Detection and characterization of recombinant DNA expressing <Emphasis Type="Italic">vip3A</Emphasis>-type insecticidal gene in GMOs—standard single,multiplex and construct-specific PCR assays

Vegetative insecticidal protein (Vip), a unique class of insecticidal protein, is now part of transgenic plants for conferring resistance against lepidopteron pests. In order to address the imminent regulatory need for detection and labeling of vip3A carrying genetically modified (GM) products, we have developed a standard single PCR and a multiplex PCR assay. As far as we are aware, this is the first report on PCR-based detection of a vip3A-type gene (vip-s) in transgenic cotton and tobacco. Our assay involves amplification of a 284-bp region of the vip-s gene. This assay can possibly detect as many as 20 natural wild-type isolates bearing a vip3A-like gene and two synthetic genes of vip3A in transgenic plants. The limit of detection as established by our assay for GM trait (vip-s) is 0.1%. Spiking with nontarget DNA originating from diverse plant sources had no inhibitory effect on vip-s detection. Since autoclaving of vip-s bearing GM leaf samples showed no deterioration/interference in detection efficacy, the assay seems to be suitable for processed food products as well. The vip-s amplicon identity was reconfirmed by restriction endonuclease assay. The primer set for vip-s was equally effective in a multiplex PCR assay format (duplex, triplex and quadruplex), used in conjunction with the primer sets for the npt-II selectable marker gene, Cauliflower mosaic virus 35S promoter and nopaline synthetase terminator, enabling concurrent detection of the transgene, regulatory sequences and marker gene. Further, the entire transgene construct was amplified using the forward primer of the promoter and the reverse primer of the terminator. The resultant amplicon served as a template for nested PCR to confirm the construct integrity. The method is suitable for screening any vip3A-carrying GM plant and food. The availability of a reliable PCR assay method prior to commercial release of vip3A-based transgenic crops and food would facilitate rapid and efficient regulatory compliance. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. An application for an Indian patent (1891/DEL2006/17.08.07) comprising a substantive part of this study has been filed. ITRC communication no. 2516.     

The synthesis of thiaolivacine and related compounds

1,5-Dimethylbenzothieno[2,3-g]isoquinoline (thiaolivacine) has been prepared from the nitro-vinyl derivative of 4-methyl-3-dibenzothiophenecarboxaldehyde. Using the same aldehyde, 4-des-methylisothiaolivacine was prepared by formation of the Schiff's base with aminoacetaldehyde diethyl acetal followed by cyclization. Similar methods yielded the pyrido-N-isomer, 1-des-methylthiaolivacine, from 4-methyl-2-dibenzothiophenecarboxaldehyde. The thiaolivacine parent unsubstituted ring system, benzothieno[2,3-g]isoquinoline, was prepared from 2-dibenzothio-pheneearboxaldehyde by the aminoacetaldehyde approach, as was the corresponding oxygen analog, benzofuro[2,3-g]isoquinoline, from 2-dibenzofurancarboxaldehyde. The 100 MHz spectra of these fused isoquinolines are recorded and correlated.     

Luminescent bacteria-based sensing method for methylmercury specific determination

