Routine application of high-performance liquid chromatography for identification of mycobacteria

Mycolic acid analysis by high-performance liquid chromatography (HPLC) was introduced in our laboratory as the routine technique for identifying all clinical isolates of mycobacteria referred to us. HPLC identified 96.1% of the 1,103 strains analyzed, whereas the biochemical procedures and/or the commercial DNA probes identified 98.3% of strains, for an overall agreement of 94.4%. Compared with the probes, there was 100% specificity and 98.9% sensitivity for Mycobacterium tuberculosis identification. HPLC allowed early detection and identification of the rare mycobacterial species M. haemophilum, M. malmoense, M. shimoidei, and M. fallax as well as uncharacteristic strains of M. simiae. After 18 months of routine use, HPLC proved to be reliable, easy to perform, rapid, and less costly than other identification methods.     

Comparison of fluorescence in situ hybridization with flow cytometry and static image analysis in ploidy analysis of paraffin-embedded prostate adenocarcinoma

Nuclear DNA ploidy has been shown to have an important prognostic association for patients with adenocarcinoma of the prostate. Flow cytometry and static image analysis are ploidy methods that have been used in prostate carcinoma. Fluorescence in situ hybridization (FISH) using chromosome-specific probes can be used to evaluate the ploidy of interphase nuclei. In this study FISH was compared with flow cytometry and static image analysis in determining ploidy in paraffin-embedded tissue from 34 prostatic adenocarcinomas. Ploidy status using FISH was determined by enumerating centromeres of two chromosomes (8 and 12) by use of directly-labeled alpha-satellite DNA probes in isolated whole nuclei obtained by the Hedley technique. All three methods identified 11 of 34 cases as diploid and 17 of 34 cases as nondiploid (82% concordance). Six cases were discordant; two cases had discrepant results by each method. Ploidy classification as determined by FISH had an 88% concordance with ploidy classification by either flow cytometry or static image analysis. In conclusion, FISH was found to be a sensitive method of ploidy analysis in isolated paraffin-embedded nuclei from prostate adenocarcinomas. When the chromosomes commonly involved in aneuploidy have been identified in prostate adenocarcinoma, FISH has the potential to provide greater sensitivity for aneuploidy detection compared with currently available methods.     

Remaining life assessment issues in high Cr martensitic steels and development of new innovative tools for damage monitoring and integrity assessment

The relatively newer high Cr martensitic steels such as P91 have now been in use in power industry for over twenty years. Over this time, there have been a number of incidents of cracking and failure in components made from P91 steel, both in thick and thin section equipments mainly due to creep damage. The thick section components have been usually failing due to Type IV cracking associated with the weldments while thin section components have been failing due to higher than expected levels of steam oxidation resulting in enhanced metal loss, increase in metal temperature above design, creep cavitation and cracking. However, it has not been possible to detect early stage creep damage/cavitation in high Cr martensitic steels using conventional replication type methods. This is because unlike the low alloy CrMoV steels, spherodisation of microstructure does not occur in high Cr martensitic steels and cavitation clearly visible by traditional methods only appears later in life when the material is about to fail. Thus there has been a need to develop new tools and more sensitive methods for integrity and damage assessment in these steels. European Technology Development (ETD) together with its industrial collaborators from Europe, Japan and North America have been looking at the development of tools and methodologies for early stage damage detection and life prediction as a part of its international multi-client project ‘P91 Integrity’. The tools which have shown successful results are portable Scanning Force Microscopy, laser guided hardness tester and more innovative use of ultrasonic probes for detecting early stage creep damage. This paper discusses the issues involved and describes some of the developments in this project.     

