Linearly Amplified Single-Stranded RNA-Derived Transcriptome Sequencing (LAST-seq).

Single-cell RNA sequencing (scRNA-seq) stands as a cutting-edge technology widely used in biological and biomedical research. Existing scRNA-seq methods rely on reverse transcription (RT) and second-strand synthesis (SSS) to convert RNA to cDNA before amplification. However, these methods often suffer from limited RT/SSS efficiency, which compromises the sensitivity of RNA detection. Here, we develop a new method, linearly amplified single-stranded RNA-derived transcriptome sequencing (LAST-seq), which directly amplifies the original single-stranded RNA without prior RT and SSS and offers high-sensitivity RNA detection and a low level of technical noise in single-cell transcriptome analysis. LAST-seq has been applied to quantify transcriptional bursting kinetics in human cells, advancing our understanding of chromatin organization's role in regulating gene expression. Key features • An RNase H/DNA polymerase-based strategy to attach the T7 promoter to single-stranded RNA. • T7 promoter mediated IVT on single stranded RNA template at single cell level.

DNA topology: A central dynamic coordinator in chromatin regulation.

Double helical DNA winds around nucleosomes, forming a beads-on-a-string array that further contributes to the formation of high-order chromatin structures. The regulatory components of the chromatin, interacting intricately with DNA, often exploit the topological tension inherent in the DNA molecule. Recent findings shed light on, and simultaneously complicate, the multifaceted roles of DNA topology (also known as DNA supercoiling) in various aspects of chromatin regulation. Different studies may emphasize the dynamics of DNA topological tension across different scales, interacting with diverse chromatin factors such as nucleosomes, nucleic acid motors that propel DNA-tracking processes, and DNA topoisomerases. In this review, we consolidate recent studies and establish connections between distinct scientific discoveries, advancing our current understanding of chromatin regulation mediated by the supercoiling tension of the double helix. Additionally, we explore the implications of DNA topology and DNA topoisomerases in human diseases, along with their potential applications in therapeutic interventions.

Synthetic Polypeptide Bioadhesive Based on Cation-π Interaction and Secondary Structure.

Bioadhesives have garnered widespread attention in the biomedical field, for wound healing and tissue sealing. However, challenges exist due to the inferior performance of bioadhesives, including weak adhesion, poor biocompatibility, or lack of biodegradability. In this work, we demonstrate the fabrication of hydrogel adhesive based on polypeptides composed of lysine and glutamic acid. The cation-π interaction between the ammonium cations and phenyl groups endows the hydrogel with strong cohesion, and the hydrophobicity of the phenyl group significantly enhances the interaction between polypeptides and the substrate interface, leading to excellent adhesive performance. The equivalent molar ratio of ammonium cations and the phenyl group is beneficial for the enhancement of adhesiveness. Furthermore, we discover that the polypeptides with an α-helix exhibit better adhesiveness than the polypeptides with a ß-sheet because the α-helical structure can increase the exposure of the side group on the polypeptide surface, which further strengthens the interaction between polypeptides and the substrate. Besides, this synthetic polypeptide adhesive can seal the tissue quickly and remain intact in water. This adhesive holds significant promise for application in wound healing and tissue sealing, and this study provides insight into the development of more peptide-based adhesives.

Chirality-Regulated Clusteroluminescence in Polypeptides.

The low emission efficiency of clusteroluminogens restricts their practical applications in the fields of sensors and biological imaging. In this work, the clusteroluminescence of ordered/disordered polypeptides was observed, and the photoluminescence (PL) intensity of polypeptides can be modulated by the chirality of amino acid residues. Polyglutamates with different chiral compositions were synthesized, and the racemic polypeptides exhibited a significantly higher PL intensity than the enantiopure ones. This emission originates from the n-π* transition between C═O groups of polypeptides and is enhanced by clusterization of polypeptides. CD and Fourier transform infrared spectra demonstrated that the enantiopure and racemic polypeptides form α-helix and random coil structures, respectively. The disordered polypeptides can form more chain entanglements and interchain interactions because of their high flexibility, leading to more clusterizations and stronger PL intensity. The rigidity of ordered helical structures restrains the chain entanglements, and the formation of intrachain hydrogen bonds between amide groups of the backbone impairs the interchain interaction between polypeptides, resulting in lower PL intensity. The PL intensity of the polypeptides can also be manipulated by the addition of urea or trifluoroacetic acid. Our study not only elucidates the chirality/order-based structure-property relationship of clusteroluminescence in peptide-based polymers but also offers implications for the rational design of fluorescent peptides/proteins.

