The first internal transcribed spacer(ITS1) of nuclear ribosomal DNA of three wild rice species and two subspecies of cultivated rice, which are distributed in China, was amplified using PCR technique and sequenced wi...The first internal transcribed spacer(ITS1) of nuclear ribosomal DNA of three wild rice species and two subspecies of cultivated rice, which are distributed in China, was amplified using PCR technique and sequenced with automated fluorescent sequencing. The sequences of ITS1 ranged from 193 bp to 218 bp in size and G/C content varied from 69.3% to 72.7%. In pairwise comparisons among the five taxa, sequence site divergence ranged from 1.5% to 10.6%. Phylogenetic analysis of ITS1 sequences using Wagner parsimony generated a single well resolved tree, which revealed that Oryza rufipogon was much more closely related to cultivated rice species than to the other two wild species. Oryza granulata was less closely related to either cultivated rice species or the other two wild species, and might be a unique and isolated taxon in the genus Oryza. The phylogenetic relationships of the three wild rice species and two cultivated rice subspecies inferred from ITS1 sequences is highly concordant with those based on the molecular evidence from isozyme, chloroplast DNA (cpDNA), mitochondrial DNA(mtDNA) and nuclear DNA (nDNA) of the genus Oryza .展开更多
[Objective] The aim was to establish a molecular biological method for identifying coccidium species.[Method]First,the pure species of Eimeria intestinalis was isolated by using single-oocyst isolation technique.Then,...[Objective] The aim was to establish a molecular biological method for identifying coccidium species.[Method]First,the pure species of Eimeria intestinalis was isolated by using single-oocyst isolation technique.Then,according to the 18s rDNA and 5.8s rDNA sequences of Eimeria coccidia published in GenBank,a pair of specific primers was designed and synthesized to amplify the internal transcribed spacer 1（ITS-1）.Finally,the PCR products were sent for sequencing.[Result]The pure species of E.intestinalis was isolated and the result of agarose gel electrophoresis showed that the PCR product was 434 bp,and at least 27-sporulated oocysts could be detected.[Conclusion]The research will provide a basis for accurate identification of coccidium species and strains.展开更多
Objective: To investigate the p21WAF1 /CIP1gene DNA sequence change and their relationship with the phenotype of human osteosarcoma. Methods: p21WAF1 /CIP1gene DNA of 36 osteosarcoma spec- ...Objective: To investigate the p21WAF1 /CIP1gene DNA sequence change and their relationship with the phenotype of human osteosarcoma. Methods: p21WAF1 /CIP1gene DNA of 36 osteosarcoma spec- imens was examined by using polymerase chain reaction-single strand conformation polymorphism (PCR- SSCP) method. The PCR products were sequenced directly. Results: In p21WAF1 /CIP1 gene exon3 of 36 cases of human osteosarcoma, the change of C→T in the p21WAF1 /CIP1gene CDNA sequence of position 609th occurred in 17 cases with the incidence being 44.4%. In 10 normal blood samples, DNA sequence analysis showed the change of C→T in the p21WAF1 /CIP1gene CDNA sequence of position 609th occurred in 8 cases with the incidence being 80%. Conclusion: The novel location of p21WAF1 /CIP1gene polymorphism of osteosarcoma, but not mutation was de?ned, and this location might provide the meaningful reference for the further research of p21WAF1/CIP1 gene.p2lWAF1/CIP1基因DNA序列分析及其与骨肉瘤表型的关系展开更多
[Objective] The study aimed at cloning and analyzing the insulin-like growth factor-1 （IGF-1） gene from liver of Hubei white swine. [Method] The total RNA was extracted by using Trizol from the liver of Hubei white ...[Objective] The study aimed at cloning and analyzing the insulin-like growth factor-1 （IGF-1） gene from liver of Hubei white swine. [Method] The total RNA was extracted by using Trizol from the liver of Hubei white swine and used as template to amplify IGF-1 gene cDNA by RT-PCR. The cDNA product was cloned into pCRII vector, screened with blue-white colonies, digested with double enzymes and sequenced. [Result] The sequencing result indicated that the IGF-1 gene consisted of 607 nucleotides, containing 5＇-untranslated region at nucleotides 1-145, a complete ORF at nucleotides 146-538 encoding 130 amino acids, and 3＇-untranslated region at nucleotides 539-607. It shared 100% homology with the porcine IGF-1 gene reported by Muller et al. [Conclusion] The successful cloning and sequencing of the Hubei white swine IGF-1 gene confirmed that IGF-I gene was highly conserved, which provided technical basis for the use of transgenic technology for breeding of Hubei white swine.展开更多
For the solid-solid transformation from formⅡto formⅠof isotactic polybutene-1(iPB),the temperature dependence of formⅠnucleation and growth was deemed to control the transformation process.However,the relationship...For the solid-solid transformation from formⅡto formⅠof isotactic polybutene-1(iPB),the temperature dependence of formⅠnucleation and growth was deemed to control the transformation process.However,the relationship between formⅠformation and formⅡdisappearance in the transformation process is not clear.In this work,the spontaneous crystal transformation from formⅡtoⅠof iPB with 81 mol%mmmm sequence concentration is studied firstly by tracking the two processes,the decay of formⅡand the yielding of formⅠin a wide range of temperature spanning from 0℃to 50℃and in a long transformation time ranging from 5 min to 65 days with in situ FTIR and WAXD.Unlike the literature reports,the decay rate of formⅡis firstly found to be lower than the yielding rate of formⅠat all studied temperatures,especially at low transition temperature.This is attributed to the amorphous chains which locate near crystal lamella participating into the nucleation of formⅡ.The regular chain folding and growth of i PB formⅠfrom amorphous chains containing short isotactic sequences also lead to an increase in crystallinity of formⅠcompared with that of initial formⅡcrystallized at 60℃.An increase in the annealing temperature results in decrease in crystallinity and increase in lamellae thickness of i PB formⅠ.展开更多
