An algorithm for simultaneous comparison of several sequences

An algorithm was developed to compare simultaneously severalDNA, RNA or protein sequences. With the algorithm, conservedregions of one sequence are located by doing pairwise comparisonswith other sequences, which is advantageous in planning site-directedmutagenesis studies. The observation matrices filled with scoresof comparisons are superimposed and added together and thosepoints having values greater than or equal to stringency areaccepted. The predicted secondary structural features can alsobe compared. Received on August 21, 1987; accepted on November 20, 1987     

Real-time PCR assay for the simultaneous quantification of nitrifying and denitrifying bacteria in activated sludge

In order to improve wastewater treatment processes, a need exists for tools that rapidly give detailed insight into the community structure of activated sludge, supplementary to chemical and physical data. In this study, the advantages of microarrays and quantitative polymerase chin reaction (PCR) methods were combined into a real-time PCR assay that allows the simultaneous quantification of phylogenetic and functional genes involved in nitrification and denitrification processes. Simultaneous quantification was possible along a 5-log dynamic range and with high linear correlation (R ² > 0.98). The specificity of the assay was confirmed by cloning and sequencing analyses of PCR amplicons obtained from activated sludge. The real-time assay was validated on mixed liquid samples of different treatment plants, which varied in nitrogen removal rate. The abundance of ammonia oxidizers was in the order of magnitude of 10⁶ down to 10⁴ ml⁻¹, whereas nitrite oxidizers were less abundant (10³–10¹ order of magnitude). The results were in correspondence with the nitrite oxidation rate in the sludge types. As for the nirS, nirK, and nosZ gene copy numbers, their abundance was generally in the order of magnitude of 10⁸–10⁵. When sludge samples were subjected to lab-scale perturbations, a decrease in nitrification rate was reflected within 18 h in the copy numbers of nitrifier genes (decrease with 1 to 5 log units), whereas denitrification genes remained rather unaffected. These results demonstrate that the method is a fast and accurate tool for the analysis of the (de)nitrifying community structure and size in both natural and engineered environmental samples. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

A novel multiplex assay for simultaneous quantification of total and S129 phosphorylated human alpha-synuclein

Background

Alpha-synuclein (asyn) has been shown to play an important role in the neuropathology of Parkinson’s disease (PD). In the diseased brain, classic intraneuronal inclusions called Lewy bodies contain abnormal formations of asyn protein which is mostly phosphorylated at serine 129 (pS129 asyn). This suggests that post-translational modifications may play a role in the pathogenic process. To date, several uniplex assays have been developed in order to quantify asyn not only in the brain but also in cerebrospinal fluid and blood samples in order to correlate asyn levels to disease severity and progression. Notably, only four assays have been established to measure pS129 asyn specifically and none provide simultaneous readout of the total and pS129 species. Therefore, we developed a sensitive high-throughput duplex assay quantifying total and pS129 human asyn (h-asyn) in the same well hence improving accuracy as well as saving time, consumables and samples.

Results

Using our newly established duplex assay we measured total and pS129 h-asyn in vitro showing that polo-like kinase 2 (PLK2) can phosphorylate asyn up to 41 % in HEK293 cells and in vivo the same kinase phosphorylated h-asyn up to 17 % in rat ventral midbrain neurons. Interestingly, no increase in phosphorylation was observed when PLK2 and h-asyn were co-expressed in rat striatal neurons. Furthermore, using this assay we investigated h-asyn levels in brain tissue samples from patients with PD as well as PD dementia and found significant differences in pS129 h-asyn levels not only between disease tissue and healthy control samples but also between the two distinct disease states especially in hippocampal tissue samples.

Conclusions

These results demonstrate that our duplex assay for simultaneous quantification is a useful tool to study h-asyn phosphorylation events in biospecimens and will be helpful in studies investigating the precise causative link between post-translational modification of h-asyn and PD pathology.

     

Colony immunoblot assay of botulinal toxin.

Botulinal neurotoxin in and around colonies of Clostridium botulinum types A, B, and E and of toxigenic Clostridium butyricum was detected by an enzyme-linked immunoassay procedure whereby the toxin was transferred from the agar medium to a nitrocellulose support and the immobilized toxin was probed with type-specific antibodies. The method identified the toxin types of the colonies grown from a mixed inoculum of C. botulinum serotypes. The specificity of the antitoxins for type A and B toxins was improved by adsorption of the antitoxins with the antigens of heterologous type cultures.     

