The Application of Nicotiana benthamiana as a Transient Expression Host to Clone the Coding Sequences of Plant Genes

Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using complementary DNA (cDNA) derived from messenger RNA (mRNA) extracted from plant tissues and generated by reverse transcription. However, some CDS are difficult to acquire through this process as they are expressed at extremely low levels or have specific spatial and/or temporal expression patterns in vivo. These challenges require the development of alternative CDS cloning technologies. In this study, we found that the genomic intron-containing gene coding sequences (gDNA) from Arabidopsis thaliana, Oryza sativa, Brassica napus, and Glycine max can be correctly transcribed and spliced into mRNA in Nicotiana benthamiana. In contrast, gDNAs from Triticum aestivum and Sorghum bicolor did not function correctly. In transient expression experiments, the target DNA sequence is driven by a constitutive promoter. Theoretically, a sufficient amount of mRNA can be extracted from the N. benthamiana leaves, making it conducive to the cloning of CDS target genes. Our data demonstrate that N. benthamiana can be used as an effective host for the cloning CDS of plant genes.

Pig pangenome graph reveals functional features of non‑reference sequences

Background The reliance on a solitary linear reference genome has imposed a significant constraint on our compre-hensive understanding of genetic variation in animals.This constraint is particularly pronounced for non-reference sequences(NRSs),which have not been extensively studied.Results In this study,we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb.Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome.Furthermore,we observed that NRSs were rarely found within coding sequences,while NRS insertions were enriched in immune-related Gene Ontology terms.Notably,our investigation also unveiled a close association between novel genes and the immune capacity of pigs.We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs,and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X.Additionally,we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in South-ern Chinese pigs.Conclusions Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.

Phylogenetic, phylogeographic and divergence time analysis of Anopheles subpictus species complex using ITS2 and COI sequences

Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2(ITS2)and cytochrome C oxidase I(COI)sequences deposited at the GenBank.Methods:Seventy-five ITS2,210 COI and 26 concatenated sequences available in the NCBI database were used.Phylogenetic analysis was performed using Bayesian likelihood trees,whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis.Genetic diversity indices and genetic differentiation were also calculated.Results:Two genetically divergent molecular forms of An.subpictus species complex corresponding to sibling species A and B are established.Species A evolved around 37-82 million years ago in Sri Lanka,India,and the Netherlands,and species B evolved around 22-79 million years ago in Sri Lanka,India,and Myanmar.Vietnam,Thailand,and Cambodia have two molecular forms:one is phylogenetically similar to species B.Other forms differ from species A and B and evolved recently in the above mentioned countries,Indonesia and the Philippines.Genetic subdivision among Sri Lanka,India,and the Netherlands is almost absent.A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances.Genetic diversity indices reveal the presence of a long-established stable mosquito population,at mutation-drift equilibrium,regardless of population fluctuations.Conclusions:An.subpictus species complex consists of more than two genetically divergent molecular forms.Species A is highly divergent from the rest.Sri Lanka and India contain only species A and B.

Mitochondrial targeting sequence of magnetoreceptor MagR:More than just targeting

Iron-sulfur clusters(ISC)are essential cofactors for proteins involved in various biological processes,such as electron transport,biosynthetic reactions,DNA repair,and gene expression regulation.ISC assembly protein IscA1(or MagR)is found within the mitochondria of most eukaryotes.Magnetoreceptor(MagR)is a highly conserved A-type iron and iron-sulfur cluster-binding protein,characterized by two distinct types of iron-sulfur clusters,[2Fe-2S]and[3Fe-4S],each conferring unique magnetic properties.MagR forms a rod-like polymer structure in complex with photoreceptive cryptochrome(Cry)and serves as a putative magnetoreceptor for retrieving geomagnetic information in animal navigation.Although the N-terminal sequences of MagR vary among species,their specific function remains unknown.In the present study,we found that the N-terminal sequences of pigeon MagR,previously thought to serve as a mitochondrial targeting signal(MTS),were not cleaved following mitochondrial entry but instead modulated the efficiency with which iron-sulfur clusters and irons are bound.Moreover,the N-terminal region of MagR was required for the formation of a stable MagR/Cry complex.Thus,the N-terminal sequences in pigeon MagR fulfil more important functional roles than just mitochondrial targeting.These results further extend our understanding of the function of MagR and provide new insights into the origin of magnetoreception from an evolutionary perspective.

