Monomer Length Research Articles

Self-Assembly of Chemically Programmed Amphiphiles into Aqueous Nanotubes with a Lipophilic Lumen.

The creation of complex hollow nanostructures with precise control over size and shape represents a great challenge in supramolecular soft materials. Here, we have further developed a bioinspired methodology for the formation of aqueous nanotubes of well-defined dimensions and pore coating through the self-assembly of amphiphiles that are chemically programmed with complementary nucleobases. These nanotubes are endowed with a hydrophobic lumen, whose diameter can be expanded as a function of the monomer length, in which apolar dyes can be efficiently encapsulated.

Self-assembled oligomeric structures of an asymmetric molecular linker; 4-isocyanophenyl disulfide on Au(111)

Para-substituted benzenes, such as 1,4-benzene dithiol and 1,4-phenyl diisocyanide, have been observed to oligomerize on the Au(111) surface by incorporating gold adatoms extracted from the substrate. This work investigates if oligomerization occurs for an analogous but asymmetric linker, 4-isocyanophenyl disulfide (ICPD) on Au(111). This molecule is comprised of both disulfide and isocyanide terminal groups attached to the phenyl ring. The resulting surface structures formed on Au(111) following exposure to ICPD are studied using scanning tunneling microscopy (STM). 1,4-isocyanophenyl thiolate (ICPT), formed through scission of ICPD’s disulfide bond, was also found to oligomerize on the surface, and potential oligomer structures and binding geometries are proposed with the aid of density functional theory (DFT) calculations, along with simulated STM images of the resulting structures. It is observed in this work that ICPT forms oligomeric structures that cover large sections of the substrate and appear to create etch pits resulting from gold atom extraction. Numerous potential binding geometries are investigated based on the distances between substrate gold atom adsorption sites compared to the monomer length. Selected structural candidates were optimized using DFT and were used to generate simulated STM images using the Tersoff–Hamann method to compare with experiment. It has been shown previously that the isocyanide- and thiol-connected oligomers conduct electrons, suggesting the possibility that the asymmetric oligomers found here might form the basis for fabricating molecular diodes.

3D-printing of biomass furan-based polyesters with robust mechanical performance and shape memory property

3D-printing provides a feasible technique for realizing new materials into structural and intelligent parts. In this work, biomass furan-based polyesters poly (ethylene furanoate) (PEF), poly (trimethylene furanoate) (PTF), and poly (butylene furanoate) (PBF) were successfully synthesized in a 5 L reactor through the melt polycondensation process and fabricated into 3D-printing feedstocks. It was demonstrated that the three furan-based polyesters were additively-manufactured into complicated structures. Besides, the mechanical and thermal properties of furan-based polyesters could be tailored by the chain length of diol monomer. The mechanical performance of 3D-printed PEF, PTF and PBF were characterized and compared with commercial filaments. The tensile strength of PEF and PTF could reach 74.6 and 63.8 MPa respectively, which exhibited superior tensile property to poly(ether-ether-ketone) (PEEK), polyamide (PA) and polylactic acid (PLA). Meanwhile, the compression results demonstrated that the PEF and PTF possessed comparable energy absorption capacity with PEEK and PLA respectively, which indicated excellent mechanical properties of furan-based polyesters. It was interesting to find that the 3D-printed structures including solid cube, bionic flower and lattice structures were employed to prove that the PTF possessed excellent shape memory properties. Therefore, the proposed biomass furan-based polymers would offer more freedom in the field of 3D-printing.

Peptonics: A new family of cell-protecting surfactants for the recombinant expression of therapeutic proteins in mammalian cell cultures.

