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.

On power series statistical convergence and new uniform integrability of double sequences

In the present paper,we mostly focus on P_(p)^(2)-statistical convergence.We will look into the uniform integrability via the power series method and its characterizations for double sequences.Also,the notions of P_(p)^(2)-statistically Cauchy sequence,P_(p)^(2)-statistical boundedness and core for double sequences will be described in addition to these findings.

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.

Graded and Quantitative Technology and Application of Coal-Bearing Reservoir Based on Seismic Reflection Characteristics

Taiyuan formation is the main exploration strata in Ordos Basin, and coals are widely developed. Due to the interference of strong reflection of coals, we cannot completely identify the effective reservoir information of coal-bearing reservoir on seismic data. Previous researchers have studied the reservoir by stripping or weakening the strong reflection, but it is difficult to determine the effectiveness of the remaining reflection seismic data. In this paper, through the establishment of 2D forward model of coal-bearing strata, the corresponding geophysical characteristics of different reflection types of coal-bearing strata are analyzed, and then the favorable sedimentary facies zones for reservoir development are predicted. On this basis, combined with seismic properties, the coal-bearing reservoir is quantitatively characterized by seismic inversion. The above research shows that the Taiyuan formation in LS block of Ordos Basin is affected by coals and forms three or two peaks in different locations. The reservoir plane sedimentary facies zone is effectively characterized by seismic reflection structure. Based on the characteristics of sedimentary facies belt and petrophysical analysis, the reservoir is semi quantitatively characterized by attribute analysis and waveform indication, and quantitatively characterized by pre stack geostatistical inversion. Based on the forward analysis of coal measure strata, this technology characterizes the reservoir facies belt through seismic reflection characteristics, and describes coal measure reservoirs step by step. It effectively guides the exploration of LS block in Ordos Basin, and has achieved good practical application effect.

Cenozoic giant coal-bearing basin belt discovered in China's sea and its adjacent areas

Sea area is an important area of oil and gas exploration in China.It has been found that China's sea area mainly consists of coal type oil and gas,and the exploration of coal-bearing series source rocks has become an important part of oil and gas exploration there.Through years of comprehensive geological research in China's sea area,it has been revealed that it has undergone multiple occurrences of tectonic opening and closing movements in varying degrees in the Paleogene,forming 26 Cenozoic sedimentary basins of various types,such as active continental margin,passive continental margin,transitional continental margin and drift rift basins.In the present study,it is observed for the first time that coal type source rocks are mainly developed in 14 continental margin basins in China's sea area,revealing that a very large C-shaped coal-bearing basin group developed there in the Cenozoic.Next,based on the coupling analysis of paleoclimate,paleobotany,paleogeography and paleostructure,it is observed that there are five coal-forming periods in China's sea area,namely the Paleocene,Eocene,early Oligocene,late Oligocene and Miocene-Pliocene,and the coal-forming age is gradually new from north to south.It is also found that the coal seams in the sea area are mainly developed in three coal-forming environments in Cenozoic,namely delta,fan delta and tidal flat-lagoon.The coal seams developed in different environments are characterized by thin thickness,many layers and poor stability.However,the coal-bearing series source rocks in China's sea area have a wide distribution range,very high thickness and large amount,thus forming a material basis for the formation of rich coal type oil and gas.

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.

Sedimentology and Paleoenvironmental Characteristics of Fine-grained Sediments in Coal-bearing Strata in the Eastern Ordos Basin:A Case Study of the Exploratory Well in the Zizhou Area

The continuously collected cores from the Permo-Carboniferous coal-bearing strata of the eastern Ordos Basin are essential for studying the hydrocarbon potential in this region.This study adopted sedimentological and geochemical methods to analyze the sedimentary environment,material composition,and geochemical characteristics of the coal-bearing strata.The differences in depositional and paleoclimatic conditions were compared;and the factors influencing the organic matter content of fine-grained sediments were explored.The depositional environment of the Benxi and Jinci formations was lagoon to tidal flat with weakly reduced waters with low salinity and dry-hot paleoclimatic conditions;while that of the Taiyuan Formation was a carbonate platform and shallow water delta front,where the water was highly reductive.The xerothermic climate alternated with the warm and humid climate.The period of maximum transgression in the Permo-Carboniferous has the highest water salinity.The Shanxi Formation was deposited in a shallow water delta front with a brackish and fresh water environment and alternative weak reductiveness.And the paleoclimate condition is dry-hot.The TOC content in fine-grained samples was averaging 1.52%.The main controlling mechanism of organic matter in this area was the input conditions according to the analysis on input and preservation of organic matter.

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.

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.

