Asia Minor: A Pleasant Refuge during Tough Times
Ada, Eren1; Perktaş, Utku1; Gür, Hakan2.
1 Department of Biology (Zoology Section), Faculty of Science, Hacettepe University, 06800, Ankara, Turkey 2 Department of Biology, Faculty of Science and Letters, Ahi Evran University, Kırşehir, Turkey
Present-day distribution patterns of many species have been affected by rapid climatic oscillations. The climatic conditions of Late Quaternary have caused range expansion and restrictions for many species. To understand how species have responded to these conditions is important in terms of their biogeographical history. There have been three well-known for Europe so far, which are Iberian, Italian and Balkan peninsulas. These refugia provided suitable climatic conditions to many European species during the Last Glacial Maximum (LGM, 21 000 ya.). However, recent studies have indicated that Anatolia has also been an important refugium for European biota. We also suggest that Anatolia was one of the major refugia for many vertebrate species.
In this study, we examined a amphibian (Triturus karelinii) species to present the refugia role of Anatolia during Last Glacial Maximum and today. We used advanced independent ecologic and phylogeographic analyses to support our hypothesis. First, ecological niche modelling (ENM) was developed to predict the geographic distribution of this species under reconstructed past (the Last Glacial Maximum) and present. Then, we used published DNA sequences to estimate phylogenetic relationships among the mtDNA haplotypes. Bayesian based historical demography analyses were used to understand expansion and contraction pattern for the species. At last, ecological niche modelling and phylogeographic results were used together to assess landscape genetic pattern of this species. All independent analyses showed that Anatolia is an important part of European biogeography and it covers a significant place in recolonized European biota.
Circulating hsa-mir-1183 in Maternal Plasma of Pre-eclamptic Women
Didem Altindirek1, Mohammad Kazem Hosseini2, Tuba Gunel2
1Istanbul University, Institute for Experimental Medicine, Department of Genetics, Istanbul,Turkey
2Istanbul University, Faculty of Science, Department of Molecular Biology and Genetics, Istanbul, Turkey
Pre-eclampsia (PE) is a serious pregnancy disorder affects 2%-7% pregnancies worldwide and leads to maternal and fetal mortality and morbidity. The only solution is the premature termination of the pregnancy. Early identification of patients with an increased risk for PE is one of the most important goals in obstetrics. Currently, testing for this disorder includes the protein markers in serum but they are lack of sufficient discrimination.
It was reported that fetal RNA derived from placenta could be detected in maternal plasma. Circulating RNA and microRNAs could be stabilized through its protection from degradation in plasma. They are originated from trophoblasts of placenta and released into maternal circulation via exosomes. Therefore, they proposed as a promising class of molecular biomarkers for non-invasive prenatal diagnosis (NIPD) of PE.
MicroRNAs regulate the expression of nearly 30% of all the human genes and participate in all fundamental cell processes. Genome-wide analysis showed that human placenta expresses more than 600 miRNAs, including placenta-specific ones during different stage of pregnancies.. Recently, circulating miRNAs of maternal plasma are considered as potential noninvasive biomarkers in pregnancies.
According to our previous microarray profiling of human miRNAs study and online bioinformatic tools hsa-mir-1183 was selected. This project’s aim is to identify expression profile of hsa-mir-1883 and investigate its putative target gene according to sequence complementarity and biological significance in maternal plasma of patients with PE and normal-term pregnancies.
We measured expression levels of hsa-mir-1183 in samples collected from 20 PE and 20 normal-term cases by Q-RT-PCR. Spike-in cel-mir-39 was used for normalization. The relative expression of hsa-mir-1183 was calculated by ΔΔCt method. Results showed that hsa-mir-1183 is differentially expressed (p<0.05) in maternal plasma of PE patients. In silico target identification of hsa-mir-1183 was studied in seven different databases. NEU3 gene wasselected as putative target. This gene remove sialic acid residues from glycoproteins and glycolipids. This plasma circulating miRNA might be used as a notable biomarker for diagnosis of PE and putative target NEU3 gene expression will be analyzed in future studies.
