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We report development and preparation of synthetic polypeptide based, coacervate core polyelectrolyte complex micelles, PCMs, in aqueous media, which were characterized and evaluated for the encapsulation and in vitro release of a model single-stranded RNA, polyadenylic acid, poly(A). Cationic, α-helical polypeptides pegylated at their N-termini, PEG113-b-5bn and PEG113-b-5cn, were designed to form coacervate core PCMs upon mixing with multivalent anions in aqueous media. Sodium tripolyphosphate (TPP) and poly(A) were used as model multivalent anions that allowed optimization of polypeptide composition and chain length for formation of stable, nanoscale PCMs. PEG113-b-5c27 was selected for preparation of PCMs that were characterized under different environmental conditions using dynamic light scattering, atomic force microscopy and cryoelectron microscopy. The PCMs were found to efficiently encapsulate poly(A), were stable at physiologically relevant pH and solution ionic strength, and were able to release poly(A) in the presence of excess polyvalent anions. These PCMs were found to be a promising model system for further development of polypeptide based therapeutic delivery vehicles.

BackgroundGenome-wide RNA-sequencing technologies are increasingly critical to a wide variety of diagnostic and research applications. RNA-seq users often first enrich for mRNA, with the most popular enrichment method being poly(A) selection. In many applications it is well-known that poly(A) selection biases the view of the transcriptome by selecting for longer tailed mRNA species.ResultsHere, we show that poly(A) selection biases Oxford Nanopore direct RNA sequencing. As expected, poly(A) selection skews sequenced mRNAs toward longer poly(A) tail lengths. Interestingly, we identify a population of mRNAs (> 10% of genes' mRNAs) that are inconsistently captured by poly(A) selection due to highly variable poly(A) tails, and demonstrate this phenomenon in our hands and in published data. Importantly, we show poly(A) selection is dispensable for Oxford Nanopore's direct RNA-seq technique, and demonstrate successful library construction without poly(A) selection, with decreased input, and without loss of quality.ConclusionsOur work expands the utility of direct RNA-seq by validating the use of total RNA as input, and demonstrates important technical artifacts from poly(A) selection that inconsistently skew mRNA expression and poly(A) tail length measurements.

Neurons provide a rich setting for studying post-transcriptional control. Here, we investigate the landscape of translational control in neurons and search for mRNA features that explain differences in translational efficiency (TE), considering the interplay between TE, mRNA poly(A)-tail lengths, microRNAs, and neuronal activation. In neurons and brain tissues, TE correlates with tail length, and a few dozen mRNAs appear to undergo cytoplasmic polyadenylation upon light or chemical stimulation. However, the correlation between TE and tail length is modest, explaining

Background: Recent literature suggests that vitamin D signaling has a protective effect against breast cancer risk. Thus, the aim of the present study was to find the association of vitamin D receptor (VDR) gene polymorphisms with breast cancer risk. Materials and Methods: Fok1, Bsm1, Apa1, and Taq1 polymorphisms were performed by polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) method, and Poly A polymorphism was carried out using PCR-SSCP in 140 breast cancer patients and 155 controls. Results: Odds ratio was significantly higher in both homozygous variant genotypes (LL) of Poly A polymorphism of VDR (odds ratio [OR] = 5.42, 95% confidence interval [CI] = 1.19–23.31, P = 0.02) and heterozygous variant genotypes (SL) of Poly A polymorphism of VDR (OR = 3.89, 95% CI = 1.10–13.7, P = 0.03). Fok1, Bsm1, Apa1, and Taq1 polymorphisms of VDR gene were not significantly associated with breast cancer risk. Conclusion: Poly A polymorphism at the 3′ untranslated region (UTR) of VDR gene was significantly associated with breast cancer risk in West Indian population. [ABSTRACT FROM AUTHOR]

RNA molecules function as messenger RNAs (mRNAs) that encode proteins and noncoding transcripts that serve as adaptor molecules, structural components, and regulators of genome organization and gene expression. Their function and regulation are largely mediated by RNA binding proteins (RBPs). Here we present RNA proximity labelling (RPL), an RNA-centric method comprising the endonuclease-deficient Type VI CRISPR-Cas protein dCas13b fused to engineered ascorbate peroxidase APEX2. RPL discovers target RNA proximal proteins in vivo via proximity-based biotinylation. RPL applied to U1 identified proteins involved in both U1 canonical and noncanonical functions. Profiling of poly(A) tail proximal proteins uncovered expected categories of RBPs and provided additional evidence for 5'-3' proximity and unexplored subcellular localizations of poly(A)+ RNA. Our results suggest that RPL allows rapid identification of target RNA binding proteins in native cellular contexts, and is expected to pave the way for discovery of novel RNA-protein interactions important for health and disease.

During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system1. Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17 tissues and organs. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif codes of their promoters. We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for one-third of differential gene expression and more than 40% of identified cell types. By integrating promoter sequence motifs with companion ENCODE epigenomic profiles, we identified a prominent promoter de-repression mechanism in neuronal expression clusters that was attributable to known and novel repressors. Focusing on the developing limb, single-cell RNA data identified 25 candidate cell types that included progenitor and differentiating states with computationally inferred lineage relationships. We extracted cell-type transcription factor networks and complementary sets of candidate enhancer elements by using single-cell RNA-seq to decompose integrative cis-element (IDEAS) models that were derived from whole-tissue epigenome chromatin data. These ENCODE reference data, computed network components and IDEAS chromatin segmentations are companion resources to the matching epigenomic developmental matrix, and are available for researchers to further mine and integrate.

