MicroRNAs (miRNAs) are derived from distinct loci in the genome and play crucial roles in RNA-mediated gene silencing mechanisms that regulate cellular processes during development and stress responses of plants. Th...MicroRNAs (miRNAs) are derived from distinct loci in the genome and play crucial roles in RNA-mediated gene silencing mechanisms that regulate cellular processes during development and stress responses of plants. The miRNAs are approximately 21 nucleotides long and code for the complementary strand to a larger genic mRNA. They are often found within the complementary primary transcript (pri-miRNAs). In the past few years, a growing number of soybean miRNAs have been discovered, however, little is known about the transcriptional regulation of these miRNAs. In this study, promoters and cis-acting elements of soybean miRNAs were analyzed using the genomic data for the first time. A total of 82 miRNAs were located among 122 loci in genome, some were present as double or multiple copies. Five clusters that included ten miRNAs were found in genome, and only one cluster share the same promoter. A total of 191 promoters from 122 loci of the soybean miRNA sequences were found and further analyzed. The results indicated that the conserved soybean miRNA genes had a greater proportion of promoters than that of non-conserved ones, and the distribution of the transcript start sites (TSSs) and TATA-boxes found had different motif styles between conserved and non-conserved miRNA genes. Furthermore, the cis-acting elements 5' of the TSSs were analyzed to obtain potential function and spatiotemporal expression pattern of miRNAs. The data obtained here may lead to the identification of specific sequences upstream of pre-miRNAs and the functional annotation of miRNAs in soybean.展开更多
The present work presents an iin silicoi analysis of Upstream Regulatory Modules (URMs) of genes expressed in tapetum specific manner in dicotyledon and monocotyledon plants. In the current analysis, we identified sev...The present work presents an iin silicoi analysis of Upstream Regulatory Modules (URMs) of genes expressed in tapetum specific manner in dicotyledon and monocotyledon plants. In the current analysis, we identified several motifs conserved in these URMs of which ten were observed to be part of known icisi-elements using tools and databases like MEME, PLACE, MAST and TFSEARCH. We also identified that binding sites for two transcription factors, DOF and WRKY71 were found to be present in majority of the URMs.展开更多
The hexanucleotide repeat mutation in the intron-1 of the chromosome 9 open reading frame (C9orf72) is a frequent cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Altered RNA folding pla...The hexanucleotide repeat mutation in the intron-1 of the chromosome 9 open reading frame (C9orf72) is a frequent cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Altered RNA folding plays a role in ALS pathogenesis in two ways: non-ATG translation of the repeat can lead to aggregates of the known C9orf72 specific dipeptide polymer, whereas the repeat also can form neurotoxic RNA inclusions that dose-responsively kill motor neurons. We report the presence of a homology in the 5’untranslated region (UTR) of the messenger RNA encoding C9orf72 with the iron responsive elements (IRE) that control expression of iron-associated transcripts and predict that this RNA structure may iron-dependently regulate C9orf72 translation. We previously report altered serum ferritin levels track with severity of ALS in patients. Here, we conduct bioinformatics analyses to determine the secondary structure of the 5’UTR in C9orf72 mRNA and find it aligned with IREs in the human mitochondrial cis-aconitase and L and H-ferritin transcripts. Comparison of the role of RNA repeats in Friedriech’s ataxia and fragile X mental retardation suggests the utility of RNA based therapies for treatment of ALS. Antisense oligonucleotides (ASO) have been reported to therapeutically target these GGGGCC repeats. At the same time, because the function of C9orf72 is unknown, knockdown strategies carry some risk of inducing or compounding haploinsufficiency. We propose, for consideration, an approach that may enhance its therapeutic dynamic range by increasing the 5’UTR driven translation of C9orf72 protein to compensate for any potential ALS-specific or ASO-induced haploinsufficieny.展开更多
The root appears to be the most relevant organ for breeding drought stress tolerance.However, our knowledge about temporal and spatial regulation of drought-associated genes in the root remains fragmented, especially ...The root appears to be the most relevant organ for breeding drought stress tolerance.However, our knowledge about temporal and spatial regulation of drought-associated genes in the root remains fragmented, especially in crop plants. We performed a meta-analysis of expression divergence of essential drought-inducible genes and analyzed their association with cis-elements in model crops and major cereal crops. Our analysis of42 selected drought-inducible genes revealed that these are expressed primarily in roots,followed by shoot, leaf, and inflorescence tissues, especially in wheat. Quantitative real-time RT-PCR analysis confirmed higher expression of TaDREB2 and TaAQP7 in roots,correlated with extensive rooting and drought-stress tolerance in wheat. A promoter scan up to 2 kb upstream of the translation start site using phylogenetic footprinting revealed708 transcription factor binding sites, including drought response elements(DREs), auxin response elements(Aux REs), MYCREs/MYBREs, ABAREs, and ERD1 in 19 selected genes.Interestingly, these elements were organized into clusters of overlapping transcription factor binding sites known as homotypic clusters(HCTs), which modulate drought physiology in plants. Taken together, these results revealed the expression preeminence of major drought-inducible genes in the root, suggesting its crucial role in drought adaptation. The occurrence of HCTs in drought-inducible genes highlights the putative evolutionary modifications of crop plants in developing drought adaptation. We propose that these DNA motifs can be used as molecular markers for breeding drought-resilient cultivars, particularly in the cereal crops.展开更多
