gcPathogen: a comprehensive genomic resource of human pathogens for public health.

Here, we present the manually curated Global Catalogue of Pathogens (gcPathogen), an extensive genomic resource designed to facilitate rapid and accurate pathogen analysis, epidemiological exploration and monitoring of antibiotic resistance features and virulence factors. The catalogue seamlessly integrates and analyzes genomic data and associated metadata for human pathogens isolated from infected patients, animal hosts, food and the environment. The pathogen list is supported by evidence from medical or government pathogenic lists and publications. The current version of gcPathogen boasts an impressive collection of 1 164 974 assemblies comprising 986 044 strains from 497 bacterial taxa, 4794 assemblies encompassing 4319 strains from 265 fungal taxa, 89 965 assemblies featuring 13 687 strains from 222 viral taxa, and 646 assemblies including 387 strains from 159 parasitic taxa. Through this database, researchers gain access to a comprehensive 'one-stop shop' that facilitates global, long-term public health surveillance while enabling in-depth analysis of genomes, sequence types, antibiotic resistance genes, virulence factors and mobile genetic elements across different countries, diseases and hosts. To access and explore the data and statistics, an interactive web interface has been developed, which can be accessed at https://nmdc.cn/gcpathogen/. This user-friendly platform allows seamless querying and exploration of the extensive information housed within the gcPathogen database.

A Robust, Flexible, Hydrophobic, and Multifunctional Pressure Sensor Based on an MXene/Aramid Nanofiber (ANF) Aerogel Film.

Pressure sensors with desirable flexibility, robustness, and versatility are urgently needed for complicated smart wearable devices. However, developing an ideal multifunctional flexible sensor is still challenging. In this work, a composite aerogel film sensor with an internal three-dimensional (3D) microporous and hierarchical structure is successfully fabricated by the self-assembly of aramid nanofiber (ANF) and conductive MXene by vacuum-assisted filtration and ice crystal growth. The resultant MXene/ANF aerogel film with a mass ratio of 3/7 (30% MAAF) presents high robustness with an outstanding tensile strength of 14.1 MPa and a modulus of 455 MPa while retaining appealing flexibility and sensitive characteristics due to the 3D microstructure. Accompanied by superior electric conductivity, the MAAF sensor performs noticeably in human motion and microexpression detection with a fast response time of 100 ms and a high sensitivity of 37.4 kPa-1. In addition, MAAF exhibits considerable thermal shielding performance based on the excellent thermostability. Moreover, it possesses prominent electrothermal property with a wide heating temperature range (32.7-242 °C) in a fast thermal response time (5 s) due to the Joule effect. Additionally, a hydrophobic SiO2 coating is introduced on the surface of MAAF to further broaden the sensing application, and the obtained MAAF@SiO2 sensor shows distinguished sensing capability underwater, which can be accurately applied to swimming monitoring. Therefore, this work provides a highly flexible, lightweight, robust, and multifunctional aerogel film sensor, showing promising potential in smart wearable sensing and healthcare devices, intelligent robots, and underwater detection.

Ultrafast formation of ANFs with kinetic advantage and new insight into the mechanism.

Aramid nanofibers (ANFs) have important applications in many fields, including electrical insulation and battery separators. However, a few limitations seriously restrict the application of ANFs currently, such as low preparation efficiency and the unclear preparation mechanism. To overcome these limitations, the present work proposes a new view-point from the perspective of reaction kinetics. The preparation efficiency was proven to essentially rely on the effective c(OH-). With a simple pre-treatment, a kinetic advantage was created and the preparation time of ANFs was reduced from multiple hours to 10 minutes, which was a considerable step towards practical applications. Moreover, the resultant ANF membranes still exhibited excellent properties in terms of mechanical strength (tensile strength > 160 MPa), thermal stability, light transmittance, and electrical insulation (above 90 kV mm-1). This work not only presents an ultrafast method to produce ANFs but also provides new insights into the mechanism that will benefit the subsequent development of ANF-based materials.

Cellulose nanofibril/mineral composites induced by H-bond/ionic coordination in co-refining system.

Mineral fillers hinder cellulosic fiber bonding and thus limit the increase of filler content in paper. Herein, precipitated calcium carbonate (PCC)/cellulose nanofibrils (CNF) composites were fabricated by a facile and efficient strategy, i.e., co-refining process (CRP). During this process, CNF and PCC were activated by mechanochemical effect and formed encapsulation structure by calcium ion coordination and hydrogen bonding. The encapsulation structure and H-bond/ionic coordination interactions not only endowed the composite with excellent size stability but also enhanced interfacial interaction between composite fillers and cellulosic fibers. Compare with the paper filled with only PCC, PCC + CNF mixture, the tensile index of the cellulosic paper containing PCC/CNF composite was increased by 44.48% and 12.14%, respectively. These results not only provide a facile and scalable approach to increase interaction between cellulosic fiber and mineral filler but also create more possibilities for special paper-based materials with requiring high content of inorganic materials.

VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes.

The genomic variations of SARS-CoV-2 continue to emerge and spread worldwide. Some mutant strains show increased transmissibility and virulence, which may cause reduced protection provided by vaccines. Thus, it is necessary to continuously monitor and analyze the genomic variations of SARS-COV-2 genomes. We established an evaluation and prewarning system, SARS-CoV-2 variations evaluation and prewarning system (VarEPS), including known and virtual mutations of SARS-CoV-2 genomes to achieve rapid evaluation of the risks posed by mutant strains. From the perspective of genomics and structural biology, the database comprehensively analyzes the effects of known variations and virtual variations on physicochemical properties, translation efficiency, secondary structure, and binding capacity of ACE2 and neutralizing antibodies. An AI-based algorithm was used to verify the effectiveness of these genomics and structural biology characteristic quantities for risk prediction. This classifier could be further used to group viral strains by their transmissibility and affinity to neutralizing antibodies. This unique resource makes it possible to quickly evaluate the variation risks of key sites, and guide the research and development of vaccines and drugs. The database is freely accessible at www.nmdc.cn/ncovn.

Flexible, Robust, and Durable Aramid Fiber/CNT Composite Paper as a Multifunctional Sensor for Wearable Applications.

Flexible paper-based sensors may be applied in numerous fields, but this requires addressing their limitations related to poor thermal and water resistance, which results in low service life. Herein, we report a paper-based composite sensor composed of carboxylic carbon nanotubes (CCNTs) and poly-m-phenyleneisophthalamide (PMIA), fabricated by a facile papermaking process. The CCNT/PMIA composite sensor exhibits an ability to detect pressures generated by various human movements, attributed to the sensor's conductive network and the characteristic "mud-brick" microstructure. The sensor exhibits the capability to monitor human motions, such as bending of finger joints and elbow joints, speaking, blinking, and smiling, as well as temperature variations in the range of 30-90 °C. Such a capability to sensitively detect pressure can be realized at different applied frequencies, gradient sagittas, and multiple twists with a short response time (104 ms) even after being soaked in water, acid, and alkali solutions. Moreover, the sensor demonstrates excellent mechanical properties and hence can be folded up to 6000 times without failure, can bear 5 kg of load without breaking, and can be cycled 2000 times without energy loss, providing a great possibility for a long sensing life. Additionally, the composite sensor shows exceptional Joule heating performance, which can reach 242 °C in less than 15 s even when powered by a low input voltage (25 V). From the perspective of industrialization, low-cost and large-scale roll-to-roll production of the paper-based sensor can be achieved, with a formed length of thousands of meters, showing great potential for future industrial applications as a wearable smart sensor for detecting pressure and temperature, with the capability of electric heating.

Improved 93-11 Genome and Time-Course Transcriptome Expand Resources for Rice Genomics.

In 2002, the first crop genome was published using the rice cultivar 93-11, which is the progenitor of the first super-hybrid rice. The genome sequence has served as a reference genome for the indica cultivars, but the assembly has not been updated. In this study, we update the 93-11 genome assembly to a gap-less sequence using ultra-depth single molecule real-time (SMRT) reads, Hi-C sequencing, reference-guided, and gap-closing approach. The differences in the genome collinearity and gene content between the 93-11 and the Nipponbare reference genomes confirmed to map the indica cultivar sequencing data to the 93-11 genome, instead of the reference. Furthermore, time-course transcriptome data showed that the expression pattern was consistently correlated with the stages of seed development. Alternative splicing of starch synthesis-related genes and genomic variations of waxy make it a novel resource for targeted breeding. Collectively, the updated high quality 93-11 genome assembly can improve the understanding of the genome structures and functions of Oryza groups in molecular breeding programs.

Effective and facile fabrication of MOFs/cellulose composite paper for air hazards removal by virtue of in situ synthesis of MOFs/chitosan hydrogel.