A bacterial biosensor method for the selective determination of a bioavailable organomercurial compound, methylmercury, is presented. A recombinant luminescent whole-cell bacterial strain responding to total mercury content in samples was used. The bacterial cells were freeze-dried and used as robust, reagent-like compounds, without batch-to-batch variations. In this bacteria-based sensing method, luciferase is used as a reporter, which requires no substrate additions, therefore allowing homogenous, real-time monitoring of the reporter gene expression. A noninducible, constitutively light-producing control bacterial strain was included in parallel for determining the overall cytotoxicity of the samples. The specificity of the total mercury sensor Escherichia coli MC1061 (pmerRBlux) bacterial resistance system toward methylmercury is due to a coexpressed specific enzyme, organomercurial lyase. This enzyme mediates the cleavage of the carbon–mercury bond of methylmercury to yield mercury ions, which induce the reporter genes and produce a self-luminescent cell. The selective analysis of methylmercury with the total mercury strain is achieved by specifically chelating the inorganic mercury species from the sample using an optimized concentration of EDTA as a chelating agent. After the treatment with the chelating agent, a cross-reactivity of 0.2% with ionic mercury was observed at nonphysiological ionic mercury concentrations (100 nM). The assay was optimized to be performed in 3 h but results can already be read after 1 h incubation. Total mercury strain E. coli MC1061 (pmerRBlux) has been shown to be highly sensitive and capable of determining methylmercury at a subnanomolar level in optimized assay conditions with a very high dynamic range of two decades. The limit of detection of 75 ng/l (300 pM) allows measurement of methylmercury even from natural samples.     

Development of bacteria-based bioassays for arsenic detection in natural waters

Arsenic contamination of natural waters is a worldwide concern, as the drinking water supplies for large populations can have high concentrations of arsenic. Traditional techniques to detect arsenic in natural water samples can be costly and time-consuming; therefore, robust and inexpensive methods to detect arsenic in water are highly desirable. Additionally, methods for detecting arsenic in the field have been greatly sought after. This article focuses on the use of bacteria-based assays as an emerging method that is both robust and inexpensive for the detection of arsenic in groundwater both in the field and in the laboratory. The arsenic detection elements in bacteria-based bioassays are biosensor–reporter strains; genetically modified strains of, e.g., Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Rhodopseudomonas palustris. In response to the presence of arsenic, such bacteria produce a reporter protein, the amount or activity of which is measured in the bioassay. Some of these bacterial biosensor–reporters have been successfully utilized for comparative in-field analyses through the use of simple solution-based assays, but future methods may concentrate on miniaturization using fiberoptics or microfluidics platforms. Additionally, there are other potential emerging bioassays for the detection of arsenic in natural waters including nematodes and clams.     

On-chip dielectrophoretic recovery and detection of a lactate sensing probiotic from model human saliva

Early detection has led to increased survival for multiple cancers; however, the 5-year survival rate of oral carcinoma (OC) has remained at 40% for the last several decades. Screening for OC is routinely done via visual examinations, followed by tissue biopsy and laboratory testing. Point-of-care testing would be a more convenient and widely available alternative for at-risk individuals. Increased lactate production is a hallmark of many head-and-neck tumors, due to the Warburg Effect, where tumor cells favor glycolysis in the place of oxidative phosphorylation. To detect excess lactate, we have modified the commensal bacterium Escherichia coli Nissle 1917 to express fluorescent reporter genes in response to extracellular lactate. Administering this commensal as a mouth wash and subsequently collecting saliva for the detection of the reporter may allow for noninvasive, early detection of cancerous lesions in at-risk individuals. Furthermore, we demonstrate a new on-chip electrokinetic technique to recover these probiotic probes from model saliva fluid to improve the detection of reporter gene activation.     

A novel preventive mechanism of gentamicin‐induced nephrotoxicity by atorvastatin

Atorvastatin (ATO) inhibits the synthesis of nonsteroidal isoprenoid compounds and possesses a pleiotropic effect. However, the detailed mechanism of ATO in preventing gentamicin (GM)‐induced renal injury remains obscure. Although underlying multifaceted mechanisms involving GM‐induced nephrotoxicity were well known, further work on elucidating the essential mechanism was needed. Using a fluorogenic derivatization–liquid chromatography tandem mass spectrometry proteomic method (FD‐LC–MS/MS method), we investigated the effects and mechanisms of ATO treatment on GM‐induced nephrotoxicity in rats. Consequently, 49 differentially expressed proteins were identified. The most significant mechanisms of nephrotoxicity caused by GM were mitochondrial dysfunction, fatty acid metabolism and oxidative stress. Their upstream regulator was found to be PPARα. The proteins involved in GM nephrotoxicity were sodium–hydrogen exchanger regulatory factor (SLC9A3R1), cathepsin V (CTSV), macrophage migration inhibitory factor (MIF) and RhoGDP dissociation inhibitor alpha (ARHGDIA). After ATO intervention, we observed a reversed enrichment pattern of their expression, especially in CTSV and SLC9A3R1 (P‐value<0.05). We predicted that ATO may improve abnormal phospholipid metabolism and phospholipidosis caused by GM and also alleviate cell volume homeostasis and reverse the interference of GM with the transporter. Furthermore, proteomic results also provided clues as to GM‐induced nephrotoxicity biomarkers such as CTSV and transthyretin.     

