Accumulation of endogenous and exogenous nucleic acids in “Touch DNA” components on hands

Successful forensic DNA profiling from handled items is increasingly routine in casework. This “touch DNA” is thought to contain both cellular and acellular nucleic acid sources. However, there is little clarity on the origins or characteristics of this material. The cellular component consists of anucleate, terminally differentiated corneocytes (assumed to lack DNA), and the occasional nucleated cell. The acellular DNA source is fragmentary, presumably cell breakdown products. This study examines the relative contributions each component makes to the hand-secretions (endogenous) and hand-accumulations (exogenous) by recovering rinses from the inside and outside of worn gloves. Additionally, cellular and acellular DNA was measured at timepoints up to 2 h after hand washing, both with and without interim contact. Microscopic examination confirmed cell morphology and presence of nucleic acids. Following the novel application of a hair keratinocyte lysis method and plasma-DNA fragment purification to hand rinse samples, DNA profiles were generated from both fractions. Exogenous cell-free DNA is shown to be a significant source of touch DNA, which reaccumulates quickly, although its amplifiable nuclear alleles are limited. Endogenous DNA is mostly cellular in origin and provides more allelic information consistently over time.     

Analysis of polyhexamethylene biguanide in multipurpose contact lens solutions

The objective of this study was to establish a reasonably simple and reliable method to measure very low concentrations of polyhexamethylene biguanide (PHMB) in multipurpose contact lens solutions (MPSs). By using a weak cation exchange solid phase extraction cartridge to extract the PHMB from MPS, followed by HPLC analysis using an evaporative light scattering detector, low levels (0.1 ppm) of PHMB were detected. Application of this method to a series of off-the-shelf MPS with PHMB as the active ingredient demonstrated these solutions contain 1 ppm. The contact lens solution with hydrogen peroxide as the active ingredient gave no peak where the PHMB peak eluted. The Polyquad^® contact lens solution generated a peak close to the retention time of PHMB. Recovery of PHMB from fortified hydrogen peroxide contact lens solution was good at 0.25 ppm and above; 105% with a RSD of 17% or less. The repeatability of the HPLC system ranged from 4 to 11% RSD; the reproducibility of the entire method was less than 17.5% RSD. Storage and stability studies indicated that storage of MPS with PHMB for chemical analysis are not temperature dependent, but are affected by the composition of the container in which the contact lens solution is stored.     

Design and validation of an STR hexaplex assay for DNA profiling of grapevine cultivars

Although the analysis of length polymorphism at STR loci has become a method of choice for grape cultivar identification, the standardization of methods for this purpose lags behind that of methods for DNA profiling in human and animal forensic genetics. The aim of this study was thus to design and validate a grapevine STR protocol with a practically useful level of multiplexing. Using free bioinformatics tools, published primer sequences, and nucleotide databases, we constructed and optimized a primer set for the simultaneous analysis of six STR loci (VVIi51, scu08vv, scu05vv, VVMD17, VrZAG47, and VrZAG83) by multiplex PCR and CE with laser‐induced fluorescence, and tested it on 90 grape cultivars. The new protocol requires subnanogram quantities of the DNA template and enables automated, high‐throughput genetic analysis with reasonable discriminatory power. As such, it represents a step toward further standardization of grape DNA profiling.     

Genetic Structure Analysis Khitan Noble of Human Remains from Necropolis

Ancient DNA was extracted from 13 skeletal remains from the burial groups of Khitan nobles, which were excavated in northeast China. The hypervariable segment Ⅰ sequences （ HVS Ⅰ ） of the mitochondrial DNA control region, in the 13 individuals, were used as genetic markers to determine the genetic relationships between the individuals and the genetic affinity to other interrelated populations by using the known database of mtDNA. Based on the phylogenetic analysis of these ancient DNA sequences, the genetic structures of two Khitan noble kindreds were obtained, including the Yel Yuzhi＇s kindred and the Xiao He＇s kindred. Furthermore, the relationships between the Khitan nobles and some modern interrelated populations were analyzed. On the basis of the result of the analysis, the gene flows of the ancient Khitans and their demographic expansion in history was deduced.     