Landscape of Sequence Variations in Homologous Copies of FAD2 and FAD3 in Rapeseed(Brassica napus L.)Germplasm with High/Low Linolenic Acid Trait

Genetic manipulation(either restraint or enhancement)of the biosynthesis pathway ofα-linolenic acid(ALA)in seed oil is an important goal in Brassica napus breeding.B.napus is a tetraploid plant whose genome often har-bors four and six homologous copies,respectively,of the two fatty acid desaturases FAD2 and FAD3,which con-trol the last two steps of ALA biosynthesis during seed oil accumulation.In this study,we compared their promoters,coding sequences,and expression levels in three high-ALA inbred lines 2006L,R8Q10,and YH25005,a low-ALA line A28,a low-ALA/high-oleic-acid accession SW,and the wildtype ZS11.The expression levels of most FAD2 and FAD3 homologs in the three high-ALA accessions were higher than those in ZS11 and much higher than those in A28 and SW.The three high-ALA accessions shared similar sequences with the pro-moters and CDSs of BnFAD3.C4 and BnFAD3.A3.In A28 and SW,substitution of three amino acid residues in BnFAD2.A5 and BnFAD2.C5,an absence of BnFAD2.C1 locus,and a 549 bp long deletion on the BnFAD3.A3 promoter were detected.The profile of BnFAD2 mutation in the two low-ALA accessions A28 and SW is different from that reported in previous studies.The mutations in BnFAD3 in the high-ALA accessions are reported for thefirst time.In identifying the sites of these mutations,we provide detailed information to aid the design of mole-cular markers for accelerated breeding schemes.

Secure Transmission of Compressed Medical Image Sequences on Communication Networks Using Motion Vector Watermarking

Medical imaging plays a key role within modern hospital management systems for diagnostic purposes.Compression methodologies are extensively employed to mitigate storage demands and enhance transmission speed,all while upholding image quality.Moreover,an increasing number of hospitals are embracing cloud computing for patient data storage,necessitating meticulous scrutiny of server security and privacy protocols.Nevertheless,considering the widespread availability of multimedia tools,the preservation of digital data integrity surpasses the significance of compression alone.In response to this concern,we propose a secure storage and transmission solution for compressed medical image sequences,such as ultrasound images,utilizing a motion vector watermarking scheme.The watermark is generated employing an error-correcting code known as Bose-Chaudhuri-Hocquenghem(BCH)and is subsequently embedded into the compressed sequence via block-based motion vectors.In the process of watermark embedding,motion vectors are selected based on their magnitude and phase angle.When embedding watermarks,no specific spatial area,such as a region of interest(ROI),is used in the images.The embedding of watermark bits is dependent on motion vectors.Although reversible watermarking allows the restoration of the original image sequences,we use the irreversible watermarking method.The reason for this is that the use of reversible watermarks may impede the claims of ownership and legal rights.The restoration of original data or images may call into question ownership or other legal claims.The peak signal-to-noise ratio(PSNR)and structural similarity index(SSIM)serve as metrics for evaluating the watermarked image quality.Across all images,the PSNR value exceeds 46 dB,and the SSIM value exceeds 0.92.Experimental results substantiate the efficacy of the proposed technique in preserving data integrity.

