Concordance of the spectral properties of dorsal wing scales with the phylogeographic structure of European male Polyommatus icarus butterflies

AbstractThe males of more than 80% of the Lycaenidae species belonging to the tribe Polyommatini exhibit structural coloration on their dorsal wing surfaces. These colors have a role in reinforcement in prezygotic reproductive isolation. The species-specific colors are produced by the cellular self-assembly of chitin/air nanocomposites. The spectral position of the reflectance maximum of such photonic nanoarchitectures depends on the nanoscale geometric dimensions of the elements building up the nanostructure. Previous work showed that the coloration of male Polyommatus icarus butterflies in the Western and Eastern Palearctic exhibits a characteristic spectral difference (20 nm). We investigated the coloration and the de novo developed DNA microsatellites of 80 P. icarus specimens from Europe from four sampling locations, spanning a distance of 1621 km. Remarkably good concordance was found between the spectral properties of the blue sexual signaling color (coincident within 5 nm) and the population genetic structure as revealed by 10 microsatellites for the P. icarus species.

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Preparation, spectral properties and biological activities of 5-bromo-6-methyl-2'-deoxyuridine and 5-iodo-6-methyl-2'-deoxyuridine

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19802364 ◽

1980 ◽

Vol 45 (8) ◽

pp. 2364-2370 ◽

Cited By ~ 3

Author(s):

Antonín Holý ◽

Erik De Clercq

Keyword(s):

Antiviral Activity ◽

Spectral Properties ◽

De Novo ◽

Biological Activities ◽

Rabbit Kidney ◽

Kidney Cells ◽

Cd Spectra ◽

Methyl Derivatives ◽

Primary Rabbit

Reaction of 3',5'-di-O-benzoyl-6-methyl-2'-deoxyuridine (IIa) with elementary bromine or iodine afforded 5-halogeno derivatives IIc and IId which on methanolysis gave 5-bromo-6-methyl-2'-deoxyurine (Ic) and 5-iodo-6-methyl-2'-deoxyurine (Id), respectively. The CD spectra of Ic, Id and 6-methyl-2'-deoxyuridine (Ia) are compared and discussed with regard to determination of the nucleoside conformation. Unlike 5-bromo- and 5-iodo-2'-deoxyuridine, the 6-methyl derivatives Ic and Id exhibit neither antibacterial nor antiviral activity. Nor do they exert any antimetabolic effect on the de novo DNA synthesis in primary rabbit kidney cells.

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Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges

Animals ◽

10.3390/ani11030904 ◽

2021 ◽

Vol 11 (3) ◽

pp. 904

Author(s):

Saif ur Rehman ◽

Faiz-ul Hassan ◽

Xier Luo ◽

Zhipeng Li ◽

Qingyou Liu

Keyword(s):

Selective Breeding ◽

Reference Genome ◽

De Novo ◽

Phenotypic Diversity ◽

Molecular Data ◽

Genomic Diversity ◽

Production Performance ◽

Phylogeographic Structure ◽

Economic Significance ◽

And Performance

The buffalo was domesticated around 3000–6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.

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In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽

10.3390/ani11082226 ◽

2021 ◽

Vol 11 (8) ◽

pp. 2226

Author(s):

Sazia Kunvar ◽

Sylwia Czarnomska ◽

Cino Pertoldi ◽

Małgorzata Tokarska

Keyword(s):

Reference Genome ◽

De Novo ◽

Bos Taurus ◽

Model Organism ◽

Genotyping By Sequencing ◽

Model Organisms ◽

European Bison ◽

Model Animal ◽

Pcr Duplicates ◽

Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

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Methionine-stabilized nonclassical growth within self-assembled de novo gold nanoparticles in conjunction with secondary nucleation inhibition

10.21203/rs.3.rs-961831/v1 ◽

2021 ◽

Author(s):

Jitendra Sahu ◽

Shahbaz Lone ◽

Kalyan Sadhu

Keyword(s):

