Cas12n nucleases, early evolutionary intermediates of type V CRISPR, comprise a distinct family of miniature genome editors.

Type V CRISPR-associated systems (Cas)12 family nucleases are considered to have evolved from transposon-associated TnpB, and several of these nucleases have been engineered as versatile genome editors. Despite the conserved RNA-guided DNA-cleaving functionality, these Cas12 nucleases differ markedly from the currently identified ancestor TnpB in aspects such as guide RNA origination, effector complex composition, and protospacer adjacent motif (PAM) specificity, suggesting the presence of earlier evolutionary intermediates that could be mined to develop advanced genome manipulation biotechnologies. Using evolutionary and biochemical analyses, we identify that the miniature type V-U4 nuclease (referred to as Cas12n, 400-700 amino acids) is likely the earliest evolutionary intermediate between TnpB and large type V CRISPR systems. We demonstrate that with the exception of CRISPR array emergence, CRISPR-Cas12n shares several similar characteristics with TnpB-ωRNA, including a miniature and likely monomeric nuclease for DNA targeting, origination of guide RNA from nuclease coding sequence, and generation of a small sticky end following DNA cleavage. Cas12n nucleases recognize a unique 5'-AAN PAM sequence, of which the A nucleotide at the -2 position is also required for TnpB. Moreover, we demonstrate the robust genome-editing capacity of Cas12n in bacteria and engineer a highly efficient CRISPR-Cas12n (termed Cas12Pro) with up to 80% indel efficiency in human cells. The engineered Cas12Pro enables base editing in human cells. Our results further expand the understanding regarding type V CRISPR evolutionary mechanisms and enrich the miniature CRISPR toolbox for therapeutic applications.

The Foxi3 transcription factor is necessary for the fate restriction of placodal lineages at the neural plate border.

The Foxi3 transcription factor, expressed in the neural plate border at the end of gastrulation, is necessary for the formation of posterior placodes and is thus important for ectodermal patterning. We have created two knock-in mouse lines expressing GFP or a tamoxifen-inducible Cre recombinase to show that Foxi3 is one of the earliest genes to label the border between the neural tube and epidermis, and that Foxi3-expressing neural plate border progenitors contribute primarily to cranial placodes and epidermis from the onset of expression, but not to the neural crest or neural tube lineages. By simultaneously knocking out Foxi3 in neural plate border cells and following their fates, we show that neural plate border cells lacking Foxi3 contribute to all four lineages of the ectoderm - placodes, epidermis, crest and neural tube. We contrast Foxi3 with another neural plate border transcription factor, Zic5, the progenitors of which initially contribute broadly to all germ layers until gastrulation and gradually become restricted to the neural crest lineage and dorsal neural tube cells. Our study demonstrates that Foxi3 uniquely acts early at the neural plate border to restrict progenitors to a placodal and epidermal fate.

Electrochemical Biosensors for Whole Blood Analysis: Recent Progress, Challenges, and Future Perspectives.

Whole blood, as one of the most significant biological fluids, provides critical information for health management and disease monitoring. Over the past 10 years, advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems for whole blood testing toward the goal of disease monitoring and treatment. Among the techniques employed for whole-blood diagnostics, electrochemical biosensors, as known to be rapid, sensitive, capable of miniaturization, reagentless and washing free, become a class of emerging technology to achieve the target detection specifically and directly in complex media, e.g., whole blood or even in the living body. Here we are aiming to provide a comprehensive review to summarize advances over the past decade in the development of electrochemical sensors for whole blood analysis. Further, we address the remaining challenges and opportunities to integrate electrochemical sensing platforms.

Deterministic Assembly of Single-Emitter Plasmonic Antenna for Ultrahigh Photoluminescence Enhancement.

Single-emitter nanoantennas play a crucial role in the fabrication of nanosensors and integrated sources. Since the coupling of single emitter to nanoantennas is largely based on stochastic methods, low qualified rate still hinders a massive deployment. Here, we proposed a deterministic, optical-force-driven method to achieve gap-plasmonic photoluminescence enhancement. Two deterministic steps are carried out in sequence: a composite nanoemitter is first synthesized by linking quantum dots to a silica-rapped gold nanoparticle, followed by an optical delivery of the nanoparticle into a nanoaperture in a gold film. We reason that the nanoparticle-in-nanoaperture (NPiNA) structure efficiently couples out-of-plane excitation light into a gap-plasmon via a transverse electromagnetic mode (TEM)-like transmission mode. An in situ photoluminescence measurement demonstrates a 3× brightness as compared to the nanoparticle-on-mirror (NPoM). This approach paves the way toward deterministic positioning of individual nanoparticles for a wide range of applications on nanophotonics structures on-a-chip.

