A multiplex assay to identify 18 European mammal species from mixtures using the mitochondrial cytochrome b gene

A novel species-specific multiplex to identify 18 common European mammalian species (badger, cat, cow, dog, donkey, fox, goat, guinea pig, harvest mouse, hedgehog, horse, house mouse, human, pig, rabbit, rat, red deer and sheep), many of which are often associated with forensic investigations, has been developed. The assay is based on the mitochondrial cytochrome b gene, which is commonly used in species identification and phylogeny studies. Areas of homology and variation were identified and were used to create universal and species-specific primers. The species-specific primers were designed such that they will only react with the species for which they were designed. Two primer sets were designed for each species making the test self-confirmatory. All primer sets produced the expected results. The multiplex was balanced at template concentration of 40 000 copies (approximately 1.36 pg). Validation was accomplished by analysing the same sample ten times to determine run variation and several samples for each species to determine between-sample variation. Twenty-eight additional mammalian species were reacted with the multiplex. The multiplex provides, for the first time, a definitive method for identification of species in a forensic context.     

基因检测技术在食品物种鉴定中的应用

食品安全关系国计民生,食品物种鉴定是食品安全链的重要环节。基因检测技术的发展使食品物种鉴定变得更加快速、准确、灵敏。本文对近十年来国内外采用基因检测技术进行食品物种鉴定的研究和应用情况进行了总结和分析,包括基因检测技术的特点、主要方法及其在动物源性食品、植物源性食品、高附加值食品和深加工食品分析中的应用以及未来的发展。     

Identification of shrimp species in raw and processed food products by means of a polymerase chain reaction-restriction fragment length polymorphism method targeted to cytochrome b mitochondrial sequences

A novel PCR-RFLP method has been developed for the identification of six commercially relevant penaeid shrimp species in raw and processed food products. The method can be completed within 8 h. To implement the method, PCR amplification with the crustF/crustR primers, targeted to the amplification of a ca. 181 bp region of the cytochrome b (cytb) mitochondrial gene in penaeid shrimps, was coupled to restriction analysis with CviJI, DdeI and NlaIV. The method was also applied successfully to the identification of shrimp species in complex processed foods, including this type of shellfish as an added-value food ingredient. The small size of this molecular target facilitates amplification from fresh, frozen, or precooked samples, where DNA fragmentation may be relevant and fragment size critical. We also report the first cytb mitochondrial sequences described to date for the species Farfantepenaeus notialis, Parapenaeus longirostris and Pleoticus muelleri, and these nearly triplicate current knowledge of reference nucleotide sequences in this mitochondrial region for this group of species. The cytb mitochondrial gene may also be considered as a molecular marker for identification and phylogenetic purposes in penaeid shrimp species.     

Development of a novel multiplex polymerase chain reaction system for forensic individual identification using insertion/deletion polymorphisms

Insertion/deletion (InDel) polymorphisms have been widely used in the fields of population genetics, genetic map constructions, and forensic investigations owing to the advantages of their low mutation rates, widespread distributions in the human genome, and small amplicon sizes. In order to provide more InDels with high discrimination power in Chinese populations, we selected and constructed one novel multiplex PCR‐InDel panel for forensic individual identification. Genetic distributions of these 35 InDels in five reference populations from East Asia showed low genetic differentiations among these populations. Forensic efficiency evaluations of these InDels revealed that these loci could perform well for forensic individual identifications in these reference populations. In the meantime, genetic diversities and forensic parameters of these InDels were further investigated in the studied Kazak group. Mean value of polymorphism information content for 35 InDels was 0.3611. Cumulative power of discrimination of 35 InDels was 0.99999999999999603 in Kazak group. Given these results, the panel is suitable for individual identifications in the studied Kazak and these reference populations.     

