Phylogenetic, phylogeographic and divergence time analysis of Anopheles subpictus species complex using ITS2 and COI sequences

Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2(ITS2)and cytochrome C oxidase I(COI)sequences deposited at the GenBank.Methods:Seventy-five ITS2,210 COI and 26 concatenated sequences available in the NCBI database were used.Phylogenetic analysis was performed using Bayesian likelihood trees,whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis.Genetic diversity indices and genetic differentiation were also calculated.Results:Two genetically divergent molecular forms of An.subpictus species complex corresponding to sibling species A and B are established.Species A evolved around 37-82 million years ago in Sri Lanka,India,and the Netherlands,and species B evolved around 22-79 million years ago in Sri Lanka,India,and Myanmar.Vietnam,Thailand,and Cambodia have two molecular forms:one is phylogenetically similar to species B.Other forms differ from species A and B and evolved recently in the above mentioned countries,Indonesia and the Philippines.Genetic subdivision among Sri Lanka,India,and the Netherlands is almost absent.A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances.Genetic diversity indices reveal the presence of a long-established stable mosquito population,at mutation-drift equilibrium,regardless of population fluctuations.Conclusions:An.subpictus species complex consists of more than two genetically divergent molecular forms.Species A is highly divergent from the rest.Sri Lanka and India contain only species A and B.

Landscape of Sequence Variations in Homologous Copies of FAD2 and FAD3 in Rapeseed(Brassica napus L.)Germplasm with High/Low Linolenic Acid Trait

Genetic manipulation(either restraint or enhancement)of the biosynthesis pathway ofα-linolenic acid(ALA)in seed oil is an important goal in Brassica napus breeding.B.napus is a tetraploid plant whose genome often har-bors four and six homologous copies,respectively,of the two fatty acid desaturases FAD2 and FAD3,which con-trol the last two steps of ALA biosynthesis during seed oil accumulation.In this study,we compared their promoters,coding sequences,and expression levels in three high-ALA inbred lines 2006L,R8Q10,and YH25005,a low-ALA line A28,a low-ALA/high-oleic-acid accession SW,and the wildtype ZS11.The expression levels of most FAD2 and FAD3 homologs in the three high-ALA accessions were higher than those in ZS11 and much higher than those in A28 and SW.The three high-ALA accessions shared similar sequences with the pro-moters and CDSs of BnFAD3.C4 and BnFAD3.A3.In A28 and SW,substitution of three amino acid residues in BnFAD2.A5 and BnFAD2.C5,an absence of BnFAD2.C1 locus,and a 549 bp long deletion on the BnFAD3.A3 promoter were detected.The profile of BnFAD2 mutation in the two low-ALA accessions A28 and SW is different from that reported in previous studies.The mutations in BnFAD3 in the high-ALA accessions are reported for thefirst time.In identifying the sites of these mutations,we provide detailed information to aid the design of mole-cular markers for accelerated breeding schemes.

To Analyze the Sensitivity of RT-PCR Assays Employing S Gene Target Failure with Whole Genome Sequencing Data during Third Wave by SARS-CoV-2 Omicron Variant

Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the community by immune evasion mechanisms. Due to mutation within S gene, most Omicron variants have reported S gene target failure (SGTF) with some commercially available PCR kits. Such diagnostic features can be used as markers to screen Omicron. However, Whole Genome Sequencing (WGS) is the only gold standard approach to confirm novel microorganisms at genetically level as similar mutations can also be found in other variants that are circulating at low frequencies worldwide. This Retrospective study is aimed to assess RT-PCR sensitivity in the detection of S gene target failure in comparison with whole genome sequencing to detect variants of Omicron. Methods: We have analysed retrospective data of SARS-CoV-2 positive RT-PCR samples for S gene target failure (SGTF) with TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) and combined with sequencing technologies to study the emerged pattern of SARS-CoV-2 variants during third wave at the tertiary care centre, Surat. Results: From the first day of December 2021 till the end of February 2022, a total of 321,803 diagnostic RT-PCR tests for SARS-CoV-2 were performed, of which 20,566 positive cases were reported at our tertiary care centre with an average cumulative positivity of 6.39% over a period of three months. In the month of December 21 samples characterized by the SGTF (70/129) were suggestive of being infected by the Omicron variant and identified as Omicron (B.1.1.529 lineage) when sequence. In the month of January, we analysed a subset of samples (n = 618) with SGTF (24%) and without SGTF (76%) with Ct values Conclusions: During the COVID-19 pandemic, it took almost more than 15 days to diagnose infection and identify pathogen by sequencing technology. In contrast to that molecular assay provided quick identification with the help of SGTF phenomenon within 5 hours of duration. This strategy helps scientists and health policymakers for the quick isolation and identification of clusters. That ultimately results in a decreased transmission of pathogen among the community.