The forming limit diagram of Ti-15-3 alloy sheet was constituted at room temperature. The effects of different punch and rubber hardness on the limit principal strain distributions were investigated experimentally. Fi...The forming limit diagram of Ti-15-3 alloy sheet was constituted at room temperature. The effects of different punch and rubber hardness on the limit principal strain distributions were investigated experimentally. Finite element analysis models of the samples with dimensions of 180 mm×180 mm were established to analyze the friction coefficients of different interfaces. Effects of various friction coefficients on the strain distributions were studied in detail. Finally, the friction coefficients in the cold forming were determined by contrasting the strain results between the experimental data and the simulated ones.展开更多
In general, triangular and quadrilateral elements are commonly applied in two-dimensional finite element methods. If they are used to compute polycrystalline materials, the cost of computation can be quite significant...In general, triangular and quadrilateral elements are commonly applied in two-dimensional finite element methods. If they are used to compute polycrystalline materials, the cost of computation can be quite significant. Polygonal elements can do well in simulation of the materials behavior and provide greater flexibility for the meshing of complex geometries. Hence, the study on the polygonal element is a very useful and necessary part in the finite element method. In this paper, an n-sided polygonal element based on quadratic spline interpolant, denoted by PS2 element, is presented using the triangular area coordinates and the B-net method. The PS2 element is conforming and can exactly model the quadratic field. It is valid for both convex and non-convex polygonal element, and insensitive to mesh distortions. In addition, no mapping or coordinate transformation is required and thus no Jacobian matrix and its inverse are evaluated. Some appropriate examples are employed to evaluate the performance of the proposed element.展开更多
A 5' flanking region of the well-conserved Toll/interleukin-1 receptor domain (TIR)-encoding sequence was isolated from the genomic DNA ofMelampsora magnusiana Wagner resistant clones of hybrid triploid poplars [(...A 5' flanking region of the well-conserved Toll/interleukin-1 receptor domain (TIR)-encoding sequence was isolated from the genomic DNA ofMelampsora magnusiana Wagner resistant clones of hybrid triploid poplars [(Populus tomentosa × P. bolleana) × P. tomentosa]. Sequencing results and alignment analysis show that the obtained TIR-specific promoter (named as PtTIRp01) was 1,732 bp in length; moreover 3' region of the PtTIRp01 contains a responds to the 5' composition of TIR-NBS type gene PtDRG02, of 747 bp long 5' region of TIR-NBS type gene PtDRG02 and its 398 bp complete TIR-encoding sequence, which significantly corindicating that the obtained TIR-specific promoter region consists upstream region of promoter (985 bp). It was found that the 5' region of TIR-NBS type gene PtDRG02 was characterized in the downstream region of the transcriptional start, named as 5'-untranslated region (5' UTR), consisting of one 93 bp 5'-untranslation exon, one 213 bp intron and one 441 bp TIR-encoding open reading frame (ORF). In addition, several putative cis-acting motifs were present in the obtained TIR-specific promoter of PtDRG02, including one TATA box, one GC-rich, one AT-rich, one P-box, one 3-AF1 binding site, two CAAT boxes, two GT-1 motifs, three typical W-boxes, four I-boxes, and one multi-cis-acting fragment (MCF). The latter contains five types of regulatory elements (E4, G-box, ABRE motif, box 1 and HVA 1 s), most of which were homologous to the cis-acting regulatory elements involved in the activation of defense genes in plants. Thus, it can be suggested that TIR-specific promoter might be a pathogen-inducible promoter and be necessary for the inducible expression of defense-related genes. Key words Toll/interleukin- 1 receptor domain, promoter, Cis-acting element, poplar展开更多
The basic principle and numerical technique for simulating two three-dimensional bubbles near a free surface are studied in detail by using boundary element method. The singularities of influence coefficient matrix ar...The basic principle and numerical technique for simulating two three-dimensional bubbles near a free surface are studied in detail by using boundary element method. The singularities of influence coefficient matrix are eliminated using coordinate transformation and so-called 4π rule. The solid angle for the open surface is treated in direct method based on its definition. Several kinds of configurations for the bubbles and free surface have been investigated. The pressure contours during the evolution of bubbles are obtained in our model and can better illuminate the mechanism underlying the motions of bubbles and free surface. The bubble dynamics and their interactions have close relation with the standoff distances, buoyancy parameters and initial sizes of bubbles. Completely different bubble shapes, free surface motions, jetting patterns and pressure distributions under different parameters can be observed in our model, as demon- strated in our calculation results.展开更多
