DNA break induces rapid transcription repression mediated by proteasome-dependent RNAPII removal.

A DNA double-strand break (DSB) jeopardizes genome integrity and endangers cell viability. Actively transcribed genes are particularly detrimental if broken and need to be repressed. However, it remains elusive how fast the repression is initiated and how far it influences the neighboring genes on the chromosome. We adopt a recently developed, very fast CRISPR to generate a DSB at a specific genomic locus with precise timing, visualize transcription in live cells, and measure the RNA polymerase II (RNAPII) occupancy near the broken site. We observe that a single DSB represses the transcription of the damaged gene in minutes, which coincides with the recruitment of a damage repair protein. Transcription repression propagates bi-directionally along the chromosome from the DSB for hundreds of kilobases, and proteasome is evoked to remove RNAPII in this process. Our method builds a foundation to measure the rapid kinetic events around a single DSB and elucidate the molecular mechanism.

GHz-rate 57-fs acousto-optic mode-locking fiber laser based on cascaded all-fiber pulse compression.

We demonstrate a compact ultrafast fiber laser system that can deliver 1.87 GHz pulse train at 1550 nm with a pulse energy of 52 pJ and an ultrashort pulse duration of 57 fs. While an acousto-optic mode-locking fiber laser was used as the seed light source at GHz rate, a stage of Er-doped fiber amplifier boosted the laser power to ∼320 mW, giving a pulse energy of ∼170 pJ. Then, a pulse compression setup was constructed, providing a high compression ratio of ∼10 with a total efficiency of ∼32%. In the cascaded compression configuration, multiple fiber samples with alternately normal and anomalous dispersion were fused together, providing efficient nonlinear spectral broadening while suppressing excessive pulse broadening over propagation. This GHz-rate ultrafast fiber laser, with compact configuration, broad optical spectrum, and high time-resolving ability could be used as the seed light source for constructing high-rate, high-power ultrafast laser systems and may find a few applications in optical measurements and microwave photonics.

Characterization of the composition, structure, and functional potential of bamboo rhizosphere archaeal communities along a chromium gradient.

Introduction: Bamboo can be used in the phytoremediation of heavy metal pollution. However, the characteristics of the bamboo rhizosphere archaeal community in Cr-contaminated soil under field conditions remain unclear. Methods: In this study, high-throughput sequencing was used to examine the rhizosphere soil archaeal communities of Lei bamboo (Phyllostachys precox) plantations along a Cr pollution gradient. Results: The results revealed U-shaped relationships between Cr [total Cr (TCr) or HCl-extractable Cr (ACr)] and two alpha indices (Chao1 and Shannon) of archaea. We also established that high Cr concentrations were associated with a significant increase in the abundance of Thaumarchaeota and significant reductions in the abundances of Crenarchaeota and Euryarchaeota. The archaeal co-occurrence networks reduced in complexity with Cr pollution, decreasing the community's resistance to environmental disturbance. Candidatus nitrosotalea and Nitrososphaeraceae_unclassified (two genera of Thaumarchaeota) were identified as keystone taxa. The community structure of soil archaeal communities was also found to be affected by TCr, ACr, pH, total organic C, and available nutrient (N, P, and K) concentrations, with pH being identified as the most reliable predictor of the archaeal community in assessed soils. Discussion: These findings enhance our understanding of microbial responses to Cr pollution and provide a basis for developing more refined approaches for the use of bamboo in the remediation of Cr-contaminated soils.

A Molecular Dynamics Study on the Defect Formation and Mechanical Behavior of Molybdenum Disulfide under Irradiation.