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.

Determination and Analysis of Mitochondrial ND2 Gene Sequence of Anas platyrhynchos

[Objective] The study was to analyze the phylogenesis of Anas platyrhynchos. [Method] Complete sequence of mitochondrial ND2 gene of 4 Anas platyrhynchos was determined by direct DNA sequencing based on PCR products. Combined with ND2 gene sequences of the Anas Linnaeus accessed in GenBank, phylogenetic tree was constructed by Neighbor-joining and maximum parsimony methods. [Result] The ND2 gene sequences of 4 Anas platyrhynchos were identical(1 041 bp in length; the nucleotide contents of A, G, T, and C were 28.91%, 13.35%, 20.75% and 36.98% respectively; A+T content approximated to that of C+G). Sequences of ND2 gene of mallard were same as spotbill duck, and had high homology with others. The phylogenetic trees indicated mallard and spotbilled duck were close in genetic relationship, both shared a haplotype; then Philippine duck, green-winged teal and northern pintail fell into branch ''A". [Conclusion] The domestic duck may be domesticated from mallard and spotbilled duck.

Sequence Analysis of HA Genes from Three H9N2 Subtype Avian Influenza Viruses

[ Objective] The study aimed to understand the genetic characters of H9N2 subtype avian influenza viruses isolated in Belling area. [ Method] HA genes of three H9N2 subtype avian influenza viruses A/Chicken/Beijing/xu/00, A/Chicken/Beijing/bei/00 and A/Chicken/Beijing/ liu/00 were amplified by RT-PCR and then sequenced. [ Result] The results of phylogenetic analysis showed that A/Chicken/Beijing/xu/00, A/ Chicken/Beijing/bei/00 and A/Chicken/Beijing/liu/00 shared the nucleotide homologies of 84.8% （ Dk/HK/Y439/97 ） -98.0% （ Ck/GX17/00 ）, 85.1% （Dk/HK/Y439/97） - 99.1% （ Ck/GXl 7/00）, 90.7% （ Ck/BJ/3/01 ） - 99.1% （Ck/GX17/00） with the isolates from Hongkong and other are- as of Chinese Mainland respectively. At the same time, the analysis of amino acid indicated that the three isolates belonged to low pathogenic H9N2 isolates of avian origin. The 226^th amino acid of them were L （ Leu）, suggesting their high binding affinity to human cells. There were seven glyco- sylation sites in HA protein, five from HA1 and two from HA2. [ Cenclusien] By analysis at molecular level, it could be concluded that A/Chicken/ Beijing/xu/00, A/Chicken/Beijing/bei/00 and A/Chicken/Beijing/liu/00 were low pathogenic H9N2 isolates of avian origin.

2型糖尿病合并感染患者肺炎克雷伯菌分布及预后影响因素分析

目的:探讨2型糖尿病(T2DM)合并感染患者肺炎克雷伯菌(KP)分布及预后影响因素分析。方法:选择226例T2DM患者为研究对象,根据是否合并KP感染分为未感染组(n=170)和感染组(n=56),分析T2DM患者感染的危险因素。收集T2DM合并感染患者KP标本,记录标本来源并进行菌种鉴定和药敏试验,并对所有菌株进行多位点序列(MLST)分型,记录预后情况。结果:基础疾病、抗生素使用、侵入性操作、血清白蛋白(ALB)、糖化血红蛋白(HbA1c)、空腹血糖(FPG)为影响T2DM发生感染的危险因素(均P<0.05)。T2DM合并感染患者体内分离56株肺炎克雷伯菌,肺炎克雷伯菌在痰液中的占比最高为44.62%,其次为尿液19.64%,血液中占比16.07%,脓液中占比12.5%,其他标本占比7.14%。56株KP总耐药率最高为氨苄西林,最低为亚胺培南,痰液标本中KP对头孢呋辛、头孢哌酮、庆大霉素耐药率高于非痰液标本,非痰液标本中KP对头孢他啶高于痰液标本(均P<0.05)。56株肺炎克雷伯菌MLST分型共发现42个ST型,ST-20型、36型、65型、347型、660型各2株,分别占3.57%,23型4株占7.14%,ST-17、25、29、35、37、45、86、189、208、211、218、322、355、412、490、519、557、595、726、776、1049、1092、1103、1319、1569、1916、2059、3014、3140、3536、4023、4194、4262、4412、4857型各1株,分别占1.78%,其他ST型7株占比12.5%。56例T2DM合并KP感染患者预后良好患者52例,预后不良患者4例,预后良好率为92.86%。结论:T2DM合并感染患者KP主要分布在痰液和尿液中,基础疾病、抗生素使用、侵入性操作、ALB、HbA1c、FPG是影响KP感染发生危险因素,T2DM合并KP感染患者根据药敏结果选择用药,有利于患者预后。