Self Assembly ◽

De Novo ◽

Noble Metal Nanoparticles ◽

Secondary Nucleation ◽

Unique Case ◽

Primary Particles ◽

Growth Reaction ◽

Aurophilic Interaction ◽

Key Steps

Abstract The key steps for seed mediated growth of noble metal nanoparticles involve primary and secondary nucleation, which depends upon the energy barrier and ligand supersaturation standards of the medium. Herein we report the unique case of methionine (Met) controlled growth reaction, which rather proceeds via impeding secondary nucleation in presence of citrate stabilized gold nanoparticle (AuNP). The interaction between freshly generated Au+ and thioether group of Met in the medium restricts the secondary nucleation process involving further Au+ reduction. This incomplete conversion of Au+ results in a significant enhancement of the zeta (ζ) potential even at low concentration of Met. Furthermore, the aurophilic interaction of Au+ controls the self-assembly process of the in situ generated emissive nucleated particles. Nucleation of primary particles on seed surface, their segregation and time dependent conversion to larger particles within self-assembly confirm the nonclassical growth, which has further been explored with Met containing bio-inspired peptides.

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High light induces species specific changes in the membrane lipid composition of Chlorella

Biochemical Journal ◽

10.1042/bcj20200160 ◽

2020 ◽

Vol 477 (13) ◽

pp. 2543-2559

Author(s):

Janka Widzgowski ◽

Alexander Vogel ◽

Lena Altrogge ◽

Julia Pfaff ◽

Heiko Schoof ◽

...

Keyword(s):

Cell Membranes ◽

De Novo ◽

Algal Cell ◽

Isotopic Labeling ◽

Biochemical Properties ◽

Membrane Lipid ◽

Light Conditions ◽

Hydrophobic Barrier ◽

Glycerolipid Composition ◽

Species Specific

Algae have evolved several mechanisms to adjust to changing environmental conditions. To separate from their surroundings, algal cell membranes form a hydrophobic barrier that is critical for life. Thus, it is important to maintain or adjust the physical and biochemical properties of cell membranes which are exposed to environmental factors. Especially glycerolipids of thylakoid membranes, the site of photosynthesis and photoprotection within chloroplasts, are affected by different light conditions. Since little is known about membrane lipid remodeling upon different light treatments, we examined light induced alterations in the glycerolipid composition of the two Chlorella species, C. vulgaris and C. sorokiniana, which differ strongly in their ability to cope with different light intensities. Lipidomic analysis and isotopic labeling experiments revealed differences in the composition of their galactolipid species, although both species likely utilize galactolipid precursors originated from the endoplasmic reticulum. However, in silico research of de novo sequenced genomes and ortholog mapping of proteins putatively involved in lipid metabolism showed largely conserved lipid biosynthesis pathways suggesting species specific lipid remodeling mechanisms, which possibly have an impact on the response to different light conditions.

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De novo centriole formation in human cells is error-prone and does not require SAS-6 self-assembly

eLife ◽

10.7554/elife.10586 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 27

Author(s):

Won-Jing Wang ◽

Devrim Acehan ◽

Chien-Han Kao ◽

Wann-Neng Jane ◽

Kunihiro Uryu ◽

...

Keyword(s):

Self Assembly ◽

De Novo ◽

Human Cells ◽

De Novo Synthesis ◽

Current Paradigm

Vertebrate centrioles normally propagate through duplication, but in the absence of preexisting centrioles, de novo synthesis can occur. Consistently, centriole formation is thought to strictly rely on self-assembly, involving self-oligomerization of the centriolar protein SAS-6. Here, through reconstitution of de novo synthesis in human cells, we surprisingly found that normal looking centrioles capable of duplication and ciliation can arise in the absence of SAS-6 self-oligomerization. Moreover, whereas canonically duplicated centrioles always form correctly, de novo centrioles are prone to structural errors, even in the presence of SAS-6 self-oligomerization. These results indicate that centriole biogenesis does not strictly depend on SAS-6 self-assembly, and may require preexisting centrioles to ensure structural accuracy, fundamentally deviating from the current paradigm.