A new multiplex for human identification using insertion/deletion polymorphisms

Human identification is usually based on the study of STRs or SNPs depending on the particular characteristics of the investigation. However, other types of genetic variation such as insertion/deletion polymorphisms (indels) have considerable potential in the field of identification, since they can combine the desirable characteristics of both STRs and SNPs. In this study, a set of 38 non‐coding bi‐allelic autosomal indels reported to be polymorphic in African, European, and Asian populations were selected. We developed a sensitive genotyping assay, which is able to characterize all 38 bi‐allelic markers using a single multiplex PCR and detected with standard CE analyzers. Amplicon length was designed to be shorter than 160 bp. Complete profiles were obtained using 0.3 ng of DNA, and full genotyping of degraded samples was possible in cases where standard STR typing had partially failed. A total of 306 individuals from Angola, Mozambique, Portugal, Macau, and Taiwan were studied and population data are presented. All indels were polymorphic in the three population groups studied and the random match probabilities of the set ranged in orders of magnitude from 10^?14 to 10^?15. Therefore, the indel‐plex represents a valuable approach in human identification studies, especially in challenging DNA cases, as a more straightforward and efficient alternative to SNP typing.     

Perceptron ensemble of graph-based positive-unlabeled learning for disease gene identification

Identification of disease genes, using computational methods, is an important issue in biomedical and bioinformatics research. According to observations that diseases with the same or similar phenotype have the same biological characteristics, researchers have tried to identify genes by using machine learning tools. In recent attempts, some semi-supervised learning methods, called positive-unlabeled learning, is used for disease gene identification. In this paper, we present a Perceptron ensemble of graph-based positive-unlabeled learning (PEGPUL) on three types of biological attributes: gene ontologies, protein domains and protein-protein interaction networks. In our method, a reliable set of positive and negative genes are extracted using co-training schema. Then, the similarity graph of genes is built using metric learning by concentrating on multi-rank-walk method to perform inference from labeled genes. At last, a Perceptron ensemble is learned from three weighted classifiers: multilevel support vector machine, k-nearest neighbor and decision tree. The main contributions of this paper are: (i) incorporating the statistical properties of gene data through choosing proper metrics, (ii) statistical evaluation of biological features, and (iii) noise robustness characteristic of PEGPUL via using multilevel schema. In order to assess PEGPUL, we have applied it on 12950 disease genes with 949 positive genes from six class of diseases and 12001 unlabeled genes. Compared with some popular disease gene identification methods, the experimental results show that PEGPUL has reasonable performance.     

A novel ATR-FTIR approach for characterisation and identification of ex situ immobilised species.

We demonstrate a novel method to analyse ex situ prepared protein chips by attenuated total reflection Fourier IR spectroscopy (ATR-FTIR), which circumvents tedious functionalisation steps of internal reflection elements (IREs), and simultaneously allows for complementary measurements by other analytical techniques. This concept is proven by utilising immobilised metal affinity capture (IMAC) chips containing about 10 mum thick films of copolymers coated with nitrilotriacetic acid (NTA) groups, which originally was manufactured for surface enhanced laser desorption ionisation (SELDI) spectrometry. Three immobilisation steps were analysed by ATR-FTIR spectroscopy: 1) NTA complexation with nickel(II) ions 2) binding of two histidine (His)-tagged synthetic peptides of 25 (25-His6) and 48 (48-His6) amino acids to the NTA-groups and 3) attachment of a ligand, mesyl amide, to the surface-bound 48-His6. Despite interference from H(2)O, both amide I and II were well resolved. Utilising peptide adsorption in the thick copolymer matrix yields a high saturation peptide concentration of approximately 100 mg mL(-1) and a dissociation constant of 116+/-11 muM, as determined by a detailed analysis of the Langmuir adsorption isotherm. The mesyl amide ligand was directly seen in the raw ATR-FTIR spectrum with specific peaks in the fingerprint region at 1172 and 1350 cm(-1). Several aspects of the fine structure of the amide I band of the peptide were analysed: influences from secondary structure, amino side chains and competing contamination product. We believe that this approach has great potential as a stand-alone or complementary analytical tool for determination of the chemical composition of functionalised surfaces. We emphasise further that with this approach no chemical treatment of IREs is needed; the chips can be regenerated and reused, and applied in other experimental set-ups.     