Shape memory hydrogels with remodelable permanent shapes and programmable cold-induced shape recovery behavior.

Most shape memory polymers apply glass transition or crystallization of domains to fix temporary shapes and shape recovery is induced by heating, which hinders their application under heat-intolerant conditions. Moreover, the permanent shapes of polymers normally cannot be altered arbitrarily after fabrication. Herein, we present a novel shape memory hydrogel with a remodelable permanent shape and programmable cold-induced shape recovery behavior. Poly(acrylic acid) (PAA) hydrogel is prepared in the presence of diethylenetriamine (DETA) and subsequently treated with calcium acetate (Ca(Ac)2). The charge-assisted hydrogen bonding between PAA and DETA imparts the hydrogel with remodelability, while the heat-induced hydrophobic aggregation of polymer chains and acetate groups results in shape fixation by heating and shape recovery by cooling. Afterwards, programmable deformable devices are obtained by assembling hydrogel blocks with different concentrations of Ca(Ac)2. This design strategy promotes the development of shape memory polymers with diverse potential applications.

A mitochondria-regulated p53-CCF circuit integrates genome integrity with inflammation.

Genomic instability and inflammation are distinct hallmarks of aging, but the connection between them is poorly understood. Understanding their interrelationship will help unravel new mechanisms and therapeutic targets of aging and age-associated diseases. Here we report a novel mechanism directly linking genomic instability and inflammation in senescent cells, through a mitochondria-regulated molecular circuit that connects the p53 tumor suppressor and cytoplasmic chromatin fragments (CCF), a driver of inflammation through the cGAS-STING pathway. Activation or inactivation of p53 by genetic and pharmacologic approaches showed that p53 suppresses CCF accumulation and the downstream inflammatory senescence-associated secretory phenotype (SASP), independent of its effects on cell cycle arrest. p53 activation suppressed CCF formation by promoting DNA repair, reflected in maintenance of genomic integrity, particularly in subtelomeric regions, as shown by single cell genome resequencing. Activation of p53 by pharmacological inhibition of MDM2 in old mice decreased features of SASP in liver, indicating a senomorphic role in vivo . Remarkably, mitochondria in senescent cells suppressed p53 activity by promoting CCF formation and thereby restricting ATM-dependent nuclear DNA damage signaling. These data provide evidence for a mitochondria-regulated p53-CCF circuit in senescent cells that controls DNA repair, genome integrity and inflammatory SASP, and is a potential target for senomorphic healthy aging interventions.

LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis.

Existing single-cell RNA sequencing (scRNA-seq) methods rely on reverse transcription (RT) and second-strand synthesis (SSS) to convert single-stranded RNA into double-stranded DNA prior to amplification, with the limited RT/SSS efficiency compromising RNA detectability. Here, we develop a new scRNA-seq method, Linearly Amplified Single-stranded-RNA-derived Transcriptome sequencing (LAST-seq), which directly amplifies the original single-stranded RNA molecules without prior RT/SSS. LAST-seq offers a high single-molecule capture efficiency and a low level of technical noise for single-cell transcriptome analyses. Using LAST-seq, we characterize transcriptional bursting kinetics in human cells, revealing a role of topologically associating domains in transcription regulation.

Secondary Structure-Governed Phase Separation Behavior in Glutamate-Based Polypeptides.

The phase separation behavior of biomacromolecules plays a key role in the fields of biology and medicine. In this work, we gain a deep insight into how the primary and secondary structures govern and regulate the phase separation behavior of polypeptides. To this end, we synthesized a series of polypeptides with tailorable hydroxyl-containing side chains. The secondary structure of polypeptides can be modulated by the local chemical environment and content of side chains. Interestingly, these polypeptides with different helical contents exhibited upper critical solution temperature behavior with marked differences in the cloud point temperature (Tcp) and the width of hysteresis. The phase transition temperature is highly relevant to the content of secondary structure and interchain interactions of polypeptides. The aggregation/deaggregation and the transition of secondary structure are completely reversible during heating-cooling cycles. Much to our surprise, the recovery rate of the α-helical structure governs the width of hysteresis. This work establishes the structure-property relationship between the secondary structure and phase separation behavior of the polypeptide and delivers new insight into the rational design of peptide-based materials with tailor-made phase separation behavior.