Microbiological diagnosis of tuberculosis

The increased incidence of tuberculosis as well as the availability of new diagnostic testing methods clearly have various implications for the routine microbiology laboratory: samples must be sent to the microbiology lab for testing immediately after being taken and microscopically investigated the same day. In other countries, difficult to treat, multi-resistant Mycobacterium tuberculosis strains have occurred. Thus decisive hygienic measures must be taken early on in cases of highly infectious patients (i.e. patients with microscopically positive sputum). Liquid media (MB Check Roche, Bactec) as well as L?wenstein Jensen media must be inoculated in the lab. Liquid media allow both faster detection of certain atypical mycobacteria and increased accuracy. Classification of culturally established agents through commercial genetic probes (AccuProbe Mycobacterien) or with high pressure liquid chromatography is possible within hours when acid-fast rods are present. Time consuming identification by determination of biochemical and culture morphological characteristics should be reserved for reference labs. Today, rapid tests like analysis of tuberculostearic acid or polymerase chain reaction are already useful for special questions like ruling out tuberculous meningitis. In most cases, however, these rapid tests cannot replace identification of microbes with culture techniques.     

In vitro fusion of phagosomes with different endocytic organelles from J774 macrophages

We describe novel biochemical and electron microscopy assays to investigate in vitro fusion of latex bead phagosomes with three different endocytic organelle fractions from J774 macrophages. After formation, early phagosomes fuse avidly with early and late endosomes and for a longer period of time with lysosomes, but they subsequently become fusion-incompetent. The fusion of early, but not late, phagosomes with all three endocytic fractions could be significantly stimulated by Rab5. In contrast to other cell types investigated, this Rab is uniquely enriched on both early and late endosomes in J774 macrophages. Moreover, exogenous Rab5 stimulates homotypic fusion between both sets of organelles. This was shown by a quantitative electron microscopy fusion assay that can directly assay fusion between any combination of morphologically defined organelles. By the same approach, we discovered an unexpected Rab5-stimulatable fusion between early and late endosomes in J774, but not in BHK cells. Thus, in J774 cells both Rab5 and the endocytic pathway seem to have evolved additional functions not yet seen in nonphagocytic cells.     

Nuclear matrix-lamina-intermediate filament system in PtK 2 cells

The advent of fluorescent ion sensitive indicators has improved our understanding of the mechanisms involved in regulating pHi and [Ca2+]i homeostasis in living cells. However, changes in [Ca2+]i can alter pHi regulatory mechanisms and vice versa, making assignment of either ion to a particular physiological response complex. A further complication is that all fluorescent Ca2+ indicators are sensitive to protons. Therefore, techniques to simultaneously measure these two ions have been developed. Although several combinations of pH and Ca2+ probes have been used, few systematic studies have been performed to assess the validity of such measurements. In vitro analysis (i.e. free acid forms of dyes) indicated that significant quenching effects occurred when using specific dye combinations. Fura-2/SNARF-1 and MagFura-2/SNARF-1 probe combinations were found to provide the most accurate pH and [Ca2+] measurements relative to Fluo-3/SNARF-1, Ca2+-Green-1/SNARF-1, or BCECF/SNARF-1. Similar conclusions were reached when probes were calibrated after loading into cells. The magnitude of interactions between pH and Ca2+ probes could be a factor which may limit the use of certain specific combinations. Loading of probes that exhibit interactions into distinct intracellular compartments (i.e. separated by a biological membrane) abolished the quenching effects. These data indicate that interactions between the probes used to simultaneously monitor pH and Ca2+ must be considered whenever probe combinations are used.     

Intracoronary radiation with a 32P source wire

With the increasing awareness of incipient and subclinical malnutrition in children several nutritional indices have been suggested for the early recognition of protein-energy malnutrition (PEM). We evaluated plasma albumin, transferrin, and fibronectin levels in 15 children with PEM and compared them with those of 10 well-nourished children. The results demonstrated that plasma albumin is a poor indicator of mild to moderate PEM. On the other hand, plasma transferrin and fibronectin are sensitive indicators of PEM as they were significantly decreased in our mild to moderately malnourished children whereas albumin was unchanged. Furthermore, malnourished children showed iron deficiency anaemia, which may interfere with the results of plasma transferrin determinations. Fibronectin is believed to have a functional role in coagulation, host immune defence, and wound healing. We suggest that the assay of fibronectin may provide a biochemical functional index of mild to moderate nutritional deficiency before overall depletion has occurred.     

