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
The nucleotide (base) sequence of the genome might reflect biological information beyond the coding sequences. The appearance frequencies of successive base sequences (key sequences) were calculated for entire genomes...The nucleotide (base) sequence of the genome might reflect biological information beyond the coding sequences. The appearance frequencies of successive base sequences (key sequences) were calculated for entire genomes. Based on the appearance frequency of the key sequences of the genome, any DNA sequences on the genome could be expressed as a sequence spectrum with the adjoining base sequences, which could be used to study the corresponding biological phenomena. In this paper, we used 64 successive three- base sequences (triplets) as the key sequences, and determined and compared the spectra of specific genes to the chromosome, or specific genes to tRNA genes in Saccharomyces cerevisiae, Schizosaccharomyces pombe and Escherichia coli. Based on these analyses, a gene and its corresponding position on the chromosome showed highly similar spectra with the same fold enlargement (approximately 400-fold) in the S. cerevisiae, S. pombe and E. coli genomes. In addition, the homologous structure of genes that encode proteins was also observed with appropriate tRNA gene(s) in the genome. This analytical method might faithfully reflect the encoded biological information, that is, the conservation of the base sequences was to make sense the conservation of the translated amino acids sequence in the coding region, and might be universally applicable to other genomes, even those that consisted of multiple chromosomes.展开更多
The satellite-based automatic identification system (AIS) receiver has to encounter the frequency offset caused by the Doppler effect and the oscillator instability. This paper proposes a non-coherent sequence detecti...The satellite-based automatic identification system (AIS) receiver has to encounter the frequency offset caused by the Doppler effect and the oscillator instability. This paper proposes a non-coherent sequence detection scheme for the satellite-based AIS signal transmitted over the white Gaussian noise channel. Based on the maximum likelihood estimation and a Viterbi decoder, the proposed scheme is capable of tolerating a frequency offset up to 5% of the symbol rate. The complexity of the proposed scheme is reduced by the state-complexity reduction, which is based on per-survivor processing. Simulation results prove that the proposed non-coherent sequence detection scheme has high robustness to frequency offset compared to the relative scheme when messages collision exists.展开更多
A novel diagrammtic method is proposed to show the angular distribution of bases of human protein sequences. Using this method, the distribution sphere[1-4] is divided into four regions with same volume. The picture i...A novel diagrammtic method is proposed to show the angular distribution of bases of human protein sequences. Using this method, the distribution sphere[1-4] is divided into four regions with same volume. The picture is clearer and more intuitive than that in [1] .A rule on the angular distribution of the representative points of bases of protein sequences is given. Besides, in 300 representative pointS of human protein sequence samples we find that there are three (not only one) points outside the sphere.展开更多
A nucleic acid sequence-based amplification（NASBA）assay was established for the detection of Macrobrachium rosenbergii Nodavirus（MrNV）.The specific primers were designed according to the high conserved region of R...A nucleic acid sequence-based amplification（NASBA）assay was established for the detection of Macrobrachium rosenbergii Nodavirus（MrNV）.The specific primers were designed according to the high conserved region of RNA2 sequence of MrNV.The 224 bp specific amplification product was obtained in positive sample determined with 3%agarose gel electrophoresis,while no product was generated from shrimp infected with other viruses including DNA viruses（IHHNV,WSSV）and RNA viruses（TSV,IMNV,YHV）.The detecting limit of the assay was 8pg nucleic acid,which is more sensitive than that of PCR method.展开更多
To understand the gene-based biological processes in-depth,the single-molecule real-time sequencing has drawn increasing attention with promoted by the Human Genome Project.Herein,a set of newly designed canonical flu...To understand the gene-based biological processes in-depth,the single-molecule real-time sequencing has drawn increasing attention with promoted by the Human Genome Project.Herein,a set of newly designed canonical fluorescent bases(A_(y),tC,G_(b),T_(p))are proposed for four-color DNA sequencing.These quasi-intrinsic probes are derived from the fluorophore replacement and ring expansion on natural bases,which still keep the pyrimidine or purine underlying skeleton and Watson–Crick hydrogen bonding face to allow minimal perturbation to the native DNA duplex.More importantly,these nucleobase analogues possess red-shifted absorption and efficient photoluminescence due to the enhancedπ-conjugation in character.Meanwhile,the four analogues could generate distinct emission wavelength(Δλ~50 nm)for real-time sequencing.To assess the biological employment of the proposed biosensors,the effects of base pairing and linking deoxyribose are also considered.展开更多
Base-level is a kind of surface which controls sedimentation and erosion. So, it can be concluded that it is base-level change that controls the formation and internal structure of a sequence. A single cycle of base-l...Base-level is a kind of surface which controls sedimentation and erosion. So, it can be concluded that it is base-level change that controls the formation and internal structure of a sequence. A single cycle of base-level change can generate four sets of different stacking patterns. They are two sets of aggradation, one progradation and one retrogradation, which affects the features of the internal structure of a sequence. Lishu fault subsidence of Songliao basin is a typical half-graben lacustrine basin. Comprehensive base-level change analysis indicates that six base-level cycles and their related six sequences can be recognized between T 4 and T 5 seismic reflection surface. The contemporaneous fault is the main controlling factor of the fault lacustrine basin. There are obvious differences exist in the composition of sedimentary systems and all systems tracts between its steep slope (the side that basin control fault existed) and flat slope. Except highstand systems tract is composed of fan delta-lacustrine system, lowstand systems tract, transgressive systems tract and regressive systems tract are all made up of fan delta-underwater fan-lacustrine sedimentary systems in the side of steep slope.展开更多
