Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance.

Improvements in cost and speed of next generation sequencing (NGS) have provided a new pathway for delivering disease diagnosis, molecular typing, and detection of antimicrobial resistance (AMR). Numerous published methods and protocols exist, but a lack of harmonisation has hampered meaningful comparisons between results produced by different methods/protocols vital for global genomic diagnostics and surveillance. As an exemplar, this study evaluated the sensitivity and specificity of five well-established in-silico AMR detection software where the genotype results produced from running a panel of 436 Escherichia coli were compared to their AMR phenotypes, with the latter used as gold-standard. The pipelines exploited previously known genotype-phenotype associations. No significant differences in software performance were observed. As a consequence, efforts to harmonise AMR predictions from sequence data should focus on: (1) establishing universal minimum to assess performance thresholds (e.g. a control isolate panel, minimum sensitivity/specificity thresholds); (2) standardising AMR gene identifiers in reference databases and gene nomenclature; (3) producing consistent genotype/phenotype correlations. The study also revealed limitations of in-silico technology on detecting resistance to certain antimicrobials due to lack of specific fine-tuning options in bioinformatics tool or a lack of representation of resistance mechanisms in reference databases. Lastly, we noted user friendliness of tools was also an important consideration. Therefore, our recommendations are timely for widespread standardisation of bioinformatics for genomic diagnostics and surveillance globally.

Spectroscopic analysis of myoglobin and cytochrome c dynamics in isolated cardiomyocytes during hypoxia and reoxygenation.

Raman microspectroscopy was applied to monitor the intracellular redox state of myoglobin and cytochrome c from isolated adult rat cardiomyocytes during hypoxia and reoxygenation. The nitrite reductase activity of myoglobin leads to the production of nitric oxide in cells under hypoxic conditions, which is linked to the inhibition of mitochondrial respiration. In this work, the subsequent reoxygenation of cells after hypoxia is shown to lead to increased levels of oxygen-bound myoglobin relative to the initial levels observed under normoxic conditions. Increased levels of reduced cytochrome c in ex vivo cells are also observed during hypoxia and reoxygenation by Raman microspectroscopy. The cellular response to reoxygenation differed dramatically depending on the method used in the preceding step to create hypoxic conditions in the cell suspension, where a chemical agent, sodium dithionite, leads to reduction of cytochromes in addition to removal of dissolved oxygen, and bubbling-N2 gas leads to displacement of dissolved oxygen only. These results have an impact on the assessment of experimental simulations of hypoxia in cells. The spectroscopic technique employed in this work will be used in the future as an analytical method to monitor the effects of varying levels of oxygen and nutrients supplied to cardiomyocytes during either the preconditioning of cells or the reperfusion of ischaemic tissue.

Mitochondrial ROS production and subsequent ERK phosphorylation are necessary for temperature preconditioning of isolated ventricular myocytes.

Hypothermia and hypothermic preconditioning are known to be profoundly cardioprotective, but the molecular mechanisms of this protection have not been fully explained. In this study, temperature preconditioning (16 °C) was found to be cardioprotective in isolated adult rat ventricular myocytes, enhancing contractile recovery and preventing calcium dysregulation after oxidative stress. Hypothermic preconditioning preserved mitochondrial function by delaying the pathological opening of the mitochondrial permeability transition pore (mPTP), whereas transient mPTP flickering remained unaltered. For the first time, reactive oxygen species (ROS) from the mitochondria are shown to be released exclusively during the hypothermic episodes of the temperature-preconditioning protocol. Using a mitochondrially targeted ROS biosensor, ROS release was shown during the brief bursts to 16 °C of temperature preconditioning. The ROS scavenger N-(2-mercaptopropionyl) glycine attenuated ROS accumulation during temperature preconditioning, abolishing the protective delay in mPTP opening. Temperature preconditioning induces ROS-dependant phosphorylation of the prosurvival kinase extracellular signal-regulated kinase (ERK)1/2. ERK1/2 activation was shown to be downstream of ROS release, as the presence of a ROS scavenger during temperature preconditioning completely blocked ERK1/2 activation. The cardioprotective effects of temperature preconditioning on mPTP opening were completely lost by inhibiting ERK1/2 activation. Thus, mitochondrial ROS release and ERK1/2 activation are both necessary to signal the cardioprotective effects of temperature preconditioning in cardiac myocytes.

Analysis of CD34 populations in mobilised peripheral blood stem cell harvests and in bone marrow by fluorescent in situ hybridisation for the bcr/abl gene fusion in patients with chronic granulocytic leukaemia.

