Strategies for the evolution of sex

We find that the hypothesis made by Jan, Stauffer and Moseley [Theory in Biosc., 119, 166 (2000)] for the evolution of sex, namely a strategy devised to escape extinction due to too many deleterious mutations, is sufficient but not necessary for the successful evolution of a steady state population of sexual individuals within a finite population. Simply allowing for a finite probability for conversion to sex in each generation also gives rise to a stable sexual population, in the presence of an upper limit on the number of deleterious mutations per individual. For large values of this probability, we find a phase transition to an intermittent, multi-stable regime. On the other hand, in the limit of extremely slow drive, another transition takes place to a different steady state distribution, with fewer deleterious mutations within the asexual population.Comment: RevTeX, 11 pages, multicolumn, including 12 figure

Self-optimization, community stability, and fluctuations in two individual-based models of biological coevolution

We compare and contrast the long-time dynamical properties of two individual-based models of biological coevolution. Selection occurs via multispecies, stochastic population dynamics with reproduction probabilities that depend nonlinearly on the population densities of all species resident in the community. New species are introduced through mutation. Both models are amenable to exact linear stability analysis, and we compare the analytic results with large-scale kinetic Monte Carlo simulations, obtaining the population size as a function of an average interspecies interaction strength. Over time, the models self-optimize through mutation and selection to approximately maximize a community fitness function, subject only to constraints internal to the particular model. If the interspecies interactions are randomly distributed on an interval including positive values, the system evolves toward self-sustaining, mutualistic communities. In contrast, for the predator-prey case the matrix of interactions is antisymmetric, and a nonzero population size must be sustained by an external resource. Time series of the diversity and population size for both models show approximate 1/f noise and power-law distributions for the lifetimes of communities and species. For the mutualistic model, these two lifetime distributions have the same exponent, while their exponents are different for the predator-prey model. The difference is probably due to greater resilience toward mass extinctions in the food-web like communities produced by the predator-prey model.Comment: 26 pages, 12 figures. Discussion of early-time dynamics added. J. Math. Biol., in pres

Tangled Nature: A model of emergent structure and temporal mode among co-evolving agents

Understanding systems level behaviour of many interacting agents is challenging in various ways, here we'll focus on the how the interaction between components can lead to hierarchical structures with different types of dynamics, or causations, at different levels. We use the Tangled Nature model to discuss the co-evolutionary aspects connecting the microscopic level of the individual to the macroscopic systems level. At the microscopic level the individual agent may undergo evolutionary changes due to mutations of strategies. The micro-dynamics always run at a constant rate. Nevertheless, the system's level dynamics exhibit a completely different type of intermittent abrupt dynamics where major upheavals keep throwing the system between meta-stable configurations. These dramatic transitions are described by a log-Poisson time statistics. The long time effect is a collectively adapted of the ecological network. We discuss the ecological and macroevolutionary consequences of the adaptive dynamics and briefly describe work using the Tangled Nature framework to analyse problems in economics, sociology, innovation and sustainabilityComment: Invited contribution to Focus on Complexity in European Journal of Physics. 25 page, 1 figur

Novel centromeric repetitive DNA elements reveal karyotype dynamics in polyploid sainfoin (Onobrychis viciifolia)

Polyploidy is a common feature in eukaryotes with one of paramount consequences leading to better environmental adaptation. Heterochromatin is often located at telomeres and centromeres and contains repetitive DNA sequences. Sainfoin (Onobrychis viciifolia) is an important perennial forage legume for sustainable agriculture. However, there are only a few studies on the sainfoin genome and chromosomes. In this study, novel tandem repetitive DNA sequences of the sainfoin genome (OnVi180, OnVi169, OnVi176 and OnVidimer) were characterized using bioinformatics, molecular and cytogenetic approaches. The OnVi180 and OnVi169 elements colocalized within functional centromeres. The OnVi176 and OnVidimer elements were localized in centromeric, subtelomeric and interstitial regions. We constructed a sainfoin karyotype that distinguishes the seven basic chromosome groups. Our study provides the first detailed description of heterochromatin and chromosome structure of sainfoin and proposes an origin of heterozygous ancestral genomes, possibly from the same ancestral diploid species, not necessarily from different species, or for chromosome rearrangements after polyploidy. Overall, we discuss our novel and complementary findings in a polyploid crop with unique and complex chromosomal features.Scientific and Technological Research Council of Turkey (TUBITAK) [118Z589]; European Cooperation in Science and Technology for COST Action CA16212-INDEPTH; Turkish Council of Higher Education for Graduate School; Ayhan Sahenk Foundation for Graduate School ScholarshipThe funding has been acknowledged from the following institutions: The Scientific and Technological Research Council of Turkey (TUBITAK) Project ID 118Z589; European Cooperation in Science and Technology for COST Action CA16212-INDEPTH; Turkish Council of Higher Education for Graduate School 100/2000 YOEK Program and Ayhan Sahenk Foundation for Graduate School Scholarship