3'-end poly(A)+ sequencing is an efficient and economical method for global measurement of mRNA levels and alternative poly(A) site usage. A common method involves oligo(dT)19V reverse-transcription (RT)-based library preparation and high-throughput sequencing with a custom primer ending in (dT)19. While the majority of library products have the first sequenced nucleotide reflect the bona fide poly(A) site (pA), a substantial fraction of sequencing reads arise from various mis-priming events. These can result in incorrect pA site calls anywhere from several nucleotides downstream to several kilobases upstream from the bona fide pA site. While these mis-priming events can be mitigated by increasing annealing stringency (e.g. increasing temperature from 37 °C to 42 °C), they still persist at an appreciable level (∼10%) and computational methods must be used to prevent artifactual calls. Here we present a bioinformatics workflow for precise mapping of poly(A)+ 3' ends and handling of artifacts due to oligo(dT) mis-priming and sample polymorphisms. We test pA site calling with three different read mapping programs (STAR, BWA, and BBMap), and show that the way in which each handles terminal mismatches and soft clipping has a substantial impact on identifying correct pA sites, with BWA requiring the least post-processing to correct artifacts. We demonstrate the use of this pipeline for mapping pA sites in the model eukaryote S. cerevisiae, and further apply this technology to non-polyadenylated transcripts by employing in vitro polyadenylation prior to library prep (IVP-seq). As proof of principle, we show that a fraction of tRNAs harbor CCU 3' tails instead of the canonical CCA tail, and globally identify 3' ends of splicing intermediates arising from inefficiently spliced transcripts.

High-throughput complementary DNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and modifications are not retained. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies. Our study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions. These native RNA reads had a median length of 771 bases, and a maximum aligned length of over 21,000 bases. Mitochondrial poly(A) reads provided an internal measure of read-length quality. We combined these long nanopore reads with higher accuracy short-reads and annotated GM12878 promoter regions to identify 33,984 plausible RNA isoforms. We describe strategies for assessing 3' poly(A) tail length, base modifications and transcript haplotypes.

MotivationAlternative polyadenylation (polyA) sites near the 3' end of a pre-mRNA create multiple mRNA transcripts with different 3' untranslated regions (3' UTRs). The sequence elements of a 3' UTR are essential for many biological activities such as mRNA stability, sub-cellular localization, protein translation, protein binding and translation efficiency. Moreover, numerous studies in the literature have reported the correlation between diseases and the shortening (or lengthening) of 3' UTRs. As alternative polyA sites are common in mammalian genes, several machine learning tools have been published for predicting polyA sites from sequence data. These tools either consider limited sequence features or use relatively old algorithms for polyA site prediction. Moreover, none of the previous tools consider RNA secondary structures as a feature to predict polyA sites.ResultsIn this paper, we propose a new deep learning model, called DeepPASTA, for predicting polyA sites from both sequence and RNA secondary structure data. The model is then extended to predict tissue-specific polyA sites. Moreover, the tool can predict the most dominant (i.e. frequently used) polyA site of a gene in a specific tissue and relative dominance when two polyA sites of the same gene are given. Our extensive experiments demonstrate that DeepPASTA signisficantly outperforms the existing tools for polyA site prediction and tissue-specific relative and absolute dominant polyA site prediction.Availability and implementationhttps://github.com/arefeen/DeepPASTA.Supplementary informationSupplementary data are available at Bioinformatics online.

BackgroundA single variant in NAA10 (c.471+2T>A), the gene encoding N-acetyltransferase 10, has been associated with Lenz microphthalmia syndrome. In this study, we aimed to identify causative variants in families with syndromic X-linked microphthalmia.MethodsThree families, including 15 affected individuals with syndromic X-linked microphthalmia, underwent analyses including linkage analysis, exome sequencing and targeted gene sequencing. The consequences of two identified variants in NAA10 were evaluated using quantitative PCR and RNAseq.ResultsGenetic linkage analysis in family 1 supported a candidate region on Xq27-q28, which included NAA10. Exome sequencing identified a hemizygous NAA10 polyadenylation signal (PAS) variant, chrX:153,195,397T>C, c.*43A>G, which segregated with the disease. Targeted sequencing of affected males from families 2 and 3 identified distinct NAA10 PAS variants, chrX:g.153,195,401T>C, c.*39A>G and chrX:g.153,195,400T>C, c.*40A>G. All three variants were absent from gnomAD. Quantitative PCR and RNAseq showed reduced NAA10 mRNA levels and abnormal 3' UTRs in affected individuals. Targeted sequencing of NAA10 in 376 additional affected individuals failed to identify variants in the PAS.ConclusionThese data show that PAS variants are the most common variant type in NAA10-associated syndromic microphthalmia, suggesting reduced RNA is the molecular mechanism by which these alterations cause microphthalmia/anophthalmia. We reviewed recognised variants in PAS associated with Mendelian disorders and identified only 23 others, indicating that NAA10 harbours more than 10% of all known PAS variants. We hypothesise that PAS in other genes harbour unrecognised pathogenic variants associated with Mendelian disorders. The systematic interrogation of PAS could improve genetic testing yields.

Poly(A) tails are non-templated additions of adenosines at the 3' ends of most eukaryotic mRNAs. In the nucleus, these RNAs are co-transcriptionally cleaved at a poly(A) site and then polyadenylated before being exported to the cytoplasm. In the cytoplasm, poly(A) tails play pivotal roles in the translation and stability of the mRNA. One challenge in studying poly(A) tails is that they are difficult to sequence and accurately measure. However, recent advances in sequencing technology, computational algorithms, and other assays have enabled a more detailed look at poly(A) tail length genome-wide throughout many developmental stages and organisms. With the help of these advances, our understanding of poly(A) tail length has evolved over the past 5 years with the recognition that highly expressed genes can have short poly(A) tails and the elucidation of the seemingly contradictory roles for poly(A)-binding protein (PABP) in facilitating both protection and deadenylation.

