Mutation scanning-coupled analysis of haplotypic variability in mitochondrial DNA regions reveals low gene flow between human and porcine Ascaris in endemic regions of China

Haplotypic variation within and among the Ascaris populations representing six provinces in China was investigated. Mitochondrial DNA regions in the cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) genes were amplified by PCR from total genomic DNA samples (n > 720) from Ascaris individuals from humans and pigs, and subjected to mutation scanning and subsequent selective sequencing. For the cox1, ten different electrophoretic profiles were recorded for human Ascaris, and the same number for pig Ascaris, one of them being common to both host species. For the nad1, 11 different profiles were detected for human Ascaris, and 15 for pig Ascaris. Having defined all haplotypes (20 for pcox1 and 26 for pnad1) by sequencing, their frequencies were estimated in each of the two host species and each of the six provinces. For each mitochondrial region, the frequency of the different haplotypes varied considerably, depending on host species and geographical origin. Analysis of the sequence data (representing all haplotypes for each mitochondrial locus) by F-statistics indicated restricted gene flow between human Ascaris and pig Ascaris, and supported the conclusions from previous molecular epidemiological investigations that pigs are not a significant source of Ascaris infection in humans in endemic regions.     

Single-strand conformation polymorphism-based analysis of mitochondrial cytochrome c oxidase subunit 1 reveals significant substructuring in hookworm populations

Sequence heterogeneity in a portion of the mitochondrial cytochrome c oxidase subunit 1 gene (pcox1) was measured for the hookworms, Ancylostoma caninum from Australia, A. duodenale from China, and Necator americanus from China and Togo using single-strand conformation polymorphism (SSCP) analysis combined with DNA sequencing. The pcox1 sequences were characterised for individual nematodes displaying genetic variation within each of the three species, and those were compared with pcox1 sequences of four other species of hookworm. While intraspecific variation in the pcox1 sequence ranged from 0.5 to 8.6% for A. caninum, 0.3 to 3.3% forA. duodenale, and 0.3 to 4.3% for N. americanus, interspecific differences varied from 4.8 to 12.9%. Sequence data also provided information on nucleotide compositions and substitution patterns. Genetically distinct groups were detected within A. caninum and A. duodenale, indicating significant population substructuring within these species. Also, N. americanus individuals from China all differed from those from Togo at four nucleotide positions, supporting a previous proposal (based on ribosomal DNA sequence data) that N. americanus may represent a species complex. The findings indicated the value of pcox1 sequence data and the mutation scanning approach for studying the genetic structures of hookworm populations, which should have important epidemiological relevance.     

Mutation scanning analysis of mitochondrial cytochrome c oxidase subunit 1 reveals limited gene flow among bovine lungworm subpopulations in Sweden

A mutation scanning approach was employed to investigate the population genetic structure of the bovine lungworm, Dictyocaulus viviparus (Nematoda: Trichostrongyloidea), in southern Sweden. A total of 252 individual nematodes were collected from cattle representing 17 farms. A portion of the mitochondrial cytochrome c oxidase subunit 1 gene (pcox1) was amplified from genomic DNA isolated from individual lungworms by the polymerase chain reaction (PCR), and then subjected to single-strand conformation polymorphism (SSCP). Samples with distinct SSCP profiles were then sequenced. In total, 12 distinct pcox1 haplotypes (393 bp) were defined for the 252 individuals, and pairwise sequence differences among the haplotypes ranged from 0.3-2.3%. Average haplotype diversity and nucleotide diversity values were 0.16 and 0.002, respectively. There was no particular correlation between pcox1 haplotypes and their geographical origin. The "overall fixation" indices F(ST) and N(ST) were calculated to be 0.77 and 0.65, respectively. The results of this study revealed that both the mitochondrial DNA sequence diversity within populations and the gene flow among populations of D. viviparus were low. This is similar to findings for some parasitic nematodes of plants and insects, but distinctly different from gastrointestinal trichostrongyloid nematodes of domesticated ruminants considered to have relatively high levels of genetic diversity and gene flow. Such differences were interpreted to relate mainly to differences in host movement as well as parasite biology, population sizes and transmission patterns, and should therefore be of epidemiological relevance.*     

