不同地理种群美洲斑潜蝇及近缘种的rDNA-ITS1序列分析和比较

目的通过对美洲斑潜蝇Liriomyzasativae Blanchard不同地理种群及近缘种间的核糖体DNA第一内转录间隔区（rDNA-ITS1）进行比较,分析美洲斑潜蝇不同地理种群间的遗传分化情况,并为美洲斑潜蝇与近缘种间提供分子鉴别标记。方法用PCR产物直接测序法及克隆测序法对我国美洲斑潜蝇8个地理种群的rDNA-ITS1序列进行测序,并调用GenBank中3个近缘种的rDNA-ITS序列,运用软件MEGA3.1对美洲斑潜蝇不同地理种群及近缘种间的rDNA-ITS1序列进行分析。结果美洲斑潜蝇8个地理种群间的分化程度较低,只有8个变异位点,遗传距离都在0.02以下,但4个近缘种间的碱基差异显著,遗传距离为0.149-0.390,有126个变异位点,12个美洲斑潜蝇特异性识别位点。结论虽然基于rDNA-ITS1序列所显示的美洲斑潜蝇各地理种群之间的遗传分化很小,但是其分化趋势与地理分布基本相吻合;得到的12个特异性识别位点不仅可以作为美洲斑潜蝇与其近缘种间鉴别的分子标记,而且可为今后设计鉴别性PCR引物提供重要的参考依据。

我国西部6省9地牛带绦虫rDNA-ITS1序列测定及分析

目的利用分子生物学技术鉴定我国6省9地是否存在牛带绦虫亚洲亚种。方法取成虫标本孕节2-3片,酚氯仿法提取DNA,PCR法扩增rDNA-ITS1片段,并纯化、克隆此片段后作序列测定。利用BioEdit,clustalx,PHYLIP,Treeview软件处理后构建系统发育树。结果广西融水（RS）、宾阳（BY）牛带绦虫标本与贵州都匀（DY）,云南大理（DL）牛带绦虫标本序列基本一致,同源性为98%-99%;新疆乌什（WS）、西藏拉萨（LS）、内蒙古（NM）、云南西双版纳（BN）牛带绦虫标本与贵州从江（CJ）牛带绦虫标本序列基本一致,同源性为98%-99%。系统发育树显示：RS、BY、DL和DY标本遗传距离较近;WS、LS、CJ、NM和BN标本遗传距离较近。而两组间遗传距离较远。结论RS、BY、DL和DY四地存在牛带绦虫亚洲亚种;WS、LS、CJ、NM和BN五地存在传统牛带绦虫。

海南地区螺旋粉虱种群mtDNA-COI和rDNA-ITS1基因的序列及系统发育分析

螺旋粉虱Aleurodicus dispersus Russell在海南是一种重要的农林害虫。本研究对海南地区不同螺旋粉虱种群的mtDNA-COI和rDNA-ITS1基因片段进行了测定并对其系统发育进行了分析。mtDNA-COI和rDNA-ITS1的序列比较发现,海南16个县市螺旋粉虱种群的mtDNA-COI序列基本一致,只有文昌番石榴Psidium guajava种群的序列发生变异,在476 bp位点的碱基C突变为碱基T。不同螺旋粉虱种群的rDNA-ITS1序列也无差异。基于mtDNA-COI序列的不同螺旋粉虱种群的系统发育树表明,已传入我国海南地区的螺旋粉虱未发生明显的遗传分化;研究还发现海南的螺旋粉虱种群与台湾的种群遗传距离最近,表明海南地区的螺旋粉虱可能由台湾传入的。基于mtDNA-COI和rDNA-ITS1序列构建的不同粉虱种群的系统发育树表明,粉虱科分为复孔粉虱亚科(Aleurodicinae)和粉虱亚科(Aleyrodinae),这一结果与其他研究结果一致。