BackgroundIn response to a wound, fibroblasts are activated to migrate toward the wound, to proliferate and to contribute to the wound healing process. We hypothesize that changes in pre-mRNA processing occurring as fibroblasts enter the proliferative cell cycle are also important for promoting their migration.ResultsRNA sequencing of fibroblasts induced into quiescence by contact inhibition reveals downregulation of genes involved in mRNA processing, including splicing and cleavage and polyadenylation factors. These genes also show differential exon use, especially increased intron retention in quiescent fibroblasts compared to proliferating fibroblasts. Mapping the 3' ends of transcripts reveals that longer transcripts from distal polyadenylation sites are more prevalent in quiescent fibroblasts and are associated with increased expression and transcript stabilization based on genome-wide transcript decay analysis. Analysis of dermal excisional wounds in mice reveals that proliferating cells adjacent to wounds express higher levels of cleavage and polyadenylation factors than quiescent fibroblasts in unwounded skin. Quiescent fibroblasts contain reduced levels of the cleavage and polyadenylation factor CstF-64. CstF-64 knockdown recapitulates changes in isoform selection and gene expression associated with quiescence, and results in slower migration.ConclusionsOur findings support cleavage and polyadenylation factors as a link between cellular proliferation state and migration.

Choanoflagellates, the closest living relatives of animals, can provide unique insights into the changes in gene content that preceded the origin of animals. However, only two choanoflagellate genomes are currently available, providing poor coverage of their diversity. We sequenced transcriptomes of 19 additional choanoflagellate species to produce a comprehensive reconstruction of the gains and losses that shaped the ancestral animal gene repertoire. We identified ~1944 gene families that originated on the animal stem lineage, of which only 39 are conserved across all animals in our study. In addition, ~372 gene families previously thought to be animal-specific, including Notch, Delta, and homologs of the animal Toll-like receptor genes, instead evolved prior to the animal-choanoflagellate divergence. Our findings contribute to an increasingly detailed portrait of the gene families that defined the biology of the Urmetazoan and that may underpin core features of extant animals.

Nearly all eukaryotic messenger RNA precursors must undergo cleavage and polyadenylation at their 3-end for maturation. A crucial step in this process is the recognition of the AAUAAA polyadenylation signal (PAS), and the molecular mechanism of this recognition has been a long-standing problem. Here, we report the cryo-electron microscopy structure of a quaternary complex of human CPSF-160, WDR33, CPSF-30, and an AAUAAA RNA at 3.4-Å resolution. Strikingly, the AAUAAA PAS assumes an unusual conformation that allows this short motif to be bound directly by both CPSF-30 and WDR33. The A1 and A2 bases are recognized specifically by zinc finger 2 (ZF2) of CPSF-30 and the A4 and A5 bases by ZF3. Interestingly, the U3 and A6 bases form an intramolecular Hoogsteen base pair and directly contact WDR33. CPSF-160 functions as an essential scaffold and preorganizes CPSF-30 and WDR33 for high-affinity binding to AAUAAA. Our findings provide an elegant molecular explanation for how PAS sequences are recognized for mRNA 3-end formation.

Alternative mRNA processing is a critical mechanism for proteome expansion and gene regulation in higher eukaryotes. The SR family proteins play important roles in splicing regulation. Intriguingly, mammalian genomes encode many poorly characterized SR-like proteins, including subunits of the mRNA 3'-processing factor CFIm, CFIm68 and CFIm59. Here we demonstrate that CFIm functions as an enhancer-dependent activator of mRNA 3' processing. CFIm regulates global alternative polyadenylation (APA) by specifically binding and activating enhancer-containing poly(A) sites (PASs). Importantly, the CFIm activator functions are mediated by the arginine-serine repeat (RS) domains of CFIm68/59, which bind specifically to an RS-like region in the CPSF subunit Fip1, and this interaction is inhibited by CFIm68/59 hyper-phosphorylation. The remarkable functional similarities between CFIm and SR proteins suggest that interactions between RS-like domains in regulatory and core factors may provide a common activation mechanism for mRNA 3' processing, splicing, and potentially other steps in RNA metabolism.

mRNA 3' end processing is an essential step in gene expression. It is well established that canonical eukaryotic pre-mRNA 3' processing is carried out within a macromolecular machinery consisting of dozens of trans-acting proteins. However, it is unknown whether RNAs play any role in this process. Unexpectedly, we found that a subset of small nucleolar RNAs (snoRNAs) are associated with the mammalian mRNA 3' processing complex. These snoRNAs primarily interact with Fip1, a component of cleavage and polyadenylation specificity factor (CPSF). We have functionally characterized one of these snoRNAs and our results demonstrated that the U/A-rich SNORD50A inhibits mRNA 3' processing by blocking the Fip1-poly(A) site (PAS) interaction. Consistently, SNORD50A depletion altered the Fip1-RNA interaction landscape and changed the alternative polyadenylation (APA) profiles and/or transcript levels of a subset of genes. Taken together, our data revealed a novel function for snoRNAs and provided the first evidence that non-coding RNAs may play an important role in regulating mRNA 3' processing.

Moso bamboo (Phyllostachys edulis) represents one of the fastest-spreading plants in the world, due in part to its well-developed rhizome system. However, the post-transcriptional mechanism for the development of the rhizome system in bamboo has not been comprehensively studied. We therefore used a combination of single-molecule long-read sequencing technology and polyadenylation site sequencing (PAS-seq) to re-annotate the bamboo genome, and identify genome-wide alternative splicing (AS) and alternative polyadenylation (APA) in the rhizome system. In total, 145 522 mapped full-length non-chimeric (FLNC) reads were analyzed, resulting in the correction of 2241 mis-annotated genes and the identification of 8091 previously unannotated loci. Notably, more than 42 280 distinct splicing isoforms were derived from 128 667 intron-containing full-length FLNC reads, including a large number of AS events associated with rhizome systems. In addition, we characterized 25 069 polyadenylation sites from 11 450 genes, 6311 of which have APA sites. Further analysis of intronic polyadenylation revealed that LTR/Gypsy and LTR/Copia were two major transposable elements within the intronic polyadenylation region. Furthermore, this study provided a quantitative atlas of poly(A) usage. Several hundred differential poly(A) sites in the rhizome-root system were identified. Taken together, these results suggest that post-transcriptional regulation may potentially have a vital role in the underground rhizome-root system.

