Polymerase Chain Reaction molecular diagnostic technology for monitoring chronic osteomyelitis

BACKGROUND

Osteomyelitis is a devastating condition whose treatment relies on the detection of bacteria. The current standard of microbiology culture may not be adequate. Molecular biology based diagnostic procedures for detecting bacteria in orthopaedic infections was previously established, but has not been applied to the setting of chronic osteomyelitis. We aim to determine the applicability of molecular diagnostic procedures for monitoring chronic osteomyelitis, and to evaluate if these procedures are superior to standard culture methods of osteomyelitis detection.

METHODS

A rabbit experimental model of chronic osteomyelitis was used; infection was induced in the proximal, medial aspect of the tibia with Staphylococcus aureus at titers ranging from 1 × 10(2) to 1 × 10(6) colony forming units. At 28 days post-infection, animals were sacrificed, and the tibias were examined radiographically, harvested, and assayed for the presence of bacteria. Two bacterial detection methods were used: (1) standard microbiological culturing, and (2) polymerase chain reaction (PCR) based diagnostic method to detect bacterial genomic DNA.

RESULTS

The molecular diagnostic method was highly sensitive and accurate, and detected low titer infections that were undetected by radiographic and microbiological methods. By using two sets of PCR primers, one for a universal bacterial gene (16S rRNA) and one for a species-specific gene (nuc), the molecular protocol allowed both the detection and speciation of the bacterial infection.

CONCLUSIONS

The use of the PCR-based method was effective for high-sensitivity detection and identification of bacteria associated with chronic osteomyelitis in a rabbit model. Our findings illustrate the applicability of PCR for monitoring chronic osteomyelitis, which may be useful for improved detection of osteomyelitis organisms in humans.

The accuracy of chromosomal microarray testing for identification of embryonic mosaicism in human blastocysts

Background

Most previous studies of chromosomal mosaicism in IVF embryos were performed by fluorescence in situ hybridization (FISH) methods. While there are reports implicating chromosome aneuploidy in implantation failure following transfer and pregnancy loss by spontaneous miscarriage, the significance of mosaicism for the developmental potential of growing embryos is unknown. However, the low prevalence of chromosomal mosaicism in chorionic villus sampling and amniotic fluid specimens suggests the presence of selection against mosaic embryos for implantation and early pregnancy. The absence of evidence for selective allocation of abnormal cells to the trophectoderm (TE) of mosaic blastocysts permits these cells to be a good proxy for embryonic mosaicism detection by chromosomal microarrays (CMA). The purpose of this study was to establish the limits of detection and the prevalence of chromosome mosaicism in day 5/6 human embryos using CMA with TE biopsies.

Results

From reconstitution experiments we established log₂ ratio thresholds for mosaicism detection. These studies indicated that chromosomal mosaicism at levels as low as between 25-37% can be consistently identified. Follow-up studies by FISH on non-transferred abnormal embryos confirmed the diagnostic accuracy of CMA testing. The number of cells in a TE biopsy can influence mosaicism detection.

Conclusions

Chromosomal microarrays can detect mosaicism in TE biopsies when present at levels as low as between 25-37% and the prevalence of day 5/6 blastocysts which were mosaic and had no other abnormalities reached 15% among a cohort of 551 embryos examined. Validated protocols for establishing detection thresholds for mosaicism are important to reduce the likelihood of transferring abnormal embryos.

MOLECULAR DETECTION OF INFECTION IN TOTAL KNEE ARTHROPLASTY: A CLINICAL CORRELATION

Total knee arthroplasty patients displaying symptoms consistent with either implant biomechanical failure or periprosthetic infection, and requiring revision surgery, had synovial fluid aspirated from the affected joint and subjected to standard microbiological culture testing for bacterial infection. In this study, an aliquot of each synovial fluid specimen was analyzed for infection using the rapid, sensitive molecular assay of polymerase chain reaction (PCR), designed to selectively amplify bacterial deoxyribonucleic acid. Decisions concerning surgical procedures performed during revision surgery were based entirely on clinical criteria, including standard preoperative evaluation for infection, independent of PCR results. In total, on the basis of pre- and/or intraoperative clinical data in conjunction with postoperative information, septic failure was determined in 31 of 50 patients, all of whom tested positive using the PCR assay. This correlative study validates the application of the PCR assay for clinical evaluation of arthroplasty infections.