Cloning and Sequence Analysis of Interferon γ-2β Full-length cDNA in Cyprinus carpio L.

[Objective] The research aimed to carry out the cloning, identification and sequence analysis of full-length cDNA of carp interferon γ-2β （IFNγ-2β）. [Method] The cDNA library of peripheral blood leucocytes which were separated from carp and stimulated with mitogen was screened by a probe labeled with DIG. The IFNγ- 2β EST sequence was picked out from the constructed cDNA library of peripheral blood leucocyte, and the full length of carp interferon γ-2β was cloned. In addition, the sequence analysis was carried out. [Result] Three positive clones were obtained. Sequence analysis indicated that the sequence had a 119 bp 5’-UTR and a 218 bp 3’-UTR, and the open reading frame （ORF）of this gene was 537 bp which putatively coded 178 amino acids and there were several instable motifs for mRNA （ATTTA） in the 3’-untranslated region. Its homology with IFN from GenBank was up to 97% . Analysis on protein sequence and structure showed that the predicted protein sequence was identified as an IFN family signature. [Conclusion] The research laid the foundation for further studying the expression manner, function characteristic and regulation mechanism of IFNγ-2β in vivo and the action mechanism in the inflammatory reaction, emergency reaction and immune response.

Sequence Comparison and Analysis of HA Gene of Four H9N2 Avian Influenza Virus Isolates

[ Objective] To determine the HA gene sequences of four H9N2 Avian influenza virus （AIV） strains and carry out comparative analysis so as to understand the difference and variation pattern of each strain from the angle of molecular biology and to know the distribution and epidemic law of H9N2 AIV. [Method] One pair of primers was designed referring to HA gene sequences of H9N2 AIV. The HA genes of A/Chicken/Hebei/WD/98 （H9N2; WD98 for short）, A/Chicken/Hebei/ZD/04 （H9N2; ZD04 for short））, A/Chicken/Beijing/MY/06 （H9N2; MY06 for short） ）, and A/Chicken/Beijing/PG/08 （H9N2; PG08 for short）） were amplified, cloned and sequenced. Then the HA gene sequences of these strains were compared with that of 10 H9N2 AIV stains in GenBank. [Result] The ORF of HA genes of the four strains was 1 683 bp in size, encoding 516 amino acids. The HA gene sequences of the four strains, WD98, MY06, PG08, and ZD04, were 82.6% -95.1%, 83.0% -99.0%, 82.7% -95.5%, and 81.3% -95.7% homologous to that of the 10 H9N2 AIV stains, respectively. And the homology of amino acid was respectively 86.6% -96.3%, 86.6% -97.9%, 87.0% -97.1%, and 86.9% -97.3%. [ Conclusion] The HA gene has greatly high homology among different strains.