An alternative infrared spectroscopy assay for the quantification of polysaccharides in bacterial samples

The ability of bacteria to produce extracellular polysaccharides has been regarded as an indication of biofilm-forming capacity. Therefore, the determination of the sugar content in bacterial samples becomes a significant parameter. The colorimetric methods currently used are rather sensitive to the nature of the sugars and therefore require knowledge of the sugar types present in the samples. Unfortunately, the types of sugars present in bacteria are generally unknown and often composed of a complex mixture. In this article, we propose an alternative method based on Fourier transform infrared (FTIR) spectroscopy for the estimation of the total sugar content in bacterial samples. The method is based on a systematic treatment of FTIR spectra obtained from dried bacteria samples. It is assumed that the total sugar amount can be estimated from the area of characteristic bands between 970 and 1182 cm(-1). In parallel, the amide II band (1560-1530 cm(-1)) associated with proteins, or the C-H stretching region (2820-3020 cm(-1)) associated with the biomass, can be used for normalization purposes. Therefore, the ratio of the band area in the sugar window over that of the amide II or C-H stretching can be used to report the sugar content in bacterial samples. This method has been validated on model bacterial mixtures containing sugars, proteins, and DNA. Results with real bacterial samples are also provided and show conclusively that increased sugar contents in biofilms can be identified. The proposed FTIR approach requires minimal sample preparation and a single acquisition, is rapid, and may be applied to any kind of bacterial growth.     

Quantitative immunoblot assay for assessment of liposomal antibody conjugation efficiency.

Routine direct assessment of immunoglobulin (Ig)-liposome(lp) conjugation efficiency has been impeded by phospholipid interference with standard protein and immunoassay methods. Rabbit IgG conjugated to anionic liposomes was quantitated in immunoblots using computer image analysis techniques. Lp-coupled Ig was separated from free Ig by dialysis in disposable Spectra/Por units (MWCO 300 kDa). Differential Lowry protein assay (DLA) of the thiolated Ig reactant and the dialyzate provided an estimate of conjugation efficiency that was compared to the results of the immunoblot assay (IBA). The color response of Ig-lp in the IBA was about an order of magnitude greater than rabbit IgG alone, requiring the synthesis of an Ig-lp standard in which the Ig conjugation efficiency was assessed by radiotracer methodology. The use of the same standard in three colorimetric protein assays verified the accuracy of the IBA and demonstrated that the colorimetric assays could be employed to determine Ig-lp conjugation efficiency. In terms of sensitivity and specificity, however, the IBA is better suited for routine assessment of laboratory-scale Ig-lp conjugation efficiencies. The DLA was found to be an unsatisfactory measure of conjugation efficiencies because an interfering substance was apparently released by Ig-lp preparations.     

An enzymatic fluorescent assay for the quantification of phosphite in a microtiter plate format

A sensitive fluorometric assay for the quantification of phosphite has been developed. The assay uses the enzymatic oxidation of phosphite to phosphate by a recombinant phosphite dehydrogenase with NAD⁺ as cosubstrate to produce the highly fluorescent reaction product resorufin. The optimized assay can be carried out in a 96-well microtiter plate format for high-throughput screening purposes and has a detection limit of 0.25 nmol phosphite. We used the method to quantify phosphite levels in plant tissue extracts and to determine phosphite dehydrogenase activity in transgenic plants. The assay is suitable for other biological or environmental samples. Because phosphite is a widely used fungicide to protect plants from pathogenic oomycetes, the assay provides a cost-effective and easy-to-use method to monitor the fate of phosphite following application.     

Multiplex RT Q-PCR assay for simultaneous quantification of three viruses used for validation of virus clearance by biopharmaceutical production

Virus removal studies are used to insure the safety of biopharmaceutical products by quantitatively estimating the viral clearance capacity by the manufacturing process. Virus quantification assays are used to measure the log₁₀ clearance factor of individual purification unit operations in spike recovery studies. We have developed a multiplex RT Q-PCR assay that detects and quantifies three commonly used model viruses X-MuLV, SV40, and MMV simultaneously. This RT Q-PCR multiplex assay has a 6 log₁₀ dynamic range with a limit of detection (LOD) of ≈1 genome copy/μL. Amplification profiles are similar to existing singleplex assays. Overall, this RT Q-PCR multiplex assay is highly quantitative, accurately identifies multiple viruses simultaneously, and may prove useful to validate viral clearance of biological products in small scale studies.     

