Population Pharmacokinetic Analysis Supports Initiation Treatment and Bridging from Sublingual Buprenorphine to Subcutaneous Administration of a Buprenorphine Depot (CAM2038) in the Treatment of Opioid Use Disorder

BACKGROUND AND OBJECTIVE

In treating opioid use disorder (OUD), subcutaneous (SC) extended-release buprenorphine (BPN) depots, e.g., CAM2038, have been shown to provide smaller and less frequent fluctuations in BPN plasma concentrations and pharmacodynamic responses, improve outcomes, reduce treatment burden, and lower risks of misuse and diversion compared to daily sublingual (SL) BPN. This analysis characterized the pharmacokinetics (PK) of BPN following intravenous and SL administration, and administration of SC CAM2038 weekly and monthly.

METHODS

Pharmacokinetic data from two Phase 1 and two Phase 2 trials in healthy participants and participants with OUD, respectively, were used to develop a population PK model using non-linear mixed effects modelling. The analysis included data from 252 participants and 10,658 BPN observations.

RESULTS

The disposition of BPN was best described by a three-compartment model with first-order elimination, and absorption of SL BPN and SC CAM2038 weekly and monthly by dual parallel absorption pathways. Model diagnostics indicated good predictive performance of BPN concentrations. Buprenorphine plasma concentration-time profiles were simulated for treatment initiation, switching from SL BPN to CAM2038 weekly and monthly, and tapering after interrupting treatment with CAM2038. Simulations predicted CAM2038 weekly and monthly doses that provided BPN plasma maximum concentration (Cmax) and trough concentration (Ctrough) values at steady state within those observed following SL BPN administration.

CONCLUSIONS

This population PK model supports the use of CAM2038 doses as individualized treatment for OUD across different treatment stages, including initiation, switching from SL BPN according to established dose conversion schedules, and tapering.

TRIAL REGISTRATIONS

ISRCTN41550730 (05/19/2014), ISRCTN24987553 (07/29/2014), NCT02611752 (11/23/2015), NCT02710526 (03/16/2016).

Population Pharmacokinetics and Exposure-Response for Dapirolizumab Pegol From a Phase 2b Trial in Patients With Systemic Lupus Erythematosus

Systemic lupus erythematosus (SLE) is a systemic, autoimmune disease characterized by chronic inflammation and organ damage. Dapirolizumab pegol inhibits CD40 ligand (CD40L) and is currently undergoing phase 3 trials for the treatment of SLE. To describe the pharmacokinetic characteristics of dapirolizumab pegol and the relationship between exposure and probability of achieving a British Isles Lupus Assessment Group-based Composite Lupus Assessment (BICLA) response, a population pharmacokinetic (popPK) model and an exposure-response model were developed, based on results of the phase 2b trial (RISE; NCT02804763) of dapirolizumab pegol in SLE. Dapirolizumab pegol pharmacokinetics were found to be dose proportional and well described by a 2-compartment model with first-order elimination from the central compartment. In the popPK model, body weight was the only significant covariate. The average concentration of dapirolizumab pegol, derived from the popPK model, was incorporated into the exposure-response model. Overall, the exposure-response model showed that treatment with dapirolizumab pegol increased the probability of transitioning from BICLA "Nonresponder" to "Responder." No significant covariates on BICLA responder status were identified. Notably, the half maximal effective concentration was greater for the transition from "Responder" to "Nonresponder" (150 µg/mL) than the transition from "Nonresponder" to "Responder" (12 µg/mL), indicating that sustained dapirolizumab pegol concentrations may be required to maintain BICLA response. In conclusion, dapirolizumab pegol pharmacokinetics were as expected for a PEGylated molecule and results from the exposure-response model indicate that a favorable dapirolizumab pegol effect was identified for both BICLA "Nonresponder" to "Responder" and "Responder" to "Nonresponder" transition probabilities.

A Population Pharmacokinetic-Pharmacodynamic Model of Pegfilgrastim

Neutropenia and febrile neutropenia (FN) are serious side effects of cytotoxic chemotherapy which may be alleviated with the administration of recombinant granulocyte colony-stimulating factor (GCSF) derivatives, such as pegfilgrastim (PG) which increases absolute neutrophil count (ANC). In this work, a population pharmacokinetic-pharmacodynamic (PKPD) model was developed based on data obtained from healthy volunteers receiving multiple administrations of PG. The developed model was a bidirectional PKPD model, where PG stimulated the proliferation, maturation, and margination of neutrophils and where circulating neutrophils in turn increased the elimination of PG. Simulations from the developed model show disproportionate changes in response with changes in dose. A dose increase of 10% from the 6 mg therapeutic dose taken as a reference leads to area under the curve (AUC) increases of ~50 and ~5% for PK and PD, respectively. A full random effects covariate model showed that little of the parameter variability could be explained by sex, age, body size, and race. As a consequence, little of the secondary parameter variability (C_max and AUC of PG and ANC) could be explained by these covariates.