Malignant precursor cells pre-exist in human breast DCIS and require autophagy for survival

Background

While it is accepted that a majority of invasive breast cancer progresses from a ductal carcinoma in situ (DCIS) precursor stage, very little is known about the factors that promote survival of DCIS neoplastic cells within the hypoxic, nutrient deprived intraductal microenvironment.

Methodology and Principal Findings

We examined the hypothesis that fresh human DCIS lesions contain pre-existing carcinoma precursor cells. We characterized these cells by full genome molecular cytogenetics (Illumina HumanCytoSNP profile), and signal pathway profiling (Reverse Phase Protein Microarray, 59 endpoints), and demonstrated that autophagy is required for survival and anchorage independent growth of the cytogenetically abnormal tumorigenic DCIS cells. Ex vivo organoid culture of fresh human DCIS lesions, without enzymatic treatment or sorting, induced the emergence of neoplastic epithelial cells exhibiting the following characteristics: a) spontaneous generation of hundreds of spheroids and duct-like 3-D structures in culture within 2–4 weeks; b) tumorigenicity in NOD/SCID mice; c) cytogenetically abnormal (copy number loss or gain in chromosomes including 1, 5, 6, 8, 13, 17) compared to the normal karyotype of the non-neoplastic cells in the source patient's breast tissue; d) in vitro migration and invasion of autologous breast stroma; and e) up-regulation of signal pathways linked to, and components of, cellular autophagy. Multiple autophagy markers were present in the patient's original DCIS lesion and the mouse xenograft. We tested whether autophagy was necessary for survival of cytogenetically abnormal DCIS cells. The lysosomotropic inhibitor (chloroquine phosphate) of autophagy completely suppressed the generation of DCIS spheroids/3-D structures, suppressed ex vivo invasion of autologous stroma, induced apoptosis, suppressed autophagy associated proteins including Atg5, AKT/PI3 Kinase and mTOR, eliminated cytogenetically abnormal spheroid forming cells from the organ culture, and abrogated xenograft tumor formation.

Conclusions

Cytogenetically abnormal spheroid forming, tumorigenic, and invasive neoplastic epithelial cells pre-exist in human DCIS and require cellular autophagy for survival.

Advances in the diagnosis of infection in prosthetic joint implants

The widespread use and dramatic success of prosthetic joint implant surgery (arthroplasty) has greatly improved the quality of life for many individuals suffering from degenerative, arthritic, or injured joints. However, in a number of cases, recipients experience discomfort at the arthroplasty site that can signal biomechanical failure, or periprosthetic infection of the joint, or both. In fact, infection remains a devastating obstacle, preventing arthroplasty from being an almost perfect medical procedure. Existing tests for the diagnosis of infection in orthopedics are disappointing because of the relatively high frequency of false negative results. To overcome this shortcoming, and to reduce the number of infected revision arthroplasties, a methodology based on molecular biology has been established. The method allows the rapid, sensitive and accurate diagnosis of orthopedic infections, and should aid the clinician with treatment regimens, surgical decisions, and overall patient management in the growing arthroplasty population.

Cloning and characterization of chicken Paraxis: a regulator of paraxial mesoderm development and somite formation

