Understanding CYP3A4 and P-gp mediated drug-drug interactions through PBPK modeling - Case example of pralsetinib

Pralsetinib, a potent and selective inhibitor of oncogenic RET fusion and RET mutant proteins, is a substrate of the drug metabolizing enzyme CYP3A4 and a substrate of the efflux transporter P-gp based on in vitro data. Therefore, its pharmacokinetics (PKs) may be affected by co-administration of potent CYP3A4 inhibitors and inducers, P-gp inhibitors, and combined CYP3A4 and P-gp inhibitors. With the frequent overlap between CYP3A4 and P-gp substrates/inhibitors, pralsetinib is a challenging and representative example of the need to more quantitatively characterize transporter-enzyme interplay. A physiologically-based PK (PBPK) model for pralsetinib was developed to understand the victim drug-drug interaction (DDI) risk for pralsetinib. The key parameters driving the magnitude of pralsetinib DDIs, the P-gp intrinsic clearance and the fraction metabolized by CYP3A4, were determined from PBPK simulations that best captured observed DDIs from three clinical studies. Sensitivity analyses and scenario simulations were also conducted to ensure these key parameters were determined with sound mechanistic rationale based on current knowledge, including the worst-case scenarios. The verified pralsetinib PBPK model was then applied to predict the effect of other inhibitors and inducers on the PKs of pralsetinib. This work highlights the challenges in understanding DDIs when enzyme-transporter interplay occurs, and demonstrates an important strategy for differentiating enzyme/transporter contributions to enable PBPK predictions for untested scenarios and to inform labeling.

Identification of GDC-1971 (RLY-1971), a SHP2 Inhibitor Designed for the Treatment of Solid Tumors

Protein tyrosine phosphatase SHP2 mediates RAS-driven MAPK signaling and has emerged in recent years as a target of interest in oncology, both for treating with a single agent and in combination with a KRAS inhibitor. We were drawn to the pharmacological potential of SHP2 inhibition, especially following the initial observation that drug-like compounds could bind an allosteric site and enforce a closed, inactive state of the enzyme. Here, we describe the identification and characterization of GDC-1971 (formerly RLY-1971), a SHP2 inhibitor currently in clinical trials in combination with KRAS G12C inhibitor divarasib (GDC-6036) for the treatment of solid tumors driven by a KRAS G12C mutation.

Shared learning from a physiologically based pharmacokinetic modeling strategy for human pharmacokinetics prediction through retrospective analysis of Genentech compounds

The quantitative prediction of human pharmacokinetics (PK) including the PK profile and key PK parameters are critical for early drug development decisions, successful phase I clinical trials, and the establishment of a range of doses to enable phase II clinical dose selection. Here, we describe an approach employing physiologically based pharmacokinetic (PBPK) modeling (Simcyp) to predict human PK and to validate its performance through retrospective analysis of 18 Genentech compounds for which clinical data are available. In short, physicochemical parameters and in vitro data for preclinical species were integrated using PBPK modeling to predict the in vivo PK observed in mouse, rat, dog, and cynomolgus monkey. Through this process, the in vitro to in vivo extrapolation (IVIVE) was determined and then incorporated into PBPK modeling in order to predict human PK. Overall, the prediction obtained using this PBPK-IVIVE approach captured the observed human PK profiles of the compounds from the dataset well. The predicted Cmax was within 2-fold of the observed Cmax for 94% of the compounds while the predicted area under the curve (AUC) was within 2-fold of the observed AUC for 72% of the compounds. Additionally, important IVIVE trends were revealed through this investigation, including application of scaling factors determined from preclinical IVIVE to human PK prediction for each molecule. Based upon the analysis, this PBPK-based approach now serves as a practical strategy for human PK prediction at the candidate selection stage at Genentech.

