Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States.

High-resolution Cas9 structures have yet to reveal catalytic conformations due to HNH nuclease domain positioning away from the cleavage site. Nme1Cas9 and Nme2Cas9 are compact nucleases for in vivo genome editing. Here, we report structures of meningococcal Cas9 homologs in complex with sgRNA, dsDNA, or the AcrIIC3 anti-CRISPR protein. DNA-bound structures represent an early step of target recognition, a later HNH pre-catalytic state, the HNH catalytic state, and a cleaved-target-DNA-bound state. In the HNH catalytic state of Nme1Cas9, the active site is seen poised at the scissile phosphodiester linkage of the target strand, providing a high-resolution view of the active conformation. The HNH active conformation activates the RuvC domain. Our structures explain how Nme1Cas9 and Nme2Cas9 read distinct PAM sequences and how AcrIIC3 inhibits Nme1Cas9 activity. These structures provide insights into Cas9 domain rearrangements, guide-target engagement, cleavage mechanism, and anti-CRISPR inhibition, facilitating the optimization of these genome-editing platforms.

In Situ Imaging of Two-Dimensional Crystal Growth Using a Heat-Resistant Optical Microscope.

Revealing low-dimensional material growth dynamics is critical for crystal growth engineering. However, in a practical high-temperature growth system, the crystal growth process is a black box because of the lack of heat-resistant imaging tools. Here, we develop a heat-resistant optical microscope and embed it in a chemical vapor deposition (CVD) system to investigate two-dimensional (2D) crystal growth dynamics. This in situ optical imaging CVD system can tolerate temperatures of ≤900 °C with a spatial resolution of ∼1 µm. The growth of monolayer MoS2 crystals was studied as a model for 2D crystal growth. The nucleation and growth process have been imaged. Model analysis and simulation have revealed the growth rate, diffusion coefficient, and spatial distribution of the precursor. More importantly, a new vertex-kink-ledge model has been suggested for monolayer crystal growth. This work provides a new technique for in situ microscopic imaging at high temperatures and fundamental insight into 2D crystal growth.

Reclassification of Some Exiguobacterium Species Based on Genome Analysis.

The Exiguobacterium genus comprises Gram-stain-positive and facultatively anaerobic bacteria. Some Exiguobacterium species have previously shown significant high 16S rRNA gene sequence similarities with each other. This study evaluates the taxonomic classification of those Exiguobacterium species through comprehensive genome analysis. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were determined for various Exiguobacterium species pairs. The ANI and dDDH values between Exiguobacterium enclense and Exiguobacterium indicum, Exiguobacterium aquaticum and Exiguobacterium mexicanum, Exiguobacterium soli and Exiguobacterium antarcticum, and Exiguobacterium sibiricum and Exiguobacterium artemiae were above the cut-off level (95-96% for ANI and 70% for dDDH) for species delineation. Based on the findings, we propose to reclassify Exiguobacterium enclense as a later heterotypic synonym of Exiguobacterium indicum, Exiguobacterium aquaticum as a later heterotypic synonym of Exiguobacterium mexicanum, Exiguobacterium soli as a later heterotypic synonym of Exiguobacterium antarcticum and Exiguobacterium sibiricum as a later heterotypic synonym of Exiguobacterium artemiae.

Taxonomic Reframe of Some Species of the Genera Haloferax and Halobellus.

Haloferax and Halobellus are the representatives of the family Haloferacaceae and they are dominant in hypersaline ecosystems. Some Haloferax and Halobellus species exhibit a close evolutionary relationship. Genomic, phylogenetic (based on 16S rRNA gene sequence), and phylogenomic analysis were performed to evaluate the taxonomic positions of the genera Haloferax and Halobellus. Based on the results we propose to reclassify Halobellus ramosii as a later heterotypic synonym of Halobellus inordinatus; Haloferax lucentense and Haloferax alexandrinum as later heterotypic synonyms of Haloferax volcanii.

A new mathematical model for evaluating surface changes in the mid-abdominal sagittal plane after two-level pedicle reduction osteotomy in patients with ankylosing spondylitis.