To investigate the molecular regulation of embryonic somite formation and development, we have cloned the full-length cDNA and characterized the embryonic expression profile of chicken Paraxis, a member of a novel family of basic helix-loop-helix (bHLH) proteins, which has been suggested to play a role in paraxial mesoderm development. Chicken Paraxis encodes a 1.35-kb mRNA and contains a 53-amino-acid residue bHLH domain, identical in sequence to that found in the mammalian Paraxis genes of mouse, hamster, and human. Northern analysis revealed significant Paraxis expression in the early embryo up to the 30- to 35-somite stage, declining from Incubation Day 4 on and becoming undetectable by Day 5. By whole-mount in situ hybridization, Paraxis expression is first seen distinctly in the emerging paraxial mesoderm of the primitive streak stage chick embryo. During gastrulation, Paraxis expression in the mesoderm defines bilaterally symmetric crescents located immediately rostral to Hensen's node and appears to pre-configure the emerging somitic mesoderm. During somite development, Paraxis expression is evident in the rostral segmental plate and the newly formed somites, although the level of expression clearly decreases in the more mature somites. By the 10-12th pair of somites, counting from the caudal end, Paraxis expression appears to be preferentially localized to the medial aspect of individual somites. Histological analysis showed that Paraxis expression is evenly distributed in the newly formed caudal epithelial somites, then localized to the medial portion of maturing somites, and preferentially localized in the dermomyotome of more rostral somites before diminishing to undetectable levels in the most cranial somites. The functional involvement of Paraxis in somite development was assessed by perturbing its expression in somitic stage chick embryos using a Paraxis-specific antisense oligonucleotide. Disruption of somite formation from the paraxial mesoderm was observed in 67% of the surviving topically treated embryos, whereas control embryos treated with sense or random sequence oligonucleotides did not show similar effects. In addition, direct injection of Paraxis-specific antisense oligonucleotide into the paraxial mesoderm produced discrete segmentation anomalies which correlated spatially with the site of injection. Whole-mount in situ hybridization revealed that the regions defective in somite formation displayed perturbed Paraxis expression and a reduction of Pax-1 expression, a marker for epithelial somites and sclerotome. Histological analysis indicated poor condensation and/or epithelization of the somitic mesoderm. Finally, embryos treated with valproic acid, a known teratogen which affects somite segmentation, showed perturbed Paraxis expression, suggesting that the mechanism of action of this teratogen involves a pathway(s) requiring Paraxis activity. These data provide evidence that Paraxis acts as an important regulator of paraxial mesoderm and somite development and functions in axial patterning of the chick embryo.

Effects of cadmium on trophoblast calcium transport

Maternal exposure to cadmium (Cd) during pregnancy has been linked to low fetal birthweight, which may be attributed to placental damage and/or dysfunction in nutrient transport. Previous studies have suggested that Cd is accumulated in the placenta, and that placental transport of calcium (Ca) and zinc (Zn) is perturbed by Cd. To investigate the mechanism of Cd perturbation of Ca transport, we used JEG-3, a human choriocarcinoma cell line which exhibits trophoblastic properties, to analyse Cd effects in vitro. Treatment with Cd at low, physiologically relevant concentrations (e.g. 0.04 microM) did not result in obvious changes in cell morphology or integrity, whereas higher concentrations (> or = 0.16 microM) affected cell integrity. With lower concentrations of Cd treatment for 24 h, activities of cellular Ca uptake and transport, and Ca2+ binding were decreased, and intracellular [Ca2+] ([Ca2+]i) profile was also altered; however, membrane-associated Ca(2+)-activated ATPase activity remained relatively unchanged. Interestingly, cellular Ca uptake activity was unaffected by short-term (30 min) Cd pretreatment. The 24-h Cd treatment also resulted in elevated expression of the metal-binding protein, metallothionein, whereas the expression of a trophoblast-specific cytosolic Ca(2+)-binding protein (HCaBP) was drastically reduced. These results strongly suggest that Cd exposure significantly compromises the Ca handling ability of trophoblastic cells; this effect is probably not due to perturbations in Ca channel or membrane Ca pump activities, but rather a consequence of alterations in subcellular, cytosolic Ca2+ binding activities.