Polymer surfactants are key components of cell culture media as they prevent mechanical damage during fermentation in stirred bioreactors. Among cell-protecting surfactants, Pluronics are widely utilized in biomanufacturing to ensure high cell viability and productivity. Monodispersity of monomer sequence and length is critical for the effectiveness of Pluronics-since minor deviations can damage the cells-but is challenging to achieve due to the stochastic nature of polymerization. Responding to this challenge, this study introduces Peptonics, a novel family of peptide and peptoid surfactants whose monomer composition and sequence are designed to achieve high cell viability and productivity at a fraction of chain length and cost of Pluronics. A designed ensemble of Peptonics was initially characterized via light scattering and tensiometry to select sequences whose phase behavior and tensioactivity align with those of Pluronics. Selected sequences were evaluated as cell-protecting surfactants using Chinese hamster ovary (CHO) cells expressing therapeutic monoclonal antibodies (mAb). Peptonics IH-T1010, ih-T1010, and ih-T1020 afforded high cell density (up to 3×107 cellsmL-1 ) and viability (up to 95% within 10 days of culture), while reducing the accumulation of ammonia (a toxic metabolite) by ≈10% compared to Pluronic F-68. Improved cell viability afforded high mAb titer (up to 5.5mgmL-1 ) and extended the production window beyond 14 days; notably, Peptonic IH-T1020 decreased mAb fragmentation and aggregation ≈5%, and lowered the titer of host cell proteins by 16% compared to Pluronic F-68. These features can improve significantly the purification of mAbs, thus increasing their availability at a lower cost to patients.

The nature and organization of satellite DNAs in Petunia hybrida, related, and ancestral genomes.

The garden petunia, Petunia hybrida (Solanaceae) is a fertile, diploid, annual hybrid species (2n=14) originating from P. axillaris and P. inflata 200 years ago. To understand the recent evolution of the P. hybrida genome, we examined tandemly repeated or satellite sequences using bioinformatic and molecular cytogenetic analysis. Raw reads from available genomic assemblies and survey sequences of P. axillaris N (PaxiN), P. inflata S6, (PinfS6), P. hybrida (PhybR27) and the here sequenced P. parodii S7 (PparS7) were used for graph and k-mer based cluster analysis of TAREAN and RepeatExplorer. Analysis of repeat specific monomer lengths and sequence heterogeneity of the major tandem repeat families with more than 0.01% genome proportion were complemented by fluorescent in situ hybridization (FISH) using consensus sequences as probes to chromosomes of all four species. Seven repeat families, PSAT1, PSAT3, PSAT4, PSAT5 PSAT6, PSAT7 and PSAT8, shared high consensus sequence similarity and organisation between the four genomes. Additionally, many degenerate copies were present. FISH in P. hybrida and in the three wild petunias confirmed the bioinformatics data and gave corresponding signals on all or some chromosomes. PSAT1 is located at the ends of all chromosomes except the 45S rDNA bearing short arms of chromosomes II and III, and we classify it as a telomere associated sequence (TAS). It is the most abundant satellite repeat with over 300,000 copies, 0.2% of the genomes. PSAT3 and the variant PSAT7 are located adjacent to the centromere or mid-arm of one to three chromosome pairs. PSAT5 has a strong signal at the end of the short arm of chromosome III in P. axillaris and P.inflata, while in P. hybrida additional interstitial sites were present. PSAT6 is located at the centromeres of chromosomes II and III. PSAT4 and PSAT8 were found with only short arrays. These results demonstrate that (i) repeat families occupy distinct niches within chromosomes, (ii) they differ in the copy number, cluster organization and homogenization events, and that (iii) the recent genome hybridization in breeding P. hybrida preserved the chromosomal position of repeats but affected the copy number of repetitive DNA.

Effect of hydrophobic chain length on the properties of polycarboxylate polymeric surfactants