Microbial genotoxicity bioreporters based on <Emphasis Type="Italic">sulA</Emphasis> activation

A bacterial genotoxicity reporter strain was constructed in which the tightly controlled strong promoter of the Escherichia coli SOS response gene sulA was fused to the alkaline phosphatase-coding phoA reporter gene. The bioreporter responded in a dose-dependent manner to three model DNA-damaging agents—hydrogen peroxide, nalidixic acid (NA), and mitomycin C (MMC)—detected 30–60 min after exposure. Detection thresholds were 0.15 μM for MMC, 7.5 μM for nalidixic acid, and approximately 50 μM for hydrogen peroxide. A similar response to NA was observed when the bioreporter was integrated into a specially designed, portable electrochemical detection platform. Reporter sensitivity was further enhanced by single and double knockout mutations that enhanced cell membrane permeability (rfaE) and inhibited DNA damage repair mechanisms (umuD, uvrA). The rfaE mutants displayed a five- and tenfold increase in sensitivity to MMC and NA, respectively, while the uvrA mutation was advantageous in the detection of hydrogen peroxide. A similar sensitivity was displayed by the double rfaE/uvrA mutant when challenged with the pre-genotoxic agents 2-amino-3-methylimidazo[4,5-f]quinoline and 2-aminoanthracene following metabolic activation with an S9 mammalian liver fraction.     

Development and validation of real-time PCR screening methods for detection of cry1A.105 and cry2Ab2 genes in genetically modified organisms

Primers and probes were developed for the element-specific detection of cry1A.105 and cry2Ab2 genes, based on their DNA sequence as present in GM maize MON89034. Cry genes are present in many genetically modified (GM) plants and they are important targets for developing GMO element-specific detection methods. Element-specific methods can be of use to screen for the presence of GMOs in food and feed supply chains. Moreover, a combination of GMO elements may indicate the potential presence of unapproved GMOs (UGMs). Primer-probe combinations were evaluated in terms of specificity, efficiency and limit of detection. Except for specificity, the complete experiment was performed in 9 PCR runs, on 9 different days and by testing 8 DNA concentrations. The results showed a high specificity and efficiency for cry1A.105 and cry2Ab2 detection. The limit of detection was between 0.05 and 0.01 ng DNA per PCR reaction for both assays. These data confirm the applicability of these new primer-probe combinations for element detection that can contribute to the screening for GM and UGM crops in food and feed samples.     

An improved synthetic approach to thieno[2,3-d]-1,2,3-thiadiazolecarboxylates via diazotization of aminothiophene derivatives

The common synthetic method for the synthesis of fused 1,2,3-thiadiazoles via diazotization is not generally applicable to aminothiophenes. A substantially improved experimental protocol for the preparation of the title compounds as a potential inducer of systemic acquired resistance in plants is reported based on a novel cyclization mechanism via a Huisgen-White type rearrangement.     