Chicken Pax-1 gene: structure and expression during embryonic somite development

Recent mouse genetic studies have implicated Pax-1, a paired-box-containing gene, in sclerotomal differentiation and vertebral body formation. To investigate Pax-1 function in somitic sclerotomal differentiation in the chick embryo, we have cloned the chicken Pax-1 gene, and its full length cDNA, and characterized its temporal and spatial expression pattern during somite development. Sequence analysis shows that chicken Pax-1 is highly homologous to murine and human Pax-1 genes with respect to the putative DNA-binding paired-box domain and the octapeptide domain. Northern analysis using probes derived from the paired-box domain and a unique non-paired box sequence of chicken Pax-1 detected 2-kb mRNA transcript. The expression profiles of Pax-1 were examined by in situ hybridization and Northern analysis. The first detectable expression of Pax-1 is seen in the most caudal epithelial somite. As the somite matures, Pax-1 expression takes on a medial distribution, thus corresponding to but preceding the emergence of the sclerotome. In the more mature, rostral somites (stage V and older), Pax-1 expression is found to be progressively localized first to the ventral-medial regions, and then to the caudal-ventral-medial quadrant of the mature somite. This pattern strongly supports the notion that Pax-1 expression is involved in somitogenesis and sclerotomal differentiation, and that it is subsequently a characteristic of the caudal half of the sclerotome, the presumptive precursor of vertebral cartilage. Northern analysis substantiated this expression profile and further revealed that the level of somitic Pax-1 expression increases as a function of embryonic development. Finally, we subjected chicken embryos to controlled heat shock treatment to perturb somite formation and segmentation. The pattern of Pax-1 expression in the anomalous somitic structures generated by controlled heat shock further supports a functional role for Pax-1 in somite development.

The Coventry Award. Polymerase chain reaction detection of bacterial infection in total knee arthroplasty

Synovial fluid aspirates from 50 patients with symptoms after total knee arthroplasty were analyzed by means of the polymerase chain reaction for the presence of bacterial deoxyribonucleic acid indicative of infection. Synovial fluid specimens were processed using a rapid bacterial lysis and extraction protocol, subjected to polymerase chain reaction amplification using universal bacterial primers, and polymerase chain reaction products analyzed by deoxyribonucleic acid hybridization methodology. Polymerase chain reaction testing on preoperative aspirates yielded 32 specimens positive for bacterial infection. Standard microbiologic culturing assays performed on the same samples gave 6 positive bacterial infection tests; intraoperative culturing identified 9 additional infected specimens. All culture positive specimens were polymerase chain reaction positive; in contrast, there were no false polymerase chain reaction positives in 21 negative control specimens obtained from aseptic joints. The synovial fluid processing protocol and polymerase chain reaction analysis can be performed with a minimum of time and may provide greater sensitivity than standard diagnostic tests. In view of the high incidence of false negative test results from standard microbiologic assays of synovial fluid specimens, the use of molecular biology based bacterial detection methodology should provide an additional, or alternative, assay to identify infected patient specimens.

Valproic acid-induced somite teratogenesis in the chick embryo: relationship with Pax-1 gene expression

The repeated pattern of the axial skeleton results from the segmentation and re-segmentation of the mesodermally derived somites. During these early events of somite development, the vertebrate embryonic axial skeleton is most susceptible to the teratogenic effects of a variety of pharmaceutical and environmental agents. One example is the anticonvulsant drug valproic acid (VPA), which has been shown to cause craniofacial and minor and major skeletal defects in human and animal embryos. We hypothesize that a candidate set of molecular targets of teratogens are the Pax family of pattern-forming genes, specifically Pax-1, which has been previously demonstrated to be an important regulator of axial skeletal patterning at the somite level. In this study, early developmental stage chick embryos were treated with VPA and dose-dependent malformations in somite development were observed. Two classes of anomalies were evident: class I included discrete sites of somitic fusions or mis-segmentation, and Class II included large areas of disorganized somite patterning. Northern blot analysis revealed a decreased level of Pax-1 expression in VPA-treated embryos. Whole mount in situ hybridization analysis showed that somite anomalies correlate spatially with regions of decreased Pax-1 expression. Finally, comparison of the VPA-induced somitic anomalies with those caused by gene-specific perturbation of Pax-1 gene expression through the use of an antisense oligonucleotide revealed significant similarities. Taken together, these results support the hypothesis that Pax-1 is a molecular target in VPA axial skeletal teratogenicity.

