requirements of earthquake-resistant precast concrete structures and to reveal the structural system design approaches. In accordance with this aim, the earthquake effect on the structures was summarized and architectural design principles that would contribute to the earthquake resistance of precast concrete structures were determined firstly. Then, earthquake-resistant structural system design approaches of frame, panel, and cell construction were evaluated separately. &nbsp

Evaluation of the efficacy of heat shock protein inhibitors and antifungal drug combinations against Candida spp.

Candida species are one of the predominant causes of fungal infections and show drug-resistant infections in immune-compromised individuals. Simultaneous targeting of existing antifungal drugs with heat shock protein 90 (Hsp90) inhibitors may be an approach that increases the efficacy of antifungal drugs. Also, since most of the patients at risk for invasive fungal infections use these anticancer or immunosuppressive drugs, synergistic interaction in combination treatment can reduce the dose of antifungal drugs and create an alternative for the toxicity problem. In this study, in vitro efficacy of commonly used antifungals (amphotericin B, caspofungin, itraconazole, voriconazole, and fluconazole) in combination with four heat shock protein inhibitors geldanamycin, 17-allylamino-17-demethoxygeldanamycin, radicicol, and novobiocin against 30 clinical Candida isolates (C. albicansn = 13, C. krusein = 7, and C. glabratan = 10) were evaluated by time kill and checkerboard methods. The significant synergistic interaction determined especially in the combinations of geldanamycin with antifungal drugs suggests that substances with inhibitory effects on Hsp90 increase the effectiveness of antifungals or reduce the antifungal resistance. Although Hsp90 inhibitors alone did not have any significant antifungal activity, they did not show adverse interactions in combination with antifungals, and at some concentrations, they increased the effectiveness of the antifungals. These in vitro results have been found promising for the development of new therapeutic approaches in the treatment of invasive fungal infections. However, detailed studies are needed.TUBITAK [112S503]This work was supported by a grant from TUBITAK (Project No. 112S503)

Antifungal Activity of Caspofungin in Combination with Amphotericin B against Candida glabrata: Comparison of Disk Diffusion, Etest, and Time-Kill Methods▿

The in vitro activities of caspofungin plus amphotericin B against 50 Candida glabrata isolates were evaluated by the time-kill, disk diffusion, and Etest methods. In vitro experiments showed a positive interaction. Even though each of these methods uses different conditions and endpoints, the results of the different methods frequently agreed

Analysis of acute impact of oleoresin capsicum on rat nasal mucosa using scanning electron microscopy

Analysis of acute cellular changes seen in nasal mucosa of Wistar-Albino rats exposed to different doses of oleoresin capsicum for various time periods by means of scanning electron microscopy. Thirty-five Wistar-Albino rats were divided into five groups of seven rats each. 6-gram oleoresin capsicum per second was sprayed into cages of the groups except group 1. Spray times and duration of exposure to pepper gasses were different for each group. Thirty minutes after the exposure, the animals were killed and specimens from their nasal mucosas were harvested and examined under scanning electron microscope. Mucosal damage was scored from 0-4 points. Mean values of nasal mucosa damage scores of the groups were calculated and compared statistically. Average damage scores of the groups exposed to identical doses of oleoresin capsicum for various exposure times were compared and a statistically significant difference was seen between Groups 2 and 3 (p 0.05). Average damage scores of the groups exposed to various doses for identical exposure times were compared, and statistically significant differences were observed between Groups 2 and 4 and also Groups 3 and 5 (p < 0.05). Outcomes of our study have demonstrated that pepper gas exerts destructive changes on rat nasal mucosa. The extent of these destructive changes increases with the prolonged exposure to higher doses. Besides, exposure time also stands out as an influential factor on the extent of the destructive changes