For a long time,classification of Demodex mites has been based mainly on their hosts and phenotypic characteristics.A new subspecies of Demodex folliculorum has been proposed,but not confirmed.Here,cox1 partial sequen...For a long time,classification of Demodex mites has been based mainly on their hosts and phenotypic characteristics.A new subspecies of Demodex folliculorum has been proposed,but not confirmed.Here,cox1 partial sequences of nine isolates of three Demodex species from two geographical sources(China and Spain) were studied to conduct molecular identification of D.folliculorum.Sequencing showed that the mitochondrial cox1 fragments of five D.folliculorum isolates from the facial skin of Chinese individuals were 429 bp long and that their sequence identity was 97.4%.The average sequence divergence was 1.24% among the five Chinese isolates,0.94% between the two geographical isolate groups(China(5) and Spain(1)),and 2.15% between the two facial tissue sources(facial skin(6) and eyelids(1)).The genetic distance and rate of third-position nucleotide transition/transversion were 0.0125,2.7(3/1) among the five Chinese isolates,0.0094,3.1(3/1) between the two geographical isolate groups,and 0.0217,4.4(3/1) between the two facial tissue sources.Phylogenetic trees showed that D.folliculorum from the two geographical isolate groups did not form sister clades,while those from different facial tissue sources did.According to the molecular characteristics,it appears that subspecies differentiation might not have occurred and that D.folliculorum isolates from the two geographical sources are of the same population.However,population differentiation might be occurring between isolates from facial skin and eyelids.展开更多
Objective To study the alternative expression and sequence of human elongation factor-1δ （human EF-1δ p31） during malignant transformation of human bronchial epithelial cells induced by cadmium chloride （CdCl2） ...Objective To study the alternative expression and sequence of human elongation factor-1δ （human EF-1δ p31） during malignant transformation of human bronchial epithelial cells induced by cadmium chloride （CdCl2） and its possible mechanism. Methods Total RNA was isolated at different stages of transformed human bronchial epithelial cells （16HBE） induced by CdCl2 at a concentration of 5.0 μM. Special primers and probe for human EF-1δ p31 were designed and expression of human EF-18 mRNA from different cell lines was detected with fluorescent quantitative PCR technique. EF-18 cDNA from different cell lines was purified and cloned into pMD 18-T vector followed by confirming and sequencing analysis. Results The expressions of human EF-1δ p31 at different stages of 16HBE cells transformed by CdCl2 was elevated （P〈0.01 or P〈0.05）. Compared with their corresponding non-transformed ceils, the overexpression level of EF-15 p31 was averagely increased 2.9 folds in Cd-pretransformed cells, 4.3 folds in Cd-transformed ceils and 7.2 folds in Cd-tumorigenic cells. No change was found in the sequence of overexpressed EF-1δ p31 at different stages of 16HBE cells transformed by CdCl2. Conclusion Overexpression of human EF-1δ p31 is positively correlated with malignant transformation of 16HBE cells induced by CdCl2, but is not correlated with DNA mutations.展开更多
AIM: To evaluate the expression of special AT-rich sequence-binding protein 1 (SATB1 ) gene in colorectal cancer and its role in colorectal cancer cell proliferation and invasion.METHODS: Immunohistochemistry was used...AIM: To evaluate the expression of special AT-rich sequence-binding protein 1 (SATB1 ) gene in colorectal cancer and its role in colorectal cancer cell proliferation and invasion.METHODS: Immunohistochemistry was used to detect the protein expression of SATB1 in 30 colorectal cancer (CRC) tissue samples and pair-matched adjacent nontumor samples. Cell growth was investigated after enhancing expression of SATB1. Wound-healing assay and Transwell assay were used to investigate the impact of SATB1 on migratory and invasive abilities of SW480 cells in vitro . Nude mice that received subcutaneous implantation or lateral tail vein were used to study the effects of SATB1 on tumor growth or metastasis in vivo . RESULTS: SATB1 was over-expressed in CRC tissues and CRC cell lines. SATB1 promotes cell proliferation and cell cycle progression in CRC SW480 cells. SATB1 over-expression could promote cell growth in vivo . In addition, SATB1 could significantly raise the ability of cell migration and invasion in vitro and promote the ability of tumor metastasis in vivo . SATB1 could up-regulate matrix metalloproteases 2, 9, cyclin D1 and vimentin, meanwhile SATB1 could down-regulate E-cadherin in CRC. CONCLUSION: SATB1 acts as a potential growth and metastasis promoter in CRC. SATB1 may be useful as a therapeutic target for CRC.展开更多
Rapeseed,the largest oil crop in China,is a boron-loving plant.Boron has an important influence on the growth and development of rapeseed.In this study,four different boron-efficient Brassica napus varieties were used...Rapeseed,the largest oil crop in China,is a boron-loving plant.Boron has an important influence on the growth and development of rapeseed.In this study,four different boron-efficient Brassica napus varieties were used as the material to analyze the structure and sequence of BnNIP7;1 gene,aiming to provide a basis for studying the role of BnNIP7;1 in the absorption and transport of boric acid in rapeseed.The results showed that BnNIP7;1 exists in multiple copies of the Brassica napus genome,consisting of five exons and four introns.There are base insertions,base deletions and more base substitutions in introns.However,there is no base insertion or base deletion in the exon,only a small number of base substitution mutations are present,bringing about three amino acid changes in the encoded protein of BnNIP7;1-ZS9b in Zhongshuang 9.The BnNIP7;1-HY7b of Huayou 7 has an ochre mutation that will lead to a protein of only 47 amino acids,thus losing its function.Bioinformatics indicates that BnNIP7;1 protein is a membrane protein with six transmembrane regions,indicating that it is involved in the absorption and transport of boric acid.展开更多