Hypocalcemia and bone mineral density changes following denosumab treatment in end-stage renal disease patients: a meta-analysis of observational studies

The incidence of hypocalcemia and bone mineral density (BMD) changes in end-stage renal disease (ESRD) patients on denosumab remains unclear. We performed this meta-analysis to assess the incidence of denosumab-associated hypocalcemia and effects of denosumab on BMD in ESRD patients. A literature search was conducted using MEDLINE, EMBASE, and Cochrane Database from inception through November 2017 to identify studies evaluating incidence of denosumab-associated hypocalcemia and changes in serum calcium, phosphate, alkaline phosphatase (ALP), parathyroid hormone (PTH), and BMD from baseline to post-treatment course of denosumab in ESRD patients. Study results were pooled and analyzed using a random-effect model. The protocol for this meta-analysis is registered with PROSPERO (International Prospective Register of Systematic Reviews; no. CRD42017081074). Six observational studies with a total of 84 ESRD patients were enrolled. The pooled estimated incidence of hypocalcemia during denosumab treatment was 42% (95% CI 29-55%, I² = 0%). Hypocalcemia occurred approximately 7 to 20 days after the first dose and reached nadir of low calcium levels in the first 2 weeks up to 2 months. However, there were no significant changes in serum calcium or phosphate from baseline to post-treatment course (≥ 3 months after treatment) with mean differences [MDs] of 0.20 mg/dL (95% CI, - 0.30 to 0.69 mg/dL) and - 0.10 mg/dL (95% CI, - 0.70 to 0.49 mg/dL). There were significant reductions in ALP and PTH levels with standardized mean differences (SMDs) of - 0.65 (95% CI - 1.13 to - 0.16) and - 1.89 (95% CI - 3.44 to - 0.34), respectively. There were significant increases in T-scores with MDs of 0.39 (95% CI 0.10 to 0.69) and 0.79 (95% CI 0.60 to 0.98) for lumbar spine and femoral neck, respectively. Our study demonstrates the estimated incidence of denosumab-associated hypocalcemia in dialysis patients of 42%. From baseline to post-treatment course, although there are no differences in serum calcium and phosphate, our findings suggest significant reductions in ALP and PTH and a significant increase in BMD. Currently, denosumab should not be considered as the treatment of choice in ESRD patients until more safety and efficacy data are available.

Chronic opioid use is associated with altered gut microbiota and predicts readmissions in patients with cirrhosis

BACKGROUND

Opioid use is epidemic in cirrhosis, which could precipitate hepatic encephalopathy (HE) potentially through gut dysbiosis and inflammation.

AIM

To define the effect of opioids on readmissions and on gut microbiota composition and functionality.

METHODS

Cohort 1 had 200 cirrhotic in-patients (with/without opioid use) followed prospectively through the index hospitalisation and 6 months post discharge. Readmissions (HE-related/unrelated) were compared between patients discharged on opioids compared to the rest, including using a multi-variable analysis. Cohort 2 consisted of 72 cirrhotics on chronic opioids who were age/model for end-stage liver disease (MELD) and prior HE-balanced with 72 cirrhotics not on opioids. Stool microbiota composition (multi-tagged sequencing), predicted functionality (PiCRUST), endotoxemia and systemic inflammation (IL-6, IL-17) were compared.

RESULTS

Cohort 1: Chronic opioid use was statistically similar between those admitted with/without HE, and was judged to be an HE precipitant in <5% of cases during the index hospitalisation. Of the 144 patients alive at 6 months, 82 were readmitted. The opioid users had a significantly higher all cause (69% vs. 48%, P = 0.008), but not HE-related readmissions (30% vs. 41%, P = 0.30). On regression, opioid therapy and female gender were predictive of readmission independent of MELD score and previous HE. Cohort 2: Significant dysbiosis was noted in the opioid cohort, especially in HE+opioid patients with lower autochthonous taxa and Bacteroidaceae relative abundance. PiCRUST showed highest aromatic amino acid and endotoxin production in opioid users. Opioid users also had higher endotoxemia and IL-6 but not IL-17.