High allelic diversity of the centromere-specific histone H3 (CENH3) in the legume sainfoin (Onobrychis viciifolia)

The centromere is a structurally and functionally specialized region on each eukaryotic chromosome and is essential for accurate and complete segregation of chromosomes during cell division. Centromeric nucleosomes differ from canonical nucleosomes by replacement of the histone H3 with its centromere-specific variant CENH3. CENH3 is essential for active centromeres in most eukaryotes. Homologs of CENH3 are identified in many organisms. Sainfoin (Onobrychis viciifolia) is an agriculturally important perennial forage and is a legume of the Fabaceae family. There is very limited information on the structure of the sainfoin genome and no data are available on its centromere structure. Here, we aim to characterize the sainfoin CENH3 homolog (OvCENH3). Using a sequence homology-based strategy with gene-specific primers, we were able to clone transcripts from sainfoin total RNA. The amplified clones were sequenced and compared by bioinformatics tools. Four distinct alleles of OvCENH3 were detected. Our study provides the first structural features on sainfoin centromeres with a possible allotetraploid origin for sainfoin. We discuss and compare our findings with that for other important legume species.Scientific and Technological Research Council of Turkey (TuBTAK) under COST Action [118Z589, CA16212]; Ayhan Sahenk Foundation; 100/2000 YoK ProgramWe wish to thank Prof. Ingo Schubert and anonymous reviewers for editing of the manuscript and critical suggestions. This project was funded by The Scientific and Technological Research Council of Turkey (TuBTAK) Project ID 118Z589 under the COST Action CA16212-INDEPTH (Impact of Nuclear Domains On Gene Expression and Plant Traits). SD has a fellowship from the 100/2000 YoK Program and Ayhan Sahenk Foundation

Bonded straight and helical flagellar filaments form ultra-low-density glasses

We study how the three-dimensional shape of rigid filaments determines the microscopic dynamics and macroscopic rheology of entangled semi-dilute Brownian suspensions. To control the filament shape we use bacterial flagella, which are micron-long helices assembled from flagellin monomers. We compare the dynamics of straight rods, helical filaments, and shape diblock copolymers composed of seamlessly joined straight and helical segments. Caged by their neighbors, straight rods preferentially diffuse along their long axis, but exhibit significantly suppressed rotational diffusion. Entangled helical filaments escape their confining tube by corkscrewing through the dense obstacles created by other filaments. By comparison, the adjoining segments of the rod-helix shape-diblocks suppress both the translation and the corkscrewing dynamics, so that shape-diblocks become permanently jammed at exceedingly low densities. We also measure the rheological properties of semi-dilute suspensions and relate their mechanical properties to the microscopic dynamics of constituent filaments. In particular, rheology shows that an entangled suspension of shape rod-helix copolymers forms a low-density glass whose elastic modulus can be estimated by accounting for how shear deformations reduce the entropic degrees of freedom of constrained filaments. Our results demonstrate that the three-dimensional shape of rigid filaments can be used to design rheological properties of semi-dilute fibrous suspensions.Comment: 24 pages, 7 figure

Novel Centromeric and Subtelomeric Repetitive DNA Sequences for Karyotyping the Bambara Groundnut (Vigna subterranea L. Verdc.)

