Marine Ecosystem Evolution in a Changing Environment (MEECE)

MEECE is a scientific research project which aims to use a combination of data synthesis, numerical simulation and targeted experimentation to further our knowledge of how marine ecosystems will respond to combinations of multiple climate change and anthropogenic drivers. With an emphasis on the European Marine Strategy (EMS), MEECE will improve the decision support tools to provide a structured link between management questions and the knowledge base that can help to address those questions. A strong knowledge transfer element will provide an effective means of communication between end-users and scientists.EU, Funded under :FP7-ENV-2007-

Exploitation of mesopelagic fish stocks can impair the biological pump and food web dynamics in the ocean

The demand for marine living resources is increasing at an unprecedented scale because of the need for continuous food provision to the world’s population. The potential of already exploited fish stocks to meet this demand is limited. Therefore, mesopelagic fish have recently become attractive potential targets for fisheries because of their vast conjectured biomass. However, the role of mesopelagic fish in marine ecosystems is poorly understood. Before developing commercial exploitation plans, the relationship between mesopelagic fish and other groups in the marine food web and biogeochemical cycles should be analyzed quantitatively. In this study, we coupled a one-dimensional biogeochemical model (North Atlantic Generic Ecosystem Model) with a higher-trophic-level food web model (Ecopath with Ecosim) for the Sargasso Sea in the North Atlantic to investigate changes in carbon export and trophodynamics under two mesopelagic fish harvesting scenarios. The coupled model represented the marine food web from plankton to fish and mammals, vertical carbon export dynamics, and their interaction with fisheries. The results showed that when mesopelagic fish were not harvested, they contributed approximately 6% of the total carbon export in the surface waters, but up to 40% of the total carbon export below 400 m. Harvesting mesopelagic fish altered the energy transfers within the food web as well as to fisheries. The ecological footprint of fisheries increased significantly. Due to declining competition in the food web, epipelagic fish increased to exert elevated grazing pressure on phytoplankton; hence, phytoplankton-mediated carbon export decreased. The total carbon export decreased by 14% due to the decreases in mesopelagic fish- and phytoplankton-mediated carbon exports. The simulated increase in zooplankton- and non-mesopelagic fish-mediated carbon exports (up to 92% and 96%, respectively) did not compensate for the total decrease in carbon exports under harvesting scenarios. The findings of this study highlighted that mesopelagic fish not only have a direct control on carbon dynamics by their metabolic releases and diel vertical migration, but also strong indirect controls through prey-predator interactions within the food web. Therefore, the implications of harvesting mesopelagic fish should be carefully considered from a holistic perspective

Procedural sedation protocols with or without ketamine in pediatric gastrointestinal endoscopy: A retrospective cohort study

Objective: A considerable difference exists in pediatric endoscopy sedation practices with the optimal sedation protocol for gastrointestinal (GI) endoscopy a subject of controversy and to investigate the safety and efficacy of sedation protocols with or without ketamine in procedural sedation for pediatric GI endoscopy. Materials and Methods: A total of 78 pediatric patients who received sedation anesthesia for GI endoscopy were included in this retrospective study. Anesthesia parameters include duration time, doses of anesthetic agents, Ramsay sedation score, respiratory and hemodynamic parameters, recovery time, modified Aldrete recovery scores, and side effects. Study parameters were evaluated with respect to ketamine dose (no ketamine group (NKG), low-dose ketamine group (LDKG, ≤0.75 mg/kg), and high-dose ketamine group (HDKG, ≥1 mg/kg). Results: The upper GI endoscopy rate (58.12% vs. 90.0%, p=0.001) was significantly lower in LDKG versus HDKG. No significant changes were observed in blood pressure levels, oxygen saturation, or heart rate compared to baseline levels. No significant difference was noted between study groups in terms of recovery time, modified Aldrete recovery scores, and nausea/vomiting. Final Ramsay sedation scores were significantly higher in NKG (p<0.05) and LDKG (p<0.01) than in HDKG. Conclusion: Our findings indicate a favorable safety and efficacy profile for ketamine as a useful adjunct to procedural sedation for pediatric GI endoscopy, enabling better quality of sedation with a low risk of cardiorespiratory suppression, or serious complications