A Clinical Decision Support System for Diabetes Patients with Deep Learning: Experience of a Taiwan Medical Center.

Background: Diabetes mellitus (DM) is a major public health problem worldwide. It involves dysfunction of blood sugar regulation resulting from insulin resistance, inadequate insulin secretion, or excessive glucagon secretion. Methods: This study collated 971,401 drug usage records of 51,009 DM patients. These data include patient identification code, age, gender, outpatient visiting dates, visiting code, medication features (included items, doses, and frequencies of drugs), HbA1c results, and testing time. We apply a random forest (RF) model for feature selection and implement a regression model with the bidirectional long short-term memory (Bi-LSTM) deep learning architecture. Finally, we use the root mean square error (RMSE) as the evaluation index for the prediction model. Results: After data cleaning, the data included 8,729 male and 9,115 female cases. Metformin was the most important feature suggested by the RF model, followed by glimepiride, acarbose, pioglitazone, glibenclamide, gliclazide, repaglinide, nateglinide, sitagliptin, and vildagliptin. The model performed better with the past two seasons in the training data than with additional seasons. Further, the Bi-LSTM architecture model performed better than support vector machines (SVMs). Discussion & Conclusion: This study found that Bi-LSTM models is a well kernel in a CDSS which help physicians' decision-making, and the increasing the number of seasons will negative impact the performance. In addition, this study found that the most important drug is metformin, which is recommended as first-line treatment OHA in various situations for DM patients.

The relationship among integrin alpha 7, CD133 and Nestin as well as their correlation with clinicopathological features and prognosis in astrocytoma patients.

OBJECTIVE: Integrin alpha 7 (ITGA7), a potential glioma stem cell marker, regulates several other stem cell markers including CD133 and Nestin in several cancers, meanwhile its high expression is related to poor prognosis in multiple solid tumor patients. However, few studies report correlation of ITGA7 with prognosis in astrocytoma patients. Hence, this study aimed to determine the astrocytoma-tissue ITGA7, CD133 and Nestin expressions to explore their relationship and clinical value for astrocytoma management. METHODS: Totally, 124 patients with primary astrocytoma were included. Their tumor tissue ITGA7, CD133 and Nestin expressions were determined by immunohistochemical (IHC) assay and scored by intensity and density ranging from 0 to 12 points. Besides, their clinical features (such as world health organization (WHO) grade, isocitrate dehydrogenase (IDH) mutation, and adjuvant therapy etc.) were collected, also their overall survival (OS) were analyzed by follow-up data. RESULTS: The mean IHC scores for ITGA7, CD133 and Nestin were 4.9 ± 2.5, 2.1 ± 2.6 and 5.8 ± 2.6, respectively. Moreover, ITGA7 high expression correlated with absence of IDH mutation (P = 0.004), advanced WHO grade (P = 0.001) and shorter OS (P = 0.005). Besides, ITGA7 positively correlated with CD133 (P = 0.001) and Nestin (P = 0.001) expressions. Regarding CD133 and Nestin, their high expression also correlated with increased WHO grade and shorter OS. Furthermore, multivariant Cox's regression analysis displayed that only CD133 high expression (P = 0.021) could independently predict reduced OS, while ITGA7 or Nestin high expression could not independently predict that. CONCLUSION: ITGA7, CD133, and Nestin are intercorrelated, also their high expressions associate with deteriorating disease conditions and poor prognosis in astrocytoma patients.

Anthracene-induced formation of highly twisted metallacycle and its crystal structure and tunable assembly behaviors.