Due to its appealing characteristics, molybdenum disulfide (MoS2) presents a promising avenue for the exploration of lubrication protection materials in high-energy irradiation scenarios. Herein, we present a comprehensive investigation into the defect behavior of multilayer MoS2 under argon (Ar) atom irradiation leveraging molecular dynamics simulations. We have demonstrated the energy shifts and structural evolution in MoS2 upon irradiation, including the emergence of Frenkel defects and intricate defect clusters. The structural damage exhibits an initial increase followed by a subsequent decrease as the incident kinetic energy increases, ultimately peaking at 2.5 keV. Moreover, we investigated the effect of postannealing on defect recovery and conducted the uniaxial tensile and interlayer shearing simulation in order to provide valuable insights for the defect evolution and its impact on mechanical and tribological properties. Furthermore, we have proposed the optimal annealing temperature. The current study reveals the atomic mechanisms underlying irradiation-induced damage on the structural integrity and mechanical performance of MoS2, thereby providing crucial guidance for its vital application in nuclear reactors and aerospace industries.

Protocol to identify DNA-binding proteins recognizing nucleotide repeat dsDNAs.

DNA-binding proteins perform diverse functions, including regulating cellular growth and orchestrating chromatin architecture. Here, we present a protocol to discover proteins specifically interacting with a hexanucleotide repeat DNA, the expansion of which is known as the most frequent genetic cause of familial C9orf72 amyotrophic lateral sclerosis and frontotemporal dementia. We describe steps to fish out DNA-binding proteins recognizing double-stranded repeat DNAs using a SILAC (stable isotope labelling by amino acids in cell culture)-based approach and validate the results using electrophoretic mobility shift assay. For complete details on the use and execution of this protocol, please refer to Liu et al.1.

Continuous tuning of pulse parameters in a soliton fiber laser by adjusting the effect of nonlinear polarization rotation: publisher's note.

This publisher's note contains a correction to Opt. Lett.49, 674 (2024)10.1364/OL.509981.

A pathologic scoring system for predicting postoperative prognosis in patients with ruptured hepatocellular carcinoma.

BACKGROUND: The accuracy of pathological factors to predict the prognosis of patients with ruptured hepatocellular carcinoma (rHCC) is unclear. We aimed to develop and validate a novel scoring system based on pathological factors to predict the postoperative survival of patients with rHCC. METHOD: Patients with rHCC who underwent hepatectomy were recruited from three hospitals and allocated to the training (n = 221) and validation (n = 194) cohorts. A new scoring system, namely the MSE (microvascular invasion-satellite foci-Edmondson Steiner) score, was established based on three pathological factors using univariate and multivariate Cox proportional hazards regression analyses, including microvascular invasion, satellite foci, and differentiation grade. Finally, patients were stratified into three groups based on their risk of prognosis (low, intermediate, or high) according to their MSE score. We also constructed MSE score-based nomograms. The performance of the nomograms was assessed by receiver operating characteristic and calibration curve analyses and validated using the validation cohort. RESULTS: Three pathological factors were significantly correlated with overall survival (OS) and recurrence-free survival (RFS), three of which were included in the MSE score. The score can clearly stratify rHCC patients after hepatectomy (P < 0.05). And we established nomograms based on the MSE score (MSE score, Barcelona Clinic Liver Cancer stage, and alpha-fetoprotein concentration) to predict postoperative OS and RFS in patients with rHCC. The nomograms showed good discrimination, with C-indices over 0.760 for OS and RFS at 1, 3, and 5 years, respectively. The calibration curve showed excellent nomogram calibration, which was also verified in the validation cohort. CONCLUSION: The clinical MSE score were accurate in predicting OS and RFS in patients with rHCC with resectable lesions after hepatectomy.

Photon Upconversion at Organic-Inorganic Interfaces.

Photon upconversion is a process that combines low-energy photons to form useful high-energy photons. There are potential applications in photovoltaics, photocatalysis, biological imaging, etc. Semiconductor quantum dots (QDs) are promising for the absorption of these low-energy photons due to the high extinction coefficient of QDs, especially in the near infrared (NIR). This allows the intriguing use of diffuse light sources such as solar irradiation. In this review, we describe the development of this organic-QD upconversion platform based on triplet-triplet annihilation, focusing on the dark exciton in QDs with triplet character. Then we introduce the underlying energy transfer steps, starting from QD triplet photosensitization, triplet exciton transport, triplet-triplet annihilation, and ending with the upconverted emission. Design principles to improve the total upconversion efficiency are presented. We end with limitations in current reports and proposed future directions. This review provides a guide for designing efficient organic-QD upconversion platforms for future applications, including overcoming the Shockley-Queisser limit for more efficient solar energy conversion, NIR-based phototherapy, and diagnostics in vivo.