Denizlerdeki Mikrobiyal Reaksiyonların Yeni Yaklaşımlar Kullanılarak Araştırılması: Genetik, Biyojeokimya ve Modelleme

TÜBİTAK ÇAYDAG15.10.2018ODTÜ Deniz Bilimleri Enstitüsü tarafından Mersin Körfezi?nde 1997 yılından bu yanasürdürülen Erdemli Zaman Serisi (ETS) programı dahilinde ölçülen degiskenlere ek olarak, buproje kapsamında toplam su kolonu derinligi 200 metre olan istasyonda altı farklı derinliktenbir yıl boyunca aylık periyotlarda deniz suyu örneklemesi yapılmıstır. Bu örneklerde yeni nesildizileme yönteminin kullanıldıgı amplikon dizilemesi (metagenomik) analizleri yapılarakbiyojeokimyasal döngülerde önemli roller oynayan bakteri türleri tayin edilmis, topluluk yapılarıve bolluklarının zamansal degisimi belirlenmistir. Taksalar arasında Pelagibacteriacea?ya aitolan SAR11 kladının tüm derinlikler ve aylarda baskınlıgı gözlenmistir. Bu kladın üyelerifonksiyonel olarak organik maddeyi oksitleyerek karbondioksit üreten heterotrofik bakterilerdirve dolayısıyla biyojeokimyasal döngülerin remineralizasyon ayagında rol almaktadırlar.SAR11 kladının bollugu yıl boyunca %22 ve %64 arasında degisim göstermistir. SAR11kladının ekotipleri olan Clade Ia ve Clade Ib ise derinlige baglı yayılım göstermektedirler.Clade Ia yüzey sularında baskınlık gösterirken Clade Ib?nin derin sularda komüniteye katkısıdaha fazla olmaktadır. Bunun yanı sıra komünite yapısını belirleyen en önemli çevreselfaktörler sıcaklık, nitrat, görünür oksijen kullanımı, sezon ve ısıklı tabaka derinligi olarakbelirlenmistir. Sezonlar arasındaki filogenetik çesitlilik, belirgin olarak farklı bulunmustur.Bunun yanı sıra bakterilerin aktif metabolizmalarını tayin etmek için sezonluk olarak mRNAörneklemesi yapılmıs ve örnekler metatranskriptom yöntemi ile analiz edilmistir. Bu yöntemaracılıgı ile bakteriler tarafından gerçeklestirilen biyokimyasal reaksiyonların aktif ve inaktifoldukları dönemler saptanmıstır. Nitrifikasyonun ilk basamagı olan amonyak oksitilenmesiKasım ayında oldukça yüksek bulunmustur. Ancak nitrifikasyonun ikinci basamagı olan nitritinnitrata oksitlenme sürecine ait olan belirteç genlere herhangi bir örnekde rastlanmamıstır.Sisteme yeni azot girdisi saglayan azot fiksasyonuna mRNA ifadelerinde rastlanmamıstır.Metatranskriptom yöntemine elde edilen bulgulara ek olarak nitrifikasyon ve azot fiksasyonsüreçleri izotop yöntemi ile de her ay dört farklı derinlikten yapılan örneklemeler ilearastırılmıstır. Nitrifikasyonun sadece afotik bölgede gerçeklesmedigi görülmüstür. Azotfiksasyonu belirteç genlerine rastlanmadıgı halde izotop yöntemi ile yapılan çalısmada azotfiksasyonu tüm yıl boyunca ve tüm derinliklerde çok düsük de olsa tespit edilmistir. Azotdöngüsüne ek olarak, metatranskriptom çalısması ile kısıtlı inorganik fosfat varlıgında aktiveolan alkalin fosfataz?ın sezonluk degisimi de göstermistir. Buna göre, ortamda düsük fosfatkonsantrasyonları gözlemlendiginde bakterilerin diger fosfor kaynaklarına yöneldigigözlemlenmistir.Bunlara ek olarak denizdeki biyokimyasal döngüleri sayısal olarak temsil eden ve tahminleridirekt olarak ölçümlerle karsılastırılabilecek bir modelleme sistemi bölgeye uyarlanmıstır. Bumodelleme sistemi bir parametre tahmin algoritması ve proje kapsamında yapılan ölçümverileri ile birlestirilerek modelde reaksiyon hızlarını kontrol eden parametrelerin tahminiyapılmıstır. Bu tahmin sonucunda ortaya çıkan nitrifikasyon hızları izotop yöntemi ile yapılannitrifikasyon hızları ile karsılastırılmıstır. Bu karsılastırma reaksiyon hızları tahmini içinmodelleme sistemi ve parametre tahmini kullanımının zor olan izotop yöntemine alternatif biryöntem olma potansiyelini göstermistir.Yapılan bir yıllık gözlemler, kullanılan izotop yöntemleri ve modelleme yaklasımı bölgedekibilimsel bilgiye önemli katkılar saglamıstır. Bakteri topluluk yapıları Türkiye kıyılarında ilk defakültür bagımsız yöntemlerle ortaya konmustur. Bunun yanı sıra izotop yöntemleri ve yapılanmetatranscriptom çalısması bölgede azot fiksasyonunun baskın bir