Detection of plant viruses--biotechnological and molecular advances

Recent advances in biotechnology and molecular biology have played a significant role in development of rapid, specific and sensitive assays for detection of plant viruses. Production of monospecific polyclonal antibodies, monoclonal antibodies have enabled to group isolates of viruses and distinction of closely related strains. In cDNA hybridization applications, there is an increasing interest to employ non-radioactive probes for detection of nucleic acids. Detection limit of nucleic acid is remarkably comparable to those of radioactive labelled probes. Application of polymerase chain reaction (PCR) has made it possible to amplify the low numbers of viral RNA/DNA molecules and their subsequent detection. Underlying principles, their advantages and disadvantages for application of monospecific polyclonal antibodies, hybridoma technology, molecular hybridization and PCR technology with reference to detection of plant viruses have been discussed in this review.     

Sertoli cells in culture and mRNA differential display provide a sensitive early warning assay system to detect changes induced by xenobiotics

We have used cultured rat Sertoli cells as an "early warning system" to monitor for morphological and biochemical changes induced by two different xenobiotics-cadmium acetate and polychlorinated biphenyls (PCBs). Sertoli cells begin to round, become vacuolized, and detach from their substrate within 24 hours of culture in the presence of cadmium at concentrations of 0.5-1.0 microM. Similar results were obtained with a lower dose of cadmium (0.01 microM) after 72 hours. When Sertoli cells are cultured for 24 hours in the presence of a mixture of PCBs (3,3',4,4'-tetrachlorobiphenyl, 2,2',4,6,6'-pentachlorophenyl, and 2,2',3,3',4,5,5', 6,6'-nonachlorobiphenyl) at concentrations of 1.0-2.0 microM, they enlarge. After 72 hours, a lower dose of PCBs (0.01 microM) produces similar cellular enlargement. Despite their changes in morphology, no reduction in Sertoli cell viability was seen at any of the concentrations or time points studied for either toxicant. Using mRNA differential display, a number of novel cDNAs were detected when cells were cultured with either cadmium or the PCBs, demonstrating that changes in gene expression accompany the changes in Sertoli cell structure. We propose that Sertoli cells in culture and mRNA differential display provide a sensitive morphological and biochemical assay system to detect early direct effects of low concentrations of toxicants on mammalian Sertoli cells.     

Real-time quantitative PCR for the detection of minimal residual disease in acute lymphoblastic leukemia using junctional region specific TaqMan probes

Analysis of minimal residual disease (MRD) can predict outcome in acute lymphoblastic leukemia (ALL). A large prospective study in childhood ALL has shown that MRD analysis using immunoglobulin (Ig) and T cell receptor (TCR) gene rearrangements as PCR targets can identify good and poor prognosis groups of substantial size that might profit from treatment adaptation. This MRD-based risk group assignment was based on the kinetics of tumor reduction. Consequently, the level of MRD has to be defined precisely in follow-up samples. However, current PCR methods do not allow easy and accurate quantification. We have tested 'real-time' quantitative PCR (RQ-PCR) using the TaqMan technology and compared its sensitivity with two conventional MRD-PCR methods, ie dot-blot and liquid hybridization of PCR amplified Ig/TCR gene rearrangements using clone-specific radioactive probes. In RQ-PCR the generated specific PCR product is measured at each cycle ('real-time') by cleavage of a fluorogenic intrinsic TaqMan probe. The junctional regions of rearranged Ig/TCR genes define the specificity and sensitivity of PCR-based MRD detection in ALL and are generally used to design a patient-specific probe. In the TaqMan technology we have chosen for the same approach with the design of patient-specific TaqMan probes at the position of the junctional regions. We developed primers/probe combinations for RQ-PCR analysis of a total of three IGH, two TCRD, two TCRG and three IGK gene rearrangements in four randomly chosen precursor-B-ALL. In one patient, 12 bone marrow follow-up samples were analyzed for the presence of MRD using an IGK PCR target. The sensitivity of the RQ-PCR technique appeared to be comparable to the dot-blot method, but less sensitive than liquid hybridization. Although it still is a relatively expensive method, RQ-PCR allows sensitive, reproducible and quantitative MRD detection with a high throughput of samples providing possibilities for semi-automation. We consider this novel technique as an important step forward towards routinely performed diagnostic MRD studies.     

