Medium-high resolution electrochemical genotyping of HLA-DQ2/DQ8 for detection of predisposition to coeliac disease

Coeliac disease is a small intestinal disorder, induced by ingestion of gluten in genetically predisposed individuals. Coeliac disease has been strongly linked to human leukocyte antigens (HLA) located on chromosome 6, with almost 100 % of coeliac disease sufferers carrying either a HLA-DQ2 or HLA-DQ8 heterodimer, with the majority carrying HLA-DQ2 encoded by the DQA1*05:01/05:05, DQB1*02:01/02:02 alleles, whereas the remaining carry the HLA-DQ8 encoded by the DQA1*03:01, DQB1*03:02 alleles. In this work, we present the development of a multiplex electrochemical genosensor array of 36 electrodes, housed within a dedicated microfluidic platform and using a total of 10 sequence-specific probes for rapid medium-high resolution HLA-DQ2/DQ8 genotyping. An evaluation of the selectivity of the designed probes was carried out with the target sequences and 44 potentially interfering alleles, including single base mismatch differentiations; good selectivity was demonstrated. The performance of the electrochemical genosensor array was validated, analyzing real human samples for the presence of HLA-DQ2/DQ8 alleles, and compared with those obtained using laboratory-based HLA typing, and an excellent correlation was obtained.

Gold nanoparticle fluorescent molecular beacon for low-resolution DQ2 gene HLA typing

Coeliac disease is an inflammation of the small intestine triggered by gluten ingestion. We present a fluorescent genosensor, exploiting molecular-beacon-functionalized gold nanoparticles, for the identification of human leukocyte antigen (HLA) DQ2 gene, a key genetic factor in coeliac disease. Optimization of sensor performance was achieved by tuning the composition of the oligonucleotide monolayer immobilized on the gold nanoparticle and the molecular beacon design. Co-immobilization of the molecular beacon with a spacing oligonucleotide (thiolated ten-thymine oligonucleotide) in the presence of ten-adenine oligonucleotides resulted in a significant increase of the sensor response owing to improved spacing of the molecular beacons and extension of the distance from the nanoparticle surface, which renders them more available for recognition. Further increase in the response (approximately 40%) was shown to be achievable when the recognition sequence of the molecular beacon was incorporated in the stem. Improvement of the specificity of the molecular beacons was also achieved by the incorporation within their recognition sequence of a one-base mismatch. Finally, gold nanoparticles functionalized with two molecular beacons targeting the DQA1*05* and DQB1*02* alleles allowed the low-resolution typing of the DQ2 gene at the nanomolar level.     

Dynamic characterization of HLA-B*44 Alleles: A comparative molecular dynamics simulation study

Human Leukocyte Antigens (HLA) are highly polymorphic proteins that play a key role in the immune system. HLA molecule is present on the cell membrane of antigen-presenting cells of the immune system and presents short peptides, originating from the proteins of invading pathogens or self-proteins, to the T-cell Receptor (TCR) molecule of the T-cells. In this study, peptide-binding characteristics of HLA-B*44:02, 44:03, 44:05 alleles bound to three nonameric peptides were studied using molecular dynamics simulations. Polymorphisms among these alleles (Asp116Tyr and Asp156Leu) result in major differences in the allele characteristics. While HLA-B*44:02 (Asp116, Asp156) and HLA-B*44:03 (Asp116, Leu156) depend on tapasin for efficient peptide loading, HLA-B*44:05 (Tyr116, Asp156) is tapasin independent. On the other hand, HLA-B*44:02 and HLA-B*44:03 mismatch is closely related to transplant rejection and acute-graft-versus-host disease. In order to understand the dynamic characteristics, the simulation trajectories were analyzed by applying Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF) calculations and hydrogen bonding analysis. Binding dynamics of the three HLA-B*44 alleles and peptide sequences are comparatively discussed. In general, peptide binding stability is found to depend on the peptide rather than the allele type for HLA-B*44 alleles.     