CONCLUSION

Chronic opioid use in cirrhosis is associated with increased endotoxemia, dysbiosis and all-cause readmissions.

Pharmacokinetic Interactions for Drugs with a Long Half-Life—Evidence for the Need of Model-Based Analysis

Pharmacokinetic drug-drug interactions (DDIs) can lead to undesired drug exposure, resulting in insufficient efficacy or aggravated toxicity. Accurate quantification of DDIs is therefore crucial but may be difficult when full concentration-time profiles are problematic to obtain. We have compared non-compartmental analysis (NCA) and model-based predictions of DDIs for long half-life drugs by conducting simulation studies and reviewing published trials, using antituberculosis drug bedaquiline (BDQ) as a model compound. Furthermore, different DDI study designs were evaluated. A sequential design mimicking conducted trials and a population pharmacokinetic (PK) model of BDQ and the M2 metabolite were utilized in the simulations where five interaction scenarios from strong inhibition (clearance fivefold decreased) to strong induction (clearance fivefold increased) were evaluated. In trial simulations, NCA systematically under-predicted the DDIs’ impact. The bias in average exposure was 29–96% for BDQ and 20–677% for M2. The model-based analysis generated unbiased predictions, and simultaneous fitting of metabolite data increased precision in DDI predictions. The discrepancy between the methods was also apparent for conducted trials, e.g., lopinavir/ritonavir was predicted to increased BDQ exposure 22% by NCA and 188% by model-based methods. In the design evaluation, studies with parallel designs were considered and shown to generally be inferior to sequential/cross-over designs. However, in the case of low inter-individual variability and no informative metabolite data, a prolonged parallel design could be favored. Model-based analysis for DDI assessments is preferable over NCA for victim drugs with a long half-life and should always be used when incomplete concentration-time profiles are part of the analysis.

A diagnostic tool for population models using non-compartmental analysis: The ncappc package for R

BACKGROUND AND OBJECTIVE

Non-compartmental analysis (NCA) calculates pharmacokinetic (PK) metrics related to the systemic exposure to a drug following administration, e.g. area under the concentration-time curve and peak concentration. We developed a new package in R, called ncappc, to perform (i) a NCA and (ii) simulation-based posterior predictive checks (ppc) for a population PK (PopPK) model using NCA metrics.

METHODS

The nca feature of ncappc package estimates the NCA metrics by NCA. The ppc feature of ncappc estimates the NCA metrics from multiple sets of simulated concentration-time data and compares them with those estimated from the observed data. The diagnostic analysis is performed at the population as well as the individual level. The distribution of the simulated population means of each NCA metric is compared with the corresponding observed population mean. The individual level comparison is performed based on the deviation of the mean of any NCA metric based on simulations for an individual from the corresponding NCA metric obtained from the observed data. The ncappc package also reports the normalized prediction distribution error (NPDE) of the simulated NCA metrics for each individual and their distribution within a population.

RESULTS

The ncappc produces two default outputs depending on the type of analysis performed, i.e., NCA and PopPK diagnosis. The PopPK diagnosis feature of ncappc produces 8 sets of graphical outputs to assess the ability of a population model to simulate the concentration-time profile of a drug and thereby evaluate model adequacy. In addition, tabular outputs are generated showing the values of the NCA metrics estimated from the observed and the simulated data, along with the deviation, NPDE, regression parameters used to estimate the elimination rate constant and the related population statistics.

CONCLUSIONS

The ncappc package is a versatile and flexible tool-set written in R that successfully estimates NCA metrics from concentration-time data and produces a comprehensive set of graphical and tabular output to summarize the diagnostic results including the model specific outliers. The output is easy to interpret and to use in evaluation of a population PK model. ncappc is freely available on CRAN (http://cran.r-project.org/web/packages/ncappc/index.html/) and GitHub (https://github.com/cacha0227/ncappc/).

miR-23b/SP1/c-myc forms a feed-forward loop supporting multiple myeloma cell growth