Subclinical Keratoconus Detection and Characterization Using Motion-Tracking Brillouin Microscopy.

PURPOSE: To characterize focal biomechanical alterations in subclinical keratoconus (SKC) using motion-tracking (MT) Brillouin microscopy and evaluate the ability of MT Brillouin metrics to differentiate eyes with SKC from normal control eyes. DESIGN: Prospective cross-sectional study. PARTICIPANTS: Thirty eyes from 30 patients were evaluated, including 15 eyes from 15 bilaterally normal patients and 15 eyes with SKC from 15 patients. METHODS: All patients underwent Scheimpflug tomography and MT Brillouin microscopy using a custom-built device. Mean and minimum MT Brillouin values within the anterior plateau region and anterior 150 µm were generated. Scheimpflug metrics evaluated included inferior-superior (IS) value, maximum keratometry (Kmax), thinnest corneal thickness, asymmetry indices, Belin/Ambrosio display total deviation, and Ambrosio relational thickness. Receiver operating characteristic (ROC) curves were generated for all Scheimpflug and MT Brillouin metrics evaluated to determine the area under the ROC curve (AUC), sensitivity, and specificity for each variable. MAIN OUTCOME MEASURES: Discriminative performance based on AUC, sensitivity, and specificity. RESULTS: No significant differences were found between groups for age, sex, manifest refraction spherical equivalent, corrected distance visual acuity, Kmax, or KISA% index. Among Scheimpflug metrics, significant differences were found between groups for thinnest corneal thickness (556 µm vs. 522 µm; P < 0.001), IS value (0.29 diopter [D] vs. 1.05 D; P < 0.001), index of vertical asymmetry (IVA; 0.10 vs. 0.19; P < 0.001), and keratoconus index (1.01 vs. 1.05; P < 0.001), and no significant differences were found for any other Scheimpflug metric. Among MT Brillouin metrics, clear differences were found between control eyes and eyes with SKC for mean plateau (5.71 GHz vs. 5.68 GHz; P < 0.0001), minimum plateau (5.69 GHz vs. 5.65 GHz; P < 0.0001), mean anterior 150 µm (5.72 GHz vs. 5.68 GHz; P < 0.0001), and minimum anterior 150 µm (5.70 GHz vs. 5.66 GHz; P < 0.001). All MT Brillouin plateau and anterior 150 µm mean and minimum metrics fully differentiated groups (AUC, 1.0 for each), whereas the best performing Scheimpflug metrics were keratoconus index (AUC, 0.91), IS value (AUC, 0.89), and IVA (AUC, 0.88). CONCLUSIONS: Motion-tracking Brillouin microscopy metrics effectively characterize focal corneal biomechanical alterations in eyes with SKC and clearly differentiated these eyes from control eyes, including eyes that were not differentiated accurately using Scheimpflug metrics. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Bacterial necromass as the main source of organic matter in saline soils.

Soil salinity poses a major threat to crop growth, microbial activity, and organic matter accumulation in agroecosystems in arid and semiarid regions. The limitations of carbon (C) accrual due to salinity can be partly mitigated by the application of organic fertilizers. Although microorganisms are crucial for soil organic carbon (SOC) stabilization, the relationships between living and dead microbial C pools and the community features of SOC accrual in saline soils are not known. A two-year field experiment was conducted to examine the effects of organic fertilizers on the microbial regulatory mechanisms of C sequestration in saline soil (chloride-sulfate salinity). Compared to manure addition alone, manure plus commercial humic acid increased SOC stock by 11% and decreased CO2 emissions by 10%, consequently facilitated soil C sequestration. We explain these results by greater bacterial necromass formation due to the dominance of r-strategists with faster turnover rate (growth and death), as well as larger necromass stability as supported by the increased aggregate stability under the addition of humic acids with manure. Humic acids increased the abundance of bacterial phylum Proteobacteria (copiotrophs) and decreased Acidobacteria (oligotrophs) compared with straw, indicating that r-strategists outcompeted K-strategists, leading to bacterial necromass accumulation. With larger C/N ratio (88), straw increased leucine aminopeptidase to mine N-rich substrates (i.e., from necromass and soil organic matter) and consequently reduced SOC stock by 8%. The decreased salinity and increased organic C availability under straw with manure addition also led to a 13% higher CO2 flux compared with manure application alone. Thus, humic acids added with manure benefited to SOC accumulation by raising bacterial necromass C and reducing CO2 emissions.

