Repeat Unit Length Research Articles

Structure, morphology, and properties of aliphatic polyurethane elastomers from bio‐based 1,3‐propanediol

AbstractThe utilization of biomass resources in the production of bio‐based or bio‐recycled polyurethanes (PUs) enhances the sustainable development and eco‐friendliness of PU. Herein, a series of new bio‐based aliphatic poly(propylene dicarboxylate) diols were synthesized using bio‐based 1,3‐propanediol (bio‐PDO) and aliphatic dicarboxylic acids with different chain lengths. These bio‐based polyester diols and 1,4‐butanediol (BDO) reacted with 4,4′‐dicyclohexylmethane diisocyanate to produce aliphatic PU elastomers (PUEs). The study aimed to evaluate the impact of the structure of poly(propylene dicarboxylate) diols on the architecture, morphology, mechanical properties, and degradation of PUEs, thereby expanding the application of bio‐PDO. The results indicate a strong correlation between the degree of microphase separation, tensile properties, and degradation behavior of the synthesized PUEs and the number of methylene groups in the repeating unit of the poly(propylene dicarboxylate) diols. Notably, the PUE derived from poly(propylene pimelate) diol demonstrates the highest level of microphase separation and superior elasticity properties because of the high flexibility of the polyester. On the other hand, PUE prepared from poly(propylene succinate) diol exhibits the fastest degradation performance due to its high density of ester groups. Bio‐PDO based polyester diols show significant potential as raw materials for PUEs with biodegradable and adjustable mechanical properties.Highlights Poly(propylene dicarboxylate) diols were prepared from bio‐based 1,3‐propanediol. The poly(propylene dicarboxylate) diols based polyurethane elastomers (PUEs) have high tensile strength (>22 MPa) and elongation at break (>920%). The morphology, mechanical properties and degradation of PUEs are highly related to the structure of the poly(propylene dicarboxylate) diols. The increasing repeating unit length of the poly(propylene dicarboxylate) diols increases elastic recovery of PUEs.

Specific Patterns in Correlations of Super-Short Tandem Repeats (SSTRs) with G+C Content, Genic and Intergenic Regions, and Retrotransposons on All Human Chromosomes.

The specific characteristics of k-mer words (2 ≤ k ≤ 11) regarding genomic distribution and evolutionary conservation were recently found. Among them are, in high abundance, words with a tandem repeat structure (repeat unit length of 1 bp to 3 bp). Furthermore, there seems to be a class of extremely short tandem repeats (≤12 bp), so far overlooked, that are non-random-distributed and, therefore, may play a crucial role in the functioning of the genome. In the following article, the positional distributions of these motifs we call super-short tandem repeats (SSTRs) were compared to other functional elements, like genes and retrotransposons. We found length- and sequence-dependent correlations between the local SSTR density and G+C content, and also between the density of SSTRs and genes, as well as correlations with retrotransposon density. In addition to many general interesting relations, we found that SINE Alu has a strong influence on the local SSTR density. Moreover, the observed connection of SSTR patterns to pseudogenes and -exons might imply a special role of SSTRs in gene expression. In summary, our findings support the idea of a special role and the functional relevance of SSTRs in the genome.

High-throughput experimentation for discovery of biodegradable polyesters

The consistent rise of plastic pollution has stimulated interest in the development of biodegradable plastics. However, the study of polymer biodegradation has historically been limited to a small number of polymers due to costly and slow standard methods for measuring degradation, slowing new material innovation. High-throughput polymer synthesis and a high-throughput polymer biodegradation method are developed and applied to generate a biodegradation dataset for 642 chemically distinct polyesters and polycarbonates. The biodegradation assay was based on the clear-zone technique, using automation to optically observe the degradation of suspended polymer particles under the action of a single Pseudomonas lemoignei bacterial colony. Biodegradability was found to depend strongly on aliphatic repeat unit length, with chains less than 15 carbons and short side chains improving biodegradability. Aromatic backbone groups were generally detrimental to biodegradability; however, ortho- and para-substituted benzene rings in the backbone were more likely to be degradable than metasubstituted rings. Additionally, backbone ether groups improved biodegradability. While other heteroatoms did not show a clear improvement in biodegradability, they did demonstrate increases in biodegradation rates. Machine learning (ML) models were leveraged to predict biodegradability on this large dataset with accuracies over 82% using only chemical structure descriptors.

