Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria

DNA fingerprinting has attracted considerable interest as means for identifying, tracing and preventing the dissemination of infectious agents. Various methods have been developed for typing of pathogenic bacteria, which differ in discriminative power, reproducibility and ease of interpretation. During recent years a typing method, which uses the information provided by whole genome sequencing of bacterial species, has gained increased attention. Short sequence repeat (SSR) motifs are known to undergo frequent variation in the number of repeated units through cellular mechanisms most commonly active during chromosome replication. A class of SSRs, named variable number of tandem repeats (VNTRs), has proven to be a suitable target for assessing genetic polymorphisms within bacterial species. This review attempts to give an overview of bacterial agents where VNTR-based typing, or multiple-locus variant-repeat analysis (MLVA) has been developed for typing purposes, together with addressing advantages and drawbacks associated with the use of tandem repeated DNA motifs as targets for bacterial typing and identification.     

9号染色体上海洛因依赖易感基因的定位

目的:筛查和定位9号染色体上海洛因依赖易感基因的位点.方法:在10例海洛因依赖者和其正常同胞对照者中用覆盖第9号染色体的20个短串联重复序列(Short Tandem Repeats,STR)进行荧光标记的基因组扫描.结果:D9S286, D9S167和D9S164位点等位基因在海洛因依赖组和其正常同胞对照组之间分布有显著性差异(x2检验,P＜0.05).其它17个STR位点D9S288,D9S285,D9S157, D9S171,D9S161,D9S1817, D9S273,D9S175,D9S283,D9S287,D9S1690,D9S1677,D9S1766, D9S1682, D9S290,D9S1826,D9S158的等位基因在海洛因依赖组和其正常同胞对照组之间分布没有显著性差异(x2检验,P＞0.05).结论:D9S286,D9S167和D9S164位点附近可能存在海洛因依赖的易感基因,多巴胺β-羟化酶基因可以作为候选基因.     

Functional Bacterial Amyloids: Understanding Fibrillation,Regulating Biofilm Fibril Formation and Organizing Surface Assemblies

Functional amyloid is produced by many organisms but is particularly well understood in bacteria, where proteins such as CsgA (E. coli) and FapC (Pseudomonas) are assembled as functional bacterial amyloid (FuBA) on the cell surface in a carefully optimized process. Besides a host of helper proteins, FuBA formation is aided by multiple imperfect repeats which stabilize amyloid and streamline the aggregation mechanism to a fast-track assembly dominated by primary nucleation. These repeats, which are found in variable numbers in Pseudomonas, are most likely the structural core of the fibrils, though we still lack experimental data to determine whether the repeats give rise to β-helix structures via stacked β-hairpins (highly likely for CsgA) or more complicated arrangements (possibly the case for FapC). The response of FuBA fibrillation to denaturants suggests that nucleation and elongation involve equal amounts of folding, but protein chaperones preferentially target nucleation for effective inhibition. Smart peptides can be designed based on these imperfect repeats and modified with various flanking sequences to divert aggregation to less stable structures, leading to a reduction in biofilm formation. Small molecules such as EGCG can also divert FuBA to less organized structures, such as partially-folded oligomeric species, with the same detrimental effect on biofilm. Finally, the strong tendency of FuBA to self-assemble can lead to the formation of very regular two-dimensional amyloid films on structured surfaces such as graphite, which strongly implies future use in biosensors or other nanobiomaterials. In summary, the properties of functional amyloid are a much-needed corrective to the unfortunate association of amyloid with neurodegenerative disease and a testimony to nature’s ability to get the best out of a protein fold.     