mRNA alternative polyadenylation (APA) is a critical mechanism for post-transcriptional gene regulation and is often regulated in a tissue- and/or developmental stage-specific manner. An ultimate goal for the APA field has been to be able to computationally predict APA profiles under different physiological or pathological conditions. As a first step toward this goal, we have assembled a poly(A) code for predicting tissue-specific poly(A) sites (PASs). Based on a compendium of over 600 features that have known or potential roles in PAS selection, we have generated and refined a machine-learning algorithm using multiple high-throughput sequencing-based data sets of tissue-specific and constitutive PASs. This code can predict tissue-specific PASs with >85% accuracy. Importantly, by analyzing the prediction performance based on different RNA features, we found that PAS context, including the distance between alternative PASs and the relative position of a PAS within the gene, is a key feature for determining the susceptibility of a PAS to tissue-specific regulation. Our poly(A) code provides a useful tool for not only predicting tissue-specific APA regulation, but also for studying its underlying molecular mechanisms.

Alkyne-modified nucleoside analogs are useful for nucleic acid localization as well as functional and structural studies because of their ability to participate in copper-catalyzed azide/alkyne cycloaddition (CuAAC) reactions. Here we describe the synthesis of the triphosphate of 7-ethynyl-8-aza-7-deazaadenosine (7-EAATP) and the enzymatic incorporation of 7-EAA into RNA. The free nucleoside of 7-EAA is taken up by HeLa cells and incorporated into cellular RNA by endogenous RNA polymerases. In addition, 7-EAATP is a substrate for both T7 RNA polymerase and poly (A) polymerase from Escherichia coli in vitro, albeit at lower efficiencies than with ATP. This work adds to the toolbox of nucleoside analogs useful for RNA labeling.

Accurate and precise annotation of 3' UTRs is critical for understanding how mRNAs are regulated by microRNAs (miRNAs) and RNA-binding proteins (RBPs). Here, we describe a method, poly(A) binding protein-mediated mRNA 3' end retrieval by crosslinking immunoprecipitation (PAPERCLIP), that shows high specificity for mRNA 3' ends and compares favorably with existing 3' end mapping methods. PAPERCLIP uncovers a previously unrecognized role of CstF64/64tau in promoting the usage of a selected group of non-canonical poly(A) sites, the majority of which contain a downstream GUKKU motif. Furthermore, in the mouse brain, PAPERCLIP discovers extended 3' UTR sequences harboring functional miRNA binding sites and reveals developmentally regulated APA shifts, including one in Atp2b2 that is evolutionarily conserved in humans and results in the gain of a functional binding site of miR-137. PAPERCLIP provides a powerful tool to decipher post-transcriptional regulation of mRNAs through APA in vivo.

Conventional molecularly imprinted polymers (MIPs) perform their functions principally depended on their three dimensional (3D) imprinted cavities (recognition sites) of templates. Here, retaining the function of recognition sites resulted from the imprinting of template molecules, the role of functional monomers is explored and expanded. Briefly, a class of dual-functional renin imprinted poly(methyldopa) (RMIP) is prepared, consisting of a drug-type function monomer (methyldopa, clinical high blood pressure drug) and a corresponding disease biomarker (renin, biomarker for high blood pressure disease). To boost target-to-receptor binding ratio and sensitivity, the microstructure of recognition sites is beforehand calculated and designed by Density Functional Theory calculations, and the whole interfacial structure, property and thickness of RMIP film is regulated by adjusting the polymerization techniques. The dual-functional applications of RMIP for biomarker detection and disease therapy in vivo is explored. Such RMIP-based biosensors achieves highly sensitive biomarker detection, where the LODs reaches down to 1.31 × 10 -6 and 1.26 × 10 -6  ng mL -1 for electrochemical and chemical polymers, respectively, and the application for disease therapy in vivo has been verified where displays the obviously decreased blood pressure values of mice. No acute and long-term toxicity is found from the pathological slices, declaring the promising clinical application potential of such engineered RMIP nanostructure., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Polyadenylation [Poly(A)] is an essential process during messenger RNA (mRNA) maturation in biological eukaryote systems. Identifying Poly(A) signals (PASs) from the genome level is the key to understanding the mechanism of translation regulation and mRNA metabolism. In this work, we propose a deep dual-dynamic context-aware Poly(A) signal prediction model, called multiscale convolution with self-attention networks (MCANet), to adaptively uncover the spatial-temporal contextual dependence information. Specifically, the model automatically learns and strengthens informative features from the temporalwise and the spatialwise dimension. The identity connectivity performs contextual feature maps of Poly(A) data by direct connections from previous layers to subsequent layers. Then, a fully parametric rectified linear unit (FP-RELU) with dual-dynamic coefficients is devised to make the training of the model easier and enhance the generalization ability. A cross-entropy loss (CL) function is designed to make the model focus on samples that are easy to misclassify. Experiments on different Poly(A) signals demonstrate the superior performance of the proposed MCANet, and an ablation study shows the effectiveness of the network design for the feature learning and prediction of Poly(A) signals.