In this work, a series of polycarboxylate polymeric surfactants were designed and synthesized from acrylate monomers with different alkyl chain lengths (alkyl chain lengths of 1, 4, 6, 12, 18), epoxy succinic acid (ESA), acrylic acid (AA) and 2-acrylamide-2-methylpropane sulfonic acid (AMPS). Their structures were confirmed by FT-IR, 1H NMR and GPC. A series of surfactant parameters, including critical micelle concentration (CMC), minimum surface tension, surface tension reduction at critical micelle concentration (Πcmc), surface tension reduction efficiency (pC20), etc, were obtained by surface activity test. The results showed that with the increase of the alkyl chain length of acrylate, surface tension and CMC of polycarboxylate polymeric surfactants gradually decreased. When the alkyl chain length of acrylate monomer was 12, the surface tension of polycarboxylate polymeric surfactants was the lowest, which was 32.6 mN/m. The results of TG, DLS and TEM showed that with the increased of the alkyl chain length of the acrylate, the micellar size of polycarboxylate polymeric surfactants decreased regularly. Meanwhile, the foaming, wetting and emulsifying properties of polycarboxylate polymeric surfactants were positively correlated with the alkyl chain length of the acrylate. The dispersing ability of polycarboxylate polymeric surfactants for calcium carbonate was 101.5 mg/g, which can dispersed Fe2O3 fouling to less than 1 μm under the condition of 0.6 g/L.

Hydrogen-Bond-Driven Peptide Nanotube Formation: A DFT Study.

DFT calculations were carried out to examine geometries and binding energies of H-bond-driven peptide nanotubes. A bolaamphiphile molecule, consisting of two N-α amido glycylglycine head groups linked by either one CH2 group or seven CH2 groups, is used as a building block for nanotube self-assembly. In addition to hydrogen bonds between adjacent carboxy or amide groups, nanotube formation is also driven by weak C-H· · ·O hydrogen bonds between a methylene group and the carboxy OH group, and between a methylene group and an amide O=C group. The intratubular O-H· · ·O=C hydrogen bonds account for approximately a third of the binding energies. Binding energies calculated with the wB97XD/DGDZVP method show that the hydrocarbon chains play a stabilizing role in nanotube self-assembly. The shortest nanotube has the length of a single monomer and a diameter than increases with the number of monomers. Lengthening of the tubular structure occurs through intertubular O-H· · ·O=C hydrogen bonds. The average intertubular O-H· · ·O=C hydrogen bond binding energy is estimated to change with the size of the nanotubes, decreasing slightly towards some plateau value near 15 kcal/mol according to the wB97XD/DGDZVP method.

Preparation of epoxy-based silicone prepolymers with applications in UV-curable coatings

PurposeThis paper aims to investigate the effects on coatings performance in the epoxy silicone resin system owing to the existence of the different chain length of open-chain epoxy monomer. In this paper, [4-Methylphenyl-(4–(2-methylpropyl) phenyl)]iodonium as photoinitiator was added into epoxy silicone resin by ultraviolet (UV)-cured polymerization to investigate the effects on coatings performance owing to the existence of the different chain length of open-chain epoxy monomer.Design/methodology/approachA simple hydrosilylation reaction was used to synthesize epoxy-based silicone prepolymers by using hydrogen-terminated polydimethylsiloxane, 1,2-epoxy-5-hexene, 1,2-epoxy-7-octene and 1,2-epoxy-9-decene as precursors.FindingsThe results revealed that the glass transition temperatures (Tg) and hydrophobicity increased with the chain length of open-chain epoxy monomer in the UV curable epoxy-based silicone coatings, and these films had excellent heat resistance, hydrophobicity, antigraffiti and ink removal properties.Research limitations/implicationsThe cationic photocuring systems are not susceptible to the effect of oxygen inhibition. However, the limitation of cationic light curing process is that it requires a long curing time.Originality/valueThe coatings prepared via the UV curing approach can provide superior antismudge effects, and thus they are promising candidates for use in various industries, especially in fields such as antismudge coatings and antigraffiti coatings.

Fluorescent cholesteric liquid crystal polymers with dual properties: design, synthesis and characterisation