A novel approach for protein identification from complex cell proteome using modified peptide mass fingerprinting algorithm

A unique peptide based search algorithm for identification of protein mixture using PMF is proposed. The proposed search algorithm utilizes binary search and heapsort programs to generate frequency chart depicting the unique peptides corresponding to all proteins in a proteome. The use of binary search program significantly reduces the time for frequency chart preparation to ～2 s for a proteome comprising ～23 000 proteins. The algorithm was applied to a three‐protein mixture identification, host cell protein (HCP) analysis, and a simulation‐generated data set. It was found that the algorithm could identify at least one unique peptide of a protein even in the presence of fourfold higher concentration of another protein. In addition, two HCPs that are known to be difficult to remove were missed by MS/MS approach and were exclusively identified using the presented algorithm. Thus, the proposed algorithm when used along with standard proteomic approaches present avenues for enhanced protein identification efficiency, particularly for applications such as HCP analysis in biopharmaceutical research, where identification of low‐abundance proteins are generally not achieved due to dynamic range limitations between the target product and HCPs.     

A modular microfluidic system for deoxyribonucleic acid identification by short tandem repeat analysis

Microfluidic technology has been utilized in the development of a modular system for DNA identification through STR (short tandem repeat) analysis, reducing the total analysis time from the ∼6 h required with conventional approaches to less than 3 h. Results demonstrate the utilization of microfluidic devices for the purification, amplification, separation and detection of 9 loci associated with a commercially-available miniSTR amplification kit commonly used in the forensic community. First, DNA from buccal swabs purified in a microdevice was proven amplifiable for the 9 miniSTR loci via infrared (IR)-mediated PCR (polymerase chain reaction) on a microdevice. Microchip electrophoresis (ME) was then demonstrated as an effective method for the separation and detection of the chip-purified and chip-amplified DNA with results equivalent to those obtained using conventional separation methods on an ABI 310 Genetic Analyzer. The 3-chip system presented here demonstrates development of a modular, microfluidic system for STR analysis, allowing for user-discretion as to how to proceed after each process during the analysis of forensic casework samples.     

A novel method for the synthesis of (Z)-α-selenyl-α,β-unsaturated ketones via acylation of (E)-α-selanylvinylstannanes

The (E)-α-selenylvinylstannanes react with acyl halides in presence of a catalytic amount of Pd(PPh₃)₄ to give the corresponding (Z)-α-selenyl-α,β-unsaturated ketones in good yield.     

A Novel Method for the Synthesis of α,β‐Unsaturated Amides Mediated by Samarium Diiodide

Promoted by Samarium diiodide (SmI₂), α,β‐unsaturated amides were formed from nitrogen anions (formed in situ by the reduction of nitro compounds) and α,β‐unsaturated esters. This reaction contrasts with the conjugate addition between amines and α,β‐unsaturated esters promoted by samarium triiodide (SmI₃) and provides an alternative attractive way to obtain α,β‐unsaturated amides using SmI₂.     

A thermodynamic criterion for the identification of the functional group of aliphatic compounds by gas chromatography

Summary A thermodynamic criterion, Q, is suggested which permits to estimate the difference in the functional group energy of interactions for two different stationary phases. The linear dependence of Q on the homolog number m of any series R_m X can be used as the thermodynamic criterion for the identification of substances by GC analysis.Enlarged text of the paper presented at the Fourth Danube Symposium on Chromatography, Bratislava, Czechoslovakia, September 1983.     

β-Caryophyllene: A Therapeutic Alternative for Intestinal Barrier Dysfunction Caused by Obesity

Obesity is an excessive accumulation of fat that exacerbates the metabolic and inflammatory processes. Studies associate these processes with conditions and dysregulation in the intestinal tract, increased concentrations of lipopolysaccharides (LPSs) in the blood, differences in the abundance of intestinal microbiota, and the production of secondary metabolites such as short-chain fatty acids. β-Caryophyllene (BCP) is a natural sesquiterpene with anti-inflammatory properties and with the potential purpose of fighting metabolic diseases. A diet-induced obesity model was performed in 16-week-old C57BL/6 mice administered with BCP [50 mg/kg]. A reduction in the expression of Claudin-1 was observed in the group with a high-fat diet (HFD), which was caused by the administration of BCP; besides BCP, the phyla Akkermansia and Bacteroidetes decreased between the groups with a standard diet (STD) vs. HFD. Nevertheless, the use of BCP in the STD increased the expression of these phyla with respect to fatty acids; a similar effect was observed, in the HFD group that had a decreasing concentration that was restored with the use of BCP. The levels of endotoxemia and serum leptin increased in the HFD group, while in the HFD + BCP group, similar values were found to those of the STD group, attributing the ability to reduce these in conditions of obesity.     

