Fast PCR amplification of AmpFlSTR Identifiler

To increase throughput for DNA typing, we examined fast PCR cycling using AmpFlSTR Identifiler by three methods. In this study, we reduced PCR running times by 1/3 to 2/3 (approximately 1-2 h). This means DNA typing, including PCR reactions, can be completed within a timeframe ranging from 90 min to 2 h and 30 min.     

大鼠皮肤挫伤后NF-κB mRNA表达与损伤时间关系

目的应用实时定量PCR技术检测大鼠皮肤挫伤后NF-κB mRNA时序性表达规律，分析其与损伤时间的关系。方法制备大鼠皮肤挫伤模型，于伤后0．5，1，6，12，18，24，30h取材，一步法提取总RNA，检测其完整性和浓度，按照0．4μg总RNA量逆转录合成第一链cDNA，以rlp32为内参基因进行荧光定量检测，采用△Ct法比较其与正常皮肤组织NF-κB mRNA表达的倍数关系。结果皮肤挫伤组织中NF-κB mRNA伤后0．5h表达显著增强（P〈0．05），6h出现高峰，12h降至正常水平，随后略有回升。结论大鼠皮肤挫伤组织NF-κB mRNA的表达，随着损伤经过时间的延长呈规律性变化。     

Evaluation of Degradation in DNA from Males with a Quantitative Gender Typing,Endpoint PCR Multiplex

Evidentiary samples submitted to a forensic DNA laboratory occasionally yield DNA that is degraded. Samples of intact chromosomal DNA (both nuclear and mitochondrial) were subjected to a heating protocol to induce DNA degradation. The DNAs were then analyzed using a multiplex PCR assay that amplifies targets of low and high molecular weight on the X/Y and mitochondrial chromosomes. If degradation is random, the amplification of larger DNA targets should be more adversely affected by degradation than smaller targets. In nuclear and mitochondrial DNA from a male donor, exhibiting degradation, DNA quantity estimates based upon higher molecular weight amplicons (HMW) are significantly lower than estimates made using low molecular weight (LMW) Q‐TAT amplicons. DNA degradation estimated using this approach correlated well with actual fluorescence associated with HMW and LMW STR alleles amplified from the same genomic DNA templates. Q‐TAT is thus useful not only as a quantitation tool, but also as an indicator of template degradation.     

广西猪圆环病毒2型感染的流行病学调查

结合流行病学、临床症状、病理变化,采用PCR技术,对2004年1月至2005年5月采自广西14个市97个疑似猪圆环病毒2型(PCV2)感染发病猪场的197份组织病料(脾、肺、淋巴结)进行了PCV2检测;同时,对鉴定为PCV2阳性的组织病料和猪场进行了猪生殖与呼吸综合征病毒(PRRSV)、猪瘟病毒(CSFV)、猪流感病毒(SIV)和猪伪狂犬病病毒(PRV)的检测,另外,对6个地(市)11个生猪屠宰场采集的外观健康屠宰猪的295份组织样品(脾、肺、淋巴结)进行了PCV2检测。结果显示,在197份组织样品中检出PCV2阳性病料108份,平均阳性率为54.82%(108/197),阳性猪场62个,平均阳性率为63.92%(62/97)。PCV2与PRRSV、CSFV、SIV、PRV混合感染的组织病料总阳性率为42.13%(83/197),混合感染的猪场总阳性率为57.73%(56/97)。从21头外观健康屠宰猪的组织样品中检测到PCV2,阳性率为7.10%。由此可见,PCV2感染在广西猪群中已普遍存在,混合感染和健康带毒现象使病情更加复杂。     

大鼠骨骼肌损伤修复中FZD4时序性变化及其应用

目的以卷曲受体4(FZD4)为例,探索细胞膜上受体蛋白的表达变化能否作为损伤时间推断的指标。方法 78只大鼠随机分为对照组和损伤后4h、8h、12h、16h、20h、24h、28h、32h、36h、40h、44h和48 h组(n=6)。麻醉后,采用重力锤自由落体方式砸伤大鼠右后肢,取股四头肌处挫伤的组织。应用免疫荧光、real-time PCR和western blotting方法检测肌肉中FZD4蛋白及m RNA的表达量。结果免疫荧光结果显示FZD4表达于骨骼肌细胞膜上,胞浆和细胞核内均未见表达;Real-time PCR结果表明FZD4 m RNA在损伤后8h、12h、36h和40h显著上调(P0.05),均超过对照组的两倍;Western blotting结果示FZD4蛋白的表达在8h、36h、40h、44h和48h组明显增加(P0.05),但均未超过对照组的两倍。结论 FZD4 m RNA和蛋白在肌肉挫伤后呈时序性变化规律可作为损伤时间推断的指标,在一定程度上FZD4 m RNA比FZD4更适用于损伤时间推断。     

Evaluating the Efficiency of Primer Extension Capture as a Method to Enrich DNA Extractions,