Genetic Structure Analysis of Human Remains from Khitan Noble Necropolis

IntroductionInformation provided by ancient mitochondrialDNA(mtDNA)has been regarded as one of the mostpowerful tools for understanding and reconstructing thepast from the genetic perspective[1].In recent years,molecular studies have been widely employed …     

Quantitative and qualitative profiling of mitochondrial DNA length heteroplasmy

Quantitative and qualitative analysis of mitochondrial DNA length heteroplasmy for the first hypervariable segment (HV1) and second hypervariable segment (HV2) regions were performed using size-based separation of fluorescently-labeled polymerase chain reaction (PCR) products by capillary electrophoresis. In this report, the relative proportions of length heteroplasmies in individuals were determined, and each length variant in the heteroplasmic mtDNA mixture was identified. The study demonstrated that 36% and 69% of Koreans show length heteroplasmy in the HV1 and HV2 regions, respectively. Electropherograms revealed that length heteroplasmy in the HV1 region resulted in over 5 length variants in an individual. The peak patterns of length heteroplasmy in the HV1 region were classified into five major types. In the HV2 region, length heteroplasmy resulted in 3-6 length variants in an individual, and showed seven variant peak patterns. The increased knowledge concerning mtDNA length heteroplasmy is believed to not only offer a useful means of determining genetic identity due to increased mitochondrial DNA haplotype diversity by allowing mtDNAs to be classified into several peak patterns, but also represent a promising tool for the diagnosis of several common diseases which are etiologically or prognostically associated with mtDNA polymorphisms.     

牛血清蛋白在共聚物水凝胶接触镜材料上的沉积过程研究

将水凝胶膜样品置于牛血清蛋白(BSA)的水溶液中,沉积一定时间后,采用染料染色结合分光光度法分析沉积前后BSA浓度的变化,计算沉积量,并采用洗脱法测试BSA与水凝胶材料的结合程度.结果表明,BSA的沉积过程为不可逆过程;BSA的沉积作用不受共聚物水凝胶材料中NVP(N-乙烯基吡咯烷酮)结构单元吸附作用的控制;BSA与水凝胶材料松散结合,很容易洗脱;沉积在水凝胶膜表面上的BSA对后续沉积过程无影响.     

高效凝胶色谱法测定角膜接触镜护理液中羟丙甲纤维素含量

采用高效凝胶色谱法测定角膜接触镜护理液中有效成分羟丙甲纤维素的含量,探讨护理液中其他润滑成份对测定的影响和评价。选择市场上含有羟丙甲纤维素的角膜接触镜护理液,以水凝胶色谱柱(TSK-Gelα3000与TSK-Gelα3000串联)为分离柱,以50mmol·L-1氯化钠溶液为流动相,流量为0.7mL·min-1,示差折光检测器测定。羟丙甲纤维素的质量浓度在0.1~5.0g·L-1范围内与其峰面积呈线性关系,检出限(3S/N)为0.056g·L-1。应用本方法对角膜接触护理液进行加标回收试验,回收率在98.0%~102%之间。对羟丙甲纤维素标准溶液平行测定6次,测定值的相对标准偏差(n=6)小于1.5%。     

Pyrosequencing‐based strategy for a successful SNP detection in two hypervariable regions: HV‐I/HV‐II of the human mitochondrial displacement loop

Forensic analysis of mitochondrial displacement loop (D‐loop) sequences using Sanger sequencing or SNP detection by minisequencing is well established. Pyrosequencing has become an important alternative because it enables high‐throughput analysis and the quantification of individual mitochondrial DNAs (mtDNAs) in samples originating from more than one individual. DNA typing of the mitochondrial D‐loop region is usually the method of choice if STR analysis fails because of trace amounts of DNA and/or extensive degradation. The main aim of the present work was to optimize the efficiency of pyrosequencing. To do this, 31 SNPs within the hypervariable regions I and II of the D‐loop of human mtDNA were simultaneously analyzed. As a novel approach, we applied two sets of amplification primers for the multiplexing assay. These went in combination with four sequencing primers for pyrosequencing. This method was compared with conventional sequencing of mtDNA from blood and biological trace materials.     

