Mechanism of transcriptional bursting in bacteria.

Transcription of highly expressed genes has been shown to occur in stochastic bursts. But the origin of such ubiquitous phenomenon has not been understood. Here, we present the mechanism in bacteria. We developed a high-throughput, in vitro, single-molecule assay to follow transcription on individual DNA templates in real time. We showed that positive supercoiling buildup on a DNA segment by transcription slows down transcription elongation and eventually stops transcription initiation. Transcription can be resumed upon gyrase binding to the DNA segment. Furthermore, using single-cell mRNA counting fluorescence in situ hybridization (FISH), we found that duty cycles of transcriptional bursting depend on the intracellular gyrase concentration. Together, these findings prove that transcriptional bursting of highly expressed genes in bacteria is primarily caused by reversible gyrase dissociation from and rebinding to a DNA segment, changing the supercoiling level of the segment.

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.

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.

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.

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.

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.

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.

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.

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.

Soft Materials with Diverse Suprastructures via the Self-Assembly of Metal-Organic Complexes.

Inspired by assemblies in the natural world, researchers have prepared diverse suprastructures with distinct spatial arrangements by artificial self-assembly, including micelles, vesicles, ribbons, films, fibers, and tubes. The field of assembly is undergoing a transition from single-component to multicomponent assembly and single-step to multistep processing. Control over the size, shape, and composition of these building blocks has enabled the formation of suprastructures with substantial structural diversity. More importantly, harnessing noncovalent interactions to create suprastructures in a controlled manner will lead to a better understanding of the formation of complex self-organized patterns. However, for the construction of multiscale self-assemblies with controllable shapes and functions, the selection of a suitable protocol remains challenging. Coordination-driven self-assembly provides a bottom-up approach to construct various metal-organic complexes (MOCs), which could be further used as building blocks with controllable shapes and sizes. Despite the tremendous progress made in the design of MOC-based supramolecular materials, most of these MOCs have dimensions of only several nanometers, and investigations of these structures rely on the characterization of their crystal structure. However, most of the functional suprastructures in living organisms have dimensions ranging from microns to centimeters and have the form of soft materials. Thus, obtaining MOC-based highly ordered materials of larger size remains a challenge. This Account focuses on our recent advances in the construction of soft suprastructure materials with MOCs. A series of functionalized MOCs was first constructed through coordination-driven self-assembly. Then, further self-assembly of the as-prepared MOCs gave rise to the formation of higher-order structures. By changing the functional groups in the acceptors and donors in the MOCs, different suprastructures, including nanospheres, nanodiamonds, nanorods, nanofibers, membranes, films, and gels, were prepared. These studies suggest that using MOCs as building blocks is a highly efficient strategy to achieve complex architectures and functional materials for the development of desired MOC-based soft materials with high precision and fidelity.

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.

Proximity-Induced Cooperative Polymerization in "Hinged" Helical Polypeptides.

Cooperative interactions and transitions are among the most important strategies utilized by biological systems to regulate a variety of physical and chemical processes. We report herein an auto-accelerated, rapid cooperative polymerization of N-carboxyanhydrides (NCAs) with initiators structurally as simple as linear aliphatic diamines for the synthesis of polypeptides. The polymerization initiated by diamines proceeds via the formation of "hinged" polypeptides, which are two blocks of helical chains connected head-to-head by the diamine molecules in the polymerization solution. The reactions follow a two-stage, cooperative polymerization kinetic; the cooperative interactions between the macrodipoles of the two hinged helical polypeptides dramatically accelerate the polymerization. Compared to the NCA polymerization initiated by the hexylamine (CH3(CH2)5NH2), the chain propagation rate of the NCA polymerization is increased by more than 600 times when initiated by its diamine analogue (1,6-diaminohexane, NH2(CH2)6NH2). This proximity-induced cooperative polymerization showcases the single helix as a remarkable cooperativity-enabling motif in synthetic chemistry.

Comprehensive analysis of presurgical factors predicting psychiatric disorders in patients with refractory temporal lobe epilepsy and mesial temporal sclerosis underwent cortico-amygdalohippocampectomy.