Divergence of gene expression and alter native splicing is a crucial driving force in the evolution of species;to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a sui...Divergence of gene expression and alter native splicing is a crucial driving force in the evolution of species;to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expressi on (ASE) and allele-specific alter native splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interferenee of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horsex don key (mule/hi nny) and cattlexyak (dzo), respectively. Results showed that 4.8%-8.7% and 10.8%-16.7% of genes exhibited ASE and ASS, respectively. Notably, IncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptati on. In con clusi on, our study dem on strated that explorati on of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.展开更多
Isoparametric quadrilateral elements are widely used in the finite element method, but the accuracy of the isoparametric quadrilateral elements will drop obviously deteriorate due to mesh distortions. Spline functions...Isoparametric quadrilateral elements are widely used in the finite element method, but the accuracy of the isoparametric quadrilateral elements will drop obviously deteriorate due to mesh distortions. Spline functions have some properties of simplicity and conformality. Two 8-node quadrilateral elements have been developed using the trian- gular area coordinates and the B-net method, which can ex- actly model the quadratic field for both convex and concave quadrangles. Some appropriate examples are employed to evaluate the performance of the proposed elements. The nu- merical results show that the two spline elements can obtain solutions which are highly accurate and insensitive to mesh distortions.展开更多
In this article,a high-order scheme,which is formulated by combining the quadratic finite element method in space with a second-order time discrete scheme,is developed for looking for the numerical solution of a two-d...In this article,a high-order scheme,which is formulated by combining the quadratic finite element method in space with a second-order time discrete scheme,is developed for looking for the numerical solution of a two-dimensional nonlinear time fractional thermal diffusion model.The time Caputo fractional derivative is approximated by using the L2-1formula,the first-order derivative and nonlinear term are discretized by some second-order approximation formulas,and the quadratic finite element is used to approximate the spatial direction.The error accuracy O(h3+t2)is obtained,which is verified by the numerical results.展开更多
This paper proposes a hybrid vertex-centered fi- nite volume/finite element method for solution of the two di- mensional (2D) incompressible Navier-Stokes equations on unstructured grids. An incremental pressure fra...This paper proposes a hybrid vertex-centered fi- nite volume/finite element method for solution of the two di- mensional (2D) incompressible Navier-Stokes equations on unstructured grids. An incremental pressure fractional step method is adopted to handle the velocity-pressure coupling. The velocity and the pressure are collocated at the node of the vertex-centered control volume which is formed by join- ing the centroid of cells sharing the common vertex. For the temporal integration of the momentum equations, an im- plicit second-order scheme is utilized to enhance the com- putational stability and eliminate the time step limit due to the diffusion term. The momentum equations are discretized by the vertex-centered finite volume method (FVM) and the pressure Poisson equation is solved by the Galerkin finite el- ement method (FEM). The momentum interpolation is used to damp out the spurious pressure wiggles. The test case with analytical solutions demonstrates second-order accuracy of the current hybrid scheme in time and space for both veloc- ity and pressure. The classic test cases, the lid-driven cavity flow, the skew cavity flow and the backward-facing step flow, show that numerical results are in good agreement with the published benchmark solutions.展开更多
Level set methods are widely used for predicting evolutions of complex free surface topologies,such as the crystal and crack growth,bubbles and droplets deformation,spilling and breaking waves,and two-phase flow pheno...Level set methods are widely used for predicting evolutions of complex free surface topologies,such as the crystal and crack growth,bubbles and droplets deformation,spilling and breaking waves,and two-phase flow phenomena.This paper presents a characteristic level set equation which is derived from the two-dimensional level set equation by using the characteristic-based scheme.An explicit finite volume element method is developed to discretize the equation on triangular grids.Several examples are presented to demonstrate the performance of the proposed method for calculating interface evolutions in time.The proposed level set method is also coupled with the Navier-Stokes equations for two-phase immiscible incompressible flow analysis with surface tension.The Rayleigh-Taylor instability problem is used to test and evaluate the effectiveness of the proposed scheme.展开更多
The importance of microRNA (miRNA) at the post-transcriptional regulation level has recently been recognized in both animals and plants. In recent years, many studies focused on miRNA target identification and funct...The importance of microRNA (miRNA) at the post-transcriptional regulation level has recently been recognized in both animals and plants. In recent years, many studies focused on miRNA target identification and functional analysis. However, little is known about the transcription and regulation of miRNAs themselves. In this study, the transcription start sites (TSSs) for 11 miRNA primary transcripts of soybean from 11 miRNA loci (of 50 loci tested) were cloned by a 5" rapid amplification of cDNA ends (5" RACE) procedure using total RNA from 30-d-old seedlings. The features consistent with a RNA polymerase II mechanism of transcription were found among these miRNA loci. A position weight matrix algorithm was used to identify conserved motifs in miRNA core promoter regions. A canonical TATA box motif was identified upstream of the major start site at 8 (76%) of the mapped miRNA loci. Several cis-acting elements were predicted in the 2 kb 5" to the TSSs. Potential spatial and temporal expression patterns of the miRNAs were found. The target genes for these miRNAs were also predicted and further elucidated for the potential function of the miRNAs. This research provides a molecular basis to explore regulatory mechanisms of miRNA expression, and a way to understand miRNA-mediated regulatory pathways and networks in soybean.展开更多