Foxi3GFP and Foxi3CreER mice allow identification and lineage labeling of pharyngeal arch ectoderm and endoderm, and tooth and hair placodes.

BACKGROUND: FOXI3 is a forkhead family transcription factor that is expressed in the progenitors of craniofacial placodes, epidermal placodes, and the ectoderm and endoderm of the pharyngeal arch region. Loss of Foxi3 in mice and pathogenic Foxi3 variants in dogs and humans cause a variety of craniofacial defects including absence of the inner ear, severe truncations of the jaw, loss or reduction in external and middle ear structures, and defects in teeth and hair. RESULTS: To allow for the identification, isolation, and lineage tracing of Foxi3-expressing cells in developing mice, we targeted the Foxi3 locus to create Foxi3GFP and Foxi3CreER mice. We show that Foxi3GFP mice faithfully recapitulate the expression pattern of Foxi3 mRNA at all ages examined, and Foxi3CreER mice can trace the derivatives of pharyngeal arch ectoderm and endoderm, the pharyngeal pouches and clefts that separate each arch, and the derivatives of hair and tooth placodes. CONCLUSIONS: Foxi3GFP and Foxi3CreER mice are new tools that will be of use in identifying and manipulating pharyngeal arch ectoderm and endoderm and hair and tooth placodes.

Cone-beam CT landmark detection for measuring basal bone width: a retrospective validation study.

BACKGROUND: Accurate assessment of basal bone width is essential for distinguishing individuals with normal occlusion from patients with maxillary transverse deficiency who may require maxillary expansion. Herein, we evaluated the effectiveness of a deep learning (DL) model in measuring landmarks of basal bone width and assessed the consistency of automated measurements compared to manual measurements. METHODS: Based on the U-Net algorithm, a coarse-to-fine DL model was developed and trained using 80 cone-beam computed tomography (CBCT) images. The model's prediction capabilities were validated on 10 CBCT scans and tested on an additional 34. To evaluate the performance of the DL model, its measurements were compared with those taken manually by one junior orthodontist using the concordance correlation coefficient (CCC). RESULTS: It took approximately 1.5 s for the DL model to perform the measurement task in only CBCT images. This framework showed a mean radial error of 1.22 ± 1.93 mm and achieved successful detection rates of 71.34%, 81.37%, 86.77%, and 91.18% in the 2.0-, 2.5-, 3.0-, and 4.0-mm ranges, respectively. The CCCs (95% confidence interval) of the maxillary basal bone width and mandibular basal bone width distance between the DL model and manual measurement for the 34 cases were 0.96 (0.94-0.97) and 0.98 (0.97-0.99), respectively. CONCLUSION: The novel DL framework developed in this study improved the diagnostic accuracy of the individual assessment of maxillary width. These results emphasize the potential applicability of this framework as a computer-aided diagnostic tool in orthodontic practice.

Simultaneous detection of dental caries and fissure sealant in intraoral photos by deep learning: a pilot study.

BACKGROUND: Deep learning, as an artificial intelligence method has been proved to be powerful in analyzing images. The purpose of this study is to construct a deep learning-based model (ToothNet) for the simultaneous detection of dental caries and fissure sealants in intraoral photos. METHODS: A total of 1020 intraoral photos were collected from 762 volunteers. Teeth, caries and sealants were annotated by two endodontists using the LabelMe tool. ToothNet was developed by modifying the YOLOX framework for simultaneous detection of caries and fissure sealants. The area under curve (AUC) in the receiver operating characteristic curve (ROC) and free-response ROC (FROC) curves were used to evaluate model performance in the following aspects: (i) classification accuracy of detecting dental caries and fissure sealants from a photograph (image-level); and (ii) localization accuracy of the locations of predicted dental caries and fissure sealants (tooth-level). The performance of ToothNet and dentist with 1year of experience (1-year dentist) were compared at tooth-level and image-level using Wilcoxon test and DeLong test. RESULTS: At the image level, ToothNet achieved an AUC of 0.925 (95% CI, 0.880-0.958) for caries detection and 0.902 (95% CI, 0.853-0.940) for sealant detection. At the tooth level, with a confidence threshold of 0.5, the sensitivity, precision, and F1-score for caries detection were 0.807, 0.814, and 0.810, respectively. For fissure sealant detection, the values were 0.714, 0.750, and 0.731. Compared with ToothNet, the 1-year dentist had a lower F1 value (0.599, p < 0.0001) and AUC (0.749, p < 0.0001) in caries detection, and a lower F1 value (0.727, p = 0.023) and similar AUC (0.829, p = 0.154) in sealant detection. CONCLUSIONS: The proposed deep learning model achieved multi-task simultaneous detection in intraoral photos and showed good performance in the detection of dental caries and fissure sealants. Compared with 1-year dentist, the model has advantages in caries detection and is equivalent in fissure sealants detection.