ABSTRACT In this study, we have synthesised fluorescent liquid crystal polymers with good fluorescence and optical properties through effective molecular design. Firstly, two series of cholesteric liquid crystal polymers (PN and PS series) were prepared by graft copolymerisation of cholesteric monomer(N1), monomer containing cyanobiphenyls with different length of carbon-chain (N2 and N3) and monomer containing bromine (6-Br) with polymethylhydrosiloxane chain as the polymer backbone. Secondly, we obtained fluorescent polymers RPN and RPS series by etherification reaction of PN and PS series with fluorescent monomer (F). The molecular structures and mesomorphic behaviour of monomers and polymers were characterised by usual ways. All the polymers are confirmed to consist with molecular design. The fluorescence of the polymers was investigated by fluorescence spectroscopy and fluorescent images. The fluorescence intensity of polymers is highly dependent on temperature. Fluorescent cholesteric liquid crystal polymers emitted different intensity fluorescence under ultraviolet irradiation and some regularities were summarised. RPN series with short carbon-chain meets our expectations for performance with dual effects of fluorescence and selective reflection, which were well verified. The effect of monomers with different chain lengths on the properties of fluorescent polymers has been described.

Effects of carbon chain length of acrylate monomer on sizing properties of sesbania gum-g-polyacrylate

A series of acrylate monomers with different carbon chain lengths including methyl acrylate (MA), ethyl acrylate (EA), butyl acrylate (BA) and 2-ethylhexyl acrylate (EHA) has been grafted onto molecular chains of native sesbania gum (SG) to obtain SG-g-polyacrylate with similar grafting ratios through Fenton’s initiator respectively. Effects of carbon chain length of the series of acrylates on sizing properties of the grafted SG on polyester yarn have been studied. It is found that, by grafting acrylates onto the molecular chains of SG, its sizing properties are improved markedly. Under the condition of similar grafting ratios, SG-g-PMA shows the highest apparent viscosity, tenacity of sizing film, wettability and adhesion strength to polyester fibre in all the grafted SG prepared. SG-g-PEA and SG-g-PEHA show the highest wear resistance and elongation of sizing film respectively. The polyester/cotton (65/35) warp yarns sized by SG-g-PMA, SG-g-PEHA and SG-g-PEA possess the highest tensile strength, tensile elongation and abrasion resistance respectively, in all the sized conditions. The SG grafted with acrylate monomers with different carbon chain lengths can meet various requirements in sizing polyester yarn.

Evolution of satDNAs on holocentric chromosomes: insights from hemipteran insects of the genus Mahanarva.

Satellite DNAs (satDNAs) constitute one of the main components of eukaryote genomes and are involved in chromosomal organization and diversification. Although largely studied, little information was gathered about their evolution on holocentric species, i.e., diffuse centromeres, which, due to differences in repeat organization, could result in different evolutionary patterns. Here, we combined bioinformatics and cytogenetic approaches to evaluate the evolution of the satellitomes in Mahanarva holocentric insects. In two species, de novo identification revealed a high number of satDNAs, 110 and 113, with an extreme monomer length range of 18-4228 bp. The overall abundance of satDNAs was observed to be 6.67% in M. quadripunctata and 1.98% in M. spectabilis, with different abundances for the shared satDNAs. Chromosomal mapping of the most abundant repeats of M. quadripunctata and M. spectabilis on other Mahanarva reinforced the dynamic nature of satDNAs. Variable patterns of chromosomal distribution for the satDNAs were noticed, with the occurrence of clusters on distinct numbers of chromosomes and at different positions and the occurrence of scattered signals or nonclustered satDNAs. Altogether, our data demonstrated the high dynamism of satDNAs in Mahanarva with the involvement of this genomic fraction in chromosome diversification of the genus. The general characteristics and patterns of evolution of satDNAs are similar to those observed on monocentric chromosomes, suggesting that the differential organization of genome compartments observed on holocentric chromosomes compared with monocentric chromosomes does not have a large impact on the evolution of satDNAs. Analysis of the satellitomes of other holocentric species in a comparative manner will shed light on this issue.

Satellitome Analysis on Talpa aquitania Genome and Inferences about the satDNAs Evolution on Some Talpidae.