The Role of Natural and Anthropogenic Drivers Shaping Current Fire Regimes in the Mediterranean-Type Ecosystems of Turkey
İsmail Bekar*1, Çağaşan Karacaoğlu1, Murat Türkeş2, Çağatay Tavşanoğlu1
1Hacettepe University, Department of Biology, Division of Ecology, Ankara/Turkey
2Middle East Technical University, Department of Statistics, Ankara/Turkey
After the Yellowstone fires of 1988, an increasing trend was seen in fire ecology studies. These studies show us that fire has diverse ecological and evolutionary effects on ecosystems. To understand the relationship between fire and ecosystems we need regional approaches. In the literature, there are several studies from many parts of Earth. Nevertheless, there is no comprehensive study on fire regimes in the Mediterranean biogeographical part of Anatolia. In this thesis, we intended to study the relative role of natural and anthropogenic factors shaping the current fire regimes in the Mediterranean region of Anatolia. We hypothesized that natural factors explain the most of the variance in recent fire regimes in the study area, but human activities contribute less. Moreover, we expect a positive relationship between the climate change and variability and fire regime changes at local scale. Fire data will include both the ground fire records of the General Directorate of Forestry and satellite records of NASA. A total of 24 bioclimatic variables will be used to investigate the effect of the climatic factors on fire regimes. Road network, demographic data, agriculture and husbandry activities will be used to investigate the effect of anthropogenic factors on fire regimes. Other natural variables will be physical geographic data and forest/vegetation structure. The data will be analyzed by generalized linear models, principal component analysis, and regression techniques. The results of the project will contribute to the up-to-date discussion on whether fire regimes are anthropogenic or natural origin
Population Genetic Structure of the Marbled Crab, Pachygrapsus Marmoratus (Fabricius, 1787) Along the Coasts of Turkey
Cansu Çetin*, Raşit Bilgin, Andrzej Furman
Bogazici University, Institute of Environmental Sciences, Istanbul/Turkey
The marbled crab, Pachygrapsus marmoratus is a common species in the Mediterranean and along the coasts of Turkey. Its global distribution extends to the north-eastern part of the Atlantic Ocean. In this study, a total of 384 specimens from 32 sites were collected from around coasts of Turkey, and genetically examined in mitochondrial CO1 gene and five nuclear microsatellites for a better understanding of its evolutionary history. High levels of genetic differentiation was found between populations of P. marmoratus distributed all around the Turkish coasts (Population C) and those constrained to the Mediterranean coasts (Population M). Both populations, however, shared the same or have very similar mtDNA CO1 haplotypes. Different scenarios are discussed referring to the biogeographical history of the Mediterranean for explaining this pattern. Two alternative explanations for the cytonuclear discordance as retention of ancestral polymorphisms or gene flow after secondary contact could not be distinguished. The use of complementary mitochondrial markers with faster mutation rates than CO1 subunit in addition to microsatellites, and sampling individuals from the rest of the Mediterranean and from the Atlantic Ocean can be useful in resolving the observed pattern.
Difference Between parkin Mutant and Its Control for Negative Geotaxis in Drosophila Melanogaster
Hacettepe University, Department of Biology, Evolutionary Genetics Laboratory, 06800 Beytepe, Ankara, Turkey
The present study consists of the first part of the work that will epistatically map the genes underlining locomotor behaviour in Drosophila melanogaster. Here in the present study we contrasted the locomotor behaviour of a mutant strain of the gene parkin with its control genetic background strain. We used negative geotaxis as the indicator of locomotion. Our results show that overall (sex-mixed) difference in geotactic behaviour between the parkin and its control is highly significant. This significance is apparent for both sexes of parkin and its control.Remarkably, males did better than the females in each genotype (parkin and its control). Another strking feature of our results is that the mutated parkin gene performed much better than the control strain. This is not unusual, however, taking into consideration the fact that newly created alleles by mutation may enhance the phenotype they influence. This finding is also promising in regard of the further mapping study we will perform in which the magnitude of the difference between the parkin and its control across many genomes will be used to reveal genes epistatically contributing to locomotion.
cDNA cloning, phylogenetic analysis and molecular clock calculations of molluscan hemocyanins
Istanbul University, Institute of Sciences, Biology Department, Zoology Programme Vezneciler, 34134 – Istanbul
Hemocyanins are oxygen-carrier proteins which are found in hemolymph of many arthropods and molluscs. Hemocyanins belong to a seperate gene family from other respiratory proteins (i.e. hemoglobin, hemerythrin) and their active sites are different. Also, while hemocyanin molecules contain copper, others contain iron as oxygen binding ion.