The development of a biomass adhesive as a substitute for petroleum-derived adhesives has been considered a viable option. However, achieving both superior bonding strength and toughness in biomass adhesives remains a significant challenge. Inspired by the human skeletal muscles structure, this study reveals a promising supramolecular structure using tannin acid (TA) functionalized poly-β-cyclodextrin (PCD) (TA@PCD) as elastic tissues and chitin nanocrystals (ChNCs) as green reinforcements to strengthen the soybean meal (SM) adhesive crosslinking network. TA@PCD acts as a dynamic crosslinker that facilitates reversible host-guest interactions, hydrogen bonds, and electrostatic interactions between adjacent stiff ChNCs and SM matrix, resulting in satisfactory strength and toughness. The resulting SM/TA@PCD/ChNCs-2 adhesive has demonstrated satisfactory wet and dry shear strength (1.25 MPa and 2.57 MPa, respectively), toughness (0.69 J), and long-term solvents resistance (80 d). Furthermore, the adhesive can exhibit desirable antimildew characteristics owing to the phenol hydroxyl groups of TA and amino groups of ChNCs. This work showcases an effective supramolecular chemistry strategy for fabricating high-performance biomass adhesives with great potential for practical applications., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

The mechanical properties of ionic conductive hydrogels (ICHs) are generally inadequate, leading to their susceptibility to breakage under external forces and consequently resulting in the failure of flexible electronic devices. In this work, a simple and convenient strategy was proposed based on the synergistic effect of ion cross-linking and salting out, in which the hydrogels consisting of polyvinyl alcohol (PVA) and xanthan gum (XG) were immersed in zinc sulfate (ZnSO 4 ) solution to obtain ICHs with exceptional mechanical properties. The salt-out effects between PVA chains and SO 4 2- ions along with the cross-linked network of XG chains and Zn 2+ ions contribute to the desirable mechanical properties of ICHs. Notably, the mechanical properties of ICHs can be adjusted by changing the concentration of ZnSO 4 solution. Consequently, the optimum fracture stress and the fracture energy can reach 3.38 MPa and 12.13 KJ m -2 , respectively. Moreover, the ICHs demonstrated a favorable sensitivity (up to 2.05) when utilized as a strain sensor, exhibiting an accurate detection of human body movements across various amplitudes., Competing Interests: Declaration of competing interest We declare that we do not have any commercial or associative interest that represents a conflict of interest in connection with the work submitted., (Copyright © 2024. Published by Elsevier B.V.)

Green polymeric foams are an important research topic for sustainable development. In this study, a natural multifunctional flame-retardant additive based on food waste was developed and evaluated for its ability to replace the commercial additives tricresyl phosphate (TCP) and trioctyl phosphate (TOP) in a polylactide/poly(butylene adipate-co-terephthalate) (PLA/PBAT) foam. A series of blend foams with additives were prepared by melt extrusion. According to the results, the blend foam with 20 phr of TCP showed the best combination of impact toughness and flame retardancy. TCP, however, poses health and environmental risks. Therefore, natural flame retardants (NFRs) were used to partially replace the commercial flame retardant (CFR). A combination of TCP and soybean residue (SB) produced an impact toughened and flame-retardant blend foam. When compared to the neat PLA/PBAT foam, the impact toughness of the best sample was increased by about 256 %. The optimal foam showed excellent flame resistance with a V-0 UL-94 rating and a high LOI value (31.8 %). SB has the potential to partially replace TCP as flame retardant and could be used in a broad range of PLA/PBAT foam applications., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Blending poly (butylene adipate-co-terephthalate) (PBAT) and polylactic acid (PLA) is a cost-effective strategy to obtain biodegradable plastic with complementary properties. However, the incompatibility between PBAT and PLA is a great challenge for fabricating high-performance composite films. Herein, the ethyl acetate fractionated lignin with the small glass transition temperature and low molecular weight was achieved and incorporated into the PBAT/PLA composite as a compatibilizer. The fractionated lignin can be uniformly dispersed within the PBAT/PLA matrix through a melt blending process and interact with the molecular chain of PBAT and PLA as a bonding bridge, which enhances the intermolecular interactions and reduces the interfacial tension of PBAT/PLA. By adding fractionated lignin, the tensile strength of the PBAT/PLA composite increased by 35.4 % and the yield strength increased by 37.7 %. Owing to lignin, the composite films possessed the ultraviolet shielding function and exhibited better water vapor barrier properties (1.73 ± 0.08 × 10 -13  g·cm/cm 2 ·s·Pa). This work conclusively demonstrated that fractionated lignin can be used as a green compatibilizer and a low-cost functional filler for PBAT/PLA materials, and provides guidance for the application of lignin in biodegradable plastics., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Base-stacking is a key factor in the energetics that determines nucleic acid structure. We measure the tensile response of single-stranded DNA as a function of sequence and monovalent salt concentration to examine the effects of base-stacking on the mechanical and thermodynamic properties of single-stranded DNA. By comparing the elastic response of highly stacked poly(dA) and that of a polypyrimidine sequence with minimal stacking, we find that base-stacking in poly(dA) significantly enhances the polymer's rigidity. The unstacking transition of poly(dA) at high force reveals that the intrinsic electrostatic tension on the molecule varies significantly more weakly on salt concentration than mean-field predictions. Further, we provide a model-independent estimate of the free energy difference between stacked poly(dA) and unstacked polypyrimidine, finding it to be ∼-0.25 kBT/base and nearly constant over three orders of magnitude in salt concentration.

