Design and construction of a single tube, quantitative endpoint, LATE-PCR multiplex assay for ventilator-associated pneumonia.

AIMS: The goal of this study was to develop a molecular diagnostic multiplex assay for the quantitative detection of microbial pathogens commonly responsible for ventilator-associated pneumonia (VAP) and their antibiotic resistance using linear-after-the-exponential polymerase chain reaction (LATE-PCR). METHOD AND RESULTS: This multiplex assay was designed for the quantitative detection and identification of pathogen genomic DNA of methicillin-resistant Staphylococcus aureus (MRSA), Acinetobacter baumannii, Pseudomonas aeruginosa, plus a control target from Lactococcus lactis. After amplification, the single-stranded amplicons were detected simultaneously in the same closed tube by hybridization to low-temperature molecular beacon probes labelled with four differently coloured fluorophores. The resulting hybrids were then analysed by determining the fluorescence intensity of each of the four fluorophores as a function of temperature. CONCLUSIONS: This LATE-PCR single tube multiplex assay generated endpoint fluorescent contours that allowed identification of all microbial pathogens commonly responsible for VAP, including MRSA. The assay was quantitative, identifying the pathogens present in the sample, no matter whether there were as few as 10 or as many 100 000 target genomes. SIGNIFICANCE AND IMPACT OF THE STUDY: This assay is rapid, reliable and sensitive and is ready for preclinical testing using samples recovered from patients suffering from ventilator-associated pneumonia.

Design of a single-tube, endpoint, linear-after-the-exponential-PCR assay for 17 pathogens associated with sepsis.

AIMS: The goal of this study was to construct a single-tube multiplex molecular diagnostic assay using linear-after-the-exponential (LATE)-PCR for the detection of 17 microbial pathogens commonly associated with septicaemia. METHODS AND RESULTS: The assay described here detects 17 pathogens associated with sepsis via amplification and analysis of gene-specific sequences. The pathogens and their targeted genes were: Klebsiella spp. (phoE); Acinetobacter baumannii (gyrB); Staphylococcus aureus (spa); Enterobacter spp. (thdF); Pseudomonas aeruginosa (toxA); coagulase-negative staphylococci (tuf), Enterococcus spp. (tuf); Candida spp. (P450). A sequence from an unidentified gene in Lactococcus lactis, served as a positive control for assay function. LATE-PCR was used to generate single-stranded amplicons that were analysed at endpoint over a wide range of temperatures in four fluorescent colours. Each target was detected by its pattern of hybridization to a sequence-specific low-temperature fluorescent probe derived from molecular beacons. CONCLUSIONS: All 17 microbial targets were detected in samples containing low numbers of pathogen genomes in the presence of high levels of human genomic DNA. SIGNIFICANCE AND IMPACT OF THE STUDY: This assay used new technology to achieve an advance in the field of molecular diagnostics: a single-tube assay for detection of pathogens commonly responsible for septicaemia.

Verification of monoplex and multiplex linear-after-the-exponential PCR gene-specific sepsis assays using clinical isolates.

AIMS: To verify monoplex and multiplex gene-specific linear-after-the-exponential polymerase chain reaction (LATE-PCR) assays for identifying 17 microbial pathogens (i.e., Klebsiella sp., Acinetobacter baumannii, Staphylococcus aureus, Enterobacter sp., Pseudomonas aeruginosa, coagulase negative staphylococci, Enterococcus sp., Candida sp.) commonly associated with septicaemia using clinical isolates. METHODS AND RESULTS: Clinical isolates of each target pathogen were collected from the University of California, Davis Medical Center (UCDMC) microbiology laboratory. Five microlitres (µl) of each culture suspension (1 × 10(8) CFU ml(-1) ) were added to 20 µl of monoplex mastermix. DNA extracted from clinical isolates was tested in multiplex. Monoplex assays demonstrated 100% sensitivity at this input level, except Enterobacter cloacae (2.7%), Ac. baumannii (57%) and Ps. aeruginosa (97.8%). All clinical isolates were positive in multiplex, with the exception of two Ac. baumannii, two Klebsiella oxytoca and two Candida parapsilosis isolates. CONCLUSIONS: Sixteen pathogens can be identified by monoplex LATE-PCR assays with sensitivities ≥ 97.8%. The multiplex assay demonstrated 91.4% sensitivity when tested with DNA extracted from 70 different target strains. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrates the potential of LATE-PCR to serve as an adjunct to culture if the reagents are optimized for sensitivity. Results warrant further testing through analytical and clinical validation of the multiplex assay.