Mutation scanning for sequence variation in three mitochondrial DNA regions for members of the Contracaecum osculatum (Nematoda: Ascaridoidea) complex

Anisakid nematodes of seals from different geographical origins, previously identified by multilocus enzyme electrophoresis as Contracaecum osculatum A (CoA), C. osculatum B (CoB), C. osculatum C (CoC), C. osculatum D (CoD), C. osculatum E (CoE) and C. osculatum baicalensis (Cob), were characterised genetically using a mutation scanning approach, in order to define genetic markers for their specific identification and differentiation. Three mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit I (COI), and the small and large subunits of rRNA (ssrRNA and IsrRNA, respectively) were amplified separately from individual nematodes by polymerase chain reaction (PCR), analysed by single-strand conformation polymorphism (SSCP), and samples displaying sequence variability were subjected to sequencing. Forty-six haplotypes were defined for 62-66 individuals (representing the six members of C. osculatum). All taxa except CoD and CoE could be identified, or delineated from one another, by nucleotide differences in the COI, ssrRNA and/or IsrRNA sequences. For all three mtDNA regions, 4 (10.5%), 7 (18.4%), 15 (39.5%) and 11 (28.9%) of 38 nucleotide positions were considered diagnostic (fixed) and could thus unequivocally delineate CoA, CoB, CoC and Cob. The lack of an unequivocal nucleotide difference in any of the three mtDNA sequences between CoD and CoE was in accordance with previous ribosomal DNA sequence data but inconsistent with multilocus enzyme electrophoretic data. Using all fixed nucleotide positions, CoA, CoD/E and CoB were genetically more similar to Cob than each was to CoC, similar to previous findings. In spite of not being able to distinguish among all six taxa of C. osculatum, the present study demonstrated clearly the usefulness and attributes of the mutation scanning approach for investigating population genetic structures of species of parasitic nematodes.     

Comparison between Echinococcus granulosus sensu stricto (G1) and E. canadensis (G6) mitochondrial genes (cox1 and nad1) and their related protein models using experimental and bioinformatics analysis

BackgroundCystic echinococcosis (CE) as a zoonotic parasitic disease, remains a health challenge in many parts of the world. There are different species of Echinococcus granulosus sensu lato with different pathogenicity and host preferences.Different procedures have been applied for characterization of Echinococcus taxa in which two mitochondrial genes, cox1 and nad1 have been used more common. They have been able to differentiate E. granulosus sensu stricto and E. canadensis species in different hosts. The affinity of E. granulosus sensu stricto and E. canadensis species for localizing different organs seems to be different. To what such affinity and related pathogenicity could be related, is not known, so far. Bioinformatics analysis may be helpful to interpret such difference by investigating the genes and their related protein models between different species infecting human and animals. The current work was designed to study the differences between E. granulosus s.s. and E. canadensis species mitochondrial genes (cox1 and nad1) and related protein models of CE cysts by experimental and bioinformatics analysis.Materials and methodsDifferent human and animal CE cysts were collected and their DNA was extracted and sequenced based on their cox1 and nad1 genes. In order to determine the E. granulosus s.s. and E. canadensis species of the samples, BLAST analysis was performed on sequenced genes. Three sequences were selected for analysis and were deposited in GenBank. Moreover, the sequence number of KT988116.1 which belonged to E. canadensis from our already deposited in GenBank was also selected. Alignment and phylogenetic analysis were performed on the sequences using BioEdit and MEGA7 software. The raw sequences of translated proteins belonged to the mentioned genes were obtained from Protein database in NCBI. The secondary structure was determined by PSIPRED Protein Sequence Analysis Workbench. The tertiary models of COX1 and NAD1 proteins in both genotypes were constructed using Modeler 9.12 software and their physicochemical features were computed using ProtParam tool in ExPASY server.ResultsBLAST analysis on sequenced genes showed that the samples belonged to E. granulosus s.s. and E. canadensis species. These sequences were deposited in GenBank with accession numbers: JN579173.1, KF437811.1, and KY924632.1.The results showed that proteins of COX1 of E. granulosus s.s., COX1of E. canadensis, NAD1of E. granulosus s.s. and NAD1of E. canadensis species, consisted of 135, 122, 120 and 124 amino acids, respectively. The aligned sequences of translated proteins belonged to COX1 and NAD1 enzymes in E. granulosus s.s. and E. canadensis species were different; such that alignment COX1 sequence between E. granulosus s.s. and E. canadensis species showed that amino acids were different in 6 positions. This difference for NAD1 sequences were different in 19 positions. The secondary structure determined by PSIPRED showed differences in coil, strand and helix chains in COX1 and NAD1 proteins in E. granulosus s.s. and E. canadensis species. Comparison between three-dimensional structures (3D) of COX1 protein model in E. granulosus s.s. and E. canadensis species demonstrated an additional helix with two conserved iron binding sites in the COX1 protein of E. granulosus s.s. species.ConclusionE. granulosus s.s. and E. canadensis species differences are reflected in two important proteins: COX1 and NAD1. These differences are demonstrable in the 3D structure of proteins of both strains. So, the present study is adding to our understanding of the difference in molecular sequences between the E. granulosus s.s. (G1) and E. canadensis (G6) which may be used for interpreting the difference between the pathogenicity and localization affinity in these two important helminthic zoonosis.     