Evaluation of bottom-up modeling of the blood-brain barrier to improve brain penetration prediction via physiologically based pharmacokinetic modeling

Predicting the brain penetration of drugs has been notoriously difficult; however, recently, permeability-limited brain models have been constructed. Lead optimization for central nervous system compounds often focuses on compounds that have low transporter efflux, where passive permeability could be a main driver in determining cerebrospinal fluid (CSF)/brain concentrations. The main objective of this study was to evaluate the translatability of passive permeability data generated from different in vitro systems and its impact on the prediction of human CSF/brain concentrations using physiologically-based pharmacokinetic (PBPK) modeling. In vitro data were generated using gMDCK and parallel artificial membrane permeability assay-blood-brain barrier for comparison and predictions using a quantitative structure-activity relationship model were also evaluated. PBPK modeling was then performed for seven compounds with moderate-high permeability and a range of efflux in vitro, and the CSF/brain mass concentrations and Kpuu were reasonably predicted. This work provides the first step of a promising approach using bottom-up PBPK modeling for CSF/brain penetration prediction to support lead optimization and clinical candidate selection.

Electrocardiogram Abnormalities Following Diphenhydramine Ingestion: A Case Report

In the United States, tricyclic antidepressants (TCA) are commonly prescribed to treat psychiatric illnesses and neuropathic pain. This class of antidepressants has been found to cause pathognomonic electrocardiogram (ECG) changes in cases of overdose.1 Specifically, TCA's cause a dominant terminal R wave in aVR and widening of the QRS complex due to their sodium channel blocking effect. Diphenhydramine, better known as Benadryl, is known to disrupt sodium channels in the same manner. In this case report, a 13-year-old female was brought into the emergency department (ED) after attempted suicide by diphenhydramine overdose. The patient presented with palpitations, nausea and confusion. She was agitated, tachycardic and exhibited opsoclonus. An ECG was performed upon the patient's arrival which showed large terminal R waves in aVR along with large S waves in lead I indicating right axis deviation. Given the patient's age and reported ingestion, it was highly suspicious that her symptoms and ECG changes were the result of a sodium channel blockade. Sodium bicarbonate was given, which resulted in notable ECG changes as well as symptomatic improvement. TCA's, and similarly diphenhydramine, have sodium channel blocking properties which can be revealed by performing an ECG. Administration of sodium bicarbonate in the ED has been shown to be a successful treatment by reversing this sodium channel blockade.

Topics

Tricyclic antidepressants, diphenhydramine, overdose, sodium channel blockage, sodium bicarbonate administration.

A highly virulent variant of HIV-1 circulating in the Netherlands

We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log₁₀ increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.

Physically principled reflection models applied to filtered camera imaging inversions in metal walled fusion machines

Ray-tracing techniques are applied to filtered divertor imaging, a diagnostic that has long suffered from artifacts due to the polluting effect of reflected light in metal walled fusion machines. Physically realistic surface reflections were modeled using a Cook-Torrance micro-facet bi-directional reflection distribution function applied to a high resolution mesh of the vessel geometry. In the absence of gonioreflectometer measurements, a technique was developed to fit the free parameters of the Cook-Torrance model against images of the JET in-vessel light sources. By coupling this model with high fidelity plasma fluid simulations, photo-realistic renderings of a number of tokamak plasma emission scenarios were generated. Finally, a sensitivity matrix describing the optical coupling of a JET divertor camera and the emission profile of the plasma was obtained, including full reflection effects. These matrices are used to perform inversions on measured data and shown to reduce the level of artifacts in inverted emission profiles.

A workforce in jeopardy: identifying the challenges of ensuring a sustainable advanced HIV nursing workforce

Background

HIV services in England face substantial challenges arising from financial pressures and changes to commissioning. A sustainable HIV specialist nursing workforce will be vital to enable them to respond to those challenges.

Aims

This paper examines the current workforce situation in HIV services across the country.

Methods

This mixed-method study involved semi-structured interviews with 19 key stakeholders and with 44 nurses/physicians from 21 purposively selected HIV services across England. Data were interpreted using a framework analysis approach.