The epidemiology of HIV-1 varies in different areas of the world, and it is possible that this complexity may leave unique footprints in the viral genome. Thus, we attempted to find significant patterns in global HIV-...The epidemiology of HIV-1 varies in different areas of the world, and it is possible that this complexity may leave unique footprints in the viral genome. Thus, we attempted to find significant patterns in global HIV-1 genome sequences. By applying the rule inference algorithm RIPPER (Repeated Incremental Pruning to Produce Error Reduction) to multiple sequence alignments of Env sequences from four classes of compiled datasets, we generated four sets of signature patterns. We found that these patterns were able to distinguish southeastern Asian from non- southeastern Asian sequences with 97.5% accuracy, Chinese from non-Chinese sequences with 98.3% accuracy, African from non-African sequences with 88.4% accuracy, and southern African from non-southern African sequences with 91.2% accuracy. These patterns showed different associations with subtypes and with amino acid positions. In addition, some signature patterns were characteristic of the geographic area from which the sample was taken. Amino acid features corresponding to the phylogenetic clustering of HIV-1 sequences were consistent with some of the deduced patterns. Using a combination of patterns inferred from subtypes B, C, and all subtypes chimeric with CRF01_AE worldwide, we found that signature patterns of subtype C were extremely common in some sampled countries (for example, Zambia in southern Africa), which may hint at the origin of this HIV-1 subtype and the need to pay special attention to this area of Africa. Signature patterns of subtype B sequences were associated with different countries. Even more, there are distinct patterns at single position 21 with glycine, leucine and isoleucine corresponding to subtype C, B and all possible recombination forms chimeric with CRF01_AE, which also indicate distinct geographic features. Our method widens the scope of inference of signature from geographic, genetic, and genomic viewpoints. These findings may provide a valuable reference for epidemiological research or vaccine design.展开更多
Water is a major limiting factor for food production and many countries fail to produce sufficient food for their population due to severe water scarcity （Jury and Vaux, 2005）. Rice is the main staple food worldwide...Water is a major limiting factor for food production and many countries fail to produce sufficient food for their population due to severe water scarcity （Jury and Vaux, 2005）. Rice is the main staple food worldwide. More than 50% of rice in the world is rain-fed and drought causes severe reduction in rice grain yield in rain-fed environments （Venuprasad et al., 2007; Zhang, 2007; Sandhu et al., 2014）. Therefore, enhancing drought resistance （DR） of rice is important for food security. However, DR is a complex trait, which is controlled by a large number of loci with small effect and is also affected by different genetic background, genotype-by-environment interaction and other stresses such as heat （Hu and Xiong, 2014）.展开更多
The rapid rise of antibiotic-resistant bacteria has created an urgent need for alternative treatments,such as bacteriophage therapy,which relies on phages to selectively eliminate specific bacterial pathogens.However,...The rapid rise of antibiotic-resistant bacteria has created an urgent need for alternative treatments,such as bacteriophage therapy,which relies on phages to selectively eliminate specific bacterial pathogens.However,the success of phage therapy hinges on accurately matching phages to their bacterial hosts,and predicting these phage–host interactions(PHIs)remains a significant challenge.The existing computational approaches for PHI prediction have major limitations.For example,the PredPHI model achieves less than 70%accuracy,and most methods predict only broad host categories(e.g.,genus levels)rather than pinpointing the exact bacterial strain.To address these gaps,we present a novel data-driven framework that predicts PHIs at the individual host strain level using only protein amino acid sequence data as input.Our approach extracts informative features from protein sequences—including amino acid composition(AAC),key chemical element abundance(AC),and molecular weight(MW)—and employs a one-dimensional convolutional neural network(1D CNN)tailored for sequential protein data.To further increase the prediction accuracy and mitigate class imbalance,we train multiple CNN models on different subsets of the data and integrate their outputs via a weighted ensemble strategy.This ensemble 1D CNN model achieves an AUC of 0.968,an AUPR of 0.976,an accuracy of 88%,and a sensitivity of 0.911,with a Matthews correlation coefficient(MCC)approximately 40%greater than that of PredPHI.Overall,this data-driven bioinformatics approach provides a powerful tool for rapid phage–host matching and custom phage design,potentially accelerating the development of targeted phage therapy.展开更多
By means of PCR,the gene encoding gD of bovine herpesvirus-1 (BHV-1) strain Luojing was amplified,cloned and sequenced.The nucleotide sequence of this gD gene was (1 251 bp,)encoding 417 amino acids.Comparied with the...By means of PCR,the gene encoding gD of bovine herpesvirus-1 (BHV-1) strain Luojing was amplified,cloned and sequenced.The nucleotide sequence of this gD gene was (1 251 bp,)encoding 417 amino acids.Comparied with the published P8-2 strain,the homology of the necleotide sequence is 99.92%,and that of the deduced amino acid sequence is 100%.The results indicated that gD of BHV-1 was highly conservative.展开更多
The M_S6. 1 earthquake was a foreshock-mainshock-aftershock type which occurred in the boundary region between Zogang and Markam counties on August 12,2013. Within 9hours before the main shock seven earthquakes of gre...The M_S6. 1 earthquake was a foreshock-mainshock-aftershock type which occurred in the boundary region between Zogang and Markam counties on August 12,2013. Within 9hours before the main shock seven earthquakes of greater than M_L2. 0 occurred,with a maximum of M_L4. 7. In this paper,the earthquake focal mechanism changing process of the Zogang-Markam M_S6. 1 earthquake sequence is studied by calculating the correlation coefficient of body wave spectral amplitudes,and the result shows that the correlation coefficients of spectral amplitude of foreshocks present high value fluctuation with an average value of 0. 86,which shows that the focal mechanism of foreshocks are similar;and the correlation coefficients of spectral amplitude of aftershocks present low value,which shows that the possibility of a large earthquake is not high after a time.展开更多
Herein, we report a very high content of simple sequence repeats (SSRs) covering 66.12% of the herpes simplex virus type 1 (HSV-1) genome when a low threshold is adopted to define SSRs, indicating that repeat sequence...Herein, we report a very high content of simple sequence repeats (SSRs) covering 66.12% of the herpes simplex virus type 1 (HSV-1) genome when a low threshold is adopted to define SSRs, indicating that repeat sequence is a very important character of the HSV-1 genome. The repeats with two iterations account for 68.33% of the total repeats. In reality, the genome of HSV-1 is prone to form shorter repeat sequences. For mono-, di- and trinucleotide repeats, the repeat numbers decreased with the increase of repeats iterations, implicating that the formation tendency of SSRs might be from low iterations to high iterations. The high iterations SSRs might have subjected to strong selected pressure and survived to perform different functions. The analysis suggested that the repeats formation may be an essential evolutionary driving force for the HSV-1 genome, and the results might be helpful for studying the genome structure, repeats genesis and genome evolution of HSV-1.展开更多
