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Phenotypic diversity and evolutionary innovation ultimately trace to variation in genomic sequence and rewiring of regulatory networks. Here, we constructed a pan-genome of the Gossypium genus using ten representative diploid genomes. We document the genomic evolutionary history and the impact of lineage-specific transposon amplification on differential genome composition. The pan-3D genome reveals evolutionary connections between transposon-driven genome size variation and both higher-order chromatin structure reorganization and the rewiring of chromatin interactome. We linked changes in chromatin structures to phenotypic differences in cotton fiber and identified regulatory variations that decode the genetic basis of fiber length, the latter enabled by sequencing 1,005 transcriptomes during fiber development. We showcase how pan-genomic, pan-3D genomic and genetic regulatory data serve as a resource for delineating the evolutionary basis of spinnable cotton fiber. Our work provides insights into the evolution of genome organization and regulation and will inform cotton improvement by enabling regulome-based approaches.

The objective factors of low permeability reservoir determine that there is obvious starting pressure gradient in waterflooding development, and the injection pressure is high. Conventional waterflooding has the technical bottleneck of “no injection and no flooding.” It highlights the development contradictions such as serious under-injection, rapid production decline and difficult production of reserves. Pressurized water injection is a new technology of unconventional water injection to enhance oil recovery, which can improve the production degree of low permeability reservoir reserves and solve the problem of water injection difficulty. In order to ensure the reliability of scheme design and the success rate of field implementation, the key technologies of unconventional oil and gas reservoir geological engineering integration are applied for the first time, including 3D geological modeling technology, geomechanics modeling technology, complex fracture network simulation technology of geological engineering integration and numerical simulation technology, and a fine 3D dynamic and static model covering all elements of geology and engineering is objectively established. Through numerical simulation research, the optimal water injection parameters of pressure flooding are determined, and the implementation effect of the optimal scheme is predicted, which provides a scientific basis for field implementation.

Cotton fiber is a unicellular seed trichome, and lint fiber initials per seed as a factor determines fiber yield. However, the mechanisms controlling fiber initiation from ovule epidermis are not understood well enough. Here, with single-cell RNA sequencing (scRNA-seq), a total of 14,535 cells were identified from cotton ovule outer integument of Xu142_LF line at four developmental stages (1.5, 1, 0.5 days before anthesis and the day of anthesis). Three major cell types, fiber, non-fiber epidermis and outer pigment layer were identified and then verified by RNA in situ hybridization. A comparative analysis on scRNA-seq data between Xu142 and its fiberless mutant Xu142 fl further confirmed fiber cluster definition. The developmental trajectory of fiber cell was reconstructed, and fiber cell was identified differentiated at 1 day before anthesis. Gene regulatory networks at four stages revealed the spatiotemporal pattern of core transcription factors, and MYB25-like and HOX3 were demonstrated played key roles as commanders in fiber differentiation and tip-biased diffuse growth, respectively. A model for early development of a single fiber cell was proposed here, which sheds light on further deciphering mechanism of plant trichome and the improvement of cotton fiber yield.

BACKGROUND Although endoscopy is the gold standard to assess disease activity and infliximab efficacy in inflammatory bowel disease (IBD), the invasive, costly, and time-consuming procedure limits its routine applications. We aimed to investigate the clinical value of serum oncostatin M (OSM) as a surrogate biomarker. METHODS Fifty healthy controls, 34 non-IBD patients, and 189 IBD patients who were pre-infliximab treatment (n = 122) or in infliximab maintenance (n = 67) were enrolled. A chemiluminescence immunoassay (CLIA) was constructed to quantify serum OSM concentrations. Receiver operator characteristic (ROC) curve analysis was used to evaluate the performance of blood biomarkers for IBD management. RESULTS The methodology of CLIA exhibited great analytical performance with a wide linear range of 31.25-25000 pg/mL, a low detection limit of 23.2 pg/mL, acceptable precision, and applicable accuracy. Patients with IBD (121.5 [43.3-249.4] pg/mL, p

Acetaminophen plays a key role in first-line Covid-19 cure as a supportive therapy of fever and pain. However, overdose of acetaminophen may give rise to severe adverse events such as acute liver failure in individual. In this work, 3D-hierarchical mesoporous carbon nanosheet (hMCNS) microspheres with superior properties were fabricated using simple and quick strategy and applied for sensitive quantification of acetaminophen in pharmaceutical formulation and rat plasmas after administration. The hMCNS microspheres are prepared via chemical etching of zinc oxide (ZnO) nanoparticles from a zinc-gallic acid precursor composite (Zn-GA) synthesized by high-temperature anaerobic pyrolysis. The obtained hMCNS could enhance analytes accessibility and accelerate proton transfer in the interface, hence increasing the electrochemical performance. Under optimized experimental conditions, the proposed electrochemical sensor achieves a detection limit of 3.5 nM for acetaminophen. The prepared electrochemical sensor has been successfully applied for quantification of acetaminophen in pharmaceutical formulations and the rat plasma samples before and after administration. Meanwhile, this sensor is compared with high-performance liquid chromatography (HPLC) as a reference technology, showing an excellent accuracy. Such an electrochemical sensor has great potential and economic benefits for applications in the fields of pharmaceutical assay and therapeutic drug monitoring (TDM).

Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the consequences for shaping 3D genomic architecture remains largely unknown in plants. Here, we report reference-grade genome assemblies for three species of cotton ranging 3-fold in genome size, namely Gossypium rotundifolium (K2), G. arboreum (A2), and G. raimondii (D5), using Oxford Nanopore Technologies. Comparative genome analyses document the details of lineage-specific TE amplification contributing to the large genome size differences (K2, 2.44 Gb; A2, 1.62 Gb; D5, 750.19 Mb) and indicate relatively conserved gene content and synteny relationships among genomes. We found that approximately 17% of syntenic genes exhibit chromatin status change between active (“A”) and inactive (“B”) compartments, and TE amplification was associated with the increase of the proportion of A compartment in gene regions (∼7,000 genes) in K2 and A2 relative to D5. Only 42% of topologically associating domain (TAD) boundaries were conserved among the three genomes. Our data implicate recent amplification of TEs following the formation of lineage-specific TAD boundaries. This study sheds light on the role of transposon-mediated genome expansion in the evolution of higher-order chromatin structure in plants.

Insulin is a critical predictor for the function of pancreatic islet beta cells, which plays a crucial role in diagnosing diabetes and diabetes-related disorders. Herein, we propose and validate a label-free and cost-effective aptamer-based optical LC biosensor for detection of insulin based on the directional recognition of biomolecular binding events at a responsive aqueous-liquid crystal (LC) interface. The binding of insulin and aptamer adsorbed on CTAB triggers a conformational change of the aptamer from G-quadruplex to stretched structure, inducing homeotropic to planar alignment and correspondingly dark to bright optical image change of the LC films. The molecular dynamic (MD) simulation validates that the orientational transition is associated with the interaction energy changes at the interface, which is in coordination with the optical observation. This LC biosensor takes advantages of simple preparation, easy operation, rapid sensing, high specificity for insulin determination in the range of 0.1-1.0 nM within 5 min. This sensor is also applicable for insulin detection in diluted human urine and serum. Additionally, the optical cell arrays allow to detection multiple samples of the same/different biomarkers at the same time. Such a strategy offers a potential basis for monitoring other clinical biomarkers, and for point-of-care testing (POCT) as well.

To understand the displacement characteristics and remaining oil displacement process by the surfactant/polymer (SP) flooding in cores with different pore structures, the effects of pore structure on the enhanced oil recovery of SP flooding was investigated at the pore, core and field scales through conducting experiments on natural core samples with three typical types of pore structures. First, the in-situ nuclear magnetic resonance core flooding test was carried out to capture the remaining oil variation features in the water flooding and SP flooding through these three types of cores. Subsequently, at the core scale, displacement characteristics and performances of water flooding and SP flooding in these three types of cores were evaluated based on the full-size core flooding tests. Finally, at the field scale, production characteristics of SP flooding in the bimodal sandstone reservoir and multimodal conglomerate reservoir were compared using the actual field production data. The results show: as the pore structure gets more and more complex, the water flooding performance gets poorer, but the incremental recovery factor by SP flooding gets higher; the SP flooding can enhance the producing degree of oil in 1–3 μm pores in the unimodal and bimodal core samples, while it produces largely oil in medium and large pores more than 3 μm in pore radius in the multimodal core sample. The core flooding test using full-size core sample demonstrates that the injection of SP solution can significantly raise up the displacement pressure of the multimodal core sample, and greatly enhance recovery factor by emulsifying the remaining oil and enlarging swept volume. Compared with the sandstone reservoir, the multimodal conglomerate reservoir is more prone to channeling. With proper profile control treatments to efficiently enlarge the microscopic and macroscopic swept volumes, SP flooding in the conglomerate reservoir can contribute to lower water cuts and longer effective durations. Key words: conglomerate reservoir, pore structure, surfactant/polymer flooding, displacement effect, oil recovery enhancement