Analysis of regulatory elements of the developmentally controlled chorion s15 promoter in transgenic Drosophila

The Drosophila s15 chorion gene is expressed only in the follicular epithelium surrounding the developing oocyte, with tight quantitative control and a very narrow temporal specificity. We have used germ-line transformation analysis to conduct an extensive mutational dissection of its promoter between -189 and -39 bp relative to the transcriptional start site. Quantitative control and temporal specificity are disrupted by several of these mutations. The results suggest that this 150-bp DNA region encompasses many positive and negative, at least partially degenerate, cis-regulatory elements, which are involved in specifying the highly precise expression pattern of the s15 gene during development.

Development of a novel, rapid processing protocol for polymerase chain reaction-based detection of bacterial infections in synovial fluids

We describe the development of a molecular detection system designed for use with synovial fluid (SF)-based infections. The methodology employs a lysis/extraction procedure that effectively disrupts microorganisms allowing for release of the microbial DNA and its amplification by polymerase chain reaction (PCR). We tested the effectiveness of adding a mixed-bed, ion-exchange resin to the extract to remove PCR inhibitory components present in the SF. After centrifugation to separate the resin, DNA contained in the supernatant is subjected to PCR using oligonucleotide primers designed for broad-spectrum microorganism detection. Amplification products are analyzed by agarose gel electrophoresis and/or DNA hybridization methodology. We report here the detection sensitivity and specificity of the protocol using SF inoculated with Escherichia coli and Staphyloccocus aureus. We have applied this new methodology to clinical SF specimens with results superior to standard laboratory culturing assays.

Chorion gene cis-regulatory DNA restricts tissue specificity of reporter gene expression in transformed Drosophila

P element mediated germ-line transformation was used to study the developmental specificity of Drosophila chorion gene regulatory sequences directing expression of the bacterial reporter genes for chloramphenicol acetyltransferase (CAT) and beta-galactosidase (lacZ). DNA fragments containing 5' flanking plus the entire 5' untranslated and the beginning of the coding region of either the s36 or the s15 chorion gene are able to confer on the reporter genes normal tissue as well as temporal specificity of expression, exclusively in the ovary of transformed female flies. However, if 5' untranslated and coding regions are omitted, normal ovarian expression is maintained but tissue specificity is relaxed: expression of the reporter gene is detected both in the ovary and in specific non-ovarian tissues of transformed females and males. The evidence suggests that the missing 5' untranslated and coding sequences may include negative elements that normally suppress expression in non-ovarian tissues, and that these putative elements are distinct from those that prevent premature expression in the ovarian follicles. The exact location of ectopic lacZ expression within the internal male genitalia depends on the constellation of 5' flanking chorion regulatory sequences included in the P element constructs. Ectopic expression of the CAT gene in the male genitalia under s15 promoter control can be abolished by mutating the hexamer TCACGT, a sequence previously shown to be essential for the normal expression of this chorion gene in the ovary.

Proteins that bind to Drosophila chorion cis-regulatory elements: a new C2H2 zinc finger protein and a C2C2 steroid receptor-like component

Gel mobility-shift assays have been used to identify proteins that bind specifically to the promoter region of the Drosophila s15 chorion gene. These proteins are present in nuclear extracts of ovarian follicles, the tissue where s15 is expressed during development, and bind to specific elements of the promoter that have been shown by transformation analysis to be important for in vivo expression. The DNA binding specificity has been used for molecular cloning of two components from expression cDNA libraries and for their tentative identification with specific DNA-binding proteins of the nuclear extracts. The mRNAs for both of these components, CF1 and CF2, are differentially enriched in the follicles. DNA sequence analysis suggests that both CF1 and CF2 are novel Drosophila transcription factors. CF2 is a member of the C2H2 family of zinc finger proteins, whereas CF1 is a member of the family of steroid hormone receptors. The putative DNA-binding domain of CF1 is highly similar to the corresponding domains of certain vertebrate hormone receptors and recognizes a region of DNA with similar, hyphenated palindromic sequences. The nature of CF1 raises the possibility of hormonal control of choriogenesis in Drosophila.