Design and optimization of a novel reverse transcription linear-after-the-exponential PCR for the detection of foot-and-mouth disease virus.

AIMS: A novel molecular assay for the detection of foot-and-mouth disease virus (FMDV) was developed using linear-after-the-exponential polymerase chain reaction (LATE-PCR). METHODS AND RESULTS: Pilot experiments using synthetic DNA targets demonstrated the ability of LATE-PCR to quantify initial target concentration through endpoint detection. A two-step protocol involving reverse transcription (RT) followed by LATE-PCR was then used to confirm the ability of the assay to detect FMDV RNA. Finally, RT and LATE-PCR were combined in a one-step duplex assay for co-amplification of an FMDV RNA segment and an internal control comprised of an Armored RNA. In that form, each of the excess primers in the reaction mixture hybridize to their respective RNA targets during a short pre-incubation, then generate cDNA strands during a 3-min RT step at 60°C, and the resulting cDNA is amplified by LATE-PCR without intervening sample processing. CONCLUSIONS: The RT-LATE-PCR assay generates fluorescent signals at endpoint that are proportional to the starting number of RNA targets and can detect a range of sequence variants using a single mismatch-tolerant probe. SIGNIFICANCE AND IMPACT OF THE STUDY: In addition to offering improvements over current laboratory-based molecular diagnostic assays for FMDV, this new assay is compatible with a novel portable ('point-of-care') device, the BioSeeq II, designed for the rapid diagnosis of FMD in the field.

Xenopus fibrinogen: characterization of the mRNAs for the three subunits.

We purified and characterized the mRNAs coding for each of the three subunits of Xenopus fibrinogen. Purification was accomplished by electrophoretic separation of liver polyadenylated RNA in a fully denaturing gel, followed by recovery of the RNA from the gel via transfer to an ion-exchange membrane. This procedure yielded fractions which were highly enriched for the mRNAs for each of the fibrinogen chains. The fibrinogen mRNAs were identified by two methods: (i) in vitro translation followed by subunit-specific cleavage with the proteases thrombin and batroxobin; and (ii) cross-hybridization with cDNA clones for individual subunits of rat fibrinogen. The results demonstrate that the A alpha and gamma chains of frog fibrinogen are each coded by a single mRNA species. The A alpha mRNA is ca. 3,100 nucleotides in length, which is nearly twice the minimum size required to code for the A alpha precursor polypeptide. The gamma chain mRNA comprises about 1,600 bases and includes only a small untranslated region. In contrast, the B beta subunit is synthesized from two mRNAs, one of which is 2,500 and the other 1,800 nucleotides long. The 2,500-base mRNA includes a large noncoding region, whereas the smaller one is near the minimum required size. The larger B beta mRNA is ca, fivefold more abundant that the smaller species.

Two-dimensional DNA gel electrophoresis as a method for analysis of eukaryotic genome structure: evaluation using Tetrahymena thermophila DNA.

There is growing interest in mapping and analyzing complete eukaryotic genomes. Yee and Inouye (in Experimental Manipulation of Gene Expression, pp. 279-290, Academic Press, New York) demonstrated that bacterial chromosomes can be resolved into interpretable patterns of DNA fragments by means of restriction enzyme digestion and electrophoresis in two dimensions. We have begun to explore applications of this procedure to analysis of eukaryotic genomes, which are far more complex. Tetrahymena thermophila was selected as a model organism because its genome is small, roughly equivalent to that of a single human chromosome. In addition, each Tetrahymena cell contains two nuclei which differ in sequence composition and methylation. Our results demonstrate that the Tetrahymena genome can be resolved into complex patterns of fragments in two dimensions. Hybridization to Southern blots of these gels with a multiply repeated sequence probe yielded analyzable patterns of a subset of the genome. The blots reveal alterations in genome structure due to methylation and rearrangement. Future extensions of the method are discussed.