2017年~2023年河南省猪圆环病毒2型的流行调查及遗传变异分析

为了解河南省猪圆环病毒2型(PCV2)的流行及变异情况,本研究采集该地区规模化猪场2017年1月~2023年6月939份表现为繁殖障碍和呼吸道症状的病猪血液或组织样品,采用PCR方法进行PCV2检测。结果显示,PCV2总阳性率为31.42%(295/939);2017年~2022年PCV2阳性率逐年降低,分别为58.65%(61/104)、49.48%(48/97)、28.57%(36/126)、16.15%(31/192)、11.52%(19/165)和7.87%(7/89),而2023年迅速上升,达到56.02%(93/166)。利用PCR扩增29份PCV2阳性样品的全基因组序列并测序,采用Meg Align分析PCV2流行株全基因组序列与Gen Bank中4株PCV2参考株全基因组序列的同源性;采用MEGA 11软件利用NJ法构建PCV2流行株ORF2基因与Gen Bank中24株PCV2参考株ORF2基因的系统发育树;采用Meg Align分析PCV2流行株Cap蛋白氨基酸序列的变异特征;采用RDP4和Sim Plot分析PCV2流行株全基因组的重组特征。全基因组同源性分析结果显示,本研究鉴定的PCV2全基因组序列之间的同源性为95.1%~100%,与PCV2参考株的同源性为93.7%~98.6%,其中与疫苗株PCV2a LG(HM038034)、PCV2b DBN-SX07-2(HM641752)和PCV2d SH(AY686763)的同源性分别为94.8%~96.2%、95.3%~98.6%和96.6%~97.8%,与来自丹麦的代表株PCV2c DK1980PMWSfree株(EU148503)的同源性为93.7%~95.1%。此外,两株2023年的PCV2流行株HN230522和HN231217与参考株的同源性仅为94.5%~97.9%。进化树结果显示,有19株PCV2流行株与PCV2d基因型参考株聚为一个分支,10株与PCV2b基因型参考株聚为一个分支。其中今年出现的PCV2流行株HN230522和HN231217株虽然属于PCV2d基因型,但处于一个相对独立的分支。Cap蛋白氨基酸序列分析结果显示,与疫苗株PCV2a LG(HM038034)、PCV2b DBN-SX07-2(HM641752)和PCV2d SH株(AY686763)相比,部分PCV2流行株在构象表位区(aa47~aa85和aa165~aa200)存在R^(48)H、A^(59)K/R、G^(85)D、P^(151)T、N^(178)S、R^(180)K和G^(197)S的突变,在基因型特异性结构域(aa190~aa191/aa206/aa210)存在K^(206)I的突变,且HN230522株在核定位信号区(NLS)(aa1~aa41)存在特有的V^(30)L突变,HN231217株在基因型特异性结构域(aa89~aa91)存在特有的^(89)RTV^(91)残基。重组分析结果显示,有高达65.52%(19/29)的PCV2流行株存在疑似的重组片段,且重组片段全部位于ORF1中。上述结果表明,今年以来河南省猪场PCV2阳性率快速上升,且流行株出现了较大变异,应加强对PCV2流行动态和遗传变异的监测。本研究为河南省PCV2分子流行病学、疫苗研究提供了参考依据。

赤眼鳟LGP2序列结构、组织表达及与MDA5互作特征

为探究赤眼鳟遗传学和生理学实验室蛋白2(laboratory of genetics and physiology 2,LGP2)的功能特征及抗草鱼呼肠孤病毒(grass carp reovirus,GCRV)育种参考潜力,实验克隆获得了2940 bp的赤眼鳟lgp2(Sclgp2)全长cDNA和721 bp的5′端上游序列。Sclgp2 cDNA编码680个氨基酸,包含DEXDc(DExD/H-box helicase domain)、HELICc(helicase superfamily C-terminal domain)和CTD(C-terminal regulatory domain)结构域;其5′端上游序列含有MafB(muscle aponeurosis fibromatosis B)和IRF3(interferon regulatory factor 3)等转录因子结合位点。不同物种LGP2的功能结构域、磷酸化修饰位点数具有相似性,同时也存在结构域排布位置及序列的差异。赤眼鳟和草鱼lgp2 cDNA序列比较初步发现2个位于RNA结合功能区的GCRV抗性关联位点。系统进化分析显示,赤眼鳟LGP2先与草鱼、鲫和青鱼聚在一起,再与鲤科鱼类等聚为一大支。荧光定量表达分析显示,赤眼鳟脾脏中sclgp2表达水平显著高于其他组织,肌肉、心脏中表达量次之,而肠中表达量最低。GCRV感染后,肝脏中ifn1表达水平在24~72 h显著下降,其他组织sclgp2和ifn1表达水平未有显著变化。相关性分析结果显示,赤眼鳟肌肉sclgp2与ifn1表达水平呈极显著正相关(0.999)。酵母双杂交互作检测发现,赤眼鳟LGP2与MDA5存在弱相互作用,而其DEXDc(1~201 aa)、HELICc(390~476 aa)以及CTD(553~668 aa)结构域与MDA5无互作。该研究成功获得了sclgp2全长cDNA及5′端上游序列,明确了其序列结构、免疫表达及与MDA5的互作特征,为赤眼鳟LGP2免疫功能属性研究奠定了基础,并为草鱼抗GCRV育种提供了参考。