süreç olmadıgını ortayakoymustur. Biyojeokimyasal bir modelleme sistemi basarıyla bölgeye uyarlanmıstır.In addition to the measured variables within the Erdemli Time Series (ETS) monitoring programcarried out in Mersin Bay since 1997 by the METU-Institute of Marine Sciences, sea watersampling was performed where the total water column depth is 200 meters and from sixdifferent depths monthly for one year. These samples were analyzed by next generationsequencing using amplicon sequencing (metagenomic) approach and the bacterial speciesthat play important roles in biogeochemical cycles and the temporal changes of communitystructures and abundances were determined. SAR11 clade belonging to Pelagibacteriaceawas the most dominant taxa in all depths and months. SAR11 is ubiquitous in the seas andreplicate under the most limiting nutrient conditions. The abundance of the SAR11 cladethroughout the year ranged between 22% and 64%. Clade Ia and Clade Ib, the ecotypes ofthe SAR11 clade, showed depth-dependent distribution. Clade Ia dominated the surfacewaters, while Clade Ib contributes the most to the community in deeper waters. The mostimportant environmental factors that determine the community composition were determinedto be; temperature, nitrate, apparent oxygen utilization, season and euphotic zone depth.Phylogenetic diversity between seasons was found to be significantly different.Furthermore, to determine the active metabolism of bacteria mRNA samples were collectedseasonally and analyzed by metatranscriptomics approach. By using this approach, active andinactive periods of biochemical reactions mediated by bacteria was discovered. Ammoniaoxidation, the first step of nitrification, was found to be high in November. However, markergenes that are belong to nitrite oxidation to nitrate which is the second step of nitrification, havenot been detected in any samples. Indicator genes of nitrogen fixation which provides newnitrogen to the system was not found in mRNA expressions. In addition to the findings obtainedfrom the metatranscriptomics study, nitrification and nitrogen fixation processes wereinvestigated using isotope measurements from four different depths each month. It wasobserved that the nitrification did not occur only in the aphotic zone. Nitrogen fixation was notdetected in the indicator genes, but in the study conducted with isotope method, even with lowlevels, nitrogen fixation was determined throughout the year and depths. Additionally, to thenitrogen cycle, the seasonal change of alkaline phosphatase activity which is active especiallyduring inorganic phosphate limitation was also identified by the metatranscriptomics study.Accordingly, when low phosphate concentrations were observed in the environment, it wasobserved that bacteria adapt to use other phosphorus sources.Furthermore, a modeling system that represents the marine biochemical cycles numericallyand whose estimates can be compared directly with the measurements was adapted to theregion. This modeling system was combined with a parameter estimation scheme and measurements obtained in the project, and the parameters controlling the reaction rates in themodel were estimated. Nitrification rates according to the estimations were cpmpared with theresults of nitrification rates obtained by isotopic measurements. This comparison showed thepotential of using modeling system and parameter estimation as an alternative approach to thehard isotope measurements for estimating reaction rates.One-year long observations, isotope methods used and modeling approach have madesignificant contributions to scientific knowledge in the region. Bacterial community structurehave been revealed by culture-independent method for the first time in the coasts of Turkey.In addition, isotope methods and metatranscriptom study showed that nitrogen fixation is nota dominant process in the region. And a biogeochemical modeling system has beensuccessfully adapted to the region