Single-strand conformation polymorphism analysis of genetic variation in Labiostrongylus longispicularis from kangaroos

Single-strand conformation polymorphism (SSCP) analysis was employed to screen for sequence heterogeneity in the second internal transcribed spacer (ITS-2) of ribosomal (r) DNA of Labiostrongylus longispicularis, a parasitic strongylid nematode occuring in some species of kangaroo in different geographical regions of Australia. The results showed that most of the nematodes screened had different SSCP profiles, which were subsequently shown to correspond to polymorphisms and/or an indel in the ITS-2 sequence. These variable sites related mainly to unpaired regions of the predicted secondary structure of the precursor rRNA molecule. SSCP profiles could be used to distinguish L. longispicularis in Macropus robustus robustus (New South Wales) from L. longispicularis in Macropus robustus erubescens and Macropus rufus (South Australia). This difference corresponded to a transversional change in the ITS-2 sequence at alignment position 82. The study demonstrated clearly the effectiveness of SSCP analysis for future large-scale population genetic studies of L. longispicularis in order to test the hypothesis that L. longispicularis from different geographical regions represents multiple sibling species.     

Applications of homemade kit in mutation detection of genes

With the accomplishment of Human Genome Project (HGP), single nucleotide polymorphism (SNP) and mutation detection in human genome are becom-ing a new researching focus. These researches can help us to understand the phenotype diversity of indi-vidual, disease susceptibility and drug resistance of different colonies. Traditional method used for muta-tion detection is slab gel electrophoresis, which re-mains labor-intensive and time-consuming because of the requirement of radioactivity or te…     

T(4-Mop)PS4卟啉与牛血清蛋白相互作用的研究

以四-(4-甲氧基-3-磺酸基苯)卟啉(T(4-Mop)PS4)为探针,通过T(4-Mop)PS4与牛血清白蛋白(BSA)的相互作用,建立了测定BSA的电化学分析方法。T(4-Mop)PS4的峰电流变化(ΔIp)与BSA在2.0×10-6～1.0×10-5mol.L-1范围内呈良好的线性关系,检出限为1.2×10-6mol.L-1;对5.0×10-6mol.L-1BSA平行测定8次,其相对标准偏差为2.0%,回收率为95%～104%。组氨酸、缬氨酸、苯丙氨酸、丝氨酸、异白氨酸、谷氨酰胺、苏氨酸等氨基酸对BSA的测定不产生干扰。采用紫外可见光度法、荧光光谱法和线性扫描伏安法(LSV)研究了T(4-Mop)PS4与BSA之间的相互作用,并测定了二者相互作用的结合常数和结合比。研究表明,T(4-Mop)PS4与BSA之间主要以疏水作用力结合,形成了1∶1的稳定复合物。     

Molecular characterization of selected dermatophytes and their identification by electrophoretic mutation scanning