Transcriptome analysis reveals FABP5 as a key player in the development of chicken abdominal fat, regulated by miR-122-5p targeting.

BACKGROUND: The development of abdominal fat and meat quality are closely related and can impact economic efficiency. In this study, we conducted transcriptome sequencing of the abdominal fat tissue of Gushi chickens at 6, 14, 22, and 30 weeks, and selected key miRNA-mRNA regulatory networks related to abdominal fat development through correlation analysis. RESULTS: A total of 1893 differentially expressed genes were identified. Time series analysis indicated that at around 6 weeks, the development of chicken abdominal fat was extensively regulated by the TGF-ß signaling pathway, Wnt signaling pathway, and PPAR signaling pathway. However, at 30 weeks of age, the apoptosis signaling pathway was the most significant, and correlation analysis revealed several genes highly correlated with abdominal fat development, including Fatty Acid Binding Protein 5 (FABP5). Based on miRNA transcriptome data, it was discovered that miR-122-5p is a potential target miRNA for FABP5. Cell experiments showed that miR-122-5p can directly target FABP5 to promote the differentiation of preadipocytes. CONCLUSION: The present study confirms that the key gene FABP5 and its target gene miR-122-5p are critical regulatory factors in the development of chicken abdominal fat. These results provide new insights into the molecular regulatory mechanisms associated with the development of abdomen-al fat in chickens.

Weighted gene co-expression network analysis identified hub genes critical to fatty acid composition in Gushi chicken breast muscle.

BACKGROUND: The composition and content of fatty acids in the breast muscle are important factors influencing meat quality. In this study, we investigated the fatty acid composition and content in the breast muscle of Gushi chickens at different developmental stages (14 weeks, 22 weeks, and 30 weeks). Additionally, we utilized transcriptomic data from the same tissue and employed WGCNA and module identification methods to identify key genes associated with the fatty acid composition in Gushi chicken breast muscle and elucidate their regulatory networks. RESULTS: Among them, six modules (blue, brown, green, light yellow, purple, and red modules) showed significant correlations with fatty acid content and metabolic characteristics. Enrichment analysis revealed that these modules were involved in multiple signaling pathways related to fatty acid metabolism, including fatty acid metabolism, PPAR signaling pathway, and fatty acid biosynthesis. Through analysis of key genes, we identified 136 genes significantly associated with fatty acid phenotypic traits. Protein-protein interaction network analysis revealed that nine of these genes were closely related to fatty acid metabolism. Additionally, through correlation analysis of transcriptome data, we identified 51 key ceRNA regulatory networks, including six central genes, 7 miRNAs, and 28 lncRNAs. CONCLUSION: This study successfully identified key genes closely associated with the fatty acid composition in Gushi chicken breast muscle, as well as their post-transcriptional regulatory networks. These findings provide new insights into the molecular regulatory mechanisms underlying the flavor characteristics of chicken meat and the composition of fatty acids in the breast muscle.

Genetic architecture and key regulatory genes of fatty acid composition in Gushi chicken breast muscle determined by GWAS and WGCNA.