Actinic Prurigo in Singaporean Chinese: A Positive Association with HLA‐DRB1*03:01

Studies have reported the association of human leukocyte antigen (HLA) genes with susceptibility to develop actinic prurigo (AP) in Caucasians, but there were no studies in Asian populations, including the Chinese. Our study was performed to determine if AP is associated with susceptibility or protective HLA alleles or haplotypes in Singaporean Chinese. All Chinese patients diagnosed with AP at National Skin Center, Singapore, from January 2002 to April 2015 were invited to participate in the study. Clinical data and phototesting results were collated, and HLA typing was performed. Among 14 patients included, 11 were male and the mean age was 49.6 (37.9–61.3) years. All patients did not have a family history of AP and none had mucosal involvement, as such these clinical features differed from Caucasian AP patients. The frequency of DRB1*03:01 in AP patients was significantly higher compared to healthy controls (43% vs 16%, P = 0.022, odds ratio (OR) 3.89). Concurrently, the frequency of HLA‐B*58:01‐DRB1*03:01 haplotype was also significantly increased (25% vs 7%, P = 0.004, OR 4.23). In conclusion, HLA‐DRB1*03:01 was associated with AP in Singaporean Chinese patients. This novel allelic association may possibly be utilized as a biological marker to aid in the diagnosis of AP in Chinese patients.     

A simple and rapid method for HLA-DQA1 genotyping by polymerase chain reaction-single strand conformation polymorphism and restriction enzyme cleavage analysis.

A simple and rapid method for identification of alleles at the human leucocyte antigen (HLA)-DQA1 locus is described. The polymorphic second exon of the HLA-DQA1 locus was amplified by the polymerase chain reaction (PCR) method. The amplified DNA was analyzed by single-strand conformation polymorphism (SSCP) and restriction enzyme cleavage assay. Using this method, the eight known DQA1 alleles could be distinguished from each other. This paper suggests that the method can be used for quick genotyping of DQA1 alleles, but detecting point mutations at various positions in a fragment as well as new HLA-DQA1 genotypes should also be possible.     

阴极铜化学标准样品的研制

经成分设计、原料选取、熔铸加工、均匀性检验等研制了阴极铜化学标准样品。以高纯铜为主原料,加入Si,Zn,S,Se等18种杂质元素制备而成,各定值元素含量呈梯度上升分布。经检验该标准样品成分均匀,稳定性好,18种杂质元素的定值结果分别为Se 0.000 02%~0.000 87%,Te 0.000 03%~0.001 1%,Bi 0.000 02%~0.001 2%,Cr 0.000 02%~0.003 2%,Mn 0.000 03%~0.002 7%,Sb 0.000 02%~0.003 1%,Cd 0.000 01%~0.003 0%,As0.000 01%~0.003 8%,P 0.000 05%~0.005 6%,Pb 0.000 03%~0.004 4%,S 0.000 15%~0.008 2%,Sn 0.000 01%~0.002 6%,Ni0.000 09%~0.006 0%,Fe 0.000 16%~0.005 4%,Si 0.000 15%~0.003 4%,Zn 0.000 04%~0.005 2%,Co 0.000 01%~0.003 5%,Ag 0.000 07%~0.007 2之间。定值结果的扩展不确定度为0.000 01%~0.000 3%(k=2)。研制的阴极铜化学标准样品已被批准为国家级标准样品,标准编号为GSB 04–2554–2010。该标准样品成分设计合理、涵盖范围广,可用于阴极铜及部分铜合金的分析检测。     

Electrophoretic human leukocyte antigen HLA-DQA1 DNA typing after polymerase chain reaction amplification.

An electrophoretic method (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) is described which permits the identification of human leukocyte antigen HLA-DQA1 types and subtypes without using allele-specific oligonucleotide probes and dot-blot methodology. The procedure can be used in miniaturized gels in combination with automated electrophoretic systems. The PhastSystem is particularly recommended since temperature control is essential. HLA-DQA1*01 and DQA1*0301 can be distinguished in homoduplexes and DQA1*01 subtypes, DQA1*0201 and DQA1*0401 in heteroduplexes (in only 5 h including DNA extraction and PCR amplification). Additional variations to those recognized using commercially available dot-blot methods can be provided since this procedure permits the identification of single base-pair substitutions. In addition, this method is faster and less expensive than commercial methods.     

稀土—4—（2—吡啶偶氮）间苯二酚螯合物的高效液相色谱分离和测定

本文讨论了反相离子对液相色谱法分离和检测稀土-4-(2-吡啶偶氮)间苯二酚螯合物的各种条件,在12 min内完成了9种稀土螫合物的分离,校正曲线的线性范围是(ppm):La(0.01～3.20),Ce(0.03～2.8),Pr(0.06～3.5),Nd(0.05～3.8),Sm(0.01～3.0),Eu(0.05～3.4),Tb(0.02～3.0),Ho(0.01～3.4),Er(0.06～4.0).变异系数小于1.2％.     