Interbacterial Chemical Communication-Triggered Nascent Proteomics

Metabolic labeling with clickable noncanonical amino acids has enabled nascent proteome profiling, which can be performed in a cell-type-specific manner. However, nascent proteomics in an intercellular communication-dependent manner remains challenging. Here we develop communication-activated profiling of protein expression (CAPPEX), which integrates the LuxI/LuxR quorum sensing circuit with the cell-type-specific nascent proteomics method to enable selective click-labeling of newly synthesized proteins in a specific bacterium upon receiving chemical signals from another reporter bacterium. CAPPEX reveals that E. coli competes with Salmonella for tryptophan as the precursor for indole, and the resulting indole suppressed the expression of virulence factors in Salmonella. This tryptophan-indole axis confers attenuation of Salmonella invasion in host cells and living mice. The CAPPEX strategy should be widely applicable for investigating various interbacterial communication processes.     

Structure of a boron-free hydrolysis product from boromycin

The structure of des-boron-des-valine-boromycin C₄₀H₆₈O₁₄ · H₂O (DBDVB), the product obtained by hydrolysis of the antibiotic boromycin C₄₅H₇₄BNO₁₅, has been determined by X-ray analysis. The molecule is remarkably similar in constitution, configuration and even in conformation to those of boromycin and des-valine-boromycin determined previously [2], showing that the overall molecular shape is retained on removal of the spiro boron atom.     

Construction of supported lipid membrane modified piezoelectric biosensor for sensitive assay of cholera toxin based on surface-agglutination of ganglioside-bearing liposomes

A novel piezoelelctric biosensor has been developed for cholera toxin (CT) detection based on the analyte-mediated surface-agglutination of ganglioside (GM1)-functionalized liposomes. To achieve a CT-specific agglutination at the surface, the gold electrode is modified by a GM1-functionalized supported lipid membrane via spontaneous spread of the liposomes on a self-assembled monolayer of a long-chain alkanethiol. In the presence of CT, the GM1-incorporated liposomes in assay medium will rapidly specifically agglutinate at the electrode surface through the binding of CT to GM1 on the electrode surface and the liposome interface. This results in an enormous mass loading on the piezoelelctric crystal as well as a significant increase of density and viscosity at the interface, thereby generating a decrease in frequency of the piezoelelctric crystal. The combination of mass loading with interfacial change in the surface-agglutination reaction allows the developed piezoelelctric biosensor to show substantial signal amplification in response to the analyte CT. The detection limit can be achieved as low as 25 ng mL⁻¹ CT. This is the first demonstration on CT detection based on specific surface-agglutination of GM1-modified liposomes. The supported lipid layer based sensing interface can be prepared readily and renewably, making the developed technique especially useful for simple, reusable and sensitive determination of proteins.     

Site‐oriented immobilization of fusion antigen directed by an affinity ligand,and its validation in an immunoassay

Immobilizing proteins on a solid surface in a site‐specific orientation and maintaining their bioactivity are crucial to the construction of high‐performance immunoassays. In this study, an affinity ligand for polystyrene (PS) surface screened from a phage display peptide library, named Lig1, was genetically fused to the N/C‐terminus of chimeric antigen HCV that could be recognized by specific antibodies against hepatitis C virus (HCV). Immunoassay characteristics of lig1‐fused HCVs immobilized on PS surface were compared to that of original HCV in both direct and indirect enzyme‐linked immunosorbent assay (ELISA). The results indicated that HCV‐Lig1 (Lig1 fused to HCV C‐terminus) was preferentially adsorbed on PS surface in a site‐oriented manner and would expose specific antibody‐binding sites well, which resulted in a substantial enhancement of detection sensitivity. AFM images showed that, compared to the original one, HCV‐Lig1 was arranged on PS surface in an ordered state and its conformational and steric distortions induced during the interfacial binding process were much slighter. As long as the specific epitope of a coating antigen is not located on both its N and C‐terminus, the ligand fusion approach could be an ideal strategy for site‐oriented protein immobilization. Copyright © 2010 John Wiley & Sons, Ltd.     

