COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Funder: Bundesministerium für Bildung und ForschungFunder: Bundesministerium für Bildung und Forschung (BMBF)We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective

Effect of spraying Pekin duck eggs obtained from different breeder age on hatchability

Onbasilar, Ebru/0000-0002-1321-0280; kocakaya, afsin/0000-0003-2023-8895WOS: 000343650800001The objective of this study was to determine the effect of spraying Pekin duck eggs obtained from different breeder age on hatchability. Hatching eggs used in this study were obtained from Pekin breeder flock. A total of 560 eggs were collected at 30 and 38-wk of breeder age at the farm. Ten eggs from each breeder age group were used to determine eggshell thickness. The other eggs for determination of hatchability and embryo development were stored for 3 d at 17 degrees C and 75% relative humidity. Eggs were incubated in the same incubator and turned from 1 to 25 days of incubation once an hour. On the 4(th) d of incubation, eggs were assigned to three treatment groups: control, spraying once a day ( Group 1), and spraying twice a day ( Group 2). Each group comprised 90 eggs which have been set to one tray each. Eggs of Group 1 and 2 were taken out of the incubator once a day and two times a day, sprayed with warm water ( 25-28 degrees C) and placed back to the incubator after 20 minutes, respectively. On the 25(th) day of incubation, all eggs were transferred singly into pedigree hatching baskets. On the 28(th) day of incubation, healthy ducklings were removed and sex and weight of the chicks was recorded. Fertility, embryonic dead and hatchability were determined. Egg weight increased ( P < 0.001) and eggshell thickness decreased ( P < 0.01) with increasing breeder age. Embryonic mortality was lower and hatchability was higher in sprayed groups than in control group ( P < 0.05) in eggs from 30 wks old hens. Increasing hen age increased the ratio of duckling weight to egg weight ( P < 0.001). Spraying of eggs affected the ratio of duckling weight to egg weight ( P < 0.001). Control and Group 1 were similar in the ratio of duckling weight to egg weight. However spraying of eggs twice a day with warm water from 4 to 25 days of incubation negatively affected the ratio of duckling weight to egg weight. It was concluded that spraying of duck eggs is partly linked to breeder hen age

Effects of brooder machine rearing method in the first week on fattening performance, carcass characteristics, meat quality and some blood parameters of Pekin ducks

kocakaya, afsin/0000-0003-2023-8895; Onbasilar, Ebru/0000-0002-1321-0280WOS: 000357000800012The aim of this study is to determine effects of brooder machine rearing method in the first week on fattening performance, carcass characteristics, meat quality and some blood parameters of male and female Pekin ducks. A total of 120 (60 male and 60 female) ducklings were used in the research. Each sex group was randomly allocated into two rearing methods. In the first group (brooder machine), ducklings were arranged in the brooder machine from 1 to 7 d then reared on the deep litter floor until day 42. In the second group (litter/control), ducklings were reared on the deep litter floor from the day 1 to the day 42 of the fattening period. At the day 41 of the fattening period, 5 ducks from each sex and rearing groups were randomly selected and bled. At the day 42 of the fattening period all ducklings were slaughtered in a commercial slaughterhouse. Hot carcass yield, organ weights and carcass characteristics were determined. Also pH, ash, fat and crude protein were determined in the breast and thigh muscles. Total body weight gain, hot carcass yield and breast percentage of ducks reared on the litter group (control group) were significantly (P<0.01; P<0.001; P<0.05) higher than those of ducks reared in the brooder machine group. Thigh fat content and breast fat content were affected by first week rearing method and these traits were higher (P<0.01) in the litter group (control group) than the brooder machine group. Only creatinin kinase level in the examined blood parameters of ducks was higher in the group reared on the litter (P<0.05). Sex affected the hatching weight, body weight gain from 1 to 42 d, feed intake from 1 to 42 d, ash of thigh meat and also ash and crude protein of breat meat (P<0.01). In conclusion, the fattening performance, hot carcass yield and percentage of breast of the pekin ducks were positively affected by the litter floor in the first week

Effect of Width and Depth of Bell Drinker and Sex on Fattening Performance and Carcass Characteristics of Pekin Ducks