N6-methyladenosine(m^(6)A)modification of mRNA is a critical post-transcriptional regulatory mechanism that modulates mRNA metabolism and neuronal function.The m^(6)A reader YTHDF1 has been shown to enhance the transl...N6-methyladenosine(m^(6)A)modification of mRNA is a critical post-transcriptional regulatory mechanism that modulates mRNA metabolism and neuronal function.The m^(6)A reader YTHDF1 has been shown to enhance the translational efficiency of m^(6)A-modified mRNAs in the brain and is essential for learning and memory.However,its role in the mature retina remains unclear.Herein,we report a novel role of Ythdf1 in the maintenance of retinal function using a genetic knockout model.Loss of Ythdf1 resulted in impaired scotopic electroretinogram(ERG)responses and progressive retinal degeneration.Detailed analyses of rod photoreceptors confirmed substantial degenerative changes in the absence of ciliary defects.Single-cell RNA sequencing revealed comprehensive molecular alterations across all retinal cell types in Ythdf1-deficient retinas.Integrative analysis of methylated RNA immunoprecipitation(MeRIP)sequencing and RIP sequencing identified Tulp1 and Dhx38,two inheritable retinal degeneration disease-associated gene homologs,as direct targets of YTHDF1 in the retina.Specifically,YTHDF1 recognized and bound m^(6)A-modified Tulp1 and Dhx38 mRNA at the coding sequence(CDS),enhancing their translational efficiency without altering mRNA levels.Collectively,these findings highlight the essential role of YTHDF1 in preserving visual function and reveal a novel regulatory mechanism of m^(6)A reader proteins in retinal degeneration,identifying potential therapeutic targets for severe retinopathies.展开更多
Viral protein U （Vpu） is an accessory protein associated with two main functions important in human immu-nodeficiency virus type 1 （HIV-1） replication and dis-semination; these are down-regulation of CD4 receptor ...Viral protein U （Vpu） is an accessory protein associated with two main functions important in human immu-nodeficiency virus type 1 （HIV-1） replication and dis-semination; these are down-regulation of CD4 receptor through mediating its proteasomal degradation and en-hancement of virion release by antagonizing tetherin/BST2. It is also well established that Vpu is one of the most highly variable proteins in the HIV-1 proteome. However it is still unclear what drives Vpu sequence variability, whether Vpu acquires polymorphisms as a means of immune escape, functional advantage, or otherwise. It is assumed that the host-pathogen inter-action is a cause of polymorphic phenotype of Vpu and that the resulting functional heterogeneity of Vpu may have critical significance in vivo . In order to compre-hensively understand Vpu variability, it is important to integrate at the population level the genetic association approaches to identify specifc amino acid residues and the immune escape kinetics which may impose Vpu functional constraints in vivo . This review will focus on HIV-1 accessory protein Vpu in the context of its sequence variability at population level and also bring forward evidence on the role of the host immune re-sponses in driving Vpu sequence variability; we will also highlight the recent findings that illustrate Vpu func-tional implication in HIV-1 pathogenesis.展开更多
2,4-dienoyl-CoA reductase 1 （ DECR1 ） is the key rate-limiting enzyme in the metabolism of polyunsaturated fatty acids. Although this protein has been studied in a variety of mammals, its role in por- cine is yet to...2,4-dienoyl-CoA reductase 1 （ DECR1 ） is the key rate-limiting enzyme in the metabolism of polyunsaturated fatty acids. Although this protein has been studied in a variety of mammals, its role in por- cine is yet to be fully elucidated. However, it is a candidate determinant/indicator of meat quality, growth traits, and carcass quality. Here, we employed RT-PCR and rapid amplification of cDNA ends （RACE） analysis to amplify the full-length cDNA of DECR1 from Mashen pig liver, and cloned it into the expression vector pET-32a＋. After confirmation by sequencing and restriction analysis, the recombinant plasmid was transformed into E. coli BL21 cells. The cDNA of pig DECR1 contained 2,352 nucleotides, including a 987 bp open reading frame flanked by a 53 bp 5＇-untranslated region （UTR） and a 1,312 bp 3＇-UTR. The pig DECR1 coding sequence encoded 328 amino acid residues, which shared 99%, 88%, 87%, 87%, 87%, 87%, and 83% identity with those of Sus scrofa （predicted）, Bos taurus, Homo sapiens, Macaca mulatta, Pan troglodytes, Equus caballus, Canis, and Mus musculus, respectively. SDS-PAGE analysis revealed that the recombinant protein was expressed and that the expression level reached its highest level after 4 h induction. Western blot analysis indicated that the molecular weight of the expressed protein was the same as that predicted, ap- proximately 35 kDa. Collectively these data provide the basis for further studies into the physiological functions and molecular mechanisms of the pig DE- CR1 gene.展开更多
基金The project supported by the Grant from Presidentof Chinese Academy of Sciences
文摘The first internal transcribed spacer(ITS1) of nuclear ribosomal DNA of three wild rice species and two subspecies of cultivated rice, which are distributed in China, was amplified using PCR technique and sequenced with automated fluorescent sequencing. The sequences of ITS1 ranged from 193 bp to 218 bp in size and G/C content varied from 69.3% to 72.7%. In pairwise comparisons among the five taxa, sequence site divergence ranged from 1.5% to 10.6%. Phylogenetic analysis of ITS1 sequences using Wagner parsimony generated a single well resolved tree, which revealed that Oryza rufipogon was much more closely related to cultivated rice species than to the other two wild species. Oryza granulata was less closely related to either cultivated rice species or the other two wild species, and might be a unique and isolated taxon in the genus Oryza. The phylogenetic relationships of the three wild rice species and two cultivated rice subspecies inferred from ITS1 sequences is highly concordant with those based on the molecular evidence from isozyme, chloroplast DNA (cpDNA), mitochondrial DNA(mtDNA) and nuclear DNA (nDNA) of the genus Oryza .