For those patients ineligible for allogeneic bone marrow transplant and who are non-responsive to interferon, autotransplant with peripheral blood stem cells (PBSC) mobilised after intensive chemotherapy, may provide a novel approach to improve prognosis in patients with chronic granulocytic leukaemia. PBSC harvests are assessed for CD34-positive cell numbers, which serve as an indicator of engraftment potential, and are also analysed cytogenetically to ascertain tumour cell contamination. However, a more accurate assessment of PBSC harvest contamination requires investigation of the Philadelphia (Ph) status of the CD34pos population, in which the cells that provide long-term engraftment are contained. In this study, we have analysed these levels in mobilised PBSC and also in bone marrow (BM) harvests, taken several weeks prior to mobilising chemotherapy. Using fluorescent in situ hybridisation for the bcr/abl gene fusion, we have shown that the median number of Ph negative cells in CD34pos isolated populations was 14.95% in BM compared to 79.05% in PBSC harvests and that in all PBSC samples tested, Ph positivity in CD34pos populations was always detectable either by FISH or one round PCR methods. In paired assessments of both PBSC and BM harvests, higher levels of Ph negative CD34pos cells (> or = 14%) isolated from BM harvests, taken prior to intensive chemotherapy, correlated with higher levels of Ph negative CD34pos cells (> or = 78.5%) in PBSC harvests. These data may aid in the selection of patients for whom PBSC harvesting, after mobilisation, is more likely to achieve an autograft product containing predominantly Ph negative CD34pos cells and may exclude those patients for whom the risk, morbidity and expense of stem cell harvesting may have no apparent benefit over a chronic phase BM harvest.

Collection of Philadelphia-negative peripheral blood progenitor cells in unselected patients with chronic granulocytic leukaemia. Northern Regional Haematology Group.

Thirty unselected patients with chronic granulocytic leukaemia (CGL), age range 22-59 years, were treated with intensive chemotherapy and G-CSF to mobilize peripheral blood progenitor cells (PBPC). Chemotherapy was well tolerated and PBPC were collected by leukapheresis early during white cell recovery. PBPC collections considered adequate for engraftment were collected in 21 patients. Cytogenetic analysis of all collections in these patients showed >75% Ph negativity (range 79-100%) in 10. Successful collections, ie those >75% Ph negative and with total cell count of >1 x 10(6) CD34+ve cells/kg or >20 x 10(4) CFU-GM/kg were further analysed by Southern blot or RT-PCR. All samples were positive for the bcr/abl transcript. Patients with a low Sokal score (<0.8) were more likely to achieve a successful collection. In contrast, there was no association between transcript expression and likelihood of successful collection. We have confirmed that it is possible to mobilize and collect Ph-negative enriched PBPC in unselected patients with CGL. This procedure is more likely to be successful earlier rather than later in the course of the disease. Whether such collections will give an advantage over unmanipulated autologous bone marrow transplantation in CGL requires further study, but our experience suggests that suitable material for autologous rescue can be obtained from approximately one third of eligible, unselected young patients.

High efficiency gene transfer to the central nervous system of rodents and primates using herpes virus vectors lacking functional ICP27 and ICP34.5.

The safe and efficient use of herpes simplex virus (HSV)-based vectors to deliver genes of potentially therapeutic benefit to the central nervous system will require their effective disablement by the inactivation of viral genes required for lytic growth. Here we report that viruses lacking functional genes for ICP27 (which is required for growth in all cell types) and ICP34.5 (which is required for growth in nondividing cell types) can deliver a marker gene to both the rodent and primate CNS with high efficiency whilst producing relatively minimal damage and having no effect on sodium currents in dorsal root ganglion neurons. Such viruses paradoxically deliver genes at much higher efficiency than the less disabled single mutant lacking ICP34.5 alone and also, as expected, produce less damage in vivo. Moreover, unlike the single mutant lacking ICP27 the double mutant viruses cannot revert to wild-type by acquistion of complimenting gene sequences during growth of virus stocks in vitro on dividing cells expressing ICP27 since artificial expression of ICP34.5 in these cells is not required. Such ICP27-; ICP34.5- viruses thus offer a platform for the development of vectors which are sufficiently safe for ultimate use in human gene therapy.

Heligmosomoides polygyrus adult worm homogenate superantigen: presentation to T cells requires MHC class I positive accessory cells.

