Protein structural differences in Cytochrome c oxidase subunit 1 of two Heterogynis species as a new approach for species delimitation

Insects are the most diverse group in the animal kingdom, accounting for about two-thirds of all animals. Cytochrome c oxidase subunit 1 (COI) is the most commonly used marker gene for animal species delineation. However, the accuracy of this approach crucially depends on the degree of overlap between the intra- and interspecific variations. Recently, we have identified a new species, Heterogynis serbica sp. n. (Lepidoptera: Zygaenoidea, Heterogynidae) found on the Mt. Kopaonik, Republic of Serbia, Balkan Peninsula. This was done by integrating taxonomic approach using morpho-anatomical characteristics by comparative scanning electron microscopy (SEM), linear wing morphometry and COI-based DNA barcoding [1]. In this study, we have used a set of bioinformatics tools available online, to determine the differences in secondary and tertiary structure of the COI proteins from H. serbica sp. n. and H. zikici. We also compared the amino acid distribution and COI motif profiles between the two species. Our results provide strong evidence that protein structure of COI can help with COI-based DNA barcoding for taxon-specific purposes of species identification and delimitation studies. Millions of COI DNA sequences deposited in the public domain (which are still growing) carry huge potential for a comprehensive assessment of genetic variation in COI among insects by using here described analysis.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202

Identifikacija genetskih osobina kukuruza (Zea mays L.) korišćenjem genetskih markera

Different genetic markers are used for estimation of breeding material, its characteristics and potential for ultimate aim - heterosis of hybrids. They also point out to the qualitative seed traits at the level of linkage with genes responsible for desirable agronomic traits. This program encompasses testing methodologies for the new seed technology. Genetic analysis of breeding material during certain phases is comprised of isozymic gene expression and degrees of their variability, but it is continued (in order to be evaluated) until determination of presence or absence of some genes existing or introduced for certain traits. Using combination of different molecular methods such as PCR, RAPD and AFLP based on polymorphism of DNA fragments, the definite aim - identification of newly created products of improvement is achieved. Testing of traits of breeding material, its genetic variability and diversity is the first stage in analysis of the maize genome. It is also the condition for determination of presence of certain genes, used for obtaining the ultimate aim - attest of identity of the genotype.Različiti genetski markeri se koriste za tumačenje selekcionog materijala njegovih osobina i osnove za krajnji cilj - heterozis hibrida. Oni su takođe pokazatelji kvaliteta semena na nivou vezanih gena za određena, tražena agronomska svojstva. Ovaj program uključuje nove metodologije za testiranje selekcionog i semenskog materijala. Genetske analize biljaka u fazama oplemenjivanja obuhvataju izoenzimsku ekspresiju gena i stepen njihove varijabilnosti, koja se nastavlja do determinacije prisustva ili odsustva gena, odgovornih za određena svojstva. Primenjuje se kombinacija različitih genetsko-molekularnih metoda, kao što su izoenzimi PCR, RAPD, AFLP, RFLP bazirani na polimorfizmu proteina i sekvenci DNK, čiji je krajnji cilj identifikacija novostvorenih genotipova i njihovo unapređenje. Utvrđivanje osobina selekcionog materijala, njegove genetske varijabilnosti i divergentnosti je prva faza u spoznaji genoma kukuruza. To je takođe uslov za determinaciju prisustva određenih gena, potrebnu za postizanje završne faze, potvrde o identitetu genotipa

Molecular characterization of some lignicolous species from fungal culture collection