Dermatophytes are fungi that can be contagious and cause infections in the keratinized skin of mammals, including humans. The etiological diagnosis of dermatophytosis relies on a combination of in vitro‐culture and microscopic methods. Effective molecular tools could overcome the limitations of conventional methods of identification. In the present study, following phenetic identification as M. canis, M. fulvum, M. gypseum, T. mentagrophytes and T. terrestre, we genetically characterized key dermatophytes, employing the sequences of the first and second internal transcribed spacers of nuclear ribosomal DNA as well as part of the chitin synthase‐1 gene, and assessed the utility of these DNA regions (based on levels of nucleotide variation within and among species/taxa) as markers for the classification of species and genotypes. Employing partial chitin synthase‐1 gene as the marker, we also established a PCR‐coupled SSCP approach as a diagnostic/analytical mutation‐scanning tool. This tool should facilitate fundamental investigations of the ecology, epidemiology and population genetics of dermatophytes and, importantly, should assist in allowing a more rapid diagnosis of dermatophytoses in humans and other animals, thus overcoming the significant delays in targeted chemotherapy following diagnosis using conventional methods. (Nucleotide sequence data reported in this paper are available in the EMBL, GenBank and DDJB datadases under accession numbers FJ897707–FJ897713 (ITS‐1), FJ897714–FJ897720 (ITS‐2) and FJ897700–FJ897706 (pchs‐1)).     

Analysis and interpretation of mixture DNA using AS‐PCR of mtDNA

Semi‐nested PCR with allele‐specific (AS) primers and sequencing of mitochondrial DNA (mtDNA) were performed to analyze and interpret DNA mixtures, especially when biological materials were degraded or contained a limited amount of DNA. SNP‐STR markers were available to identify the minor DNA component using AS‐PCR; moreover, SNPs in mtDNA could be used when the degraded or limited amounts of DNA mixtures were not successful with SNP‐STR markers. Five pairs of allele‐specific primers were designed based on three SNPs (G15043A, T16362C, and T16519C). The sequence of mtDNA control region of minor components was obtained using AS‐PCR and sequencing. Sequences of the amplification fragments were aligned and compared with the sequences of known suspects or databases. When this assay was used with the T16362C and T16519C SNPs, we found it to be highly sensitive for detecting small amounts of DNA (～30 pg) and analyzing DNA mixtures of two contributors, even at an approximately 1‰ ratio of minor and major components. An exception was tests based on the SNP G15043A, which required approximately 300 pg of a 1% DNA mixture. In simulated three contributor DNA mixtures (at rate of 1:1:1), control region fragments from each contributor were detected and interpreted. AS‐PCR combined with semi‐nested PCR was successfully used to identify the mtDNA control region of each contributor, providing biological evidence for excluding suspects in forensic cases, especially when biological materials were degraded or had a limited amount of DNA.     

Mutation scanning-based analysis of anisakid larvae from Sillago flindersi from Bass Strait, Australia

Anisakidosis is an important fish-borne disease caused by the larvae of anisakid nematodes, which affects humans and a range of other animals. The accurate identification of members of this nematode group is central to investigating the epidemiology of the parasites and in the surveillance and control of anisakidosis. It is now well known that morphological identification alone does not allow specific identification, particularly of larval stages. To better understand the epidemiology of anisakid nematodes in southern Australian fishes and the potential risks posed to human health, a survey of 50 specimens of the commercially important fish, Sillago flindersi, from Bass Strait, Australia was conducted. We characterised anisakid larvae by PCR-coupled mutation scanning, sequencing and phylogenetic analyses of the first and second internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA. This study revealed that 92% of the S. flindersi examined were infected with anisakids (n=194), which were represented by seven genotypes. Phylogenetic analyses of the genotypes defined herein, together with reference sequence for Anisakis pegreffii and Hysterothylacium sp. from public databases (i.e. GenBank), revealed the presence of A. pegreffii (n=24), Hysterothylacium larval type IV (n=90) and Hysterothylacium larval type VIII (n=80) in S. flindersi. Thus, the PCR-coupled mutation scanning approach employed herein is an effective tool for the genetic characterisation of anisakid nematodes for diagnostic and analytical purposes (nucleotide sequences reported in this paper are available in the GenBank database under accession nos. JN631796-809).     