Doğu Akdeniz'de mevcut farklı ekosistemlerin - upwelling bölgeleri, açık deniz ve kıta sahanlığı suları - dinamikleri, bakteriyel ve birincil üretim potansiyelleri, üst trofik seviyelere yansımaları

TÜBİTAK ÇAYDAG15.10.2014Türkiye denizleri, su bütçesi, atmosferik ve karasal girdiler, taban topoğrafyası, iklimsel evrim gibi temel etkenlerin belirlediği fiziksel, kimyasal, biyolojik özellikler bakımından büyük farklılıklar içeren zengin ve değişken deniz ekosistemlerini barındırmaktadır. Birincil üretim potansiyelleri açısından Karadeniz’in özellikle kuzeybatı kıta sahanlığı ötrofik, Marmara Denizi ve körfezleri ileri derecede ötrofik, Ege Denizi ve Doğu Akdeniz oligotrofik yapı sergilemektedir. Özgün bir dinamiği olan Doğu Akdeniz, genelde bir uç oligotrofik sistem olarak tanımlansa da, kendi içinde önemli bölgesel farklılıklar göstermektedir. Özellikle karasal tatlı su ve besin girdilerinden etkilenen kuzeydoğu kıta sahanlığı (Mersin ve İskenderun Körfezleri) ve ‘upwelling’ dinamiğinden etkilenen Rodos döngüsünde önemli düzeylerde birincil üretim potansiyeline sahiptirler ve daha yoksul olan açık denizden farklıdırlar. Aktif dinamik yapıya ve zengin biyolojik çeşitliliğe sahip kıyısal denizlerimizin sürekli gözlem, analiz ve model öngörüleri aracılığıyla araştırılmasının sürdürülmesi, büyük stratejik önemi haizdir. Çalışma O.D.T.Ü. Deniz Bilimleri Enstitüsü Araştırma Gemisi Bilim-2 ile anılan sahalarda ve istasyonlarda mevsimsel bazda gerçekleştirilmiştir. Bu çalışma ile fonksiyonel olarak üç farklı ekosistemi teşkil eden alanlarda bakteriden balıklara uzanan besin zincirinde olası yapısal farklılıklar, üretim potansiyelleri, dinamikleri karşılaştırılmış, toplanan diğer çevre faktörleri ile etkileşimleri irdelenmiştir.Turkish seas accommodate rich and varied marine ecosystems which are diverse in their physical, chemical, biological characteristics as a result of differences in basic driving factors such as the water budget, atmospheric and land-based inputs, bottom topography, climatic evolution. In terms of primary production potential, the Black Sea especially the northwestern continental shelf exhibits eutrophic characteristics, while Marmara Sea and its bays are highly eutrophic, and Aegean and Eastern Mediterranean Seas display oligotrophic structure. Although the Eastern Mediterranean with its rather unique characteristics is often defined as an ultra-oligotrophic system, there are significant regional differences within the system. The northeastern continental shelf (Mersin and İskenderun Bays) influenced by land-based fresh water and nutrient sources and the Rhodes Gyre influenced by ‘upwelling’ dynamics have potential for high primary production, while the open sea is relatively poor. Continued research through continuous observations, analyses and model predictions have immense strategic importance for the well being of our coastal seas possessing energetic dynamics and rich biological diversity. It is proposed that the physical-biochemical variability of the diverse northern Levantine Sea ecosystems be investigated through systematic observations during oceanographic cruises, as well as model-based predictions. Study has been conducted seasonally aboard Research Vessel Bilim-2 of the Institute of Marine Sciences of Middle East Technical University in the referred areas and stations. Throughout the study, in areas that represent the three different functional ecosystems, possible structural differences, productivity potential, and dynamics were compared in the food chain spanning bacteria to fish, and their interactions with the other environmental factors were investigated