Synthesis and Characterization of a One-Dimensional Malleable Spin-Crossover Polymer Complex Modified by Methoxy Polyethylene Glycol.

A novel one-dimensional malleable spin-crossover (SCO) complex {[Fe(MPEG-trz)3](BF4)2} has been successfully synthesized by molecular self-assembly between 4-amino-1,2,4-triazoles (MPEG-trz) grafted with a long flexible chain methoxy polyethylene glycol (MPEG) and metallic complex Fe(BF4)2•6H2O. The detailed structure information was illustrated by using FT-IR and 1H NMR measurements, while the physical behaviors of the malleable SCO complexes were systematically investigated by using magnetic susceptibility measurements using superconductivity quantum interference device (SQUID) and differential scanning calorimetry (DSC). This new metallopolymer exhibits a remarkable spin crossover transition behavior, between two spin quantum states (Fe2+ ions): high spin (HS) state (quintet state) and low spin (LS) state (singlet state), at a specific critical temperature with a slender hysteresis loop of 1 K. DFT computations revealed the partial rules of HOMO-LUMO energy levels and spin density distributions of different four-position substituted [Fe(1,2,4-triazole)3]2+ derivatives with different length of repeat units in polymer complexes. This can go a step further to depict the spin and magnetic transition behaviors of SCO polymer complexes. Furthermore, the coordination polymers possess an excellent processability due to an outstanding malleability, which can be easily shaped into a polymer film with spin magnetic switching properties.

Solvent-soluble thiophene-benzene based electrochromic polymers as electrode materials for supercapacitor

The bis(alkoxy) group para-substituted para-phenylene (p-phenylene) based conjugated polymers exhibit good electronic property due to the existence of intra-molecular non-covalent interaction between oxygen and heteroatom. However, the strong inter-molecular aggregation inhibits the ionic transport of polymer. Here, the strategy of changing side chain substitution position is employed to improve the properties of conjugated polymer. Three organic solvent-soluble conjugated polymers based on the bis(hexyloxy) group ortho-substituted p-phenylene were synthesized. The three polymers display small dihedral angles between thiophene and benzene. As the conjugated chain length of repeat units increasing, the redox potentials of polymers decrease gradually. From P1 to P2 to P3, their optical absorption regions red shift gradually, leading to neutral polymers display yellow for P1, orange for P2, magenta for P3, respectively. And the three polymers display good electrochromic properties (coloration efficiency: 641 cm2 C−1; response time: 0.2 s; optical contrast: 54%). Also, P2 possess the specific capacitance value of 170 F g−1, which is higher than that of most reported soluble conjugated polymers. Combining energy storage and electrochromic performance of the three polymers, their visualization monitor of energy storage were investigated.

Review of the Developments of Bacterial Medium-Chain-Length Polyhydroxyalkanoates (mcl-PHAs).

Synthetic plastics derived from fossil fuels—such as polyethylene, polypropylene, polyvinyl chloride, and polystyrene—are non-degradable. A large amount of plastic waste enters landfills and pollutes the environment. Hence, there is an urgent need to produce biodegradable plastics such as polyhydroxyalkanoates (PHAs). PHAs have garnered increasing interest as replaceable materials to conventional plastics due to their broad applicability in various purposes such as food packaging, agriculture, tissue-engineering scaffolds, and drug delivery. Based on the chain length of 3-hydroxyalkanoate repeat units, there are three types PHAs, i.e., short-chain-length (scl-PHAs, 4 to 5 carbon atoms), medium-chain-length (mcl-PHAs, 6 to 14 carbon atoms), and long-chain-length (lcl-PHAs, more than 14 carbon atoms). Previous reviews discussed the recent developments in scl-PHAs, but there are limited reviews specifically focused on the developments of mcl-PHAs. Hence, this review focused on the mcl-PHA production, using various carbon (organic/inorganic) sources and at different operation modes (continuous, batch, fed-batch, and high-cell density). This review also focused on recent developments on extraction methods of mcl-PHAs (solvent, non-solvent, enzymatic, ultrasound); physical/thermal properties (Mw, Mn, PDI, Tm, Tg, and crystallinity); applications in various fields; and their production at pilot and industrial scales in Asia, Europe, North America, and South America.