Deregulated microRNA (miR)/transcription factor (TF)-based networks represent a hallmark of cancer. We report here a novel c-Myc/miR-23b/Sp1 feed-forward loop with a critical role in multiple myeloma (MM) and Waldenstrom's macroglobulinemia (WM) cell growth and survival. We have found miR-23b to be downregulated in MM and WM cells especially in the presence of components of the tumor bone marrow milieu. Promoter methylation is one mechanism of miR-23b suppression in myeloma. In gain-of-function studies using miR-23b mimics-transfected or in miR-23b-stably expressing MM and WM cell lines, we observed a significant decrease in cell proliferation and survival, along with induction of caspase-3/7 activity over time, thus supporting a tumor suppressor role for miR-23b. At the molecular level, miR-23b targeted Sp1 3'UTR and significantly reduced Sp1-driven nuclear factor-κB activity. Finally, c-Myc, an important oncogenic transcription factor known to stimulate MM cell proliferation, transcriptionally repressed miR-23b. Thus MYC-dependent miR-23b repression in myeloma cells may promote activation of oncogenic Sp1-mediated signaling, representing the first feed-forward loop with critical growth and survival role in myeloma.

Prevalence and Predictors of Alcohol Consumption among the Squatter of Kathmandu Valley

BACKGROUND

Alcohol consumption has grown up sharply over the past decades in Nepal. Conversely, little is known about this phenomenon among the urban poor. We assessed pattern, frequency, context, and type of alcohol consumption among the urban poor of Nepal.

METHODS

We executed a cross-sectional study, taking 422 households from four squatter settlements of Kathmandu Valley. Modified Nepalese version standard questionnaire was used for data collection. Data was objectively analyzed in SPSS full version 19.

RESULTS

The study reported 39.81% (95% CI: 32.41-47.21) current drinkers, with male (65.99%, 95% CI: 57.85-74.13) outnumbering female (16.89%, 95% CI: 4.98-28.80). One out of ten drinkers drank daily (male: 13.08%, female: 13.16%). A third (30.36%) of all current drinkers acknowledged drinking more than one type of alcohol (male: 28.46%, female: 36.84%). Nearly half (47.60%) of the drinkers drank in social gathering (male: 47.90%, female: 47.60%). Home was the place of drinking for nearly one-fifth (18.60%) of the drinkers. Males most commonly drank alcohol with their friends (34.60%), whereas female drank with family members (25.60%). Nearly half of the drinkers drank during evening hour (45.24%). Multivariable analysis detected likelihood of drinking 5.86 times (95% CI: 2.50-13.72) in male and 3.16 times (95% CI: 1.39-7.13) in those with family history of alcohol.

CONCLUSIONS

We found high prevalence of alcohol consumption than the national average among the urban poor with a marked gender difference by pattern. Gender sensitive alcohol prevention and control programs need a greater start.

SAR650984 directly induces multiple myeloma cell death via lysosomal-associated and apoptotic pathways, which is further enhanced by pomalidomide

The anti-CD38 monoclonal antibody SAR650984 (SAR) is showing promising clinical activity in treatment of relapsed and refractory multiple myeloma (MM). Besides effector-mediated antibody-dependent cellular cytotoxicity and complement-mediated cytotoxicity, we here define molecular mechanisms of SAR-directed MM cell death and enhanced anti-MM activity triggered by SAR with Pomalidomide (Pom). Without Fc-cross-linking agents or effector cells, SAR specifically induces homotypic aggregation (HA)-associated cell death in MM cells dependent on the level of cell surface CD38 expression, actin cytoskeleton and membrane lipid raft. SAR and its F(ab)'2 fragments trigger caspase 3/7-dependent apoptosis in MM cells highly expressing CD38, even with p53 mutation. Importantly, SAR specifically induces lysosome-dependent cell death (LCD) by enlarging lysosomes and increasing lysosomal membrane permeabilization associated with leakage of cathepsin B and LAMP-1, regardless of the presence of interleukin-6 or bone marrow stromal cells. Conversely, the lysosomal vacuolar H+-ATPase inhibitor blocks SAR-induced LCD. SAR further upregulates reactive oxygen species. Pom enhances SAR-induced direct and indirect killing even in MM cells resistant to Pom/Len. Taken together, SAR is the first therapeutic monoclonal antibody mediating direct cytotoxicity against MM cells via multiple mechanisms of action. Our data show that Pom augments both direct and effector cell-mediated MM cytotoxicity of SAR, providing the framework for combination clinical trials.

The effect of noggin interference in a rabbit posterolateral spinal fusion model

STUDY DESIGN

Noggin protein levels and spinal fusion rates were compared in a rabbit model after application of siRNA against BMP antagonist noggin in paraspinal muscle.