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Species-Specific Marker Discovery in Tilapia

Scientific Reports ◽

10.1038/s41598-019-48339-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 9

Author(s):

Mochamad Syaifudin ◽

Michaël Bekaert ◽

John B. Taggart ◽

Kerry L. Bartie ◽

Stefanie Wehner ◽

...

Keyword(s):

Phylogenetic Trees ◽

Restriction Site ◽

De Novo ◽

Snp Markers ◽

Specific Marker ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Species Analysis ◽

Species Specific ◽

Marker Discovery

Abstract Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.

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Capacity of the Golgi Apparatus for Biogenesis from the Endoplasmic Reticulum

Molecular Biology of the Cell ◽

10.1091/mbc.e03-06-0437 ◽

2003 ◽

Vol 14 (12) ◽

pp. 5011-5018 ◽

Cited By ~ 62

Author(s):

Sapna Puri ◽

Adam D. Linstedt

Keyword(s):

Endoplasmic Reticulum ◽

Golgi Apparatus ◽

Self Assembly ◽

De Novo ◽

Brefeldin A ◽

The Other ◽

Matrix Proteins ◽

Er Export ◽

Golgi Matrix

It is unclear whether the mammalian Golgi apparatus can form de novo from the ER or whether it requires a preassembled Golgi matrix. As a test, we assayed Golgi reassembly after forced redistribution of Golgi matrix proteins into the ER. Two conditions were used. In one, ER redistribution was achieved using a combination of brefeldin A (BFA) to cause Golgi collapse and H89 to block ER export. Unlike brefeldin A alone, which leaves matrix proteins in relatively large remnant structures outside the ER, the addition of H89 to BFA-treated cells caused ER accumulation of all Golgi markers tested. In the other, clofibrate treatment induced ER redistribution of matrix and nonmatrix proteins. Significantly, Golgi reassembly after either treatment was robust, implying that the Golgi has the capacity to form de novo from the ER. Furthermore, matrix proteins reemerged from the ER with faster ER exit rates. This, together with the sensitivity of BFA remnants to ER export blockade, suggests that presence of matrix proteins in BFA remnants is due to cycling via the ER and preferential ER export rather than their stable assembly in a matrix outside the ER. In summary, the Golgi apparatus appears capable of efficient self-assembly.

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Interfacial zippering-up of coiled-coil protein filaments

Physical Chemistry Chemical Physics ◽

10.1039/c5cp05938k ◽

2015 ◽

Vol 17 (46) ◽

pp. 31055-31060 ◽

Cited By ~ 6

Author(s):

Emiliana De Santis ◽

Valeria Castelletto ◽

Maxim G. Ryadnov

Keyword(s):

Self Assembly ◽

De Novo ◽

Coiled Coil ◽

Morphological Control

A de novo self-assembly topology for engineering protein nanostructures under morphological control is reported.

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MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems

Nucleic Acids Research ◽

10.1093/nar/gkaa200 ◽

2020 ◽

Vol 48 (9) ◽

pp. 5135-5146 ◽

Cited By ~ 7

Author(s):

Christopher Maffeo ◽

Aleksei Aksimentiev

Keyword(s):

Self Assembly ◽

De Novo ◽

Dna Nanotechnology ◽

Equilibrium Structure ◽

Molecular Graphics ◽

Structure And Dynamics ◽

Self Assembled ◽

Actual Shape ◽

And Function ◽

Assembly Principles

Abstract Although the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of experimental characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resolution simulation framework, mrdna, that, in 30 min or less, can produce an atomistic-resolution structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equilibrium structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e. wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied electric field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and molecular graphics tools.

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