Estrogen induction of a 45 kDa secreted protein coordinately with vitellogenin in Xenopus liver.

In the frog Xenopus laevis, vitellogenin is the major estrogen-induced protein in the liver. We have characterized an additional secreted protein, of 45,000 Da and designated Ep45, which is also responsive to estrogen treatment. Like vitellogenin, Ep45 is not normally found in the plasma nor synthesized by the liver of the male frog. Its synthesis increases 6-fold between days 2 and 8 following a single 2 mg injection of estradiol-17 beta. For comparison, we have also studied a third estrogen-regulated protein, Ep20, with a molecular weight of approximately 20,000. This protein exhibits a different set of characteristics with regard to hormone responsiveness. Ep20 is synthesized in the liver of normal males and therefore is not absolutely hormone-dependent. Its level increases only about 4-fold following estrogen stimulation. The messenger RNAs for both Ep45 and Ep20 have been identified and purified, using a high-resolution RNA fractionation technique. By this procedure, it was possible to demonstrate that following high doses of estrogen the predominant mRNAs in the liver are those coding for vitellogenin, Ep45 and Ep20. Thus estrogen suppression of virtually all other liver proteins appears to act at the messenger RNA level for intracellular as well as secreted proteins.

Injection of Xenopus eggs before activation, achieved by control of extracellular factors, improves plasmid DNA replication after activation.

Injection of molecular probes into unfertilized Xenopus eggs requires suppression of activation. But the unfertilized egg is poised for activity, and pricking, like sperm penetration, triggers the start of the first cell cycle. Methods of suppressing activation generally rely on introduction of drugs into the cell, but some of these techniques are irreversible. I report here that injection without activation can also be accomplished by simply limiting extracellular free Ca2+ to 1-2 microM. The site of injection heals, but the cortex does not contract. Gentle modification of the vitelline envelope, which causes it to become tougher, improves the rate of healing to about 100%. Healed eggs are stable for hours and can be activated when needed. Injection of a plasmid derived from type 1 bovine papilloma virus revealed that replication occurs only after activation, but preloading the DNA markedly increased the efficiency of first-round replication. DNA interaction with the unactivated egg cytoplasm may therefore be required for efficient replication of exogenous DNA. The new procedures described here are likely to be of general utility.

The view from Cairo.

PIP: The author, a Brandeis University biologist who attended the 1994 International Conference on Population and Development, cautions against optimism regarding the global impact of this gathering in the absence of revolutionary changes in four areas: reproductive practices, sexual behavior, human consumption of natural resources, and population crowding. Few speakers at Cairo addressed the ecologic and climatologic consequences of overpopulation and environmental destruction, despite indications that the earth is reaching the limits of its environmental support system. Another concern is the conflict between contraceptive methods that are most effective in preventing pregnancy and the condom use that is essential to halt the spread of acquired immunodeficiency syndrome (AIDS). In countries such as China, where the AIDS epidemic's threat has been minimized by the government, massive educational campaigns will be required to convince sterilized couples that they must now practice safe sex. Also criticized is the assumption that population stabilization is achievable through a balance in birth and death rates. It is likely that environmental instability and other factors will lead to substantially increased mortality in the years ahead. Needed is a new global ethics based on biological realities and valuation of the environment.^ieng

Liver parenchymal cell proliferation during secondary induction with estradiol-17 beta in Xenopus.