The wide application of fully biodegradable polylactic acid/polybutylene terephthalate (PLA/PBAT) blends in environmentally friendly packaging were limited because of poor compatibility. Normal compatibilizers suffer from poor thermal stability and non-biodegradability. In this work, epoxy copolymer (MDOG) with different molecular structures were made of 2-methylene-1, 3-dioxoheptane, and glycidyl methacrylate as raw materials by free radical copolymerization. MDOG copolymers have good biodegradability and a high thermal decomposition temperature of 361 °C. The chemical reaction of the epoxy groups in MDOG with PLA and PBAT during the melting reaction improved the interfacial bonding by decreasing the particle size of PBAT. Compared to the PLA/PBAT blends, the tensile strength and fracture toughness of PLA/PBAT/MDOG blends were enhanced to 34.6 MPa and 115.8 MJ/m 3 , which are 25 % and 81 % higher, respectively. As a result, this work offers new methods for developing thermally stable and biodegradable compatibilizers, which will hopefully promote the development of packaging industry., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Electro-conductive hydrogels emerge as a stretchable conductive materials with diverse applications in the synthesis of flexible strain sensors. However, the high-water content and low cross-links density cause them to be mechanically destroyed and freeze at subzero temperatures, limiting their practical applications. Herein, we report a one-pot strategy by co-incorporating cellulose nanofiber (CNF), Poly pyrrole (PPy) and glycerol with polyvinyl alcohol (PVA) to prepare hydrogel. The addition of PPy endowed the hydrogel with good conductivity (∼0.034 S/m) compared to the no PPy@CNF group (∼0.0095 S/m), the conductivity was increased by 257.9 %. The hydrogel exhibits comparable ionic conductivity at -18 °C as it does at room temperature. It's attributed to the glycerol as a cryoprotectant and the formation of hydrated [Zn(H 2 O) n ] 2+ ions via strong interaction between Zn 2+ and water molecules. Moreover, the cellulose nanofiber intrinsically assembled into unique hierarchical structures allow for strong hydrogen bonds between adjacent cellulose and PPy polymer chains, greatly improve the mechanical strength (stress∼0.65 MPa, strain∼301 %) and excellent viscoelasticity (G'max ∼ 82.7 KPa). This novel PPy@CNF-PVA hydrogel exhibits extremely high Gauge factor (GF) of 2.84 and shows excellent sensitivity, repeatability and stability. Therefore, the hydrogel can serve as reliable and stable strain sensor which shows excellent responsiveness in human activities monitoration., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

Developing biobased materials is a considerably effective approach to save fossil resources and reduce emissions. Biobased polyamide 56 (PA56) is an excellent engineering material, but it has low toughness. Herein, to enhance the toughness of PA56, an ultra-tough biodegradable material, i.e., poly (butylene adipate-co-terephthalate) (PBAT) was introduced into PA56. Moreover, a self-synthesized epoxy-terminated hyperbranched polyester (EHBP) was used to improve the compatibility of the blended materials. The results of differential scanning calorimetry and Fourier-transform infrared spectroscopy indicated that the epoxide group of EHBP could react with PA56 and PBAT to form a block-like polymer structure and limit the crystallization behavior of the blends. The scanning electron microscopy results show that the addition of EHBP considerably reduced the dispersed-phase size in the blends, forming a nanoscale island structure. Moreover, the hydrogen bonds formed between EHBP and PA56/PBAT enhanced the intermolecular interaction between the two materials. Thus, PA56 blends with ultrahigh toughness were successfully prepared. The prepared PA56/PBAT/EHBP blend exhibited a notch impact strength of 20.71 kJ/m 2 and a breaking elongation of 38.3 %, which represent increases of 427.3 % and 252.8 %, respectively, compared with those of pure PA56. Thus, the proposed method is suitable for toughening PA56 and broadening its applications., Competing Interests: Declaration of competing interest The authors declare that there is no conflict of interest., (Copyright © 2024. Published by Elsevier B.V.)

Conductive hydrogels have shown a great potential in the field of flexible electronic devices. However, conductive hydrogels prepare by traditional methods are difficult to combine high strength and toughness, which limits their application in various fields. In this study, a strategy for preparing conductive hydrogels with high strength and toughness by using the synergistic effect of biomineralization and salting-out was pioneered. In simple terms, by immersing the CaCl 2 doped soy protein isolate/poly(vinyl alcohol)/dimethyl sulfoxide (SPI/PVA/DMSO) hydrogel in Na 2 CO 3 and Na 3 Cit complex solution, the biomineralization aroused by Ca 2+ and CO 3 2- , and the salting-out effect of both NaCl and Na 3 Cit would enhance the mechanical properties of SPI/PVA/DMSO hydrogel. Meanwhile, the ionic conductivity of the hydrogel would also increase due the introduction of cation and anion. The mechanical and electrical properties of SPI/PVA/DMSO/CaCO 3 /Na 3 Cit hydrogels were significantly enhanced by the synergistic effect of biomineralization and salting-out. The optimum tensile strength, toughness, Young's modulus and ionic conductivity of the hydrogel were 1.4 ± 0.08 MPa, 0.51 ± 0.04 MPa and 1.46 ± 0.01 S/m, respectively. The SPI/PVA/DMSO/CaCO 3 /Na 3 Cit hydrogel was assembled into a strain sensor. The strain sensor had good sensitivity (GF = 3.18, strain in 20 %-500 %) and could be used to accurately detect various human movements., Competing Interests: Declaration of competing interest We declare that we have no financial and personal relationships with other people or organizations that can inappropriately influence our work, there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the position presented in, or the review of, the manuscript entitled., (Copyright © 2023. Published by Elsevier B.V.)

State-of-the-art Li batteries suffer from serious safety hazards caused by the reactivity of lithium and the flammable nature of liquid electrolytes. This work develops highly efficient solid-state electrolytes consisting of imidazolium-containing polyionic liquids (PILs) and lithium bis(trifluoromethane sulfonyl)imide (LiTFSI). By employing PIL/LiTFSI electrolyte membranes blended with poly(propylene carbonate) (PPC), we addressed the problem of combining ionic conductivity and mechanical properties in one material. It was found that PPC acts as a mechanically reinforcing component that does not reduce but even enhances the ionic conductivity. While pure PILs are liquids, the tricomponent PPC/PIL/LiTFSI blends are rubber-like materials with a Young's modulus in the range of 100 MPa. The high mechanical strength of the material enables fabrication of mechanically robust free-standing membranes. The tricomponent PPC/PIL/LiTFSI membranes have an ionic conductivity of 10 -6 S·cm -1 at room temperature, exhibiting conductivity that is two orders of magnitude greater than bicomponent PPC/LiTFSI membranes. At 60 °C, the conductivity of PPC/PIL/LiTFSI membranes increases to 10 -5 S·cm -1 and further increases to 10 -3 S·cm -1 in the presence of plasticizers. Cyclic voltammetry measurements reveal good electrochemical stability of the tricomponent PIL/PPC/LiTFSI membrane that potentially ranges from 0 to 4.5 V vs. Li/Li+. The mechanically reinforced membranes developed in this work are promising electrolytes for potential applications in solid-state batteries.