The shoot apical meristem (SAM) is a special category of tissue with pluripotency that forms new organs and individuals, especially floral individuals. However, little is known about the fate of cotton SAMs as a tunica corpus structure. Here, we demonstrate that cotton SAM fate decisions depend on light signals and circadian rhythms, and the genes GhFKF1, GhGI, GhCRY1 and GhCO were responsible for SAM fate decisions and highlighted via RNA sequencing (RNA-seq) analysis of different cotton cultivars, as confirmed by genetic analysis via the CRISPR–Cas9 system. In situ hybridization (ISH) analysis showed that the GhCO gene, induced by a relatively high blue light proportion, was highly upregulated during the initiation of floral meristems (FMs). Further blue light treatment analysis showed that the transition from vegetative to reproductive growth of SAM was promoted by a high proportion of blue light, coupled with high expression of the blue light-responsive genes GhCO and GhCRY1. Taken together, our study suggests that blue light signalling plays a key role in the fate decision of cotton SAM. These results provide a strategy to regulate the SAM differentiation of cotton by using the CRISPR–Cas9 system to change the ratio of red and blue light absorption to breed early-maturity cotton.One-sentence summaryThe SAM differentiation especially the initiation of floral meristem of upland cotton were mediated by genes GhCO and GhCRY1 which in response to blue light.

Background Despite remarkable advances in our knowledge of epigenetically mediated transcriptional programming of cell differentiation in plants, little is known about chromatin topology and its functional implications in this process. Results To interrogate its significance, we establish the dynamic three-dimensional (3D) genome architecture of the allotetraploid cotton fiber, representing a typical single cell undergoing staged development in plants. We show that the subgenome-relayed switching of the chromatin compartment from active to inactive is coupled with the silencing of developmentally repressed genes, pinpointing subgenome-coordinated contribution to fiber development. We identify 10,571 topologically associating domain-like (TAD-like) structures, of which 25.6% are specifically organized in different stages and 75.23% are subject to partition or fusion between two subgenomes. Notably, dissolution of intricate TAD-like structure cliques showing long-range interactions represents a prominent characteristic at the later developmental stage. Dynamic chromatin loops are found to mediate the rewiring of gene regulatory networks that exhibit a significant difference between the two subgenomes, implicating expression bias of homologous genes. Conclusions This study sheds light on the spatial-temporal asymmetric chromatin structures of two subgenomes in the cotton fiber and offers a new insight into the regulatory orchestration of cell differentiation in plants.

C-reactive protein (CRP) is one of the most sensitive acute-phase reactants, which is an early stage indicator of cardiovascular disease and infectious inflammation in clinic. However, it is still challenging to accurately quantification the trace content of CRP molecules in plasma samples. In this work, we propose an ultrasensitive electrochemical CRP aptasensor based on rhomboid dodecahedra carbonized-ZIF

Since the discovery of exosomes, their potential diagnostic value has been the focus of considerable research. However, the lack of a rapid and simple technique for the quantitative analysis of exosomes greatly limits the application of exosomes in clinical research. In this study, we describe a newly developed one-step chemiluminescence immunoassay for the rapid quantitative analysis of exosomes from biofluids. Our new technique, named ExoNANO, adopts a double-antibody sandwich strategy using anti-CD63 antibody-conjugated superparamagnetic iron oxide particles (SIOPs) and acridinium ester (ACE)-labeled anti-CD9 antibodies. SIOPs have narrow size distribution and high magnetic susceptibility, and ACE has excellent chemiluminescent properties such as low background signal and no need for a catalyst. We demonstrated that ExoNANO allows the quantitative analysis of exosomes in the range of 2.92 ×105 to 2.80×108 particles/μL, with a limit of detection of 2.63×105 particles/μL. Using ExoNANO, we quantified exosomes in cell culture medium and clinical biofluids such as serum, saliva, ascitic fluid, and cerebrospinal fluid. We believe that ExoNANO might pave the way for the rapid isolation and quantitative analysis of exosomes for routine clinical applications.

Droplet manipulation is a critical step for microfluidic applications. We present digital microfluidic devices based on electrowetting-on-dielectric (EWOD) for reliable and repeatable droplet manipulation. The EWOD device consists of two flexible conductive films as top and bottom electrodes, and one flexible liquid-infused membrane (LIM) as the hydrophobic insulating layer. LIMs made by infusing various fluids (air, fluorocarbon, silicone and hydrocarbon oils) into polytetrafluoroethylene (PTFE) membranes are evaluated by electrowetting performance of a sessile water droplet. Silicone oil is selected as the filling insulating oil according to its excellent electrowetting performance in good reversibility, low contact angle hysteresis, and negligible volatility. Fast (85 mm⋅s−1), repeatable (>5000 times without obvious decay) and continuous droplet (designed routes) moving, merging, mixing and positioning have been demonstrated. The factors affecting droplet transport velocity are investigated, including the infused oil viscosity, the conductive volume and the top-to-bottom gap distance. Both the conductive film and LIM are replaceable and robust, showing reliable and long-term stability. Quantitative chromogenic reactions and a flexible EWOD device are demonstrated. These devices are easy-to-fabricate, replaceable-in-material and robust-in-performance, showing high potential for applications in sample preparation, and flexible sensing and display devices.