Human DNA extraction from highly degraded skeletal remains: How to find a suitable method?

Retrieving DNA from highly degraded human skeletal remains is still a challenge due to low concentration and fragmentation, which makes it difficult to extract and purify. Recent works showed that silica-based methods allow better DNA recovery and this fact may be attributed to the type of bones and the quality of the preserved tissue. However, more systematic studies are needed to evaluate the efficiency of the different silica-based extraction methods considering the type of bones. The main goal of the present study is to establish the best extraction method and the type of bone that can maximize the recovery of PCR-amplifiable DNA and the subsequent retrieval of mitochondrial and nuclear genetic information. Five individuals were selected from an archaeological site located in Catalonia–Spain dating from 5th to 11th centuries AD. For each individual, five samples from different skeletal regions were collected: petrous bone, pulp cavity and cementum of tooth, and rib and limb bones. Four extraction methods were tested, three silica-based (silica in-suspension, HE column and XS plasma column) and the classical method based on phenol–chloroform. Silica in-suspension method from petrous bone and pulp cavity showed the best results. However, the remains preservation will ultimately be the key to the molecular result success.     

Multiplex amplified product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations

We present a reliable, rapid, and economical multiplex amplified product-length polymorphism (APLP) method for analyzing the haplogroup-diagnostic mitochondrial single-nucleotide polymorphisms (mtSNPs) in East Asian populations. By examining only 36 haplogroup-specific mtSNPs in the coding region by using four 9-multiplex polymerase chain reaction (PCR) and subsequent electrophoresis, we could safely assign 1815 individuals from 8 populations of Japanese, Korean, Chinese, and Germans to 45 relevant haplogroups. This multiplex APLP analysis of coding-region mtSNPs for haplogrouping is especially useful not only for molecular phylogenetic studies but also for large-scale association studies due to its rapid and economical nature. This is the first panel of mtSNPs in the coding region to be used for haplogrouping of East Asian populations.     

A simple,one‐tube assay for the simultaneous detection and diagnosis of ten Australian poultry Eimeria

Coccidiosis is a costly worldwide enteric disease of chickens caused by parasites of the genus Eimeria. At present, there are seven described species that occur globally and a further three undescribed, operational taxonomic units (OTUs X, Y, and Z) that are known to infect chickens from Australia. Species of Eimeria have both overlapping morphology and pathology and frequently occur as mixed‐species infections. This makes definitive diagnosis with currently available tests difficult and, to date, there is no test for the detection of the three OTUs. This paper describes the development of a PCR‐based assay that is capable of detecting all ten species of Eimeria, including OTUs X, Y, and Z in field samples. The assay is based on a single set of generic primers that amplifies a single diagnostic fragment from the mitochondrial genome of each species. This one‐tube assay is simple, low‐cost, and has the capacity to be high throughput. It will therefore be of great benefit to the poultry industry for Eimeria detection and control, and the confirmation of identity and purity of vaccine strains.     

Mutations in mitochondrial-encoded cytochrome c oxidase subunits I, II, and III genes detected in Alzheimer's disease using single-strand conformation polymorphism

