Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low-copy loci

Fagus L. is a key component in temperate deciduous broadleaf forests of the Northern Hemisphere. However, its biogeographic history has not been examined under the framework of a fully resolved and reasonably time-calibrated phylogeny. In this study, we sequenced 28 nuclear single/low-copy loci (18 555 bp in total) of 11 Fagus species/segregates and seven outgroups. Phylogenetic trees were reconstructed using both concatenation-based (maximum parsimony, maximum likelihood, and Bayesian inference) and coalescent-based methods (StarBEAST2, ASTRAL). The monophyly of two subgenera (Fagus and Engleriana) and most sections was well supported, except for sect. Lucida, which was paraphyletic with respect to sect. Longipetiolata. We also found a major phylogenetic conflict among North American, East Asian, and West Eurasian lineages of subgen. Fagus. Three segregates that have isolated distribution (F. mexicana, F. multinervis, and F. orientalis) were independent evolutionary units. Biogeographic analysis with fossils suggested that Fagus could have originated in the North Pacific region in late early Eocene. Major diversifications coincided with a climate aberration at the Eocene/Oligocene boundary and the global cooling since mid-Miocene. The late Miocene accelerated global cooling and the Pleistocene glaciations would have driven beeches into East Asia, North America, and West Eurasia. Meanwhile, range reduction and extinction in high latitudes, central Asia, and western North America converged to form the beech modern distribution pattern. This study provides a first attempt to disentangle the biogeographic history of beeches in the context of a nearly resolved and time-calibrated phylogeny, which could shed new insights into the formation of the temperate biome in the Northern Hemisphere.This work was supported by the National Natural Science Foundation of China (Grant Nos. 31770236, 30760016, and 31560064) and the Strategic Priority Research Program of Chinese Academy of Sciences (XDB31000000).1 Introduction 2 Material and Methods 2.1 Taxon sampling 2.2 Screening of nuclear single/low-copy orthologous locus 2.3 DNA extraction, PCR protocol, and sequencing 2.4 Phylogenetic analyses and molecular dating 2.5 Ancestral area reconstruction 3 Results 3.1 Concatenated tree 3.2 Species tree and molecular dating 3.3 Ancestral area reconstruction 4 Discussion 4.1 Nearly resolved and well supported phylogeny of Fagus 4.2 Species delimitation of three segregates within Fagus 4.3 Biogeographic history of beech species Acknowledgement

Development of SSR (simple sequence repeat) dna markers in saffron (Crocus sativus L.) and their transferability to the closer relative species of saffron.