Results

'Building a career in HIV nursing' identified problems associated with retention and recruitment. Changes in commissioning are disrupting common career routes from sexual health to HIV nursing, and a perceived lack of a clear career pathway was seen as a barrier to recruitment. 'Developing a specialist workforce' explored the professional development of the current workforce, which was hampered by poor access to funding or study time for advanced study and the absence of an HIV-specific advanced nursing qualification.

Conclusions

The HIV nursing workforce, which provides an increasing proportion of HIV care, is facing serious recruitment and retention challenges. A strategic approach to workforce development and training is essential to overcome systemic barriers and secure the next generation of skilled practitioners.

An analysis of baseline data from the PROUD study: an open-label randomised trial of pre-exposure prophylaxis

Background

Pre-exposure prophylaxis (PrEP) has proven biological efficacy to reduce the sexual acquisition of the human immunodeficiency virus (HIV). The PROUD study found that PrEP conferred higher protection than in placebo-controlled trials, reducing HIV incidence by 86 % in a population with seven-fold higher HIV incidence than expected. We present the baseline characteristics of the PROUD study population and place the findings in the context of national sexual health clinic data.

Methods

The PROUD study was designed to explore the real-world effectiveness of PrEP (tenofovir-emtricitabine) by randomising HIV-negative gay and other men who have sex with men (GMSM) to receive open-label PrEP immediately or after a deferral period of 12 months. At enrolment, participants self-completed two baseline questionnaires collecting information on demographics, sexual behaviour and lifestyle in the last 30 and 90 days. These data were compared to data from HIV-negative GMSM attending sexual health clinics in 2013, collated by Public Health England using the genitourinary medicine clinic activity database (GUMCAD).

Results

The median age of participants was 35 (IQR: 29–43). Typically participants were white (81 %), educated at a university level (61 %) and in full-time employment (72 %). Of all participants, 217 (40 %) were born outside the UK. A sexually transmitted infection (STI) was reported to have been diagnosed in the previous 12 months in 330/515 (64 %) and 473/544 (87 %) participants reported ever having being diagnosed with an STI. At enrolment, 47/280 (17 %) participants were diagnosed with an STI. Participants reported a median (IQR) of 10 (5–20) partners in the last 90 days, a median (IQR) of 2 (1–5) were condomless sex acts where the participant was receptive and 2 (1–6) were condomless where the participant was insertive. Post-exposure prophylaxis had been prescribed to 184 (34 %) participants in the past 12 months. The number of STI diagnoses was high compared to those reported in GUMCAD attendees.

Conclusions

The PROUD study population are at substantially higher risk of acquiring HIV infection sexually than the overall population of GMSM attending sexual health clinics in England. These findings contribute to explaining the extraordinary HIV incidence rate during follow-up and demonstrate that, despite broad eligibility criteria, the population interested in PrEP was highly selective.

Trial registration

Current Controlled TrialsISRCTN94465371. Date of registration: 28 February 2013.

Electronic supplementary material

The online version of this article (doi:10.1186/s13063-016-1286-4) contains supplementary material, which is available to authorized users.

The development and validation of a meta-tool for quality appraisal of public health evidence: Meta Quality Appraisal Tool (MetaQAT)

OBJECTIVES

Most quality appraisal tools were developed for clinical medicine and tend to be study-specific with a strong emphasis on risk of bias. In order to be more relevant to public health, an appropriate quality appraisal tool needs to be less reliant on the evidence hierarchy and consider practice applicability. Given the broad range of study designs used in public health, the objective of this study was to develop and validate a meta-tool that combines public health-focused principles of appraisal coupled with a set of design-specific companion tools.

STUDY DESIGN

Several design methods were used to develop and validate the tool including literature review, synthesis, and validation with a reference standard.

METHODS

A search of critical appraisal tools relevant to public health was conducted; core concepts were collated. The resulting framework was piloted during three feedback sessions with public health practitioners. Following subsequent revisions, the final meta-tool, the Meta Quality Appraisal Tool (MetaQAT), was then validated through a content analysis of appraisals conducted by two groups of experienced public health researchers (MetaQAT vs generic appraisal form).