A combination immunoblot for the simultaneous detection and differentiation of HIV-1 and HIV-2

We have developed a combination immunoblot (combi-blot) for simultaneous detection and differentiation of HIV-1 and HIV-2 antibodies using HIV-1 lysate and HIV-1 and HIV-2 synthetic peptide antigens in a single assay. Minimal modification in antigen strip preparation and no modification in assay procedure of the current HIV-1 Western blot protocol was required. Implementation of this combi-blot following the use of the combination HIV-1/-2 enzyme immunoassay would simplify the current HIV testing algorithm and increase the accuracy of HIV-2 surveillance.     

Double-layer plaque assay for quantification of enteroviruses

We describe here a double-layer plaque assay for the quantification of enteroviruses, combining a monolayer plaque assay and a suspended-cell plaque assay. The double-layer assay provides significantly greater counts than other methods of virus quantification of both suspensions of pure culture viruses and naturally occurring viruses. The counts obtained by this method are approximately one order of magnitude greater than those obtained with the more commonly used method, the monolayer plaque assay. We conclude that the methods available for quantifying viruses rank in efficiency as follows: double-layer plaque assay >or=suspended-cell plaque assay > counting cytopathogenic virus adsorbed to cellulose nitrate membrane filters >or= most probable number of cytopathogenic units > monolayer plaque assay. Moreover, the double-layer plaque assay allows the use of two different cell lines in the two layers. Using the human colonic carcinoma cell line CaCo2 facilitates the recovery of a greater number and diversity of naturally occurring enteroviruses in water than the monolayer agar method. In addition, the pretreatment of cells with 5-iodo-2'-deoxyuridine (IDU) prior to the quantification of enteroviruses by the double-layer plaque assay provides significantly higher recoveries than the use of IDU does with the other methods of quantification.     

Western blot (immunoblot) analysis of the fimbrial antigens of Bacteroides nodosus

The roles of the fimbrial subunit and the putative basal protein antigens in the serological classification of Bacteroides nodosus have been examined by Western blot (immunoblot)-antibody binding studies of fimbriae isolated from a wide range of strains representative of different serogroups and serotypes. Fimbrial subunits were recognized by antiserum against the homologous serogroup but not generally by heterologous antisera, whereas recognition of the basal antigen was independent of serological classification. Secondary cross-reaction patterns among fimbrial subunits indicated that some serogroups may be more closely related than others. Examples include serogroups C and G and serogroups D and H. Similar analyses of isolates classified within serotypes A1 and A2, with serotype-specific antisera, showed that this subdivision is also determined by the fimbrial subunit and that significant variation does occur even at this level. These studies suggest that the various serogroups and serotypes of B. nodosus comprise a series of overlapping sets of antigenically related strains.     

Simple, rapid and sensitive assay method for simultaneous quantification of urinary nicotine and cotinine using gas chromatography-mass spectrometry

Nicotine is a major addictive compound in cigarette. Its smoke is rapidly and extensively metabolized to several metabolites in human. Cotinine as a major metabolite of nicotine is commonly used as a biomarker to determine active and passive smokers. Cotinine has a longer half-life ( approximately 20 h) compared to nicotine ( approximately 2h). A simple, sensitive, rapid and high throughput GC-MS method was developed for simultaneous quantification of urinary nicotine and cotinine in passive and active smokers. In the sample preparation method, the analytes and internal standard were first basified and followed by liquid-liquid extraction. Upon completion, anhydrous sodium sulphate was added to the solvent mixture to trap moistures. The clear extract obtained was directly injected into GC-MS, operating under selective ion monitoring (SIM) mode. Calibration curves in the range of 0.5-5000 ng/mL of the analytes in urine matrix were established with linear correlation coefficients (r(2)) greater than 0.997. The limit of detection for both nicotine and cotinine were 0.20 ng/mL. The mean recoveries for nicotine and cotinine were 93.0 and 100.4%, respectively. The within- and between-assay accuracies were between 2.1 and 7.9% for nicotine and between 0.7 and 11.1% for cotinine. Within- and between-assay precisions of 3.3-9.5% for nicotine and 3.4-9.8% for cotinine were also achieved. The method can be used in routine assessment and monitoring of active smoking and exposure to environmental tobacco smoke. The applicability of the assay was demonstrated in a small-scale comparison study between smokers and non-smokers.     

