Comparison of three different primer sets for sexing birds

Because many bird species are monomorphic or only sexually dimorphic in adult stages, it is difficult to determine their sexes, which may cause significant problems in population and conservation studies. DNA-based sexing relies on the chromodomain helicase DNA binding (CHD) gene located on the W chromosome and its homolog on the Z chromosome, giving distinct banding patterns on agarose gel as a result of length differences in intronic regions within this gene. We used 3 specific primer sets, CHD1F/CHD1R, 2550F/2718R, and P2/P8, for sex determination of 230 samples from 77 avian species. We report here the records for 70 of those species analyzed using the CHD1F/CHD1R primer set, and 49 species using 2550F/2718R, and 46 species using P2/P8. CHD1F/CHD1R PCR products on agarose gel generally showed an apparent single band in males and 2 bands in females, but the products of 2550F/2718R (61%) and P2/P8 (42%) showed distinct banding patterns for separate bird orders. However, when PCR products of these last 2 primer pairs labeled with fluorescent dye were run in a capillary gel and detected using a DNA analyzer, P2/P8 gave 2 distinguishable peaks in females, whereas 2550F/2718R results remained the same. DNA sexing with any of those 3 primer sets can be used for all sexually monomorphic avian taxa although the primer sets should be compared before choosing the most efficient one for molecular sexing of the studied species

Quantification of Three-Dimensional Cell-Mediated Collagen Remodeling Using Graph Theory

Background: Cell cooperation is a critical event during tissue development. We present the first precise metrics to quantify the interaction between mesenchymal stem cells (MSCs) and extra cellular matrix (ECM). In particular, we describe cooperative collagen alignment process with respect to the spatio-temporal organization and function of mesenchymal stem cells in three dimensions. Methodology/Principal Findings: We defined two precise metrics: Collagen Alignment Index and Cell Dissatisfaction Level, for quantitatively tracking type I collagen and fibrillogenesis remodeling by mesenchymal stem cells over time. Computation of these metrics was based on graph theory and vector calculus. The cells and their three dimensional type I collagen microenvironment were modeled by three dimensional cell-graphs and collagen fiber organization was calculated from gradient vectors. With the enhancement of mesenchymal stem cell differentiation, acceleration through different phases was quantitatively demonstrated. The phases were clustered in a statistically significant manner based on collagen organization, with late phases of remodeling by untreated cells clustering strongly with early phases of remodeling by differentiating cells. The experiments were repeated three times to conclude that the metrics could successfully identify critical phases of collagen remodeling that were dependent upon cooperativity within the cell population. Conclusions/Significance: Definition of early metrics that are able to predict long-term functionality by linking engineere

Genetic diversity is retained in a bottlenecked Cinereous Vulture population in Turkey

Bilgin, C Can/0000-0001-9284-307XWOS: 000486728800007Vulture populations worldwide have suffered precipitous declines in recent decades. the Cinereous Vulture Aegypius monachus, a highly philopatric scavenger distributed across southern Europe and the central Asian plateau, is threatened in many parts of its range. Turkey holds the second largest population of this species in the Western Palaearctic, but there has been no research on its genetic structure and the possible implications of this structure for the future of the species. Here we report nuclear diversity and relatedness determined by short tandem repeat genotyping of 81 individuals from the four largest colonies. Our results demonstrated no significant genetic structuring, suggesting a single panmictic metapopulation connected by frequent dispersal. Furthermore, we show that the study population has retained moderate levels of genetic diversity, despite passing through a recent demographic bottleneck. We estimated the effective population size to be 112 individuals (95% confidence interval 74-201). Our results imply that the observed lack of increase in population size since the 1990s has not been caused by lowered fitness due to genetic inbreeding but rather by increased mortality via demographic processes. in the short term, we suggest that conservation efforts should treat the Turkish subpopulations as a single management unit and aim to increase population size through effective protection, especially during the breeding season

Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean

The Neolithic transition in west Eurasia occurred in two main steps: the gradual development of sedentism and plant cultivation in the Near East and the subsequent spread of Neolithic cultures into the Aegean and across Europe after 7000 cal BCE. Here, we use published ancient genomes to investigate gene flow events in west Eurasia during the Neolithic transition. We confirm that the Early Neolithic central Anatolians in the ninth millennium BCE were probably descendants of local hunter-gatherers, rather than immigrants from the Levant or Iran. We further study the emergence of post-7000 cal BCE north Aegean Neolithic communities. Although Aegean farmers have frequently been assumed to be colonists originating from either central Anatolia or from the Levant, our findings raise alternative possibilities: north Aegean Neolithic populations may have been the product of multiple westward migrations, including south Anatolian emigrants, or they may have been descendants of local Aegean Mesolithic groups who adopted farming. These scenarios are consistent with the diversity of material cultures among Aegean Neolithic communities and the inheritance of local forager know-how. The demographic and cultural dynamics behind the earliest spread of Neolithic culture in the Aegean could therefore be distinct from the subsequent Neolithization of mainland Europe.WoSScopu