RESULTS

The MetaQAT framework consists of four domains: relevancy, reliability, validity, and applicability. In addition, a companion tool was assembled from existing critical appraisal tools to provide study design-specific guidance on validity appraisal. Content analysis showed similar methodological and generalizability concerns were raised by both groups; however, the MetaQAT appraisers commented more extensively on applicability to public health practice.

CONCLUSIONS

Critical appraisal tools designed for clinical medicine have limitations for use in the context of public health. The meta-tool structure of the MetaQAT allows for rigorous appraisal, while allowing users to simultaneously appraise the multitude of study designs relevant to public health research and assess non-standard domains, such as applicability.

Pre-exposure prophylaxis to prevent the acquisition of HIV-1 infection (PROUD): effectiveness results from the pilot phase of a pragmatic open-label randomised trial

BACKGROUND

Randomised placebo-controlled trials have shown that daily oral pre-exposure prophylaxis (PrEP) with tenofovir-emtricitabine reduces the risk of HIV infection. However, this benefit could be counteracted by risk compensation in users of PrEP. We did the PROUD study to assess this effect.

METHODS

PROUD is an open-label randomised trial done at 13 sexual health clinics in England. We enrolled HIV-negative gay and other men who have sex with men who had had anal intercourse without a condom in the previous 90 days. Participants were randomly assigned (1:1) to receive daily combined tenofovir disoproxil fumarate (245 mg) and emtricitabine (200 mg) either immediately or after a deferral period of 1 year. Randomisation was done via web-based access to a central computer-generated list with variable block sizes (stratified by clinical site). Follow-up was quarterly. The primary outcomes for the pilot phase were time to accrue 500 participants and retention; secondary outcomes included incident HIV infection during the deferral period, safety, adherence, and risk compensation. The trial is registered with ISRCTN (number ISRCTN94465371) and ClinicalTrials.gov (NCT02065986).

FINDINGS

We enrolled 544 participants (275 in the immediate group, 269 in the deferred group) between Nov 29, 2012, and April 30, 2014. Based on early evidence of effectiveness, the trial steering committee recommended on Oct 13, 2014, that all deferred participants be offered PrEP. Follow-up for HIV incidence was complete for 243 (94%) of 259 patient-years in the immediate group versus 222 (90%) of 245 patient-years in the deferred group. Three HIV infections occurred in the immediate group (1·2/100 person-years) versus 20 in the deferred group (9·0/100 person-years) despite 174 prescriptions of post-exposure prophylaxis in the deferred group (relative reduction 86%, 90% CI 64-96, p=0·0001; absolute difference 7·8/100 person-years, 90% CI 4·3-11·3). 13 men (90% CI 9-23) in a similar population would need access to 1 year of PrEP to avert one HIV infection. We recorded no serious adverse drug reactions; 28 adverse events, most commonly nausea, headache, and arthralgia, resulted in interruption of PrEp. We detected no difference in the occurrence of sexually transmitted infections, including rectal gonorrhoea and chlamydia, between groups, despite a suggestion of risk compensation among some PrEP recipients.

INTERPRETATION

In this high incidence population, daily tenofovir-emtricitabine conferred even higher protection against HIV than in placebo-controlled trials, refuting concerns that effectiveness would be less in a real-world setting. There was no evidence of an increase in other sexually transmitted infections. Our findings strongly support the addition of PrEP to the standard of prevention for men who have sex with men at risk of HIV infection.

FUNDING

MRC Clinical Trials Unit at UCL, Public Health England, and Gilead Sciences.

Colorectal cancer is reliably excluded in the frail and elderly population by minimal preparation CT

BACKGROUND

This study aimed to retrospectively assess the accuracy of minimal preparation computed tomography (MPCT) in the detection of colorectal cancer (CRC) within the frail and elderly population and to evaluate the relevance of extra-colonic findings (ECF).