Simple reversed-phase liquid chromatographic assay for simultaneous quantification of free mycophenolic acid and its glucuronide metabolite in human plasma

A reversed-phase HPLC-UV method, involving simple instrumental setup and mobile phase without ion-pairing reagent, was developed and validated for direct simultaneous quantification of free mycophenolic acid (MPA) and its major metabolite MPA-glucuronide (MPAG) in human plasma. Both free MPA and MPAG were isolated from plasma samples using ultrafiltration prior to analysis. Each chromatographic run was completed within 13 min. The optimized method showed good performance in terms of specificity, linearity (r(2)=0.9999), sensitivity (limit of quantitation (LOQ): 0.005 mg/L for MPA; 1 mg/L for MPAG), and intra- and inter-day precision (R.S.D.<7%). This assay was successfully applied to free MPA and MPAG measurements in clinical samples.     

An intradermal assay for quantification and kinetics studies of tumor angiogenesis in mice.

A method is reported for the study of early phases of neovascularization in syngeneic murine tumors and human tumor xenografts in nude mice. Using this method, the effect of irradiation of tumor cells or tumor bed on tumor angiogenesis was studied. Tumor cells were injected intradermally in the abdominal skin flap, which was reopened at 2-day intervals to quantify newly formed blood vessels at the site of tumor cell injection. Both tumor cell injection and blood vessel counting were performed under a dissecting microscope. Using three syngeneic murine tumors and two clones of a human colonic adenocarcinoma, it was observed that new blood vessels started appearing within a few days after tumor cell injection and that this event preceded measurable tumor growth. The number of blood vessels increased exponentially for several days but then their further growth slowed. The extent of angiogenesis depended on the tumor type and the number of tumor cells injected. The exposure of the skin flap to ionizing radiation prior to tumor cell injection reduced neovascularization. We further observed that heavily irradiated tumor cells retained their ability to induce angiogenic response and that lymphoid cells (peritoneal exudate and spleen cells) could also elicit an angiogenic response, although it is weaker than the response elicited by tumor cells. Thus this method is suitable for quantification and kinetics of early phases of tumor angiogenesis in individual mice bearing transplants of syngeneic tumors or human tumor xenografts, and it can be useful for investigating various regulators of tumor angiogenesis.     

Simultaneous quantification of total and conjugated ubiquitin levels in a single immunoblot

Ubiquitin (Ub) is a posttranslational modifier, and total Ub (Ub_T) is always in dynamic equilibrium among free Ub (Ub_F), activated Ub (Ub_A), and conjugated Ub (Ub_C) in the forms of mono-Ub, thioester-bond-linked Ub, and peptide-bond-linked Ub, respectively. In this study, we developed a simple method to simultaneously determine the levels of Ub_T, Ub_F + Ub_A, and Ub_C in a single immunoblot and demonstrated its reliability and reproducibility by determining [Ub_T], [Ub_F + Ub_A], and [Ub_C] in various mouse tissues and cultured cells.     

An In vitro assay useful to determine the potency of several bitter compounds

Gustducin and transducin are guanine nucleotide binding regulatory proteins (G proteins) expressed in taste receptor cells and implicated in transducing taste cell responses to certain compounds that humans consider bitter or sweet. These G proteins can be activated in vitro by taste receptor-containing membranes plus any of several bitter compounds. This activation can be monitored using limited trypsin digestion, sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting. Scanning of the autoradiograms enables one to quantitate the level of activation (defined as an activation index), obtain dose-response profiles and estimate the potency of the tastant. This assay may provide a useful substitute for, or adjunct to, the time-consuming human psychophysical analysis and costly animal studies typically used in taste sensory analysis. It may be used to identify and determine the concentration-response function of many bitter components of oral pharmaceuticals and food ingredients. A potential limitation of the assay is that only about half of all bitter compounds tested demonstrated in vitro activity, perhaps due to the presence of multiple transduction pathways. Nevertheless, the rapid throughput and microsample handling capability of this assay make it an ideal method to screen for high-potency bitterness inhibitors.     

Enzyme-linked immunolysis assay for tumour-specific surface antigens

Expression of the activity of the cytosolic enzyme lactate dehydrogenase released on cell lysis by tumour specific antibodies in the presence of complement was investigated by direct assay of the expression of the occluded enzyme in tumour cell suspensions. This method, called Enzyme Linked Immunolysis Assay (ELILA) was shown to be more sensitive than conventional cytotoxic assays. The data fit well in the linear regression model, so that the technique can be used for quantitation of the antibody titres.