Polycyclic aromatic hydrocarbons (PAHs) continue to attract increasing interest with respect to their applications as luminescent materials. The ordered structure of the metal-organic complex facilitates the selective integration of PAHs that can be tuned to function cooperatively. Here, a unique highly twisted anthracene-based organoplatinum metallacycle was prepared via coordination-driven self-assembly. Single-crystal X-ray diffraction analysis revealed that the metallacycle was twisted through the cooperation of strong π···π stacking interactions and steric hindrance between two anthracene-based ligands. Notably, the intramolecular twist and aggregation behavior introduced restrictions to the conformational change of anthracenes, which resulted in increased emission intensity of the metallacycle in solution. The emission behaviors and suprastructures based on the highly twisted metallacycle can be modulated by the introduction of different solvents. This study demonstrates that this metallacycle with highly twisted structure is a promising candidate for sensing and bioimaging applications.

Neuronal enhancers are hotspots for DNA single-strand break repair.

Defects in DNA repair frequently lead to neurodevelopmental and neurodegenerative diseases, underscoring the particular importance of DNA repair in long-lived post-mitotic neurons1,2. The cellular genome is subjected to a constant barrage of endogenous DNA damage, but surprisingly little is known about the identity of the lesion(s) that accumulate in neurons and whether they accrue throughout the genome or at specific loci. Here we show that post-mitotic neurons accumulate unexpectedly high levels of DNA single-strand breaks (SSBs) at specific sites within the genome. Genome-wide mapping reveals that SSBs are located within enhancers at or near CpG dinucleotides and sites of DNA demethylation. These SSBs are repaired by PARP1 and XRCC1-dependent mechanisms. Notably, deficiencies in XRCC1-dependent short-patch repair increase DNA repair synthesis at neuronal enhancers, whereas defects in long-patch repair reduce synthesis. The high levels of SSB repair in neuronal enhancers are therefore likely to be sustained by both short-patch and long-patch processes. These data provide the first evidence of site- and cell-type-specific SSB repair, revealing unexpected levels of localized and continuous DNA breakage in neurons. In addition, they suggest an explanation for the neurodegenerative phenotypes that occur in patients with defective SSB repair.

Self-Assembly of Metallacages into Centimeter Films with Tunable Size and Emissions.

The coupling of material systems at different length scales enables new ways to take advantage of the unique properties of nano-/macroscale materials. Here, the self-organization of assembled metallacages generated ultralong nanowires, followed by the formation of nanowire-based soft films with diameters up to 6.5 cm. In contrast to previous reports that mainly focused on the preparation of metallacage assemblies with dimensions on the nano-/micrometer scale, the preparation of centimeter assemblies can serve as the bridge between nanostructures and the macroscopic world.

A Regenerable Hydrogel Electrolyte for Flexible Supercapacitors.

Easy regenerability of core components such as electrode and electrolyte is highly required in advanced electrochemical devices. This work reports a reliable, regenerable, and stretchable hydrogel electrolyte based on ionic bonds between polyacrylic acid (PAA) and polyallylamine (PAH). PAA-PAH electrolyte (1M LiCl addition) exhibits high ionic conductivity (0.050 S·cm-1) and excellent mechanical property (fracture strain of 1,688%). Notably, the electrolyte can be regenerated to any desired shape under mild conditions and remains 96% and 90% of the initial ionic conductivity after the first and second regeneration, respectively. PAA-PAH/LiCl-based supercapacitor exhibits nearly 100% capacitance retention upon rolling, stretching, and 5,000 charge-discharge cycles, whereas the regenerated device holds 97.6% capacitance of the initial device and 90.9% after 5,000 cycles. This low-cost, high-efficiency, and regenerable hydrogel electrolyte reveals very promising use in solid-state/flexible supercapacitors and possibly becomes a standard commercial hydrogel electrolyte for sustainable electrochemical energy devices.

Self-Assembly of Porphyrin-Based Metallacages into Octahedra.

Despite rapid progress in recent years, it has remained challenging to prepare well-defined metal-organic complex-based suprastructures. As a result, the physicochemical mechanisms leading to their geometrical complexity remain perplexing. Here, a porphyrin-based metallacage was used as a building block to construct octahedra via self-assembly, and the mechanism for the evolution of the metallacages into octahedra was disclosed by both experiments and theoretical simulations.

Blastobotrys baotianmanensis sp. nov. and Blastobotrys xishuangbannaensis f.a., sp. nov., two novel yeast species associated with insects and rotting wood.

