Genomic and chromosomal organization of Ty1- copia-like sequences in Olea europaea and evolutionary relationships of Olea retroelements

The Ty1- copia-like retrotransposon is one of the commonest class of transposable elements in the plant kingdom, often comprising several percent of the total DNA content. We aimed to study the evolutionary relationships of Olea retroelements, using part of the reverse transcriptase domain, as well as the genomic and chromosomal organization of these sequences in Olea europaea chromosomes and their transcription activity and copy number. Fourteen clones, that were isolated from four different species, were sequenced and a phylogenetic tree was constructed based on their predicted amino acids. Five clones derived from O. europaea were clustered together with a 87% nucleotide sequence homology and two Olea oleaster clones showed 98% sequence homology. The rest of the clones showed heterogeneity among them, leading to a common ancestral transposon that existed before the genus arose. The Ty1- copia-like sequences have a dispersed genomic organization, physically distributed on all chromosomes, showing minor clustering in some cases and low copy numbers in the smallest chromosome pair. The total copy number in the O. europaea genome was estimated by dot blotting to be 40,000 in a haploid nucleus, but a number of these are non-functional since the sequenced clones contained stop codons and frame-shifts. Some Ty1- copia-like copies, present in O. europaea, were found to be methylated, while no differences in methylation were observed between DNA isolated from young leaves and callus-suspension cultures

The close relationship between the A and B genomes in Avena L. (Poaceae) determined by molecular cytogenetic analysis of total genomic, tandemly and dispersed repetitive DNA sequences

The genus Avena L. (Poaceae) consists of diploid, tetraploid, and hexaploid species, with the B genome known only in tetraploid species and the D genome in the hexaploid species. DNA:DNA in situ hybridization, using total genomic DNA from diploid Avena strigosa Schreb. (A8 genome) as a probe, labelled all 28 chromosomes of the AB tetraploid Avena vaviloviana (Malz.) Mordv. strongly and uniformly, revealing the close relationship between these two genomes. Comparison of patterns of size-separated DNA restriction fragments between the diploid A. strigosa and the tetraploid A. valviloviana, using 32 different restriction enzymes, revealed no differences. Southern hybridization using total AB genomic DNA as a probe also gave no differences in banding patterns between the two genomes, even when a large excess of A genomic DNA was used as a block. From an A. vaviloviana genomic library, 1800 colonies were blotted and probed sequentially with A and AB genomic DNA, but no colony was identified to be B genome specific DNA digests of AB genome tetraploids with restriction enzyme HaeIII gave a strong band at 4.2 kb. Clone pAbKB3, derived from the 4.2 kb band, was found to be part of a Tyl-copia-like retrotransposon present in A and B genome chromosomes. Cloned rRNA genes were used for in situ hybridization and showed that diploid A. strigosa has four major sites for 18S-25S rDNA and two pairs of sites for 5SrDNA (pairs on the same satellited chromosome, on different chromosome arms), while 4x A. vaviloviana has eight major sites for 18S-25S rDNA and four pairs of sites for 5S rDNA (pairs on the same satellited chromosome, on different chromosome arms). A repetitive sequence from rye pSc119.2, showed dispersed hybridization, while the telomeric sequence in clone pLT11 hybridized to telomeres. Again no discrimination was possible between A and B genome chromosomes. The molecular similarities between the diploid A. strigosa and the barbara group tetraploids clearly indicate that the barbara group of tetraploids arose from A8 diploids through autotetraploidization

Olive Oil Polyphenols in Neurodegenerative Pathologies

Neurodegenerative diseases lead to the death of nerve cells in the brain or the spinal cord. A wide range of diseases are included within the group of neurodegenerative disorders, with the most common ones being dementia, Alzheimer’s, and Parkinson’s diseases. Millions of older people are suffering from such pathologies. The global increase of life expectancy unavoidably leads to a consequent increase in the number of people who will be at some degree affected by neurodegenerative-related diseases. At this moment, there is no effective therapy or treatment that can reverse the loss of neurons. A growing number of studies highlight the value of the consumption of medical foods, and in particular olive oil, as one of the most important components of the Mediterranean diet. A diet based on extra virgin olive oil seems to contribute toward the lowering of risk of age-related pathologies due to high phenol concentration. The link of a polyphenol found in extra virgin olive oil, namely, tyrosol, with the protein tyrosinase, associated to Parkinson’s disease is underlined as a paradigm of affiliation between polyphenols and neurodegenerative disorders. © Springer Nature Switzerland AG 2020