Affinity capillary electrophoresis for the assessment of binding affinity of carbohydrate‐based cholera toxin inhibitors

Developing tools for the study of protein carbohydrate interactions is an important goal in glycobiology. Cholera toxin inhibition is an interesting target in this context, as its inhibition may help to fight against cholera. For the study of novel ligands an affinity capillary electrophoresis (ACE) method was optimized and applied. The method uses unlabeled cholera toxin B‐subunit (CTB) and unlabeled carbohydrate ligands based on ganglioside GM1‐oligosaccharides (GM1os). In an optimized method at pH 4, adsorption of the protein to the capillary walls was prevented by a polybrene‐dextran sulfate‐polybrene coating. Different concentrations of the ligands were added to the BGE. CTB binding was observed by a mobility shift that could be used for dissociation constant (K_d) determination. The K_d values of two GM1 derivatives differed by close to an order of magnitude (600 ± 20 nM and 90 ± 50 nM) which was in good agreement with the differences in their reported nanomolar IC₅₀ values of an ELISA‐type assay. Moreover, the selectivity of GM1os towards CTB was demonstrated using Influenza hemagglutinin (H5) as a binding competitor. The developed method can be an important platform for preclinical development of drugs targeting pathogen‐induced secretory diarrhea.     

Hexaplex PCR assay and liquid bead array for detection of stacked genetically modified cotton event 281-24-236×3006-210-23

A hexaplex system based on multiplex polymerase chain reaction (PCR) coupled with liquid bead array was developed to assist detection of stacked genetically modified (GM) cotton event 281-24-236 × 3006-210-23 (Widestrike) expressing two kinds of endotoxin from Bacillus thuringiensis (Bt). The efficiency of this multiplex detection system was assessed. Specific primer sets for simultaneous detection of six targets in the stacked GM cotton event were constructed and used for the PCR assay. Each of the six targets was amplified, and the amplicons could be separated as discrete bands by agarose gel electrophoresis. A liquid bead array assay for the stacked GM cotton was performed using the hexaplex PCR products followed by hybridization between the biotinylated targets and anti-tagged microsphere beads. The hybridization products produced fluorescent signals that were detected by the Luminex system. Signal strengths were analyzed by their median fluorescent intensity values. Comparison of the assays showed that results from the liquid bead array using specific probes agreed with those from the PCR, and detection of the different target elements was found to be very specific with no cross-reaction. Therefore, the combination of hexaplex PCR and liquid bead array for detection of stacked GM events can be a useful and efficient system for screening and analyzing multiple transgenes for simultaneous qualitative analysis.     

Separation of Phenols from the Leaves of Toona Sinensis (Meliaceae) by Capillary Electrophoresis

A micellar electrokinetic capillary chromatography (MEKC) method, using UV detection, was developed for the determination of polyphenols in Toona sinensis (Meliaceae); the procedure involved precipitation of polyphenols from the leaves of T. sinensis using methanol. The structures can be established with fifteen compounds including methyl gallate, gallic acid, kaempferol, quercitin, quercitrin, rutin, kaempferol‐glucoside, catechin, epicatechin, stearic acid, palmitic acid, β‐sitosterol, stigmasterol, β‐sitosteryl‐glucoside, and stigmasteryl‐glucoside by spectroscopic analysis. However, there has been no investigation to quantitate the polyphenols that form T. sinensis. Thus, seven polyphenols of T. sinensis with UV absorbance, catechin (C), epicatechin (EC), methyl gallate (MG), rutin (R), gallic acid (G), quercitrin (Q), and kaempferol (K) were separated within 10 min with a 40 cm uncoated fused‐silica column, with the RSD < 3% (migration times), voltage at 15 kV using this method. On‐column detection was carried out at 254 nm. The detection limit of this method for all analytes ranged from 19.5 to 0.02 μM (RSD < 3.1%). The method provided a rapid and sensitive identification of polyphenols of interest in T. sinensis and is suitable for biological activity studies.     