We have previously demonstrated that injection of adult male frogs with estradiol-17 beta causes extensive proliferation of liver parenchymal cells together with the induction of vitellogenin (R. J. Spolski, W. Schneider, and L. J. Wangh (1985) Dev. Biol. 108, 332-340). In addition, purified parenchymal cells placed in culture synthesize DNA in an estrogen-dependent manner (B. S. Aprison, L. Martin-Morris, R. J. Spolski, and L. J. Wangh (1986) In Vitro 22, 457-464). We now describe conditions under which secondary exposure to estradiol-17 beta, either in vivo or in vitro, can lead to further DNA synthesis and cell division. The extent of this proliferation depends upon both the magnitude of the primary dose and the length of time elapse before secondary stimulation. A hormone dose of 0.5 mg, which causes little cell proliferation initially, allows for maximal secondary proliferation in response to 2.0 mg, while a maximal primary dose of 2.0 mg substantially inhibits further division in response to a secondary treatment with the same hormone dose. Cell culture experiments demonstrate that the failure of liver cells, in maximally stimulated males, to synthesize DNA in response to estrogen is not irreversible. But, cell crowding in culture does restrict DNA synthesis. The restrictions seen in vivo may therefore be due to structural features of the intact tissue rather than to terminal differentiation at the genetic level. These results are discussed with regard to our understanding of hormone-dependent differentiation in the frog liver system.

Xenopus fibrinogen synthesis and secretion. Analysis of precursor polypeptides and their post-translational modification.

Xenopus fibrinogen is distinct from that of mammals in that the B beta subunit of the secreted protein has a higher apparent molecular weight than either the A alpha or the gamma subunit. A precursor polypeptide for each subunit was identified among the products translated in vitro from liver mRNA. Pre-A alpha is larger than pre-B beta and pre-gamma is the smallest of the three. Purified liver parenchymal cells cultured in the presence of tunicamycin secrete fibrinogen polypeptides which lack carbohydrate moieties. Our analysis of these forms of Xenopus fibrinogen demonstrated the presence of a signal peptide on each of the precursor polypeptides, the loss of a COOH-terminal peptide from the pre-A alpha chain, and the presence of one carbohydrate moiety on the mature gamma chain and two carbohydrate moieties on the mature B beta chain. The B fibrinopeptide on the NH2-terminus of the B beta chain is unusually large. The number of amino acids in this peptide is approximately twice that characteristic of mammalian B fibrinopeptides and it is glycosylated. On the basis of these data, together with information in the literature, we propose that when vertebrates first arose the B fibrinopeptide was a large glycosylated peptide. It retained this basic structure during the evolution of all subsequent vertebrates, with the exception of mammals. In contrast, the A fibrinopeptide increased in length early in vertebrate evolution. The alpha portion of the A alpha subunit of fibrinogen appears to have originally been a polypeptide about the same length as the beta chain. Concomitant with the evolution of mammals, the alpha polypeptide significantly increased in length.

Efficient recovery of functionally intact mRNA from agarose gels via transfer to an ion-exchange membrane.

A simple method is described for the efficient recovery of intact mRNA from high resolution agarose gels. Fractionation of RNA is accomplished by gel electrophoresis under denaturing conditions using methylmercuric hydroxide. The RNA in the gel is then transferred electrophoretically to a diethylaminoethyl (DEAE)-membrane. After reversing the methylmercuric modification of the RNA, the membrane is sliced into narrow sections and the RNA is eluted at 65 degrees with a high ionic strength buffer containing 6M guanidine hydrochloride. RNA isolated by this procedure is suitable for subsequent enzymatic reactions, including in vitro translation and reverse transcription. The major advantages offered by this procedure are: 1) The membrane-bound RNA is a replica of the high resolution fractionation pattern achieved in the gel. 2) The immobilization and concentration of RNA and the removal of gel matrix contaminants are all accomplished in one step. 3) Small quantities of RNA are efficiently recovered and are suitable for subsequent biochemical manipulations. The method is of general utility for any biological system. We have applied its use to the fractionation, recovery, and analysis of mRNA from Xenopus liver and have identified cDNA clones complementary to albumin mRNA.

Synthesis of vitellogenin in cultures of male and female frog liver regulated by estradiol treatment in vitro.