Comparing the Efficacy of Video-Assisted Thoracoscopic Surgery and Open Thoracotomy in Sleeve Lobectomy for the Treatment of Central-Type Non-small Cell Lung Cancer: A Systematic Review and Meta-Analysis.

Objective: Central-type Non-small Cell Lung Cancer (NSCLC) treatment involves different surgical techniques, including Video-Assisted Thoracoscopic Surgery (VATS) and Open Thoracotomy Sleeve Lobectomy. However, there remains a lack of consensus on the most effective treatment modality. Methods: This study strictly adhered to PRISMA guidelines. Four electronic databases were searched without time or language limitation, and studies comparing VATS and Open Thoracotomy in patients with central-type NSCLC undergoing sleeve lobectomy were included. Primary outcomes were perioperative outcomes (blood loss, operation time, intraoperative lymph node dissection count, postoperative hospital stay, and complication rates), 3-year Progression-Free Survival (PFS) rate, and Overall Survival (OS) rate. Results: The meta-analysis included six studies with 569 patients. VATS was associated with longer operation time [SMD = 0.75, 95% CI (0.29, 1.21)], less intraoperative blood loss [SMD = -0.23; 95% CI (-0.44, -0.01)], and shorter hospital stay [SMD = -0.53; 95% CI (-0.73, -0.34)]. There were no significant differences in the number of lymph nodes dissected, postoperative complications, and 3-year PFS and OS rates between the two groups. Conclusions: VATS sleeve lobectomy for central-type NSCLC results in less surgical trauma and quicker postoperative recovery without adversely impacting tumor prognosis compared to open thoracotomy sleeve lobectomy. Despite a longer operation time, VATS could be considered an alternative to open thoracotomy sleeve lobectomy. VATS sleeve lobectomy is a safe and effective alternative to open thoracotomy in treating central-type NSCLC, as it results in less surgical trauma and quicker postoperative recovery without impacting tumor prognosis negatively. More well-designed randomized controlled trials are required to verify these findings.

Integrated Genomics and Transcriptomics Provide Insights into Salt Stress Response in Bacillus subtilis ACP81 from Moso Bamboo Shoot (Phyllostachys praecox) Processing Waste.

Salt stress is detrimental to the survival of microorganisms, and only a few bacterial species produce hydrolytic enzymes. In this study, we investigated the expression of salt stress-related genes in the salt-tolerant bacterial strain Bacillus subtilis ACP81, isolated from bamboo shoot processing waste, at the transcription level. The results indicate that the strain could grow in 20% NaCl, and the sub-lethal concentration was 6% NaCl. Less neutral protease and higher cellulase and ß-amylase activities were observed for B. subtilis ACP81 under sub-lethal concentrations than under the control concentration (0% NaCl). Transcriptome analysis showed that the strain adapted to high-salt conditions by upregulating the expression of genes involved in cellular processes (membrane synthesis) and defense systems (flagellar assembly, compatible solute transport, glucose metabolism, and the phosphotransferase system). Interestingly, genes encoding cellulase and ß-amylase-related (malL, celB, and celC) were significantly upregulated and were involved in starch and sucrose metabolic pathways, and the accumulated glucose was effective in mitigating salt stress. RT-qPCR was performed to confirm the sequencing data. This study emphasizes that, under salt stress conditions, ACP81 exhibits enhanced cellulase and ß-amylase activities, providing an important germplasm resource for saline soil reclamation and enzyme development.

Continuous tuning of pulse parameters in a soliton fiber laser by adjusting the effect of nonlinear polarization rotation.