Organic molecules are of great interest for gas sensing applications. However, achieving high-performance gas sensors with high sensitivity, fast response, low consumption, and workability in humid conditions is still challenging. Herein, we report the rational design and synthesis of an ion-in-conjugation polymer, PADC (poly-4,4'-azodianiline-croconamide), obtained by the condensation of croconic acid with 4-4'diaminoazobenzene for gas sensing under humid conditions. The as-fabricated PADC-based gas sensor exhibits ultrahigh sensitivity (802.7 ppm -1 at 1 ppm), subppb detection limit, and high selectivity under humid air with an 80% humidity effect at a temperature down to 350 K. PADC shows good planarity, excellent thermostability, and a narrow band gap of 1.2 eV because of azobenzene fragments spacing previously repulsed biphenyl rings. Compared to previous humidity immunity works, PADC-based sensors realized humidity immunity at a relatively lower temperature, resulting in lower energy consumption.

The textile industry produces high volumes of colored effluents that require multiple treatments to remove non-adsorbed dyes, which could be recalcitrant due to their complex chemical structure. Most of the studies have dealt with the biodegradation of mono or diazo dyes but rarely with poly-azo dyes. Therefore, the aim of this paper was to study the biodegradation of a four azo-bond dye (Sirius grey) and to optimize its decolorization conditions. Laccase-containing cell-free supernatant from the culture of a newly isolated fungal strain, Coriolopsis gallica strain BS9 was used in the presence of 1-hydroxybenzotriazol (HBT) to optimize the dye decolorization conditions. A Box-Benken design with four factors, namely pH, enzyme concentration, HBT concentration, and dye concentration, was performed to determine optimal conditions for the decolorization of Sirius grey. The optimal conditions were pH 5, 1 U/mL of laccase, 1 mM of HBT, and 50 mg/L of initial dye concentration, ensuring a decolorization yield and rate of 87.56% and 2.95%/min, respectively. The decolorized dye solution showed a decrease in its phytotoxicity (Germination index GI = 80%) compared to the non-treated solution (GI = 29%). This study suggests that the laccase-mediator system could be a promising alternative for dye removal from textile wastewater.

The cationic platinum(II) organometallic complex [Pt(terpy)Me] + (terpy = 2,2':6',2″-terpyridine) at mild acidic pH interacts with poly(L-glutamic acid) (L-PGA) in its α-helix conformation, affording chiral supramolecular adducts. Their kinetics of formation have been investigated in detail as a function of the concentrations of both reagents and changing pH, ionic strength, the length of the polymeric scaffold and temperature. After a very fast early stage, the kinetic traces have been analyzed as three consecutive steps, suggesting a mechanism based on the electrostatic fast formation of a not-organized aggregate that subsequently evolves through different rearrangements to form the eventual supramolecular adduct. A model for this species has been proposed based on (i) the attractive electrostatic interaction of the cationic platinum(II) complexes and the polyelectrolyte and (ii) the π-stacking interactions acting among the [Pt(terpy)Me] + units.

Polymer nanocomposites filled with carbon nanoparticles (CNPs) are a hot topic in materials science. This article discusses the current research on the use of these materials as interfacial electron transfer films for solid contact potentiometric membrane sensors (SC-PMSs). The results of a comparative study of plasticized poly (vinyl chloride) (pPVC) matrices modified with single-walled carbon nanotubes (SWCNTs), fullerenes-C60, and their hybrid ensemble (SWCNTs-C60) are reported. The morphological characteristics and electrical conductivity of the prepared nanostructured composite films are reported. It was found that the specific electrical conductivity of the pPVC/SWCNTs-C60 polymer film was higher than that of pPVC filled with individual nanocomponents. The effectiveness of this composite material as an electron transfer film in a new potentiometric membrane sensor for detecting phenylpyruvic acid (in anionic form) was demonstrated. Screening for this metabolic product of phenylalanine in body fluids is of significant diagnostic interest in phenylketonuria (dementia), viral hepatitis, and alcoholism. The developed sensor showed a stable and fast Nernstian response for phenylpyruvate ions in aqueous solutions over the wide linear concentration range of 5 × 10 -7 -1 × 10 -3 M, with a detection limit of 10 -7.2 M.

In this study, a novel film of poly(vinyl alcohol) (PVA)/pullulan (PULL) with improved surface characteristics was prepared from poly(vinyl acetate) (PVAc)/PULL blend films with various mass ratios after the saponification treatment in a heterogeneous medium. According to proton nuclear magnetic resonance ( 1 H-NMR), Fourier transform infrared, and X-ray diffraction results, it was established that the successful fabrication of saponified PVA/PULL (100/0, 90/10, and 80/20) films could be obtained from PVAc/PULL (100/0, 90/10, and 80/20) films, respectively, after 72 h saponification at 50 °C. The degree of saponification calculated from 1 H-NMR analysis results showed that fully saponified PVA was obtained from all studied films. Improved hydrophilic characteristics of the saponified films were revealed by a water contact angle test. Moreover, the saponified films showed improved mechanical behavior, and the micrographs of saponified films showed higher surface roughness than the unsaponified films. This kind of saponified film can be widely used for biomedical applications. Moreover, the reported saponified film dressing extended the lifespan of dressing as determined by its self-healing capacity and considerably advanced in vivo wound-healing development, which was attributed to its multifunctional characteristics, meaning that saponified film dressings are promising candidates for full-thickness skin wound healing.