Conjugated Oligothiophene Derivatives Based on Bithiophene with Unsaturated Bonds as Building Blocks for Solution‐Processed Bulk Heterojunction Organic Solar Cells

A new building block ATVTA that uses stiff carbon–carbon triple bonds (A) on 1,2‐di(2‐thienyl)‐ethene (TVT) has been developed. Oligothiophene derivatives S‐01 with a TVT unit, S‐02 with a 5,5′‐diethynyl‐2,2′‐dithienyl (AT2) unit and S‐03 with ATVTA were synthesized to compare their effects in a systematic study. Due to the better π‐conjugation extension of the TVT unit, S‐01 exhibits the most red‐shifted absorption profile among them, whereas S‐02 possesses the deepest HOMO level. While the HOMO level of S‐03 is down‐shifted by 0.02 eV relative to that of S‐01 , the alkyne linkages can effectively down‐shift the HOMO level. By replacing the terminal units of S‐03 with stronger electron acceptors, S‐04 and S‐05 exhibited broader absorption profiles and lower HOMO levels than those of S‐03 . Organic solar cells based on these molecules were fabricated and an S‐03 :PC₆₀BM (1:1, w/w) based device afforded the highest V_oc value of 0.96 V and a power conversion efficiency (PCE) of 2.19 %.     

DNA damage promotes mistyping in the allele specific oligonucleotide probing analysis of forensic samples

Five polymerase chain reaction (PCR) products which could not be reliably typed by allele-specific oligonucleotide (ASO) probing at the human leukocyte antigen (HLA) DQA1 locus were analyzed by polyacrylamide gel electrophoresis and direct sequencing. The first method revealed the preferential amplification of only one of the two alleles in two cases. Direct sequencing of PCR products allowed unambiguous genetic typing but a high number of artifacts was observed. Several of these artifacts occurred in the sequences recognized by the ASOs. This finding provides an explanation for the mistyping in the ASO probing procedure because Taq polymerase errors both created new genetic specificities and eliminated site-specific polymorphisms. Reversed-phase HPLC-MS of the five forensic templates showed a high degree of DNA damage. These data together indicate that the risk of mistyping when using the ASO probing procedure cannot be neglected in the forensic analysis of damaged DNA samples.     

Application of silver staining to the rapid typing of the polymorphism of HLA-DQ alleles by enzymatic amplification and allele-specific restriction fragment length polymorphism.

A rapid and highly sensitive silver staining method, originally developed for the detection of proteins, was slightly modified to detect nucleic acids in polyacrylamide gels. The second exons of the histocompatibility antigen HLA-DQA 1 and DQB 1 genes were selectively amplified from genomic DNA by the polymerase chain reaction (PCR). Digestion of the PCR products by endonucleases, followed by their size-separation on polyacrylamide gels and visualization by silver staining, allowed us to define the HLA-DQ alleles of the genomic DNA. The intensity of staining of digested PCR-amplified DNA is linear from at least 8 to 18 ng for fragments of lengths ranging from approximately 40 to 200 bp. Thus, silver staining in combination with PCR and allele-specific restriction fragment length polymorphism provides a simple, safe, and rapid method for accurate definition of HLA-DQ alleles at the nucleotide level in the clinical typing laboratory.     

Genetic polymorphisms of the A and B subunits of human coagulation factor XIII in mainland Italy and Sardinia: description of a new FXIIIA variant allele.

The distribution of the two alleles of FXIIIA and the three alleles of FXIIIB were studied in populations from mainland Italy and from Sardinia. The frequencies of the FXIIIA*2 allele were 0.266 and 0.265. The frequencies of FXIIIB*1 were 0.787 and 0.765; of B*2, 0.070 and 0.094; of B*3, 0.143 and 0.141. A new cathodal FXIIIA allele (A*7) was described in the Rome sample. No significant difference in the distribution of allele frequencies for either system was found between the two populations studied. For typing both markers, good results were also obtained by using whole blood instead of plasma.     

Computational investigation of peptide binding stabilities of HLA-B*27 and HLA-B*44 alleles

Major Histocompatibility Complex (MHC) is a cell surface glycoprotein that binds to foreign antigens and presents them to T lymphocyte cells on the surface of Antigen Presenting Cells (APCs) for appropriate immune recognition. Recently, studies focusing on peptide-based vaccine design have allowed a better understanding of peptide immunogenicity mechanisms, which is defined as the ability of a peptide to stimulate CTL-mediated immune response. Peptide immunogenicity is also known to be related to the stability of peptide-loaded MHC (pMHC) complex. In this study, ENCoM server was used for structure-based estimation of the impact of single point mutations on pMHC complex stabilities. For this purpose, two human MHC molecules from the HLA-B*27 group (HLA-B*27:05 and HLA-B*27:09) in complex with four different peptides (GRFAAAIAK, RRKWRRWHL, RRRWRRLTV and IRAAPPPLF) and three HLA-B*44 molecules (HLA-B*44:02, HLA-B*44:03 and HLA-B*44:05) in complex with two different peptides (EEYLQAFTY and EEYLKAWTF) were analyzed. We found that the stability of pMHC complexes is dependent on both peptide sequence and MHC allele. Furthermore, we demonstrate that allele-specific peptide-binding preferences can be accurately revealed using structure-based computational methods predicting the effect of mutations on protein stability.     