TEZ10255Tez (Doktora) -- Çukurova Üniversitesi, Adana, 2016.Kaynakça (s. 101-116) var.xi, 117 s. : res. (bzs. rnk.), tablo ; 29 cm.Bu çalışma safran için SSR markörlerini geliştirmek ve bu markörlerin safranın yakın yabani akrabalarına aktarılabilirliğini araştırmak amacıyla yürütülmüştür. Safranbolu bölgesinden toplanmış safran genotipine ait DNA kullanılarak farklı tekrar motifleriyle zenginleştirilmiş dört adet genomik kütüphaneden toplam 528 adet klon sekanslanmış, 350`sinde (%66.3) tekrar motifi belirlenmiş ve 235 adet (%67.1) klon için SSR primer çifti dizayn edilmiştir. Gradient PCR analizi sonucunda, 188 adet SSR primerinin (% 80.0) DNA`ya optimum bağlanma sıcaklığı belirlenmiş olup, 128 adet SSR primer çifti 27 adet safran genotipinde genetik çeşitliliği araştırmak için kullanılmıştır. Polimorfik bulunan 21 adet (%16,4) SSR primer çifti 27 adet safran genotipinde toplam 78 adet bant üretmiş, bunlardan 52 tanesi polimorfik bulunmuştur. Polimorfizm Bilgi İçeriği 0.071 ile 0.499 arasında değişmiş olup, ortalama 0.211 olarak bulunmuştur. Geliştirilen 138 adet SSR primer çiftinden; 114 tanesinin C.asumaniae`da, 129 tanesinin C.cartwrightianus`da, 121 tanesinin C. pallasi x C. mathewi`de, 124 tanesinin C. mathewi`de, 122 tanesinin C. pallasii ssp. pallasii`de, 122 tanesinin C. pallasii ssp. turcicus`da, 120 tanesinin C. pallasii ssp. dispathaceus`a PCR ürünü verdiği saptanmıştır. Crocus serisine ait taksonlarda yapılan filogenetik analiz sonucunda, kültürü yapılan safran genotiplerine en yakın yabani türün C. cartwrightianus olduğu belirlenmiştir. Geliştirilen SSR primer çiftlerinin hem safran bitkisinde genetik çeşitliliğin belirlenmesinde hem de Crocus serisinin filogenetik ve evrimsel çalışmalarında kullanılabileceği sonucuna varılmıştır.The aims of this study were to develop microsatellite markers for Crocus sativus (saffron) and to test them for the transferability into the close wild relatives of saffron. Four genomic libraries, which were enriched with different microsatellite motifs, were developed by using genomic saffron DNA of Safranbolu genotype. 350 of the 528 clones sequenced (% 66,3) contained microsatellites and 235 (%67,1) of the primers were designed. Optimum annealing temperature was determined for 188 (% 80.0) SSR markers with Gradient PCR protocol. The 21 (%16,4) out of 128 microsatellite primer pairs generated polymorphic bands among 27 saffron genotypes and 78 fragments were obtained. 52 of them were polymorphic. The average PIC value was 0.211, ranging from 0.071 to 0.499. Out of 138 SSRs developed, 114 in C.asumaniae, 129 in C.cartwrightianus, 121 in C. pallasi x C. mathewi, 124 in C. mathewi,122 in C. pallasii ssp. pallasii,122 in C. pallasii ssp. turcicus and 120 in C. pallasii ssp. dispathaceus gave amplicons. The results of phylogenetic analysis in taxa of Crocus series showed that the closest relative wild species of saffron could be C. cartwrightianus. From the results of the study, it was concluded that themicrosatellite markers developed in this study could bee useful both for evaluating genetic diversity in saffron and phylogenetic, taxonomic and evolutionary studies in Crocus species.Bu çalışma Ç.Ü. Bilimsel Araştırma Projeleri Birimi tarafından desteklenmiştir. Proje No: ZF2013D25

Bazı mürdümük (lathyrus satvus L.) varyete, hat ve çeşitleri arasındaki morfolojik, tarımsal ve moleküler farklılıkların saptanması üzerine bir araştırma

TEZ6576Tez (Yüksek Lisans) -- Çukurova Üniversitesi, Adana, 2007.Kaynakça (s.55-60) var.x, 61 s. ; 29 cm.The purpose of this study conducted at the Field Crops Department of Agricultural Faculty of Cukurova University during the growing season of 2005-2006 was to determine morphological and molecular diversity among 5 varieties, 4 lines and one cultivar of grasspea. Morphological diversity was studied in the field experiment arranged in randomized complete block design with three replications at the research area of Field Crops Department. Molecular diversity was studied by using 10 of ISSR primers. The results of the study showed that the varieties, lines and cultivar studied were statistically significant different in plant height, stem length, number of stems per plant, number of leaves on lengthiest stem of plant, green forage and hay yield per plant, days to 50 % flowering, number of pods per plant, pod length, pod width, number of seeds per pod, 1000 seed weight and seed yield per plant. According to the Jaccard's similarity index, similarity index values between varieties, lines and cultivar ranged from a minimum of 0.33 to a maximum of 0.79, the average being 0.58. From these coefficient values, it was concluded that L. Sativus var. albus and L.sativus var. azureus were close related varieties.Bu çalışma 2006-2007 yetiştirme sezonunda 5 mürdümük varyetesi, 4 mürdümük hattı ve bir adet tescil edilmiş mürdümük çeşidi arasındaki morfolojik, tarımsal ve moleküler farklılıkları saptamak amacıyla yürütülmüştür. Morfolojik ve tarımsal farklılıklar Çukurova Üniversitesi Tarla Bitkileri Bölümü araştırma alanında kurulan üç tekrarlamalı tarla denemelerinde, moleküler farklılık ise 10 adet ISSR primerı kullanılarak saptanmıştır. Çalışma sonuçları, incelenen çeşit varyete ve hatlar arasında, bitki boyu, sap uzunluğu ve kalınlığı, bitki başına ana dal sayısı, en uzun saptaki yaprak sayısı, bitki başına yaş ve kuru ot verimi, % 50 çiçeklenme süresi, bitki başına dolu ve boş meyve sayısı, meyve uzunluğu ve genişliği, bakla başına tohum sayısı ve verimi ile bin dane ağırlığı açısından önemli farklılıklar olduğunu göstermiştir. Jaccard benzerlik katsayısı 0.33 ile 0.79 arasında değişmiş ve ortalama 0.58 olarak bulunmuştur. 0.79 Jaccard benzerlik katsayısıyla L. Sativus var. albus ve L. sativus var. azureus 'un genetik olarak birbirlerine en yakın varyeteler olduğu saptanmıştır. L. sativus var. coloratus varyetesi ile 452 nolu hat 0.33 Jaccard benzerlik katsayısı ile birbirlerineBu çalışma Ç.Ü. Bilimsel Araştırma Projeleri Birimi Tarafından Desteklenmiştir. Proje No