In view of the high accuracy and predictability, high-resolution sequence stratigraphy had been extensively applied to oil exploration and gotten prominent practicable results. This article takes the first layer, uppe...In view of the high accuracy and predictability, high-resolution sequence stratigraphy had been extensively applied to oil exploration and gotten prominent practicable results. This article takes the first layer, upper second submember, Shahejie （沙河街） Formation from Pucheng （濮城） oilfield as an example to analyze the application of high-resolution sequence stratigraphy in reservoir study on the basis of a comprehensive study of core log data. Firstly, facies analysis of this area reveals the corresponding terminal fan system occurring where sediment-laden streams decrease in size and vanish as a result of evaporation and transmission losses. The model includes a tripartite zonation of terminal fan into feeder, distributary, and basinal zones. Secondly, electrofacies were made by well-log analysis and then matched with sedimentary facies defined by core analysis. Four electrofacies characterizing the main sedimentary facies association and depositional environments within target area are defined （channel, lag deposit, lake or flood-plain, and overflow deposits）. Thirdly, related correlations based on high-resolution sequence stratigraphy were established. By observing the stacking arrangement of genetic sequences, different scales of stratigraphic cycle can be identified. Within scale and duration, the stratigraphic cycles are termed as genetic sequences, genetic sequence sets, and minor cycles.展开更多
The reservoirs within the Chang 8 Member of Yanchang （延长） Formation in the south- western Ordos basin are characterized by low permeability. It is significant to build a high-resolution sequence stratigraphic fram...The reservoirs within the Chang 8 Member of Yanchang （延长） Formation in the south- western Ordos basin are characterized by low permeability. It is significant to build a high-resolution sequence stratigraphic framework for the exploration and development of these reservoirs. Based on an integrated investigation of well logs, seismic data, cores and outcrops, the Chang 8 Member is interpreted as a 3rd-order transgressive-regressive （T-R） sequence, which consists of six 4th-order T-R se- quences, namely, K1, K2, K3, K4, K5 and K6, respectively, from base to top. Each 4th-order sequence comprises a transgressive systems tract overlain by a regressive systems tract. From K1 to transgressive systems tract of K4, it is characterized by the landward shifts of facies and overall retrogradational sequence stacking pattern due to accommodation increase more than sediment supply during the 3rd-order base-level rise. The distributary channels are mainly deposited in the transgressive systems tracts, and the interdistributary bays, sheet sands, and small-scale mouth bars are primarily developed in the regressive systems tracts in response to the 4th-order base-level fluctuations. From the regressivesystems tracts of K4 to K6, it is characterized by the basinward shifts of facies and overall progradational sequence stacking pattern because of accommodation increase less than sediment sup- ply during a fall in 3rd-order base level. The distributary channels are mainly accumulated in the transgressive systems tracts, and distributary channels and mouth bars are deposited in the regressive systems tracts as a result of the 4th-order base-level changes. Detailed stratigraphic and sedimentoiogical analyses indicate that sequences K1, K2, K5 and K6, as well as the basin edge of K3 and K4, remain potential for exploration and development due to their high reservoir quality in response to the low accommodation and more sediment supply.展开更多
Aging is linked to the deterioration of many physical and cognitive abilities and is the leading risk factor for Alzheimer’s disease. The growing aging population is a significant healthcare problem globally that res...Aging is linked to the deterioration of many physical and cognitive abilities and is the leading risk factor for Alzheimer’s disease. The growing aging population is a significant healthcare problem globally that researchers must investigate to better understand the underlying aging processes. Advances in microarrays and sequencing techniques have resulted in deeper analyses of diverse essential genomes(e.g., mouse, human, and rat) and their corresponding cell types, their organ-specific transcriptomes, and the tissue involved in aging. Traditional gene controllers such as DNA-and RNA-binding proteins significantly influence such programs, causing the need to sort out long non-coding RNAs, a new class of powerful gene regulatory elements. However, their functional significance in the aging process and senescence has yet to be investigated and identified. Several recent researchers have associated the initiation and development of senescence and aging in mammals with several well-reported and novel long non-coding RNAs. In this review article, we identified and analyzed the evolving functions of long non-coding RNAs in cellular processes, including cellular senescence, aging, and age-related pathogenesis, which are the major hallmarks of long non-coding RNAs in aging.展开更多