Bambara groundnut (Vigna subterranea L. Verdc.) is an un-derutilized minor legume crop with climate resilience and great potential use in world agriculture. This study aimed to cytogenetically characterize the genome and chromosome properties of Bambara groundnut. We cloned, sequenced, and mapped a 50-bp centromere-specific tandem repeat on all chromosomes. In addition, a 400-bp subtelomeric repeat was discovered and mapped on a single pair of chromosomes. A Bambara groundnut karyotype was constructed using these novel repeats along with ribosomal RNA genes (45S and 5S) and telomeric DNA sequences. This study provides the first analysis of the genome and chromosome properties of Bambara groundnut. We discuss our findings in relation to genetic improvement of Bambara groundnut and centromere evolution in legume species.Ayhan Sahenk FoundationDoctoral scholarships for S.D.K.OE. and H.Y. are awarded by Ayhan Sahenk Foundation. There are no other funding sources to report

Geçmişten günümüze genetik ve kromozom mühendisliği çalışmalarının sürdürülebilir tarım ve bitki islahına katkısı

It is predicted that by 2050 the population will reach 9.2 billion and the demands for equal and basic needs must be met worldwide. Until today, various studies have been carried out to increase agricultural production. However, new technologies and methods that ensure higher Abstract: It is predicted that by 2050 the population will reach 9.2 billion and the demands for equal and basic needs must be met worldwide. Until today, various studies have been carried out to increase agricultural production. However, new technologies and methods that ensure higher yields per unit area should be developed and integrated into plant breeding programs. While contradictory practices to sustainable agriculture should still be reduced, productivity in agriculture can be increased by understanding plant biology, evolution, and genome structure. In addition, efficient use of genetic diversity, adaptation of knowledge from model plants to breeding programs, and the genetic resource potential of orphan plants will contribute to the development of new genotypes. So far, modern technologies such as gene transformation, DNA sequencing, genome mapping and genome editing have played an active role in understanding the genome structure in plants. Numerous chromosome engineering methods such as FISH, GISH, chromosome truncation via telomeres, mini chromosomes, detection of syntenic chromosomal loci between organisms, discovery of repetitive DNA elements and the use of structural CENH3 protein will also be a driving force in agricultural development. Agricultural research, benefiting from the advances in basic sciences, will support achieving the desired goal in the long term. Potentially, chromosome engineering methods contribute to the increase of agricultural production in the future. In this review article, we aim to create a discussion platform for researchers by providing unique perspectives synthesized from agriculture, breeding and genetics and bringing together the current and rapidly developing interdisciplinary thematic studies. © 2021, Centenary University. All rights reserved.European Cooperation in Science and Technology, COST, (CA16212); Türkiye Bilimsel ve Teknolojik Araştirma Kurumu, TÜBITAK, (118O670, 118Z589

Elucidation of key odorants and sensory propertiesof five different extra virgin olive oils from Turkey by GC-MS-Olfactometry

The present study investigates the aroma, key odorants and sensory profile of extra virgin olive oils from five well-known Turkish cultivars. The aromatic extract obtained by the purge and trap extraction system, according to a sensory analysis, resembled the odor of olive oil. A total of 22, 21, 18, 22 and 21 aroma-active compounds were detected in the extracts of Ayvalık, Memecik, Gemlik, Sarı Ulak and Beylik olive oils, respectively. The results show that Ayvalık has the highest flavor dilution (FD) value of 1024 with hexanal, (E)-2-hexenal and α-farnesene. Memecik has the highest FD value at 2048 with (E)-2-hexenal. Gemlik has the highest FD value of 1024 with (Z)-3-hexenyl acetate, (E)-2-hexen-1-ol and α-farnesene. Sarı Ulak has the highest FD value at 2048 with (E)-2-hexenal. Beylik has the highest FD value of 2048 with (E)-2-hexenal and hexanal. All cultivars represent the characteristic green, cut-grass, fruity odor notes

Magnetoelectric Effect in Hydrogen Harvesting: Magnetic Field as a Trigger of Catalytic Reactions (Adv. Mater. 19/2022)

Magnetic fields have been regarded as an additional stimulus for electro- and photocatalytic reactions, but not as a direct trigger for catalytic processes. Multiferroic/magnetoelectric materials, whose electrical polarization and surface charges can be magnetically altered, are especially suitable for triggering and control of catalytic reactions solely with magnetic fields. Here, we demonstrate that magnetic fields can be employed as an independent input energy source for hydrogen harvesting by means of the magnetoelectric effect. Composite multiferroic CoFe2O4-BiFeO3 core-shell nanoparticles act as catalysts for the hydrogen evolution reaction (HER) that is triggered when an alternating magnetic field is applied to an aqueous dispersion of the magnetoelectric nanocatalysts. Based on density functional calculations, we propose that the hydrogen evolution is driven by changes in the ferroelectric polarization direction of BiFeO3 caused by the magnetoelectric coupling. We believe our findings will open new avenues towards magnetically induced renewable energy harvesting