Hemocyanins are assumed to be evolved from tyrosinase-like ancestral oxygen-binding proteins. DNA sequencing, phylogenetic studies and molecular clock calculations show that these occured independently around 740 million years ago and 600 million years ago in case of molluscan and arthropod hemocyanins, respectively. Although having similar active sites, molluscan and arthropod hemocyanins differ in the primary, ternary and quaternary structures and considered as seperate protein super families.
Hemocyanins are studied in a number of mollusks such as Helix lucorum and Nucula nucleus both structurally and in the sense of sequence data. While structural data is important for understanding the evolution of the molecule, amino acid sequences are also required to determine the complete covalent structure. cDNA cloning is a method used for obtaining complete cDNA sequences. Obtained cDNA sequences are also used for phylogenetic analysis and molecular clock calculations.
In search of fire ephemerals in the Mediterranean Basin
Gökhan Ergan¹, Golshan Zare², Barış Özüdoğru², Çağatay Tavşanoğlu¹
(¹)Fire Ecology and Seed Research Lab, Division of Ecology, Department of Biology, Hacettepe University, Turkey,
(²)Division of Botany, Department of Biology, Hacettepe University, Turkey
Plant community structure in fire-prone ecosystems is mainly shaped by wildfire. Early post-fire habitats in Mediterranean-type ecosystems include many unique species with fire-adaptations such as resprouting and heat shock-/ smoke-stimulated germination, i.e. fire ephemerals. Fire ephemerals are plants species that appear immediately after the fire, have a short life span, and then disappear until next fire. Although Mediterranean-type ecosystems of South Africa, California and South Australia include many fire ephemerals, none is recorded in the Mediterranean Basin yet. The aim of the study is to determine the role of fire ephemerals in early post-fire Mediterranean environments. We selected a recently burned site and three more habitats (P. brutia forest, roadside environment, and old burned forest) to study in Muğla, Turkey. For each habitat type, five replicate plots 1 ha in size were sampled to determine plant species using the belt transect method between February and November 2014. Using the seeds of the species in study sites, we performed germination experiments including heat shock and smoke treatments to assess the germination response of the plant species to fire. Preliminary results show that species richness in the recently burned area is higher than other habitats. Several species were only found in the recently burned area, and many species only germinated after smoke and/or heat shock treatments. Particularly, multiple fire cues synergistically increased the germination in rare annual species, and smoke stimulated the resprouting in a geophyte species. Our results suggest that many species are candidates of fire ephemerals in our study area.
Spatial and temporal modeling of Fabrea salina (Ciliophora, Heterotrichida) Population Size in Konya Closed Basin Lakes?
Serhat Ertugrul, Nazlı Deniz Eyice, Sırma Çapar Dinçer
Hacettepe Üniversitesi, Fen fakültesi, Biyoloji Bölümü, 06800 Beytepe-ANKARA
The aquatic ecosystems are accepted as an important part of a natural landscape and play a part in the bio-diversity. The restoration and the protection of the aquatic ecosystems are important for the environmental management. Increasing temperature and consequently evaporation due to global climate change, induces salinity changes of aquatic ecosystems.
This situation causes the deterioration of aquatic ecosystems, pollution and biodiversity to be in danger. Global climate change and the raise of heat and consequently evaporation alter the aquatic ecosystems.
There are present problems with our understanding of ciliate responses which greatly affect our ability to manage water quality this study will try to bring new concepts and models are which urgently needed in protozoological world.
Fabrea salina occupations will be figured out by correlation with the set of climatic variables which comprehensively represent general trends (days of sun), extreme values(salinity), and seasonal variation. Based on model evaluation criteria, several approaches will be performed to prediction of species distribution. Thus, these models are spatially explicit and likely to predict future salinity probabilities.
Today, this complex system approach often used to refer the types of distributions and to made ecological analysis, also to identify areas in the near future distribution of species across various climate change scenarios, this study will shed light on these types of studies however also to see the effects of discharged pollutants into the lake ,on the basis of economic activities carried out by people and factories, by using ciliates model approach will provide data to the implementing agencies of the wetland management plan.