Estimating the elastic modulus of unidirectional over-braided multilayer composites

Unidirectional over-braiding was developed based on two-dimensional over-braiding. Unidirectional over-braided multilayer composites have excellent mechanical properties and broad application prospects. It is necessary to estimate accurately the elastic modulus of unidirectional over-braided multilayer composites. In this study, the representative unit cell geometry model of unidirectional over-braided multilayer composites was established. As the braid angle increased from the first to the last layer, two model analytical methods were proposed to predict the elastic modulus of unidirectional over-braided multilayer composites. The prediction results of the two methods had good correlation with the experimental results. The smaller the increment of the braid angle from the first to the last layer, the smaller the difference between the results of the two methods. As a result of the increase in undulation amplitude, the longitudinal modulus of two-dimensional over-braided multilayer composites showed a decrease (7.94%) in comparison to the unidirectional over-braided multilayer composites. In over-braided multilayer composites, the outer layer compacted the inner layer due to the braid tension. In unidirectional over-braided multilayer composites, the interaction between layers could be ignored. In two-dimensional over-braided multilayer composites, the inner layer was obviously compacted by the outer layer. However, as the amplitude and length of the undulation repeat unit of the braided yarn were not affected by the compaction, the reduction in the longitudinal modulus of two-dimensional over-braided multilayer composites caused by compaction was very slight.

Cross-sectional Neuromuscular Phenotyping Study of Patients With Arhinia With SMCHD1 Variants.

Facioscapulohumeral muscular dystrophy type 2 (FSHD2) and arhinia are 2 distinct disorders caused by pathogenic variants in the same gene: SMCHD1. The mechanism underlying this phenotypic divergence remains unclear. In this study, we characterize the neuromuscular phenotype of individuals with arhinia caused by SMCHD1 variants and analyze their complex genetic and epigenetic criteria to assess their risk for FSHD2. Eleven individuals with congenital nasal anomalies, including arhinia, nasal hypoplasia, or anosmia, underwent a neuromuscular examination, genetic testing, muscle ultrasound, and muscle MRI. Risk for FSHD2 was determined by combined genetic and epigenetic analysis of 4q35 haplotype, D4Z4 repeat length, and methylation profile. We also compared expression levels of pathogenic DUX4 mRNA in primary myoblasts or dermal fibroblasts (upon myogenic differentiation or epigenetic transdifferentiation, respectively) in these individuals vs those with confirmed FSHD2. Among the 11 individuals with rare, pathogenic, heterozygous missense variants in exons 3-11 of SMCHD1, only a subset (n = 3/11; 1 male, 2 female; age 25-51 years) met the strict genetic and epigenetic criteria for FSHD2 (D4Z4 repeat unit length <21 in cis with a 4qA haplotype and D4Z4 methylation <30%). None of the 3 individuals had typical clinical manifestations or muscle imaging findings consistent with FSHD2. However, the patients with arhinia meeting the permissive genetic and epigenetic criteria for FSHD2 displayed some DUX4 expression in dermal fibroblasts under the epigenetic de-repression by drug treatment and in the primary myoblasts undergoing myogenic differentiation. In this cross-sectional study, we identified patients with arhinia who meet the full genetic and epigenetic criteria for FSHD2 and display the molecular hallmark of FSHD-DUX4 de-repression and expression in vitro-but who do not manifest with the typical clinicopathologic phenotype of FSHD2. The distinct dichotomy between FSHD2 and arhinia phenotypes despite an otherwise poised DUX4 locus implies the presence of novel disease-modifying factors that seem to operate as a switch, resulting in one phenotype and not the other. Identification and further understanding of these disease-modifying factors will provide valuable insight with therapeutic implications for both diseases.

Polymorphism of microsatellite markers linked with &lt;i&gt;Rf1&lt;/i&gt; and &lt;i&gt;Pl5/Pl8&lt;/i&gt; loci in sunflower &lt;i&gt;Helianthus annuus&lt;/i&gt; L.