In the genus Talpa a new species, named Talpa aquitania, has been recently described. Only cytogenetic data are available for the nuclear genome of this species. In this work, we characterize the satellitome of the T. aquitania genome that presents 16 different families, including telomeric sequences, and they represent 1.24% of the genome. The first satellite DNA family (TaquSat1-183) represents 0.558%, and six more abundant families, including TaquSat1-183, comprise 1.13%, while the remaining 11 sat-DNAs represent only 0.11%. The average A + T content of the SatDNA families was 50.43% and the median monomer length was 289.24 bp. The analysis of these SatDNAs indicated that they have different grades of clusterization, homogenization, and degeneration. Most of the satDNA families are present in the genomes of the other Talpa species analyzed, while in the genomes of other more distant species of Talpidae, only some of them are present, in accordance with the library hypothesis. Moreover, chromosomal localization by FISH revealed that some satDNAs are localized preferentially on centromeric and non-centromeric heterochromatin in T. aquitania and also in the sister species T. occidentalis karyotype. The differences observed between T. aquitania and the close relative T. occidentalis and T. europaea suggested that the satellitome is a very dynamic component of the genomes and that the satDNAs could be responsible for chromosomal differences between the species. Finally, in a broad context, these data contribute to the understanding of the evolution of satellitomes on mammals.

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Residue-residue distance information is useful for predicting tertiary structures of protein monomers or quaternary structures of protein complexes. Many deep learning methods have been developed to predict intra-chain residue-residue distances of monomers accurately, but few methods can accurately predict inter-chain residue-residue distances of complexes. We develop a deep learning method CDPred (i.e., Complex Distance Prediction) based on the 2D attention-powered residual network to address the gap. Tested on two homodimer datasets, CDPred achieves the precision of 60.94% and 42.93% for top L/5 inter-chain contact predictions (L: length of the monomer in homodimer), respectively, substantially higher than DeepHomo’s 37.40% and 23.08% and GLINTER’s 48.09% and 36.74%. Tested on the two heterodimer datasets, the top Ls/5 inter-chain contact prediction precision (Ls: length of the shorter monomer in heterodimer) of CDPred is 47.59% and 22.87% respectively, surpassing GLINTER’s 23.24% and 13.49%. Moreover, the prediction of CDPred is complementary with that of AlphaFold2-multimer.

A Pipeline NanoTRF as a New Tool for De Novo Satellite DNA Identification in the Raw Nanopore Sequencing Reads of Plant Genomes.

High-copy tandemly organized repeats (TRs), or satellite DNA, is an important but still enigmatic component of eukaryotic genomes. TRs comprise arrays of multi-copy and highly similar tandem repeats, which makes the elucidation of TRs a very challenging task. Oxford Nanopore sequencing data provide a valuable source of information on TR organization at the single molecule level. However, bioinformatics tools for de novo identification of TRs in raw Nanopore data have not been reported so far. We developed NanoTRF, a new python pipeline for TR repeat identification, characterization and consensus monomer sequence assembly. This new pipeline requires only a raw Nanopore read file from low-depth (<1×) genome sequencing. The program generates an informative html report and figures on TR genome abundance, monomer sequence and monomer length. In addition, NanoTRF performs annotation of transposable elements (TEs) sequences within or near satDNA arrays, and the information can be used to elucidate how TR–TE co-evolve in the genome. Moreover, we validated by FISH that the NanoTRF report is useful for the evaluation of TR chromosome organization—clustered or dispersed. Our findings showed that NanoTRF is a robust method for the de novo identification of satellite repeats in raw Nanopore data without prior read assembly. The obtained sequences can be used in many downstream analyses including genome assembly assistance and gap estimation, chromosome mapping and cytogenetic marker development.

Living polymerization in nano-scale volumes. Impact of process conditions on polymerization kinetics and product characteristics

Living polymerization processes, irreversible and reversible, proceeding in a large number of isolated (no mass exchange) nano-scale reactors (droplets) were modeled using stochastic (Monte Carlo) and deterministic simulations and analytical solutions of derived mathematical equations. Monomer and living unimer used as initiator were redistributed in droplets uniformly or accordingly to the Poisson distribution, resulting in nanoreactors containing a small number of growing chains. Stochasticity of reactions involving low number of molecules affects the concentration of monomer and chain length distributions in individual droplets, both differing from ones accounted in macroscopic system. The developed mathematical description, based on values of rate constants of propagation (kp) and depropagation (kd) reactions and on initial monomer and living unimer concentrations, as well as numerical simulations, allow predicting kinetics of the process and of several characteristics of the products resulting therefrom, e.g. chain length distribution. Moreover, they allow also following evolution of droplet subpopulations that differ in composition. Moreover, for the reversible process the equilibrium monomer concentration in a droplets system [M]eq can be calculated. As living ionic and coordination polymerization and the controlled radical polymerization in nano-scale dispersions are rather little explored the theoretical predictions shown in this work could facilitate their further development.