In this study, ciliated protists, which can live even in extreme environmental conditions and detect pollution at lower levels in the trophic chain of factors, and react quickly to environmental changes , will enable us to use them, as an early warning. Essentially a practice of the temporal and spatial scales if variability in both marine and freshwater planktonic environments and the algal responses to those scales. I assert that that are problemswith our present understanding of the scales and the use of inappropriate assumptions concerning the occurrence of steady-state conditions.
Investigating marine microbial reactions using novel approaches: genetics, biogeochemistry and modeling
Selin KUCUKAVSAR, Şadi Sinan ARKIN and Barış SALİHOĞLU
Middle East Technical University, Institue of Marine Sciences, Mersin/Turkey
In the marine environment, organic matter produced by phytoplankton is decomposed by bacteria producing the inorganic nutrients necessary for marine plants. This recycling performed by bacteria make them a central component of the marine biogeochemical cycles, which in turn signifies their importance in some of the most important environment problems facing the world. Despite the many important roles they play, bacteria are one of the least known components of the marine biogeochemical cycles. Recently developed methods of metagenomics and metatranscriptomics allow a detailed study of bacterial communities. The goal of the study is to determine the temporal dynamics of the species composition, the community structure and the abundances of the bacteria that play important roles in the biogeochemical cycles of the Mediterranean as well as determining the rates of the reactions that the bacteria perform using a combination of genetic analyses, high-frequency biochemical measurements and numerical models. In order to achieve these goals, metagenomics and metatranscriptomic analysis will be performed on samples taken from a regular monitoring station near Erdemli. Furthermore, a modeling system whose output can directly be compared to the results of the metagenomic and metatranscriptomic analysis will be developed and the rates of the reactions performed by the bacteria will be obtained from the model. Finally, the bacterial reaction rates determined by a combination of the numerical modeling system and the measurements at the station will be validated using isotope tracer experiments.
Comparative analysis of EF-Tu proteins sequences obtained from extant and modern bacterial homologs
Gokce Senger*1, Nurcan Tuncbag2, Betul Kacar3 1 Izmir Institute of Technology, Department of Molecular Biology and Genetics; 2Department of Health Informatics, Graduate School of Informatics, Middle East Technical University; 3Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, 3Blue Marble Space Institute of Science, Seattle, WA firstname.lastname@example.org, email@example.com, firstname.lastname@example.org
Elongation factor protein (EF-Tu), plays an important role in the protein synthesis machinery of microbial cell systems (1). Various ancestral EF-Tu protein sequences have been reconstructed previously, through a method referred as “Ancestral Sequence Reconstruction” (2,3). An in vitro translation system composed of modern Escherichia coli translational machinery components was utilized to measure the activity of the reconstructed ancestral EF-Tu proteins (4), demonstrating that the majority of the ancestral EF-Tu proteins are capable of interacting with the components of the modern translation system. To develop a further explanation for these results and complement on-going in-vivo studies, various EF-Tu protein sequences representing modern and ancestral forms are compared to identify the conserved and diverged regions within the protein. Sequence similarity, identity and differences of various EF-Tu protein sequences are used to speculate as to how observed differences may affect protein function. These data, in conjunction with a preliminary network behavior model of EF-Tu protein homologs, may shed light on the evolutionary pattern of EF-Tu proteins.