Background. Microsatellite (SSR) markers are an effective tool for certifying collections of plant genetic resources, as well as for identifying genes that determine valuable biological and agronomic traits. The knowledge of their polymorphism is important for characterizing genetic diversity within the sunflower (Helianthus annuus L.) collection. The present study was aimed at analyzing nucleotide polymorphism of SSR-markers linked with the genes for fertility restoration (Rf1) and downy mildew resistance (Pl5/Pl8). Materials and methods. The material included 84 self-pollinated lines of VIR sunflower genetic collection, F1 and F2 hybrids from crosses between fertile lines VIR 365 and RIL130, and offspring from test crosses. Polymorphism of SSR markers ORS224, ORS511, ORS799 and НА4011 was studied by means of PCR analysis. To determine the microsatellite structure and variability, the amplified fragments were cloned and sequenced. Results. The unique alleles which differed from the typical ones (characteristic for most genotypes) were revealed in the ORS224 marker locus of four lines, and the unique alleles in the ORS511 locus were observed in 10 lines. The ORS511 unique allele of line VIR 365 included two 161 and 240 bp fragments, while line RIL130 was characterized by a typical 159 bp fragment. The profiles of typical and unique markers were inherited as allelic variants of the same locus in F2 of (VIR 365 × RIL130) and a population from VIR 111A × (VIR 365 × RIL130). The nucleotide sequences of unique alleles differed from typical allelic variants in the length and number of repeat units (GA in ORS224 and AT/GT in ORS511), and also by the presence of indels and nucleotide substitutions. Differences in length of НА4011 marker 240 and 200 bp allele variants were caused by 80, 47 and 44 bp indels. Conclusions. A number of lines in the VIR sunflower genetic collection are marked by the unique alleles of microsatellite loci ORS224 and ORS511, which differ from the frequently occurring variants in the length and number of repeat units, as well as in the presence of indels and nucleotide substitutions. Polymorphism of allele variants of HA4011 microsatellite is associated with the presence of indels of 80, 47 and 4 bp.

Molecular and FISH analysis of 45S rDNA on BAC molecule of Saccharina japonica

IGS is abundant in polymorphism, which is widely used in the analysis of intraspecific genetic diversity and phylogenetic relationships among geographical populations. In this study, the 45S rDNA repeat unit of Saccharina japonica was obtained for the first time by BAC clone sequencing. The total length of the 45S rDNA repeat unit of S. japonica was 8 995 bp, including 5 420 bp of 18S-5.8S–25S rDNA, and 3 575 bp of IGS (Intergenic Spacer), with the GC content of 51.4 %. The IGS was composed of a 465 bp of 3′-outer transcribed spacer (ETS), an 874 bp 5′-ETS, and a 2 236 bp non-transcribed spacer (NTS), with the GC content of 50.1 %. Fiber-FISH (fiber-fluorescence in situ hybridization) analysis of the distribution of 45S rDNA repeat units on the bacterial artificial chromosome illustrated that each fiber had at least five continuously moniliform hybridization signal points. This study provided a new candidate molecular marker for detecting intraspecific polymorphisms of S. japonica. In addition, the successful fiber-FISH analysis of the 45S rDNA on BAC molecule would contribute to the construction of the physical map and map-based cloning of this kelp.

Five Mitochondrial Genomes of the Genus Eysarcoris Hahn, 1834 with Phylogenetic Implications for the Pentatominae (Hemiptera: Pentatomidae).

Simple SummaryPentatominae is the largest subfamily in the Pentatomidae, and most of its species are considered important agricultural pests. The phylogenetic relationships of tribes within Pentatominae remain controversial despite the fact that many studies have been performed using various molecular markers. In this study, five mitogenomes of the genus Eysarcoris were sequenced and analyzed, and the phylogenetic relationships of tribes within Pentatominae were reconstructed. The gene arrangement of the five mitochondrial genomes were found to be conserved and identical to other heteropteran mitogenomes. Differences in start codon usage and tandem repeats within control regions were found between E. gibbosus and the other four Eysarcoris species. In addition, the phylogenetic analyses showed that E. gibbosus is the first diverging clade within Eysarcorini. The results support the proposal to transfer E. gibbosus to the Stagonomus, another genus of Eysarcorini. Our results clarified the phylogenetic relationships among tribes of Pentatominae and laid a foundation for the further studies of Pentatominae.Four complete mitogenomes of Eysarcoris rosaceus, E. montivagus, E. gibbosus, E. annamita and one near-complete mitochondrial genome of E. ventralis were sequenced and used to explore the phylogenetic relationships of tribes within the subfamily Pentatominae. The mitogenomes range from 15,422 to 16,043 base pairs (bp) in length and encode 37 genes, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes (21 in E. ventralis), and a control region. Similar to other heteropteran species, the AT contents of the sequenced species were higher than their GC contents. The most frequently used start/stop codon was ATN/TAA. GTG was only found in atp6 and atp8 of E. gibbosus. All transfer RNA genes (tRNAs) exhibit the typical cloverleaf secondary structure, except for the trnS1 and trnV, which lacks the stem of the DHU arm. The length and copy number of repeat units were conserved within Eysarcoris, with the exception of E. gibbosus. Phylogenetic analyses based on mitogenomes using both maximum likelihood (ML) and Bayesian inference (BI) methods strongly supported the relationship among tribes within Pentatominae and confirmed that Graphosoma should be an intermediate lineage of Pentatominae. The relationship between Eysarcoris and Carbula was strongly supported and combined with our previous geometric morphometrics and chromosomal studies, suggest the Eysarcoris should belong to the tribe Eyasrcorini. This work will help to enhance our understanding of mitochondrial genomic evolution and phylogenetic relationships in Pentatominae.