基金Supported by the Program of National Rabbit Industrial Production Technology System of Ministry of Agriculture~~
文摘[Objective] The aim was to establish a molecular biological method for identifying coccidium species.[Method]First,the pure species of Eimeria intestinalis was isolated by using single-oocyst isolation technique.Then,according to the 18s rDNA and 5.8s rDNA sequences of Eimeria coccidia published in GenBank,a pair of specific primers was designed and synthesized to amplify the internal transcribed spacer 1（ITS-1）.Finally,the PCR products were sent for sequencing.[Result]The pure species of E.intestinalis was isolated and the result of agarose gel electrophoresis showed that the PCR product was 434 bp,and at least 27-sporulated oocysts could be detected.[Conclusion]The research will provide a basis for accurate identification of coccidium species and strains.
文摘Objective: To investigate the p21WAF1 /CIP1gene DNA sequence change and their relationship with the phenotype of human osteosarcoma. Methods: p21WAF1 /CIP1gene DNA of 36 osteosarcoma spec- imens was examined by using polymerase chain reaction-single strand conformation polymorphism (PCR- SSCP) method. The PCR products were sequenced directly. Results: In p21WAF1 /CIP1 gene exon3 of 36 cases of human osteosarcoma, the change of C→T in the p21WAF1 /CIP1gene CDNA sequence of position 609th occurred in 17 cases with the incidence being 44.4%. In 10 normal blood samples, DNA sequence analysis showed the change of C→T in the p21WAF1 /CIP1gene CDNA sequence of position 609th occurred in 8 cases with the incidence being 80%. Conclusion: The novel location of p21WAF1 /CIP1gene polymorphism of osteosarcoma, but not mutation was de?ned, and this location might provide the meaningful reference for the further research of p21WAF1/CIP1 gene.p2lWAF1/CIP1基因DNA序列分析及其与骨肉瘤表型的关系
基金Supported by Projects for Transgenic Research (2008ZX08006-002,2008ZX08006-003,2008ZX08010-003,2008ZX08011-004)Hubei Key Laboratory Project (2011ZD127)~~
文摘[Objective] The study aimed at cloning and analyzing the insulin-like growth factor-1 （IGF-1） gene from liver of Hubei white swine. [Method] The total RNA was extracted by using Trizol from the liver of Hubei white swine and used as template to amplify IGF-1 gene cDNA by RT-PCR. The cDNA product was cloned into pCRII vector, screened with blue-white colonies, digested with double enzymes and sequenced. [Result] The sequencing result indicated that the IGF-1 gene consisted of 607 nucleotides, containing 5＇-untranslated region at nucleotides 1-145, a complete ORF at nucleotides 146-538 encoding 130 amino acids, and 3＇-untranslated region at nucleotides 539-607. It shared 100% homology with the porcine IGF-1 gene reported by Muller et al. [Conclusion] The successful cloning and sequencing of the Hubei white swine IGF-1 gene confirmed that IGF-I gene was highly conserved, which provided technical basis for the use of transgenic technology for breeding of Hubei white swine.
基金financially supported by the Major Science and Technology Innovation Project of Shandong Province(No.2019JZZY010352)Natural Science Foundation of Shandong Province(ZR2019MB072)Taishan Scholar Program
文摘For the solid-solid transformation from formⅡto formⅠof isotactic polybutene-1(iPB),the temperature dependence of formⅠnucleation and growth was deemed to control the transformation process.However,the relationship between formⅠformation and formⅡdisappearance in the transformation process is not clear.In this work,the spontaneous crystal transformation from formⅡtoⅠof iPB with 81 mol%mmmm sequence concentration is studied firstly by tracking the two processes,the decay of formⅡand the yielding of formⅠin a wide range of temperature spanning from 0℃to 50℃and in a long transformation time ranging from 5 min to 65 days with in situ FTIR and WAXD.Unlike the literature reports,the decay rate of formⅡis firstly found to be lower than the yielding rate of formⅠat all studied temperatures,especially at low transition temperature.This is attributed to the amorphous chains which locate near crystal lamella participating into the nucleation of formⅡ.The regular chain folding and growth of i PB formⅠfrom amorphous chains containing short isotactic sequences also lead to an increase in crystallinity of formⅠcompared with that of initial formⅡcrystallized at 60℃.An increase in the annealing temperature results in decrease in crystallinity and increase in lamellae thickness of i PB formⅠ.