METHODS

Radiology reports, clinical notes and follow-up reports from 207 patients who underwent MPCT to investigate for CRC between 2005 and 2009 were analysed. Patients were scanned following the administration of oral contrast for 48 h, without bowel preparation or colonic insufflation. MPCT results were measured against patient outcomes, with a minimum of 2 years of follow-up.

RESULTS

Twelve cases of clinically relevant CRC were confirmed (5.8 %). MPCT correctly identified 11 of these lesions (sensitivity 91.6 %). Thirty-one patients had a possible CRC identified by MPCT, which was not confirmed by further examination (specificity 84.1 %). This results in a positive predictive value of 26.2 % and a negative predictive value of 99.4 %. Five of the patients with colon cancer underwent curative surgery. Sixty-eight clinically relevant ECF were confirmed, including 14 previously undiagnosed extra-colonic malignancies. ECF were considered to account for the presenting complaint in 15.0 % (31/207) of all patients.

CONCLUSIONS

Minimal preparation computed tomography is an effective and reliable investigation for the exclusion of clinically relevant CRC in this population. It provides clinicians with a valuable and pragmatic alternative to colonoscopy and CT colonography when invasive examination or cathartic bowel preparation will be poorly tolerated and small polyps are of limited significance. MPCT has an advantage over purely luminal imaging in the detection of extra-colonic pathology and appears to have an equally important role in the detection of CRC.

Comparison of cleaning efficacy between in-use disinfectant and electrolysed water in an English residential care home

BACKGROUND

Infection control in hospitals and care homes remains a key issue. They are regularly inspected regarding standards of hygiene, but visual assessment does not necessarily correlate with microbial cleanliness. Pathogens can persist in the inanimate environment for extended periods of time.

AIM

This prospective study compared the effectiveness of a novel sanitizer containing electrolysed water, in which the active ingredient is stabilized hypochlorous acid (Aqualution™), with the effectiveness of the quaternary ammonium disinfectant in current use for microbial removal from hand-touch surfaces in a care home. The study had a two-period crossover design.

METHODS

Five surfaces were cleaned daily over a four-week period, with screening swabs taken before and after cleaning. Swabs were cultured in order to compare levels of surface microbial contamination [colony-forming units (cfu)/cm(2)] before and after cleaning with each product.

FINDINGS

Cleaning with electrolysed water reduced the mean surface bacterial load from 2.6 [interquartile range (IQR) 0.30-30.40] cfu/cm(2) to 0.10 (IQR 0.10-1.40) cfu/cm(2) [mean log(10) reduction factor 1.042, 95% confidence interval (CI) 0.79-1.30]. Cleaning with the in-use quaternary ammonium disinfectant increased the bacterial load from 0.90 (IQR 0.10-8.50) cfu/cm(2) to 93.30 (IQR 9.85-363.65) cfu/cm(2) (mean log(10) reduction -1.499, 95% CI -1.87 to -1.12) (P < 0.0001). Using two proposed benchmark standards for surface microbial levels in hospitals, electrolysed water resulted in a higher 'pass rate' than the in-use quaternary ammonium disinfectant (80-86% vs 15-21%, P < 0.0001).

CONCLUSION

Electrolysed water exerts a more effective bacterial kill than the in-use quaternary ammonium disinfectant, which suggests that it may be useful as a surface sanitizer in environments such as care homes.

A model for rewarding professional growth in the diagnostic molecular oncology laboratory

The University of Texas M.D. Anderson Cancer Center (UTMDACC), Department of Pathology and Laboratory Medicine is committed to the endless pursuit of innovative research, education, training and administration for the prevention, diagnosis and clinical management of cancer and associated diseases. The molecular genetic technology professional development model promotes personal development, recognizes increased competencies, and sets high standards for all skills and services provided. There are four competency levels that comprise our Professional Development Model (PDM): Discovery, Application, Maturation, and Expert. The skill, knowledge, education, and certification requirements for each level are defined based on the business needs of each lab. When a genetic technologist successfully completes all skills, knowledge, proficiency, education and certification requirements within the appropriate time frame for a particular competency level, his/her salary would be adjusted to the entry point for the competency level he/she has completed.