Current barriers and recommendations on the diagnosis of transthyretin amyloid cardiomyopathy: a Delphi study

ObjectivesThis study has been conducted to investigate the non-invasive diagnostic journey of patients with a transthyretin amyloid cardiomyopathy (aTTR-CM) in Turkey, identify the challenges and uncertainties encountered on the path to diagnosis from the perspectives of expert physicians, and develop recommendations that can be applied in such cases.MethodsThis study employed a three-round modified Delphi method and included 10 cardiologists and five nuclear medicine specialists. Two hematologists also shared their expert opinions on the survey results related to hematological tests during a final face-to-face discussion. A consensus was reached when 80% or more of the panel members marked the “agree/strongly agree” or “disagree/strongly disagree” option.ResultsThe panelists unanimously agreed that the aTTR-CM diagnosis could be established through scintigraphy (using either 99mTc-PYP, 99mTc-DPD, or 99mTc-HMPD) in a patient with suspected cardiac amyloidosis (CA) without a further investigation if AL amyloidosis is ruled out (by sFLC, SPIE and UPIE). In addition, scintigraphy imaging performed by SPECT or SPECT-CT should reveal a myocardial uptake of Grade ≥2 with a heart-to-contralateral (H/CL) ratio of ≥1.5. The cardiology panelists recommended using cardiovascular magnetic resonance (CMR) and a detailed echocardiographic scoring as a last resort before considering an endomyocardial biopsy in patients with suspected CA whose scintigraphy results were discordant/inconclusive or negative but still carried a high clinical suspicion of aTTR-CM.ConclusionThe diagnostic approach for aTTR-CM should be customized based on the availability of diagnostic tools/methods in each expert clinic to achieve a timely and definitive diagnosis

Operational Ecosystem: Ecosystem forecast products to enhace marine GMES applications (OPEC)

OPEC will undertake research and development to develop Operational Ecology to augment the capabilities of the GMES Marine Service. Using the Marine Service as a framework, OPEC will OPEC will contribute ‘to the establishment of innovative new GMES products or applications by’ establishing the infrastructure for the performance of ecology in the European Regional Seas by implementing a prototype regional ecological Marine Forecast System in 4 European Regions (NE Atlantic Baltic, Mediterranean and Black Seas, which include hydrodynamics, lower (plankton) and higher trophic (e.g. fish) and biological data assimilation. OPEC will deliver ‘new products’ in terms of rapid environmental assessments as well as hindcasts for environmental management by providing regular ‘geo-spatially referenced’ error quantified information products (ECV’s and indicators of GES) for European Coastal Seas in both lower and higher trophic levels. By assessing the potential spatial and temporal scales of predictability of seasonal forecast appropriate to both lower and higher trophic levels OPEC will also lay the foundations for the next generation of operational ecological products. In doing so OPEC will provide high quality 3D ecosystem indicators covering a range of temporal and spatial scale appropriate for different policy needs as new service aimed at supporting policy, environmental management and other downstream services by providing error quantified hindcast estimates of the state of the environment in the recent past systems. OPEC will contribute directly to policy requirements such as the MSFD, CFP, the monitoring of climate change and to the assessment of mitigation and adaptation policies. Through engagement with SME’s, OPEC will implement new water quality related data products and delivery systems for implementation in downstream services. In addition OPEC will define and deliver the S&T Roadmap and make recommendations for future data requirements for Operational Ecology.EU, Funded under :FP7-SPACE-2011-

megaCITY - Zoom for the ENvironment (CITYZEN)