In this work, a 3D-framework of functionalized multi-walled carbon nanotubes (fMWCNTs) decorated with molecularly imprinted polymer (MIP), has been fabricated to achieve fast and ultrasensitive electrochemical molecular sensing. The cavity networks of MIP layer from Norfloxacin (NFX) molecules offers simultaneous identification and quantification of NFX; and thus, ensures its high selectivity. The porous structure of fMWCNT 3D-framwork effectively increases the specific surface area, and the copolymer of fMWCNTs and MIP shows synergistic effect for electrocatalytic reaction of NFX at the modified sensor. Under optimized conditions, the fabricated sensors show wide linear detection ranges of 0.003-0.391 μM and 0.391–3.125 μM, low limit of determination (LOD) of 1.58 nM, and excellent selectivity in discriminating NFX according to its structural analogues and possible interferences. Precise and fast quantification of NFX in pharmaceutical formulations (Yunnan Baiyao and Ouyi Pharmaceutical) and rat plasma samples (N = 4) suggests its simplicity and reliability. The recoveries from pharmaceutical formulations ranged from 97.36 to 109.58% with the precisions (relative standard deviations, RSD, n = 3) of 1.74–3.41%; and the recoveries from rat plasma samples ranged from 83.00 to 115.67% with RSDs (n = 3) of 0.45–10.30%. Considering the advantages of easy fabrication, and selective and sensitive detection, such sensors with different types of MIPs would be widely applied in the fields of pharmaceutical analysis, and environmental and clinical therapeutic drug monitoring.

The objective of the presented work is to verify a delayed detached eddy simulation (DDES) model for simulating transitional swirling flow in a micro-scale multi-inlet vortex reactor (MIVR). The DDES model is a k- ω based turbulence model with a low Reynolds number correction applied to the standard k- ω model such that the Reynolds-averaged Navier-Stokes (RANS) component of the DDES model is able to account for low Reynolds number flow. By limiting the dissipation rate in the k-equation, the large-eddy simulation (LES) part of the DDES model behaves similarly to a one-equation sub-grid model. The turbulent Reynolds number is redefined to represent both modeled and resolved turbulence level so that underestimation of the RANS length scale in the LES range can be reduced. Applying the DDES model to simulate both laminar and transitional flow in the micro-scale MIVR produces an accurate prediction of mean velocity and turbulent intensity compared with experimental data. It is demonstrated that the proposed DDES model is capable of simulating transitional flow in the complex geometry of the micro-scale MIVR. These simulation results also help to understand the flow and mixing patterns in the micro-scale MIVR and provide guidances to optimize the reactor for the application of producing functional nanoparticles.

BackgroundMillennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components.ResultsWe construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost fromGossypium hirsutumandGossypium barbadensereference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV). We document the landscape of PAV selection accompanied by asymmetric gene gain and loss and identify 124 PAVs linked to favorable fiber quality and yield loci.ConclusionsThis variation repertoire points to genomic divergence during cotton domestication and improvement, which informs the characterization of favorable gene alleles for improved breeding practice using a pan-genome-based approach.

Background Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analyses extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy that targeting multiple genes is of great value in cotton functional genomics and genetic engineering. Results To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR/Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium, we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues. Conclusion All targeted genes were successfully edited with high specificity. Our pooled sgRNAs assembly offers a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.

Background : Upland cotton ( Gossypium hirsutum ), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analysis extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy that targeting multiple genes is of great value in cotton functional genomics and genetic engineering. Results : To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR/Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium , we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues.Conclusion : All targeted genes were successfully edited with high specificity. Our pooled sgRNAs assembly offers a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.