Genetic diversity and relationships among Pistacia species and cultivars

Iran is one of the two major centres of Pistacia diversity and the main producer of pistachios in the world. About 282 Iranian pistachio genotypes (Pistacia spp.), together with 22 foreign cultivars (P. vera), were genotyped using 10 simple sequence repeat (SSR) markers to analyse the genetic diversity and relationships among Pistacia species and cultivars. The results revealed that the genetic diversity within P. atlantica subsp. kurdica was considerably lower than in P. vera or P. khinjuk. Principal coordinate analysis revealed a clear separation between the different Pistacia spices, as well as between the Iranian and foreign cultivars. AMOVA analysis showed that the variation between the species, between different populations, and within populations accounted for 41, 9, and 50% of the total variation, respectively. The results demonstrated that the study of genetic diversity and relationships among Pistacia species and cultivars using SSR markers provides important information for the collection and conservation of pistachio germplasm. In addition, the Iranian cultivars had a broader genetic background than that of the foreign cultivars. Thus, they are very important for genetic conservation and the planning of future breeding programmes. We also determined the different levels of genetic diversity that exist between and within the species and populations and showed that gene flow occurs between the Iranian cultivars and wild-type P. vera populations. The study provides practical information that policy-makers and scientists can apply to the conservation and sustainable use of all the species studied. © Springer Science+Business Media B.V. 2009

Microbiome Hijacking Towards an Integrative Pest Management Pipeline

Pesticides are necessary to fight agricultural pests, yet they are often nonspecific, and their widespread use is a hazard to the environment and human health. The genomic era allows for new approaches to specifically target agricultural pests, based on analysis of their genome and their microbiome. We present such an approach, to combat Bactrocera oleae, a widespread pest whose impact is devastating on olive production. To date, there is no specific pesticide to control it. Herein, we propose a novel strategy to manage this pest via identifying novel pharmacological targets on the genome of its obligate endosymbiotic bacterium Candidatus Erwinia dacicola. Three genes were selected as pharmacological targets. The 3D models of the Helicase, Polymerase, and Protease-C gene products were designed and subsequently optimized by means of molecular dynamics simulations. Successively, a series of structure-based pharmacophore models were elucidated in an effort to pave the way for the efficient high-throughput virtual screening of libraries of low molecular weight compounds and thus the discovery of novel modulating agents. Our methodology provides the means to design, test, and identify highly specific pest control substances that minimize the impact of toxic chemicals on health, economy, and the environment. © Springer Nature Switzerland AG 2020

Effectiveness of SSR molecular markers in evaluating the phylogenetic relationships among eight Actinidia species

The aim of the present study is to evaluate a set of microsatellites and their effectiveness in determining the phylogenetic relationships among Actinidia species. A set of 14 genotypes belonging to eight Actinidia species were subjected to PCR using SSRs as molecular markers. The PCR products were analyzed on denaturing polyacrylamide gels. The discriminating ability of SSRs was based on the number of alleles and the indices DI, I and PIC. All SSR primer pairs were polymorphic and identified a total number of 61 alleles corresponding to an average of 7.8 alleles per locus. Data showed that the di-nucleotide microsatellites were more polymorphic, than the tri-nucleotide and penta-nucleotide, and were more efficient in establishing genetic similarities. The genetic similarity of the genotypes calculated with Jaccard and/or Dice similarity coefficients varied from 0.100 to 0.579, indicating a broad genetic base for the genetic material tested. Both similarity matrices clustered either with UPGMA or NJ, produced similar topology with minor clustering differences among genotypes. Thus, the eight species were clustered in two main groups and each main group in two subgroups. Data showed a close genetic relationship among Actinidia chinensis and Actinidia deliciosa species. The same conclusions were, also, drawn using the principal coordinate analysis. (C) 2008 Elsevier B.V. All fights reserved

Drugena: A Fully Automated Immunoinformatics Platform for the Design of Antibody-Drug Conjugates Against Neurodegenerative Diseases

Antibodies are proteins that are the first line of defense in the adaptive immune response of vertebrates. Thereby, they are involved in a multitude of biochemical mechanisms and clinical manifestations with significant medical interest, such as autoimmunity, the regulation of infection, and cancer. An emerging field in antibody science that is of huge medicinal interest is the development of novel antibody-interacting drugs. Such entities are the antibody-drug conjugates (ADCs), which are a new type of targeted therapy, which consist of an antibody linked to a payload drug. Overall, the underlying principle of ADCs is the discerning delivery of a drug to a target, hoping to increase the potency of the original drug. Drugena suite is a pioneering platform that employs state-of-the-art computational biology methods in the fight against neurodegenerative diseases using ADCs. Drugena encompasses an up-to-date structural database of specialized antibodies for neurological disorders and the NCI database with over 96 million entities for the in silico development of ADCs. The pipeline of the Drugena suite has been divided into several steps and modules that are closely related with a synergistic fashion under a user-friendly graphical user interface. © Springer Nature Switzerland AG 2020