Development of rapid detection strategies that target potentially pathogenic bacteria has gained increasing attention due to the increasing awareness for better health and safety. In this study, we evaluate an intrinsically antimicrobial polymer, 2Gdm, which is a poly(norbornene)-based functional polymer featuring guanidinium groups as side chains, for bacterial detection by the means of triboelectric nanogenerators (TENGs) and triboelectric nanosensors (TENSs). Attachment of bacteria to the sensing layer is anticipated to alter the overall triboelectric properties of the underlying polymer layer. The positively charged guanidinium functional groups can interact with the negatively charged phospholipid bilayer of bacteria and lead to bacterial death, which can then be detected by optical microscopy, X-ray photoelectron microscopy, and more advanced self-powered sensing techniques such as TENGs and TENSs. The double bonds present along the poly(norbornene) backbone allow for thermally induced cross-linking to obtain X-2Gdm and thus rendering materials remain stable in water. By monitoring the change in voltage output after immersion in various concentrations of Gram-negative Escherichia coli ( E. coli ) and Gram-positive Streptococcus pneumoniae ( S. pneumoniae ), we have demonstrated the utility of X-2Gdm as a new polymer dielectric for autonomous bacterial detection. As the bacterial concentration increases, the amount of adsorbed bacteria also increases, resulting in a decrease in the surface potential of the X-2Gdm thin film; this reduction in surface potential can cause a decrease in the triboelectric output for both TENGs and TENSs, which serves as a key working mechanism for facile bacterial detection. TENG and TENS systems are capable of detecting E. coli and S. pneumoniae within a range of 4 × 10 5 to 4 × 10 8 CFU/mL with a limit of detection of 10 6 CFU/mL. This report highlights the promising prospects of employing TENGs and TENSs as innovative sensing technologies for rapid bacterial detection by leveraging the electrostatic interactions between bacterial cell membranes and cationic groups present on polymer surfaces.

The design of a novel electrochemical impedimetric biosensor for label-free analysis of resistin, a biomarker for obesity, is reported. For the fabrication of the immunosensor, a novel approach composed of electrochemical copolymerization of double epoxy groups-substituted thiophene (ThidEp) and 3,4-Ethylenedioxythiophene (EDOT) monomers was utilized. Anti-resistin antibodies were covalently attached to the copolymer-coated electrode. The capture of resistin antigens by anti-resistin antibodies caused significant variations in charge transfer resistance (R ct ) because of the immunoreactions between these proteins. Under optimum experimental variables, the changes in impedance signals were employed for the determination of resistin antigen concentration, and the prepared immunosensor based on conjugated copolymer illustrated a wide linear range between 0.0125 and 22.5 pg/mL, a low detection limit (LOD) of 3.71 fg/mL, and a good sensitivity of 1.22 kΩ pg -1 mL cm 2 . The excellent analytical performance of the resistin immunosensor in terms of selectivity, sensitivity, repeatability, reproducibility, storage stability, and low detection limit might be attributed to the conductive copolymer film layer generation on the disposable indium tin oxide (ITO) platform. The capability of this system for the determination of resistin in human serum and saliva samples was also tested. The immunosensor results were in accordance with the enzyme-linked immunosorbent assay (ELISA) results. The matrix effects of human serum and saliva were also investigated, and the proposed immunosensor displayed good recovery ranging from 95.91 to 106.25%. The engineered immunosensor could open new avenues for obesity monitoring., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)

A sequence of deadenylation events, or the shortening of the poly(A) tail, is a highly regulated process during the life cycle of mRNAs. Advances in biochemistry have enabled the study of deadenylation events at single-nucleotide resolution. Here we describe mathematical models and their applications to estimate the kinetics of a single deadenylation event in vitro. We demonstrate how this quantitative approach is used for assessing reactions with synthetic RNA with poly(A) tails and the CCR4-NOT complex. This method is also applicable to investigating the catalytic activities of other exonucleases and RNA substrates. All example data and custom software are available on GitHub: https://github.com/2yngsklab/deadenylation-kinetics ., (© 2024. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.)

Cell survival in changing environments requires appropriate regulation of gene expression, including posttranscriptional regulatory mechanisms. From reporter gene studies in glucose-starved yeast, it was proposed that translationally silenced eukaryotic mRNAs accumulate in P bodies and can return to active translation. We present evidence contradicting the notion that reversible storage of nontranslating mRNAs is a widespread and general phenomenon. First, genome-wide measurements of mRNA abundance, translation, and ribosome occupancy after glucose withdrawal show that most mRNAs are depleted from the cell coincident with their depletion from polysomes. Second, only a limited subpopulation of translationally repressed transcripts, comprising fewer than 400 genes, can be reactivated for translation upon glucose readdition in the absence of new transcription. This highly selective posttranscriptional regulation could be a mechanism for cells to minimize the energetic costs of reversing gene-regulatory decisions in rapidly changing environments by transiently preserving a pool of transcripts whose translation is rate-limiting for growth.

Binding of recombinant prion protein with small highly structured RNAs, prokaryotic and eukaryotic prion protein mRNA pseudoknots, tRNA and polyA has been studied by the change in fluorescence anisotropy of the intrinsic tryptophan groups of the protein. The affinities of these RNAs to the prion protein and the number of sites where the protein binds to the nucleic acids do not vary appreciably although the RNAs have very different compositions and structures. The binding parameters do not depend upon pH of the solution and show a poor co-operativity. The reactants form larger nucleoprotein complexes at pH 5 compared to that at neutral pH. The electrostatic force between the protein and nucleic acids dominates the binding interaction at neutral pH. In contrast, nucleic acid interaction with the incipient nonpolar groups exposed from the structured region of the prion protein dominates the reaction at pH 5. Prion protein of a particular species forms larger complexes with prion protein mRNA pseudoknots of the same species. The structure of the pseudoknots and not their base sequences probably dominates their interaction with prion protein. Possibilities of the conversion of the prion protein to its infectious form in the cytoplasm by nucleic acids have been discussed.