Hepatocellular carcinoma(HCC) is one of the most common malignancies leading to high mortality rates in the general population and the sixth most common cancer worldwide. HCC is characterized by deregulation of multip...Hepatocellular carcinoma(HCC) is one of the most common malignancies leading to high mortality rates in the general population and the sixth most common cancer worldwide. HCC is characterized by deregulation of multiple genes and signalling pathways. These genetic effects can involve both protein coding genes as well as non-coding RNA genes. Long noncoding RNAs(lnc RNAs) are transcripts longer than 200 nt, constituting a subpopulation of nc RNAs. Their biological effects are not well understood comparedto small non-coding RNA(micro RNAs), but they have been recently recognized to exert a crucial role in the regulation of gene expression and modulation of signalling pathways. Notably, several studies indicated that lnc RNAs contribute to the pathogenesis and progression of HCC. Investigating the molecular mechanisms underlying lnc RNAs expression opens potential applications in diagnosis and treatment of liver disease. This editorial provides three examples(MALAT-1 metastasis associated lung adenocarcinoma transcript, HULC highly upregulated in liver cancer and HOTAIR HOX transcript antisense intergenic RNA) of well-known lnc RNAs upregulated in HCC, whose mechanisms of action are known, and for which therapeutic applications are delineated. Targeting of lnc RNAs using several approaches(siR NA-mediated silencing or changing their secondary structure) offers new possibility to treat HCC.展开更多
Long non-coding RNAs(lncRNAs)are abundantly expressed in the central nervous system and exert a critical role in gene regulation via multiple biological processes.To uncover the functional significance and molecular m...Long non-coding RNAs(lncRNAs)are abundantly expressed in the central nervous system and exert a critical role in gene regulation via multiple biological processes.To uncover the functional significance and molecular mechanisms of lncRNAs in spinal cord injury(SCI),the expression signatures of lncRNAs were profiled using RNA sequencing(RNA-seq)technology in a Sprague-Dawley rat model of the 10th thoracic vertebra complete transection SCI.Results showed that 116 of 14,802 detected lncRNAs were differentially expressed,among which 16—including eight up-regulated(H19,Vof16,Hmox2-ps1,LOC100910973,Ybx1-ps3,Nnat,Gcgr,LOC680254)and eight down-regulated(Rmrp,Terc,Ngrn,Ppp2r2b,Cox6a2,Rpl37a-ps1,LOC360231,Rpph1)—demonstrated fold changes>2 in response to transection SCI.A subset of these RNA-seq results was validated by quantitative real-time PCR.The levels of 821 mRNAs were also significantly altered post-SCI;592 mRNAs were up-regulated and 229 mRNAs were down-regulated by more than 2-fold.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analyses showed that differentially expressed mRNAs were related to GO biological processes and molecular functions such as injury and inflammation response,wound repair,and apoptosis,and were significantly enriched in 15 KEGG pathways,including cell phagocytosis,tumor necrosis factor alpha pathway,and leukocyte migration.Our results reveal the expression profiles of lncRNAs and mRNAs in the rat spinal cord of a complete transection model,and these differentially expressed lncRNAs and mRNAs represent potential novel targets for SCI treatment.We suggest that lncRNAs may play an important role in the early immuno-inflammatory response after spinal cord injury.This study was approved by the Administration Committee of Experimental Animals,Guangdong Province,China.展开更多
Based on non-homogeneous model, a modified model is proposed. The new model deals with codon preference in protein-coding regions, reflects more accurately the key biological features of the regions. In addition, it i...Based on non-homogeneous model, a modified model is proposed. The new model deals with codon preference in protein-coding regions, reflects more accurately the key biological features of the regions. In addition, it is demonstrated, via an example, the modified model offers better solutions than previous model does.展开更多
Bicoid is one of the important Drosophila maternal genes involved in the control of embryo polarity and larvae segmentation. To clone and characterize the rice bicoid-related genes, one cDNA clone, Rb24 (EMBL accessio...Bicoid is one of the important Drosophila maternal genes involved in the control of embryo polarity and larvae segmentation. To clone and characterize the rice bicoid-related genes, one cDNA clone, Rb24 (EMBL accession number: AJ2771380), was isolated by screening of rice unmature seed cDNA library. Sequence analysis indicates that Rb24 contains a putative amino acid sequence, which is homologous to unique 8 amino acids sequence within Drosophila bicoid homeodomain (50% identity, 75% similarity) and involves a lys-9 in putative helix 3. Northern blot analysis of rice RNA has shown that this sequence is expressed in a tissue-specific manner. The transcript was detected strongly in young panicles, but less in young leaves and roots. This results are further confirmed with paraffin section in situ hybridization. The signal is intensive in rice globular embryo and located at the apical tip of the embryo, then, along with the development of embryo, the signal is getting reduced and transfers into both sides of embryo. The existence of bicoid-related sequence in rice embryo and the similarity of polar distribution of bicoid and Rb24 mRNA in early embryo development may implicates a conserved maternal regulation mechanism of body axis presents in Drosophila and in rice.展开更多
Evolutionary algorithm is applied for distillation separation sequence optimization synthesis problems with combination explosion. The binary tree data structure is used to describe the distillation separation sequenc...Evolutionary algorithm is applied for distillation separation sequence optimization synthesis problems with combination explosion. The binary tree data structure is used to describe the distillation separation sequence, and it is directly applied as the coding method. Genetic operators, which ensure to prohibit illegal filial generations completely, are designed by using the method of graph theory. The crossover operator based on a single parent or two parents is designed successfully. The example shows that the average ratio of search space from evolutionary algorithm with two-parent genetic operation is lower, whereas the rate of successful minimizations from evolutionary algorithm with single parent genetic operation is higher.展开更多