The role of Clinical Support Workers in reducing junior doctors' hours and improving quality of patient care

AIM

The aim of the study was to see if the introduction of Clinical Support Workers (CSWs) at a teaching hospital could reduce the medical work intensity for junior doctors without compromising the quality of patient care.

BACKGROUND

The 'New Deal' and 'European Working Time Directive' have prompted hospitals to take a close look at junior doctors' hours and work intensity in order to make posts compliant. Following the Department of Health's publication 'reducing junior doctors' hours', it was felt that certain clinical duties could be shared with nursing staff.

METHODS

Two audits were undertaken 8 months apart. The first was to determine the areas where the introduction of CSW would make the biggest impact. The second was to determine if this impact had had an effect on the intensity of work carried out by the junior doctors.

FINDINGS

The CSW greatly reduced the number of cannulations and venepunctures performed by the doctors without any compromise to patient care.

RELEVANCE TO CLINICAL PRACTICE

This study shows that other allied health professionals can be trained to carry out certain tasks that previously were only performed by doctors. This not only reduces the impact on junior doctors' hours but can also improve patient care, with fewer delays encountered when patients are waiting for a procedure.

The role of clinical support workers in reducing junior doctors' hours and improving quality of patient care

AIM

The aim of the study was to see if the introduction of clinical support workers (CSWs) at a teaching hospital could reduce the medical work intensity for junior doctors without compromising the quality of patient care.

BACKGROUND

The 'New Deal' and 'European Working Time Directive' have prompted hospitals to take a close look at junior doctors' hours and work intensity in order to make posts compliant. Following the Department of Health's publication 'reducing junior doctors' hours', it was felt that certain clinical duties could be shared with nursing staff.

METHODS

Two audits were undertaken 8 months apart. The first was to determine the areas where the introduction of CSW would make the biggest impact. The second was to determine if this impact had had an effect on the intensity of work carried out by the junior doctors.

FINDINGS

The CSW greatly reduced the number of cannulations and venepunctures performed by the doctors without any compromise to patient care.

RELEVANCE TO CLINICAL PRACTICE

This study shows that other allied health professionals can be trained to carry out certain tasks that previously were only performed by doctors. This not only reduces the impact on junior doctors' hours but can also improve patient care, with fewer delays encountered when patients are waiting for a procedure.

A mathematical model for assessing control strategies against West Nile virus

Since its incursion into North America in 1999, West Nile virus (WNV) has spread rapidly across the continent resulting in numerous human infections and deaths. Owing to the absence of an effective diagnostic test and therapeutic treatment against WNV, public health officials have focussed on the use of preventive measures in an attempt to halt the spread of WNV in humans. The aim of this paper is to use mathematical modelling and analysis to assess two main anti-WNV preventive strategies, namely: mosquito reduction strategies and personal protection. We propose a single-season ordinary differential equation model for the transmission dynamics of WNV in a mosquito-bird-human community, with birds as reservoir hosts and culicine mosquitoes as vectors. The model exhibits two equilibria; namely the disease-free equilibrium and a unique endemic equilibrium. Stability analysis of the model shows that the disease-free equilibrium is globally asymptotically stable if a certain threshold quantity (R0), which depends solely on parameters associated with the mosquito-bird cycle, is less than unity. The public health implication of this is that WNV can be eradicated from the mosquito-bird cycle (and, consequently, from the human population) if the adopted mosquito reduction strategy (or strategies) can make R0<1. On the other hand, it is shown, using a novel and robust technique that is based on the theory of monotone dynamical systems coupled with a regular perturbation argument and a Liapunov function, that if R0>1, then the unique endemic equilibrium is globally stable for small WNV-induced avian mortality. Thus, in this case, WNV persists in the mosquito-bird population.