We demonstrate that through inserting a short length of highly birefringent small-core photonic crystal fiber (Hi-Bi SC-PCF) into a soliton fiber laser, the nonlinear polarization rotation effect in this laser can be manipulated, leading to continuous tuning of the output pulse parameters. In experiments, we observed that by adjusting the polarization state of light launched into the Hi-Bi SC-PCF and varying the cavity attenuation, the laser spectral width can be continuously tuned from ∼7.1 to ∼1.7 nm, corresponding to a pulse-width-tuning range from ∼350 fs to ∼1.56 ps. During the parameter tuning, the output pulses strictly follow the soliton area theory, giving an almost constant time-bandwidth-product of ∼0.31. This soliton fiber laser, being capable of continuous parameter tuning, could be applied as the seed source in ultrafast laser systems and may find some applications in nonlinear-optics and soliton-dynamics experiments.

Growth of BiSBr Microsheet Arrays for Enhanced Photovoltaics Performance.

In this study, single-crystalline BiSBr is synthesized using a solution-based approach and conducted a systematic characterization of its photoelectric properties and photovoltaic performances. UV photoelectron spectroscopy and density functional theory (DFT) calculations reveal that BiSBr is an indirect p-type semiconductor, characterized by distinct positions and compositions of the valence band maximum and conduction band minimum. The BiSBr single crystal microrod features a significant electrical conductivity of 14 800 S m-1 along the c-axis, denoting minimal carrier resistance in this direction. For photovoltaic performance assessment, the authors successfully fabricated two homogeneous BiSBr films on TiO2 porous substrates: A microsheet array film via physical vapor deposition (PVD) and solvothermal treatment, and a BiSBr microsheet film via PVD and thermal treatment. The solar cell, comprising a BiSBr microsheet array film with an architecture of fluorine-doped tin oxide FTO/TiO2/BiSBr/(I3 -/I-)/Pt, demonstrated a power conversation efficiency of 1.40%, ≈11 times that of BiSBr microsheet film counterpart. These preliminary results underscore the potential of BiSBr microsheet arrays, producible through low-cost solution processes, as adept light absorbers, enhancing photovoltaic efficiency through effective light scattering and promoting efficient electron-hole separation and transport.

G-quadruplex in the TMV Genome Regulates Viral Proliferation and Acts as Antiviral Target of Photodynamic Therapy.

Plant viruses seriously disrupt crop growth and development, and classic protein-targeted antiviral drugs could not provide complete protection against them. It is urgent to develop antiviral compounds with novel targets. Photodynamic therapy shows potential in controlling agricultural pests, but nonselective damage from reactive oxygen species (ROS) unexpectedly affects healthy tissues. A G-quadruplex (G4)-forming sequence in the tobacco mosaic virus (TMV) genome was identified to interfere the RNA replication in vitro, and affect the proliferation of TMV in tobacco. N-methyl mesoporphyrin IX stabilizing the G4 structure exhibited inhibition against viral proliferation, which was comparable to the inhibition effect of ribavirin. This indicated that G4 could work as an antiviral target. The large conjugate planes shared by G4 ligands and photosensitizers (PSs) remind us that the PSs could work as antiviral agents by targeting G4 in the genome of TMV. Chlorin e6 (Ce6) was identified to stabilize the G4 structure in the dark and selectively cleave the G4 sequence by producing ROS upon LED-light irradiation, leading to 92.2% inhibition against TMV in vivo, which is higher than that of commercial ningnanmycin. The inhibition of Ce6 was lost against the mutant variants lacking the G4-forming sequence. These findings indicated that the G-quadruplex in the TMV genome worked as an important structural element regulating viral proliferation, and could act as the antiviral target of photodynamic therapy.

Experimental studies on the core-structure dependence of backward Brillouin gain in solid-core photonic crystal fibers.