A perspectiva dos estudantes pré-clínicos sobre o ensino da ética médica: um estudo de grupo focal na Turquia

Aim: We aimed to receive the opinions of the preclinical medical students on medical ethics education, and to present some suggestions for the education program. Methods: Focus group discussions were held with third-grade medical students. The analyses were implemented using Creswell’s six-step qualitative data analysis. Results: During the data analysis, themes with the following titles were identified: necessity of the education, content, education methods, assessment, participation, contribution of the education, moving to clinical training and suggestions. Discussion: The students stated that the discussions on movies/books/case-based scenarios are more useful than lectures. Although they believed that student assessment was necessary for the medical ethics education, they had negative attitudes towards Multiple Choice Questions. At the stage of moving to the clinical training, their feelings and thoughts about the learning outcomes they would gain from ethical education were contradictory. Conclusion: Each theme and code obtained from the students’ expressions may contribute to improving medical ethics education for all institutions. Besides student education, it is also necessary the faculty development programs on medical ethics education for clinical teachers. Additionally, further studies can be conducted on the actions that need to be taken to help students internalize the ethical issues and feel the need of learning more.Nuestro objetivo consistió en recibir las opiniones de estudiantes de medicina en pre-clínica sobre educación en ética médica y presentar algunas sugerencias para el programa de educación. Métodos: Se mantuvo discusiones de grupo focal con estudiantes de medicina de tercer grado. Se implementó el análisis cualitativo de datos de seis pasos de Creswell. Resultados: Mediante el análisis de datos, se identificaron los siguientes temas: necesidad de la educación, contenido, métodos de educación, evaluación, participación, contribución de la educación, el paso a formación clínica y sugerencias. Discusión: Los estudiantes consideraron que las discusiones sobre películas/libros/escenarios de casos eran más útiles que las clases dictadas. Aunque pensaban que la evaluación de los estudiantes era necesaria para la educación en ética médica, no valoraron positivamente las pruebas de preguntas con respuesta múltiple. En el paso a la formación clínica, sus sentimientos y pensamientos sobre los resultados del aprendizaje en educación ética eran contradictorios. Conclusión: Cada tema y código obtenido de las propuestas de los estudiantes puede contribuir a mejorar la educación en ética médica en las instituciones. Además de la educación, también es necesario desarrollar programas sobre educación ética médica para los profesores clínicos. Además, se pueden realizar más estudios sobre las acciones que se necesitan tomar para ayudar a los estudiantes a internalizar los temas éticos y sentir la necesidad de aprender más.Objetivo: tivemos como objetivo coletar as opiniões dos estudantes pré-clínicos de medicina no ensino da ética médica e apresentar algumas sugestões para o programa de ensino. Métodos: foram realizadas discussões em grupos focais com estudantes do 3º período de medicina. As análises foram implementadas usando o método qualitativo de seis etapas de Creswell. Resultados: Durante a análise de dados, os seguintes temas foram identificados: a necessidade da educação, conteúdo, métodos de ensino, avaliação, participação, contribuição da educação, transição para o treinamento clínico e sugestões. Discussão: Os alunos concluíram que as discussões sobre filmes/livros/estudos de caso são mais úteis que aulas expositivas. Embora eles acreditassem que a avaliação de alunos era necessária para o ensino da ética médica, eles tinham atitudes negativas em relação a questões de múltipla escolha. Na fase de transição para o treinamento clínico, seus sentimentos e pensamentos sobre os resultados da aprendizagem, que eles obteriam com o ensino da ética eram contraditórios. Conclusão: Cada tema e código obtidos das opiniões dos alunos podem contribuir para melhorar o ensino da ética médica para todas as instituições. Além do ensino dirigido ao aluno, é necessário que haja também programas de desenvolvimento do corpo docente acerca da educação de ética médica. Ademais, mais estudos podem ser realizados sobre as ações que precisam ser tomadas para ajudar os alunos a interiorizar as questões éticas e sentir a necessidade de aprender mais a respeito