本文在综合文献的基础上,建立了尿中三唑苯二氮(艹卓)及其主要代谢物的鉴定方法。本法以20ml尿样,在PH为9时,用乙醚提取。提取物用无水硫酸钠脱水,K、D、浓缩到0.5ml,固体进样杆直接进行EI/CI/MS分析;质谱分析在Finnigan Mat 1020 GC/MS...本文在综合文献的基础上,建立了尿中三唑苯二氮(艹卓)及其主要代谢物的鉴定方法。本法以20ml尿样,在PH为9时,用乙醚提取。提取物用无水硫酸钠脱水,K、D、浓缩到0.5ml,固体进样杆直接进行EI/CI/MS分析;质谱分析在Finnigan Mat 1020 GC/MS/DS仪上进行。EI、CI源,甲烷作反应气,源室压力0.35吒。2ul样品由固体进样杆进样,其温度程序:初温60℃,以120℃/min速率升温到350℃。所建立的分析方法快速、灵敏,口服给药量为0.5mg时,可检出尿中1—羟甲基三唑苯二氮(艹卓)。展开更多
Our previous studies have revealed that the Th CAP gene plays a vital role in transgenic Populus(P.davidiana 9 P.bolleana) in response to cold stress.However,the regulatory mechanism of Th CAP gene expression has been...Our previous studies have revealed that the Th CAP gene plays a vital role in transgenic Populus(P.davidiana 9 P.bolleana) in response to cold stress.However,the regulatory mechanism of Th CAP gene expression has been unclear.In this study,the 50 flanking region of the Th CAP promoter(PTh CAP) was cloned using a genomewalking method.By analyzing cis-acting regulatory elements of PTh CAP,a DRE motif and MYC and MYB elements were found to be located in the promoter.To identify the regulatory elements that control the expression of the Th CAP gene promoter,a series of deletion derivatives ofPTh CAP,P1–P5,from the translation start code(-1538,-1190,-900,-718 and-375 bp),were fused to the GUS reporter gene,and then each deletion was stably introduced into Arabidopsis thaliana plants.Deletion analysis of the promoter suggested that only the P2 fragment had strong GUS expression in leaves and roots of A.thaliana exposed to low temperature stress.These results suggest that this290-bp region(-1190 to-900 bp),as an important part in PTh CAP,was associated with cold tolerance of A.thaliana.Our results provide evidence for the regulatory mechanism of Th CAP gene involved in the response to cold stress,and that the gene is promising candidate gene for genetic improvement of crops.展开更多
<strong>Background:</strong> Recently, Coronavirus Disease 2019 (COVID-19) has been affected by the extreme acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has developed important global health a...<strong>Background:</strong> Recently, Coronavirus Disease 2019 (COVID-19) has been affected by the extreme acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has developed important global health anxiety. At this time, the treatment options for this disease are only moderately successful. Smoking has been related to COVID-19 and its mortality, and it has the potential to affect bacteriological and viral conversion, clinical effects, and treatment outcomes. <strong>Methods:</strong> The aim of this study was to determine the relationship between critical essential trace {zinc (Zn), iron (Fe), and copper (Cu)} and toxic {cadmium (Cd) and nickel (Ni)} elements in human biological samples such as scalp hair, serum, saliva, blood, nasal fluid, and sputum of smoking and nonsmoking male COVID-19 patients (n = 139, age range 25 - 38 years) from Hyderabad, Pakistan. For comparative purposes, the biological specimens of referent persons (n = 83), pulmonary Tuberculosis (T.B) patients (n = 67), Pneumonia (n = 56) of the same age groups were also be analyzed. Microwave oven mediated digestion method was employed, and digestion of samples was carried out with the help of 2:1 mixture solution of HNO<sub>3</sub> (65%) and H<sub>2</sub>O<sub>2</sub> (30%). Atomic absorption spectrometry was employed for the determination of elemental concentrations from the microwave oven employed digested samples. <strong>Results:</strong> The found average of essential elements (Zn, Fe, and Cu) in biological specimens of smoker and nonsmoker male COVID-19, T.B, and Pneumonia patients was found to lower, whilst cadmium and nickel were found to be higher when compared with samples from referents (p < 0.001). <strong>Conclusions:</strong> Improved elemental (Cu, Fe, Zn) concentrations may also decrease the risk of bacterial co-infection by enhancing the mucociliary clearance and respiratory epithelial barrier function, in addition to providing direct antibacterial effects against <i>S. pneumoniae</i>. Our findings also suggest that higher Cd and Ni concentrations are linked to cigarette smoking, which could lead to COVID-19 and other lung-infected diseased recurrences. However, further clinical and experimental research is required.展开更多
A three - dimenslonal finite element model is developed to deal with the polymeric liquid flow in coat - hanger die. This model is used to predict the flow behavior of the 2% CMC/watsr solution in the coat - hanger d...A three - dimenslonal finite element model is developed to deal with the polymeric liquid flow in coat - hanger die. This model is used to predict the flow behavior of the 2% CMC/watsr solution in the coat - hanger die with linearly taper manifolds and its validity is experimentally verified quantitatively and qualitatively by using Laser Doppler Velocimetry and Particle Image Velocimetry respectively.展开更多