Stimulated Brillouin scattering (SBS) in solid-core photonic crystal fibers (PCFs) differs significantly from that in standard optical fibers due to the tight confinement of both optical and acoustic fields in their µm-sized fiber cores, as resultantly evident in their Brillouin gain spectra. Despite many theoretical studies based on either simplified models or numerical simulations, the structural dependency of Brillouin gain spectra in small-core PCFs has not been characterized comprehensively using PCFs with elaborated parameter controls. In this work we report a comprehensive characterization on the core-structure dependences of backward SBS effects in solid-core PCFs that are drawn with systematically varied core-diameter, revealing several key trends of the fiber Brillouin spectrum in terms of its gain magnitude, Brillouin shift and multi-peak structure, which have not been reported in detail previously. Our work provides some practical guidance on PCF design for potential applications like Brillouin fiber lasers and Brillouin fiber sensing.

Joining of metallic glasses in liquid via ultrasonic vibrations.

Joining processes especially for metallic materials play critical roles in manufacturing industries and structural applications, therefore they are essential to human life. As a more complex technique, under-liquid joining has far-reaching implications for national defense, offshore mining. Furthermore, up-to-now, the effective joining of metals in extreme environments, such as the flammable organo-solvent or the arctic liquid nitrogen, is still uninvestigated. Therefore, an efficient under-liquid joining approach is urgently called for. Here we report a method to join different types of metallic glasses under water, seawater, alcohol and liquid-nitrogen. The dynamic heterogeneity and liquid-like region expansion induces fluid-like behavior under ultrasonic vibration to promote oxide layer dispersion and metal bonding, allowing metallic glasses to be successfully joined in heat-free conditions, while still exhibiting excellent tensile strength (1522 MPa), bending strength (2930 MPa) and improved corrosion properties. Our results provide a promising strategy for manufacturing under offshore, polar, oil-gas and space environments.

A magnetic field-driven multi-functional "medical ship" for intestinal tissue collection in vivo.

The incidence of intestinal cancer has risen significantly. Because of the many challenges posed by the complex environment of the intestine, it is difficult to diagnose accurately and painlessly using conventional methods, which requires the development of new body-friendly diagnostic methods. Micro- and nanomotors show great potential for biomedical applications in restricted environments. However, the difficulty of recycling has been a constraint in the collection of biological tissues for diagnostic purposes. Here, we propose a multi-functional "medical ship" (MFMS) that can be rapidly driven by a magnetic field and can reversibly "open" and "close" its internal storage space under NIR laser irradiation. It provides a transportation and recovery platform for micro- and nanomotors and cargoes. In addition, fast selection of the MFMS and magnetic nanoparticles (MNPs) can be realized through adjusting the strength and frequency of the external magnetic field. Rapid encapsulation of intestinal tissues by MNPs was achieved using a low-frequency rotating magnetic field. In addition, we demonstrated the controlled release of MNPs using the MFMS and the collection of intestinal tissues. The proposed MFMS is an intelligent and controllable transportation platform with a simple structure, which is expected to be a new tool for performing medical tasks within the digestive system.

Preparation and characterization of Pickering emulsion with directionally embedded antimicrobial peptide MOp2 and its preservation effect on grass carp.

The peptide MOp2 obtained from Moringa oleifera seeds showed good antimicrobial activity. However, the stability of its activity has not yet been studied. In the present study, MOp2-loaded thiolated chitosan-stabilized (CMOp2) Pickering emulsion was prepared and applied to prolong the shelf life of grass carp. The encapsulation rate of MOp2 was 57.7% in CMOp2. In addition, the effects of different concentrations of CMOp2 solid particles and pH on droplet size, zeta optional and storage stability of Pickering emulsions were evaluated; the best condition for preparing Pickering emulsion through experiment was 1.75% CMOp2 solid particles at pH 9.5. Moreover, morphological observations and rheological analysis indicated that Pickering emulsions were considered a water-in-oil emulsion with typical non-Newtonian fluid characteristics. Furthermore, the prepared Pickering emulsion could significantly inhibit the growth of Escherichia coli and Staphylococcus aureus. Besides, Pickering emulsion effectively prevented spoilage of grass carp, and the Pickering emulsion-treated group reduced its pH, TVB-N and color values, inhibited microbial growth, and extended shelf life to 9 day at the storage of 4 °C. Overall, the present findings provide a reference for the application of MOp2-loaded Pickering emulsions in food preservation.