A crucial residue in the hydrophobic core of the solenoid structure of leucine rich repeats

Leucine rich repeats (LRRs) with 20–30 residues form a super helix arrangement. Individual LRRs are separated into a highly conserved segment with a highly conserved (HCS) and a variable segment (VS). In LRRs short β-strands in HCS stack in parallel, while VS adopts various secondary structures. Among eleven classes recognized, only RI-like, Cysteine-containing (CC), and GALA classes adopt an α-helix. However, the repeat unit lengths are usually different from each other. We performed some analyses based on the atomic coordinates in the known LRR structures. In the VS consensuses of the three classes, position 8 in the VS part is, in common, occupied by conserved aliphatic residue adopting an α-helix. This aliphatic residue is near to the two conserved hydrophobic residues at position 4 (in the center of β-strands) in two adjacent HCS parts. The conserved aliphatic residue plays a crucial role to preserve two parallel β-strands.

Genome-wide survey of tandem repeats by nanopore sequencing shows that disease-associated repeats are more polymorphic in the general population

BackgroundTandem repeats are highly mutable and contribute to the development of human disease by a variety of mechanisms. It is difficult to predict which tandem repeats may cause a disease. One hypothesis is that changeable tandem repeats are the source of genetic diseases, because disease-causing repeats are polymorphic in healthy individuals. However, it is not clear whether disease-causing repeats are more polymorphic than other repeats.MethodsWe performed a genome-wide survey of the millions of human tandem repeats using publicly available long read genome sequencing data from 21 humans. We measured tandem repeat copy number changes using tandem-genotypes. Length variation of known disease-associated repeats was compared to other repeat loci.ResultsWe found that known Mendelian disease-causing or disease-associated repeats, especially CAG and 5′UTR GGC repeats, are relatively long and polymorphic in the general population. We also show that repeat lengths of two disease-causing tandem repeats, in ATXN3 and GLS, are correlated with near-by GWAS SNP genotypes.ConclusionsWe provide a catalog of polymorphic tandem repeats across a variety of repeat unit lengths and sequences, from long read sequencing data. This method especially if used in genome wide association study, may indicate possible new candidates of pathogenic or biologically important tandem repeats in human genomes.

Shrinking of repeating unit length in leucine-rich repeats from double-stranded DNA viruses.

Leucine-rich repeats (LRRs) are present in over 563,000 proteins from viruses to eukaryotes. LRRs repeat in tandem and have been classified into fifteen classes in which the repeat unit lengths range from 20 to 29 residues. Most LRR proteins are involved in protein-protein or ligand interactions. The amount of genome sequence data from viruses is increasing rapidly, and although viral LRR proteins have been identified, a comprehensive sequence analysis has not yet been done, and their structures, functions, and evolution are still unknown. In the present study, we characterized viral LRRs by sequence analysis and identified over 600 LRR proteins from 89 virus species. Most of these proteins were from double-stranded DNA (dsDNA) viruses, including nucleocytoplasmic large dsDNA viruses (NCLDVs). We found that the repeating unit lengths of 11 types are one to five residues shorter than those of the seven known corresponding LRR classes. The repeating units of six types are 19 residues long and are thus the shortest among all LRRs. In addition, two of the LRR types are unique and have not been observed in bacteria, archae or eukaryotes. Conserved strongly hydrophobic residues such as Leu, Val or Ile in the consensus sequences are replaced by Cys with high frequency. Phylogenetic analysis indicated that horizontal gene transfer of some viral LRR genes had occurred between the virus and its host. We suggest that the shortening might contribute to the survival strategy of viruses. The present findings provide a new perspective on the origin and evolution of LRRs.