基金supported by the National High-Tech R&D Program of China (863 Program,2006AA100104-4)the Project of 948 from Ministryof Agriculture of China (2006-G5)+5 种基金the National Nature Science Foundation of China (30971810,60932008)the National Basic Research Program ofChina (973 Program, 2009CB118400)the Postdoctoral Fund in Heilongjiang Province, China (LBH-Z07228)the Foundation Projects of Northeast Agricultural University, Chinathe Technology Project of Education Ministry of Heilongjiang Province, China(11541025)the Technology Project of Harbin,China (2009RFQXN085)
文摘MicroRNAs (miRNAs) are derived from distinct loci in the genome and play crucial roles in RNA-mediated gene silencing mechanisms that regulate cellular processes during development and stress responses of plants. The miRNAs are approximately 21 nucleotides long and code for the complementary strand to a larger genic mRNA. They are often found within the complementary primary transcript (pri-miRNAs). In the past few years, a growing number of soybean miRNAs have been discovered, however, little is known about the transcriptional regulation of these miRNAs. In this study, promoters and cis-acting elements of soybean miRNAs were analyzed using the genomic data for the first time. A total of 82 miRNAs were located among 122 loci in genome, some were present as double or multiple copies. Five clusters that included ten miRNAs were found in genome, and only one cluster share the same promoter. A total of 191 promoters from 122 loci of the soybean miRNA sequences were found and further analyzed. The results indicated that the conserved soybean miRNA genes had a greater proportion of promoters than that of non-conserved ones, and the distribution of the transcript start sites (TSSs) and TATA-boxes found had different motif styles between conserved and non-conserved miRNA genes. Furthermore, the cis-acting elements 5' of the TSSs were analyzed to obtain potential function and spatiotemporal expression pattern of miRNAs. The data obtained here may lead to the identification of specific sequences upstream of pre-miRNAs and the functional annotation of miRNAs in soybean.
文摘The present work presents an iin silicoi analysis of Upstream Regulatory Modules (URMs) of genes expressed in tapetum specific manner in dicotyledon and monocotyledon plants. In the current analysis, we identified several motifs conserved in these URMs of which ten were observed to be part of known icisi-elements using tools and databases like MEME, PLACE, MAST and TFSEARCH. We also identified that binding sites for two transcription factors, DOF and WRKY71 were found to be present in majority of the URMs.
文摘The hexanucleotide repeat mutation in the intron-1 of the chromosome 9 open reading frame (C9orf72) is a frequent cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Altered RNA folding plays a role in ALS pathogenesis in two ways: non-ATG translation of the repeat can lead to aggregates of the known C9orf72 specific dipeptide polymer, whereas the repeat also can form neurotoxic RNA inclusions that dose-responsively kill motor neurons. We report the presence of a homology in the 5’untranslated region (UTR) of the messenger RNA encoding C9orf72 with the iron responsive elements (IRE) that control expression of iron-associated transcripts and predict that this RNA structure may iron-dependently regulate C9orf72 translation. We previously report altered serum ferritin levels track with severity of ALS in patients. Here, we conduct bioinformatics analyses to determine the secondary structure of the 5’UTR in C9orf72 mRNA and find it aligned with IREs in the human mitochondrial cis-aconitase and L and H-ferritin transcripts. Comparison of the role of RNA repeats in Friedriech’s ataxia and fragile X mental retardation suggests the utility of RNA based therapies for treatment of ALS. Antisense oligonucleotides (ASO) have been reported to therapeutically target these GGGGCC repeats. At the same time, because the function of C9orf72 is unknown, knockdown strategies carry some risk of inducing or compounding haploinsufficiency. We propose, for consideration, an approach that may enhance its therapeutic dynamic range by increasing the 5’UTR driven translation of C9orf72 protein to compensate for any potential ALS-specific or ASO-induced haploinsufficieny.
基金supported by German–Pakistani Research Cooperation(grant no.56453308)via German Academic Exchange Service(DAAD)to build German–Pakistani research and academic exchange and partnerships
文摘The root appears to be the most relevant organ for breeding drought stress tolerance.However, our knowledge about temporal and spatial regulation of drought-associated genes in the root remains fragmented, especially in crop plants. We performed a meta-analysis of expression divergence of essential drought-inducible genes and analyzed their association with cis-elements in model crops and major cereal crops. Our analysis of42 selected drought-inducible genes revealed that these are expressed primarily in roots,followed by shoot, leaf, and inflorescence tissues, especially in wheat. Quantitative real-time RT-PCR analysis confirmed higher expression of TaDREB2 and TaAQP7 in roots,correlated with extensive rooting and drought-stress tolerance in wheat. A promoter scan up to 2 kb upstream of the translation start site using phylogenetic footprinting revealed708 transcription factor binding sites, including drought response elements(DREs), auxin response elements(Aux REs), MYCREs/MYBREs, ABAREs, and ERD1 in 19 selected genes.Interestingly, these elements were organized into clusters of overlapping transcription factor binding sites known as homotypic clusters(HCTs), which modulate drought physiology in plants. Taken together, these results revealed the expression preeminence of major drought-inducible genes in the root, suggesting its crucial role in drought adaptation. The occurrence of HCTs in drought-inducible genes highlights the putative evolutionary modifications of crop plants in developing drought adaptation. We propose that these DNA motifs can be used as molecular markers for breeding drought-resilient cultivars, particularly in the cereal crops.