Electrophoretic detection of population variation within Contracaecum ogmorhini (Nematoda: Ascaridoidea: Anisakidae)

This study examined genetic variation among specimens of Contracaecum ogmorhini from different otariid hosts and geographical origins using a polymerase chain reaction (PCR)-based mutation detection approach. The first (ITS-1) and second (ITS-2) internal transcribed spacers (ITS) of ribosomal DNA (rDNA) were amplified individually by PCR, scanned for sequence variation by single-strand conformation polymorphism (SSCP), and samples displaying variable SSCP profiles were subjected to cycle sequencing. While C. ogmorhini individuals from Arctocephalus pusillus pusillus (CoAPP) from South Africa and those from Arctocephalus pusillus doriferus (CoAPD) from Australia had very similar SSCP profiles for both ITS-1 and ITS-2, individuals of C. ogmorhini from Zalophus californianus (CoZC) from Pacific Canada could be unequivocally distinguished based on their profiles. In accordance with SSCP results, both CoAPP and CoAPD had identical ITS consensus sequences, whereas CoZC differed in sequence from both CoAPP and CoAPD populations by 0.2% (one base in the ITS-1) and 0.7% (two bases in the ITS-2). Based on the nucleotide difference in the ITS-2 sequence, a PCR-linked restriction fragment length polymorphism (RFLP) could be employed to distinguish individuals representing CoZC from those of both CoAPP and CoAPD. The findings suggest that C. ogmorhini may represent a complex of at least two species.     

Analysis of variation in the ovine ultra‐high sulphur keratin‐associated protein KAP5‐4 gene using PCR‐SSCP technique

Keratin‐associated proteins (KAPs) are one of the main structural components of the wool fibre. Variation in the KAP genes (KRTAPs) may affect the structure of KAPs and hence wool characteristics. In this study, we used PCR‐SSCP to analyse ovine KRTAP5‐4, a gene encoding a member of the KAP5 family. Five different PCR‐SSCP patterns were detected in the 250 sheep that were analysed. Either one or a combination of two patterns was observed for each sheep, which was consistent with these sheep being either homozygous or heterozygous at this locus. DNA sequencing revealed that these patterns represent five different DNA sequences. One of the sequences was identical to a published ovine KRTAP5‐4 sequence. The remaining four were unique, but shared a high homology with the published ovine KRTAP5‐4 sequence, suggesting that these sequences represent allelic variants of KRTAP5‐4. There were a total of six SNPs and one length polymorphism in the sequences. Of the five SNPs found in the coding region, four were non‐synonymous SNPs and would result in amino acid changes. The length polymorphism would affect the cysteine content of the putative peptide and this along with the SNPs may have an impact on the structure of KAP5‐4, and hence affect wool traits.     

Theoretical Investigation on Mechanism,Thermochemistry, and Kinetics of the Gas-phase Reaction of 2-Propargyl Radical with Formaldehyde

Gas-phase mechanism and kinetics of the reactions of the 2-propargyl radical(H2CCCH), an important intermediate in combustion processes, with formaldehyde were investigated using ab initio molecular orbital theory at the coupled-cluster CCSD(T)//B3LYP/6-311++G(3df,2p) method in conjunction with transition state theory(TST), variational transition state theory(VTST) and Rice-Ramsperger-Kassel-Marcus(RRKM) calculations for rate constants. The potential energy surface(PES) constructed shows that the H2CCCH+HCHO reaction has six main entrances, including two H-abstraction and four additional channels, in which the former is energetically more favorable. The H-abstraction channels slide down to two quite weak pre-complexes COM-01(-9.3 kJ/mol) and COM-02(-kJ/mol) before going via energy barriers of 71.3(T0/P1) and 63.9 kJ/mol(T0/P2), respectively. Two post-complexes, COM-1(-17.8 kJ/mol) and COM-2(-23.4 kJ/mol) created just after coming out from T0/P1 and T0/P2, respectively, can easily be decomposed via barrier-less processes yielding H2CCCH2+CHO(P1,-12.4 kJ/mol) and HCCCH3+CHO(P2,-16.5 kJ/mol), respectively. The additional channels occur initially by formation of four intermediate states, H2CCCHCH2O(I1, 1.1 kJ/mol), HCCCH2CH2O(I3, 4.5 kJ/mol), H2CCCHOCH2(I4, 10.2 kJ/mol), and HCCCH2OCH2(I6, 19.1 kJ/mol) via energy barriers of 66.3, 59.2, 112.2, and 98.6 kJ/mol at T0/1, T0/3, TOM, and TO/6, respectively. Of which two channels producing 14 and 16 can be ignored due to coming over tlie high barriers TOM and TO/6, respectively. The rate constants and product branching ratios for the low-energy channels calculated show that the H2CCCH+HCHO reaction is almost pressure-independent. Altliough the H2CCCH+HCHO→Ⅰ1 and H2CCCH+HCHO→Ⅰ3 channels become dominant at low temperature, however, they are less competitive channels at high temperature.     

