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 co...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.展开更多
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...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.展开更多
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 Tran...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.展开更多
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 whil...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.展开更多
This paper introduces an improvement to a currently published algorithm to compute both Lucas 'sister' sequences Vk and Uk. The proposed algorithm uses Lucas sequence properties to improve the running time by ...This paper introduces an improvement to a currently published algorithm to compute both Lucas 'sister' sequences Vk and Uk. The proposed algorithm uses Lucas sequence properties to improve the running time by about 20% over the algorithm published in [1].展开更多
In this study, we first give the definitions of (s,t)-Jacobsthal and (s,t)-Jacobsthal Lucas sequence. By using these formulas we define (s,t)-Jacobsthal and (s,t)-Jacobsthal Lucas matrix sequences. After that we estab...In this study, we first give the definitions of (s,t)-Jacobsthal and (s,t)-Jacobsthal Lucas sequence. By using these formulas we define (s,t)-Jacobsthal and (s,t)-Jacobsthal Lucas matrix sequences. After that we establish some sum formulas for these matrix sequences.展开更多
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 p...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.展开更多
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 th...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.展开更多
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 ...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.展开更多
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...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.展开更多
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 oper...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.展开更多
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.I...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.展开更多
文摘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.
基金This work was supported by the National Key Research and Development Program of China(grant no.2022YFF1000500)National Natural Science Foundation of China(grant no.31941007)Zhejiang province agriculture(livestock)varieties breeding Key Technology R&D Program(grant no.2016C02054-2).
文摘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.
文摘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.
基金supported by the Yayasan Universiti Teknologi PETRONAS Grants,YUTP-PRG(015PBC-027)YUTP-FRG(015LC0-311),Hilmi Hasan,www.utp.edu.my.
文摘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.
文摘This paper introduces an improvement to a currently published algorithm to compute both Lucas 'sister' sequences Vk and Uk. The proposed algorithm uses Lucas sequence properties to improve the running time by about 20% over the algorithm published in [1].
文摘In this study, we first give the definitions of (s,t)-Jacobsthal and (s,t)-Jacobsthal Lucas sequence. By using these formulas we define (s,t)-Jacobsthal and (s,t)-Jacobsthal Lucas matrix sequences. After that we establish some sum formulas for these matrix sequences.
文摘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.
基金supported by the National Natural Science Foundation of China (31830084, 32070466)Fundamental Research Funds for the Central Universities,Nankai University (96172158,96173250, 91822294)。
文摘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.
基金supported by the National Natural Science Foundation of China(grant number:31571361).
文摘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.
基金supported by the National Natural Science Foundation of China(NSFC)(Grant Nos.42272221,41930863)the Fundamental Research Funds for the Central Universities(Grant No.300102272901)+1 种基金the Foundation of the State Key Laboratory of Loess and Quaternary Geology(Institute of Earth and Environment,CAS)(SKLLQG1905,SKLLQGPY2006)the Second Tibet Plateau Scientific Expedition and Research Program(STEP)(2019QZKK0704,2019QZKK0101)。
文摘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.
文摘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.
基金Supported by the National Natural Science Foundation of China(11501250)Zhejiang Provincial Natural Science Foundation of China(LY18A010020)Innovation of Jiaxing City:a program to support the talented persons。
文摘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.