文摘The forming limit diagram of Ti-15-3 alloy sheet was constituted at room temperature. The effects of different punch and rubber hardness on the limit principal strain distributions were investigated experimentally. Finite element analysis models of the samples with dimensions of 180 mm×180 mm were established to analyze the friction coefficients of different interfaces. Effects of various friction coefficients on the strain distributions were studied in detail. Finally, the friction coefficients in the cold forming were determined by contrasting the strain results between the experimental data and the simulated ones.
基金supported by the National Natural Science Foundation of China (60533060, 10672032, 10726067)Science Foundation of Dalian University of Technology (SFDUT07001)
文摘In general, triangular and quadrilateral elements are commonly applied in two-dimensional finite element methods. If they are used to compute polycrystalline materials, the cost of computation can be quite significant. Polygonal elements can do well in simulation of the materials behavior and provide greater flexibility for the meshing of complex geometries. Hence, the study on the polygonal element is a very useful and necessary part in the finite element method. In this paper, an n-sided polygonal element based on quadratic spline interpolant, denoted by PS2 element, is presented using the triangular area coordinates and the B-net method. The PS2 element is conforming and can exactly model the quadratic field. It is valid for both convex and non-convex polygonal element, and insensitive to mesh distortions. In addition, no mapping or coordinate transformation is required and thus no Jacobian matrix and its inverse are evaluated. Some appropriate examples are employed to evaluate the performance of the proposed element.
文摘A 5' flanking region of the well-conserved Toll/interleukin-1 receptor domain (TIR)-encoding sequence was isolated from the genomic DNA ofMelampsora magnusiana Wagner resistant clones of hybrid triploid poplars [(Populus tomentosa × P. bolleana) × P. tomentosa]. Sequencing results and alignment analysis show that the obtained TIR-specific promoter (named as PtTIRp01) was 1,732 bp in length; moreover 3' region of the PtTIRp01 contains a responds to the 5' composition of TIR-NBS type gene PtDRG02, of 747 bp long 5' region of TIR-NBS type gene PtDRG02 and its 398 bp complete TIR-encoding sequence, which significantly corindicating that the obtained TIR-specific promoter region consists upstream region of promoter (985 bp). It was found that the 5' region of TIR-NBS type gene PtDRG02 was characterized in the downstream region of the transcriptional start, named as 5'-untranslated region (5' UTR), consisting of one 93 bp 5'-untranslation exon, one 213 bp intron and one 441 bp TIR-encoding open reading frame (ORF). In addition, several putative cis-acting motifs were present in the obtained TIR-specific promoter of PtDRG02, including one TATA box, one GC-rich, one AT-rich, one P-box, one 3-AF1 binding site, two CAAT boxes, two GT-1 motifs, three typical W-boxes, four I-boxes, and one multi-cis-acting fragment (MCF). The latter contains five types of regulatory elements (E4, G-box, ABRE motif, box 1 and HVA 1 s), most of which were homologous to the cis-acting regulatory elements involved in the activation of defense genes in plants. Thus, it can be suggested that TIR-specific promoter might be a pathogen-inducible promoter and be necessary for the inducible expression of defense-related genes. Key words Toll/interleukin- 1 receptor domain, promoter, Cis-acting element, poplar
基金supported by the Funds for Creative Research Groups of China (50921001)the State Key Development Program for Basic Research of China (2010CB832704)
文摘The basic principle and numerical technique for simulating two three-dimensional bubbles near a free surface are studied in detail by using boundary element method. The singularities of influence coefficient matrix are eliminated using coordinate transformation and so-called 4π rule. The solid angle for the open surface is treated in direct method based on its definition. Several kinds of configurations for the bubbles and free surface have been investigated. The pressure contours during the evolution of bubbles are obtained in our model and can better illuminate the mechanism underlying the motions of bubbles and free surface. The bubble dynamics and their interactions have close relation with the standoff distances, buoyancy parameters and initial sizes of bubbles. Completely different bubble shapes, free surface motions, jetting patterns and pressure distributions under different parameters can be observed in our model, as demon- strated in our calculation results.
基金supported by grants from the National Natural Science Foundation of China(31572381)National Thousand Youth Talents Plan of the International Science and Technology Cooperation Project of China(2013DFA31420)Science and Technology Innovation Capability Promotion Program of the Science and Technology Department of Qinghai Province(2015-ZJ-712)
文摘Divergence of gene expression and alter native splicing is a crucial driving force in the evolution of species;to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expressi on (ASE) and allele-specific alter native splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interferenee of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horsex don key (mule/hi nny) and cattlexyak (dzo), respectively. Results showed that 4.8%-8.7% and 10.8%-16.7% of genes exhibited ASE and ASS, respectively. Notably, IncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptati on. In con clusi on, our study dem on strated that explorati on of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.