A "mitochondrial hypothesis" of late onset Alzheimer's disease (AD) has been proposed. Biochemical studies indicate that there is a significant decrease in cytochrome oxidase (CO) activity as well as perturbed CO I and CO III mRNA levels in platelets and brain tissue from Alzheimer's patients. Using the electrophoretic mutation detection technique SSCP and DNA sequencing, we have identified 20 point mutations in the mitochondrial-encoded CO subunits (CO I, II, and III) in AD and age-matched control brain samples. Eight of the mutations are new variants of the mitochondrial genome. The efficiency of SSCP in detecting mutations in the CO subunits was estimated to be 80% when compared to dideoxy sequencing. One of the mutations (at position 9,861) results in a phenylalanine-->leucine substitution at a highly conserved residue in CO III. CO activity was reduced by an average of 35% in all AD brains compared to age-matched control samples, which agrees with previous reports. CO activity in one of the AD brain samples carrying the 9,861 mutation decreased by 80% relative to control brain samples, suggesting that the phenotypic expression of this mutation may result in reduced CO activity and compromised mitochondrial function.     

Recombination analysis of autosomal short tandem repeats in Chinese Han families

Recombination fractions between forensic STRs can be extrapolated from the International HapMap Project, but the concordance between recombination fractions predicated from genetic maps and derived from observation of STR transmissions in families is still ambiguous for autosomal STRs because of limited family studies. Therefore, the main goal of this study is to compare recombination fractions estimated by pedigree analysis with those derived from HapMap phase SNP data. Genotypes of nine autosomal STR pairs (TPOX‐D2S1772, D5S818‐CSF1PO, D7S3048‐D7S820, D8S1132‐D8S1179, TH01‐D11S2368, vWA‐D12S391, D13S325‐D13S317, D18S51‐D18S1364, and D21S11‐PentaD) from 207 two‐generation families with two to five children (the number of families with five, four, three, and two children was 2, 3, 20, and 182, respectively) were used to analyze the recombination. The linkage analysis showed that significant linkage was observed at six STR pairs (D5S818‐CSF1PO, D8S1132‐D8S1179, TH01‐D11S2368, vWA‐D12S391, D13S325‐D13S317, and D18S51‐D18S1364) with genetic distances <36.22 cM in HapMap. Their recombination fractions calculated from family data were very close to those derived from HapMap. However, three STR pairs of TPOX‐D2S1772, D7S3048‐D7S820, and D21S11‐PentaD showed no significant linkage with genetic distances from 43.38 to 91.49 cM. Our results indicate that recombination fractions extrapolated from HapMap can provide a substitute if empirical data are unavailable for the linkage STR pair with a genetic distance spanned <36.22 cM.     

DNA微阵列原位合成中的氧化剂体系改进

DNA芯片的制备方法主要有离片合成法和在片合成法．离片合成是用点样法将DNA探针固定在基片上;在片合成是在基片表面直接原位合成寡核苷酸探针阵列．目前国外已有多种DNA芯片原位合成方法的报道,但其中仅Fordor等提出的光脱保护DNA固相原位合成技术已商品化,该方法制备成本高,     

Who touched the document?: A new overall strategy for collection and identification of DNA from the questioned documents as a supportive evidence

The questions on which judges/prosecutors apply for expertise are mostly about by whom a document was drafted/signed. In this study, a new collective strategy was constructed including a collection method, a modified-silica-based DNA isolation method, and a novel purification method on four contact traces formed on four different paper surface during writing, using PCR with AmpFlSTR®GlobalFiler™ STR kit (after experimental comparison between three different kits) and identification using CE. This collective analysis approach is more sensitive and superior to its equivalents on questioned documents in literature because quantifiable amounts of touch DNA and profiles with high loci percentages (100% on day 1, 72.72% after 1 week) were obtained up to 1 week even after the most challenging conditions of sample forming that a forensic scientist can meet; as washing hands just before drafting and using a very low pressure in a shorter time (simulating a simple contact real conditions while drafting), using no visualizing technique that damages the document. Using the strategy, four most commonly used paper types were compared, to see in which of them DNA could be recovered better. The success of this strategy was shown on the 1-day to 10-year-old real samples from a diary and some archive documents from a law office (including the mix-DNA and different ballpoint pens). Thus, it became possible to show if a person had touched the document, in high success rates up to 1 week as a secondary evidence, when primary evidences are insufficient for the detection of document fraud offenses.