菱角萤叶甲不同地理种群及近缘种rDNA-ITS1基因序列初步分析

通过对我国菱角萤叶甲Galerucella birmanica Jacoby6个地理种群和褐背小萤叶甲Galerucella grisescens Joannis扬州种群的核糖体DNA第1内转录间隔区(rDNA-ITS1)的测序,并调用GenBank中该属其它4种昆虫的同源序列,运用软件DNAStar的MegAlign程序对小萤叶甲属种间、同种不同地理种群之间的ITS1序列的遗传分歧及相似性进行了分析,运用Mega3.0软件建立系统发育关系。序列分析结果表明,rDNA-ITS1基因在小萤叶甲属昆虫中进化速度较快,种下具有一定的差异,种间差异明显。该基因适合小萤叶甲属种间和种下的分类鉴定研究。进化树显示,菱角萤叶甲泰安种群和扬州种群形成一个分支,益阳种群和新余种群形成一个分支,苏州种群和上海青浦种群形成一个分支,这一现象说明6个地理种群的菱角萤叶甲分化与寄主和地理距离之间具有较高的相关性。

ITS1 SEQUENCES OF NUCLEAR RIBOSOMAL DNA IN WILD RICES AND CULTIVATED RICES OF CHINA AND THEIR PHYLOGENETIC IMPLICATIONS

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 .

云贵两省三地牛带绦虫核糖体rDNA-ITS1序列分析

目的：采用PCR克隆测序方法，对采自贵州省都匀、从江及云南省大理三地牛带绦虫，与台湾桃园牛带绦虫亚洲亚种标本进行比较，为贵州都匀、从江及云南大理牛带绦虫标本鉴别提供分子生物学证据，并进一步探讨牛带绦虫亚洲亚种分类学地位。方法：取贵州都匀株、贵州从江株、云南大理株和台湾桃园株成虫节片，抽提DNA，PCR扩增rDNA-ITS1区段，克隆测序；结合GenBank中已知猪带绦虫rDNA-ITS1序列，构建系统发育树。结果：贵州都匀、云南大理牛带绦虫标本、台湾牛带绦虫亚洲亚种标本的ITS1序列基本一致，同源性达98％～99％；贵州从江牛带绦虫标本ITS1序列与前三者有30个碱基差异，与台湾桃园、贵州都匀和云南大理同源性均为97％。系统发育树显示：贵州都匀和云南大理牛带绦虫标本与台湾牛带绦虫亚洲亚种标本的遗传距离最接近，距贵州从江牛带绦虫标本较远，与猪带绦虫则更远。结论：（1）贵州都匀和云南大理牛带绦虫标本属于牛带绦虫亚洲亚种，贵州从江牛带绦虫标本属于传统牛带绦虫。（2）rDNA-ITS1序列分析可以用于牛带绦虫亚洲亚种与传统带绦虫分类学研究。

10株巨型艾美球虫rDNA-ITS-1部分序列测定与分析

用一对种特异性引物,对国内10株巨型艾美球虫ITS-1区进行PCR扩增,对扩增产物纯化、测序与分析,并用DNAStar软件对所检测的10株巨型艾美球虫与GenBank中的所有巨型艾美球虫的ITS-1相应序列进行系统发生进化关系分析。结果显示,扬州株、龙岩株和福州株的ITS-1部分序列片段长度为152bp,其余各株均为151bp。10株巨型艾美球虫的同源性为90.7%～100%,在构建的系统发生进化树中分成2大系群,凤阳株形成一个单系群,其余9株为另一系群。虫株间的亲缘关系与地理位置不尽一致,与免疫交叉保护力无相关性。

p21^(WAF1/CIP1) Gene DNA Sequence Change and Their Relationship with the Phenotype of Human Osteosarcoma

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

Cloning and Sequence Analysis on IGF-1 Gene of Hubei White Swine

[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.

Detection of Novel BEST1 Variations in Autosomal Recessive Bestrophinopathy Using Third-generation Sequencing