In this study, we sought to document the efficiency of primer extension capture (PEC) as a method to enrich DNA eluates of targeted DNA molecules and remove nontarget molecules from pools containing both. Efficiency of the method was estimated by comparing number of “copies in” to “copies out” by quantitative polymerase chain reaction. PEC retention of DNA targets ranging 109‐288 base pairs (bps) in length was 15.88–2.14% (i.e., loss of 84.12–97.86% of target molecules). Experimental modifications of the PEC method resulted in no significant improvements. However, the benefit of PEC was revealed in its ability to remove most nontarget DNA molecules (99.99%). We also discovered that many (56.69%) of the target molecules are “lost” prior to their immobilization on the streptavidin‐coated beads. These estimates of methodological efficiency are directly comparable to previous ones observed following “fishing” for DNA, an alternative method for DNA enrichment.     

建立检测制式长枪上DNA多态性的新方法

目的建立快速、准确检测制式长枪上基因分型的新方法。方法联合使用直扩法、硅膜法对48支制式长枪上5个不同部位共240份检材进行DNA检测。结果联合使用直扩法及硅膜法,在48支制式长枪中检测出DNA完整分型42支,检出率达87.50%。结论联合使用直扩法、硅膜法,可有效快速、准确地检测出制式长枪上DNA多态性。     

山羊关节炎脑炎病毒SYBR GreenⅠ荧光定量PCR方法的建立及应用

为建立检测山羊关节炎脑炎病毒(caprine arthritis-encephalitis virus,CAEV)的快速诊断方法,本研究根据CAEV甘肃株Gag基因设计1对引物,并以含有CAEV甘肃株全基因组序列的质粒pUC57-CAEV为模板,建立CAEV的SYBR GreenⅠ荧光定量PCR检测方法,并验证其特异性、灵敏性和重复性。结果显示,本研究所建立的SYBRGreenⅠ荧光定量PCR检测方法的Ct值与标准品模板在1.19×109~1.19×10^1 copies/μL范围内呈良好的线性关系,相关系数为0.997,斜率为-3.74,检测下限为1.19×10^1 copies/μL,且对痘苗病毒、山羊痘病毒均无扩增。重复性试验结果显示,批间与批内变异系数均小于1%,重复性好。本研究首次建立了CAEVGag基因的SYBRGreenⅠ荧光定量PCR检测方法,为CAEV的快速检测和病毒感染预防提供了技术手段。     

Test for contamination in connection with renovation of post-PCR laboratories

The Teilum building housing the Department of Forensic Medicine at the University of Copenhagen was renovated in 2021/22. All windows were replaced, and the heating system was upgraded. During the renovation, the usual measures to prevent PCR products from escaping the post-PCR laboratories could not be maintained, since construction workers had to move in and out of the rooms carrying tools and debris. Instead, new measures were introduced, that included 1) the construction of a changing room for the workers with immediate access to the post-PCR laboratories, 2) clothing and shoes for the workers, that should only be worn inside the post-PCR laboratories, and 3) strict limitations on the areas the workers could enter, while renovating the post-PCR laboratories. Samples were taken before, during and after the renovation to monitor the possible spread of PCR products from the post-PCR areas. Mixtures of gDNA and PCR products were detected in only three of the 303 samples. All three samples were collected from the post-PCR areas prior to the renovation began, which indicated that the renovation did not cause wide-spread contamination of PCR products.     

Experimental long-distance haplotyping of OCA2-HERC2 variants

The regulatory HERC2 SNP, rs12913832, is strongly associated with blue and brown eye colour. However, eye colour in heterozygous rs12913832 individuals is observed to vary greatly. Missense mutations in OCA2, such as rs1800407 and rs74653330, are associated with lighter eye colour in some but not all heterozygous rs12913832 individuals. Determining the physical linkage of these variants might help to further explain eye colour variation. So far, experimental haplotyping of these variants has been challenging because the genomic distance between them (∼ 135 kb) exceeds the fragment lengths produced by commonly used DNA isolation kits. The aim for this study was to explore novel methods for long distance haplotyping to assess associations between OCA2-HERC2 haplotypes and eye colour. DNA was isolated from frozen blood samples collected from Norwegians that are known to be heterozygous for both HERC2 rs12913832 and OCA2 SNPs, either rs1800407 (n = 23) or rs74653330 (n = 17), using the newly commercially available Monarch® HMW (heigh molecular weight) DNA Extraction Kit (New England BioLabs_inc). We successfully isolated DNA fragments up to 210 kb, which were long enough to haplotype OCA2-HERC2 loci by droplet digital PCR (ddPCR). Three haplotypes were observed in the study population: rs12913832:A-rs1800407:T in 22/23 individuals, rs12913832:A-rs1800407:C in 1/23 individuals and rs12913832:A-rs74653330:T in 16/16 individuals. As expected, all individuals with the rs12913832:A-rs74653330:T haplotype had intermediate to blue eye colour. However, the rs12913832:A-rs1800407:T haplotype was observed in both blue and brown-eyed individuals, suggesting more research is needed.