Culture collections of microorganisms, including fungi, are strain deposits recognised as Biological Resource Centers (BRCs) with a great importance in science, industry and education. Their objective is to preserve the purity, viability and genomic integrity of every single strain as a member of such collection. Since improvement of molecular methods nowadays brought many novel approaches in manipulation with strains of microorganisms, they can also be useful for characterization of existing stored strains. ITS1 region in nuclear DNA is preferred barcoding marker for taxon identification, which can be explained by its great inter-species variability. This paper presents results from analysing ITS1 region sequences (17) obtained from fungal DNA of culture collection of autochthonous, lignicolous genera Piptoporus, Pleurotus, Ganoderma and Schizophyllum cultured on malt agar plates for 14 days at 25°C. BLAST (Basic Local Alignment Search Tool) was used for comparison with online databases, while alignment of sequences was made with MEGA 5.10 software. Morphological determination of species or genus was confirmed for 13 cultures, while the others were disproved. The resulting alignment indicated small intra-species variability of ITS1 region and pointed to it as an ideal marker for verification of fungal culture collections' authenticity. [Projekat Ministarstva nauke Republike Srbije, br. III43002 and by the Provincial Secretariat for Science and Technological Development, Vojvodina, Serbia APV 114-4513592/2013-03: Molecular and phenotypic diversity of taxa of economical and epidemiological importance, and endangered and endemic species in Europe

Molecular Technologies in Serbian Lowland Forestry under Climate Changes - Possibilities and Perspectives

Background and Purpose: Vojvodina province, the northern part of the Republic of Serbia, is predominantly lowland agricultural region with over 75% of arable land which in previous years, has been highly impacted by drought. The annual precipitation is lower than 700 mm and it is the limit for the growth and development of natural forest vegetation. Unfortunately, the atmospheric precipitation is still a major source of water for plant biodiversity. Taking these facts into account, it is highly recommended to primarily use the xerothermic tree species, which have a well-developed root system for “classical” afforestation. Some species from Salicaceae and Fagaceae like poplars, willows, oaks and beeches are surely the best option for afforestation in temperate zones strongly influenced by drought. Conclusions: In order to develop stress-based genomic information in Populus and the rest of woody plant species from Vojvodina, an integrated genetic research needs to be done. The aim of this particular paper is to analyse and summarize data regarding stress-based biotechnology perspectives in Vojvodina and to give recommendations for future forest tree breeding. Drought as a strong negative ecological factor must be carefully considered. In order to achieve sustainability, new forest management plans must consider wide approaches, from molecular to ecosystem level

Molecular mechanisms of woody plant species abiotic stress response

Sve učestalije i intenzivnije promene faktora spoljašnje sredine deluju na biljke kao stres. Suočene sa ovim promenama biljke su razvile mehanizme tolerancije i adaptacije, koji im omogućavaju opstanak. Ovi mehanizmi funkcionišu na morfološkom, fiziološkom, biohemijskom i molekularnom nivou, međusobno su povezani, regulisani i usklađeni u integrisani sistem odgovora na promene u životnoj sredini. Mnogi ključni regulatorni i funkcionalni molekuli koji učestvuju u odgovoru na abiotički stres su identifikovani i time je otvorena mogućnost primene novih strategija u upravljanju stresom. Tema ovog rada su molekularni i biohemijski mehanizmi odgovora drvenastih vrsta biljaka na različite tipove abiotičkog stresa, sa posebnim osvrtom na topole.More frequent and more intense changes in environmental factors act as a stress on the plants. Faced with these changes, plants have developed mechanisms of tolerance and adaptation, which enable them to survive. These mechanisms operate on the morphological, physiological, biochemical and molecular level, are interconnected, regulated and coordinated in an integrated system response to changes in the environment. Many key regulatory and functional molecules involved in the response to abiotic stress are identified, thus opening the possibility for implementation of new strategies in the stress management. This paper outlines the molecular and biochemical mechanisms of response of woody plants to different types of abiotic stress, with special emphasis on poplars

Relationship among eastern cottonwood genotypes according to early rooting traits

The relationship between twelve genotypes of eastern cottonwood (Populus deltoides Bartr.) was analyzed according to sixteen early rooting traits and cutting survival. Principal component analysis (PCA) and cluster analysis were used on data that were standardized by common and by one alternative way of standardization. Alternative way of standardization (standardization with within-genotype standard deviation instead of standard deviation of genotypes’ means) was used in order to emphasize the contribution of genotype to the effect of differences among genotypes on total variation. After bought ways the first principal component had high correlation with the most of rooting traits and cutting survival, while the second was mainly related to the traits of root formation on the basal cut of cutting (wound roots). Three difficult-to-root genotypes (S6-7, S1-3, 129/81) were distinctly grouped against other examined genotypes, by bought principal component and cluster analysis. There was a slight difference in grouping of easy-to-root genotypes (B-229 and PE19/66) among examined ways of standardization