Latent S alleles are widespread in cultivated self-compatible Brassica napus

The genetic control of self-incompatibility in Brassica napus was investigated using crosses between resynthesized lines of B. napus and cultivars of oilseed rape. These crosses introduced eight C-genome S alleles from Brassica oleracea (S16, S22, S23, S25, S29, S35, S60, and S63) and one A-genome S allele from Brassica rapa (SRM29) into winter oilseed rape. The inheritance of S alleles was monitored using genetic markers and S phenotypes were determined in the F1, F2, first backcross (B1), and testcross (T1) generations. Two different F1 hybrids were used to develop populations of doubled haploid lines that were subjected to genetic mapping and scored for S phenotype. These investigations identified a latent S allele in at least two oilseed rape cultivars and indicated that the S phenotype of these latent alleles was masked by a suppressor system common to oilseed rape. These latent S alleles may be widespread in oilseed rape varieties and are possibly associated with the highly conserved C-genome S locus of these crop types. Segregation for S phenotype in subpopulations uniform for S genotype suggests the existence of suppressor loci that influenced the expression of the S phenotype. These suppressor loci were not linked to the S loci and possessed suppressing alleles in oilseed rape and non-suppressing alleles in the diploid parents of resynthesized B. napus lines.

Unsupervised feature dimension reduction for classification of MR spectra

We present an unsupervised feature dimension reduction method for the classification of magnetic resonance spectra. The technique preserves spectral information, important for disease profiling. We propose to use this technique as a preprocessing step for computationally demanding wrapper-based feature subset selection. We show that the classification accuracy on an independent test set can be sustained while achieving considerable feature reduction. Our method is applicable to other classification techniques, such as neural networks, support vector machines, etc.

TNF-alpha and interleukin 1 activate gastrin gene expression via MAPK- and PKC-dependent mechanisms

Helicobacter pylori and proinflammatory cytokines have a direct stimulatory effect on gastrin release from isolated G cells, but little is known about the mechanism by which these factors regulate gastrin gene expression. We explored whether tumor necrosis factor (TNF)-alpha and interleukin (IL)-1 directly regulate gastrin gene expression and, if so, by what mechanism. TNF-alpha and IL-1 significantly increased gastrin mRNA in canine G cells to 181 +/- 18% and 187 +/- 28% of control, respectively, after 24 h of treatment. TNF-alpha and IL-1 stimulated gastrin promoter activity to a maximal level of 285 +/- 12% and 415 +/- 26% of control. PD-98059 (a mitogen-activated protein kinase kinase inhibitor), SB-202190 (a p38 kinase inhibitor), and GF-109203 (a protein kinase C inhibitor) inhibited the stimulatory action of both cytokines on the gastrin promoter. In conclusion, both cytokines can directly regulate gastrin gene expression via a mitogen-activated protein kinase- and protein kinase C-dependent mechanism. These data suggest that TNF-alpha and IL-1 may play a direct role in Helicobacter pylori-induced hypergastrinemia.

Comparative estrogenicity of estradiol, ethynyl estradiol and diethylstilbestrol in an in vivo, male sheepshead minnow (Cyprinodon variegatus), vitellogenin bioassay

An in vivo bioasssay for vitellogenin (VTG) synthesis was developed to screen individual chemicals or mixtures of chemicals for potentially estrogenic effects in a marine teleost model. An enzyme-linked immunosorbent assay (ELISA) was used to quantitate VTG synthesis in male sheepshead minnows (Cyprinodon variegatus) exposed to five concentrations of the natural estrogen (17beta-estradiol), a synthetic, steroidal pharmaceutical estrogen (17alpha-ethynyl estradiol), or a synthetic, non-steroidal, pharmaceutical estrogen (diethystilbestrol) for 16 days. At an exposure concentration of 20 ng/l, only diethystilbestrol elicited a vitellogenic response. At all test concentrations greater than 100 ng/l, VTG appeared in the plasma in a dose-dependent manner for the three estrogen treatments. Liver VTG mRNA measurements were also made, exhibiting no clear correlations between quantities, nor temporal appearance of the message and mature protein were apparent. This assay is short-term, relatively inexpensive, shows a direct response, and easily quantitated.

Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39

The genome sequences of Chlamydia trachomatis mouse pneumonitis (MoPn) strain Nigg (1 069 412 nt) and Chlamydia pneumoniae strain AR39 (1 229 853 nt) were determined using a random shotgun strategy. The MoPn genome exhibited a general conservation of gene order and content with the previously sequenced C.trachomatis serovar D. Differences between C.trachomatis strains were focused on an approximately 50 kb 'plasticity zone' near the termination origins. In this region MoPn contained three copies of a novel gene encoding a >3000 amino acid toxin homologous to a predicted toxin from Escherichia coli O157:H7 but had apparently lost the tryptophan biosyntheis genes found in serovar D in this region. The C. pneumoniae AR39 chromosome was >99.9% identical to the previously sequenced C.pneumoniae CWL029 genome, however, comparative analysis identified an invertible DNA segment upstream of the uridine kinase gene which was in different orientations in the two genomes. AR39 also contained a novel 4524 nt circular single-stranded (ss)DNA bacteriophage, the first time a virus has been reported infecting C. pneumoniae. Although the chlamydial genomes were highly conserved, there were intriguing differences in key nucleotide salvage pathways: C.pneumoniae has a uridine kinase gene for dUTP production, MoPn has a uracil phosphororibosyl transferase, while C.trachomatis serovar D contains neither gene. Chromosomal comparison revealed that there had been multiple large inversion events since the species divergence of C.trachomatis and C.pneumoniae, apparently oriented around the axis of the origin of replication and the termination region. The striking synteny of the Chlamydia genomes and prevalence of tandemly duplicated genes are evidence of minimal chromosome rearrangement and foreign gene uptake, presumably owing to the ecological isolation of the obligate intracellular parasites. In the absence of genetic analysis, comparative genomics will continue to provide insight into the virulence mechanisms of these important human pathogens.

Intermediate not indeterminate care

Increasing demands, limited resources and an aging population are driving the development of alternatives to the full acute hospital bed. This review considers some opportunities and pitfalls, and proposes some principles for practice.

Complete genome sequence of Treponema pallidum, the syphilis spirochete

The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006 base pairs containing 1041 predicted coding sequences (open reading frames). Systems for DNA replication, transcription, translation, and repair are intact, but catabolic and biosynthetic activities are minimized. The number of identifiable transporters is small, and no phosphoenolpyruvate:phosphotransferase carbohydrate transporters were found. Potential virulence factors include a family of 12 potential membrane proteins and several putative hemolysins. Comparison of the T. pallidum genome sequence with that of another pathogenic spirochete, Borrelia burgdorferi, the agent of Lyme disease, identified unique and common genes and substantiates the considerable diversity observed among pathogenic spirochetes.

Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi

The genome of the bacterium Borrelia burgdorferi B31, the aetiologic agent of Lyme disease, contains a linear chromosome of 910,725 base pairs and at least 17 linear and circular plasmids with a combined size of more than 533,000 base pairs. The chromosome contains 853 genes encoding a basic set of proteins for DNA replication, transcription, translation, solute transport and energy metabolism, but, like Mycoplasma genitalium, it contains no genes for cellular biosynthetic reactions. Because B. burgdorferi and M. genitalium are distantly related eubacteria, we suggest that their limited metabolic capacities reflect convergent evolution by gene loss from more metabolically competent progenitors. Of 430 genes on 11 plasmids, most have no known biological function; 39% of plasmid genes are paralogues that form 47 gene families. The biological significance of the multiple plasmid-encoded genes is not clear, although they may be involved in antigenic variation or immune evasion.