Onbasilar, Ebru/0000-0002-1321-0280; kocakaya, afsin/0000-0003-2023-8895WOS: 000328082800002The aim of this study was to determine the effects of width and depth of bell drinker and sex on fattening performance and carcass characteristics of Pekin ducks. A total of sixty male and sixty female ducklings (Star 53 H.Y., Grimaud Freres) were used. Each sex group was randomly allocated into two bell drinker groups (narrow bell drinker with 47 mm water depth and 48 mm water width and wide bell drinker with 78 mm water depth and 90 mm water width) each of 30 ducklings. Groups were located in floor pens of 170 x 94 cm width x length, each of 6 chicks, in a naturally ventilated house. Sex affected the hatching weight (P<0.01), total body weight gain (P<0.001), feed intake (d 22 to 42 and d 1 to 42, P<0.05), feed conversion ratio (d 1 to 21, P<0.05), slaughter weight (P<0.001) and percentages of hot carcass (P<0.05). Wide bell drinker increased the body weight gain (d 22 to 42 and d 1 to 42, P<0.001), feed efficiency (d 22 to 42 and d 1 to 42, P<0.01), slaughter weight (P<0.001) and percentages of breast and wings (P<0.01), however decreased the percentages of skin subcutaneous fat (P<0.01). More width and depth bell drinker was positively contributed to the fattening performance in rearing of Pekin ducks

Effect of Yucca schidigera Spraying in Different Litter Materials on Some Litter Traits and Breast Burn of Broilers at the Fifth Week of Production

Onbasilar, Ebru/0000-0002-1321-0280; kocakaya, afsin/0000-0003-2023-8895; UNAL, NECMETTIN/0000-0001-5250-7063; Torlak, Emrah/0000-0003-4636-7791WOS: 000328082700003This study was carried out to determine the effects of different levels of Yucca schidigera spraying in different litter materials on some litter traits (moisture, pH, ammonia, total colony count, number of Enterobacteriaceae and number of yeast and mold) and breast burn of broilers at the 5th week of production. A total of four hundred thirty two 1-d-old male broiler chicks (ROSS-308) were used. In this study 12 chicks were put in each pen having 170x94x90 cm (depth x length x height). Half of the litter was wood shavings, the other was rice hull. Yucca schidigera extract was pulverized weekly at the level of 0, 4% and 8% to each pen from the second week of the study. Litter materials and Yucca schidigera spraying at different level did not affect the examined litter traits and breast burns of broilers (P>0.05) at the 5th week of production.TUBITAK FundTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [110O933]This study was supported by TUBITAK Fund (Project No: 110O933

Bayazıt Ailesinin Türkiye’deki yeri ve Türkiye'ye kazandırdığı isimler

Ankara : İhsan Doğramacı Bilkent Üniversitesi İktisadi, İdari ve Sosyal Bilimler Fakültesi, Tarih Bölümü, 2017.This work is a student project of the The Department of History, Faculty of Economics, Administrative and Social Sciences, İhsan Doğramacı Bilkent University.by Öztürk, İbrahim Mert

Effect of Yucca schidigera additions to different litter materials on broiler performance, footpad dermatitis and litter characteristics

kocakaya, afsin/0000-0003-2023-8895; Onbasilar, Ebru/0000-0002-1321-0280; UNAL, NECMETTIN/0000-0001-5250-7063WOS: 000343649800001The objective of this study was to determine the effects of different levels of Yucca schidigera additions to different litter materials on broiler performance, footpad dermatitis and litter characteristics. A total of five hundred seventy six 1-d-old male broiler chicks (ROSS-308) was randomly assigned to 48 pens. Chicks were randomly allocated to 2 litter and 4 Yucca schidigera treatments (0, 4, 8, 12%) with 6 replication pens. Each pen consisted of 12 chicks. Performances of broilers, ratio of footpad dermatitis and litter characteristics were not affected by Yucca schidigera additions to the litter materials. However, body weight gain and feed conversion from 1 to 21 days, total feed intake, total colony counts and number of Enterobacteriaceae in the litter were changed by litter material. Litter material by level of Yucca schidigera interaction was significant for body weight gain and feed conversion. Further studies will be done with different doses and applications of Yucca schidigera additions to the litter.TUBITAKTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [110O933]A part of this study was supported by TUBITAK Fund (Project No: 110O933). We thank the Beypilic for supplying chicks and Ekol Gida for supplying Yucca schidigera extract to us