Metal-organic frameworks (MOFs) have potential in the removal of air hazards such as particulate matter. Cellulose paper is low-cost, renewable and highly industrialized matrix. A facile strategy was proposed in the present work to efficiently integrate MOFs with cellulose paper, with zeolitic imidazolate framework-8 (ZIF-8) as the model. ZIF-8 was in situ synthesis in chitosan gel and subsequently added to the cellulose pulp to fabricate composite paper. The retention rate of ZIF-8 was 75.73 %, which was significantly superior to conventional filling method (4.15 %) and in situ precipitation method (6.52 %). Moreover, ZIF-8 in the composite paper functioned well in aspects of adsorption, filtration and sterilization. The PM2.5 removal efficiency was 99.68 % with basis weight 60 g·m-2, while the removal efficiency and pressure drop can be modulated by changing the basis weight of composite paper. This strategy may offer ideas to design MOFs/cellulose-based composite materials for particulate matter removal.

Sugar-Based Aggregation-Induced Emission Luminogens: Design, Structures, and Applications.

Sugars are abundant natural sources existing in biological systems, and bioactive saccharides have attracted much more attention in the field of biochemistry and biomaterials. For better understanding of the sugar-based biomaterials and biological sciences, aggregation-induced emission luminogens (AIE-gens) have been widely employed for detection, tracing, and imaging. This review covers the applications of AIE molecules on sugar-based biomaterials by three parts, polysaccharide, oligosaccharide, and monosaccharide, mainly focusing on saccharide detection, stimuli response materials preparation, bioimaging, and study of the AIE mechanism. These excellent works suggest the promising future of the sugar-based AIE bioconjugates, considering that the naturally designed and elaborately functionalized saccharides play discriminate roles in biological processes and AIE-tagged species may work as an indicator in each case. However, there are a lot of sugar-based biological species that have not been touched, such as mucopolysaccharides and glycoproteins on the cell surface and in the cell plasma. Based on these features, we enthusiastically look forward to more glorious developments in this bright research area.

Lightweight and porous cellulose-based foams with high loadings of zeolitic imidazolate frameworks-8 for adsorption applications.

The excess emission of toxic gases in atmosphere and heavy metal ions in drinking water is still a serious threat to human health. In this paper, a lightweight and porous zeolitic imidazolate frameworks-8@cellulose nanofiber@cellulose foam (ZIF-8@CNF@cellulose foam) with excellent gas adsorption and heavy metal ions removal properties was prepared using a simple in situ green growth method. The nitrogen adsorption property of ZIF-8@CNF@cellulose foam was 30 times higher than pure cellulose foam. Furthermore, the adsorption testing demonstrated that the composite foam showed high adsorption capacity for fluorescent dyes (24.6 mg g-1 for rhodamine B), heavy metal ions (35.6 mg g-1 for Cr (VI)) and organic solvents (45.2 g g-1 for DMF). Additionally, the ZIF-8/cellulose-based foam with 40 wt.% CNF exhibited an excellent mechanical performance, reaching a compressive strength value of 1.30 MPa. Herein, this work provides a feasible method to prepare ZIF-8@CNF@cellulose foam composite materials, which could adsorb gas molecules and heavy metal ions and show a great potential in atmosphere and water treatment.

Highly mineralized chitosan-based material with large size, gradient mineral distribution and hierarchical structure.

Nature materials constituted with organic and inorganic components have hierarchical structure and superior performance. Although a variety of techniques have been developed to mimic microstructure and properties of natural mineralized materials, facile and rapid fabrication of large-size bulk materials with high calcium content under ambient conditions still remains a major challenge. Here, we present a feasible and versatile route to a highly mineralized material with an in situ preparation method where gelation and mineralization occur simultaneously. Meanwhile, hierarchically ordered hydrogel microstructures are formed during the gelation, and controllable inorganic gradient distribution forms along with mineralization spontaneously. With the achievement of high mineral content by the assistance of urea, this fabrication route is facile and efficient, only taking several hours to complete the gelation and mineralization, and large-scale materials are prepared readily. This chitosan matrix-directed mineralization represents a rational and promising strategy for fast fabrication of highly mineralized material with hierarchical structure on a large scale, and the chitosan-based mineralized material has great potential for applications in bone repairing and tissue engineering.

Construction of ordered structure in polysaccharide hydrogel: A review.

Hydrogels are three-dimensional, hydrophilic, polymeric networks, held together by a variety of physical or chemical crosslinks. Among the numerous polymers that can be employed to fabricate hydrogel, polysaccharides have attracted enormous attention due to their peculiar properties that make them suitable for various applications. Compared with homogeneous hydrogels, hydrogels with ordered structures on various length scales are endowed with excellent properties and promising applications in materials science. In the present review, a wide range of techniques were introduced and discussed, which had been utilized to construct ordered hierarchical structures in polysaccharide hydrogels. These techniques focused on the construction of multi-layered and orientated structure, which are two typical and very important forms of hierarchical structure.