A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae.

Background Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales.FindingsUsing Oxford Nanopore Technologies, chromosome conformation capture (Hi-C), Illumina and RNA survey sequence, supported by molecular cytogenetics, we report a high-quality 481.5 Mb genome assembly with 9 pseudo-chromosomes and 36,836 genes. A total of 55% of the genome is composed of repetitive sequences with predominantly LTR-retroelements (37%) and DNA transposons (7%). The single 5S ribosomal DNA locus had an exceptionally long monomer length of 1,056 bp, more than twice that of the monomers at multiple loci in Musa. A tandemly repeated satellite (1.1% of the genome, with no similar sequence in Musa) was present around all centromeres, together with a few copies of a long interspersed nuclear element (LINE) retroelement. The assembly enabled us to characterize in detail the chromosomal rearrangements occurring between E. glaucum and the x = 11 species of Musa. One E. glaucum chromosome has the same gene content as Musa acuminata, while others show multiple, complex, but clearly defined evolutionary rearrangements in the change between x= 9 and 11.ConclusionsThe advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles, copy number variation, and a reference for structural variation available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly shows the nature of chromosomal fusion and translocation events during speciation, and features of rapid repetitive DNA change in terms of copy number, sequence, and genomic location, critical to understanding its role in diversity and evolution.

Polyimide-supported Cu/2,2,6,6-tetramethyl-1-piperidine-N-oxyl catalytic systems: Aromatic donor-acceptor interaction-directed cooperative catalysis

Non-covalent immobilization of multifunctional catalysts onto polymer supports is a promising technique to build highly efficient heterogeneous cooperative catalysts. Here, we present a strategy to build polyimide-supported Cu/2,2,6,6-tetramethyl-1-piperidine-N-oxyl (TEMPO) catalytic systems based on hydrophobic interactions and aromatic donor-acceptor interactions. Pyrene-containing catalytic species and naphthalene diimide (NDI)-based polyimides were chosen for the preparation of nanoparticle catalysts using the nanoprecipitation technique. The cooperative behaviors of catalytic components were evaluated by the catalytic activities of aerobic oxidation of benzyl alcohol (BnOH) in water. We studied the influence of effective constituent ratio of polymers, chain length of monomer, and the incorporation of a second monomer on catalytic activities. The aggregate structures were investigated by X-ray powder diffraction (XRD) patterns and small angle X-ray scattering (SAXS), and speculated to be random distributions of aromatic stacking clusters within nanoparticle catalysts. This strategy will find applications in the construction of other multifunctional heterogeneous catalysts.

Subfamily-specific differential contribution of individual monomers and the tether sequence to mouse L1 promoter activity