Optimal mining sequence for coal faces under a bedding slope:insight from landslide prevention

Repetitive mining beneath bedding slopes is identified as a critical factor in geomorphic disturbances, especially landslides and surface subsidence. Prior research has largely concentrated on surface deformation in plains due to multi-seam coal mining and the instability of natural bedding slopes, yet the cumulative impact of different mining sequences on bedding slopes has been less explored. This study combines drone surveys and geological data to construct a comprehensive three-dimensional model of bedding slopes. Utilizing FLAC3D and PFC2D models, derived from laboratory experiments, it simulates stress, deformation, and failure dynamics of slopes under various mining sequences. Incorporating fractal dimension analysis, the research evaluates the stability of slopes in relation to different mining sequences. The findings reveal that mining in an upslope direction minimizes disruption to overlying strata. Initiating extraction from lower segments increases tensile-shear stress in coal pillar overburdens, resulting in greater creep deformation towards the downslope than when starting from upper segments, potentially leading to localized landslides and widespread creep deformation in mined-out areas. The downslope upward mining sequence exhibits the least fractal dimensions, indicating minimal disturbance to both strata and surface. While all five mining scenarios maintain good slope stability under normal conditions, recalibrated stability assessments based on fractal dimensions suggest that downslope upward mining offers the highest stability under rainfall, contrasting with the lower stability and potential instability risks of upslope downward mining. These insights are pivotal for mining operations and geological hazard mitigation in multi-seam coal exploitation on bedding slopes.

Method and Description of Sedimentary System Characterization Based on Sequence Stratigraphy

A Oilfield is the most representative mid to deep oil field in the Bohai Sea, with the main oil bearing intervals being the upper and middle Shahejie-3 sections of the Paleogene Shahejie Formation. By combining well seismic analysis, the middle section of Shahejie-3 is divided into high-level system tract and forced lake retreat system tract, corresponding to the II oil formation and I oil formation, respectively. Using sequence stratigraphy methods, based on seismic profiles and drilling lithological cycles, the high stand system tract is divided into 5 stages of delta progradation. The first and second stages are high angle S-type progradation with large sedimentary thickness, the third stage is oblique progradation, and the fourth and fifth stages are S-oblique composite progradation;By combining seismic data, we characterized the large-scale (8 small-scale) progradation bodies of 5 periods, clarified the distribution characteristics of reservoir planes, and laid the foundation for the later exploration of oilfield potential.

Coseismic Coulomb stress changes induced by a 2020-2021 M_(W)>7.0 Alaska earthquake sequence in and around the Shumagin gap and its influence on the Alaska-Aleutian subduction interface

Three M_(W)>7.0 earthquakes in 2020-2021 occurred in the Shumagin seismic gap and its adjacent area of the Alaska-Aleutian subduction zone,including the Mw7.8 Simeonof thrust earthquake on July 22,2020,the M_(W)7.6 Sand Point strike-slip earthquake on October 19,2020,and the M_(W)8.2 Chignik thrust earthquake on July 29,2021.The spatial and temporal proximity of these three earthquakes prompts us to probe stress-triggering effects among them.Here we examine the coseismic Coulomb stress change imparted by the three earthquakes and their influence on the subduction interface.Our results show that:(1)The Simeonof earthquake has strong loading effects on the subsequent Sand Point and Chignik earthquakes,with the Coulomb stress changes of 3.95 bars and 2.89 bars,respectively.The Coulomb stress change caused by the Sand Point earthquake at the hypocenter of the Chignik earthquake is merely around 0.01 bars,suggesting the negligible triggering effect on the latter earthquake;(2)The triggering effects of the Simeonof,Sand Point,and Chignik earthquakes on aftershocks within three months are not well pronounced because of the triggering rates of 38%,14%,and 43%respectively.Other factors may have played an important role in promoting the occurrence of these aftershocks,such as the roughness of the subduction interface,the complicated velocity structure of the lithosphere,and the heterogeneous prestress therein;(3)The three earthquakes caused remarkable coseismic Coulomb stress changes at the subduction interface nearby these mainshocks,with an average Coulomb stress change of 3.2 bars in the shallow region directly inwards the trench.