Microhomologies Are Associated with Tandem Duplications and Structural Variation in Plant Mitochondrial Genomes.

Short tandem repeats (STRs) contribute to structural variation in plant mitochondrial genomes, but the mechanisms underlying their formation and expansion are unclear. In this study, we detected high polymorphism in the nad7-1 region of the Pinus tabuliformis mitogenome caused by the rapid accumulation of STRs and rearrangements over a few million years ago. The STRs in nad7-1 have a 7-bp microhomology (TAG7) flanking the repeat array. We then scanned the mitogenomes of 136 seed plants to understand the role of microhomology in the formation of STR and mitogenome evolution. A total of 13,170 STRs were identified, and almost half of them were associated with microhomologies. A substantial amount (1,197) of microhomologies was long enough to mediate structural variation, and the length of microhomology is positively correlated with the length of tandem repeat unit. These results suggest that microhomology may be involved in the formation of tandem repeat via microhomology-mediated pathway, and the formation of longer duplicates required greater length of microhomology. We examined the abundance of these 1,197 microhomologies, and found 75% of them were enriched in the plant mitogenomes. Further analyses of the 400 prevalent microhomologies revealed that 175 of them showed differential enrichment between angiosperms and gymnosperms and 186 differed between angiosperms and conifers, indicating lineage-specific usage and expansion of microhomologies. Our study sheds light on the sources of structural variation in plant mitochondrial genomes and highlights the importance of microhomology in mitochondrial genome evolution.

Comparative genomics in phytopathogenic prokaryotes reveals the higher relative abundance and density of long-SSRs in the smallest prokaryotic genome.

Frequency and distribution of long-SSRs were studied in 18 phytopathogenic prokaryotes. Higher relative abundance of the long-SSRs was observed in phytopathogenic prokaryotes when compared to non-pathogenic control. The frequency of these SSRs was positively correlated with size and GC content of the genomes of phytopathogenic prokaryotes. Interestingly, phytopathogens with higher GC content in the genome were found to posses longer repeat motifs of SSRs, whereas those having lesser GC content were harbouring shorter repeat motifs. Higher abundance of tri- and hexa-nucleotide repeat motifs were the characteristic of actinomycetes, where as higher abundance of mono- and tetra-nucleotide repeats were the characteristic of the mollicutes. The maximum relative abundance and relative density of SSR were found in the smallest genome of host-adapted pathogen Aster yellow, however, length of microsatellite repeat units was the least. On the basis of presence of SSRs in the housekeeping genes, a phylogenetic relationship between these phytopathogenic prokaryotes was deduced and compared with the phylogeny developed based on 16S ribosomal RNA gene.

Redefining polyamide property profiles via renewable long-chain aliphatic segments: Towards impact resistance and low water absorption

A series of renewable, long-chain, fatty acid-derived polyamides (PA) ranging from PA 6,14 to PA 6,18 were synthesized via polycondensation, yielding very high molecular weights and a remarkable property profile distinct from short-chain commercial grades. Most notably, synthesized polyamides exhibited good impact resistance, excellent stiffness-to-toughness balance and very low water absorption yet high oxygen and water vapour permeability; with this property profile being exemplified by PA 6,18. The increased repeating unit length and reduced number of amide linkages able to participate in interchain hydrogen bonding imparted a strong influence on material properties. The data highlights the benefits and technical advantages of utilising long-chain polyamides, while also significantly expanding the repertoire, knowledge and property profile of the long-chain aliphatic polyamide family, and providing a basis for further development of polyamides from renewable sources.