结直肠癌组织中K-ras基因突变的毛细管电泳检测

通过对PCR扩增的76例结直肠癌组织及癌旁正常组织DNA基因组共152个样本纯化变性后,采用毛细管电泳-激光诱导荧光检测(CE-LIF)结合单链构象多态性(SSCP)分析方法检测了人结直肠癌组织及癌旁正常组织中K-ras基因第12/13位密码子突变。所检测的76例结直肠癌患者中有30例患者存在基因突变,并对异常片段进行测序验证,测序证实以碱基G→A点突变为主。结果表明所建立的CE-LIF技术结合SSCP分析检测K-ras基因突变的方法高效、快速、灵敏、准确,适合于临床上大样本结直肠癌中K-ras基因突变分析,对选择抗结直肠癌药物有一定的指导作用。     

微波辅助萃取-固相微萃取-气相色谱法同时测定茶叶中的有机氯和拟除虫菊酯农药残留

建立了微波辅助萃取-固相微萃取-气相色谱(MAE-SPME-GC)同时测定茶叶中六六六(α-BHC,β-BHC,γ-BHC,δ-BHC 4种异构体)、滴滴涕类(DDD,DDE,o,p′-DDT,p,p′-DDT)、氯氰菊酯(cypermethrin)和氰戊菊酯(fenvalerate)等10种农药残留的方法。采用外标法定量,除氰戊菊酯外,农药的质量浓度与其色谱峰面积在一定范围内有较好的线性关系,相关系数为0.9705～0.9984。10种组分的加标回收率为64%～121%,相对标准偏差为10.4%～22.9%,检测限为1～50 ng/L。应用该方法测定了市场上3种茶叶中上述农药残留的含量。     

Multilocus mutation scanning for the analysis of genetic variation within Malassezia (Basidiomycota: Malasseziales)

Members of the genus Malassezia are budding yeasts, characterized by a thick cell wall. Recently, these yeasts have received attention as emerging pathogens. They are common commensals on the skin of animals and can become pathogenic under the influence of various predisposing factors. Central to studying their taxonomy, systematics, and ecology and to diagnosis is the accurate identification of species or operational taxonomic units. To overcome the limitations of current phenotypic and biochemical methods of identification, a PCR-coupled SSCP approach, utilizing sequence variation (0.4-33.5%) in short regions (approximately 250-270 bp) of the first internal transcribed spacer (ITS-1) of nuclear ribosomal DNA and the chitin synthase-2 gene (chs-2), was assessed for the identification and differentiation of different species/genotypes of Malassezia, characterized previously by DNA sequencing. Genomic DNA samples (n = 30) from Malassezia isolates cultured from canine skin scrapings were assessed by SSCP analysis of the two different genetic loci, and unequivocal delineation between genotypes and species was achieved. This SSCP approach is considered to provide a practical tool for the rapid and reliable genetic characterization of Malassezia genotypes/species from dogs and for investigating their population genetics and ecology. It will also provide a powerful tool for studies of Malassezia isolates from other animal species.     