基金Project(No. 81271856)supported by the National Natural Science Foundation of China
文摘For a long time,classification of Demodex mites has been based mainly on their hosts and phenotypic characteristics.A new subspecies of Demodex folliculorum has been proposed,but not confirmed.Here,cox1 partial sequences of nine isolates of three Demodex species from two geographical sources(China and Spain) were studied to conduct molecular identification of D.folliculorum.Sequencing showed that the mitochondrial cox1 fragments of five D.folliculorum isolates from the facial skin of Chinese individuals were 429 bp long and that their sequence identity was 97.4%.The average sequence divergence was 1.24% among the five Chinese isolates,0.94% between the two geographical isolate groups(China(5) and Spain(1)),and 2.15% between the two facial tissue sources(facial skin(6) and eyelids(1)).The genetic distance and rate of third-position nucleotide transition/transversion were 0.0125,2.7(3/1) among the five Chinese isolates,0.0094,3.1(3/1) between the two geographical isolate groups,and 0.0217,4.4(3/1) between the two facial tissue sources.Phylogenetic trees showed that D.folliculorum from the two geographical isolate groups did not form sister clades,while those from different facial tissue sources did.According to the molecular characteristics,it appears that subspecies differentiation might not have occurred and that D.folliculorum isolates from the two geographical sources are of the same population.However,population differentiation might be occurring between isolates from facial skin and eyelids.
基金Supported by the National Natural Science Foundation of China (No. 30771781)the Natural Science Foundation of Guangdong Province (No.06022672)
文摘Objective To study the alternative expression and sequence of human elongation factor-1δ （human EF-1δ p31） during malignant transformation of human bronchial epithelial cells induced by cadmium chloride （CdCl2） and its possible mechanism. Methods Total RNA was isolated at different stages of transformed human bronchial epithelial cells （16HBE） induced by CdCl2 at a concentration of 5.0 μM. Special primers and probe for human EF-1δ p31 were designed and expression of human EF-18 mRNA from different cell lines was detected with fluorescent quantitative PCR technique. EF-18 cDNA from different cell lines was purified and cloned into pMD 18-T vector followed by confirming and sequencing analysis. Results The expressions of human EF-1δ p31 at different stages of 16HBE cells transformed by CdCl2 was elevated （P〈0.01 or P〈0.05）. Compared with their corresponding non-transformed ceils, the overexpression level of EF-15 p31 was averagely increased 2.9 folds in Cd-pretransformed cells, 4.3 folds in Cd-transformed ceils and 7.2 folds in Cd-tumorigenic cells. No change was found in the sequence of overexpressed EF-1δ p31 at different stages of 16HBE cells transformed by CdCl2. Conclusion Overexpression of human EF-1δ p31 is positively correlated with malignant transformation of 16HBE cells induced by CdCl2, but is not correlated with DNA mutations.
基金Supported by The National Natural Science Foundation of China, No. 81101580
文摘AIM: To evaluate the expression of special AT-rich sequence-binding protein 1 (SATB1 ) gene in colorectal cancer and its role in colorectal cancer cell proliferation and invasion.METHODS: Immunohistochemistry was used to detect the protein expression of SATB1 in 30 colorectal cancer (CRC) tissue samples and pair-matched adjacent nontumor samples. Cell growth was investigated after enhancing expression of SATB1. Wound-healing assay and Transwell assay were used to investigate the impact of SATB1 on migratory and invasive abilities of SW480 cells in vitro . Nude mice that received subcutaneous implantation or lateral tail vein were used to study the effects of SATB1 on tumor growth or metastasis in vivo . RESULTS: SATB1 was over-expressed in CRC tissues and CRC cell lines. SATB1 promotes cell proliferation and cell cycle progression in CRC SW480 cells. SATB1 over-expression could promote cell growth in vivo . In addition, SATB1 could significantly raise the ability of cell migration and invasion in vitro and promote the ability of tumor metastasis in vivo . SATB1 could up-regulate matrix metalloproteases 2, 9, cyclin D1 and vimentin, meanwhile SATB1 could down-regulate E-cadherin in CRC. CONCLUSION: SATB1 acts as a potential growth and metastasis promoter in CRC. SATB1 may be useful as a therapeutic target for CRC.
基金Supported by "System Construction of Rapeseed Industry" by Yunnan Agriculture Department(2017KJTX005-05)"Yunnan Oil Crop Innovative Team" of Yunnan Science and Technology Department(2017HC021)~~
文摘Rapeseed,the largest oil crop in China,is a boron-loving plant.Boron has an important influence on the growth and development of rapeseed.In this study,four different boron-efficient Brassica napus varieties were used as the material to analyze the structure and sequence of BnNIP7;1 gene,aiming to provide a basis for studying the role of BnNIP7;1 in the absorption and transport of boric acid in rapeseed.The results showed that BnNIP7;1 exists in multiple copies of the Brassica napus genome,consisting of five exons and four introns.There are base insertions,base deletions and more base substitutions in introns.However,there is no base insertion or base deletion in the exon,only a small number of base substitution mutations are present,bringing about three amino acid changes in the encoded protein of BnNIP7;1-ZS9b in Zhongshuang 9.The BnNIP7;1-HY7b of Huayou 7 has an ochre mutation that will lead to a protein of only 47 amino acids,thus losing its function.Bioinformatics indicates that BnNIP7;1 protein is a membrane protein with six transmembrane regions,indicating that it is involved in the absorption and transport of boric acid.