AIM: To study genetic difference of mitochondrial DMA (mtDNA) between two hepatocarcinoma cell lines (Hca-F and Hca-P) with diverse metastatic characteristics and the relationship between mtDNA changes in cancer cells...AIM: To study genetic difference of mitochondrial DMA (mtDNA) between two hepatocarcinoma cell lines (Hca-F and Hca-P) with diverse metastatic characteristics and the relationship between mtDNA changes in cancer cells and ttieir oncogenic phenotype. METHODS: Mitochondrial DMA D-loop, tRNAMet+Glu+Ile and ND3 gene fragments from the hepatocarcinoma cell lines with 1100,1126 and 534 bp in length respectively were analysed by PCR amplification and restriction fragment length polymorphism techniques. The D-loop 3′ end sequence of the hepatocarcinoma cell lines was determined by sequencing. RESULTS: No amplification fragment length polymorphism and restriction fragment length polymorphism were observed in tRNAMet+Glu+Ile, ND3 and D-loop of mitochondrial DNA of the hepatocarcinoma cells. Sequence differences between Hca-F and Hca-P were found in mtDNA D-loop. CONCLUSION: Deletion mutations of mitochondrial DNA restriction fragment may not play a significant role in carcinogenesis. Genetic difference of mtDNA D-loop between Hca-F and Hca-P, which may reflect the environmental and genetic influences during tumor progression, could be linked to their tumorigenic phenotypes.展开更多
In this paper, we mainly discuss the images of certain spaces under closed sequencecovering maps. It is showed that the property with a locally countable weak base is preserved by closed sequence-covering maps. And th...In this paper, we mainly discuss the images of certain spaces under closed sequencecovering maps. It is showed that the property with a locally countable weak base is preserved by closed sequence-covering maps. And the following question is discussed： Are the closed sequence-covering images of spaces with a point-countable sn-network sn-first countable？展开更多
Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent work has uncovered a growing number of bacterial small RNAs （sRNAs）, some of which have been shown to regulate critical ce...Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent work has uncovered a growing number of bacterial small RNAs （sRNAs）, some of which have been shown to regulate critical cellular processes. Computational approaches, in combination with molecular experiments, have played an important role in the identification of these sRNAs. At present, there is no information on the presence of small non-coding RNAs and their genes in the Agrobacterium tumefaciens genome. To identify potential sRNAs in this important bacterium, deep sequencing of the short RNA populations isolated from Agrobacterium tumefaciens C58 was carried out. From a data set of more than 10,000 short sequences, 16 candidate sRNAs have been tentatively identified based on computational analysis. All of these candidates can form stem-loop structures by RNA folding predictions and the majority of the secondary structures are rich in GC base-pairs：：Some are followed by a short stretch of U residues, indicative of a rho-independent transcription terminator, whereas some of the short RNAs are found in the stem region of the hairpin, indicative of eukaryotic-like sRNAs. Experimental strategies will need to be used to verify these candidates. The study of an expanded list of candidate sRNAs in Agrobacterium will allow a more complete understanding of the range of roles played by regulatory RNAs in prokaryotes.展开更多
The base sequence in genome was governed by some fundamental principles such as reverse-complement symmetry, multiple fractality and so on, and the analytical method of the genome structure, the “Sequence Spectrum Me...The base sequence in genome was governed by some fundamental principles such as reverse-complement symmetry, multiple fractality and so on, and the analytical method of the genome structure, the “Sequence Spectrum Method (SSM)”, based on the structural features of genomic DNA faithfully visualized these principles. This paper reported that the sequence spectrum in SSM closely reflected the biological phenomena of protein and DNA, and SSM could identify the interactive region of protein-protein and DNA-protein uniformly. In order to investigate the effectiveness of SSM we analyzed the several protein-protein and DNA-protein interaction published primarily in the genome of Saccharomyces cerevisiae. The method proposed here was based on the homology of sequence spectrum, and it advantageously and surprisingly used only base sequence of genome and did not require any other information, even information about the amino-acid sequence of protein. Eventually it was concluded that the fundamental principles in genome governed not only the static base sequence but also the dynamic function of protein and DNA.展开更多
In the field of automatic target recognition and tracking,traditional image complexity metrics,such as statistical variance and signal-to-noise ratio,all focus on single-frame images.However,there are few researches a...In the field of automatic target recognition and tracking,traditional image complexity metrics,such as statistical variance and signal-to-noise ratio,all focus on single-frame images.However,there are few researches about the complexity of image sequence.To solve this problem,a criterion of evaluating image sequence complexity is proposed.Firstly,to characterize this criterion quantitatively,two metrics for measuring the complexity of image sequence,namely feature space similarity degree of global background(FSSDGB)and feature space occultation degree of local background(FSODLB)are developed.Here,FSSDGB reflects the ability of global background to introduce false alarms based on feature space,and FSODLB represents the difference between target and local background based on feature space.Secondly,the feature space is optimized by the grey relational method and relevant features are removed so that FSSDGB and FSODLB are more reasonable to establish complexity of single-frame images.Finally,the image sequence complexity is not a linear sum of the single-frame image complexity.Target tracking errors often occur in high-complexity images and the tracking effect of low-complexity images is very well.The nonlinear transformation based on median(NTM)is proposed to construct complexity of image sequence.The experimental results show that the proposed metric is more valid than other metrics,such as sequence correlation(SC)and interframe change degree(IFCD),and it is highly relevant to the actual performance of automatic target tracking algorithms.展开更多
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.