Unsustainable harvest of water frogs in southern Turkey for the European market

Frogs have been harvested from the wild for the last 40 years in Turkey. We analysed the population dynamics of Anatolian water frogs (Pelophylax spp.) in the Seyhan and Ceyhan Deltas during 2013–2015. We marked a total of 13,811 individuals during 3 years, estimated population sizes, simulated the dynamics of a harvested population over 50 years, and collated frog harvest and export statistics from the region and for Turkey as a whole. Our capture estimates indicated a population reduction of c. 20% per year, and our population modelling showed that, if overharvesting continues at current rates, the harvested populations will decline rapidly. Simulations with a model of harvested population dynamics resulted in a risk of extinction of > 90% within 50 years, with extinction likely in c. 2032. Our interviews with harvesters revealed their economic dependence on the frog harvest. However, our results also showed that reducing harvest rates would not only ensure the viability of these frog populations but would also provide a source of income that is sustainable in the long term. Our study provides insights into the position of Turkey in the ‘extinction domino’ line, in which harvest pressure shifts among countries as frog populations are depleted and harvest bans are effected. We recommend that harvesting of wild frogs should be banned during the mating season, hunting and exporting of frogs < 30 g should be banned, and harvesters should be trained on species knowledge and awareness of regulations

Türkiye Bal Arıları Genetik Farklarının Koloni Dayanıklılığına (Vitality) Etkileri

TÜBİTAK KBAG Proje01.11.201

Trophic interactions are key to understanding the effects of global change on the distribution and functional role of the brown bear

Biotic interactions are expected to influence species' responses to global changes, but they are rarely considered across broad spatial extents. Abiotic factors are thought to operate at larger spatial scales, while biotic factors, such as species interactions, are considered more important at local scales within communities, in part because of the knowledge gap on species interactions at large spatial scales (i.e., the Eltonian shortfall). We assessed, at a continental scale, (i) the importance of biotic interactions, through food webs, on species distributions, and (ii) how biotic interactions under scenarios of climate and land-use change may affect the distribution of the brown bear (Ursus arctos). We built a highly detailed, spatially dynamic, and empirically sampled food web based on the energy contribution of 276 brown bear food species from different taxa (plants, vertebrates, and invertebrates) and their ensemble habitat models at high resolution across Europe. Then, combining energy contribution and predicted habitat of food species, we modelled energy contribution across space and included these layers within Bayesian-based models of the brown bear distribution in Europe. The inclusion of biotic interactions considerably improved our understanding of brown bear distribution at large (continental) scales compared with Bayesian models including only abiotic factors (climate and land use). Predicted future range shifts, which included changes in the distribution of food species, varied greatly when considering various scenarios of change in biotic factors, providing a warning that future indirect climate and land-use change are likely to have strong but highly uncertain impacts on species biogeography. Our study confirmed that advancing our understanding of ecological networks of species interactions will improve future projections of biodiversity change, especially for modelling species distributions and their functional role under climate and land-use change scenarios, which is key for effective conservation of biodiversity and ecosystem service

Manyas Kuşcenneti Milli Parkı'nda (Kuzeybatı Anadolu) Söğüt Bülbülü'nün (phylloscopus trochilus linnaeus 1758) sonbahar göç dinamiği, aırlığı, yağ yükü ve konaklama davranışı.

Turkey lies on one of major migratory routes between Palearctic and Afrotropical regions.Despite its importance for many species, few studies exist on bird migration over Turkey. In this study, autumn migration dynamics and stopover behaviour of Willow Warbler (Phylloscopus trochilus), a small insectivorous passerine, was documented and analyzed at Manyas Kuşcenneti National Park (northwestern Turkey). Birds were mistnetted, ringed, measured, weighed and fat-scored from mid August in 2002 and end of August in 2003 to end of October in both years. Totally 543 and 929 Willow Warblers were ringed in 2002 and 2003 respectively. For 2002 and 2003 respectively, fat score values (mean±SE) are 4.63±0.06 and 3.84±0.05 and body mass values are 11.38±0.07 and 10.37±0.05 grams for birds captured the first time.Fat scores in 2003 show a bimodal distribution with peaks of T2 and T5, indicating populations or age classes with different migratory strategies.The number of retraps constituted 9.2-12.1 % of the total in 2002 and 2003. In both years,minimum stopover length ranged from 1 to 15 or 16 days with a median of 5 days. The majority of the retraps put on significant fat in both years. Retraps continued to put on weight for up to two weeks after they arrived. In this first ever study documenting passerine migration at Manyas Kuşcenneti National Park, it was revealed that such wetlands provide crucial stopover habitat for many migrant passerines, enables them to gain necessary fat loads before crossing two ecological barriers,the Mediterranean Sea and the Sahara