Single‑cell RNA sequencing opens a new era for cotton genomic research and gene functional analysis

Single-cell RNA sequencing(scRNA-seq)is one of the most advanced sequencing technologies for studying transcriptome landscape at the single-cell revolution.It provides numerous advantages over traditional RNA-seq.Since it was first used to profile single-cell transcriptome in plants in 2019,it has been extensively employed to perform different research in plants.Recently,scRNA-seq was also quickly adopted by the cotton research community to solve lots of scientific questions which have been never solved.In this comment,we highlighted the significant progress in employing scRNA-seq to cotton genetic and genomic study and its future potential applications.

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.

Identification and validation of a pyroptosis-related prognostic model for colorectal cancer based on bulk and single-cell RNA sequencing data

BACKGROUND Pyroptosis impacts the development of malignant tumors,yet its role in colorectal cancer(CRC)prognosis remains uncertain.AIM To assess the prognostic significance of pyroptosis-related genes and their association with CRC immune infiltration.METHODS Gene expression data were obtained from The Cancer Genome Atlas(TCGA)and single-cell RNA sequencing dataset GSE178341 from the Gene Expression Omnibus(GEO).Pyroptosis-related gene expression in cell clusters was analyzed,and enrichment analysis was conducted.A pyroptosis-related risk model was developed using the LASSO regression algorithm,with prediction accuracy assessed through K-M and receiver operating characteristic analyses.A nomo-gram predicting survival was created,and the correlation between the risk model and immune infiltration was analyzed using CIBERSORTx calculations.Finally,the differential expression of the 8 prognostic genes between CRC and normal samples was verified by analyzing TCGA-COADREAD data from the UCSC database.RESULTS An effective pyroptosis-related risk model was constructed using 8 genes-CHMP2B,SDHB,BST2,UBE2D2,GJA1,AIM2,PDCD6IP,and SEZ6L2(P<0.05).Seven of these genes exhibited differential expression between CRC and normal samples based on TCGA database analysis(P<0.05).Patients with higher risk scores demonstrated increased death risk and reduced overall survival(P<0.05).Significant differences in immune infiltration were observed between low-and high-risk groups,correlating with pyroptosis-related gene expression.CONCLUSION We developed a pyroptosis-related prognostic model for CRC,affirming its correlation with immune infiltration.This model may prove useful for CRC prognostic evaluation.

Leachate Lithium Characteristics of Loess-paleosol Sequences on the Chinese Loess Plateau and their Paleoclimatic Significance

The geochemical components of the leachate from loess-paleosol deposits can provide information about climaterelated post-depositional processes.For example,leachate lithium([Li]_(leachate))is a potential paleoclimate proxy because lithium is a typical lithophile element that is readily adsorbed by clay minerals during weathering and pedogenesis,and thus stratigraphic variations in[Li]leachatecan reflect these processes.We investigated the[Li]leachatevalues of two loess-paleosols profiles(the Luochuan and Weinan sections),on a north-south climatic gradient on the Chinese Loess Plateau.Independent paleoclimate information was provided by measurements of magnetic susceptibility,grain size,Rb/Sr ratios,and clay mineral content.During the last glacial-interglacial period,[Li]leachateincreased from 0.39 to 1.97μg/g at Luochuan and from 0.67 to 2.45μg/g at Weinan,mainly due to increasing pedogenesis.Based on these results we developed a conceptual model to explain the variations in[Li]leachate,Li^(+)within loess layers is mainly derived from dust input and the decomposition of primary minerals,influenced by the East Asian winter monsoon,while in paleosol layers Li is mainly derived from clay mineral adsorption during pedogenic processes,influenced by the East Asian summer monsoon.

Association between childhood obesity and gut microbiota:16S rRNA gene sequencing-based cohort study