Temporal regulation in development: negative and positive cis regulators dictate the precise timing of expression of a Drosophila chorion gene

We have used germ-line transformation to dissect the cis regulatory elements responsible for the transcriptional control of an internally marked Drosophila chorion gene (s15-P) during development. A 73-base-pair segment of the proximal 5'-flanking DNA contains sequences essential for the tissue-specific expression and the precise "late" temporal regulation of that gene. A substitute s36-1 segment of similar location can provide the tissue-specific function and imparts an early temporal regulation characteristic of gene s36-1. Within the regulatory DNA of s15-P, at least three adjacent elements are recognizable: an essential operationally positive element (TCACGT) that is shared by s36-1 and other chorion genes, irrespective of temporal specificity; a second positive element that is required for the normal late expression of s15-P; and, farthest upstream, a negative element that represses precocious expression during the early choriogenic stages.

Both early and late Drosophila chorion gene promoters confer correct temporal, tissue and sex specificity on a reporter Adh gene

In vivo transformation studies have been performed using fusion constructs of chorion DNA and the alcohol dehydrogenase (Adh) structural gene. The results indicate that almost exclusively 5' flanking DNA regions of the early (s36) and late (s15) chorion genes suffice for conferring normal chorion developmental specificity (sex, tissue and temporal) on the reporter gene. In the case of s15, the proximal 5' flanking DNA up to position -370 is sufficient for specificity. However, quantitative analysis indicates that one or more elements within or downstream of the s15 gene are required, either transcriptionally or post-transcriptionally, for attainment of an mRNA level comparable to that of the endogenous s15 gene (corrected for amplification); in the absence of such element(s), the average level of Adh transcript produced by fusion gene constructs is 18-fold lower.

Gene amplification in a single cell cycle in Chinese hamster ovary cells

We have employed Chinese hamster ovary cells synchronized by mitotic selection to study the replication and amplification of the dihydrofolate reductase gene. Using bromodeoxyuridine to differentially label newly replicated DNA, we show that the dihydrofolate reductase gene is replicated during the first 2 h of S phase, a time when, at most, 10% of the total genome has been replicated. We find that a 6-h inhibition of DNA synthesis by hydroxyurea beginning 2 h after the initiation of S phase markedly increases the frequency with which cells become resistant to a 100-fold increment in methotrexate. When DNA synthesis resumes following removal of the hydroxyurea, virtually all of the DNA replicated prior to inhibition, including the dihydrofolate reductase gene, is rereplicated. Analysis of the dihydrofolate reductase enzyme content of cells 24 h after treatment with hydroxyurea using the fluorescence-activated cell sorter reveals a subset of cells with elevated dihydrofolate reductase. It is this subset that contains additional copies of the dihydrofolate reductase gene and from which emerge highly methotrexate-resistant cells. We propose that the initial event of amplification is the rereplication of a variable, but relatively large, amount of the genome. As cells are subsequently placed under selection, a number of processes, including recombination events and loss of nonselected DNA sequences occur, resulting in what appears as differential gene amplification.

S phase-specific synthesis of dihydrofolate reductase in Chinese hamster ovary cells

We investigated the cell cycle modulation of dihydrofolate reductase (DHFR; tetrahydrofolate dehydrogenase, 7,8-dihydroxyfolate:NADP+ oxidoreductase, EC 1.5.1.3) levels in methotrexate-resistant Chinese hamster ovary cells synchronized by mitotic selection. DNA content and DHFR concentration were analyzed throughout the cell cycle by standard biochemical techniques and by double fluorescence staining utilizing the fluorescence-activated cell sorter. We found an S phase-specific period of DHFR biosynthetic activity. Commencing within hour 2 of S phase and continuing throughout the duration of S phase, there is a 90% increase in DHFR specific activity. This results from an approximately 2.5-fold increase in the level of DHFR, while total soluble protein increases 50% during the same period. This increase is the result of new synthesis of DHFR molecules initiated after the cell is physiologically committed to DNA replication. This increase in DHFR activity through S phage parallels the increasing rate of [3H]thymidine incorporation during the same interval. The maximum peak of DHFR activity is coincident with the maximum rate of DNA synthesis, both activities occurring during the bulk of DNA replication within the last stages of the 6.5-hr S phase.