OBJECTIVE

To test whether endogenous BMPs are sufficient to form bone in the absence of their antagonists, using noggin siRNA to interrupt the negative feedback loop on endogenous BMP within the paraspinal muscles in rabbits. Unused Posterolateral lumbar fusion is a standard surgical treatment for many spinal disorders, yet even under ideal conditions the rate of non-fusion approaches 25 %. BMPs are effective in promoting bone formation, and are inhibited by antagonists such as noggin. We have previously shown that in this model, endogenous BMPs are present and endogenous BMP antagonist noggin is strongly increased during spinal fusion. Previous studies have found that noggin siRNA enhanced spinal fusion in combination with supra-physiological amounts of exogenous BMP; however, the effect of the siRNA alone remains unknown.

METHODS

A posterolateral intertransverse rabbit lumbar fusion was utilized, as established by Boden et al. SiRNA against noggin was electroporated into paraspinal muscle to determine its effect on fusion. Outcome measures included noggin protein expression, and assessment of spinal fusion at 6 weeks.

RESULTS

SiRNAs were effective in reducing overexpressed noggin in vitro. Noggin protein was successfully knocked down in vivo for the initial 7 days in our rabbit model and returned to detectable levels by 4 weeks and to normal levels by 6 weeks. The overall fusion rate was not significantly enhanced compared to established controls from our earlier work (Tang et al.).

CONCLUSIONS

Early noggin suppression does not appear to enhance the BMP activity sufficiently to significantly affect final fusion rates in our model.

PeptiSite: a structural database of peptide binding sites in 4D

We developed PeptiSite, a comprehensive and reliable database of biologically and structurally characterized peptide-binding sites, in which each site is represented by an ensemble of its complexes with protein, peptide and small molecule partners. The unique features of the database include: (1) the ensemble site representation that provides a fourth dimension to the otherwise three dimensional data, (2) comprehensive characterization of the binding site architecture that may consist of a multimeric protein assembly with cofactors and metal ions and (3) analysis of consensus interaction motifs within the ensembles and identification of conserved determinants of these interactions. Currently the database contains 585 proteins with 650 peptide-binding sites. http://peptisite.ucsd.edu/ link allows searching for the sites of interest and interactive visualization of the ensembles using the ActiveICM web-browser plugin. This structural database for protein-peptide interactions enables understanding of structural principles of these interactions and may assist the development of an efficient peptide docking benchmark.

CRM1 inhibition induces tumor cell cytotoxicity and impairs osteoclastogenesis in multiple myeloma: molecular mechanisms and therapeutic implications

The key nuclear export protein CRM1/XPO1 may represent a promising novel therapeutic target in human multiple myeloma (MM). Here we showed that chromosome region maintenance 1 (CRM1) is highly expressed in patients with MM, plasma cell leukemia cells and increased in patient cells resistant to bortezomib treatment. CRM1 expression also correlates with increased lytic bone and shorter survival. Importantly, CRM1 knockdown inhibits MM cell viability. Novel, oral, irreversible selective inhibitors of nuclear export (SINEs) targeting CRM1 (KPT-185, KPT-330) induce cytotoxicity against MM cells (ED50<200 nM), alone and cocultured with bone marrow stromal cells (BMSCs) or osteoclasts (OC). SINEs trigger nuclear accumulation of multiple CRM1 cargo tumor suppressor proteins followed by growth arrest and apoptosis in MM cells. They further block c-myc, Mcl-1, and nuclear factor κB (NF-κB) activity. SINEs induce proteasome-dependent CRM1 protein degradation; concurrently, they upregulate CRM1, p53-targeted, apoptosis-related, anti-inflammatory and stress-related gene transcripts in MM cells. In SCID mice with diffuse human MM bone lesions, SINEs show strong anti-MM activity, inhibit MM-induced bone lysis and prolong survival. Moreover, SINEs directly impair osteoclastogenesis and bone resorption via blockade of RANKL-induced NF-κB and NFATc1, with minimal impact on osteoblasts and BMSCs. These results support clinical development of SINE CRM1 antagonists to improve patient outcome in MM.