BACKGROUND This study aimed to identify characteristic gut genera in obese and normal-weight children(8-12 years old)using 16S rDNA sequencing.The research aimed to provide insights for mechanistic studies and prevention strategies for childhood obesity.Thirty normal-weight and thirty age-and sex-matched obese children were included.Questionnaires and body measurements were collected,and fecal samples underwent 16S rDNA sequencing.Significant differences in body mass index(BMI)and body-fat percentage were observed between the groups.Analysis of gut microbiota diversity revealed lowerα-diversity in obese children.Differences in gut microbiota composition were found between the two groups.Prevotella and Firmicutes were more abundant in the obese group,while Bacteroides and Sanguibacteroides were more prevalent in the control group.AIM To identify the characteristic gut genera in obese and normal-weight children(8-12-year-old)using 16S rDNA sequencing,and provide a basis for subsequent mechanistic studies and prevention strategies for childhood obesity.METHODS Thirty each normal-weight,1:1 matched for age and sex,and obese children,with an obese status from 2020 to 2022,were included in the control and obese groups,respectively.Basic information was collected through questionnaires and body measurements were obtained from both obese and normal-weight children.Fecal samples were collected from both groups and subjected to 16S rDNA sequencing using an Illumina MiSeq sequencing platform for gut microbiota diversity analysis.RESULTS Significant differences in BMI and body-fat percentage were observed between the two groups.The Ace and Chao1 indices were significantly lower in the obese group than those in the control group,whereas differences were not significant in the Shannon and Simpson indices.Kruskal-Wallis tests indicated significant differences in unweighted and weighted UniFrac distances between the gut microbiota of normal-weight and obese children(P<0.01),suggesting substantial disparities in both the species and quantity of gut microbiota between the two groups.Prevotella,Firmicutes,Bacteroides,and Sanguibacteroides were more abundant in the obese and control groups,respectively.Heatmap results demonstrated significant differences in the gut microbiota composition between obese and normal-weight children.CONCLUSION Obese children exhibited lowerα-diversity in their gut microbiota than did the normal-weight children.Significant differences were observed in the composition of gut microbiota between obese and normal-weight children.

About Upper and Lower Strong Fractional Weighted Mean Convergence by Moduli for Triple Sequences

In article, I present a study on upper and lower statistical convergence, and upper and lower strong fractional weighted mean convergence by moduli for triple sequences. One of the generalizations of the discrete operator Cesàro, was weighted mean operators, which are linear operators, too. Given a modulus function f, I established that a triple sequence that is f-upper or lower strong fractional weighted mean convergent, in some supplementary conditions, is also f-lower or upper statistically convergent. The results of this paper adapt the results obtained in [1] and [2] to upper and lower strong fractional weighted mean convergence and to triple sequence concept. Furthermore, new concepts can be applied to the approximation theory, topology, Fourier analysis, analysis interdisciplinary with applications electrical engineering, robotics and other domains.

The asymptotic relation between the first crossing point and the last exit time of Gaussian order statistics sequences

In this paper,we study the asymptotic relation between the first crossing point and the last exit time for Gaussian order statistics which are generated by stationary weakly and strongly dependent Gaussian sequences.It is shown that the first crossing point and the last exit time are asymptotically independent and dependent for weakly and strongly dependent cases,respectively.The asymptotic relations between the first crossing point and the last exit time for stationary weakly and strongly dependent Gaussian sequences are also obtained.

A study of sequence stratigraphy of the Early Cretaceous coal-bearing series in the southeastern Songliao Basin, NE China

The Early Cretaceous is an important coal accumulation period in China.Abundant coal resources were formed in the southeastern margin of Songliao Basin.Sequence stratigraphy and coal accumulation of the Early Cretaceous in the southeastern margin of Songliao Basin have been studied on the basis of extensive outcrop and borehole data.Based on regional unconformity,basal erosional surfaces of incised valley fills,and abrupt depositional facies-reversal surface,six sequence boundaries have been identified,which subdivide the Early Cretaceous coal-bearing series into 5 third-order sequences.Sequence I corresponds to Huoshiling Formation,sequences II and III correspond to member I and member II of Shahezi Formation.Sequences IV and V correspond to member I and member II of Yingcheng Formation.Sequence I developed at the initial subsiding stage,sequence II and III developed during the stable subsiding stage,while sequence IV and V developed during the basin shrinkage stage.The major coal seams were developed in the sequence II and III,which ensured the relative balance between the increase rate of the accommodation space and the rate of peat accumulation for a longer period,thus forming a thick coal seam.

Development of a High-throughput Sequencing Platform for Detection of Viral Encephalitis Pathogens Based on Amplicon Sequencing

Objective Viral encephalitis is an infectious disease severely affecting human health.It is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other viruses.The laboratory diagnosis of viral encephalitis is a worldwide challenge.Recently,high-throughput sequencing technology has provided new tools for diagnosing central nervous system infections.Thus,In this study,we established a multipathogen detection platform for viral encephalitis based on amplicon sequencing.Methods We designed nine pairs of specific polymerase chain reaction(PCR)primers for the 12 viruses by reviewing the relevant literature.The detection ability of the primers was verified by software simulation and the detection of known positive samples.Amplicon sequencing was used to validate the samples,and consistency was compared with Sanger sequencing.Results The results showed that the target sequences of various pathogens were obtained at a coverage depth level greater than 20×,and the sequence lengths were consistent with the sizes of the predicted amplicons.The sequences were verified using the National Center for Biotechnology Information BLAST,and all results were consistent with the results of Sanger sequencing.Conclusion Amplicon-based high-throughput sequencing technology is feasible as a supplementary method for the pathogenic detection of viral encephalitis.It is also a useful tool for the high-volume screening of clinical samples.