Application Potential of Bacterial Volatile Organic Compounds in the Control of Root-Knot Nematodes

Plant-parasitic nematodes (PPNs) constitute the most damaging group of plant pathogens. Plant infections by root-knot nematodes (RKNs) alone could cause approximately 5% of global crop loss. Conventionally, chemical-based methods are used to control PPNs at the expense of the environment and human health. Accordingly, the development of eco-friendly and safer methods has been urged to supplement or replace chemical-based methods for the control of RKNs. Using microorganisms or their metabolites as biological control agents (BCAs) is a promising approach to controlling RKNs. Among the metabolites, volatile organic compounds (VOCs) have gained increasing attention because of their potential in the control of not only RKNs but also other plant pathogens, such as insects, fungi, and bacteria. This review discusses the biology of RKNs as well as the status of various control strategies. The discovery of VOCs emitted by bacteria from various environmental sources and their application potential as BCAs in controlling RKNs are specifically addressed.     

A novel pathogen detection system based on high‐resolution CE‐SSCP using a triblock copolymer matrix

Although CE‐SSCP analysis combined with 16S ribosomal RNA gene‐specific PCR has enormous potential as a simple and versatile pathogen detection technique, low resolution of CE‐SSCP causes the limited application. Among the experimental conditions affecting the resolution, the polymer matrix is considered to be most critical to improve the resolution of CE‐SSCP analysis. However, due to the peak broadening caused by the interaction between hydrophobic moiety of polymer matrices and DNA, conventional polymer matrices are not ideal for CE‐SSCP analysis. A poly(ethyleneoxide)‐poly(propyleneoxide)‐poly(ethyleneoxide) (PEO‐PPO‐PEO) triblock copolymer, with dynamic coating ability and a propensity to form micelles to minimize exposure of hydrophobic PPO block to DNA, can be an alternative matrix. In this study, we examined the resolution of CE‐SSCP analysis using the PEO‐PPO‐PEO triblock copolymer as the polymer matrix and four same‐sized DNA fragments of similar sequence content. Among 48 commercially available PEO‐PPO‐PEO triblock copolymers, three were selected due to their transparency in the operable range of viscosity and PEO₁₃₇PPO₄₃PEO₁₃₇ exhibited the most effective separation. Significant improvement in resolution allowed discrimination of the similar sequences, thus greatly facilitated CE‐SSCP analysis compared to the conventional polymer matrix. The results indicate that PEO‐PPO‐PEO triblock copolymer may serve as an ideal matrix for high‐resolution CE‐SSCP analysis.     

Triblock copolymer matrix‐based capillary electrophoretic microdevice for high‐resolution multiplex pathogen detection

Rapid and simple analysis for the multiple target pathogens is critical for patient management. CE‐SSCP analysis on a microchip provides high speed, high sensitivity, and a portable genetic analysis platform in molecular diagnostic fields. The capability of separating ssDNA molecules in a capillary electrophoretic microchannel with high resolution is a critical issue to perform the precise interpretation in the electropherogram. In this study, we explored the potential of poly(ethyleneoxide)‐poly(propyleneoxide)‐poly(ethyleneoxide) (PEO‐PPO‐PEO) triblock copolymer as a sieving matrix for CE‐SSCP analysis on a microdevice. To demonstrate the superior resolving power of PEO‐PPO‐PEO copolymers, 255‐bp PCR amplicons obtained from 16S ribosomal RNA genes of four bacterial species, namely Proteus mirabilis, Haemophilus ducreyi, Pseudomonas aeruginosa, and Neisseria meningitidis, were analyzed in the PEO‐PPO‐PEO matrix in comparison with 5% linear polyacrylamide and commercial GeneScan? gel. Due to enhanced dynamic coating and sieving ability, PEO‐PPO‐PEO copolymer displayed fourfold enhancement of resolving power in the CE‐SSCP to separate same‐sized DNA molecules. Fivefold input of genomic DNA of P. aeruginosa and/or N. meningitidis produced proportionally increased corresponding amplicon peaks, enabling correct quantitative analysis in the pathogen detection. Besides the high‐resolution sieving capability, a facile loading and replenishment of gel in the microchannel due to thermally reversible gelation property makes PEO‐PPO‐PEO triblock copolymer an excellent matrix in the CE‐SSCP analysis on the microdevice.