内皮细胞特异性骨形态发生蛋白2对血管新生的影响:生物信息学分析和实验验证

背景:血管新生是心血管疾病的主要干预靶点,骨形态发生蛋白2具有调控血管新生作用,但内皮细胞特异性骨形态发生蛋白2对血管新生的调控作用不清楚。目的:探讨内皮细胞特异性骨形态发生蛋白2对血管新生的影响。方法:(1)生物信息学分析:通过Panglao DB公共基因表达数据库单细胞转录组荟萃分析观察骨形态发生蛋白2细胞群表达丰度和定位。血管新生小鼠和内皮(心内膜)过表达骨形态发生蛋白2小鼠转录组测序数据集探索内皮细胞骨形态发生蛋白2对血管新生信号通路的调控作用。(2)体内实验验证:建立小鼠后肢缺血模型,对比模型小鼠患侧与健侧缺血后肢7,14和21 d血流灌注情况,免疫荧光和免疫组织化学染色评估小鼠骨形态发生蛋白2和CD31的表达定位情况。(3)体外实验验证:体外培养人脐静脉内皮细胞,分为对照组、缺氧组和骨形态发生蛋白2抑制剂(Noggin蛋白)干预组,培养24 h,观察各组内皮细胞血管新生情况。结果与结论:(1)内皮细胞是表达骨形态发生蛋白2的重要细胞亚群,在血管新生内皮细胞和骨形态发生蛋白2过表达内皮细胞转录组再分析均发现骨形态发生蛋白2表达明显升高,血管新生通路明显激活。(2)缺血7 d小鼠新生血管周围骨形态发生蛋白2阳性血管明显增加(P<0.05),缺血2周骨形态发生蛋白2阳性血管明显减少(P<0.001)。(3)体外培养人脐静脉内皮细胞,缺氧干预后,内皮细胞迁移能力和血管出芽明显增加,血管新生因子血管内皮生长因子和血小板衍生生长因子的表达明显升高,Noggin明显减少了缺氧诱导的内皮细胞血管新生(P<0.001),并下调血管内皮生长因子和血小板衍生生长因子的表达(P<0.01)。(4)结果证实,内皮细胞特异性骨形态发生蛋白2具有调控血管新生作用,靶向性内皮细胞骨形态发生蛋白2可望改善血管新生。

上皮细胞转化序列2通过调控p33生长抑制因子1表达影响食管鳞状细胞癌细胞的体外转移活性

目的探讨上皮细胞转化序列2(ECT2)与p33生长抑制因子1(p33ING1)的表达水平对食管鳞状细胞癌(ESCC)细胞转移活性的影响。方法采用免疫组织化学法和免疫印迹法检测食管鳞癌组织和癌旁组织中ECT2和p33ING1的表达情况。将人食管鳞癌细胞系KYSE140细胞分为4组:空白组、阴性对照组(pcDNA 3.1 NC)组、过表达组(pcDNA 3.1 ECT2)和抑制表达组(si ECT2)。采用MTT法和细胞集落形成实验研究细胞的增殖和生长能力,Transwell实验和划痕实验研究细胞的侵袭和迁移能力,并用流式细胞术检测细胞凋亡率和细胞周期,Western blotting检测ECT2对p33ING1蛋白的影响。结果在食管鳞癌组织中ECT2表达增加,p33ING1表达降低。过表达ECT2能够显著增加KYSE140细胞的生长、集落形成、迁移以及侵袭能力,并能降低KYSE140细胞的凋亡率和p33ING1的表达;此外,抑制ECT2表达后能够逆转上述变化。结论ECT2高表达能够促进食管鳞癌KYSE140细胞的生长、转移,并抑制其凋亡,其机制可能与ECT2能够抑制p33ING1表达相关。