Long-term effect of light rare earth element neodymium on Anammox process.

During the mining of rare earth minerals, the application of neodymium-containing manures, and the treatment of spent neodymium iron boron magnet, the generation of ammonia wastewater containing neodymium is increasing. Thus, the effects of neodymium (Nd(III)) on anaerobic ammonium oxidation (Anammox) were investigated from the aspects of performance, kinetics, statistics, microbial community and sludge morphology, and the recovery strategy of EDTA-2Na wash was discussed. The nitrogen removal efficiency of the Anammox reactor decreased significantly and eventually collapsed at the Nd(III) dosing levels of 20 and 40 mg L-1, respectively. And the toxicity of Nd(III) to AnAOB was determined by the amount internalized into the cells. The EDTA-2Na wash successfully increased the total nitrogen removal rate (TNRR) of Nd(III)-inhibited Anammox to 41.60% of its initial value within 30 days, and the modified Boltzmann model accurately simulated this recovery process. The transient and extended effects of Nd(III), self-recovery, and EDTA-2Na wash on Anammox were effectively assessed using a one-sample t-test. 16S rRNA gene sequencing indicated that Nd(III) remarkably decreased the relative abundance of Planctomycetes and Candidatus Brocadia. The scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS) revealed crystal-like neodymium particles on the surface of Anammox sludge. The above-mentioned results demonstrate that the concentration of Nd(III) should be below the toxicity threshold (20 mg L-1) when treating ammonia wastewater containing neodymium by Anammox, and also emphasize the importance of an appropriate recovery strategy.

Beyond Solvothermal: Alternative Synthetic Methods for Covalent Organic Frameworks.

Covalent organic frameworks (COFs) are crystalline porous organic materials that hold a wealth of potential applications across various fields. The development of COFs, however, is significantly impeded by the dearth of efficient synthetic methods. The traditional solvothermal approach, while prevalent, is fraught with challenges such as complicated processes, excessive energy consumption, long reaction times, and limited scalability, rendering it unsuitable for practical applications. The quest for simpler, quicker, more energy-efficient, and environmentally benign synthetic strategies is thus paramount for bridging the gap between academic COF chemistry and industrial application. This Review provides an overview of the recent advances in alternative COF synthetic methods, with a particular emphasis on energy input. We discuss representative examples of COF synthesis facilitated by microwave, ultrasound, mechanic force, light, plasma, electric field, and electron beam. Perspectives on the advantages and limitations of these methods against the traditional solvothermal approach are highlighted.

Photoresponsive hydrogel-based soft robot: A review.

Soft robots have received a lot of attention because of their great human-robot interaction and environmental adaptability. Most soft robots are currently limited in their applications due to wired drives. Photoresponsive soft robotics is one of the most effective ways to promote wireless soft drives. Among the many soft robotics materials, photoresponsive hydrogels have received a lot of attention due to their good biocompatibility, ductility, and excellent photoresponse properties. This paper visualizes and analyzes the research hotspots in the field of hydrogels using the literature analysis tool Citespace, demonstrating that photoresponsive hydrogel technology is currently a key research direction. Therefore, this paper summarizes the current state of research on photoresponsive hydrogels in terms of photochemical and photothermal response mechanisms. The progress of the application of photoresponsive hydrogels in soft robots is highlighted based on bilayer, gradient, orientation, and patterned structures. Finally, the main factors influencing its application at this stage are discussed, including the development directions and insights. Advancement in photoresponsive hydrogel technology is crucial for its application in the field of soft robotics. The advantages and disadvantages of different preparation methods and structures should be considered in different application scenarios to select the best design scheme.