UTJECAJ ONEČIŠĆENOSTI TLA TEŠKIM METALIMA NA KLONOVE TOPOLA IZ SRBIJE

Oxidative stress is known as disturbed balance between antioxidative protection mechanism and production of reactive oxygen species, which can negatively influence on normal biological and metabolical processes in living organisms, such as poplar species. Phytoremediation is promising biotechnical method of cleaning of polluted soils by various pollutants: heavy metals, organic contaminants, pesticides, oil etc. Until today, poplars showed potential for regenerating polluted soils during phytoremediation process. This study represents results of oxidative stress profiles of three poplar clones (M1, B229 and PE 19/66) shoots from Institute of Lowland Forestry and Environment, University of Novi Sad, Serbia, while being treated by different concentration of three heavy metals in soil: Ni3+, Cu2+ and Cd2+. Biochemical parameters of oxidative stress which have been analyzed were: content of soluble proteins, intensity of lipid peroxidation, antioxidative capacity by ferric reducing antioxidative power assay and activity of superoxid dismutase. Results showed that the most acceptable phytoremediation response to heavy metal pollution in soil showed clone M1. Great differences between B229 and PE 19/66 clones were in response on soil heavy metal contamination, directly suggesting of not being suitable for possible phytoremediation application.Oksidacijski stres je poznat kao narušena ravnoteža između antioksidacijskog mehanizma zaštite i proizvodnje reaktivnih kisikovih vrsta, što može negativno utjecati na normalne biološke i metaboličke procese u živim organizmima, kao na primjer kod topola. U cilju opstanka, aerobni organizmi su stekli mehanizme antioksidacijske zaštite, gdje su od enzimskih najistraženije aktivnosti antioksidativnih enzima kao što su katalaze, peroksidaze, glutation peroksidaze i superoksid dismutaza. Fitoremedijacija je obećavajuća biotehnička metoda čišćenja zagađenih tala raznim onečišćujućim tvarima poput: teških kovina, organskih kontaminanata, pesticida i dr. Do danas, topole su pokazale potencijal za regeneraciju onečišćenih tala tijekom fitoremedijacijskog procesa.Biokemijsko profiliranje statusa oksidacijskog stresa u drvenastim biljkama nije često istraživana u Srbiji i stoga je cilj ovoga pokusa bio ispitati utjecaj različitih koncentracija tri jona teških kovina, Ni3+, Cu2+ i Cd2+ na razinu oksidacijskog stresa tri klona, dvije različite vrste topole (Populus euramericana-M1; PE 19/66 i B-229 oba Populus deltoides vrsta). Biokemijski parametri za određivanje razine oksidacijskog stresa su: lipidna peroksi­dacija (LPx), test redukcijske snage željeza (FRAP), superoksid dismutaze (SOD) aktivnost i sadržina topivih bjelančevina. Ovi rezultati mogli bi dati smjernice u odabiru klonova iz kolekcije Instituta za nizijsko šumarstvo i životnu sredinu Univerziteta u Novom Sadu za buduće fitoremedijacijske uporabe ovih genotipova topola. Pješčano fluvisol tlo u pokusnim posudama je zagađeno različitim tretmanima teških kovina, koji su prikazani u tablici 1. Biljni ekstrakti izrađeni su od 2 g biljnog materijala (izbojci) i homogenizirani s kvarcnim pijeskom i suspenzirani u 10 cm3 0,1 mol/dm3 K2HPO4 pH 7,0. Homogenati su centrifugirani za 10 min na 4000 g (Quy Hai sur., 1975). Sva očitavanja apsorbancija za sadržaj topivih proteina, SOD i FRAP odrađeno pomoću Janway UV / VIS spektrofotometra 6505 i za čitanje količine nastalog MDA korišten je višefrekvencijski Spectrum Termo Corporation.Sve analize izvedene su u tri ponavljanja. Statistička usporedba između uzoraka izvedena je u programu Statistica 9, koristeći Duncan test, s statističkom značajnosti p <0,05. Dobiveni rezultati prikazani su grafički preko histograma (slike 1. do 4.) i iznad njih su slova koja označuju statistički značajne razlike između rezultata i kontrola (od a do e).Usporedni postotak je izračunat prema formuli: Δ (%) = (100 * uzorak / kontrola) –100, gdje vrijednosti mogu rezultirati pozitivno (+) ako je došlo do povećanja u odnosu na kontrolu i rezultiralo negativno (–), ako je došlo do smanjenja u odnosu na kontrolu.Trudić i sur. (2012) analizirali su kroz iste metode okdisacijskog stresa ekstrakte lišća i korijena spomenutih klonova topola. Uspoređujući ove rezultate, B229 klon je kroz lišće i korijenje pokazao više prihvatljiv antioksidacijski odgovor, dok je, u ovom istraživanju, M1 klon pokazao najprihvatljivije antioksidacijske odgovore kroz ekstrakte izbojaka. Parametri iz Pilipović i sur. (2012), Trudić i sur. (2012) i naše studije, mogu predstavljati udružen fiziološki i antioksidacijski marker sustav za buduće različite fitoremedijacijske primjene ovih klonova na tlima onečišćenim raznim tvarima.Rezultati ovog istraživanja mogu ukazati na genotipske specifičnosti svih ispitivanih biokemijskih parametara i obilježava klonove topola, kao što je M1 kao primarni, a B229 klon kao potencijalno sljedeći u primjeni fitoremedijacije tala onečišćenih teškim kovinama. Ipak, za stjecanje novih, dubljih rezultata u vezi s oksidacijskim stresom izazvanim onečišćavanjem tala teškim kovinama, potrebne su dalje in vitro antioksidacijske analize