Intelligent extraction of road cracks based on vehicle laser point cloud and panoramic sequence images

In light of the limited efficacy of conventional methods for identifying pavement cracks and the absence of comprehensive depth and location data in two-dimensional photographs,this study presents an intelligent strategy for extracting road cracks.This methodology involves the integration of laser point cloud data obtained from a vehicle-mounted system and a panoramic sequence of images.The study employs a vehicle-mounted LiDAR measurement system to acquire laser point cloud and panoramic sequence image data simultaneously.A convolutional neural network is utilized to extract cracks from the panoramic sequence image.The extracted sequence image is then aligned with the laser point cloud,enabling the assignment of RGB information to the vehicle-mounted three dimensional(3D)point cloud and location information to the two dimensional(2D)panoramic image.Additionally,a threshold value is set based on the crack elevation change to extract the aligned roadway point cloud.The three-dimensional data pertaining to the cracks can be acquired.The experimental findings demonstrate that the use of convolutional neural networks has yielded noteworthy outcomes in the extraction of road cracks.The utilization of point cloud and image alignment techniques enables the extraction of precise location data pertaining to road cracks.This approach exhibits superior accuracy when compared to conventional methods.Moreover,it facilitates rapid and accurate identification and localization of road cracks,thereby playing a crucial role in ensuring road maintenance and traffic safety.Consequently,this technique finds extensive application in the domains of intelligent transportation and urbanization development.The technology exhibits significant promise for use in the domains of intelligent transportation and city development.

Influence of Production Sequence of Aluminum Alloy Hot Rolling on Strip Surface Quality

With the intensification of market competition in the aluminum alloy strip processing industry,it is dif-ficult to control the mass production of the same specifications,which is bound to affect the hot rolling production.This paper studied the effect of the hot rolling order of aluminum alloy on the surface quality of strip,such as roll printing,color difference,anodic oxidation,etc.,reasonable discharge sequence and corresponding optimization measures were formulated.

Biostratigraphy,Microfacies,Sedimentary Environments and Sequence Stratigraphy of the Late Devonian-Carboniferous Deposits at the Anarak Section,Central Iran

The Late Devonian-early Carboniferous deposits of the Anarak section in northeastern Isfahan,Central Iran,evaluated based on conodont biostratigraphy,sedimentary environment and sequence stratigraphy.According to the field observations,five lithological units were identified.Investigating the conodont fauna of the Late Devonian-Carboniferous(Mississippian-Pennsylvanian)deposits of Bahram,Shishtu,and Qaleh(Sardar 1)formations in Anarak section led to the identification of 67 species of 18 conodont genera,and accordingly 22 conodont biozones were differentiated.The correlation of sea-level change curves,regarding to the conodont biofacies with the global sea-level curve,demonstrates the relative correlation in the mentioned times due to the shallow condition of the central Iran basin compared to the European and American basins.The microfacies analysis led to the identification of 12 microfacies related to the open sea,bioclastic barrier,lagoon and tidal flat sub-sedimentary environments in a homoclinal carbonate ramp environment.Based on sequence stratigraphy studies,three 3rd order sequences were identified.The first sequence,which is of the Late Devonian(upper part of the Bahram Formation,32.5 m),the second sequence(12.5 m)is the Late Devonian(uppermost part of the Bahram Formation),and the third sequence(68 m)is the early Carboniferous(the Shishtu I Formation).

Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs

Background Pork quality can directly affect customer purchase tendency and meat quality traits have become valu-able in modern pork production.However,genetic improvement has been slow due to high phenotyping costs.In this study,whole genome sequence(WGS)data was used to evaluate the prediction accuracy of genomic best linear unbiased prediction(GBLUP)for meat quality in large-scale crossbred commercial pigs.Results We produced WGS data(18,695,907 SNPs and 2,106,902 INDELs exceed quality control)from 1,469 sequenced Duroc×(Landrace×Yorkshire)pigs and developed a reference panel for meat quality including meat color score,marbling score,L*(lightness),a*(redness),and b*(yellowness)of genomic prediction.The prediction accuracy was defined as the Pearson correlation coefficient between adjusted phenotypes and genomic estimated breeding values in the validation population.Using different marker density panels derived from WGS data,accuracy differed substantially among meat quality traits,varied from 0.08 to 0.47.Results showed that MultiBLUP outperform GBLUP and yielded accuracy increases ranging from 17.39%to 75%.We optimized the marker density and found medium-and high-density marker panels are beneficial for the estimation of heritability for meat quality.Moreover,we conducted genotype imputation from 50K chip to WGS level in the same population and found average concord-ance rate to exceed 95%and r^(2)=0.81.Conclusions Overall,estimation of heritability for meat quality traits can benefit from the use of WGS data.This study showed the superiority of using WGS data to genetically improve pork quality in genomic prediction.

A Novel Method of Deinterleaving Radar Pulse Sequences Based on a Modified DBSCAN Algorithm

A modified DBSCAN algorithm is presented for deinterleaving of radar pulses in modern EW environments.A main characteristic of the proposed method is that using only time of arrival of pulses,the method can sort the pulses efficiently.Other PDW information such as rise time,carrier frequency,pulse width,modulation on pulse,fall time and direction of arrival are not required.To identify the valid PRIs in a set of interleaved pulses,an innovative modification of the DBSCAN algorithm is introduced which is accurate and easy to implement.The proposed method determines valid PRIs more accurately and neglects the spurious ones more efficiently as compared to the classical histogram based algorithms such as SDIF.Furthermore,without specifying any input parameter,the proposed method can deinterleave radar pulses while up to 30%jitter is present in the associated PRI.The accuracy and efficiency of the proposed method are verified by computer simulations and real data results.Experimental simulations are based on different real and operational scenarios where the presence of missing and spurious pulses are also considered.So,the simulation results can be of practical significance.

PRI modulation recognition and sequence search under small sample prerequisite

Pulse repetition interval(PRI)modulation recognition and pulse sequence search are significant for effective electronic support measures.In modern electromagnetic environments,different types of inter-pulse slide radars are highly confusing.There are few available training samples in practical situations,which leads to a low recognition accuracy and poor search effect of the pulse sequence.In this paper,an approach based on bi-directional long short-term memory(BiLSTM)networks and the temporal correlation algorithm for PRI modulation recognition and sequence search under the small sample prerequisite is proposed.The simulation results demonstrate that the proposed algorithm can recognize unilinear,bilinear,sawtooth,and sinusoidal PRI modulation types with 91.43% accuracy and complete the pulse sequence search with 30% missing pulses and 50% spurious pulses under the small sample prerequisite.

Reaction视频中用户弹幕信息交互行为的情感反应生成机理研究

深入挖掘Reaction视频中弹幕信息交互行为的情感反应机理有助于理解用户弹幕创作背后的情感生成原因及情感变化过程。本文基于情感反应模型,利用定向内容分析法对哔哩哔哩网站中11个热门视频的弹幕信息资源、视频内容以及reactor反应情况展开编码研究,构建了Reaction视频中用户弹幕信息交互行为的情感反应生成机理模型。研究发现,Reaction视频弹幕信息交互行为中的情感反应生成机理总体上遵循“信息刺激-情感反应”的路径,信息刺激有时会独立唤醒情绪或特定情感态度,有时也会通过唤醒特定情感态度进而影响情绪或内化情感态度的生成。该模型有助于提升情感反应理论在计算机协助交流中的情境化探索,也将为社交媒体中用户与信息交互提供优化建议。