Using the frog Xenopus laevis, we show that the addition of physiological concentrations of estradiol to cultures of liver from untreated males rapidly induces the synthesis of large amounts of vitellogenin. Sustained synthesis of vitellogenin requires continuous exposure to estradiol. A nonestrogenic steroid, dexamethasone, does not induce vitellogenin synthesis but does induce increased synthesis of a different protein in liver cultures.

New insights into the mechanisms of nuclear segmentation in human neutrophils.

During human neutrophil differentiation, large portions of the genome condense and associate with the nuclear envelope to form filament-like structures. As a result, the nucleus of the mature neutrophil typically consists of a linear array of three or four lobes joined by thin, DNA-containing filaments. Despite the medical significance of neutrophil nuclear morphology, little is known about the events regulating neutrophil nuclear differentiation and its pathological states. This work presents a new model of the mechanisms governing nuclear filament formation in human neutrophils. This model is based on recent chromosome mapping studies in human neutrophils and on studies of genetic and pathological conditions affecting neutrophil nuclear shape. According to this model, filament assembly is initiated by factors that interact with specific regions of the genome in a hierarchical and dose-dependent manner. In this regard, the strategies governing the molecular interactions responsible for filament formation appear to resemble those involved in transcriptional silencing, a phenomenon that also affects the properties of extended chromosomal regions. According to the silencing paradigm, bound filament control Factors must recruit additional Filament Foehn factors which spread along adjacent DNA to mediate filament formation. A better understanding of the factors that shape the neutrophil nucleus may lead to new clinical tools for the diagnosis and manipulation of abnormal neutrophil differentiation.

Fluorescent in situ hybridization (FISH) analysis of the relationship between chromosome location and nuclear morphology in human neutrophils.

Human neutrophil nuclei typically consist of three of four large heterochromatic lobes joined by thin, DNA-containing filaments. In addition, some lobes exhibit appendages of various sizes and shapes. Classical genetic and cytological studies suggest that some appendages contain specific chromosomes. The studies reported here provide the first detailed analysis of the spatial relationship between individual chromosomes and recognizable structures in neutrophil nuclei using fluorescent in situ hybridization. Analysis of DNA sequences in chromosomes 2, 18, X, and Y demonstrate that specific lobes in a population of neutrophil nuclei do not have a fixed chromosome content. This result implies that chromosomes partition randomly among lobes during neutrophil differentiation. However, neutrophil nuclear topography is not entirely fortuitous. For instance, none of the sequences probed in this study mapped to a filament and most centromeres lie in clusters near the nuclear periphery. In addition, one of the X chromosome centromeres in females and the Y chromosome centromere in males consistently associate with specific nuclear appendages found in a subset of neutrophil nuclei. Chromosomes 2 and 18 occupy discrete nd separate territories within individual lobes and neither territory ever extends into a filament. Surprisingly, the sizes of these territories are not proportional to chromosome length, suggesting that individual neutrophil chromosomes vary in their degree of compaction. These results are discussed in the light of models that attempt to explain nuclear morphology in terms of chromosome spatial organization.

Estrogen-dependent DNA synthesis and parenchymal cell proliferation in the liver of adult male Xenopus frogs.

Estradiol-17 beta treatment of adult male Xenopus laevis induces liver parenchymal cells to synthesize DNA and proliferate. DNA synthesis begins 3 to 4 days after estrogen treatment and continues for approximately 10 days. Over this 2-week period, the total number of liver parenchymal cells increases fourfold, the wet weight of the liver remains constant, and there is a 50% reduction in cell volume. The elevated number of cells persists for several months and then returns to the control value. The extent of proliferation is hormone dose dependent. Pulse-chase experiments demonstrate that as a result of hormone treatment a minority of the parenchymal cells in the initial population enter the cell cycle, and via repeated divisions become the majority (79%) of the population by Day 14. The implications of this phenomenon for estrogen-induced liver cell differentiation and vitellogenin gene function are discussed.

The efficiency and timing of plasmid DNA replication in Xenopus eggs: correlations to the extent of prior chromatin assembly.