文摘The nucleotide (base) sequence of the genome might reflect biological information beyond the coding sequences. The appearance frequencies of successive base sequences (key sequences) were calculated for entire genomes. Based on the appearance frequency of the key sequences of the genome, any DNA sequences on the genome could be expressed as a sequence spectrum with the adjoining base sequences, which could be used to study the corresponding biological phenomena. In this paper, we used 64 successive three- base sequences (triplets) as the key sequences, and determined and compared the spectra of specific genes to the chromosome, or specific genes to tRNA genes in Saccharomyces cerevisiae, Schizosaccharomyces pombe and Escherichia coli. Based on these analyses, a gene and its corresponding position on the chromosome showed highly similar spectra with the same fold enlargement (approximately 400-fold) in the S. cerevisiae, S. pombe and E. coli genomes. In addition, the homologous structure of genes that encode proteins was also observed with appropriate tRNA gene(s) in the genome. This analytical method might faithfully reflect the encoded biological information, that is, the conservation of the base sequences was to make sense the conservation of the translated amino acids sequence in the coding region, and might be universally applicable to other genomes, even those that consisted of multiple chromosomes.
文摘The satellite-based automatic identification system (AIS) receiver has to encounter the frequency offset caused by the Doppler effect and the oscillator instability. This paper proposes a non-coherent sequence detection scheme for the satellite-based AIS signal transmitted over the white Gaussian noise channel. Based on the maximum likelihood estimation and a Viterbi decoder, the proposed scheme is capable of tolerating a frequency offset up to 5% of the symbol rate. The complexity of the proposed scheme is reduced by the state-complexity reduction, which is based on per-survivor processing. Simulation results prove that the proposed non-coherent sequence detection scheme has high robustness to frequency offset compared to the relative scheme when messages collision exists.
文摘A novel diagrammtic method is proposed to show the angular distribution of bases of human protein sequences. Using this method, the distribution sphere[1-4] is divided into four regions with same volume. The picture is clearer and more intuitive than that in [1] .A rule on the angular distribution of the representative points of bases of protein sequences is given. Besides, in 300 representative pointS of human protein sequence samples we find that there are three (not only one) points outside the sphere.
基金Supported by Special Fund for Agro-scientific Research in the Public Interest(201103034)Huzhou Science and Technology Project(2012GN08,2011ZD2005)Science and Technology Innovation Team Project of Freshwater Aquaculture of Zhejiang Province(2012R10026-11)
文摘A nucleic acid sequence-based amplification（NASBA）assay was established for the detection of Macrobrachium rosenbergii Nodavirus（MrNV）.The specific primers were designed according to the high conserved region of RNA2 sequence of MrNV.The 224 bp specific amplification product was obtained in positive sample determined with 3%agarose gel electrophoresis,while no product was generated from shrimp infected with other viruses including DNA viruses（IHHNV,WSSV）and RNA viruses（TSV,IMNV,YHV）.The detecting limit of the assay was 8pg nucleic acid,which is more sensitive than that of PCR method.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11804195,11847224,11674198,and 12274265)the Natural Science Foundation of Shandong Province,China(Grant Nos.ZR2018BA034 and ZR2022MA006)。
文摘To understand the gene-based biological processes in-depth,the single-molecule real-time sequencing has drawn increasing attention with promoted by the Human Genome Project.Herein,a set of newly designed canonical fluorescent bases(A_(y),tC,G_(b),T_(p))are proposed for four-color DNA sequencing.These quasi-intrinsic probes are derived from the fluorophore replacement and ring expansion on natural bases,which still keep the pyrimidine or purine underlying skeleton and Watson–Crick hydrogen bonding face to allow minimal perturbation to the native DNA duplex.More importantly,these nucleobase analogues possess red-shifted absorption and efficient photoluminescence due to the enhancedπ-conjugation in character.Meanwhile,the four analogues could generate distinct emission wavelength(Δλ~50 nm)for real-time sequencing.To assess the biological employment of the proposed biosensors,the effects of base pairing and linking deoxyribose are also considered.