Sequence of events leading to primary biliary cholangitis

Primary biliary cholangitis(PBC)is a chronic cholestatic liver disease that is observed more frequently in middle-aged women.This disorder is considered an autoimmune disease,since liver injury is sustained by the presence of selfdirected antimitochondrial antibodies targeting the bile duct cells.The prognosis may vary depending on an early diagnosis and response to therapy.However,nearly a third of patients can progress to liver cirrhosis,thus requiring a liver transplant.Traditional immunosuppressive therapies,commonly employed for other autoimmune diseases,have limited effects on PBC.In fact,dramatic functional changes that occur in the biliary epithelium in the course of inflammation play a major role in perpetuating the injury.In this minireview,after a background on the disease and possible predisposing factors,the sequential cooperation of cellular/molecular events leading to end-stage PBC is discussed in detail.The rise and maintenance of the autoimmune process,as well as the response of the biliary epithelia during inflammatory injury,are key factors in the progression of the disease.The so-called“ductular reaction(DR)”,intended as a reactive expansion of cells with biliary phenotype,is a process frequently observed in PBC and partially understood.However,recent findings suggest a strict relationship between this pathological picture and the progression to liver fibrosis,cell senescence,and loss of biliary ducts.All these issues(onset of chronic inflammation,changes in secretive and proliferative biliary functions,DR,and its relationship with other pathological events)are discussed in this manuscript in an attempt to provide a snapshot,for clinicians and researchers,of the most relevant and sequential contributors to the progression of this human cholestatic disease.We believe that interpreting this disorder as a multistep process may help identify possible therapeutic targets to prevent evolution to severe disease.

Tuning electronic structure of RuO_(2)by single atom Zn and oxygen vacancies to boost oxygen evolution reaction in acidic medium

The poor stability of RuO_(2)electrocatalysts has been the primary obstacles for their practical application in polymer electrolyte membrane electrolyzers.To dramatically enhance the durability of RuO_(2)to construct activity-stability trade-off model is full of significance but challenging.Herein,a single atom Zn stabilized RuO_(2)with enriched oxygen vacancies(SA Zn-RuO_(2))is developed as a promising alternative to iridium oxide for acidic oxygen evolution reaction(OER).Compared with commercial RuO_(2),the enhanced Ru–O bond strength of SA Zn-RuO_(2)by forming Zn-O-Ru local structure motif is favorable to stabilize surface Ru,while the electrons transferred from Zn single atoms to adjacent Ru atoms protects the Ru active sites from overoxidation.Simultaneously,the optimized surrounding electronic structure of Ru sites in SA ZnRuO_(2)decreases the adsorption energies of OER intermediates to reduce the reaction barrier.As a result,the representative SA Zn-RuO_(2)exhibits a low overpotential of 210 mV to achieve 10 mA cm^(-2)and a greatly enhanced durability than commercial RuO_(2).This work provides a promising dual-engineering strategy by coupling single atom doping and vacancy for the tradeoff of high activity and catalytic stability toward acidic OER.

Complicated expansion trajectories of insertion sequences and potential association with horizontal transfer of Wolbachia DNA

DEAR EDITOR,Insertion sequences(ISs) are the simplest structural transposable elements(TEs) in prokaryotes, consisting only of a transposase coding sequence and its bilateral short terminal inverted repeats. Due to their gradually streamlined genomic construction, TEs rarely exist in the genomes of obligate endosymbionts. However, TE content, especially ISs.

Identification of clade-wide putative cis-regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes

Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms.Many conserved non-coding sequences(CNSs)function as cis-regulatory elements.They control the development of various lineages.How-ever,predicting clade-wide cis-regulatory elements across several closely related species remains challenging.Based on the relationship between CNSs and cis-regulatory elements,we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes.Using 12-way whole-genome alignment,we first obtained 632112 CNSs in Cucurbitaceae.Next,we identified 16552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants.Furthermore,we predicted 3271 potential regulatory pairs in the cucumber genome,of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages.The CNSs,Cucurbitaceae-wide cis-regulatory elements,and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/.These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.