Five yeast strains were isolated from the gut of the groundbeetle Pterostichus gebleri and rotting wood, which were collected from two different localities in China. These strains were identified as representing two novel species of the genus Blastobotrys through comparison of sequences in the D1/D2 domains of the LSU rRNA gene and other taxonomic characteristics. Blastobotrys baotianmanensis sp. nov. produces two to three spherical ascospores per ascus, and is most closely related to the type strains of B. elegans, B. capitulata, B. arbuscula, and an undescribed species represented by strain BG02-7-20-006A-3-1. Blastobotrys baotianmanensis sp. nov. differed from these strains by 3.6-8.4 % divergence (21-46 substitutions and 0-4 gaps) in the D1/D2 sequences. Blastobotrys xishuangbannaensis f.a., sp. nov. is closely related to B. nivea, B. elegans and B. aristata but the formation of ascospores was not observed on various sporulation media, and it differed from its relatives by 6.2-8.5 % divergence (34-43 substitutions and 2-6 gaps) in the D1/D2 sequences. The holotype of Blastobotrys baotianmanensis sp. nov. is NYNU 1581 and the holotype of Blastobotrys xishuangbannaensis f.a., sp. nov. is NYNU 181030.

Recent developments in the construction and applications of platinum-based metallacycles and metallacages via coordination.

Coordination-driven suprastructures have attracted much interest due to their unique properties. Among these structures, platinum-based architectures have been broadly studied due to their facile preparation. The resultant two- or three-dimensional (2D or 3D) systems have many advantages over their precursors, such as improved emission tuning, sensitivity as sensors, and capture and release of guests, and they have been applied in biomedical diagnosis as well as in catalysis. Herein, we review the recent results related to platinum-based coordination-driven self-assembly (CDSA), and the text is organized to emphasizes both the synthesis of new metallacycles and metallacages and their various applications.

Multiple-Responsive and Amphibious Hydrogel Actuator Based on Asymmetric UCST-Type Volume Phase Transition.

Thermoresponsive hydrogel actuators have attracted tremendous interest due to their promising applications in artificial muscles, soft robotics, and flexible electronics. However, most of these materials are based on polymers with lower critical solution temperature (LCST), while those from upper critical solution temperature (UCST) are rare. Herein, we report a multiple-responsive UCST hydrogel actuator based on the complex of poly(acrylic acid) (PAAc) and poly(acrylamide) (PAAm). By applying a heterogeneous photopolymerization, a bilayer hydrogel was obtained, including a layer of the interpenetrating network (IPN) of PAAm/PAAc and a layer of a single network of PAAm. When cooled down below the UCST, the PAAm/PAAc layer contracted due to the hydrogen bonding of the two polymers while the PAAm layer stays in swelling state, driving the hydrogel to curl. By adjusting the composition of the two layers, the amplitude of actuation behavior could be regulated. By creating patterned IPN domains with photomasks, the hydrogel could deform into complex two-dimensional (2D) and three-dimensional (3D) shapes. An active motion was realized in both water and oil bath, thanks to the internal water exchange between the two layers. Interestingly, the hydrogel actuator is also responsive to urea and salts (Na2SO4, NaCl, NaSCN), due to that the strength of the hydrogen bonds in the IPN changes with the additives. Overall, the current study realized an anisotropic UCST transition by introducing asymmetrically distributed polymer-polymer hydrogen bonds, which would inspire new inventions of intelligent materials.

Synthesis of polypeptides via bioinspired polymerization of in situ purified N-carboxyanhydrides.

Ribozymes synthesize proteins in a highly regulated local environment to minimize side reactions caused by various competing species. In contrast, it is challenging to prepare synthetic polypeptides from the polymerization of N-carboxyanhydrides (NCAs) in the presence of water and impurities, which induce monomer degradations and chain terminations, respectively. Inspired by natural protein synthesis, we herein report the preparation of well-defined polypeptides in the presence of competing species, by using a water/dichloromethane biphasic system with macroinitiators anchored at the interface. The impurities are extracted into the aqueous phase in situ, and the localized macroinitiators allow for NCA polymerization at a rate which outpaces water-induced side reactions. Our polymerization strategy streamlines the process from amino acids toward high molecular weight polypeptides with low dispersity by circumventing the tedious NCA purification and the demands for air-free conditions, enabling low-cost, large-scale production of polypeptides that has potential to change the paradigm of polypeptide-based biomaterials.