A series of experiments were carried out to further characterize the previously discovered Heligmosomoides polygyrus, adult worm homogenate (AWH), superantigen. AWH, in contrast to staphylococcal enterotoxin B (SEB) superantigen, was totally unable to stimulate naive thymocytes, in either the presence or the absence of exogenous accessory cells (AC). Experiments using AC from B10 congenic mice failed to indicate a requirement for a specific MHC haplotype for successful presentation of the AWH superantigen and also indicated that the presence or absence of the H-2,E molecule on AC did not affect AWH stimulation of T cell hybridomas. Furthermore, AWH was found to require the presence of MHC class I-positive AC in order to stimulate T cell hybridomas, while, in contrast, the absence of MHC Class II on AC did not affect the superantigenic properties of AWH. Initial characterization of the T cell hybridomas stimulated by the AWH superantigen, indicated that all were CD4-positive and that three of them expressed TCR V beta 8.1. Hence AWH superantigen can stimulate TCR V beta 8.1/CD4-positive T cells only in the presence of MHC Class I-positive AC.

Adult worm homogenate of the nematode parasite Heligmosomoides polygyrus induces proliferation of naive T lymphocytes without MHC restriction.

The documented in vitro response of mouse T cells to parasite antigens is typically anamnestic and H-2 restricted. As yet, there have been no confirmed reports of the existence of a non-H-2-restricted, superantigen type of response to the antigens of metazoan parasites. Reported here are data which show that antigens produced by the adult stage of the nematode parasite Heligmosomoides polygyrus (= Nematospiroides dubius) can stimulate naive T cells in vitro to proliferate and produce IL-2. A series of T cell hybridomas has been used to show that adult worm homogenate of H. polygyrus can stimulate parasite antigen naive T cells. This response is independent of the H-2 haplotype of the antigen-presenting accessory cells and does not appear to be influenced by the presence or absence of an H-2 E molecule. However, successful presentation of the H. polygyrus superantigen does require the presence of metabolically active accessory cells and fixation of the accessory cells with paraformaldehyde abrogates the response of the target cells. This discovery has important implications for the study of the role of superantigens in host/parasite interactions and will also help to expand current knowledge about the relationship between chronic intestinal nematodes and the host immune system.

Brugia malayi: patterns of expression of surface-associated antigens.

Patterns of expression of surface-associated antigens were analyzed in the filarial nematode Brugia malayi immediately prior, and during development in the vertebrate host. Two surface-associated protein molecules, i.e., accessible to surface radioiodination and soluble in aqueous buffers, were investigated: Mrs 29-30,000 and 16,000, both of which are antigenic in infected animals. The Mr 29-30,000 glycoprotein is expressed in a surface-associated manner by adult worms and by fourth-stage larvae, but is not detectable in preparasitic third-stage larvae. The 16,000 component, which appears not to be glycosylated, is surface-associated in adult worms and fourth-stage larvae. In contrast to the 29-30,000 glycoprotein, the 16,000 protein is also expressed both by pre- and postparastic third-stage larvae. However, it becomes surface-associated only after infection. Thus, immediately prior, and during development within the vertebrate host, B. malayi displays at least two different patterns of expression of surface-associated antigens: (i) de novo, intiated either immediately after infection (phase specific) or during genesis of the fourth-stage larva (stage specific); (ii) continuous, but with phase-dependent surface exposure of previously cryptic antigens, during the transition from intermediate to definitive host.

Ectopic pregnancy.

The incidence of ectopic pregnancy has been increasing for many years and currently is two to three times higher than it was 20 or 25 years ago. The reasons for this are complex and include increased rates of pelvic and tubal infection, the use of the IUD, surgery in the pelvis for infertility, sterilization and other surgical procedures, in vitro fertilization, and improved diagnosis. Normal tubal physiology, the findings in affected tubes, and the mechanisms of how the ectopic pregnancy develops and involves the tube are considered. The cardinal points of the history and physical examination are presented in considerable detail. Further, the evolution of the tools of diagnosis--curettage, culdocentesis, laparotomy, laparoscopy, hormonal tests, and ultrasound-is considered. The different approaches to therapy are presented. Salpingectomy was once the method of accepted therapy, but currently conservative management (salpingostomy) is the most acceptable approach. More recently, selected patients are being treated with observation and a small subgroup are being managed with methotrexate and other chemical agents injected directly into the ectopic pregnancy. Ectopic pregnancy is still a leading cause of maternal death despite improved diagnosis and therapy. It should be remembered, however, that the total number of women who die from this condition is less than ever before and this is despite the rising incidence of ectopic pregnancy. There is still much to be learned about ectopic pregnancy, its etiology, diagnosis, and management.

Anti-idiotypic antibodies function as a surrogate surface epitope of Brugia malayi infective larvae.