BACKGROUND: The purpose of this study was to create a mathematical model to precalculate the acreage change in the abdominal median sagittal plane (ac-AMSP) of patients with ankylosing spondylitis (AS) for whom two-level pedicle subtraction osteotomy (PSO) was planned. METHODS: A single-centre retrospective review of prospectively collected data was conducted among 11 adults with AS. Acreage of the abdominal median sagittal plane (a-AMSP) was performed. The distances and angles between the osteotomy apexes, anterosuperior edge of T12, xiphoid process, superior edge of the pubis, and anterosuperior corner of the sacrum were measured on preoperative thoracolumbar computed tomography. A mathematical model was created using basic trigonometric functions in accordance with the abdominal parameters. Planned osteotomized vertebra angles (POVAs) were substituted into the mathematical model, and the predictive ac-AMSP (P-AC) was obtained. A paired sample t test was performed to determine the differences between the P-AC and actual ac-AMSP (A-AC) and between the predictive acreage change rate (P-CR) and actual acreage change rate (A-CR). RESULTS: The mean age and GK were 44.4 ± 8.99 years and 102.9° ± 19.17°, respectively. No significant difference exists between A-CR and P-CR via mathematical modeling (p > 0.05). No statistically significant difference existed between POVA and actual osteotomized vertebra angles (AOVA) (p > 0.05). A statistically significant difference was observed between preoperative and postoperative measurements of LL, SVA, and GK variables (p < 0.001). CONCLUSIONS: The novel mathematical model was reliable in predicting the ac-AMSP in AS patients undergoing two-level PSO.

Liquid Phase Edge Epitaxy of Transition-Metal Dichalcogenide Monolayers.

Precise monolayer epitaxy is important for two-dimensional (2D) semiconductors toward future electronics. Here, we report a new self-limited epitaxy approach, liquid phase edge epitaxy (LPEE), for precise-monolayer epitaxy of transition-metal dichalcogenides. In this method, the liquid solution contacts 2D grains only at the edges, which confines the epitaxy only at the grain edges and then precise monolayer epitaxy can be achieved. High-temperature in situ imaging of the epitaxy progress directly supports this edge-contact epitaxy mechanism. Typical transition-metal dichalcogenide monolayers (MX2, M = Mo, W, and Re; X = S or Se) have been obtained by LPEE with a proper choice of molten alkali halide solvents (AL, A = Li, Na, K, and Cs; L = Cl, Br, or I). Furthermore, alloying and magnetic-element doping have also been realized by taking advantage of the liquid phase epitaxy approach. This LPEE method provides a precise and highly versatile approach for 2D monolayer epitaxy and can revolutionize the growth of 2D materials toward electronic applications.

Local-Nonlinearity-Enabled Deep Subdiffraction Control of Acoustic Waves.

Diffraction sets a natural limit for the spatial resolution of acoustic wave fields, hindering the generation and recording of object details and manipulation of sound at subwavelength scales. We propose to overcome this physical limit by utilizing nonlinear acoustics. Our findings indicate that, contrary to the commonly utilized cumulative nonlinear effect, it is in fact the local nonlinear effect that is crucial in achieving subdiffraction control of acoustic waves. We theoretically and experimentally demonstrate a deep subwavelength spatial resolution up to λ/38 in the far field at a distance 4.4 times the Rayleigh distance. This Letter represents a new avenue towards deep subdiffraction control of sound, and may have far-reaching impacts on various applications such as acoustic holograms, imaging, communication, and sound zone control.

Adsorption Behavior of Diclofenac on Polystyrene and Poly(butylene adipate-co-terephthalate) Microplastics: Influencing Factors and Adsorption Mechanism.