BackgroundThe internal promoter in L1 5’UTR is critical for autonomous L1 transcription and initiating retrotransposition. Unlike the human genome, which features one contemporarily active subfamily, four subfamilies (A_I, Gf_I and Tf_I/II) have been amplifying in the mouse genome in the last one million years. Moreover, mouse L1 5’UTRs are organized into tandem repeats called monomers, which are separated from ORF1 by a tether domain. In this study, we aim to compare promoter activities across young mouse L1 subfamilies and investigate the contribution of individual monomers and the tether sequence.ResultsWe observed an inverse relationship between subfamily age and the average number of monomers among evolutionarily young mouse L1 subfamilies. The youngest subgroup (A_I and Tf_I/II) on average carry 3–4 monomers in the 5’UTR. Using a single-vector dual-luciferase reporter assay, we compared promoter activities across six L1 subfamilies (A_I/II, Gf_I and Tf_I/II/III) and established their antisense promoter activities in a mouse embryonic fibroblast cell line and a mouse embryonal carcinoma cell line. Using consensus promoter sequences for three subfamilies (A_I, Gf_I and Tf_I), we dissected the differential roles of individual monomers and the tether domain in L1 promoter activity. We validated that, across multiple subfamilies, the second monomer consistently enhances the overall promoter activity. For individual promoter components, monomer 2 is consistently more active than the corresponding monomer 1 and/or the tether for each subfamily. Importantly, we revealed intricate interactions between monomer 2, monomer 1 and tether domains in a subfamily-specific manner. Furthermore, using three-monomer 5’UTRs, we established a complex nonlinear relationship between the length of the outmost monomer and the overall promoter activity.ConclusionsThe laboratory mouse is an important mammalian model system for human diseases as well as L1 biology. Our study extends previous findings and represents an important step toward a better understanding of the molecular mechanism controlling mouse L1 transcription as well as L1’s impact on development and disease.

Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda.

Spodoptera frugiperda (fall armyworm) is a member of the superfamily Noctuoidea that accounts for more than a third of all Lepidoptera and includes a considerable number of agricultural and forest pest species. Spodoptera frugiperda is a polyphagous species that is a significant agricultural pest worldwide, emphasizing its economic importance. Spodoptera frugiperda’s genome size, assembly, phylogenetic classification, and transcriptome analysis have all been previously described. However, the different studies reported different compositions of repeated DNA sequences that occupied the whole assembled genome, and the Spodoptera frugiperda genome also lacks the comprehensive study of dynamic satellite DNA. We conducted a comparative analysis of repetitive DNA across geographically distant populations of Spodoptera frugiperda, particularly satellite DNA, using publicly accessible raw genome data from eight different geographical regions. Our results showed that most transposable elements (TEs) were commonly shared across all geographically distant samples, except for the Maverick and PIF/Harbinger elements, which have divergent repeat copies. The TEs age analysis revealed that most TEs families consist of young copies 1–15 million years old; however, PIF/Harbinger has some older/degenerated copies of 30–35 million years old. A total of seven satellite DNA families were discovered, accounting for approximately 0.65% of the entire genome of the Spodoptera frugiperda fall armyworm. The repeat profiling analysis of satellite DNA families revealed differential read depth coverage or copy numbers. The satellite DNA families range in size from the lowest 108 bp SfrSat06-108 families to the largest (1824 bp) SfrSat07-1824 family. We did not observe a statistically significant correlation between monomer length and K2P divergence, copy number, or abundance of each satellite family. Our findings suggest that the satellite DNA families identified in Spodoptera frugiperda account for a considerable proportion of the genome’s repetitive fraction. The satellite DNA families’ repeat profiling revealed a point mutation along the reference sequences. Limited TEs differentiation exists among geographically distant populations of Spodoptera frugiperda.

Poly-L-Arginine Molecule Properties in Simple Electrolytes: Molecular Dynamic Modeling and Experiments.

Physicochemical properties of poly-L-arginine (P-Arg) molecules in NaCl solutions were determined by molecular dynamics (MD) modeling and various experimental techniques. Primarily, the molecule conformations, the monomer length and the chain diameter were theoretically calculated. These results were used to interpret experimental data, which comprised the molecule secondary structure, the diffusion coefficient, the hydrodynamic diameter and the electrophoretic mobility determined at various ionic strengths and pHs. Using these data, the electrokinetic charge and the effective ionization degree of P-Arg molecules were determined. In addition, the dynamic viscosity measurements for dilute P-Arg solutions enabledto determine the molecule intrinsic viscosity, which was equal to 500 and 90 for ionic strength of 10−5 and 0.15 M, respectively. This confirmed that P-Arg molecules assumed extended conformations and approached the slender body limit at the low range of ionic strength. The experimental data were also used to determine the molecule length and the chain diameter, which agreed with theoretical predictions. Exploiting these results, a robust method for determining the molar mass of P-Arg samples, the hydrodynamic diameter, the radius of gyration and the sedimentation coefficient was proposed.