The Genus Heterogynis Rambur, 1866 (Heterogynidae, Lepidoptera): Congruence of Molecular, Morphological and Morphometric Evidence Reveal New Species in Serbia

The Heterogynidae are a small family of moths consisting of a single genus Heterogynis and sixteen described species distributed in the Mediterranean region. A species new to science, Heterogynis serbica sp. nov., is described from the locality of Srebrenac, Mt. Kopaonik, Republic of Serbia, Balkan Peninsula, by applying an integrative taxonomic approach using morpho-anatomical characteristics, wing morphometics and DNA barcoding. Male genitalia, scanning electron micrographs of adult male head anatomy, abdominal tergites/sternites, cocoons and habitats of the closely related species H. serbica sp. nov. and H. zikici are discussed and illustrated. Photographs of adult males and females, cocoons, plants in which the cocoons were found and habitats are shown. Importantly, marked differences in genital structure and other morphological characters were noted. These differences were confirmed with forewing morphometrics and COI-based DNA barcoding results. Additionally, DNA barcodes for H. serbica sp. nov. and H. zikici were compared against previously available data for the genus to evaluate the phylogenetic relationships. We conclude that deep, previously unknown and unexpected intrageneric morphological diversity exists in the genus Heterogynis.The authors wish to express their gratitude to Goran Anaˇckov, a Director of The Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, for his support; he enabled the usage of the equipment in the University Center for Electronic Microscopy (UCEM-NS), at the University of Novi Sad for this research. The authors are also very grateful to the Director and the Executive Director of the National Park “Kopaonik” Bojan Milovanovi´c and Predrag Šumarac for their long-term cooperation and support in this research. Finally, the authors deeply appreciate the support from Vladimir Žiki´c, from the University of Niš, Faculty of Sciences and Mathematics, Department of Biology and Ecology, who has kindly provided the analysed samples of H. zikici

Antioxidative response of poplar tissue culture exposed to peg 6000

The aim of this work was to investigate the influence of the water deficit in poplar tissue culture (M-1 genotype) through proline content, level of lipid peroxidation and activities of antioxidative enzymes. Plants were exposed to PEG 6000 (100 and 200 mOsm) in in vitro conditions for 6 days. Malondialdehyde (MDA) content showed an increase only at 200 mOsm stress. Under the 100 mOsm stress, catalase and guaiacol peroxidase activities were induces indicating their important role in elimination of reactive oxygen species (ROS). Under the 200 mOsm stress, superoxide dismutase and guaiacol peroxidase activities were induced