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

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

Türkiye Bal Arıları Genetik Farklarının Koloni Dayanıklılığına (Vitality) Etkileri

TÜBİTAK KBAG Proje01.11.201

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

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

Doğu, Güneydoğu Anadolu, Karadeniz bölgesi ve iç Anadolu'nun doğusunda dağılış gösteren su kurbağalarının genetik çeşitliliğinin belirlenmesi

TÜBİTAK TBAG Proje01.08.201

Büyük Memeli Türlerinin Yerel Yayılışlarının Fotokapan Kullanarak Belirlenmesinde Tür Kompozisyonu Ve Habitat Yapısının Etkisi

Bu projenin amacı, Türkiye’nin farklı özellikler gösteren bölgelerinde (kıyı Ege, İç Anadolu, Doğu Karadeniz) yapılacak fotokapan çalışmaları ile alana özgü niteliklerin, tür envanteri, yerleşiklik ve populasyon tahminlerinin başarısını nasıl etkilediğini araştırmak, yaban hayatı ekologları ve yöneticiler için benzer çalışmaların başarısını arttıracak bir dizi öneri üretmektir. Proje Türkiye’nin üç farklı yöresinde gerçekleştirilecektir. Ege Bölgesi’nde Dilek Yarımadası Milli Parkı (Aydın) ve Karaburun ilçesinde (İzmir) çalışılacaktır. İç Anadolu Bölgesi’nde Beypazarı ve Nallıhan ilçelerinde, Doğu Karadeniz Bölgesi’nde Yusufeli ilçesinde (Artvin) çalışma yapılacaktır. Bu alanlar iklim, topoğrafya, bitki örtüsü ve büyük memeli kompozisyonu açısından birbirlerinden farklıdırlar. Araştırma kapsamında her alanda en az 30 gün süre ile, duruma göre 15-25 arasında değişen sayılarda fotokapan yerleştirilecektir. Bahar döneminde fotokapanlar en az 2 km aralıkla, yaban hayvanlarının kullandığı patikalar veya su kaynaklarının yakınına yerleştirilecektir. Fotokapan çalışmasının devam ettiği bu süre boyunca çalışma alanında arazi gözlemleri, dışkı ve iz takibi de yapılacaktır. Her fotokapan çalışmasının sonunda pil ve kartları laboratuvara getirilip şarj edilecek ve dijital ortama aktarılacaktır. Fotokapanlardan elde edilen veriler, tür teşhisinden ve davranış analizinden sonra bir veritabanına girilecektir. Bu veriler daha sonra PRESENCE yazılımı ile yerleşiklik analizine tabii tutulacak, elde edilecek sonuçlar habitat ve topoğrafik parametreler ve tür kompozisyonları açısından değerlendirilecektir. Bulgular ve projeden kazanılan deneyimler, Türkiye’de farklı coğrafya ve habitatlarda benzeri çalışmalar için kurallar ve öneriler geliştirmede kullanılacaktır

Discordance between ventral colour and mtDNA haplotype in the water frog Rana (ridibunda) caralitana, 1988 Arikan

The water frog form caralitana was first described as a subspecies of Rana ridibunda by Arikan (1988) from southwestern Turkey. Its orange ventral colour has been used as a diagnostic character since its description. After testing for a correlation between body size and ventral colour, we compared mtDNA and venter colour of adult specimens from 27 localities to assess the validity of this character for systematics of Anatolian water frogs. We mapped the distribution of each category and tested whether there is concordance between mtDNA haplotype and ventral colour of sampled individuals at the watershed level. Furthermore, we analyzed relationships between ventral colour and altitude. Size and ventral colouration were found to be significantly correlated. The distribution of orange ventral colour exhibited a complex clinal variation especially west of the Lake District where different coloured individuals are seen syntopically. In other regions, there were abrupt changes, presumably because of geographic barriers such as mountains. Our results indicate that although there is significant concordance between caralitana-specific mtDNA and orange venter colour, there are certain watersheds where the majority of sampled individuals exhibits discordance in mtDNA and ventral colouration. In all periphery regions, some degree of genetic introgression is indicated. These patterns clearly indicate gene flow between the caralitana lineage and non-caralitana lineages and is supported by lack of evidence for habitat-specific selection, the assignment of individuals from the same population into distinct clades, and the occurrence of an intermediate character between different forms in transition zones