A Ligand That Targets CUG Trinucleotide Repeats

The development of small molecules that can recognize specific RNA secondary and tertiary structures is currently an important research topic for developing tools to modulate gene expression and therapeutic drugs. Expanded CUG trinucleotide repeats, known as toxic RNA, capture the splicing factor MBNL1 and are causative of neurological disorder myotonic dystrophy type 1 (DM1). Herein, the rational molecular design, synthesis, and binding analysis of 2,9‐diaminoalkyl‐substituted 1,10‐phenanthroline (DAP), which bound to CUG trinucleotide repeats, is described. The results of melting temperature (T_m) analyses, surface plasmon resonance (SPR) assay, and electrospray spray ionization time‐of‐flight (ESI‐TOF) mass spectrometry showed that DAP bound to r(CUG)₉ but not to r(CAG)₉ and r(CGG)₉. The dual luciferase assay clearly indicated DAP bound to the r(CUG)_n repeat by affecting the translation in vitro.     

A novel diagnostic strategy for trisomy 21 using short tandem repeats

Molecular technique with STRs can rapidly diagnose aneuploidy. In order to improve its fidelity, we developed a novel STR-based strategy for fast diagnosis of trisomy 21 and constructed a multimarker diagnostic system according to it. The system is based on nine STRs, of which two were previously known and seven were newly identified from the genomic sequence of the long arm of chromosome 21. They were confirmed to be highly polymorphic in the Chinese population by PCR amplification and gel electrophoresis. The combination of nine STR markers, when applied to DNA from 102 Chinese individuals with normal karyotype, did not yield any false-positives, and clearly revealed three different alleles in DNA from 15 out of 18 trisomy 21 patients. The results show that our new strategy can provide an alternative molecular technique for the rapid detection of aneuploidy.     

Development and validation of a forensic six-dye multiplex assay with 29 STR loci

This paper describes the development and validation of a novel 31-locus, six-dye STR multiplex system, which is designed to meet the needs of the rapidly growing Chinese forensic database. This new assay combines 20 extended-CODIS core loci (D3S1358, D5S818, TPOX, CSF1PO, TH01, vWA, D7S820, D21S11, D8S1179, D18S51, D16S539, D13S317, FGA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045), nine highly polymorphic loci in Chinese Han population (D3S3045, D6S1043, D6S477, D8S1132, D10S1435, D15S659, D19S253, Penta D, and Penta E), and two gender determining markers, amelogenin and Y-Indel, which could amplify DNA from extracts, as well as direct amplification from substrates. To demonstrate the suitability for forensic applications, this system was validated by precision and accuracy evaluation, concordance tests, case sample tests, sensitivity, species specificity, stability, stutter calculation, and DNA mixtures, according to the guidelines described by the Scientific Working Group on DNA Analysis Methods (SWGDAM) and regulations published by the China Ministry of Public Security. The validation results indicate the robustness and reliability of this new system, and it could be a potentially helpful tool for human identification and paternity testing in the Chinese population, as well as facilitating global forensic DNA data sharing.     

Analytical validation of quality control materials for Huntington’s disease examination

The expansion of molecular diagnostics using nucleic acid technologies in clinical and public health practice has increased the need for appropriate reference materials and verified quality-control materials for quality assurance, test validation, proficiency testing and the development of new examination procedures. Good laboratory practice requires the use of reference materials to establish an examination procedure and assess the variability of the results. Reference materials are also required to assess the assay on a daily basis and to normalize results collected among different laboratories. Despite the growing volume, the rapidly increasing number of tests being offered, and the necessary routine use, certified reference materials are often not available. There is a wide range of human genetic bio-assays for which there are no available traceable certified reference materials. Several initiatives have been organized to provide well-characterized quality control specimens (e.g., cell lines) with known DNA mutations for use in diagnostics. Mutations are confirmed with bi-directional DNA sequence analysis, which is considered the reference examination procedure. In the field of personalized medicine, NIST has created and validated Standard Reference Material^® 2399 for fragile X examinations. Herein we describe our characterization of candidate reference materials for Huntington’s disease genetic examination. Bi-directional DNA sequencing confirmed the size of the CAG repeat contained on each allele from patient derived materials. Amplification and capillary electrophoresis of the CAG repeats had an uncertainty ranging from 2.06%CV to 7.83%CV.