A small molecule agonist of EphA2 receptor tyrosine kinase inhibits tumor cell migration in vitro and prostate cancer metastasis in vivo

During tumor progression, EphA2 receptor can gain ligand-independent pro-oncogenic functions due to Akt activation and reduced ephrin-A ligand engagement. The effects can be reversed by ligand stimulation, which triggers the intrinsic tumor suppressive signaling pathways of EphA2 including inhibition of PI3/Akt and Ras/ERK pathways. These observations argue for development of small molecule agonists for EphA2 as potential tumor intervention agents. Through virtual screening and cell-based assays, we report here the identification and characterization of doxazosin as a novel small molecule agonist for EphA2 and EphA4, but not for other Eph receptors tested. NMR studies revealed extensive contacts of doxazosin with EphA2/A4, recapitulating both hydrophobic and electrostatic interactions recently found in the EphA2/ephrin-A1 complex. Clinically used as an α1-adrenoreceptor antagonist (Cardura®) for treating hypertension and benign prostate hyperplasia, doxazosin activated EphA2 independent of α1-adrenoreceptor. Similar to ephrin-A1, doxazosin inhibited Akt and ERK kinase activities in an EphA2-dependent manner. Treatment with doxazosin triggered EphA2 receptor internalization, and suppressed haptotactic and chemotactic migration of prostate cancer, breast cancer, and glioma cells. Moreover, in an orthotopic xenograft model, doxazosin reduced distal metastasis of human prostate cancer cells and prolonged survival in recipient mice. To our knowledge, doxazosin is the first small molecule agonist of a receptor tyrosine kinase that is capable of inhibiting malignant behaviors in vitro and in vivo.

Interaction of uranium with a filamentous, heterocystous, nitrogen-fixing cyanobacterium, Anabaena torulosa

The filamentous, heterocystous, diazotrophic cyanobacterium, Anabaena torulosa was found to bind uranium from aqueous solutions containing 100 μM uranyl carbonate at pH 7.8. The uranyl sequestration kinetics exhibited (a) an initial rapid phase, binding 48% uranium within 30 min resulting in a loading of 56 mg U g(-1) of dry wt, followed by (b) a slower phase, binding 65% uranium with resultant loading of 77.35 mg U g(-1) in 24h. Energy Dispersive X-ray fluorescence spectroscopy of uranium loaded biomass revealed all components of UL X-rays (UL(l), UL(α), UL(β1) and UL(β2)). Heat killed cells or extracellular polysaccharides derived from live cells exhibited limited uranyl binding (~26%) highlighting the importance of cell viability for optimum uranyl binding. The present study revealed the involvement of acid soluble polyphosphates in uranium accumulation by this brackish water cyanobacterium.

Identification of novel nonsteroidal compounds as substrates or inhibitors of hASBT

A prodrug approach that employs the human apical sodium dependent bile acid transporter (hASBT) for absorption requires a recognition moiety for hASBT. Bile acids are natural ligands for hASBT, but are hormones with high molecular weight, such that a recognition moiety that is not a bile acid may be advantageous. The objective was to identify nonsteroidal small molecules that could potentially serve as promoieties in the design of prodrugs that target hASBT. Three searches for bile acid analogues were conducted and it involved molecular fingerprints as the computational tools for similarity searching, as well as traditional medicinal chemistry pattern recognition. Sixty-three compounds were tested using a hASBT-Madin-Darby canine kidney cell monolayer model. Twenty-three of these compounds were found to be hASBT inhibitors and represent novel hASBT inhibitors. Three were selected for hASBT uptake studies. Two were substrates, which represent the first reported nonsteroidal substrates of hASBT. Interestingly, each compound lacked a negative charge. These compounds promise to serve as leads to identify hASBT recognition moieties in a prodrug approach to target hASBT to increase drug absorption.

Structural determinants for transport across the intestinal bile acid transporter using C-24 bile acid conjugates

The human apical sodium dependent bile acid transporter (hASBT) reabsorbs gram quantities of bile acid daily and is a potential prodrug target to increase oral drug absorption. In the absence of a high resolution hASBT crystal structure, 3D-QSAR modeling may prove beneficial in designing prodrug targets to hASBT. The objective was to derive a conformationally sampled pharmacophore 3D-QSAR (CSP-SAR) model for the uptake of bile acid conjugates by hASBT. A series of bile acid conjugates of glutamyl chenodeoxycholate were evaluated in terms of K(m) and normalized V(max) (normV(max)) using hASBT-MDCK cells. All monoanionic conjugates were potent substrates. Dianions, cations and zwitterions, which bound with a high affinity, were not substrates. CSP-SAR models were derived using structural and physicochemical descriptors, and evaluated via cross validation. The best CSP-SAR model for K(m) included two structural and two physiochemical descriptors, where substrate hydrophobicity enhanced affinity. A best CSP-SAR model for K(m)/normV(max) employed one structural and three physicochemical descriptors, also indicating hydrophobicity enhanced efficiency. Overall, the bile acid C-24 region accommodated a range of substituted anilines, provided a single negative charge was present near C-24. In comparing uptake findings to prior inhibition results, increased hydrophobicity enhanced activity, with dianions and zwitterions hindering activity.