文摘Base-level is a kind of surface which controls sedimentation and erosion. So, it can be concluded that it is base-level change that controls the formation and internal structure of a sequence. A single cycle of base-level change can generate four sets of different stacking patterns. They are two sets of aggradation, one progradation and one retrogradation, which affects the features of the internal structure of a sequence. Lishu fault subsidence of Songliao basin is a typical half-graben lacustrine basin. Comprehensive base-level change analysis indicates that six base-level cycles and their related six sequences can be recognized between T 4 and T 5 seismic reflection surface. The contemporaneous fault is the main controlling factor of the fault lacustrine basin. There are obvious differences exist in the composition of sedimentary systems and all systems tracts between its steep slope (the side that basin control fault existed) and flat slope. Except highstand systems tract is composed of fan delta-lacustrine system, lowstand systems tract, transgressive systems tract and regressive systems tract are all made up of fan delta-underwater fan-lacustrine sedimentary systems in the side of steep slope.
基金supported by the National Key Technology R&D Program (No. 2006BAC18B05)
文摘In view of the high accuracy and predictability, high-resolution sequence stratigraphy had been extensively applied to oil exploration and gotten prominent practicable results. This article takes the first layer, upper second submember, Shahejie （沙河街） Formation from Pucheng （濮城） oilfield as an example to analyze the application of high-resolution sequence stratigraphy in reservoir study on the basis of a comprehensive study of core log data. Firstly, facies analysis of this area reveals the corresponding terminal fan system occurring where sediment-laden streams decrease in size and vanish as a result of evaporation and transmission losses. The model includes a tripartite zonation of terminal fan into feeder, distributary, and basinal zones. Secondly, electrofacies were made by well-log analysis and then matched with sedimentary facies defined by core analysis. Four electrofacies characterizing the main sedimentary facies association and depositional environments within target area are defined （channel, lag deposit, lake or flood-plain, and overflow deposits）. Thirdly, related correlations based on high-resolution sequence stratigraphy were established. By observing the stacking arrangement of genetic sequences, different scales of stratigraphic cycle can be identified. Within scale and duration, the stratigraphic cycles are termed as genetic sequences, genetic sequence sets, and minor cycles.
基金supported by the National Natural Science Foundation of China (No. 40702024)
文摘The reservoirs within the Chang 8 Member of Yanchang （延长） Formation in the south- western Ordos basin are characterized by low permeability. It is significant to build a high-resolution sequence stratigraphic framework for the exploration and development of these reservoirs. Based on an integrated investigation of well logs, seismic data, cores and outcrops, the Chang 8 Member is interpreted as a 3rd-order transgressive-regressive （T-R） sequence, which consists of six 4th-order T-R se- quences, namely, K1, K2, K3, K4, K5 and K6, respectively, from base to top. Each 4th-order sequence comprises a transgressive systems tract overlain by a regressive systems tract. From K1 to transgressive systems tract of K4, it is characterized by the landward shifts of facies and overall retrogradational sequence stacking pattern due to accommodation increase more than sediment supply during the 3rd-order base-level rise. The distributary channels are mainly deposited in the transgressive systems tracts, and the interdistributary bays, sheet sands, and small-scale mouth bars are primarily developed in the regressive systems tracts in response to the 4th-order base-level fluctuations. From the regressivesystems tracts of K4 to K6, it is characterized by the basinward shifts of facies and overall progradational sequence stacking pattern because of accommodation increase less than sediment sup- ply during a fall in 3rd-order base level. The distributary channels are mainly accumulated in the transgressive systems tracts, and distributary channels and mouth bars are deposited in the regressive systems tracts as a result of the 4th-order base-level changes. Detailed stratigraphic and sedimentoiogical analyses indicate that sequences K1, K2, K5 and K6, as well as the basin edge of K3 and K4, remain potential for exploration and development due to their high reservoir quality in response to the low accommodation and more sediment supply.
文摘Aging is linked to the deterioration of many physical and cognitive abilities and is the leading risk factor for Alzheimer’s disease. The growing aging population is a significant healthcare problem globally that researchers must investigate to better understand the underlying aging processes. Advances in microarrays and sequencing techniques have resulted in deeper analyses of diverse essential genomes(e.g., mouse, human, and rat) and their corresponding cell types, their organ-specific transcriptomes, and the tissue involved in aging. Traditional gene controllers such as DNA-and RNA-binding proteins significantly influence such programs, causing the need to sort out long non-coding RNAs, a new class of powerful gene regulatory elements. However, their functional significance in the aging process and senescence has yet to be investigated and identified. Several recent researchers have associated the initiation and development of senescence and aging in mammals with several well-reported and novel long non-coding RNAs. In this review article, we identified and analyzed the evolving functions of long non-coding RNAs in cellular processes, including cellular senescence, aging, and age-related pathogenesis, which are the major hallmarks of long non-coding RNAs in aging.