A rolling circle amplification chemiluminescence immunoassay (RCA-CLIA) was developed for precise quantitation of Aβ in plasma. Capture antibodies conjugated with magnetic beads and detection antibodies with collateral single-stranded DNA (ssDNA) were bound to Aβ42/Aβ40 antigens to form a typical double-antibody sandwich structure. The RCA reaction was triggered by the addition of ssDNA, which generated products with a large number of sites for the binding of acridinium ester (AE)-labeled detection probes, thereby realizing the purpose of the amplification. The RCA-CLIA method had higher sensitivity than conventional CLIA without loss of specificity. Under optimum conditions, the linear range of Aβ42 and Aβ40 detection was 3.9-140 pg/mL and 3.9-180 pg/mL, respectively, with corresponding low detection limits of 1.99 pg/mL and 3.14 pg/mL, respectively. Plasma Aβ42 and Aβ40 were detected in the blood of 21 AD patients and 22 healthy people, wherein this ratio could significantly distinguish AD patients from healthy individuals with a sensitivity of 90.48% and specificity of 63.64% for a cutoff value of 154. The Aβ42/Aβ40 ratio of plasma acts as an accurate indicator for AD diagnosis; therefore, detection of plasma Aβ using the RCA-CLIA exhibits great potential in noninvasive diagnosis and progressive assessment of AD.

Additional file 2. Figures S1-S30.

Additional file 3. Supplementary Notes.

Additional file 4. Review history.

Background: Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome consists of A and D subgenomes. The genes in have multiple copies with high sequence similarity that makes genetic, genomic and functional analysis extremely challenging. The recent accessibility of CRISPR/Cas9 tool offers the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy to target multiple genes is of great value in cotton functional genomics and practical applications of genetic engineering.Results: To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR-Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium, we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues. Conclusion: All targeted genes were successfully edited with high specificity which makes our pooled sgRNAs assembly a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.

Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the effect on shaping of 3D genomic architecture remains largely unknown in plants. Here, we report three reference-grade cotton genome assemblies of Gossypium rotundifolium (K2), G. arboreum (A2) and G. raimondii (D5) using Oxford Nanopore sequencing technology. Comparative genome analyses document the details of lineage-specific TE amplification contributing to three-fold change of genome size (K2, 2.44 Gb; A2, 1.62 Gb; D5, 750.19 Mb), and indicate a relatively conserved gene content and synteny relationship among genomes. We found that approximately 17% of syntenic genes exhibit chromatin status switching of A/B compartment, and active TE amplification increases the proportion of A compartment in gene regions in K2 and A2 relative to D5. We also found that only 42% of topologically associating domain (TAD) boundaries were conserved by comparing three genomes, and abundant TE amplification was linked to the organization of lineage-specific TADs. This study sheds light on the regulatory role of transposon-mediated genome expansion in the evolution of higher-order chromatin structure in plants.

The 2019 novel coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected all aspects of human life. Rapid, accurate, sensitive and user friendly detection method is urgently needed to facilitate early intervention and control the spread of SARS-CoV-2. Here, we propose a one-pot visual SARS-CoV-2 detection system named “opvCRISPR” by integrating reverse transcription loop-mediated isothermal amplification (RT-LAMP) and Cas12a cleavage in a single reaction system. We demonstrate that the collateral activity against single-stranded DNA (ssDNA) reporters of activated Cas12a triggered by RT-LAMP amplicon increases detection sensitivity and makes detection results observable with naked eye. The opvCRISPR enables detection at nearly single molecule level in 45 min. We validate this method with 50 SARS-CoV-2 potentially infected clinical samples. The opvCRISPR diagnostic results provide 100% agreement with the Centers for Disease Control and Prevention (CDC)-approved quantitative RT-PCR assay. The opvCRISPR holds great potential for SARS-CoV-2 detection in next-generation point-of-care molecular diagnostics., Highlights • We have proposed an ultrasensitive visual SARS-CoV-2 detection method that could be accomplished within 45 min. • This visual detection method has fundamental differences with colorimetric methods. • This method integrated RT-LAMP and CRISPR/Cas cleavage in one-pot and totally avoided amplicon contamination. • The operation is greatly simplified with only a thermoblock and blue light required. • This method could detect SARS-CoV-2 at nearly single molecule level and demonstrated 100% positive predictive agreement.

In this work, a new application of Mn-doped ZnS quantum dots (Mn-ZnS QDs) was developed to screen chloramphenicol (CAP) and tetracycline (TC) residues simply and rapidly. Mn-ZnS QDs synthesized by a hydration method and modified by L-cysteine for better stability emit phosphorescence at 583 nm with the excitation wavelength at 289 nm. Based on the overlap of the Mn-ZnS QDs excitation spectra and CAP or TCs ultraviolet spectra, the excited light of the Mn-ZnS QDs was partially absorbed by CAP or TCs owing to the inner-filter effect (IFE), leading to a decrease in the phosphorescence intensity. The phosphorescence intensities of the samples prepared by mixing different TCs and CAP were in good agreement with the expected results from adding a single antibiotic sample. Therefore, the total molar concentrations of CAP and TCs could be screened based on the linear equation of a single standard substance. Represented by tetracycline (TC), as a member of the tetracycline family, under optimized conditions, showed a good linear relational concentration range over 4 orders of magnitude from 50 to 1.5 × 105 nM with a limit of detection (LOD; S/N ratio = 3) down to 8.6 nM. The phosphorescent sensor was also used to detect total TCs in actual samples successfully. The evaluations of the recovery rate and selectivity were good. These results demonstrated that the presented phosphorescent sensor can be a simple and rapid screening platform for CAP and TCs.