基金the funding by the Chinese Key National Science and Technology Program in the 12th Five-Year Period, grant 2012ZX10001006-002
文摘The epidemiology of HIV-1 varies in different areas of the world, and it is possible that this complexity may leave unique footprints in the viral genome. Thus, we attempted to find significant patterns in global HIV-1 genome sequences. By applying the rule inference algorithm RIPPER (Repeated Incremental Pruning to Produce Error Reduction) to multiple sequence alignments of Env sequences from four classes of compiled datasets, we generated four sets of signature patterns. We found that these patterns were able to distinguish southeastern Asian from non- southeastern Asian sequences with 97.5% accuracy, Chinese from non-Chinese sequences with 98.3% accuracy, African from non-African sequences with 88.4% accuracy, and southern African from non-southern African sequences with 91.2% accuracy. These patterns showed different associations with subtypes and with amino acid positions. In addition, some signature patterns were characteristic of the geographic area from which the sample was taken. Amino acid features corresponding to the phylogenetic clustering of HIV-1 sequences were consistent with some of the deduced patterns. Using a combination of patterns inferred from subtypes B, C, and all subtypes chimeric with CRF01_AE worldwide, we found that signature patterns of subtype C were extremely common in some sampled countries (for example, Zambia in southern Africa), which may hint at the origin of this HIV-1 subtype and the need to pay special attention to this area of Africa. Signature patterns of subtype B sequences were associated with different countries. Even more, there are distinct patterns at single position 21 with glycine, leucine and isoleucine corresponding to subtype C, B and all possible recombination forms chimeric with CRF01_AE, which also indicate distinct geographic features. Our method widens the scope of inference of signature from geographic, genetic, and genomic viewpoints. These findings may provide a valuable reference for epidemiological research or vaccine design.
基金supported by grants from the National Program for Basic Research of China(No.2012CB114305)the National Program on High Technology Development(No. 2012AA10A303)the Oversea Graduate Program from Ministry of Education to K.Songyikhangsuthor
文摘Water is a major limiting factor for food production and many countries fail to produce sufficient food for their population due to severe water scarcity （Jury and Vaux, 2005）. Rice is the main staple food worldwide. More than 50% of rice in the world is rain-fed and drought causes severe reduction in rice grain yield in rain-fed environments （Venuprasad et al., 2007; Zhang, 2007; Sandhu et al., 2014）. Therefore, enhancing drought resistance （DR） of rice is important for food security. However, DR is a complex trait, which is controlled by a large number of loci with small effect and is also affected by different genetic background, genotype-by-environment interaction and other stresses such as heat （Hu and Xiong, 2014）.
基金supported by the Beijing Genomics Institute under grant numbers 62203134,6220020329 and 62176164Scientific Foundation for Youth Scholars of Shenzhen University 868-000001033385.The author gratefully acknowledges the support provided by the“Design of phage tail protein based on adversarial machine learning”project and the“Construction of artificial phage model based on deep generative adversarial network learning”project.And the datasets is provided by BGI-Shenzhen.
文摘The rapid rise of antibiotic-resistant bacteria has created an urgent need for alternative treatments,such as bacteriophage therapy,which relies on phages to selectively eliminate specific bacterial pathogens.However,the success of phage therapy hinges on accurately matching phages to their bacterial hosts,and predicting these phage–host interactions(PHIs)remains a significant challenge.The existing computational approaches for PHI prediction have major limitations.For example,the PredPHI model achieves less than 70%accuracy,and most methods predict only broad host categories(e.g.,genus levels)rather than pinpointing the exact bacterial strain.To address these gaps,we present a novel data-driven framework that predicts PHIs at the individual host strain level using only protein amino acid sequence data as input.Our approach extracts informative features from protein sequences—including amino acid composition(AAC),key chemical element abundance(AC),and molecular weight(MW)—and employs a one-dimensional convolutional neural network(1D CNN)tailored for sequential protein data.To further increase the prediction accuracy and mitigate class imbalance,we train multiple CNN models on different subsets of the data and integrate their outputs via a weighted ensemble strategy.This ensemble 1D CNN model achieves an AUC of 0.968,an AUPR of 0.976,an accuracy of 88%,and a sensitivity of 0.911,with a Matthews correlation coefficient(MCC)approximately 40%greater than that of PredPHI.Overall,this data-driven bioinformatics approach provides a powerful tool for rapid phage–host matching and custom phage design,potentially accelerating the development of targeted phage therapy.
文摘By means of PCR,the gene encoding gD of bovine herpesvirus-1 (BHV-1) strain Luojing was amplified,cloned and sequenced.The nucleotide sequence of this gD gene was (1 251 bp,)encoding 417 amino acids.Comparied with the published P8-2 strain,the homology of the necleotide sequence is 99.92%,and that of the deduced amino acid sequence is 100%.The results indicated that gD of BHV-1 was highly conservative.
基金jointly sponsored by the Special Program of Earthquake Science and Technology of Earthquake Administration of Sichuan Province(LY1302) the National Key Technology R&D Program of China(2012BAK19802)
文摘The M_S6. 1 earthquake was a foreshock-mainshock-aftershock type which occurred in the boundary region between Zogang and Markam counties on August 12,2013. Within 9hours before the main shock seven earthquakes of greater than M_L2. 0 occurred,with a maximum of M_L4. 7. In this paper,the earthquake focal mechanism changing process of the Zogang-Markam M_S6. 1 earthquake sequence is studied by calculating the correlation coefficient of body wave spectral amplitudes,and the result shows that the correlation coefficients of spectral amplitude of foreshocks present high value fluctuation with an average value of 0. 86,which shows that the focal mechanism of foreshocks are similar;and the correlation coefficients of spectral amplitude of aftershocks present low value,which shows that the possibility of a large earthquake is not high after a time.