To unveil the intricacies surrounding the interaction between microplastics (MPs) and pollutants, diligent investigation is warranted to mitigate the environmental perils they pose. This exposition delves into the sorption behavior and mechanism of diclofenac sodium (DCF), a contaminant, upon two distinct materials: polystyrene (PS) and poly(butylene adipate-co-terephthalate) (PBAT). Experimental adsorption endeavors solidify the observation that the adsorption capacity of DCF onto the designated MPs amounts to Q(PBAT) = 9.26 mg g-1 and Q(PS) = 9.03 mg g-1, respectively. An exploration of the factors governing these discrepant adsorption phenomena elucidates the influence of MPs and DCF properties, environmental factors, as well as surfactants. Fitting procedures underscore the suitability of the pseudo-second-order kinetic and Freundlich models in capturing the intricacies of the DCF adsorption process onto MPs, corroborating the notion that the mentioned process is characterized by non-homogeneous chemisorption. Moreover, this inquiry unveils that the primary adsorption mechanisms of DCF upon MPs encompass electrostatic interaction, hydrogen bonding, and halo hydrogen bonding. An additional investigation concerns the impact of commonly encountered surfactants in aqueous environments on the adsorption of DCF onto MPs. The presence of surfactants elicits modifications in the surface charge properties of MPs, consequently influencing their adsorption efficacy vis-à-vis DCF.

Enhanced photocatalytic degradation of tetracycline by a H2O2-assisted Bi3NbO7/Bi2Sn2O7 composite under visible light.

A Z-scheme BNO/BSO composite photocatalyst has been successfully prepared using an in situ solvothermal method. The phase component, microstructure and optical properties of the as-prepared samples were characterized using X-ray diffractometry, scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, photoluminescence spectroscopy and other means. The photocatalytic performance of the BNO/BSO composite was evaluated via the degradation of the typical antibiotic tetracycline (TC) under hydrogen peroxide assistance and visible light irradiation. The "cata + H2O2 + vis" system shows the best photocatalytic activity, and its apparent rate constant reaches 0.03164 min-1, which is 4.9 times and 5.7 times that of the "cata + vis" system and the "cata + H2O2" system, respectively. Compared with pristine that of BSO alone, the reaction rate constant of the 15% BNO/BSO composite increases 1.8 times. The enhanced photocatalytic activity is attributed to the construction of a unique Z-scheme-type heterojunction, which effectively suppresses the recombination of electron-hole pairs. In addition, the addition of H2O2 promotes the generation of more active species. Moreover, a possible photocatalytic degradation mechanism is also further proposed.

Desorption of sulfamethoxazole from polyamide 6 microplastics: Environmental factors, simulated gastrointestinal fluids, and desorption mechanisms.

Microplastics (MPs) can enrich pollutants after being released into the environment, and the contaminants-loaded MPs are usually ingested by organisms, resulting in a potential dual biotoxic effect. In this paper, the adsorption behavior of Sulfamethoxazole (SMX) on Polyamide 6 (PA6) MPs was systematically investigated and simulated by the kinetic and isotherm models. The effect of environmental conditions (pH, salinity) on the adsorption process was studied, and the desorption behavior of SMX-loaded PA6 MPs was focused on simulating the seawater, ultrapure water, gastric and intestinal fluids. We found that lower pH and solubilization of SMX by gastrointestinal components (bovine serum albumin (BSA), sodium taurocholate (NaT), and pepsin) can reduce the electrostatic interaction between the surface charge of PA6 MPs and SMX. The result will lead to an increase in the desorption capacity of SMX-loaded PA6 MPs in gastrointestinal fluids and therefore will provide a reasonable mechanism for the desorption of SMX-loaded PA6 MPs in the gastrointestinal fluids. This study will provide a theoretical reference for studying the desorption behavior of SMX-loaded PA6 MPs under gastrointestinal conditions.

CdSSe Nano-Flowers for Ultrasensitive Raman Detection of Antibiotics.

Surface-enhanced Raman scattering (SERS) technique is widely used for the highly sensitive detection of trace residues due to its unparalleled signal amplification ability and plays an important role in food safety, environmental monitoring, etc. Herein, CdSSe nano-flowers (CdSSe NFs) are synthesized via the chemical vapor deposition (CVD) method. CdSSe NFs thin film is used as a SERS substrate with an ultralow limit of detection (LOD, 10-14 M), high apparent enhancement factor (EF, 3.62 × 109), and excellent SERS stability (relative standard deviation, RSD = 3.05%) for probe molecules of Rh6G. Further, CdSSe NFs substrate is successfully applied in the sensitive, quantitative, and label-free analysis of ciprofloxacin (CIP) and enrofloxacin (ENR) antibiotics, which exhibit LODs of below 0.5 ppb. This excellent SERS platform may be widely utilized for sensitive life science and environmental sensing.