细胞分裂后期促进复合亚基2在肝细胞癌组织中的表达及临床意义

目的探究细胞分裂后期促进复合亚基2(Anaphase promoting complex subunit 2,ANAPC2)在肝细胞癌(Hepatocellular carcinoma,HCC)组织中的表达和其相关潜在功能机制。方法使用组织芯片免疫组化评估HCC及正常肝脏组织中ANAPC2蛋白表达的水平,并基于基因芯片和RNA测序的高通量数据库,计算ANAPC2 mRNA在HCC中的表达水平。利用单细胞测序技术进一步验证ANAPC2在HCC细胞层面的表达水平,并运用CRISPR敲除探究ANAPC2基因对HCC细胞生长的影响。使用Pearson相关分析筛选出ANAPC2的共表达基因,对该基因集进行功能富集分析。结果与正常肝组织相比,HCC组织中ANAPC2蛋白的表达出现了上调趋势。高通量数据集检索共纳入3861个HCC和3136个非癌肝组织样本,发现ANAPC2 mRNA在HCC组织中高表达(SMD=0.18,95%CI:0.04~0.32,P<0.05),sROC曲线下面积为0.67(95%CI:0.63~0.71)。在HCC单细胞水平也证实了ANAPC2的表达上调,ANAPC2基因的敲除可显著抑制HCC细胞的生长。ANAPC2共表达基因显著富集的信号通路包括细胞周期和有丝分裂等。结论HCC中,ANAPC2在转录及翻译阶段均表达上调,发挥了一定的促癌功能。

X连锁迟发性脊椎骨骺发育不良家系TRAPPC2基因缺失突变的高通量测序分析

目的·研究一个X连锁迟发性脊椎骨骺发育不良(spondyloepiphyseal dysplasia tarda,SEDT)家系的致病基因及突变类型。方法·提取一个SEDT家系6名成员外周血基因组DNA。应用Clearseq遗传性疾病试剂盒靶向捕获先证者基因组样本中与罕见遗传性疾病相关的致病区域,并进行高通量测序,过滤去除高频突变。采用外显子组隐马尔科夫模型(exome hidden Markov model,XHMM)分析拷贝数变异(copy number variant,CNV),并进一步对6名家系成员基因缺失片段的拷贝数进行实时定量PCR分析。结果·高通量测序分析结果显示,先证者X染色体存在2.5 kb缺失(chrX:13732385~13734927),该区域覆盖转运蛋白复合体亚单位2(transport protein particle complex subunit 2,TRAPPC2)基因的第4~6个外显子。定量PCR结果证实先证者及其表哥均存在该缺失,先证者母亲为杂合缺失,先证者父亲、姐姐和表型正常的舅舅拷贝数均正常。结论·TRAPPC2基因第4~6个外显子片段的缺失为SEDT的致病性突变;同时高通量测序分析中运用XHMM算法可检测到致病基因多个外显子的缺失。

Molecular Cloning and Sequence Analysis ofBoPGIP2 Gene from Brassica oleracea L. var. alboglabra

PGIP gene was obtained from Brassica oleracea L. var. alboglabra, named BoPGIP2. The full length of BoPGIP2 gene is 1 102 bp and the exon is 993 bp which encodes a protein of 330 amino acids with a predicted molecular mass of 37.1 kDa, interrupted by one intron of 95 bp in, length. Sequence analysis revealed that it has five potential N-giycosylation sites, two protein kinase C phosphrylation sites, five casin kinase Ⅱ phosphrylation sites and four N-myristoylation sites. The amino acids sequences alignment confirmed that ^145 LRR stucture was highly conserved in all aligned PGIP sequences.

结直肠神经内分泌肿瘤患者ESD后淋巴结转移情况及其与SATB2的相关性

目的探讨结直肠神经内分泌肿瘤(NENs)患者内镜黏膜下剥离术(ESD)后淋巴结转移情况及与特异性AT序列结合蛋白2(SATB2)的相关性。方法纳入2018年1月至2023年1月汉中市中心医院收治的158例结直肠NENs患者,均行ESD治疗。记录所有患者的手术和随访结果,包括整块切除率、切缘阳性率、淋巴结转移率。根据患者随访期间淋巴结转移情况分为转移组和对照组,记录两组的临床资料并进行比较。使用二元Logistic回归分析影响结直肠NENs患者ESD后淋巴结转移的危险因素,用受试者工作特征(ROC)曲线分析SATB2对患者ESD后淋巴结转移的预测价值。结果158例患者ESD均为整块切除,整块切除率为100.00%,14例(8.86%)患者切缘阳性。随访期间淋巴结转移21例(13.29%)纳入转移组,无淋巴转移137例纳入对照组。两组的肿瘤分期、肿瘤直径、淋巴管浸润、SATB2阳性比较,差异具有统计学意义(P<0.05)。二元Logistic回归分析结果显示,肿瘤分期、肿瘤直径、淋巴管浸润为结直肠NENs患者ESD后淋巴结转移的危险因素,SATB2阳性为保护性因素(P<0.05)。ROC曲线显示,SATB2对结直肠NENs患者ESD后淋巴结转移预测的曲线下面积(AUC)为0.747(95%CI 0.626~0.867),灵敏度为57.69%,特异度为91.67%。结论结直肠NENs患者ESD后淋巴结转移的发生与肿瘤分期、肿瘤直径、淋巴管浸润、SATB2表达相关,其中SATB2可作为患者淋巴结转移评估的有效指标。