BACKGROUND: Fatty acids composition in poultry muscle is directly related to its tenderness, flavour, and juiciness, whereas its genetic mechanisms have not been elucidated. In this study, the genetic structure and key regulatory genes of the breast muscle fatty acid composition of local Chinese chicken, Gushi-Anka F2 resource population by integrating genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA) strategies. GWAS was performed based on 323,306 single nucleotide polymorphisms (SNPs) obtained by genotyping by sequencing (GBS) method and 721 chickens from the Gushi-Anka F2 resource population with highly variable fatty acid composition traits in the breast muscle. And then, according to the transcriptome data of the candidate genes that were obtained and phenotypic data of fatty acid composition traits in breast muscle of Gushi chickens at 14, 22, and 30 weeks of age, we conducted a WGCNA. RESULTS: A total of 128 suggestive significantly associated SNPs for 11 fatty acid composition traits were identified and mapped on chromosomes (Chr) 2, 3, 4, 5, 13, 17, 21, and 27. Of these, the two most significant SNPs were Chr13:5,100,140 (P = 4.56423e-10) and Chr13:5,100,173 (P = 4.56423e-10), which explained 5.6% of the phenotypic variation in polyunsaturated fatty acids (PUFA). In addition, six fatty acid composition traits, including C20:1, C22:6, saturated fatty acid (SFA), unsaturated fatty acids (UFA), PUFA, and average chain length (ACL), were located in the same QTL intervals on Chr13. We obtained 505 genes by scanning the linkage disequilibrium (LD) regions of all significant SNPs and performed a WGCNA based on the transcriptome data of the above 505 genes. Combining two strategies, 9 hub genes (ENO1, ADH1, ASAH1, ADH1C, PIK3CD, WISP1, AKT1, PANK3, and C1QTNF2) were finally identified, which could be the potential candidate genes regulating fatty acid composition traits in chicken breast muscle. CONCLUSION: The results of this study deepen our understanding of the genetic mechanisms underlying the regulation of fatty acid composition traits, which is helpful in the design of breeding strategies for the subsequent improvement of fatty acid composition in poultry muscle.

Asymmetric Total Synthesis of Cephalotaxus Diterpenoids: Cephinoid P, Cephafortoid A, 14-epi-Cephafortoid A and Fortalpinoids M-N, P.

The asymmetric total syntheses of cephalotaxus C19 diterpenoids, bearing a unique cycloheptene A ring with a chiral methyl group at C-12, were disclosed based on a universal strategy. Six members, including cephinoid P, cephafortoid A, 14-epi-cephafortoid A and fortalpinoids M-N, P, were accomplished for the first time. The concise approach relies on two crucial steps: (1) a Nicholas/Hosomi-Sakurai cascade reaction was developed to efficiently generate the cycloheptene ring bearing a chiral methyl group; (2) an intramolecular Pauson-Khand reaction was followed to facilitate the construction of the complete skeleton of target molecules. Our studies provide a new strategy for the synthetic analysis of cephalotaxus diterpenoids and structurally related polycyclic natural products.

Robust algorithm for precise XCO2 retrieval using single observation of IPDA LIDAR.

CO2 column-weighted dry-air mixing ratio (XCO2) products with high precision and spatial resolution are essential for inverting CO2 fluxes and promoting our understanding of global climate change. Compared with passive remote sensing methods, IPDA LIDAR, as an active remote sensing technique, offers many advantages in measuring XCO2. However, a significant random error in IPDA LIDAR measurements causes XCO2 values calculated directly from LIDAR signals to be unqualified as the final XCO2 products. Hence, we propose an efficient particle filter-based inversion of CO2 for single observation (EPICSO) algorithm to precisely retrieve the XCO2 of every LIDAR observation while preserving the high spatial resolution of LIDAR measurements. The EPICSO algorithm adopts the sliding average results as the first estimate of the local XCO2; subsequently, it estimates the difference between two adjacent XCO2 points and calculates the posterior probability of XCO2 based on particle filter theory. To evaluate the performance of the EPICSO algorithm numerically, we perform an EPICSO to process pseudo-observation data. The simulation results show that the results retrieved by the EPICSO algorithm satisfy the required high precision and that the algorithm is robust to a significant amount of random errors. In addition, we utilize LIDAR observation data from actual experiments in Hebei, China, to validate the performance of the EPICSO algorithm. The results retrieved by the EPICSO algorithm are more consistent with the actual local XCO2 than those of the conventional method, indicating that the EPICSO algorithm is efficient and practical for retrieving XCO2 with high precision and spatial resolution.

The effect of albumin and hemoglobin levels on the prognosis of early-stage cervical cancer: a prospective, single-center-based cohort study.