Comparison of liver and bone health of two laying hen strains kept in different cage systems

Onbasilar, Ebru/0000-0002-1321-0280; kocakaya, afsin/0000-0003-2023-8895; UNAL, NECMETTIN/0000-0001-5250-7063WOS: 000371289800001Concerns have been increasing about conventional cages for laying hens in connection with welfare. Liver and bone disorders of laying hens are major problems. Therefore, the aim of this experiment was to investigate the differences in liver and bone traits of two laying strains kept in conventional and enriched cages. A total of 532 two Lohmann Brown Classic (LB) and 532 Lohmann LSL Classic (LW) hens were housed from 16 to 73 weeks in either conventional cages or enriched cages. Enriched cages had a nesting area, scratch pad, perch and claw shortener. At 73 weeks of age, blood parameters (alanine amino transferase (ALT), aspartate amino transferase (AST), alkaline phosphatase (ALP), calcium (Ca), phosphor (P), cholesterol and triglycerides), relative liver weight, fatty liver score and bone parameters (weight, length, diameter, maximum load, deformation at maximum load and stiffness of tibia and femur) were determined. The cage type affected only serum ALT, AST, ALP and cholesterol levels. Differences of liver and bone parameters between both cage types were not statistically significant. Serum ALT, ALP and P level and also weight and diameter of examined bones were affected by strain. This study indicates that cage type and cage type x strain interactions have limited effect on the liver and bone health.Ankara UniversityAnkara University [BAP-10A3338005]This research was supported by Ankara University BAP-10A3338005

Effects of cage type on performance, welfare, and microbiological properties of laying hens during the molting period and the second production cycle

As most of the unenriched cages will soon switch to enriched cages, it is important to characterize all the effects in the laying hens for sustainable production. Laying hens can be used in several production periods by applying molting. The aim of this study was to determine the cage type (unenriched and enriched) on performance, welfare, and microbiological properties of laying hens during the molting period and the second production cycle. Overall, 840 brown laying hybrids were used in the experiment. Laying hens were reared on two different cage types (unenriched cage (UEC) and enriched cage (EC)) in the same poultry house. When the hybrids were 75 weeks old, they were subjected to force molting with whole grain barley. Performance, welfare, microbiological, and serological data of laying hens were obtained from 73 to 107 weeks of age. Egg production, egg weight, feed conversion ratio, breaking strength, albumen and yolk index, Haugh unit, feather condition, and breaking force of femur and metatarsus were better in the post-molting period. However, keel bone deformities and Newcastle disease virus antibody titers are the worst in the post-molting period. Stiffness of femur and metatarsus was increased with period. These results indicate that necessary precautions should be taken against the problems that may occur in the direction of bone and health. During the molting period, hens kept in EC had lower egg production but they returned to egg production at a high rate. EC type had a positive effect on egg production, feed conversion ratio, feather and foot condition, and breaking force of metatarsus

Ribavirin shows antiviral activity against SARS-CoV-2 and downregulates the activity of TMPRSS2 and the expression of ACE2 In Vitro

Ribavirin is a guanosine analog and has a broad-spectrum antiviral activity against RNA viruses. Based on this, we aimed to show the anti-SARS-CoV-2 activity of this drug molecule via in vitro, in silico and molecular techniques. Ribavirin showed antiviral activity in Vero E6 cells following SARS-CoV-2 infection whereas the drug itself did not show any toxic effect over the concentration range tested. In silico analysis suggested that Ribarivin has a broad-spectrum impact on SARS-CoV-2, acting at different viral proteins. According to the detailed molecular techniques, Ribavirin was shown to decrease the expression of TMPRSS2 both at mRNA and protein levels 48 hours after treatment. The suppressive effect of Ribavirin in ACE2 protein expression was shown to be dependent on cell types. Finally, proteolytic activity assays showed that Ribavirin also showed an inhibitory effect on TMPRSS2 enzyme. Based on these results, we hypothesized that Ribavirin may inhibit the expression of TMPRSS2 by modulating the formation of inhibitory G-quadruplex structures at the TMPRSS2 promoter. As a conclusion, Ribavirin is a potential antiviral drug for the treatment against SARS-CoV-2, and it interferes with the effect of TMPRSS2 and ACE2 expression.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author