Evaluation of five imidazopyrazinone-type chemiluminescent superoxide probes and their application to the measurement of superoxide anion generated by Listeria monocytogenes

Superoxide-triggered chemiluminescence of five new imidazopyrazinone derivatives was investigated using the hypoxanthine-xanthine oxidase system as the source of superoxide anion. The results showed that they are highly sensitive and have favorable properties in measuring superoxide anion. With those new probes, the generation of superoxide anion from the bacteria Listeria monocytogenes was examined. The results confirmed the previous report that L. monocytogenes is an unusual organism that extracellularly and continuously generates a high level of superoxide anion in the presence of acetaldehyde. The data indicated that two of the probes, 3,7-dihydro-2-methyl-6-phenylethynylimidazo[1,2-a]pyrazin-3- one (4) and its methoxy derivative (5), are highly sensitive and useful in the measurements of superoxide anion and are clearly superior to 3,7-dihydro-2-methyl-6-(4-methoxyphenyl)imidazo[1,2-a]pyrazin-3-on e (MCLA), which-has been generally considered the most sensitive superoxide probe in the past. When tested at a probe concentration of 3.3 microM, the luminescence response and the signal-background ratio of compound 4 were 1.5 and 2.5 times those of MCLA, respectively, and the signal-background ratio of compound 5 was almost 15 times that of MCLA, though the luminescence response of this compound was slightly lower than that of MCLA. The low probe concentration used enhances the usefulness of probes in the measurements of superoxide in functioning biological systems.     

On nonaxisymmetric entry flow at very low Reynolds numbers

We describe the construction and testing of a structural model at the nucleotide level for conformation CH of the central hairpin of genomic RNA from coliphage Q beta. The model was developed with the computer program MFOLD using both optimal and suboptimal predictions. Structural information obtained by electron microscopic analysis of Kleinschmidt spreadings of Q beta RNA was used to guide the modeling. The model was tested in solution with three enzymatic probes: RNase T1, RNase T2, and RNase V1, as well as four chemical probes: dimethylsulfate, diethylpyrocarbonate, kethoxal and 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate (CMCT). The structural analyses in solution are consistent with the predicted structural model. The model is also supported by comparative structural analysis with the related coliphage SP. The model provides a structural basis for published biochemical and genetic studies implicating large, long-range structural features in the co-regulation of viral coat and replicase expression. In addition, we show that the read-through region of the viral protein A1 forms a separate structural domain, and we suggest that it functions as a nucleation site that participates in the folding and refolding of the molecule during replication and translation. In addition to the central hairpin, we have analyzed the structure of the viral coat initiation region. Our studies show that the entire region consists of small local hairpins and that 26 nucleotides immediately surrounding the coat initiation codon are single-stranded.     