文摘Hepatocellular carcinoma(HCC) is one of the most common malignancies leading to high mortality rates in the general population and the sixth most common cancer worldwide. HCC is characterized by deregulation of multiple genes and signalling pathways. These genetic effects can involve both protein coding genes as well as non-coding RNA genes. Long noncoding RNAs(lnc RNAs) are transcripts longer than 200 nt, constituting a subpopulation of nc RNAs. Their biological effects are not well understood comparedto small non-coding RNA(micro RNAs), but they have been recently recognized to exert a crucial role in the regulation of gene expression and modulation of signalling pathways. Notably, several studies indicated that lnc RNAs contribute to the pathogenesis and progression of HCC. Investigating the molecular mechanisms underlying lnc RNAs expression opens potential applications in diagnosis and treatment of liver disease. This editorial provides three examples(MALAT-1 metastasis associated lung adenocarcinoma transcript, HULC highly upregulated in liver cancer and HOTAIR HOX transcript antisense intergenic RNA) of well-known lnc RNAs upregulated in HCC, whose mechanisms of action are known, and for which therapeutic applications are delineated. Targeting of lnc RNAs using several approaches(siR NA-mediated silencing or changing their secondary structure) offers new possibility to treat HCC.
基金financially supported by the National Natural Science Foundation of China,No.81371366(to HFW)Characteristic Innovation Project of Colleges and Universities in Guangdong Province of China,No.2018KTSCX075(to HFW)+3 种基金the Key Project of Social Development of Dongguan of China,No.20185071521640(to HFW)College Students’ Science and Technology Innovation Training Project,China,Nos.201810571058,GDMU2018024,GDMU2018056,GDMU2018061(to HFW)College Students’ Innovative Experimental Project in Guangdong Medical University,China,No.ZZDS001(to HFW)College Students’ Science and Technology Innovation Cultivation Project in Guangdong of China,No.pdjh2019b0217(to HFW)
文摘Long non-coding RNAs(lncRNAs)are abundantly expressed in the central nervous system and exert a critical role in gene regulation via multiple biological processes.To uncover the functional significance and molecular mechanisms of lncRNAs in spinal cord injury(SCI),the expression signatures of lncRNAs were profiled using RNA sequencing(RNA-seq)technology in a Sprague-Dawley rat model of the 10th thoracic vertebra complete transection SCI.Results showed that 116 of 14,802 detected lncRNAs were differentially expressed,among which 16—including eight up-regulated(H19,Vof16,Hmox2-ps1,LOC100910973,Ybx1-ps3,Nnat,Gcgr,LOC680254)and eight down-regulated(Rmrp,Terc,Ngrn,Ppp2r2b,Cox6a2,Rpl37a-ps1,LOC360231,Rpph1)—demonstrated fold changes>2 in response to transection SCI.A subset of these RNA-seq results was validated by quantitative real-time PCR.The levels of 821 mRNAs were also significantly altered post-SCI;592 mRNAs were up-regulated and 229 mRNAs were down-regulated by more than 2-fold.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analyses showed that differentially expressed mRNAs were related to GO biological processes and molecular functions such as injury and inflammation response,wound repair,and apoptosis,and were significantly enriched in 15 KEGG pathways,including cell phagocytosis,tumor necrosis factor alpha pathway,and leukocyte migration.Our results reveal the expression profiles of lncRNAs and mRNAs in the rat spinal cord of a complete transection model,and these differentially expressed lncRNAs and mRNAs represent potential novel targets for SCI treatment.We suggest that lncRNAs may play an important role in the early immuno-inflammatory response after spinal cord injury.This study was approved by the Administration Committee of Experimental Animals,Guangdong Province,China.
文摘Based on non-homogeneous model, a modified model is proposed. The new model deals with codon preference in protein-coding regions, reflects more accurately the key biological features of the regions. In addition, it is demonstrated, via an example, the modified model offers better solutions than previous model does.
文摘Bicoid is one of the important Drosophila maternal genes involved in the control of embryo polarity and larvae segmentation. To clone and characterize the rice bicoid-related genes, one cDNA clone, Rb24 (EMBL accession number: AJ2771380), was isolated by screening of rice unmature seed cDNA library. Sequence analysis indicates that Rb24 contains a putative amino acid sequence, which is homologous to unique 8 amino acids sequence within Drosophila bicoid homeodomain (50% identity, 75% similarity) and involves a lys-9 in putative helix 3. Northern blot analysis of rice RNA has shown that this sequence is expressed in a tissue-specific manner. The transcript was detected strongly in young panicles, but less in young leaves and roots. This results are further confirmed with paraffin section in situ hybridization. The signal is intensive in rice globular embryo and located at the apical tip of the embryo, then, along with the development of embryo, the signal is getting reduced and transfers into both sides of embryo. The existence of bicoid-related sequence in rice embryo and the similarity of polar distribution of bicoid and Rb24 mRNA in early embryo development may implicates a conserved maternal regulation mechanism of body axis presents in Drosophila and in rice.
文摘Evolutionary algorithm is applied for distillation separation sequence optimization synthesis problems with combination explosion. The binary tree data structure is used to describe the distillation separation sequence, and it is directly applied as the coding method. Genetic operators, which ensure to prohibit illegal filial generations completely, are designed by using the method of graph theory. The crossover operator based on a single parent or two parents is designed successfully. The example shows that the average ratio of search space from evolutionary algorithm with two-parent genetic operation is lower, whereas the rate of successful minimizations from evolutionary algorithm with single parent genetic operation is higher.