BACKGROUND: Serum albumin (ALB) and hemoglobin (HGB) are important serum biochemical indices of the nutritional status of patients and are associated with cancer development. We investigated the relationship between ALB and HGB levels and clinicopathologic characteristics of early-stage cervical cancer to determine the influence of ALB and HGB on the prognosis of early-stage cervical cancer. METHODS: The clinical data of 560 patients with International Federation of Gynaecology and Obstetrics (FIGO, 2009) stage IA1-IIA2 cervical cancer from January 2005 to December 2010 were retrospectively analyzed. The relationship between serum ALB and HGB levels and clinicopathological characteristics of patients were analyzed. The patients were followed-up for 12-138 months. The effects of ALB and HGB levels on the prognosis were analyzed by Cox regression, log-rank test, and the Kaplan-Meier method. RESULTS: The rate of patients with pelvic lymph node metastasis (PLNM), tumor diameter ≥ 4 cm, lymphovascular space invasion (LVSI), and deep stromal invasion was significantly higher in the anemia and hypoalbuminemia group than in the normal group (P < 0.05). The progression-free survival (PFS) and overall survival (OS) of patients in the hypoalbuminemia group and anemia group were significantly lower than that of the normal group (P < 0.05). FIGO stage, tumor diameter, PLNM, depth of stromal invasion, LVSI, the levels of ALB and HGB were risk factors for the prognosis of cervical cancer patients (P < 0.05). CONCLUSION: Patients with hypoproteinemia and anemia in early-stage cervical cancer are more likely to have higher tumor stage, larger tumor size, PLNM, LVSI, and deep stromal invasion. In addition, patients with hypoproteinemia and anemia have a poorer prognosis than those without the condition. Therefore, it is of great significance to detect the ALB and HGB levels of patients and improve the nutritional status of patients in a timely manner for better prognosis of cervical cancer.

Directivity-Enhanced Detection of a Single Nanoparticle Using a Plasmonic Slot Antenna.

In situ refractive index sensors integrated with nanoaperture-based optical tweezers possess stable and sensitive responsivity to single nanoparticles. In most existing works, detection events are only identified using the total light intensity with directivity information ignored, leading to a low signal-to-noise ratio. Here, we propose to detect an optically trapped 20 nm silica particle by monitoring directivity of a plasmonic antenna. The main and secondary radiation lobes of the antenna reverse upon trapping because the particle-induced perturbation negates the relative phase between two antenna elements, leading to a significant change of the antenna front-to-back ratio. As a result, we obtain a signal-to-noise ratio of 20, with an order-of-magnitude improvement as compared to the intensity-only detection scheme.

Once-middle amount of straw interlayer enhances saline soil quality and sunflower yield in semi-arid regions of China: Evidence from a four-year experiment.

Straw deep returning as an interlayer is a novel practice to enhance soil carbon and nutrients. However, the impact of applying various amounts of straw as an interlayer on soil quality still remain unclear in the saline soil. Therefore, a field experiment was carried out over four years (2015-2018) in Hetao Irrigation District, China. The aim was to evaluate the impact of four straw interlayer rates (i.e., 0, 6, 12, and 18 Mg ha-1) applied at 40 cm depth on soil quality index (SQI) and its relationship to sunflower yield in saline soil. Our results showed that, in comparison to no straw interlayer (CK), straw interlayers applied at rates of 6, 12, and 18 Mg ha-1 improved SQI on average by 2.0, 2.7, and 3.0 times in four years, respectively (p < 0.05). This suggested that straw deep returning as an interlayer improved SQI, especially for middle and high amounts (12 and 18 Mg ha-1). Partial least squares path model (PLSPM) illustrated that the improvement of SQI was due to the high-moisture and low-salt environment created by straw interlayer in the early two years (2015-2016), while the higher soil nutrients released from straw decomposition in the subsequent years (2017-2018). The improvement of SQI contributed to sunflower yield, which was related to the decrease of soil salinity, the increase of soil moisture, soil organic carbon (SOC), total nitrogen (TN), and available nutrients under straw interlayers. The sunflower yield was increased by 8.7-13.4% under straw interlayers (p < 0.05), following the order of 18 = 12 > 6 >0 Mg ha-1. The greater increment of yield was detected during the initial phase of burying straw interlayers, which indicated that straw as an interlayer played a more important role than nutrient supply from straw decomposition. The findings highlighted that appropriate straw return amount (i.e., 12 Mg ha-1) as an interlayer is an economic practice to benefit soil quality and crop yield synchronously in salt-affected soils.