References: 1) Kacar et al. (2013). “Experimental evolution of protein–protein interaction networks”. Biochem J, 453(Pt 3): 311–319. doi:10.1042/BJ20130205
2) Gaucher et al. (2008). “Palaeotemperature trend for Precambrian life inferred from resurrected proteins”. Nature 451, 704-707. doi:10.1038/nature06510
3) Thornton et al. (2004). “Resurrecting ancient genes: experimental analysis of extinct molecules”. Nature Reviews Genetics 5, 366-375. doi:10.1038/nrg1324
4) Zhou et al. (2012).” Reconstitution of translation from Thermus thermophilus reveals a minimal set of components sufficient for protein synthesis at high temperatures and functional conservation of modern and ancient translation components”. Nucleic Acid Research, 40(16):7932-45. doi:10.1093/nar/gks568
Distribution of Genetic Diversity and Gene Expression Response to Environmental Forcing in Posidonia oceanica (L.) Delile, 1813
Özge TUTAR1 , Gabriele Procaccini2, Lazaro Marίn-Guirao2, Emanuela Dattolo2
1 University of Milano-Bicocca – Piazza dell’Ateneo Nuovo, 1 – 20126, Milano
2 Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 – Napoli, Italy
Genetic diversity increases the resistance of seagrass to environmental disturbance. The connectivity between populations alters the genetic diversity and it defines the evolutionary potential of population. In environmental disturbance, plant may respond by evolving or they can be plastic enough to adapt. While genetically drifted populations are vulnerable to changes, populations with high clonal diversity tend to be more plastic. Knowing evolution potential of P. oceanica in the Mediterranean basin will give the chance to understand survival potential of different populations in the basin. This is accomplished by studying genetic diversity and connectivity, with neutral markers, and studying gene expression of environmental responsive genes. Two projects are developed to understand the survival potential of P. oceanica under stress conditions. The first one is genetic characterization of P. oceanica populations along the coasts of Turkey, from where no extensive data are available in comparison with other regions of the Mediterranean area. The aim of the second project is to examine gene expression response of shallow and deep P. oceanica plants to oxidative stress which is induced by a short-term and long-term simulated heat wave.
The Pleistocene history of a passerine bird species: phylogeography and ecological niche modeling of the blackcap
Onur Uluar1, Can Elverici1, Eren Ada1, Utku Perktaş1,2
1- Department of Biology (Zoology Section), Faculty of Science, Hacettepe University, 06800, Beytepe, Ankara
2- Department of Ornithology, American Museum of Natural History, Central Park West @79th Street, New York, 10024, NY, USA
Global climate oscillations through the Quaternary glacial–interglacial cycles have had significant impacts on the geographic distribution and genetic structure of bird species. The effects of these climatic fluctuations have been well documented by numerous different phylogeographic studies. In this study, we would like to test whether multiple refugia existed for the blackcap (Sylvia atricapilla) during the Last Glacial Maximum. To achieve this aim, an ecological niche modeling was developed to predict the geographic distribution of breeding populations of the blackcap under reconstructed past and present. In addition, we also performed coalescent analyses based on Bayesian approach to understand historical demography of the blackcap. Results are discussed with regard to ecological niche modeling and phylogeography.
Determining the effects of the climate changes in glacial and interglacial periods on Quercus robur’s western paleartctic’s distribution by ecological niche modelling
Elif Deniz ÜLKER
Hacettepe University, Faculty of Science, Department of Ecology, Ankara/TURKEY
Late Quaternary has undergone several climate changes which caused many glacial and interglacial periods. The late interglacial period and the last glacial maximum were the predominants of configuration the present biota in particular. The glacial periods has mostly took effect in the Northern Hemisphere where temperate species contracted their distributions and restricted to glacial refugia with suitable climatic conditions. The expansion and contraction of species’ distribution could predictable by using Ecological Niche Modelling (ENM) approach, by this way it would be possible to predict the responses and the distributions of species’ in a possible global climate change in future. In this study Quercus robur’s, a temperate plant species, potantial distributions has evaluated by using ecological niche modelling for the last interglacial period (120.000 years ago), the last glacial maximum (21.000 years ago), mid-Holocene (6.000 years ago), present and determined the most effective climate variables on its distribution. According to the results mean temperature of the warmest quarter, temperature seasonality, mean temperature of the driest quarter and temperature annual range has the main determinants of Q. robur’s distribution. On the other hand, Anatolia has determined as a glacial refugia together with other refugia in the Mediterrenean for Q. robur in the last glacial maximum.
Whole genome methylation analysis in idiopathic generalized epilepsies
Özkan Özdemir1, Sibel Uğur İşeri1, Osman Uğur Sezerman2, Ece Egemen2, Nerses Bebek3, Betül Baykan3,Uğur Özbek1
1- Istanbul University, Institute for Experimental Medicine, Dept. of Genetics, Istanbul Turkey
2- Sabanci University, Biological Sciences and Bioengineering, Faculty of Engineering, Istanbul, Turkey
3- Istanbul University, Istanbul Medical Faculty, Dept. of Neurology
Genetic factors play a predominant role in the etiology of common idiopathic generalized epilepsy(IGE) syndromes. An increased rate of maternal inheritance and excess number of affected females implicate involvement of epigenetic effects in the etiology of IGE syndromes.