Background A member of the S100 family of Ca2+-binding proteins, S100A1 is highly expressed in cardiac muscle tissue. Although this protein is considered an indicator of acute myocardial infarction (AMI), high-throughput and sensitive detection methods are still urgently needed. We constructed a rapid and sensitive method for detecting S100A1 and to investigate the clinical utility of S100A1 as a biomarker for the early diagnosis of AMI and subsequent prognostic assessments. We developed an automated chemiluminescent immunoassay to detect S100A1. We then analyzed the performance of the newly developed assay including evaluation of the analytical sensitivity, analytical selectivity, linear range, accuracy and repeatability. Methods We recruited 87 patients with AMI or angina pectoris to explore the value of this marker for the early diagnosis and prognostic assessment. Results The chemiluminescent-immune-based S100A1 assay had functional analytical sensitivity with a detection limit of 0.13 ng/ml, and a wide linear range of 0.13–31.66 ng/ml. It also exhibited good repeatability with intra-assay and inter-assay findings of 1.02 ng/ml) was notably associated with the poor prognosis of AMI patients after first PCI. Conclusions Measurement of circulating S100A1 concentrations with our newly developed chemiluminescent-immune-based assay shows potential for use in the clinic. This assay could enable early identification and prognostic assessment of AMI.

A novel rapid and sensitive fluorescence probe based on silicon quantum dots (Si QDs) fluorescence was fabricated for selective detection of tetracyclines (TCs) residues. Si QDs were innovatively prepared via facile One-Pot Solvent-Free Method and characterized by TEM, FT-IR, UV absorption, fluorescence, XPS and XRD. In aqueous solution, Cu2+ and Si QDs complexed together and the fluorescence of Si QDs quenched (static quenching) to a certain extent. TCs can be early in binding to Cu2+ and prevent Si QDs fluorescence quenching. As a consequence, quantitative screening of TCs can be achieved. The assay is highly selective for TCs. Represented by chlortetracycline (CTC), a member of TCs, under optimized conditions, good linear relationship in the range of 11.32–1086.72 nM was obtained, and the detection limit (LOD; S/N ratio = 3) of this assay for CTC is 0.92 nM. It was successfully applied to the determination of CTC in spiked bee honey and total TCs in actual honey samples. And the evaluation of selectivity, reproducibility and stability of the probe were favorable. These results demonstrated that the presented fluorescent probe can be a promising sensing platform for TCs analysis.

Human insulin-like growth factor-I (IGF-I) is a pleiotropic polypeptide hormone, which has been widely utilized for the diagnosis and management of growth hormone (GH) related disorders and diseases. In this work, we verify a label-free optical biosensor based on nematic liquid crystals (LCs) of 4-cyano-4-pentylbiphenyl (5CB) for ultrasensitive sensing of trace IGF-I in human serum samples. 5CB shows unique birefringence driven by the reorientation of the self-assembled N, N-dimethyl-N-(3-(trimethoxysilyl)propyl)−1-octadecanaminiuchloride (DMOAP) on glass. IGF-I antibody (AbIGF-I), as a specific recognition element, can be immobilized onto modified glass surface through a cross-linker of glutaradehyde (GA) and (3-aminopropyl) trimethoxysilane (APTES). Based on the number of specific recognition and binding between antibody (AbIGF-1) and antigen (AgIGF-1), the LC film exhibits gradual change from dark to bright under crossed polarizer. Under optimized conditions, the constructed LC-based biosensor demonstrates high sensitivity to IGF-I with a detection limit (LOD) of 1.0 ng/mL and a linear range of 10.0–2000.0 ng/mL (R2 = 0.989). This detection method possesses the advantages of easy construction, rapid sensing, good stability and repeatability, and high specificity for distinguishing IGF-I from other interfering proteins. Meanwhile, the format of biosensor could quickly detect IGF-I within a physiological range, providing profound information for prevention and treatment of GH-IGF-I axis related diseases in clinical diagnosis.