METAL OXIDE DOPED ANTIBACTERIAL POLYMERIC COATED TEXTILE MATERIALS AND ASSESSEMENT OF ANTIBACTERIAL ACTIVITY WITH ELECTRON SPIN RESONANCE

Antibacterial activity of a food conveyor belt is an essential property in some cases. However, every antibacterial chemical is not suitable to contact with food materials. Many metal oxides are suitable option for this purpose. The aim of this study was to investigate antibacterial properties of zinc oxide doped PVC polymer coated with electron spin resonance technique. Therefore, optimum zinc oxide containing PVC paste was prepared and applied to textile surface. Coating construction was designed as double layered, first layer did not contain antibacterial agent, thin second layer contained zinc oxide at 10-35% concentration. Oxygen radicals released from zinc oxide containing polymeric coated surface were spin trapped with DMPO (dimethylpyrroline-N-oxide) spin trap and measured with Electron Spin Resonance (ESR). Besides conveyor belt samples, oxygen radical release from zinc oxide surface was measured with ESR under UV light and dark conditions. Oxygen radical release was determined even at dark conditions. Antibacterial properties were tested with ISO 22196 standard using Listeria innocua species. Measured antibacterial properties were related with ESR results. Higher concentration of zinc oxide resulted in higher antibacterial efficiency. DCFH-DA flourometric assay was carried out to determine oxidative stress insidebacteria. It is tought that, this technique will lead to decrease on the labour and time needed for conventional antibacterial tests

Production of Metal Oxide Containing Antibacterial Coated Textile Material and Investigation of the Mechanism of Action

The main aim of this study was to produce PVC coated textile based antibacterial textile material and to investigate the antibacterial mechanism with detailed analyzes. Metal oxide (calcium oxide, zinc oxide, magnesium oxide) powders were used to provide antibacterial functionality to coated materials. Metal oxide concentrations were varied between 5-35 %. Antibacterial tests were performed according to ISO 22196-2011 standard. Antibacterial efficiency of the samples was tested for each metal oxide type and concentration with L. innocua species. The antibacterial mechanism was investigated with ESR technique, fluorescent microscobe and microplate reader using DCFH-DA probe, UV-vis spectrometer using fluorescein probe. The results indicated that the antibacterial effect of used metal oxides was strongly arisen from radical oxygen species. The morphology of coatings was investigated with SEM and the distribution of metal oxide particles on the surface was examined with EDX analysis and EDX mapping. The changes on the molecular basis of the coating due to the metal oxide addition was analyzed with FT-IR spectroscopy. High antibacterial efficiencies (up to 100 %) were detected. It is suggested that the non-toxic metal oxides can be used as an effective and economically feasible alternative to conventional antibacterial additives for industrial applications such as conveyor belts