Competition adsorption of malachite green and rhodamine B on polyethylene and polyvinyl chloride microplastics in aqueous environment.

Microplastics (MPs) will cause compound pollution by combining with organic pollutants in the aqueous environment. It is important for environmental protection to study the adsorption mechanism of different MPs for pollutants. In this study, the adsorption behaviors of malachite green (MG) and rhodamine B (RhB) on polyethylene (PE) and polyvinyl chloride (PVC) were studied in single systems and binary systems, separately. The results show that in single system, the adsorptions of between MPs for pollutants (MG and RhB) are more consistent with the pseudo-second-order kinetics and Freundlich isotherm model, the adsorption capacity of both MPs for MG is greater than that of RhB. The adsorption capacities of MG and RhB were 7.68 mg/g and 2.83 mg/g for PVC, 4.52 mg/g and 1.27 mg/g for PE. In the binary system, there exist competitive adsorption between MG and RhB on MPs. And the adsorption capacities of PVC for the two dyes are stronger than those of PE. This is attributed to the strong halogen-hydrogen bond between the two dyes and PVC, and the larger specific surface area of PVC. This study revealed the interaction and competitive adsorption mechanism between binary dyes and MPs, which is of great significance for understanding the interactions between dyes and MPs in the multi-component systems.

Scalable production of intrinsic WX2(X = S, Se, Te) quantum sheets for efficient hydrogen evolution electrocatalysis.

Mass production of transition-metal dichalcogenides has attracted much attention to replace platinum-based catalysts for the hydrogen evolution reaction (HER). Herein, we demonstrate a general strategy for the scalable production of the intrinsic tungsten dichalcogenide (WX2(X = S, Se, Te)) quantum sheets (QSs) by an all-physical top-down method. The method combines silica-assisted ball-milling and sonication-assisted solvent exfoliation and thus enables production of WS2QSs, WSe2QSs, and WTe2QSs in exceedingly high yields of 28.2, 21.3, 19.9 wt%, respectively. The WX2QSs are confirmed as intrinsic and defect-free, which could be determinative to their improved HER performance. The overpotentials of 285, 331, 435 mV at the current density of 10 mA cm-2and Tafel slopes of 116, 78, 162 mV dec-1in acidic media, as well as charge transfer resistance values of 171, 242, 1973 Ω, are derived for WS2QSs, WSe2QSs, and WTe2QSs, respectively, which are much better than those of bulk materials. The WX2QSs exhibit high stability during the electrocatalysis as well. This work offers a powerful approach for fabrication of intrinsic QSs as efficient and robust electrocatalysts.

Magnetic porous carbon derived from Zn/Co metal-organic framework as an adsorbent for extraction and determination of carbamates.

A novel magnetic porous carbon with a high specific surface and magnetization saturation, derived from a Zn/Co-MOF-5, was fabricated by direct carbonization of Zn/Co-MOF-5 without the need of additional carbon precursors under optimum pyrolysis temperature. The material was employed as an adsorbent for magnetic solid-phase extraction of four carbamates from water and tomato samples prior to high-performance liquid chromatography-tandem quadrupole mass spectrometry analysis. Under optimum conditions, the method displayed good linearity (r > 0.9987) within the concentration range 0.05-20 ng mL-1 for water samples and 0.1-40 ng g-1 for tomato samples. The limits of detection (S/N = 3) for the four carbamate pesticides were in the range 0.0006-0.013 ng mL-1 for water samples and 0.001-0.01 ng g-1 for tomato samples and satisfactory spiked recoveries in the range 86.1 to 109.1% were obtained with the relative standard deviation values from 2.1 to 14.0%. Graphical abstract.