Structural requirements of the ASBT by 3D-QSAR analysis using aminopyridine conjugates of chenodeoxycholic acid

The human apical sodium-dependent bile acid transporter (ASBT) is a validated drug target and can be employed to increase oral bioavailability of various drug conjugates. The aim of the present study was to investigate the chemical space around the 24-position of bile acids that influences both inhibition and uptake by the transporter. A series of 27 aminopyridine and aminophenol conjugates of glutamyl-chenodeoxycholate were synthesized and their ASBT inhibition and transport kinetics (parametrized as K(i), K(t), and J(max)) measured using stably transfected ASBT-MDCK cells. All conjugates were potent ASBT inhibitors. Monoanionic conjugates exhibited higher inhibition potency than neutral conjugates. However, neutral conjugates and chloro-substituted monoanionic conjugates were not substrates, or at least not apparent substrates. Kinetic analysis of substrates indicated that similar values for K(i) and K(t) implicate substrate binding to ASBT as the rate-limiting step. Using 3D-QSAR, four inhibition models and one transport efficiency model were developed. Steric fields dominated in CoMFA models, whereas hydrophobic fields dominated CoMSIA models. The inhibition models showed that a hydrophobic or bulky substitute on the 2 or 6 position of a 3-aminopyridine ring enhanced activity, while a hydrophobic group on the 5 position was detrimental. Overall, steric and hydrophobic features around the 24 position of the sterol nucleus strongly influenced bile acid conjugate interaction with ASBT. The relative location of the pyridine nitrogen and substituent groups also modulated binding.

Molecular switch controlling the binding of anionic bile acid conjugates to human apical sodium-dependent bile acid transporter

The human apical sodium-dependent bile acid transporter (hASBT) may serve as a prodrug target for oral drug absorption. Synthetic, biological, NMR, and computational approaches identified the structure-activity relationships of mono- and dianionic bile acid conjugates for hASBT binding. Experimental data combined with a conformationally sampled pharmacophore/QSAR modeling approach (CSP-SAR) predicted that dianionic substituents with intramolecular hydrogen bonding between hydroxyls on the cholane skeleton and the acid group on the conjugate's aromatic ring increased conjugate hydrophobicity and improved binding affinity. Notably, the model predicted the presence of a conformational molecular switch, where shifting the carboxylate substituent on an aromatic ring by a single position controlled binding affinity. Model validation was performed by effectively shifting the spatial location of the carboxylate by inserting a methylene adjacent to the aromatic ring, resulting in the predicted alteration in binding affinity. This work illustrates conformation as a determinant of ligand physiochemical properties and ligand binding affinity to a biological transporter.

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems.

Synthesis and Characterization of a Novel Diels - Alder Adduct of Codeine

The Diels - Alder reaction was applied to 4,5-epoxymorphinan opioids to generate a novel aromatic cycloadduct at C(7) - C(8): Thermolytic cleavage of sultine 8 produced the reactive diene o-quinodimethane 7 which condensed favorably with codeine (11), but not with codeinone (9) or 14- hydroxycodeinone (10), producing the desired tetrahydronaphtho adduct 12 with (7R,8R) geometry (Scheme). The configuration of the cycloadduct was determined by 1D- and 2D-NMR experiments. The unanticipated reactivity of these codeine derivatives was investigated by quantum-mechanical calculations, and it was determined that steric effects of the 6-keto and 14-hydroxy group likely precluded condensation by raising the molecular energy of their respective transition states.