Standardized genotyping of HLA STR by CE as surrogate for HLA class I and II markers and for identification of HLA identical siblings

Linkage disequilibria (LD) between alleles and haplotypes of human leucocyte antigen, locus A (HLA) and STR loci located in the human major histocompatibility complex were analyzed in order to investigate whether or not HLA alleles and haplotypes are predictable by alleles or haplotypes of HLA STRs. Standardized genotyping of eight STR loci (D6S2972, D6S2906, D6S2691, D6S2678, D6S2792, D6S2789, D6S273, and DQIV) was performed by CE on 600 individuals from 150 Austrian Caucasoid families with known HLA‐A,‐B,‐C and –DRB1 typing. From those, 576 full haplotypes of four HLA and eight STR loci were obtained. Haplotypes of two flanking STRs predicted HLA alleles and two‐locus HLA haplotypes better than single STR alleles, except HLA‐DRB1 alleles (92% were in LD with DQIV alleles only). A percentage of 65–86% of three and four‐locus HLA haplotypes were in LD with haplotypes of three, four, and eight of their flanking STR loci including numerous clear‐cut predictions (20–61%). All eight and a set of the four most informative STR loci D6S2972, D6S2678, D6S2792, and DQIV could identify all HLA identical and nonidentical siblings in 138 pairs of siblings. The results of this proof of concept study in Austrian Caucasoids show, that HLA STRs can aid the definition of HLA‐A,‐B,‐C,‐DRB1 haplotypes and the selection of sibling donors for stem cell transplantation.     

Orosomucoid 1 and orosomucoid 2 types in the Taiwanese and Japanese: evidence for five new orosomucoid variants

The genetic polymorphisms of orosomucoid, ORM1 and ORM2, were analyzed by isoelectric focusing on polyacrylamide gels and subsequent immunoprinting. Sera from 600 unrelated individuals in Taiwan and Japan were examined. Five new alleles, designated ORM1*7, ORM1*8, ORM1*4.2, ORM2*8 and ORM2*10, were observed together with common and rare alleles that have been found in the Japanese and the Filipinos. As compared with the Japanese, the Taiwanese have a higher frequency of ORM1*1, and a significantly lower frequency of ORM1*2.1.     

Fine specificity of antigen binding to two class I major histocompatibility proteins (B*2705 and B*2703) differing in a single amino acid residue

Starting from the X-ray structure of a class I majorhistocompatibility complex (MHC)-encoded protein (HLA-B*2705), a naturallypresented self-nonapeptide and two synthetic analogues were simulated in thebinding groove of two human leukocyte antigen (HLA) alleles (B*2703 andB*2705) differing in a single amino acid residue. After 200 ps moleculardynamics simulations of the solvated HLA–peptide pairs, some molecularproperties of the complexes (distances between ligand and protein center ofmasses, atomic fluctuations, buried versus accessible surface areas,hydrogen-bond frequencies) allow a clear discrimination of potent from weakMHC binders. The binding specificity of the three nonapeptides for the twoHLA alleles could be explained by the disruption of one hydrogen-bondingnetwork in the binding pocket of the HLA-B*2705 protein where the singlemutation occurs. Rearrangements of interactions in the B pocket, which bindsthe side chain of peptidic residue 2, and a weakening of interactionsinvolving the C-terminal end of the peptide also took place. In addition,extension of the peptide backbone using a -Ala analogue did notabolish binding to any of the two HLA-B27 subtypes, but increased theselectivity for B*2703, as expected from the larger peptide binding groovein this subtype. A better understanding of the atomic details involved inpeptide selection by closely related HLA alleles is of crucial importancefor unraveling the molecular features linking particular HLA alleles toautoimmune diseases, and for the identification of antigenic peptidestriggering such pathologies.     