Rapid Detection of Adulterants in Whey Protein Supplement by Raman Spectroscopy Combined with Multivariate Analysis.

The growing demand for whey protein supplements has made them the target of adulteration with cheap substances. Therefore, Raman spectroscopy in tandem with chemometrics was proposed to simultaneously detect and quantify three common adulterants (creatine, l-glutamine and taurine) in whey protein concentrate (WPC) powder. Soft independent modeling class analogy (SIMCA) and partial least squares discriminant analysis (PLS-DA) models were built based on two spectral regions (400-1800 cm-1 and 500-1100 cm-1) to classify different types of adulterated samples. The most effective was the SIMCA model in 500-1100 cm-1 with an accuracy of 96.9% and an error rate of 5%. Partial least squares regression (PLSR) models for each adulterant were developed using two different Raman spectral ranges (400-1800 cm-1 and selected specific region) and data pretreatment methods. The determination coefficients (R2) of all models were higher than 0.96. PLSR models based on typical Raman regions (500-1100 cm-1 for creatine and taurine, the combination of range 800-1000 cm-1 and 1300-1500 cm-1 for glutamine) were superior to models in the full spectrum. The lowest root mean squared error of prediction (RMSEP) was 0.21%, 0.33%, 0.42% for creatine, taurine and glutamine, and the corresponding limit of detection (LOD) values for them were 0.53%, 0.71% and 1.13%, respectively. This proves that Raman spectroscopy with the help of multivariate approaches is a powerful method to detect adulterants in WPC.

A Noninvasive Accurate Measurement of Blood Glucose Levels with Raman Spectroscopy of Blood in Microvessels.

Raman spectra of human skin obtained by laser excitation have been used to non-invasively detect blood glucose. In previous reports, however, Raman spectra thus obtained were mainly derived from the epidermis and interstitial fluid as a result of the shallow penetration depth of lasers in skin. The physiological process by which glucose in microvessels penetrates into the interstitial fluid introduces a time delay, which inevitably introduces errors in transcutaneous measurements of blood glucose. We focused the laser directly on the microvessels in the superficial layer of the human nailfold, and acquired Raman spectra with multiple characteristic peaks of blood, which indicated that the spectra obtained predominantly originated from blood. Incorporating a multivariate approach combining principal component analysis (PCA) and back propagation artificial neural network (BP-ANN), we performed noninvasive blood glucose measurements on 12 randomly selected volunteers, respectively. The mean prediction performance of the 12 volunteers was obtained as an RMSEP of 0.45 mmol/L and R2 of 0.95. It was no time lag between the predicted blood glucose and the actual blood glucose in the oral glucose tolerance test (OGTT). We also applied the procedure to data from all 12 volunteers regarded as one set, and the total predicted performance was obtained with an RMSEP of 0.27 mmol/L and an R2 of 0.98, which is better than that of the individual model for each volunteer. This suggested that anatomical differences between volunteer fingernails do not reduce the prediction accuracy and 100% of the predicted glucose concentrations fall within Region A and B of the Clarke error grid, allowing acceptable predictions in a clinically relevant range. The Raman spectroscopy detection of blood glucose from microvessels is of great significance of non-invasive blood glucose detection of Raman spectroscopy. This innovative method may also facilitate non-invasive detection of other blood components.

Time-delay-induced dynamical behaviors for an ecological vegetation growth system driven by cross-correlated multiplicative and additive noises.

In this paper, the modified potential function, the stationary probability distribution function (SPDF), the mean growth time and the mean degeneration time for a vegetation growth system with time delay are investigated, where the vegetation system is assumed to be disturbed by cross-correlated multiplicative and additive noises. The results reveal some fact that the multiplicative and additive noises can both reduce the stability and speed up the decline of the vegetation system, while the strength of the noise correlation and time delay can both enhance the stability of the vegetation and slow down the depression process of the ecological system. On the other hand, with regard to the impacts of noises and time delay on the mean development and degeneration processes of the ecological system, it is discovered that 1) in the development process of the vegetation population, the increase of the noise correlation strength and time delay will restrain the regime shift from the barren state to the boom one, while the increase of the additive noise can lead to the fast regime shift from the barren state to the boom one. 2) Conversely, in the depression process of the ecological system, the increase of the strength of the correlation noise and time delay will prevent the regime shift from the boom state to the barren one. Comparatively, the increase of the additive and multiplicative noises can accelerate the regime shift from the boom state to the barren state.