A Drosophila homolog of bovine smg p25a GDP dissociation inhibitor undergoes a shift in isoelectric point in the developmental mutant quartet

The Drosophila developmental mutation quartet causes late larval lethality and small imaginal discs and, when expressed in the adult female, has a lethal effect on early embryogenesis. These developmental defects are associated with mitotic defects, which include a low mitotic index in larval brains and incomplete separation of chromosomes in mitosis in the early embryo. quartet mutations also have a biochemical effect, i.e., a basic shift in isoelectric point in three proteins. We have purified one of these proteins, raised an antibody to it, and isolated and sequenced its cDNA. At the amino acid level, the sequence shows 68% identity and 81% similarity to bovine smg p25a GDP dissociation inhibitor (GDI), a regulator of ras-like small GTPases of the rab/SEC4/YPT1 subfamily. The correlation between a basic shift in isoelectric point in Drosophila GDI in quartet mutant tissue and the quartet developmental phenotype raises the possibility that a posttranslational modification of GDI is necessary for its function and that GDI function is essential for development.     

Sequential analysis of early hematopoietic reconstitution following allogeneic bone marrow transplantation with fluorescence in situ hybridization (FISH)

Using in situ hybridization with an X and Y chromosome probe mixture, we have sequentially studied peripheral blood samples from 10 patients (four males/six females) in an HLA-matched allogeneic setting in order to monitor the kinetics of early hematopoietic reconstitution. Interphase cells from smears consisting of purified granulocytic and lymphocytic populations respectively were studied in three patients at 24, 48, 72 and 96 h post-transplant. This period was arbitrarily defined as the immediate post-transplant period. These three patients plus seven others were studied sequentially at days 5, 10, 15, 20, 25 and 50 post-transplant, defined as the intermediate post-transplant period. The X and Y probes were indirectly labelled with rhodamine and fluoresceine isothiocyanate, respectively. Donor neutrophils were detected as early as 24 h post marrow infusion followed by a significant expansion at 48 h. At 96 h post-transplant, the median percentage of donor neutrophils was > 90%. In the immediate post-transplant period, most of the lymphocytes were of recipient origin. However, we have documented a significant expansion in donor lymphocytes, starting at day 5 post-transplant in most patients. Almost complete chimerism for the myeloid and lymphoid lineages was established at days 10 and 25 post-transplant, respectively. All patients engrafted normally according to standard clinical criteria. Follow-up data for those surviving > or = 100 days (eight patients), showed persistence of this pattern of hematopoietic reconstitution in all but one patient. Molecular monitoring of early engraftment has enabled us to unravel a distinct biphasic pattern of myeloid and lymphoid engraftment.     

Selective pathway choice of a single central axonal fascicle by a subset of peripheral neurons during leech development

In the CNS of leech, the central projections of peripheral sensory neurons segregate into three distinct axonal tracts during early development. We have previously shown that a subset of these neurons, recognized by the monoclonal antibody lan 4-2, projects axons into only one of these fascicles (Johansen et al., 1992, Neuron 8, 599). Here we report on a developmental and biochemical characterization of another fascicle-specific antigen labeled by the monoclonal antibody lan 3-6. By immunocytochemistry and double labelings we demonstrate that the lan 3-6 epitope is expressed only by a small subgroup of the peripheral neurons in Macrobdella embryos. The axons of these neurons selectively fasciculate in the CNS, but to only one of the three lan 3-2-positive tracts, which is different from the previously described lan 4-2-positive tract. These observations support the existence of a hierarchy of guidance cues mediating specific tract formation in this system. A biochemical analysis of the antigen suggests that it is likely to be a glycosylated protein with a molecular weight of approximately 200 kDa. Thus, the restricted expression of the lan 3-6 antigen and its biochemical properties are consistent with the hypothesis that this antigen may be playing a role in axonal guidance.     

Controlled chemical modification of hyaluronic acid: synthesis, applications, and biodegradation of hydrazide derivatives

Controlled modification of the carboxylic acid moieties of hyaluronic acid with mono- and polyfunctional hydrazides leads to biochemical probes, biopolymers with altered physical and chemical properties, tethered drugs for controlled release, and crosslinked hydrogels as biocompatible scaffoldings for tissue engineering. Methods for polyhydrazide synthesis, for prodrug preparation, for hydrogel crosslinking, and for monitoring biodegradation are described.