Injection of the circular plasmid FV1 (derived from type I bovine papilloma virus) into Xenopus eggs before the start of the first cell cycle dramatically increases the efficiency of plasmid replication once eggs are chemically activated. We call this the preloading effect and report kinetic and quantitative characterization of this phenomenon here. The timing and the amount of FV1 synthesis were measured by both BrdUTP density labelling and an optimized method of selective enzymatic digestion of replicated and unreplicated molecules using the three methyladenosine-sensitive isoschizomers, DpnI, MboI and Sau3a. DpnI in 100 mM NaCl proved particularly useful for distinguishing and quantitating unreplicated, once-replicated, and repeatedly replicated molecules accumulated over several cell cycles. Our results reveal that both the amount of DNA replicated and the timing of synthesis during the first S-phase correlate with the length of the preloading period. Longer preloading leads to larger amounts of DNA being replicated sooner. In fact, up to 30-50% of 1 ng injected plasmid can replicate in a semiconservative cell cycle-dependent manner during the first S-phase. But such high levels of synthesis during the first cell cycle appear to limit the egg's ability to rereplicate this material in subsequent cell cycles. The preloading effect does not depend on synthesis of either viral or egg proteins, but does appear to correlate with the extent of plasmid assembly into chromatin before the start of the cell cycle. We postulate that each plasmid molecule must achieve a critical degree of chromatin assembly before it can proceed along the replication pathway. These observations illuminate some of the difficulties inherent in building a vector for gene insertion into Xenopus embryos, but also suggest an experimental strategy toward this aim.

Nonrandom location and orientation of the inactive X chromosome in human neutrophil nuclei.

The nuclei of human neutrophils typically consist of a linear array of three or four lobes joined by DNA-containing filaments. Terminal lobes are connected to internal lobes via a single filament, while internal lobes have two filaments, each to an adjacent lobe. Some lobes also have appendages of various shapes and sizes. In particular, up to 17% of neutrophil nuclei of healthy women exhibit a drumstick-shaped appendage that contains the inactive X chromosome. This report provides a detailed analysis of the relationship between nuclear morphology and the location of the X and Y chromosomes in human neutrophils. Fluorescent in situ hybridization analysis revealed that the X and the Y chromosomes of male neutrophil nuclei are randomly distributed among nuclear lobes. Similarly, in female neutrophil nuclei with a drumstick appendage, the active X chromosome is also randomly distributed among lobes. In contrast, the inactive X chromosome is preferentially located in a terminal lobe in over 90% nuclei with drumsticks. Within the terminal lobe of nuclei with drumsticks, the inactive X chromosome lies distal to the point of filament attachment in 80% of the nuclei. The inactive X chromosome also exhibits a specific orientation within the drumstick appendage, with over 95% of nuclei having the X centromere located toward the tip of the appendage. Female nuclei without a drumstick appendage also have one of the X chromosomes (presumably the inactive chromosome) preferentially situated in a terminal lobe. Nonrandom distribution of the inactive X chromosome is discussed in the context of a model that considers chromosomes as determinants of neutrophil nuclear morphology.

Replication of Xenopus erythrocyte nuclei in a homologous egg extract requires prior proteolytic treatment.

Reactivation and reinitiation of DNA replication in quiescent frog erythrocyte nuclei has been analyzed following incubation in extracts prepared from activated Xenopus eggs. Nuclear decondensation and DNA synthesis only occurred if nuclei were pretreated with low doses of trypsin. This protease treatment did not digest histones, but did degrade several nonhistone proteins. Activated erythrocyte nuclei swell and begin DNA synthesis by 30 min after being mixed with the egg extract. In some extracts virtually complete genome replication was achieved in all nuclei after 2-3 hr. Addition of several protease inhibitors during sperm nuclear isolation significantly reduced the template efficiency of these preparations. We concluded that proteolytic alteration of nonhistone nuclear structural proteins may be a general mechanism which permits quiescent nuclei to reenter the replication cycle. Erythrocyte nuclei and egg extracts provide an excellent experimental system in which to investigate the processes of nuclear reactivation.