Scanning the beta-globin gene for mutations in large populations by denaturing capillary and gel electrophoresis

Separation of mutant from nonmutant DNA sequences of 100 bp may be accomplished by using defined denaturing conditions of chemical denaturant and/or elevated temperature during electrophoresis on either polyacrylamide slab gels (denaturing gradient gel electrophoresis, DGGE) or capillary gels (constant denaturant capillary electrophoresis, CDCE). In analysis of mutant directly from a polymerase chain reaction (PCR) product mixture, both have detection sensitivities of approximately 1%. CDCE that facilitates an intermediate mutant enrichment step permits detection of mutants at fractions as low as 2 x 10(-6). Here we report the successful application of both approaches to scan for mutations of the human beta-globin gene (HBB) in two human population samples of approximately 5000 persons in the HBB. Using DGGE, the coding region and flanking intronic splice sites of HBB were scanned in a population of 4949 Han Chinese individuals in pool sizes of 48 individual DNA samples. Four point mutations ranging in mutant frequency from 0.5 to 0.0002 were identified. Using CDCE with a mutant enrichment step, these same sequences were scanned in a population of 5028, predominantly African-American juveniles (<9 years) as a single pooled DNA sample. Three point mutations were identified ranging in mutant frequency from 0.13 to 0.0005. This study shows that both the DGGE/small pool and the CDCE/large pool approaches offer the means to define the fine structure map of genetic variation in large population samples, and with appropriately engineered facilities to provide high throughput, should be useful in pangenomic scans to discover genes carrying casual mutations for common diseases.     

A facile and efficient one‐step strategy for the preparation of β‐cyclodextrin monoliths

A novel, facile, and efficient one‐step copolymerization strategy was developed for the preparation of β‐cyclodextrin (β‐CD) methacrylate monolithic columns using click chemistry. The novel mono‐(1H‐1,2,3‐triazol‐4‐ylmethyl)‐2‐methylacryl‐β‐CD monomer was synthesized by a click reaction between propargyl methacrylate and mono‐6‐azido‐β‐CD, and then monolithic columns were prepared through a one‐step in situ copolymerization of the mono‐(1H‐1,2,3‐triazol‐4‐ylmethyl)‐2‐methylacryl‐β‐CD monomer and ethylene dimethacrylate. The physicochemical properties and column performance of the fabricated monolithic columns were characterized by elemental analysis, SEM, and micro‐HPLC. Satisfactory column permeability, efficiency, and separation performance were obtained for the optimized poly(mono‐(1H‐1,2,3‐triazol‐4‐ylmethyl)‐2‐methylacryl‐β‐CD‐co‐ethylene dimethacrylate) monolithic columns. Additionally, typical hydrophilic interaction chromatography retention behavior was observed on the monoliths at high acetonitrile content in the mobile phase. Although the enantioselectivity of our monolithic columns did not meet the level of other reported β‐CD monolithic columns, this one‐step strategy based on click chemistry still provides an interesting and effective model as it offers the possibility to easily prepare related novel CD methacrylate monoliths through a one‐step copolymerization strategy.     

A palladium-catalyzed route for α-alkylation of ketones by primary alcohols

Ketones react with primary alcohols in dioxane at 100 °C in the presence of a catalytic amount of Pd/C and KOH along with 1-decene as a sacrificial hydrogen acceptor to give the corresponding coupled ketones in moderate to good yields. The catalytic pathway seems to be proceeded via a sequence involving initial oxidation of primary alcohols to aldehydes, cross aldol condensation, and regioselective reduction.     

A novel strategy to prepare LDH networks loaded carbon structure by C-MEMS techniques for glucose detection

NiAl-layered double hydroxide (NiAl-LDH) networks loaded carbon microcylinder (CMC) hybrid was synthesized for the first time using typical carbon based microelectromechanical systems (C-MEMS) techniques combined with in situ growth progress. The incorporation of NiAl-LDH on C-MEMS structures via a simple pyrolysis of modified photoresist was investigated. With proper control of parameters in lithography and hydrothermal processes, the NiAl-LDH/CMC composites with suitable morphology were fabricated. When the composites applied as new catalytic material for glucose detection, this simple sensor showed satisfying electrocatalytic properties towards glucose oxidation owing to its unique structure and excellent electric conductivity. It is also worth pointing out that this novel fabrication process can equip carbon microfeatures with various nanostructures, and have wide potential applications in scaling up carbon based nanocomposites.     