BACKGROUND: This study aimed to evaluate the predictive value of presurgical factors for psychiatric disorders (PD) in refractory temporal lobe epilepsy and mesial temporal sclerosis (TLE-MTS) patients underwent cortico-amygdalohippocampectomy (CAH). METHODS: A total of 98 refractory TLE-MTS patients underwent CAH were consecutively enrolled in this cohort study. Several presurgical factors were recorded, such as married status, employment status, highest education, disease duration, family history of epilepsy, and disorganized VEEG background activity. RESULTS: There were 17 (17.3%) refractory TLE-MTS patients occurring PD after CAH, including 8 (8.2%) mood disorders, 7 (7.1%) anxiety disorders, 8 (8.2%) psychoses, and 1 (1.0%) interictal dysphoric disorder. Employed status correlated with low PD occurrence, while disease duration and asymmetric VEEG background activity positively correlated with PD occurrence. Multivariate logistic analysis revealed employed status (P = 0.009) could independently predict lower PD occurrence, while highest education (P = 0.027), disease duration (P = 0.028), seizure frequencies (P = 0.015), and asymmetric VEEG background activity (P = 0.034) could independently predict higher PD occurrence. Receiver operating characteristic curve showed combination of these five factors (area under curve (AUC) = 0.871, 95%CI: 0.783-0.960) disclosed a great predictive value of PD occurrence. The sensitivity and specificity were 70.6% and 92.6% at the best cutoff point. In addition, the percentage of PD was increased with higher Engel classification (P = 0.003). CONCLUSION: Employed status, highest education, disease duration, seizure frequencies, and asymmetric VEEG background activity correlate with PD occurrence independently in epileptic patients.

Self-Assembly of Metallacages into Multidimensional Suprastructures with Tunable Emissions.

Cubic metallacages were arranged into multidimensional (one-, two-, and three-dimensional) suprastructures via multistep assembly. Four new shape-controllable, hybrid metallacages with modified substituents and tunable electronic properties were prepared using dicarboxylate ligands with various substituents (sodium sulfonate, nitro, methoxyl, and amine), tetra-(4-pyridylphenyl) ethylene, and cis-(PEt3)2Pt(OTf)2. The as-prepared metallacages were used as building blocks for further assembly. Diverse suprastructures with tunable emissions (λmax from 451 to 519 nm) and various substituents (-SO3Na, -NO2, -OCH3, and -NH2) were prepared depending on the substituents and solvents used.

Synthetic polypeptides: from polymer design to supramolecular assembly and biomedical application.

Synthetic polypeptides from the ring-opening polymerization of N-carboxyanhydrides (NCAs) are one of the most important biomaterials. The unique features of these synthetic polypeptides, including their chemical diversity of side chains and their ability to form secondary structures, enable their broad applications in the field of gene delivery, drug delivery, bio-imaging, tissue engineering, and antimicrobials. In this review article, we summarize the recent advances in the design of polypeptide-based supramolecular structures, including complexes with nucleic acids, micelles, vesicles, hybrid nanoparticles, and hydrogels. We also highlight the progress in the chemical design of functional polypeptides, which plays a crucial role to manipulate their assembly behaviours and optimize their biomedical performances. Finally, we conclude the review by discussing the future opportunities in this field, including further studies on the secondary structures and cost-effective synthesis of polypeptide materials.

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.

A convenient single-cell newly synthesized transcriptome assay reveals gene expression dynamics during early-stage T-cell activation.

Sequencing newly synthesized transcriptome alongside regular transcriptome in single cells enables the study of gene expression temporal dynamics during rapid chromatin and gene regulation processes. However, existing assays to profile single-cell newly synthesized transcriptome require in-house technical expertise to achieve high cellular throughput, limiting their widespread application. Here, we developed NOTE-seq, a method that simultaneously profiles regular and newly synthesized transcriptomes in single cells. NOTE-seq integrates 4-thiouridine labeling of newly synthesized RNA, thiol-alkylation-based chemical conversion, and a streamlined workflow on the 10X Genomics platform, offering high cellular throughput that is accessible and convenient for regular biology laboratories without specialized single-cell expertise. Using NOTE-seq, we characterized the temporal dynamics of gene expression during early-stage T-cell activation in Jurkat and naïve T cells, identified transcription factors and regulons, and discovered Fli-1 as a master transcription factor for gene regulation upon T-cell stimulation. Interestingly, chemotherapeutic topoisomerase inhibitor affects Fli-1 level in T cells, indicating potential complications for the immune system.