文摘Herein, we report a very high content of simple sequence repeats (SSRs) covering 66.12% of the herpes simplex virus type 1 (HSV-1) genome when a low threshold is adopted to define SSRs, indicating that repeat sequence is a very important character of the HSV-1 genome. The repeats with two iterations account for 68.33% of the total repeats. In reality, the genome of HSV-1 is prone to form shorter repeat sequences. For mono-, di- and trinucleotide repeats, the repeat numbers decreased with the increase of repeats iterations, implicating that the formation tendency of SSRs might be from low iterations to high iterations. The high iterations SSRs might have subjected to strong selected pressure and survived to perform different functions. The analysis suggested that the repeats formation may be an essential evolutionary driving force for the HSV-1 genome, and the results might be helpful for studying the genome structure, repeats genesis and genome evolution of HSV-1.
基金supported by the National Natural Science Foundation of China(82371083,82471100,82121003,82271084)Program of Science and Technology International Cooperation Project of Qinghai province(China)(2022-HZ-814)。
文摘N6-methyladenosine(m^(6)A)modification of mRNA is a critical post-transcriptional regulatory mechanism that modulates mRNA metabolism and neuronal function.The m^(6)A reader YTHDF1 has been shown to enhance the translational efficiency of m^(6)A-modified mRNAs in the brain and is essential for learning and memory.However,its role in the mature retina remains unclear.Herein,we report a novel role of Ythdf1 in the maintenance of retinal function using a genetic knockout model.Loss of Ythdf1 resulted in impaired scotopic electroretinogram(ERG)responses and progressive retinal degeneration.Detailed analyses of rod photoreceptors confirmed substantial degenerative changes in the absence of ciliary defects.Single-cell RNA sequencing revealed comprehensive molecular alterations across all retinal cell types in Ythdf1-deficient retinas.Integrative analysis of methylated RNA immunoprecipitation(MeRIP)sequencing and RIP sequencing identified Tulp1 and Dhx38,two inheritable retinal degeneration disease-associated gene homologs,as direct targets of YTHDF1 in the retina.Specifically,YTHDF1 recognized and bound m^(6)A-modified Tulp1 and Dhx38 mRNA at the coding sequence(CDS),enhancing their translational efficiency without altering mRNA levels.Collectively,these findings highlight the essential role of YTHDF1 in preserving visual function and reveal a novel regulatory mechanism of m^(6)A reader proteins in retinal degeneration,identifying potential therapeutic targets for severe retinopathies.
基金Supported by A Grant-in-Aid for Scientific Research from the Ministry of Education,Science,Sports,and Culture(MEXT)of JapanA Grant-in-Aid for AIDS Research from the Ministry of Health,Labor,and Welfare of Japan+1 种基金The Scholarship for the International Priority Graduate Programs,to Hasan Z and Kamori DAdvanced Graduate Courses for International Students(Doctoral Course),MEXT,Japan,to Hasan Z and Kamori D
文摘Viral protein U （Vpu） is an accessory protein associated with two main functions important in human immu-nodeficiency virus type 1 （HIV-1） replication and dis-semination; these are down-regulation of CD4 receptor through mediating its proteasomal degradation and en-hancement of virion release by antagonizing tetherin/BST2. It is also well established that Vpu is one of the most highly variable proteins in the HIV-1 proteome. However it is still unclear what drives Vpu sequence variability, whether Vpu acquires polymorphisms as a means of immune escape, functional advantage, or otherwise. It is assumed that the host-pathogen inter-action is a cause of polymorphic phenotype of Vpu and that the resulting functional heterogeneity of Vpu may have critical significance in vivo . In order to compre-hensively understand Vpu variability, it is important to integrate at the population level the genetic association approaches to identify specifc amino acid residues and the immune escape kinetics which may impose Vpu functional constraints in vivo . This review will focus on HIV-1 accessory protein Vpu in the context of its sequence variability at population level and also bring forward evidence on the role of the host immune re-sponses in driving Vpu sequence variability; we will also highlight the recent findings that illustrate Vpu func-tional implication in HIV-1 pathogenesis.
文摘2,4-dienoyl-CoA reductase 1 （ DECR1 ） is the key rate-limiting enzyme in the metabolism of polyunsaturated fatty acids. Although this protein has been studied in a variety of mammals, its role in por- cine is yet to be fully elucidated. However, it is a candidate determinant/indicator of meat quality, growth traits, and carcass quality. Here, we employed RT-PCR and rapid amplification of cDNA ends （RACE） analysis to amplify the full-length cDNA of DECR1 from Mashen pig liver, and cloned it into the expression vector pET-32a＋. After confirmation by sequencing and restriction analysis, the recombinant plasmid was transformed into E. coli BL21 cells. The cDNA of pig DECR1 contained 2,352 nucleotides, including a 987 bp open reading frame flanked by a 53 bp 5＇-untranslated region （UTR） and a 1,312 bp 3＇-UTR. The pig DECR1 coding sequence encoded 328 amino acid residues, which shared 99%, 88%, 87%, 87%, 87%, 87%, and 83% identity with those of Sus scrofa （predicted）, Bos taurus, Homo sapiens, Macaca mulatta, Pan troglodytes, Equus caballus, Canis, and Mus musculus, respectively. SDS-PAGE analysis revealed that the recombinant protein was expressed and that the expression level reached its highest level after 4 h induction. Western blot analysis indicated that the molecular weight of the expressed protein was the same as that predicted, ap- proximately 35 kDa. Collectively these data provide the basis for further studies into the physiological functions and molecular mechanisms of the pig DE- CR1 gene.