Sensitive impulsive stimulated Brillouin spectroscopy by an adaptive noise-suppression Matrix Pencil.

Impulsive stimulated Brillouin spectroscopy (ISBS) plays a critical role in investigating mechanical properties thanks to its fast measurement rate. However, traditional Fourier transform-based data processing cannot decipher measured data sensitively because of its incompetence in dealing with low signal-to-noise ratio (SNR) signals caused by a short exposure time and weak signals in a multi-peak spectrum. Here, we propose an adaptive noise-suppression Matrix Pencil method for heterodyne ISBS as an alternative spectral analysis technique, speeding up the measurement regardless of the low SNR and enhancing the sensitivity of multi-component viscoelastic identification. The algorithm maintains accuracy of 0.005% for methanol sound speed even when the SNR drops 33 dB and the exposure time is reduced to 0.4 ms. Moreover, it proves to extract a weak component that accounts for 6% from a polymer mixture, which is inaccessible for the traditional method. With its outstanding ability to sensitively decipher weak signals without spectral a priori information and regardless of low SNRs or concentrations, this method offers a fresh perspective for ISBS on fast viscoelasticity measurements and multi-component identifications.

Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease.

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have been harnessed as powerful genome editing tools in diverse organisms. However, the off-target effects and the protospacer adjacent motif (PAM) compatibility restrict the therapeutic applications of these systems. Recently, a Streptococcus pyogenes Cas9 (SpCas9) variant, xCas9, was evolved to possess both broad PAM compatibility and high DNA fidelity. Through determination of multiple xCas9 structures, which are all in complex with single-guide RNA (sgRNA) and double-stranded DNA containing different PAM sequences (TGG, CGG, TGA, and TGC), we decipher the molecular mechanisms of the PAM expansion and fidelity enhancement of xCas9. xCas9 follows a unique two-mode PAM recognition mechanism. For non-NGG PAM recognition, xCas9 triggers a notable structural rearrangement in the DNA recognition domains and a rotation in the key PAM-interacting residue R1335; such mechanism has not been observed in the wild-type (WT) SpCas9. For NGG PAM recognition, xCas9 applies a strategy similar to WT SpCas9. Moreover, biochemical and cell-based genome editing experiments pinpointed the critical roles of the E1219V mutation for PAM expansion and the R324L, S409I, and M694I mutations for fidelity enhancement. The molecular-level characterizations of the xCas9 nuclease provide critical insights into the mechanisms of the PAM expansion and fidelity enhancement of xCas9 and could further facilitate the engineering of SpCas9 and other Cas9 orthologs.

Structural and functional characterizations and heterogenous expression of the antimicrobial peptides, Hidefensins, from black soldier fly, Hermetia illucens (L.).

Insect defensins are effector components of the innate defense system. Defensins, which are widely distributed among insects, are a type of small cysteine-rich plant antimicrobial peptides with broad-spectrum antimicrobial activity. Here, the cDNAs of the black soldier fly, Hermetia illucens (L.), encoding six defensins, designated herein as Hidefensin1-1, 2, 3, 4, 5, 6. Moreover, Hidefensin1-1, 2, and 5 were identified for the first time by genome-targeted analysis. These Hidefensins were found to mainly adopt α-helix and ß-sheet conformation homology as modeled by PRABI, Swiss-Model and ProFunc server. Six conserved cysteine residues that contribute to three disulfide bonds formed the spacing pattern "C-X12-C-X3-C-X9-C-X5-C-X-C", which play a vital role in the molecular stability of Hidefensins. Phylogenetic analysis revealed that the homology of five Hidefensins (except Hidefensin4) was about 59%-92% compared with other insect defensins, indicating that they are novel antimicrobial peptides genes in black soldier fly. Furthermore, the Hidefensin1-1 was expressed in the Escherichia coli strain BL21(DE3) as a fusion protein with thioredoxin. Results showed that the purified TRX-Hidefensin1-1 exerted strong inhibitory effects against the Gram-positive bacteria Staphylococcus aureus and the Gram-negative bacteria Escherichia coli. The inhibitory efficacy of TRX-Hidefensin1-1 against Gram-positive bacteria was better than that against Gram-negative bacteria. These results indicated that Hidefensin1-1 has potent antimicrobial activities against test pathogens.