Çocuk Acil Servisinin En Küçük Misafirleri: Yenidoğanlar

Amaç Yenidoğan dönemi çocukluk çağının en savunmasız dönemlerinden biridir. Çalışmamızda çocuk acil servisine getirilen yenidoğan bebeklerin başvuru nedenleri ile izlem özelliklerini değerlendirmeyi amaçladık. Gereç ve Yöntemler 01.09.2018-01.09.2019 tarihleri arasında İstanbul Şehit Prof. Dr. İlhan Varank Sancaktepe Eğitim ve Araştırma Hastanesi çocuk acil servisine başvuran yenidoğanların demografik ve klinik bilgileri hastane veri tabanından alınarak geriye dönük olarak incelendi. Hastaların yaş, cinsiyet, başvuru nedeni, başvuru zamanı ve klinik seyirleri değerlendirildi. Bulgular İncelenen 12 aylık süreçte çocuk acile başvuran hasta sayısı 209.030 idi. Yenidoğanlar (0-28 gün) başvuruların %1,54’ünü (3224) oluşturuyordu, %46,96’sı (1.514) kız, %53,04’ü (1.710) erkekti. Vakaların en sık başvuru yaşının %63,94 (2062) ile 7-28 günler arasında olduğu görüldü. Sarılık (n=1.193, %37) en sık başvuru nedeniydi. En fazla başvuru Ağustos ayında (n=428, %13,28) olduğu görüldü. Hastaların %89,61’i (2.890) ayaktan, %10,39’u (334) yatırılarak izlendi. Takip sırasında kaybedilen olgumuz olmadı. Sonuç Çalışmamızda, yenidoğan başvurularının büyük çoğunluğunu normal sağlıklı yenidoğan bebeklerin oluşturduğu görülmüştür. Ailelere doğum öncesi ve sonrası eğitim verilmesinin acil servise gereksiz başvuruları azaltabileceğini ve ciddi bulguları olan bebeklerin erken başvurularını sağlayabileceğini düşünüyoruz.Objective The neonatal period is one of the most vulnerable periods of childhood. In our study, we aimed to evaluate the reasons for admission and follow-up characteristics of newborn babies admitted to the pediatric emergency department. Material and Methods Demographic and clinical characteristics of newborns applied to the pediatric emergency department of Istanbul Sancaktepe Training and Research Hospital between 01.09.2018 and 01.09.2019 were taken from the hospital database and analyzed retrospectively. Age, gender, reason for admission, time of admission and clinical course of the patients were evaluated. Results The number of patients admitted to the pediatric emergency department during the 12-month period was 209.030. Newborns (0-28 days old) constituted 1.54% (3224) of the admission, 46.96% (1,514) were girls, 53.04% (1,710) were boys. The most of the cases (63.94%, n=2062) were between 7 and 28 days old. Jaundice (n=1,193, 37%) was the most common reason for admission. The highest number (n=428, 13.28%) of admissions was in August, 89.61% (2,890) of the patients were followed up outpatient and 10.39% (334) of them were hospitalized. We did not have any mortality cases during follow-up. Conclusion In our study, it was observed that the majority of newborn admissions consisted of normal healthy newborn babies. We think that providing education to families before and after delivery can reduce unnecessary admissions to the emergency department and provide early admissions of babies with severe symptoms

GENETIC DIVERSITY OF CROCUS SATIVUS AND ITS CLOSE RELATIVE SPECIES ANALYZED BY iPBS-RETROTRANSPOSONS

WOS: 000418419700011Saffron (Crocus L.) is a member of Crocoideae, the biggest of four subfamilies in the Iridaceae family. It has 2n = 3x = 24 chromosomes and is triploid; thus, it is sterile. In previous research, different molecular DNA markers were used but molecular characterization and genetic diversity of this complex genus have not yet been clarified. Therefore, current study aimed to determine the molecular characterization of saffron and its close relative species using inter-primer binding site (iPBS)-retrotransposon markers. Eighty-three iPBS-retrotransposon primers were used in 28 C. sativus genotypes and 17 close relative species of saffron to identify their genetic diversity. Sixteen polymorphic iPBS-retrotransposon primers generated a total of 401 polymorphic scorable bands. The mean PIC value, Nei's genetic diversity and Shannon's information index (I) were calculated as 0.85, 0.16 and 0.29, respectively. The results of the Unweighted Pair Group Method with Arithmetic mean UPGMA dendrogram and Principal Coordinates Analysis PCoA analysis indicated a spatial representation of the relative genetic distances among 28 saffron samples and the 17 close relative species were categorized under two distinct groups. Saffron genotypes showed very limited genetic variation and according to the iPBS-retrotransposon data, its close relatives were C. cartwrightianus and C. pallasii subsp. pallasii.University of Cukurova, Scientific Research Projects UnitCukurova University [FBA-2014-2704]The authors express their gratitude to University of Cukurova, Scientific Research Projects Unit for their financial support (FBA-2014-2704)