Dear-DIA^(XMBD): Deep Autoencoder Enables Deconvolution of Data-Independent Acquisition Proteomics

Data-independent acquisition(DIA)technology for protein identification from mass spectrometry and related algorithms is developing rapidly.The spectrum-centric analysis of DIA data without the use of spectra library from data-dependent acquisition data represents a promising direction.In this paper,we proposed an untargeted analysis method,Dear-DIA^(XMBD),for direct analysis of DIA data.Dear-DIA^(XMBD) first integrates the deep variational autoencoder and triplet loss to learn the representations of the extracted fragment ion chromatograms,then uses the k-means clustering algorithm to aggregate fragments with similar representations into the same classes,and finally establishes the inverted index tables to determine the precursors of fragment clusters between precursors and peptides and between fragments and peptides.We show that Dear-DIA^(XMBD) performs superiorly with the highly complicated DIA data of different species obtained by different instrument platforms.

Visually monitoring the etching process of gold nanoparticles by KI/12 at single-nanoparticle level using scattered-light dark-field microscopic imaging

Real-time monitoring of reaction processes is helpful for understanding the reaction mechanisms. In this study we investigated the etching mechanism of gold nanopartides （AuNPs） by iodine on a single-nanopartide level because AuNPs have become important nanoprobes with applications in sensing and bioimaging fields owing to their specific localized surface plasmon resonance （LSPR） properties. By using a scattered-light dark-field microscopic imaging （iDFM） technique, the in situ KI/I2-treated etching processes of various shapes of AuNPs, including nanospheres （AuNSs）, nanorods （AuNRs）, and nanotrigonal prisms （AuNTs）, were monitored in real time. It was found that the scattered light of the different shapes of AuNPs exhibited noticeable color changes upon exposure to the etching solution. The scattering spectra during the etching process showed obvious blue-shifts with decreasing scattered intensity owing to the oxidation of Au atoms into [AuI2]-. Both finite-difference time-domain （FDTD） simulations and monitoring of morphological variations proved that the etching was a thermodynamic-dependent process through a chamfering mechanism coupled with layer-by-layer peeling, resulting in isotropic spheres with decreased particle sizes.

A multiplexed circulating tumor DNA detection platform engineered from 3D-coded interlocked DNA rings

Circulating tumor DNA(ctDNA)is a critical biomarker not only important for the early detection of tumors but also invaluable for personalized treatments.Currently ctDNA detection relies on sequencing.Here,a platform termed three-dimensional-coded interlocked DNA rings(3D-coded ID rings)was created for multiplexed ctDNA identification.The ID rings provide a ctDNA recognition ring that is physically interlocked with a reporter ring.The specific binding of ctDNA to the recognition ring initiates target-responsive cutting via a restriction endonuclease;the cutting then triggers rolling circle amplification on the reporter ring.The signals are further integrated with internal 3D codes for multiplexed readouts.ctDNAs from non-invasive clinical specimens including plasma,feces,and urine were detected and validated at a sensitivity much higher than those obtained through sequencing.This 3D-coded ID ring platform can detect any multiple DNA fragments simultaneously without sequencing.We envision that our platform will facilitate the implementation of future personalized/precision medicine.

Dispen-Seq: a single-microparticle dispenser based strategy towards flexible cell barcoding for single-cell RNA sequencing

Single-cell RNA sequencing(sc RNA-seq)has become one of the most powerful tools to understand the heterogeneity of biological systems.While barcoding strategies have revolutionized the field of high-throughput sc RNA-seq,it is still challenging to achieve highly efficient,direct and universal cell barcoding with cost-effectiveness and minimal sample loss.Herein,a single micro-particle dispenser approach for rapid single barcode bead/cell manipulation and pairing,enabling highly efficient cell barcoding for sc RNA-seq(Dispen-Seq)was developed.Notably,Dispen-Seq provides a versatile platform which can enrich cell subgroups of interest while unlimited by input sample amounts,and can respond to changes in sample composition with high resolution and reproducibility.It is anticipated that Dispen-Seq will increase the scope of sc RNA-seq from academic research to practical applications.

Biochar contributes to resistance against root rot disease by stimulating soil polyphenol oxidase

Biochar has been considered an effective approach as soil amendment for decreasing incidences of disease and regulating microbial populations in continuous-cropping soil.Although researches have extensively focused on changes of soil microbes and unbalance of nutrition in continuous-cropping soil,the relationship between soil properties and pathogens by biochar application remains poorly understood.In this study,we applied ITS ribosomal RNA gene profiling to analyze tobacco root microbiota of biochar and non-biochar treatment in a 3-year continuous-cropping tobacco field,comparing firstly planting tobacco as control.We found that biochar application decreased the relative abundance of the soil fungal pathogens(Ceratobasidium and Monosporascus),which are the prime pathogens of tobacco root rot in continuous-cropping soil.Using RDA,co-occurrence and PLS-PM approaches,we provided evidence that there was a negative correlation between fungal genera(especially for Ceratobasidium and Monosporascus)and soil polyphenol oxidase(PPO)activity(R^(2) incidence rate=−0.930,R^(2) disease index=−0.905,both p<0.001).The PPO was up-regulated by different biochar treatment intensities.Together,we demonstrated that biochar in continuouscropping soil regulated the soil PPO activity to suppress pathogens,and further decrease incidence of root rot.Notably,biochar application forward continuous cropping was more effective for the continuous-cropping soil improvement than the other treatments.The data should help in appropriate timing of biochar application for alleviating continuous-cropping obstacle.

Control of slope-pattern on the deposition of fan-delta systems:a case study of the Upper Karamay Formation,Junggar Basin

The Mesozoic fan deltas in the north-west margin of the Junggar Basin,as important petroleum reservoirs,exhibited complex facies change and internal structures with strong heterogeneity which were controlled by the transformation of slope-patterns,bringing great challenges to the study of sedimentary characteristics.The Upper Karamay Formation at north-west margin of the Junggar Basin was the objective in this paper which attempts to clarify the mechanism of sedimentary response and sand-body distribution of fan delta systems under the control of slope-pattern change.Based on a data set of cores,well logs and seismic,two types of slope-pattern were identified in the study area,which include steep-to-gentle in the south and gentle-to-steep in the north.The control of difference slope-patterns on the sand-body distribution was clarified based on the analysis of the sedimentary dynamics,facies characteristics,and depositional evolution of the fan deltas.The study shows that the transport mechanism of sediments on the steep-slope was dominated by debris flows,developing coarse-grained,thick-bedded lobes with poor structural maturity of clasts.On the gentle-slope,the deposition was dominated by hyperconcentrated-traction currents,forming relatively fine-grained,thin-bedded lobes with increased sandy matrix.The sand-bodies show frequent bar-channel transformation and channel down-cutting under the steep slope setting,which exhibit migration of isolated river channels on the gentle slopes.Under the steep-to-gentle pattern,the coase-grained sediments were mainly accumulated at slope toe,generally developed equiaxial lobes.However,the coarse-grained clasts were preserved both at proximal and distal lobes on the gentle-to-steep slopes,showing obvious lateral extension of the fan delta.The slope patterns controlled sedimentary respond rates of the fan deltas during lake level change.By comparing the modern cases of fan systems worldwide,the control of slope patterns on deposition of coarse-grained fans was clarified,providing insight into hydrocarbon exploration on basin margins.