Hg(II) is one of the most toxic heavy metal ions. The bioconcentration and degradation-resistant of Hg(II) bring about serious harm to the ecosystem and humans. Therefore, the establishment of an accurate and effective method for detecting mercury ions is of great significance to environmental protection, food safety and human health. In this work, a new fluorescent nanoprobe was presented using nitrogen-doped carbon quantum dots (N-CQDs) for Hg(II) sensing with high stability and selectivity. On this basis, a paper-based chip was innovatively developed for visualization detection of Hg(II). The N-CQDs were prepared through a one-step hydrothermal reaction using catechol and ethylenediamine as carbon and nitrogen sources, respectively. As-prepared N-CQDs exhibit the strong green fluorescence at the excitation/emission wavelength of 370/511 nm. In aqueous solution, a rapid and highly sensitive detection method of Hg(II) was established by the joint of dynamic and static quenching effect of Hg(II) on N-CQDs fluorescence. Under the optimized conditions, there was a stable correlation between the fluorescence intensity change of N-CQDs and the concentrations of Hg(II) in the range of 15 ∼ 104 nM, and the detection limit was down to 8 nM (S/N = 3). The recoveries of water, sorghum and rice were 91.60 to 102.46%, which was consistent with ICP-MS. More importantly, the N-CQDs nanoprobe was further integrated in nitrocellulose membrane to develop paper-based chip for Hg(II) visualization detection, and the detection performance was also excellent. This strategy had significant implications for achieving low-cost, on-site real-time monitoring of mercury (II) in the environment and food.

A molecular beacon (MB) is an oligonucleotide hybridization probe with a hairpin-shaped structure that leads to specific and instantaneous nucleic acid hybridization, enabling a variety of applications. However, integration of additional module sequences interferes with the performance of MBs and increases the complexity of sequence design. Herein, we develop and characterize a toehold integrated molecular beacon (ToMB) strategy for nucleic acid hybridization, where the reaction rate can be flexibly regulated by a target-induced MB conformational switch. Using this basic mechanism, the ToMB is capable of identifying nucleic acids with high specificity and a wider linearity range compared with the conventional molecular beacon system. We further applied the ToMB to the construction of a hybridization chain reaction system and a basic OR logic gate VJHto explore its programmability and versatility. Our results strongly suggest that the novel ToMB can act as a powerful nano-module to construct universal and multifunctional biosensors or molecular computations. Graphical abstract Molecular beacon is employed as a flexible and switchable spacer to control the toehold-mediated strand displacement reaction.

Water-weakening effect is one of the most important causes triggering large deformation and failure of soft-rock engineering; however, few studies have paid attention to damage evolution and constitutive relationship of rock in water-weakening process. In this paper, laboratory tests are first carried out to estimate the evolution of mechanical properties along with changes of immersion time for shale samples. Then with the aid of X-ray diffraction and scanning electron microscope, mechanism of parameter degradation for shale under immersion conditions is investigated from the microscopic perspective. Based on the generalized strain equivalent principle and the theory of statistical microscopic damage mechanics, a damage constitutive model of rock subjected to water-weakening effect and uniaxial loading is established by considering the influence of void-compression stage, and the proposed model is verified to be in good agreement with the experiment results. This paper provides an effective approach to analyze the constitutive relationship of rock subjected to water-weakening effect and uniaxial loading.

Typical large-deformation phenomena of soft rock occurred frequently during the tunneling process in Huangjiazhai Tunnel, Hubei Province, China, including extrusion at the tunnel wall and severe damage of the primary support and secondary lining. To reveal the mechanisms of these anomalies, comprehensive investigations have been undertaken combining engineering, laboratory, and microscopic analyses. Since the monitoring results show that there might be a close relationship between the large deformation phenomena and water infiltration into the tunnel, the water–rock interaction is the research focus in the investigations. The experimental results reveal that the deforming resistance and strength of shales exposed at the excavation face weaken quickly in the first 20 days after the shales have contact with water. The results obtained by mineral composition detection and microstructure observation illustrate the microscopic reasons for the decreasing strength and deforming resistance of the tunnel surrounding rock after water infiltration. The results from in situ geostress tests indicate that as a result of high tectonic stress and low rock strength, the field of Huangjiazhai Tunnel is an extremely high geostress area. By combining analyses from the mechanical and geological perspectives, there are two main reasons for the large deformations in the Huangjiazhai Tunnel: the plastic flow caused by tunnel excavation under high geostress and low rock strength and a hydrated-mechanical coupling process between the shales and water.