Anti-idiotypic (AB2) antibodies were generated in rabbits following immunization with a murine IgM monoclonal antibody (AB1) recognizing a surface determinant of Brugia malayi infective stage larvae. AB2 specifically inhibited the binding of AB1 to B. malayi larvae. Furthermore, AB2 had the ability to mimic the original antigen since mice immunized with AB2 possessed serum antibodies (AB3) specific for the B. malayi surface determinant. The presence of anti-surface antibodies (AB3 and AB1) induced either by AB2 immunization or by administration of AB1, did not alter the outcome of an intraperitoneal infection of B. malayi larvae in BABL/c mice when compared to untreated animals. AB3 antibodies like AB1, were IgM, thus indicating an isotype restricted response to the B. malayi epitope. There were no detectable cell mediated responses to the surface determinant in mice immunized with AB2, assessed by lymphocyte blastogenesis or IL3 production in vitro in response to the idiotope as presented by living larvae. The lack of cellular responses and/or the previously demonstrated rapid shedding of the epitope may explain the inability of AB1 or AB2 to protect mice against larval challenge in this study.

The response of primary cultured adult mouse sensory neurons to ethanol, propanol, acetaldehyde and acrolein treatments.

Primary cultures of adult mouse sensory neurons maintained for 8 days in vitro (8 div), in both the presence of non-neuronal cell (NNC) outgrowth and in NNC-reduced cultures, were exposed to doses of ethanol, propanol, acetaldehyde and acrolein. The effects on cell viability were monitored: LD50's of 600 microM acrolein and 100 mM propanol were obtained after 24 h exposures and after 48 h with 1 mM acetaldehyde and 500 mM ethanol. Morphological effects were evident by scanning electron microscopy with sub-acute doses for each agent, using both lower concentrations and shorter exposures. Membrane pitting of the perikaryon and a reduction in the proportion of neurons bearing neurites were common signs of toxic insult. The neurites of treated cells were thicker and more irregular than those of untreated cells; this proved a good indicator of specific neurotoxicity rather than merely a cytotoxic response. Fetal calf serum in the medium lessened the response of neurons to ethanol treatments. Comparison with other in vitro studies suggests these primary cultures are a more sensitive system than established cell lines of neuronal origin for use in neurotoxicity testing.

Acanthocheilonema viteae (Dipetalonema viteae) in mice: attempts to correct the low responder phenotype of the BALB/c host.

Attempts were made to correct the low responder phenotype of microfilaraemic Acanthocheilonema viteae (Dipetalonema viteae) infected BALB/c mice through the transfer of immune spleen cells and immune serum from amicrofilaraemic B10 background mice. The transfer of immune cells and serum prior to infection failed to influence development of microfilaraemia in BALB/c recipients. Attempts to alter the course of an established microfilaraemia in BALB/c mice through the transfer of 3 x 10(7) immune spleen cells were unsuccessful but transfer of 3 x 10(8) cells reduced microfilaraemia temporarily. Treating microfilaraemic BALB/c mice with immune serum brought about a rapid reduction in microfilaraemia. This effect was only temporary and numbers of circulating microfilariae returned to control levels within a short time. Repeated serum transfers reduced the microfilaraemia only during the period of treatment. Similar results were obtained when immune serum was given to microfilaraemic, immunodeficient CBA/N mice.

Evidence for prazosin-resistant, rauwolscine-sensitive alpha-adrenoceptors mediating contractions in the isolated vascular bed of the rat tail.

1. The postjunctional alpha-adrenoceptors mediating contractions in the isolated vascular bed of the perfused rat tail have been investigated, in the presence and absence of an increase in perfusion pressure by arginine vasopressin (AVP). 2. In the absence of AVP, bolus doses of noradrenaline (NA) and phenylephrine produced pressor responses of similar time course, while UK-14,304 was practically inactive. Responses to noradrenaline were inhibited more by 0.05 microM prazosin than by 1 microM rauwolscine, suggesting the presence of alpha1-adrenoceptors. 3. Following a sustained elevation in perfusion pressure by AVP, both UK-14,304 and NA (the latter in the presence of 0.05 microM prazosin to inhibit alpha 1-adrenoceptors) elicited dose-dependent pressor responses. The maximum response to UK-14,304 under these conditions was approximately 30% of the maximum response to NA in the absence of prazosin and AVP. Responses to phenylephrine were not affected by the AVP-induced increase in vascular tone. 4. In the presence of AVP, pressor responses to UK-14,304 were resistant to 0.05 microM prazosin and susceptible to antagonism by 1 microM rauwolscine (-log Kb 7.65 +/- 0.15). Similarly, responses to NA in the presence of 0.05 microM prazosin and AVP were inhibited by 1 microM rauwolscine. This represents the first demonstration of prazosin-resistant, rauwolscine-sensitive alpha 2-adrenoceptor-mediated responses in the vasculature of the rat tail. 5. These results suggest that in isolated vascular preparations, functional populations of postjunctional alpha 2-adrenoceptors may be 'uncovered' by the presence of AVP.