Effects of solvent casted poly (lactic acid)/poly(ethylene glycol)/paraben derivative triazine films on antibacterial performance and cytotoxicity

A series of poly(lactic acid) (PLA) films that including fully paraben substituted triazine derivatives having anti-bacterial properties have been prepared by utilizing the solvent-casting method. PLA as biodegradable polymer, poly(ethylene glycol) (PEG) as a plasticizing agent and s-triazine molecules (TA01, TA02, TA03, TA04, and TA05) behaving as an anti-bacterial component have been utilized in the experiments. The influence of TA compounds on the antibacterial performance of PLA/PEG films was investigated for the first time against Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus aureus (S. aureus) bacteria via the contact active method. TA01-03-05 incorporated PLA/PEG films gave the best results against E.coli bacteria and log10 reductions of these films were 0.78, 0.64, and 0.65 respectively. The effect of TA compounds on the cell viability was investigated against cancer and non-cancerous cell lines using an MTS assay. The results showed that TA compounds had a positive effect on cell growth in non-cancerous cells, while they had a negative effect on cell growth in cancer cells. Furthermore, the addition of TA considerably increased the decomposition temperatures from 349° to 361° and char yield from 0.65 for PLA/PEG film to 2.3 for PLA/PEG/TA05. All of the films had good transparency and low opacity which was 7.2 for pure PLA used for control and the maximum opacity value was 11.2 observed for PLA/PEG/01. TA03 and TA04 caused a decrement of water vapor permission when compared to PLA/PEG films from 1439 to 749 and 664. It was also observed that pure PLA/PEG film lost weight rapidly over time during degradation tests. On the other hand, weight loss wasn't observed in PLA/PEG/TA films. This study focused on demonstrating the use of our new, flexible PLA/PEG derivatives in food and medical packaging.     

磺酸基共聚凝胶在混合有机溶剂中的体积相变

2-丙烯酰胺基-2-甲基丙磺酸(AMPS)与甲基丙烯酸-2-羟基丙酯(HPM)在乙二醇/水(1:1,质量比)中70℃下进行共聚,AMPS/HPM(8:2,摩尔比)为该体系的恒比共聚点.在此组成加入交联剂N,N'-亚甲基双丙烯酰胺2%、3%和5%(摩尔分数)制备了凝胶试样GO2、GO3、GO5.它们在DMSO/THF混合溶剂中THF达55%～60%(体积百分数)时发生体积相变;在乙醇/THF混合溶剂中GO3的体积随THF的加入连续缩小,但不出现体积相变.此现象可用高分子链溶剂化层的变化以及低极性介质中离子对之间的偶极-偶极相互作用来说明.     

化学修饰的吸附树脂对2,4,6-三氯苯酚的吸附研究

合成了用邻羧基苯甲酰基或苯甲酰基修饰的新型聚苯乙烯-二乙烯苯吸附树脂ZH-01, ZH-02和ZH-03, 利用瓶点法研究了它们和Amberlite XAD-4对288～318 K下水溶液中2,4,6-三氯苯酚的静态吸附和静态脱附特征以证实吸附质与吸附剂之间存在化学吸附, 并利用半经验分子轨道法(AM1)计算的几种吸附剂和2,4,6-三氯苯酚的前线轨道近似能级进行了解释. 结果表明: 经邻羧基苯甲酰基或苯甲酰基化学修饰后的树脂ZH-01, ZH-02和ZH-03对水溶液中2,4,6-三氯苯酚的吸附过程在合适温度时会使酚羟基和吸附剂表面的羰基发生作用, 对吸附剂进行适当的化学修饰后, 对2,4,6-三氯苯酚的穿透吸附容量均为Amberlite XAD-4树脂的150%, 饱和吸附容量是Amberlite XAD-4树脂的114％～128％.     

The ultrafast dynamics and nonlinear optical properties of tribranched styryl derivatives based on 1,3,5-triazine

By using the femtosecond laser spectroscopic techniques, we have studied the ultrafast response and the nonlinear optical properties of three molecules with donor-acceptor structure (denoted as T01, T02, and T03). Two-photon absorption (2PA) cross sections measured by the open aperture Z-scan technique were determined to be 77, 90, and 410 GM for T01, T02, and T03, respectively. The relaxation dynamics of the excited states were measured by two-color femtosecond pump-probe and time-resolved photoluminescence (PL) experiments. By changing the solvent from chloroform (CHCl3) to dimethyl sulfoxide (DMSO), the transient dynamics was found changed significantly and the decay time of PL emission decreased dramatically because DMSO with large dipole moment accelerates the cross-transfer process and the nonradiative process in the molecules.