Functional characterisation of metal(loid) processes in planta through the integration of synchrotron techniques and plant molecular biology

Functional characterisation of the genes regulating metal(loid) homeostasis in plants is a major focus for phytoremediation, crop biofortification and food security research. Recent advances in X-ray focussing optics and fluorescence detection have greatly improved the potential to use synchrotron techniques in plant science research. With use of methods such as micro X-ray fluorescence mapping, micro computed tomography and micro X-ray absorption near edge spectroscopy, metal(loids) can be imaged in vivo in hydrated plant tissues at submicron resolution, and laterally resolved metal(loid) speciation can also be determined under physiologically relevant conditions. This article focuses on the benefits of combining molecular biology and synchrotron-based techniques. By using molecular techniques to probe the location of gene expression and protein production in combination with laterally resolved synchrotron techniques, one can effectively and efficiently assign functional information to specific genes. A review of the state of the art in this field is presented, together with examples as to how synchrotron-based methods can be combined with molecular techniques to facilitate functional characterisation of genes in planta. The article concludes with a summary of the technical challenges still remaining for synchrotron-based hard X-ray plant science research, particularly those relating to subcellular level research.     

A Direct Competitive Homogeneous Immunoassay for Progesterone – the Redox Quenching Immunoassay

A direct competitive amperometric immunoassay format for the detection of haptens and proteins was developed. The method is based on the quenching of electroactivity of ferrocenium, which is coupled to the antigen and used as the primary reporter, upon binding to a monoclonal anti‐ferrocenium antibody, which is coupled to the detection antibody and used as a secondary reporter. A separation‐free progesterone immunoassay with a lower detection limit of 1 ng mL^?1 (3.18 nmol L^?1) in 1 : 2 diluted blood serum was realised by combining two bifunctional conjugates, a ferrocenium‐PEG‐progesterone tracer and a bioconjugate of one anti‐progesterone and one anti‐ferrocenium antibody. The immune complex is formed within 30 s upon addition of progesterone, resulting in a total analysis time of 1.5 min.     

Novel Thermostable Flavin‐binding Fluorescent Proteins from Thermophilic Organisms

Flavin‐binding fluorescent proteins (FbFPs) are small, oxygen‐independent in vivo reporters, derived from Light Oxygen Voltage (LOV) domains of photoreceptors. Here, we investigated the thermostability of existing, as well as novel FbFPs, whose genes were identified in genome sequences of various thermophilic bacteria as well as metagenomic libraries from hot springs in the Yellowstone National Park. Detailed in vitro analyses revealed that two of those fluorescent reporter proteins were highly thermostable, exhibiting melting temperatures above 75°C.     

Highly Pure Synthesis,Spectral Assignments,and Two‐Photon Properties of Cruciform Porphyrin Pentamers Fused with Benzene Units

Tetrameric porphyrin formation of 2‐hydroxymethylpyrrole fused with porphyrins through a bicyclo[2.2.2]octadiene unit gave bicyclo[2.2.2]octadiene‐fused porphyrin pentamers. Thermal conversion of the pentamers gave fully π‐conjugated cruciform porphyrin pentamers fused with benzene units in quantitative yields. UV/Vis spectra of fully π‐conjugated porphyrin pentamers showed one very strong Q absorption and were quite different from those of usual porphyrins. From TD‐DFT calculations, the HOMO level is 0.49 eV higher than the HOMO?1 level. The LUMO and LUMO+1 levels are very close and are lower by more than 0.27 eV than those of other unoccupied MOs. The strong Q absorption was interpreted as two mutually orthogonal single‐electron transitions (683 nm: 86 %, HOMO→LUMO; 680 nm: 86 %, HOMO→LUMO+1). The two‐photon absorption (TPA) cross section value (σ⁽²⁾) of the benzene‐fused porphyrin pentamer was estimated to be 3900 GM at 1500 nm, which is strongly correlated with a cruciform molecular structure with multidirectional π‐conjugation pathways.