A promising transparent and UV-shielding composite film prepared by aramid nanofibers and nanofibrillated cellulose.

An aramid nanofibers (ANFs)-functionalized nanofibrillated cellulose (NFC) composite film is effectively fabricated by the incorporation of ANFs into nanocellulose matrix. The fabrication of the composite film imitates the traditional paper-making process after homogenous mixing. The as-prepared composite film shows excellent UV-shielding performance due to the incorporation of ANFs. Thus the effect of ANFs contents is evaluated in aspects of the surface morphology, physicochemical properties including crystallinity, chemical structure and photothermal stability of composite film. Results show that the composite film with 2 wt.% of ANFs has improved mechanical properties, surface wettability compared to pure NFC film, and presents excellent UV-shielding performance ranging up to 400 nm while still retaining its high transparency. Moreover, the composite film shows high photostability even after continuous UV irradiation (365 nm) for over 12 h. The findings in the present work indicate that the ANFs-functionalized NFC composite films are promising as UV-shielding and transparent materials.

Design of double-component metal-organic framework air filters with PM2.5 capture, gas adsorption and antibacterial capacities.

A biodegradable cellulose-based air filter (Ag-MOFs@CNF@ZIF-8) with multi-layer structure was fabricated by in situ generation of double-component metal-organic frameworks (MOFs) and reinforcement of cellulose nanofiber (CNF). It exhibits good filtration performance, gas adsorption, antibacterial activity and mechanical property. The presence of MOFs could enhance the interaction between the filter and particulate matter (PM) and significantly improve the specific surface area of the composite filter. Thus, the filtration efficiency of the composite filter could reach 94.3% for PM2.5 and the nitrogen adsorption capacity increased to 109 cm3 g-1. Furthermore, the Ag-MOFs@CNF@ZIF-8 filter exhibited excellent antibacterial activity against Escherichia coli with an inhibition zone diameter of 18.1 mm. The compressive strength of the composite filter could be up to 501 kPa, approximately 3.8 times higher than that of pure cellulose filter. Herein, this composite filter has a great application potential in PM2.5 removal, toxic gas adsorption and healthcare fields.

Low- and High-LET Ionizing Radiation Induces Delayed Homologous Recombination that Persists for Two Weeks before Resolving.

Genome instability is a hallmark of cancer cells and dysregulation or defects in DNA repair pathways cause genome instability and are linked to inherited cancer predisposition syndromes. Ionizing radiation can cause immediate effects such as mutation or cell death, observed within hours or a few days after irradiation. Ionizing radiation also induces delayed effects many cell generations after irradiation. Delayed effects include hypermutation, hyper-homologous recombination, chromosome instability and reduced clonogenic survival (delayed death). Delayed hyperrecombination (DHR) is mechanistically distinct from delayed chromosomal instability and delayed death. Using a green fluorescent protein (GFP) direct repeat homologous recombination system, time-lapse microscopy and colony-based assays, we demonstrate that DHR increases several-fold in response to low-LET X rays and high-LET carbon-ion radiation. Time-lapse analyses of DHR revealed two classes of recombinants not detected in colony-based assays, including cells that recombined and then senesced or died. With both low- and high-LET radiation, DHR was evident during the first two weeks postirradiation, but resolved to background levels during the third week. The results indicate that the risk of radiation-induced genome destabilization via DHR is time limited, and suggest that there is little or no additional risk of radiation-induced genome instability mediated by DHR with high-LET radiation compared to low-LET radiation.

Chitosan Hydrogel Structure Modulated by Metal Ions.

As one of the most important polysaccharide, chitosan (CS) has generated a great deal of interest for its desirable properties and wide applications. In the utilization of CS materials, hydrogel is a major and vital branch. CS has the ability to coordinate with many metal ions by a chelation mechanism. While most researchers focused on the applications of complexes between CS and metal ions, the complexes can also influence gelation process and structure of CS hydrogel. In the present work, such influence was studied with different metal ions, revealing two different kinds of mechanisms. Strong affinity between CS and metal ions leads to structural transition from orientation to multi-layers, while weak affinity leads to composite gel with in-situ formed inorganic particles. The study gave a better understanding of the gelation mechanism and provided strategies for the modulation of hydrogel morphology, which benefited the design of new CS-based materials with hierarchical structure and facilitated the utilization of polysaccharide resources.

Difference between Chitosan Hydrogels via Alkaline and Acidic Solvent Systems.