We will determine the air pollution distribution and change in and around hotspots over the last decade from extensive satellite and in-situ observations and we will employ a series of different scale models in order to analyze the impacts of air pollution hot spots on regional and global air quality including potential future changes for various climate scenarios. Focus is on ozone and particulate matter with chemical and physical characterization, and their precursors. The Eastern Mediterranean (Istanbul, Athens, Cairo), the Po Valley, the BeNeLux region, the Pearl River Delta in China (with megacities Guangzhou and Hong Kong) and the hot and polluted European summer 2003 are chosen for intensive case studies. The consortium includes groups from China, Turkey, Greece and Italy, in addition to France, Germany, UK and Norway, with experts on the observations, emission data and models. A set of chemical transport models which connect all the most important spatial and temporal scales will be developed and used to quantify how the observed air pollution arises. The models and emission inventories will be evaluated, errors identified and improved on the urban, regional and global spatial scales. Climate change may cause changes in air pollution in and around hotspots, and hotspot pollution can change precipitation and temperature/albedo. These feedbacks will be studied in scale-bridging model systems based on global climate model scenarios, and in a coupled high resolution chemistry-climate model. The model systems evaluated in the project will be applied to analyse mitigation options in and around hotpots, also taking into account climate change. Best available technologies and sectoral changes will be studied. Several partners have key roles in the technical underpinning of policy. They will ensure that the improved emission inventories, scale-bridging model systems and the systematic observational evidence will have a significant, broad and lasting impact.EU, Funded under:FP7-ENV-2007-

European Union Basin-scale Analysis, Synthesis and Integration (EURO-BASIN)

EURO-BASIN is designed to advance our understanding on the variability, potential impacts, and feedbacks of global change and anthropogenic forcing on the structure, function and dynamics of the North Atlantic and associated shelf sea ecosystems as well as the key species influencing carbon sequestering and ecosystem functioning. The ultimate goal of the program is to further our capacity to manage these systems in a sustainable manner following the ecosystem approach. Given the scope and the international significance, EURO-BASIN is part of a multidisciplinary international effort linked with similar activities in the US and Canada. EURO-BASIN focuses on a number of key groups characterizing food web types, e.g. diatoms versus microbial loop players; key species copepods of the genus Calanus; pelagic fish, herring (Clupea harengus), mackerel (Scomber scombrus), blue whiting (Micromesistius poutassou) which represent some of the largest fish stocks on the planet; piscivorous pelagic bluefin tuna (Thunnus thynnus) and albacore (Thunnus alalunga) all of which serve to structure the ecosystem and thereby influence the flux of carbon from the euphotic zone via the biological carbon pump. In order to establish relationships between these key players, the project identifies and accesses relevant international databases and develops methods to integrate long term observations. These data will be used to perform retrospective analyses on ecosystem and key species/group dynamics, which are augmented by new data from laboratory experiments, mesocosm studies and field programs. These activities serve to advance modelling and predictive capacities based on an ensemble approach where modelling approaches such as size spectrum; mass balance; coupled NPZD; fisheries; and “end to end” models and as well as ecosystem indicators are combined to develop understanding of the past, present and future dynamics of North Atlantic and shelf sea ecosystems and their living marine resources.EU, Funded under :FP7-ENV-201

Options for Delivering Ecosystem-Based Marine Management (ODEMM)

The overall aim of the ODEMM project is to develop a set of fully-costed ecosystem management options that would deliver the objectives of the Marine Strategy Framework Directive, the Habitats Directive, the European Commission Blue Book and the Guidelines for the Integrated Approach to Maritime Policy. This will be achieved by: (i) providing a comprehensive knowledge base to support policy for the development of sustainable and integrated management of European marine ecosystems; (ii) developing Operational Objectives to achieve the High-Level Policy Objectives set by the MSFD and the HD, and with reference to the proposed Maritime Policy; (iii) identifying Management Options (individual management tools and combinations of tools) to meet the Operational Objectives; (iv) providing a risk assessment framework for the evaluation of Management Options and to assess the risk associated with the different options; (v) conducting a cost-benefit analysis of a range of Management Options using appropriate techniques; (vi) identifying stakeholder opinions on the creation of governance structures directed towards implementation of the ecosystem approach, and to elaborate different scenarios for changing governance structures and legislation to facilitate a gradual transition from the current fragmented management approach towards fully integrated ecosystem management; (vii) documenting the steps necessary for the transition from the current fragmented management scheme to a mature and integrated approach, and providing a toolkit that could be used to evaluate options for delivering ecosystem-based management; and (viii) communicating and consulting on the outcomes of the project effectively with policy makers and other relevant user groups.EU, Funded under FP7-ENV-2009-