基金Supported by the National Natural Science Foundation of China, No. 39900173
文摘AIM: To study genetic difference of mitochondrial DMA (mtDNA) between two hepatocarcinoma cell lines (Hca-F and Hca-P) with diverse metastatic characteristics and the relationship between mtDNA changes in cancer cells and ttieir oncogenic phenotype. METHODS: Mitochondrial DMA D-loop, tRNAMet+Glu+Ile and ND3 gene fragments from the hepatocarcinoma cell lines with 1100,1126 and 534 bp in length respectively were analysed by PCR amplification and restriction fragment length polymorphism techniques. The D-loop 3′ end sequence of the hepatocarcinoma cell lines was determined by sequencing. RESULTS: No amplification fragment length polymorphism and restriction fragment length polymorphism were observed in tRNAMet+Glu+Ile, ND3 and D-loop of mitochondrial DNA of the hepatocarcinoma cells. Sequence differences between Hca-F and Hca-P were found in mtDNA D-loop. CONCLUSION: Deletion mutations of mitochondrial DNA restriction fragment may not play a significant role in carcinogenesis. Genetic difference of mtDNA D-loop between Hca-F and Hca-P, which may reflect the environmental and genetic influences during tumor progression, could be linked to their tumorigenic phenotypes.
基金Supported by National Natural Science Foundation of China (Grant Nos.1120141410971185+2 种基金11171162)the Natural Science Foundation of Fujian Province (Grant No.2012J05013)Training Programme Foundation for Excellent Youth Researching Talents of Fujian’s Universities (Grant No.JA13190)
文摘In this paper, we mainly discuss the images of certain spaces under closed sequencecovering maps. It is showed that the property with a locally countable weak base is preserved by closed sequence-covering maps. And the following question is discussed： Are the closed sequence-covering images of spaces with a point-countable sn-network sn-first countable？
文摘Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent work has uncovered a growing number of bacterial small RNAs （sRNAs）, some of which have been shown to regulate critical cellular processes. Computational approaches, in combination with molecular experiments, have played an important role in the identification of these sRNAs. At present, there is no information on the presence of small non-coding RNAs and their genes in the Agrobacterium tumefaciens genome. To identify potential sRNAs in this important bacterium, deep sequencing of the short RNA populations isolated from Agrobacterium tumefaciens C58 was carried out. From a data set of more than 10,000 short sequences, 16 candidate sRNAs have been tentatively identified based on computational analysis. All of these candidates can form stem-loop structures by RNA folding predictions and the majority of the secondary structures are rich in GC base-pairs：：Some are followed by a short stretch of U residues, indicative of a rho-independent transcription terminator, whereas some of the short RNAs are found in the stem region of the hairpin, indicative of eukaryotic-like sRNAs. Experimental strategies will need to be used to verify these candidates. The study of an expanded list of candidate sRNAs in Agrobacterium will allow a more complete understanding of the range of roles played by regulatory RNAs in prokaryotes.
文摘The base sequence in genome was governed by some fundamental principles such as reverse-complement symmetry, multiple fractality and so on, and the analytical method of the genome structure, the “Sequence Spectrum Method (SSM)”, based on the structural features of genomic DNA faithfully visualized these principles. This paper reported that the sequence spectrum in SSM closely reflected the biological phenomena of protein and DNA, and SSM could identify the interactive region of protein-protein and DNA-protein uniformly. In order to investigate the effectiveness of SSM we analyzed the several protein-protein and DNA-protein interaction published primarily in the genome of Saccharomyces cerevisiae. The method proposed here was based on the homology of sequence spectrum, and it advantageously and surprisingly used only base sequence of genome and did not require any other information, even information about the amino-acid sequence of protein. Eventually it was concluded that the fundamental principles in genome governed not only the static base sequence but also the dynamic function of protein and DNA.
基金supported by the National Natural Science Foundation of China(61703337)Shanghai Aerospace Science and Technology Innovation Fund(SAST2017-082)
文摘In the field of automatic target recognition and tracking,traditional image complexity metrics,such as statistical variance and signal-to-noise ratio,all focus on single-frame images.However,there are few researches about the complexity of image sequence.To solve this problem,a criterion of evaluating image sequence complexity is proposed.Firstly,to characterize this criterion quantitatively,two metrics for measuring the complexity of image sequence,namely feature space similarity degree of global background(FSSDGB)and feature space occultation degree of local background(FSODLB)are developed.Here,FSSDGB reflects the ability of global background to introduce false alarms based on feature space,and FSODLB represents the difference between target and local background based on feature space.Secondly,the feature space is optimized by the grey relational method and relevant features are removed so that FSSDGB and FSODLB are more reasonable to establish complexity of single-frame images.Finally,the image sequence complexity is not a linear sum of the single-frame image complexity.Target tracking errors often occur in high-complexity images and the tracking effect of low-complexity images is very well.The nonlinear transformation based on median(NTM)is proposed to construct complexity of image sequence.The experimental results show that the proposed metric is more valid than other metrics,such as sequence correlation(SC)and interframe change degree(IFCD),and it is highly relevant to the actual performance of automatic target tracking algorithms.