Chitosan (CS) has generated considerable interest for its desirable properties and wide applications. Hydrogel has been proven to be a major and vital form in the applications of CS materials. Among various types of CS hydrogels, physical cross-linked CS hydrogels are popular, because they avoided the potential toxicity and sacrifice of intrinsic properties caused by cross-linking or reinforcements. Alkaline solvent system and acidic solvent system are two important solvent systems for the preparation of physical cross-linked CS hydrogels, and also lay the foundations of CS hydrogel-based materials in many aspects. As members of physical cross-linked CS hydrogels, gel material via alkaline solvent system showed significant differences from that via acidic solvent system, but the reasons behind are still unexplored. In the present work, we studied the difference between CS hydrogel via alkaline system and acidic system, in terms of gelation process, hydrogel structure and mechanical property. In-situ/pseudo in-situ studies were carried out, including fluorescent imaging of gelation process, which provided dynamic visualization. Finally, the reasons behind the differences were explained, accompanied by the discussion about design strategy based on gelation behavior of the two systems.

Gelation process visualized by aggregation-induced emission fluorogens.

Alkaline-urea aqueous solvent system provides a novel and important approach for the utilization of polysaccharide. As one of the most important polysaccharide, chitosan can be well dissolved in this solvent system, and the resultant hydrogel material possesses unique and excellent properties. Thus the sound understanding of the gelation process is fundamentally important. However, current study of the gelation process is still limited due to the absence of direct observation and the lack of attention on the entire process. Here we show the entire gelation process of chitosan LiOH-urea aqueous system by aggregation-induced emission fluorescent imaging. Accompanied by other pseudo in situ investigations, we propose the mechanism of gelation process, focusing on the formation of junction points including hydrogen bonds and crystalline.

DNA Damage Response Proteins and Oxygen Modulate Prostaglandin E2 Growth Factor Release in Response to Low and High LET Ionizing Radiation.

Common cancer therapies employ chemicals or radiation that damage DNA. Cancer and normal cells respond to DNA damage by activating complex networks of DNA damage sensor, signal transducer, and effector proteins that arrest cell cycle progression, and repair damaged DNA. If damage is severe enough, the DNA damage response (DDR) triggers programed cell death by apoptosis or other pathways. Caspase 3 is a protease that is activated upon damage and triggers apoptosis, and production of prostaglandin E2 (PGE2), a potent growth factor that can enhance growth of surviving cancer cells leading to accelerated tumor repopulation. Thus, dying tumor cells can promote growth of surviving tumor cells, a pathway aptly named Phoenix Rising. In the present study, we surveyed Phoenix Rising responses in a variety of normal and established cancer cell lines, and in cancer cell lines freshly derived from patients. We demonstrate that IR induces a Phoenix Rising response in many, but not all cell lines, and that PGE2 production generally correlates with enhanced growth of cells that survive irradiation, and of unirradiated cells co-cultured with irradiated cells. We show that PGE2 production is stimulated by low and high LET ionizing radiation, and can be enhanced or suppressed by inhibitors of key DDR proteins. PGE2 is produced downstream of caspase 3 and the cyclooxygenases COX1 and COX2, and we show that the pan COX1-2 inhibitor indomethacin blocks IR-induced PGE2 production in the presence or absence of DDR inhibitors. COX1-2 require oxygen for catalytic activity, and we further show that PGE2 production is markedly suppressed in cells cultured under low (1%) oxygen concentration. Thus, Phoenix Rising is most likely to cause repopulation of tumors with relatively high oxygen, but not in hypoxic tumors. This survey lays a foundation for future studies to further define tumor responses to radiation and inhibitors of the DDR and Phoenix Rising to enhance the efficacy of radiotherapy with the ultimate goal of precision medicine informed by deep understanding of specific tumor responses to radiation and adjunct chemotherapy targeting key factors in the DDR and Phoenix Rising pathways.

Using absorbable chitosan hemostatic sponges as a promising surgical dressing.

As absorbable hemostatic dressings, chitosan with a deacetylation degree of 40% (CS-40) and 73% (CS-73) have been fabricated into sponges via a modified method. The hemostatic, biocompatible and biodegradable properties were evaluated through in vivo assays. In a hepatic hemorrhage model, the chitosan sponges, with excellent blood compatibility, achieved less blood loss than the gelation sponge (GS). In addition, CS-40 showed better hemostatic capability and biodegradability than CS-73. After implantation, a histological analysis indicated that CS-40 exhibited the best biodegradability, tissue regeneration and least tissue adhesion. By contrasting CS-40 and CS-73, the deacetylation degree is confirmed to be a key factor for the hemostatic effect, biodegradability, biocompatibility and tissue regeneration. Our overall results demonstrated the potential application of CS-40 for use in absorbable hemostatic dressings.