基金supported by the National Natural Science Foundation of China(11001037,11102037 and 11290143)the Fundamental Research Funds for the Central Universities
文摘Isoparametric quadrilateral elements are widely used in the finite element method, but the accuracy of the isoparametric quadrilateral elements will drop obviously deteriorate due to mesh distortions. Spline functions have some properties of simplicity and conformality. Two 8-node quadrilateral elements have been developed using the trian- gular area coordinates and the B-net method, which can ex- actly model the quadratic field for both convex and concave quadrangles. Some appropriate examples are employed to evaluate the performance of the proposed elements. The nu- merical results show that the two spline elements can obtain solutions which are highly accurate and insensitive to mesh distortions.
基金the National Natural Science Fund(11661058,11761053)Natural Science Fund of Inner Mongolia Autonomous Region(2016MS0102,2017MS0107)+1 种基金Program for Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region(NJYT-17-A07)National Undergraduate Innovative Training Project of Inner Mongolia University(201710126026).
文摘In this article,a high-order scheme,which is formulated by combining the quadratic finite element method in space with a second-order time discrete scheme,is developed for looking for the numerical solution of a two-dimensional nonlinear time fractional thermal diffusion model.The time Caputo fractional derivative is approximated by using the L2-1formula,the first-order derivative and nonlinear term are discretized by some second-order approximation formulas,and the quadratic finite element is used to approximate the spatial direction.The error accuracy O(h3+t2)is obtained,which is verified by the numerical results.
基金supported by the Natural Science Foundation of China (11061021)the Program of Higher-level talents of Inner Mongolia University (SPH-IMU,Z200901004)the Scientific Research Projection of Higher Schools of Inner Mongolia(NJ10016,NJ10006)
文摘This paper proposes a hybrid vertex-centered fi- nite volume/finite element method for solution of the two di- mensional (2D) incompressible Navier-Stokes equations on unstructured grids. An incremental pressure fractional step method is adopted to handle the velocity-pressure coupling. The velocity and the pressure are collocated at the node of the vertex-centered control volume which is formed by join- ing the centroid of cells sharing the common vertex. For the temporal integration of the momentum equations, an im- plicit second-order scheme is utilized to enhance the com- putational stability and eliminate the time step limit due to the diffusion term. The momentum equations are discretized by the vertex-centered finite volume method (FVM) and the pressure Poisson equation is solved by the Galerkin finite el- ement method (FEM). The momentum interpolation is used to damp out the spurious pressure wiggles. The test case with analytical solutions demonstrates second-order accuracy of the current hybrid scheme in time and space for both veloc- ity and pressure. The classic test cases, the lid-driven cavity flow, the skew cavity flow and the backward-facing step flow, show that numerical results are in good agreement with the published benchmark solutions.
基金King Mongkut’s University of Technology North Bangkok (KMUTNB)the Office of the Higher Education Commission (OHEC)the National Metal and Materials Technology Center (MTEC) for supporting this research work
文摘Level set methods are widely used for predicting evolutions of complex free surface topologies,such as the crystal and crack growth,bubbles and droplets deformation,spilling and breaking waves,and two-phase flow phenomena.This paper presents a characteristic level set equation which is derived from the two-dimensional level set equation by using the characteristic-based scheme.An explicit finite volume element method is developed to discretize the equation on triangular grids.Several examples are presented to demonstrate the performance of the proposed method for calculating interface evolutions in time.The proposed level set method is also coupled with the Navier-Stokes equations for two-phase immiscible incompressible flow analysis with surface tension.The Rayleigh-Taylor instability problem is used to test and evaluate the effectiveness of the proposed scheme.
基金supported by the National High-Tech R&D Program of China (2006AA10Z1F1)the National Core Soybean Genetic Engineering Project, China(2011ZX08004-002)+3 种基金the National Natural Science Foundation of China (60932008, 30971810)the National Basic Research Program of China (2009CB118400)the Ministry of Education Innovation Team of Soybean Molecular Design,Chinathe Innovation Team of the Education Bureau of Heilongjiang Province, China
文摘The importance of microRNA (miRNA) at the post-transcriptional regulation level has recently been recognized in both animals and plants. In recent years, many studies focused on miRNA target identification and functional analysis. However, little is known about the transcription and regulation of miRNAs themselves. In this study, the transcription start sites (TSSs) for 11 miRNA primary transcripts of soybean from 11 miRNA loci (of 50 loci tested) were cloned by a 5" rapid amplification of cDNA ends (5" RACE) procedure using total RNA from 30-d-old seedlings. The features consistent with a RNA polymerase II mechanism of transcription were found among these miRNA loci. A position weight matrix algorithm was used to identify conserved motifs in miRNA core promoter regions. A canonical TATA box motif was identified upstream of the major start site at 8 (76%) of the mapped miRNA loci. Several cis-acting elements were predicted in the 2 kb 5" to the TSSs. Potential spatial and temporal expression patterns of the miRNAs were found. The target genes for these miRNAs were also predicted and further elucidated for the potential function of the miRNAs. This research provides a molecular basis to explore regulatory mechanisms of miRNA expression, and a way to understand miRNA-mediated regulatory pathways and networks in soybean.