In this study, we have performed a whole genome methylation analysis for 15 parent-offspring trios with vertical inheritance of the IGE trait. DNA samples were subjected to bisulphite conversion prior to IlluminaHuman Methylation 450K Beadarray application. Beadchips were scanned through Illumina iScan platform. We used a comprehensive R-Bioconductor package, namely “RnBeadsV0.99.11”, which implements an analysis workflow that can be used for paired and unpaired differential methylation analysis.
After data normalization, quality control, filtering and methylation profiling steps, differential methylation analysis revealed 239 genes with p-values smaller than 0.05. As an alternative approach, we have run a pathway-based analysis to see if genes with differential methylation values map to common pathways. This analysis with PANOGA software revealed various pathways particularly with synaptic and immunological functions.
Analysis of high throughput methylation data has proven to be challenging where various pipelines with alternative normalization and filtering methods should be applied. Two approaches presented herein have resulted in identification of new epilepsy related genes and pathways that could as well be applied to analysis of other trio based methylation studies.
Feeding Biology of the Family Mullidae
Suna Tüzün and Cem Dalyan
Istanbul University, Faculty of Science, Department of Biology, Division of Hydrobiology
There are five species of the family Mullidae in Turkish waters. Besides their ecological significance, Mullus barbatus, M. surmuletus, Upeneus pori and U. moluccensis are of economic value due to their high importance in fisheries. While the Iskenderun Bay inhabits all five mullid species, only the local species M.barbatus and M.surmuletus are present in the coasts of the Imbros Island.
The mullids obtained from the Iskenderun Bay and Imbros Island will be compared in terms of feeding biology. The trawl sampling will take place in four different periods over a course of one year, using a fishing vessel. Obtained individuals will be frozen and brought to the laboratory. Following length and weight measurements, individuals will be dissected, the sexes will be determined and the stomachs will be removed. First the full stomachs, then the empty stomachs will be weighed, and the stomach contents will be fixed in 50% ethanol solution. Additionally, the otoliths will be removed for age determination.
With the obtained data, the trophic level of the species will be estimated, and some indexes used for comparison, such as Index of Relative Importance (IRI) and Shoener’s diet overlap index, will be used.
In this comparison, depth, spatial distribution, growth in length and age and sex ratios will be examined as parameters potentially effecting the feeding of the mullid species. We will also try to estimate the effect of lessepsian species on the feeding of mullids. Moreover, the stomach contexts of the same species in two different substrates (sandy/muddy and hard substrate in Iskenderun Bay and Imbors Island, respectively) will be compared.
Preferences of zooplankton in alpine lakes: bottom structure or temperature?
Sinop University, Fisheries Faculty, Department of Hydrobiology, Sinop/Turkey
Temperature is a more important factor for alpine lakes compared to lowland lakes. Alpine freshwater ecosystems are defined as harsh and fragile environments because of low temperature, lack of nutrient and short development time. It is known that lake temperature is affected by differences in bottom structure and lake depth. This study was done in eleven alpine lakes that are located in southern and northern regions of Verçenik Mountain (Rize, Kaçkar Mountain Range) during August (2010) and July (2011). Considering the temperature values in both months, the lakes with muddy bottom structure were warmer than those with rocky bottom.
According to PCA, temperature is negatively correlated with altitude and positively correlated with electrical conductivity. nMDS analysis was done with the Bray-Curtis Similarity shows that rocky lakes create a group among themselves but according to ANOSIM and SIMPER results, there is no significant differences between two types of lakes.
Species diversity and evenness values showed highest value in August at South Lake 2 because Lake 2 has advantage of more daylight, muddy bottom structure and shallowness. When analyzed in terms of richness, lakes of North 1 and North 4, that are located in northern region and has rocky bottom structures shows higher richness in August while July shows low richness.
It was observed that, rocky bottom structured lakes shows higher species diversity and richness although muddy bottom structured lakes has higher temperature value