The authors describe a method for DNA target recognition and signal amplification that is based on the target-induced formation of a three way junction. The subsequent assembly of two DNA probes releases the inhibitory strand and triggers a downstream strand displacement amplification. This causes the formation of a G-rich single sequence that binds to a hemin monomer with its peroxidase-mimicking properties. The resulting peroxidase (POx) activity is quantified by using H2O2 and TMB as the substrate. In the presence of an inhibitor, in contrast, the POx-like activity is strongly reduced. This forms the basis for a highly sensitive DNA assay. It has a 0.8 pM detection limit when operated at a wavelength of 450 nm and was applied to the isothermal determination of target DNA with high selectivity.

Background: Myocardial infarction is one of the leading causes of morbidity and mortality worldwide, triggering irreversible myocardial cell damage and heart failure. The role of low-density lipoprotein receptor-related proteins 5 and 6 (LRP5/6) as coreceptors of the Wnt/β-catenin pathway in the adult heart remain unknown. Insulin-like growth factor binding protein 4 and dickkopf-related protein 1 (Dkk1) are 2 secreted LRP5/6 binding proteins that play a crucial role in heart development through preventing Wnt/β-catenin pathway activation. However, their roles in the adult heart remain unexplored. Methods: To understand the role of LRP5/6 and β-catenin in the adult heart, we constructed conditional cardiomyocyte-specific LRP5/6 and β-catenin knockout mice and induced surgical myocardial infarction. We also directly injected recombinant proteins of insulin-like growth factor binding protein 4 and Dkk1 into the heart immediately following myocardial infarction to further examine the mechanisms through which these proteins regulate LRP5/6 and β-catenin. Results: Deletion of LRP5/6 promoted cardiac ischemic insults. Conversely, deficiency of β-catenin, a downstream target of LRP5/6, was beneficial in ischemic injury. It is interesting to note that although both insulin-like growth factor binding protein 4 and Dkk1 are secreted Wnt/β-catenin pathway inhibitors, insulin-like growth factor binding protein 4 protected the ischemic heart by inhibiting β-catenin, whereas Dkk1 enhanced the injury response mainly through inducing LRP5/6 endocytosis and degradation. Conclusions: Our findings reveal previously unidentified dual roles of LRP5/6 involved in the cardiomyocyte response to ischemic injury. These findings suggest new therapeutic strategies in ischemic heart disease by fine-tuning LRP5/6 and β-catenin signaling within the Wnt/β-catenin pathway.

Large scientific data centers have recently begun providing a number of different types of data storage, to satisfy the various needs of their users. Users with interactive accounts, for example, might want a posix interface for easy access to the data from their interactive machines. Grid computing sites, on the other hand, likely need to provide an X509 based storage protocol, like SRM and GridFTP, since the data management system is built on top of them. Meanwhile, an experiment producing large amounts of data typically demands a service that provides archival storage for the safe keeping of their unique data. To access these various types of data, users must use specific sets of commands tailored for the respective storage, making access to their data complex and difficult. BNLBox is an attempt to provide a unified and easy to use storage service for all BNL users, scientists and engineers, to store their important documents, code and data. It is a cloud storage system with an intuitive web interface for novice users. It provides an automated synchronization feature that enables users to upload data to their cloud storage without manual intervention, freeing them to focus on analysis rather than data management software. It provides a posix interface for local interactive users, which simplifies data access from batch jobs as well. At the same time, it also provides users with a straightforward mechanism for archiving large data sets for later processing. The storage space can be used for both code and data within the compute job environment. This presentation will cover the various aspects of the BNLBox storage service.

The mechanical properties of rock materials are remarkably affected by water content. To reveal the effect of water content on the strength and deformation properties of siltstone, which was collected from the quarry of Zhundong Coalmine, the scanning electron microscope and uniaxial compression tests of siltstone specimens were carried out with a water content of 0%, 0.5%, 1.5%, and 2.8%. Conventional triaxial compression test was conducted in dry and saturated conditions. The test results showed that the strength and deformation parameters of siltstone are weakened with different degrees after water absorption. The deformation of the plastic yield stage in the stress-strain curve decreases with rising of water content, while the loss rate of uniaxial compression strength continues to increase until reached saturated state. The strength of dry and saturated specimens varies regularly with confining pressure, and their relationship can be described with the exponential criterion. In addition, it is observed that microscopic damage of siltstone specimens accumulates as water content increases. The hydration of clay minerals reduces the local cohesion of specimens, and the hydrolysis of quartz minerals in crack tip region promotes subcritical crack growth during the loading process, which collaboratively results in the bearing capacity of saturated specimen decrease. The results can provide a reference for the analysis of rock strength and damage mechanism under the action of water erosion.