Prenatal sensitisation in experimental filariasis: observations on Acanthocheilonema viteae infections in mice.

The probability that in utero exposure to filarial antigens may influence the outcome of a subsequent infection has been investigated using a laboratory model whereby BALB/c mice are implanted with adult, female Acanthocheilonema viteae in order to generate a high-level, long lasting microfilaraemia. When infected using this procedure, BALB/c and (BALB/c x B10) F1 mice can be defined as susceptible and resistant respectively in terms of the microfilaraemia produced. By using microfilaraemic BALB/c mice as mothers, BALB/c and F1 offspring were exposed to the possibility of in utero infection. The finding of microfilariae in foetal tissues and their presence in the blood of two week old mice confirmed the transplacental transmission of parasites in both cases, BALB/c and F1 progeny born to microfilaraemic mothers failed to support a full infection from the L3 stage; similarly, progeny implanted with female worms were as sus-ceptible and resistant respectively as unexposed BALB/c and F1 controls. Spleen cells from in utero exposed, two week old BALB/c and F1 mice recognised filarial antigens in lymphocyte proliferation assays, as did their microfilaraemic mothers. In Western Blot studies, sera from such mice and from foetal, in utero exposed BALB/c mice recognised the same spectrum of A. viteae antigens as their mothers, which strongly suggests the transplacental transfer of maternal antibody. These results demonstrate that the A. viteae-mouse model may be useful in studying transplacental transmission and prenatal sensitisation in experimental filariasis.

Immunity to Dipetalonema viteae (Filarioidea) infections in resistant and susceptible mice.

The course of infection with Dipetalonema viteae in mice shows marked genetically-determined strain variation. Subcutaneous implantation of 5 female D. viteae into C57BL/10 (B10) mice results in a short term, low level microfilaraemia compared with that seen in similar infections in BALB/c mice. Adult worm survival is similar, thus the different patterns of infections reflect responses directed against the microfilariae larvae (mf). A number of immunological parameters have been monitored during infection in an attempt to identify strain differences which may be correlated with levels of resistance. Blast cell activity in the spleen and lymph nodes showed little strain difference, peaking on day 10 and declining as mf disappeared from the circulation. Total serum IgG levels doubled in both strains during infection, the response being more rapid in B10 mice. Serum IgM levels increased threefold in BALB/c mice but fourteen-fold in B10. Radiosorbent assays identified comparable anti-adult antibody and anti-mf homogenate IgM antibody responses in both strains. Immunofluorescent assay showed that the appearance of IgM antibodies directed against the mf surface correlated with the clearance of mf from the blood of B10 mice, whereas similar antibodies were not detected in BALB/c mice. It is proposed that the efficient clearance of mf in B10 is mediated through an IgM-dependent mechanism and that the chronic microfilariaemia seen in BALB/c mice is facilitated by the absence of a specific IgM response to mf surface antigens.

Analgesic efficacy of meclofenamate sodium in episiotomy pain.

Meclofenamate sodium was compared, double-blind, with codeine and placebo for the treatment of acute episiotomy pain. One hundred sixty-eight women with moderate or severe episiotomy pain after normal delivery were assigned randomly to one of four treatment groups: one received meclofenamate sodium 200 mg at dose 1 and 100 mg at doses 2 and 3; one received meclofenamate sodium 100 mg at dose 1 and 50 mg at doses 2 and 3; one received codeine 60 mg at all three doses; and one received placebo at all three doses. Efficacy measurements were evaluated periodically for 6 hours after medication. After the first administration, both doses of meclofenamate sodium were significantly superior to placebo and to codeine from 2-6 hours in pain intensity difference and pain relief. For second and third doses, data were available for too few patients to allow valid analysis and interpretation. Adverse effects occurred in 4 patients in each meclofenamate sodium group, and in 8 in the codeine group and in 6 in the placebo group. The study indicates that single 100- and 200-mg doses of meclofenamate sodium are as safe as, and significantly more effective than, codeine 60 mg or placebo for episiotomy pain.