Surveillance of emerging SARS-CoV-2 variants by nanopore technology-based genome sequencing

Objective:To surveill emerging variants by nanopore technology-based genome sequencing in different COVID-19 waves in Sri Lanka and to examine the association with the sample characteristics,and vaccination status.Methods:The study analyzed 207 RNA positive swab samples received to sequence laboratory during different waves.The N gene cut-off threshold of less than 30 was considered as the major inclusion criteria.Viral RNA was extracted,and elutes were subjected to nanopore sequencing.All the sequencing data were uploaded in the publicly accessible database,GISAID.Results:The Omicron,Delta and Alpha variants accounted for 58%,22%and 4%of the variants throughout the period.Less than 1%were Kappa variant and 16%of the study samples remained unassigned.Omicron variant was circulated among all age groups and in all the provinces.Ct value and variants assigned percentage was 100%in Ct values of 10-15 while only 45%assigned Ct value over 25.Conclusions:The present study examined the emergence,prevalence,and distribution of SARS-CoV-2 variants locally and has shown that nanopore technology-based genome sequencing enables whole genome sequencing in a low resource setting country.

Generation of iPS cells using defined factors linked via the self-cleaving 2A sequences in a single open reading frame

Generation of induced pluripotent stem （iPS） cells from somatic cells has been achieved successfully by simultaneous viral transduction of defined reprogramming transcription factors （TFs）. However, the process requires multiple viral vectors for gene delivery. As a result, generated iPS cells harbor numerous viral integration sites in their genomes. This can increase the probability of gene mutagenesis and genomic instability, and present significant barriers to both research and clinical application studies of iPS cells. In this paper, we present a simple lentivirus reprogramming system in which defined factors are fused in-frame into a single open reading frame （ORF） via self-cleaving 2A sequences. A GFP marker is placed downstream of the transgene to enable tracking of transgene expression. We demonstrate that this polycistronic expression system efficiently generates iPS cells. The generated iPS cells have normal karyotypes and are similar to mouse embryonic stem cells in morphology and gene expression. Moreover, they can differentiate into cell types of the three embryonic germ layers in both in vitro and in vivo assays. Remarkably, most of these iPS cells only harbor a single copy of viral vector. This system provides a valuable tool for generation of iPS cells, and our data suggest that the balance of expression of transduced reprogramming TFs in each cell is essential for the reprogramming process. More importantly, when delivered by non-integrating gene-delivery systems, this re-engineered single ORF will facilitate efficient generation of human iPS cells free of genetic modifications.

Interference-Free Pilot Design and Channel Estimation Using ZCZ Sequences for MIMO-OFDM-Based C-V2X Communications

Cellular vehicle-to-everything(C-V2X) communications is regarded as a promising and feasible solution for 5G-enabled vehicular communications and networking. In this paper, we investigate the pilot design and channel estimation problem in MIMO-OFDM-based C-V2X systems with severe co-channel interference due to spectrum reusing among different V2X communication links. By using zero-correlation zone(ZCZ) sequences, we provide an interference-free pilot design scheme and a corresponding time-domain(TD) correlation-based channel estimation(TD-CCE) method. We employ the ZCZ sequences from the same family set to be designed as the TD pilot symbols and guarantee the pilot sequeneces for neighboring V2X communication links are code-division multiplexing(CDM). The co-channel pilot interference of the deisgned pilot symbols can be effectively eliminated by exploiting the provided TD-CCE method. Simulation results indicate that the accuracy of channel estimation can be effectively improved by the proposed scheme, whose performance is close to that of the non-interference situation.