Requirement or exclusion of inverted repeat sequences with cruciform-forming potential in Escherichia coli revealed by genome-wide analyses

Inverted repeat (IR) sequences are DNA sequences that read the same from 5′ to 3′ in each strand. Some IRs can form cruciforms under the stress of negative supercoiling, and these IRs are widely found in genomes. However, their biological significance remains unclear. The aim of the current study is to explore this issue further. We constructed the first Escherichia coli genome-wide comprehensive map of IRs with cruciform-forming potential. Based on the map, we performed detailed and quantitative analyses. Here, we report that IRs with cruciform-forming potential are statistically enriched in the following five regions: the adjacent regions downstream of the stop codon-coding sites (referred to as the stop codons), on and around the positions corresponding to mRNA ends (referred to as the gene ends), ~ 20 to ~45 bp upstream of the start codon-coding sites (referred to as the start codons) within the 5′-UTR (untranslated region), ~ 25 to ~ 60 bp downstream of the start codons, and promoter regions. For the adjacent regions downstream of the stop codons and on and around the gene ends, most of the IRs with a repeat unit length of ≥ 8 bp and a spacer size of ≤ 8 bp were parts of the intrinsic terminators, regardless of the location, and presumably used for Rho-independent transcription termination. In contrast, fewer IRs were present in the small region preceding the start codons. In E. coli, IRs with cruciform-forming potential are actively placed or excluded in the regulatory regions for the initiation and termination of transcription and translation, indicating their deep involvement or influence in these processes.

Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results

Some of the expected advantages of next generation sequencing (NGS) for short tandem repeat (STR) typing include enhanced mixture detection and genotype resolution via sequence variation among non-homologous alleles of the same length. However, at the same time that NGS methods for forensic DNA typing have advanced in recent years, many caseworking laboratories have implemented or are transitioning to probabilistic genotyping to assist the interpretation of complex autosomal STR typing results. Current probabilistic software programs are designed for length-based data, and were not intended to accommodate sequence strings as the product input. Yet to leverage the benefits of NGS for enhanced genotyping and mixture deconvolution, the sequence variation among same-length products must be utilized in some form.Here, we propose use of the longest uninterrupted stretch (LUS) in allele designations as a simple method to represent sequence variation within the STR repeat regions and facilitate – in the nearterm – probabilistic interpretation of NGS-based typing results. An examination of published population data indicated that a reference LUS region is straightforward to define for most autosomal STR loci, and that using repeat unit plus LUS length as the allele designator can represent greater than 80% of the alleles detected by sequencing. A proof of concept study performed using a freely available probabilistic software demonstrated that the LUS length can be used in allele designations when a program does not require alleles to be integers, and that utilizing sequence information improves interpretation of both single-source and mixed contributor STR typing results as compared to using repeat unit information alone. The LUS concept for allele designation maintains the repeat-based allele nomenclature that will permit backward compatibility to extant STR databases, and the LUS lengths themselves will be concordant regardless of the NGS assay or analysis tools employed. Further, these biologically based, easy-to-derive designations uphold clear relationships between parent alleles and their stutter products, enabling analysis in fully continuous probabilistic programs that model stutter while avoiding the algorithmic complexities that come with string based searches. Though using repeat unit plus LUS length as the allele designator does not capture variation that occurs outside of the core repeat regions, this straightforward approach would permit the large majority of known STR sequence variation to be used for mixture deconvolution and, in turn, result in more informative mixture statistics in the near term. Ultimately, the method could bridge the gap from current length-based probabilistic systems to facilitate broader adoption of NGS by forensic DNA testing laboratories.

High-throughput analysis unveils a highly shared satellite DNA library among three species of fish genus Astyanax

The high-throughput analysis of satellite DNA (satDNA) content, by means of Illumina sequencing, unveiled 45 satDNA families in the genome of Astyanax paranae, with repeat unit length (RUL) ranging from 6 to 365 bp and marked predominance of short satellites (median length = 59 bp). The analysis of chromosomal location of 35 satDNAs in A. paranae, A. fasciatus and A. bockmanni revealed that most satellites are shared between the three species and show highly similar patterns of chromosome distribution. The high similarity in satellite DNA content between these species is most likely due to their recent common descent. Among the few differences found, the ApaSat44-21 satellite was present only on the B chromosome of A. paranae, but not on the A or B chromosomes of the two other species. Likewise, the ApaSat20-18 satellite was B-specific in A. paranae but was however present on A and B chromosomes of A. fasciatus and A. bockmanni. The isochromosome nature of B chromosomes in these species was evidenced by the symmetric location of many satDNAs on both B chromosome arms, and the lower symmetry observed in the A. fasciatus BfMa chromosome suggests that it is older than those analyzed in A. paranae and A. bockmanni.