Objective:Autosomal recessive bestrophinopathy(ARB),a retinal degenerative disease,is characterized by central visual loss,yellowish multifocal diffuse subretinal deposits,and a dramatic decrease in the light peak on electrooculogram.The potential pathogenic mechanism involves mutations in the BEST1 gene,which encodes Ca2+-activated Cl−channels in the retinal pigment epithelium(RPE),resulting in degeneration of RPE and photoreceptor.In this study,the complete clinical characteristics of two Chinese ARB families were summarized.Methods:Pacific Biosciences(PacBio)single-molecule real-time(SMRT)sequencing was performed on the probands to screen for disease-causing gene mutations,and Sanger sequencing was applied to validate variants in the patients and their family members.Results:Two novel mutations,c.202T>C(chr11:61722628,p.Y68H)and c.867+97G>A,in the BEST1 gene were identified in the two Chinese ARB families.The novel missense mutation BEST1 c.202T>C(p.Y68H)resulted in the substitution of tyrosine with histidine in the N-terminal region of transmembrane domain 2 of bestrophin-1.Another novel variant,BEST1 c.867+97G>A(chr11:61725867),located in intron 7,might be considered a regulatory variant that changes allele-specific binding affinity based on motifs of important transcriptional regulators.Conclusion:Our findings represent the first use of third-generation sequencing(TGS)to identify novel BEST1 mutations in patients with ARB,indicating that TGS can be a more accurate and efficient tool for identifying mutations in specific genes.The novel variants identified further broaden the mutation spectrum of BEST1 in the Chinese population.

Alterative Expression and Sequence of Human Elongation Factor-1δ during Malignant Transformation of Human Bronchial Epithelial Cells Induced by Cadmium Chloride

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.

Accurate Diagnosis of SARS-CoV-2 JN.1 by Sanger Sequencing of Receptor-Binding Domain Is Needed for Clinical Evaluation of Its Immune Evasion

Background: Omicron JN.1 has become the dominant SARS-CoV-2 variant in recent months. JN.1 has the highest number of amino acid mutations in its receptor binding domain (RBD) and has acquired a hallmark L455S mutation. The immune evasion capability of JN.1 is a subject of scientific investigation. The US CDC used SGTF of TaqPath COVID-19 Combo Kit RT-qPCR as proxy indicator of JN.1 infections for evaluation of the effectiveness of updated monovalent XBB.1.5 COVID-19 vaccines against JN.1 and recommended that all persons aged ≥ 6 months should receive an updated COVID-19 vaccine dose. Objective: Recommend Sanger sequencing instead of proxy indicator to diagnose JN.1 infections to generate the data based on which guidelines are made to direct vaccination policies. Methods: The RNA in nasopharyngeal swab specimens from patients with clinical respiratory infection was subjected to nested RT-PCR, targeting a 398-base segment of the N-gene and a 445-base segment of the RBD of SARS-CoV-2 for amplification. The nested PCR amplicons were sequenced. The DNA sequences were analyzed for amino acid mutations. Results: The N-gene sequence showed R203K, G204R and Q229K, the 3 mutations associated with Omicron BA.2.86 (+JN.1). The RBD sequence showed 24 of the 26 known amino acid mutations, including the hallmark L455S mutation for JN.1 and the V483del for BA.2.86 lineage. Conclusions: Sanger sequencing of a 445-base segment of the SARS-CoV-2 RBD is useful for accurate determination of emerging variants. The CDC may consider using Sanger sequencing of the RBD to diagnose JN.1 infections for statistical analysis in making vaccination policies.

Special AT-rich sequence-binding protein 1 promotes cell growth and metastasis in colorectal cancer

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.

Inference of Global HIV-1 Sequence Patterns and Preliminary FeatureAnalysis

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.

Cloning and Sequence Analysis of Glycoprotein D Gene of Bovine Herpesvirus-1 Strain Luojing

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.

Study on Focal Mechanism Changing Characteristics of the 2013 Zogang-Markam Ms6. 1 Earthquake Sequence

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.

The genome of herpes simplex virus type 1 is prone to form short repeat sequences

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.

Role of host immune responses in sequence variability of HIV-1 Vpu

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.

Cloning, Sequence Analysis, and Prokaryotic Expression of the Porcine DECR1 Gene

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.

Isolation and Complete Nucleotide Sequence of the Measles Virus IMB-1 Strain in China

The complete nucleotide sequence of the measles virus strain IMB-1,which was isolated in China,was determined.As in other measles viruses,its genome is 15,894 nucleotides in length and encodes six proteins.The full-length nucleotide sequence of the IMB-1 isolate differed from vaccine strains (including wild-type Edmonston strain) by 4%-5% at the nucleotide sequence level.This isolate has amino acid variations over the full genome,including in the hemagglutinin and fusion genes.This report is the first to describe the full-length genome of a genotype H1 strain and provide an overview of the diversity of genetic characteristics of a circulating measles virus.