文摘本文在综合文献的基础上,建立了尿中三唑苯二氮(艹卓)及其主要代谢物的鉴定方法。本法以20ml尿样,在PH为9时,用乙醚提取。提取物用无水硫酸钠脱水,K、D、浓缩到0.5ml,固体进样杆直接进行EI/CI/MS分析;质谱分析在Finnigan Mat 1020 GC/MS/DS仪上进行。EI、CI源,甲烷作反应气,源室压力0.35吒。2ul样品由固体进样杆进样,其温度程序:初温60℃,以120℃/min速率升温到350℃。所建立的分析方法快速、灵敏,口服给药量为0.5mg时,可检出尿中1—羟甲基三唑苯二氮(艹卓)。
基金supported by the State Key Laboratory of Tree Genetics and Breeding(Northeast Forestry University)(201102)Natural Science Foundation of Heilongjiang Province(QC2012C057)+2 种基金China Postdoctoral Science Foundation(2013M531005)Foundation for the Postdoctoral of Heilongjiang Province(LBH-Z12007)National Natural Science Foundation of China(31200510)
文摘Our previous studies have revealed that the Th CAP gene plays a vital role in transgenic Populus(P.davidiana 9 P.bolleana) in response to cold stress.However,the regulatory mechanism of Th CAP gene expression has been unclear.In this study,the 50 flanking region of the Th CAP promoter(PTh CAP) was cloned using a genomewalking method.By analyzing cis-acting regulatory elements of PTh CAP,a DRE motif and MYC and MYB elements were found to be located in the promoter.To identify the regulatory elements that control the expression of the Th CAP gene promoter,a series of deletion derivatives ofPTh CAP,P1–P5,from the translation start code(-1538,-1190,-900,-718 and-375 bp),were fused to the GUS reporter gene,and then each deletion was stably introduced into Arabidopsis thaliana plants.Deletion analysis of the promoter suggested that only the P2 fragment had strong GUS expression in leaves and roots of A.thaliana exposed to low temperature stress.These results suggest that this290-bp region(-1190 to-900 bp),as an important part in PTh CAP,was associated with cold tolerance of A.thaliana.Our results provide evidence for the regulatory mechanism of Th CAP gene involved in the response to cold stress,and that the gene is promising candidate gene for genetic improvement of crops.
文摘<strong>Background:</strong> Recently, Coronavirus Disease 2019 (COVID-19) has been affected by the extreme acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has developed important global health anxiety. At this time, the treatment options for this disease are only moderately successful. Smoking has been related to COVID-19 and its mortality, and it has the potential to affect bacteriological and viral conversion, clinical effects, and treatment outcomes. <strong>Methods:</strong> The aim of this study was to determine the relationship between critical essential trace {zinc (Zn), iron (Fe), and copper (Cu)} and toxic {cadmium (Cd) and nickel (Ni)} elements in human biological samples such as scalp hair, serum, saliva, blood, nasal fluid, and sputum of smoking and nonsmoking male COVID-19 patients (n = 139, age range 25 - 38 years) from Hyderabad, Pakistan. For comparative purposes, the biological specimens of referent persons (n = 83), pulmonary Tuberculosis (T.B) patients (n = 67), Pneumonia (n = 56) of the same age groups were also be analyzed. Microwave oven mediated digestion method was employed, and digestion of samples was carried out with the help of 2:1 mixture solution of HNO<sub>3</sub> (65%) and H<sub>2</sub>O<sub>2</sub> (30%). Atomic absorption spectrometry was employed for the determination of elemental concentrations from the microwave oven employed digested samples. <strong>Results:</strong> The found average of essential elements (Zn, Fe, and Cu) in biological specimens of smoker and nonsmoker male COVID-19, T.B, and Pneumonia patients was found to lower, whilst cadmium and nickel were found to be higher when compared with samples from referents (p < 0.001). <strong>Conclusions:</strong> Improved elemental (Cu, Fe, Zn) concentrations may also decrease the risk of bacterial co-infection by enhancing the mucociliary clearance and respiratory epithelial barrier function, in addition to providing direct antibacterial effects against <i>S. pneumoniae</i>. Our findings also suggest that higher Cd and Ni concentrations are linked to cigarette smoking, which could lead to COVID-19 and other lung-infected diseased recurrences. However, further clinical and experimental research is required.
文摘A three - dimenslonal finite element model is developed to deal with the polymeric liquid flow in coat - hanger die. This model is used to predict the flow behavior of the 2% CMC/watsr solution in the coat - hanger die with linearly taper manifolds and its validity is experimentally verified quantitatively and qualitatively by using Laser Doppler Velocimetry and Particle Image Velocimetry respectively.