Tapered fluorotellurite microstructured fibers for broadband supercontinuum generation.

Fluorotellurite microstructured fibers (MFs) based on TeO2-BaF2-Y2O3 glasses are fabricated by using a rod-in-tube method. Tapered fluorotellurite MFs with varied transition region lengths are prepared by employing an elongation machine. By using a tapered fluorotellurite MF with a transition region length of ∼3.3 cm as the nonlinear medium and a 1560 nm femtosecond fiber laser as the pump source, broadband supercontinuum generation covering from 470 to 2770 nm is obtained. The effects of the transition region length of the tapered fluorotellurite MF on supercontinuum generation are also investigated. Our results show that tapered fluorotellurite MFs are promising nonlinear media for generating broadband supercontinuum light expanding from visible to mid-infrared spectral region.

Polydopamine-armored zeolitic imidazolate framework-8-incorporated zwitterionic hydrogel with multifunctional properties for infected wound healing.

Diabetic skin wound healing is compromised by bacterial infections, oxidative stress, and vascular disruption, leading to delayed recovery and potential complications. This study developed an antibacterial, antioxidant, and adhesive hydrogel dressing that promotes rapid bacterial-infected diabetic wound healing using the biological macromolecule of polydopamine (PDA). This hydrogel comprised PDA-armored zeolitic imidazolate framework-8 nanoparticles (PDA@ZIF-8 NPs) combined with a second armor of zwitterionic polymer network (poly(acrylamide-co-sulfobetaine methacrylate); PAS), realizing low concentration Zn2+ release, good adhesion (14.7 kPa for porcine skin), and improved tensile strength (83.2 kPa). The hydrogel exhibited good antibacterial efficacy against both Staphylococcus aureus (S. aureus, 92.8 %), Escherichia coli (E. coli, 99.6 %) and methicillin-resistant S. aureus (MRSA, 99.2 %), which was attributed to the properties of the incorporated PDA@ZIF-8 NPs. Notably, in vitro, the PDA@ZIF-8 PAS hydrogel not only promoted fibroblast proliferation and migration but also facilitated endothelial cell angiogenesis. In vivo, the PDA@ZIF-8 PAS hydrogel retained its Zn2+-releasing function and effectively suppressed bacterial growth in infected wounds, thereby accelerating the regeneration of both normal and diabetic wounds. This multiarmored hydrogel is a promising sustained-release carrier for functional metal ions and drugs, making it applicable for not only skin healing, but potentially the regeneration of other complex tissues.

Dimerization and liquid-liquid phase separation of the nonrepetitive domains of pyriform spidroin 1 controls the pyriform silk formation.

Spiders spin high performance silks with diverse mechanical properties for specific biological functions. Of these spider silk types, pyriform silk stands out as a unique combination of wet glue and dry fibers. Investigation of self-assembly process of spider silk proteins is necessary for elucidating the silk formation mechanism. However, the functions of nonrepetitive domains in the silk formation of pyriform spidroins from liquid proteins to solid fibers are still unclear, making it difficult to achieve efficient biomimetic preparations of pyriform silk with good mechanical properties. In this study, we investigate the roles of the N-linker repeat (NLR) and both terminal domains of pyriform spidroin 1 (PySp1) in the silk formation. We demonstrate for the first time that the PySp1 NLR alone is sufficient to self-assemble into high strength fibers. Moreover, we showed that the ability to promote the pyriform silk formation by the addition of the NLR. We also found that the pH-sensitive dimerization property for N-terminal domain and the liquid-liquid phase separation (LLPS) coupled with acidification triggers the self-assembly mediated by the C-terminal domain. Overall, our results provide new insight into the role of nonrepetitive domains in the pyriform silk formation mechanism and the basis for producing new protein-based materials derived from spider pyriform silk.