A novel silk‐based segmented block copolymer containing GlyAlaGlyAla β‐sheets templated by phenoxathiin

A novel segmented block copolymer, containing polyethylene glycol segment and GlyAlaGlyAla sequence derived from B. mori silk, has been prepared as a model for silk‐based materials using both solution and interfacial techniques. Inherent viscosity, size exclusion chromatography, and light‐scattering measurements gave molecular weight between M_w 34,000–39,000. Evidence for phase separation was provided by differential scanning calorimetry, which gave two T_g's at −57 °C and 111 °C, and transmission electron microscopy, which showed a morphology in which the peptide domain, estimated to be about 20–50 nm, was dispersed in the continuous polyether phase. Solid‐state FTIR spectroscopic results showed that the polymer contained both parallel and antiparallel β‐sheet stacks, and that the solution‐polymerized material has the higher β‐sheet content. This was further confirmed by ¹³C NMR, which gave about 80% total β‐sheet content for the solution‐polymerized product and about 40% for the polymer obtained by interfacial polymerization. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 352–366, 2000     

Monoaryloxo ytterbium(III) chlorides supported by β‐diketiminato ligands as novel initiators for the living ring‐opening polymerization of ε‐caprolactone

Ring‐opening polymerization of ε‐caprolactone (ε‐CL) was carried out using β‐diketiminato‐supported monoaryloxo ytterbium chlorides L¹Yb(OAr)Cl(THF) (1) [L¹ = N,N′‐bis(2,6‐dimethylphenyl)‐2,4‐pentanediiminato, OAr = 2,6‐di‐tert‐butylphenoxo‐], and L²Yb(OAr′)Cl(THF) (2) [L² = N,N′‐bis(2,6‐diisopropylphenyl)‐2,4‐pentanediiminato, OAr′ = 2,6‐di‐tert‐butyl‐4‐methylphenoxo‐], respectively, as single‐component initiator. The influence of reaction conditions, such as polymerization temperature, polymerization time, initiator, and initiator concentration, on the monomer conversion, molecular weight, and molecular weight distribution of the resulting polymers was investigated. Complex 1 was well characterized and its crystal structure was determined. Some features and kinetic behaviors of the CL polymerization initiated by these two complexes were studied. The polymerization rate is first order with respect to monomer. The M_n of the polymer increases linearly with the increase of the polymer yield, while polydispersity remained narrow and unchanged throughout the polymerization in a broad range of temperatures from 0 to 50 °C. The results indicated that the present system has a “living character”. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 1147–1152, 2006     

A validated HPLC‐PDA method for identification and quantification of two bioactive alkaloids,ephedrine and cryptolepine,in different Sida species

A simple, rapid, accurate and reproducible reverse‐phase HPLC method has been developed for the identification and quantification of two alkaloids ephedrine and cryptolepine in different extracts of Sida species using photodiode array detection. Baseline separation of the two alkaloids was achieved on a Waters RP‐18 X‐terra column (250 × 4.6 mm, 5 µm) using a solvent system consisting of a mixture of water containing 0.1% Trifluoroacetic acid (TFA) and acetonitrile in a gradient elution mode with detection at 210 and 280 nm for ephedrine and cryptolepine, respectively. The calibration curves were linear in a concentration range of 10–250 µg/mL for both the alkaloids with correlation coefficient values >0.99. The limits of detection and quantification for ephedrine and cryptolepine were 5 and 10 µg/mL and 2.5 and 5 µg/mL, respectively. Relative standard deviation values for intra‐day and inter‐day precision were 1.22 and 1.04% for ephedrine and 1.71 and 2.06% for cryptolepine, respectively. Analytical recovery ranged from 92.46 to 103.95%. The developed HPLC method was applied to identify and quantify ephedrine and cryptolepine in different extracts of Sida species. Copyright © 2013 John Wiley & Sons, Ltd.