Age-specific differences in oncogenic pathway deregulation and chemosensitivity in patients with acute myeloid leukemia: Strategies to maximize response to induction chemotherapy

7013

Background: Despite all the advances made in understanding the poor prognosis of acute myeloid leukemia (AML) in the elderly, the underlying biology at a molecular signaling pathway level has yet to be defined. Methods: Clinically annotated, microarray data from 425 patients with newly diagnosed AML from two publicly available datasets GSE1159 and GSE12417 were analyzed. Age-specific cohorts (young ≤45 years; n = 175 and elderly ≥55 years; n = 144) were prospectively identified. Gene expression analysis was conducted by applying previously defined and tested signature profiles reflecting deregulation of oncogenic signaling pathways, altered tumor environment, and signatures of chemotherapy sensitivity. Standard Kaplan-Meier survival curves were generated using the two-sided log-rank test and individual differences in the probability of oncogenic pathway deregulation between young vs. elderly were analyzed via the non-parametric Mann-Whitney U test and a one-sided p-value ≤ 0.05 was considered statistically significant. Results: Elderly AML patients had worse OS (median 8.8 months vs. 24.1 months in younger patients; p = 0.001) and EFS (median 7.1 months vs. 15.3 months in younger patients; p < 0.0001). Analysis of oncogenic pathways revealed that older patients had higher probability of Ras, Src, and TNF pathway activation, p < 0.0001. Older patients were also less sensitive to anthracycline compared to younger AML patients, p < 0.0001. Unsupervised hierarchical clustering of younger AML patients revealed two clusters and clinically better survival for cluster 1 compared to cluster 2 (high Ras, Src, TNF pathway activation) and the latter were in turn less sensitive to adriamycin. However, in elderly patients those in cluster 2 also had high Ras, Src, TNF but this did not translate into differences in survival or chemotherapy sensitivity. Conclusions: AML arising in the elderly represents a distinct biologic entity characterized by unique patterns of deregulated signaling pathways that contributes to poor survival and resistance to adriamycin. We hope these findings will enable clinically meaningful adjustments of treatment strategies in the older patient population.

No significant financial relationships to disclose.

Characterizing the clinical relevance of an embryonic stem cell phenotype in lung adenocarcinoma

11001

Background: Cancer cells possess traits reminiscent of those ascribed to normal stem cells. It is unclear whether these phenotypic similarities between normal/embryonic stem cells and mature tumor cells, specific to lung cancer, are a result of underlying biologic processes, such as specific molecular pathways and regulatory networks. Methods: Using a large cohort of lung cancer cell lines with associated gene expression data, genes associated with an embryonic stem cell identity were used to develop a ‘signature’ representative of embryonic stemness (ES) activity specific to lung adenocarcinoma. Differential biology was evaluated using Gene Set Enrichment Analysis (GSEA) and signatures of oncogenic pathway deregulation. The ES signature was applied to three independent early (stage I - IIIa) lung adenocarcinoma data sets (N = 634) with clinically annotated gene expression data. The relationship between the ES phenotype and cisplatin sensitivity was also evaluated. Results: Using Bayesian regression analysis, a 100 gene signature representative of ES activity in lung adenocarcinoma was developed and validated in a leave-one-out-analysis. GSEA identified gene sets significantly represented in the ES signature: signature of neoplastic transformation, signature of undifferentiated cancer, BRCA pathway, and fibroblast serum response pathway, all associated with cancer invasiveness. Adenocarcinomas with ES demonstrated increased activation of RAS (p = 0.0002), MYC (p = 0.0057), wound healing (angiogenesis) (p < 0.0001), chromosomal instability (p < 0.0001), and invasiveness (p < 0.0001) gene signatures. Adenocarcinomas (N= 634) with ES had a decreased survival (p<0.04). The ES signature was not prognostic in prostate, ovarian, or breast adenocarcinomas. Lung tumors (N=634) and adenocarcinoma cell lines (N=31) with ES were more resistant to cisplatin (p<0.0001 and p=0.0063, respectively). Conclusions: Lung adenocarcinomas that share a common gene expression pattern with normal stem cells were associated with decreased survival and increased likelihood of resistance to cisplatin, indicating the aggressiveness of lung tumors with a stem cell phenotype.

No significant financial relationships to disclose.

Integration of mRNA and microRNA profiles as prognostic and predictive markers in lung adenocarcinoma

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Background: Lung adenocarcinoma (ADC) is a distinct biologic entity with unique gene amplifications (Weir B, Nature 2008). Yet, comprehensive transcriptomic analysis, including microRNAs, specific to lung ADC are lacking. Methods: Using mRNA expression data from a discovery cohort of 154 patients with histologically proven early stage (I and II) lung ADC, signatures of oncogenic pathway and tumor microenvironment status were applied and further organized by hierarchical clustering to develop a metagene model. Further, using in vitro assays in a large cohort of lung ADC cell lines (n = 42) with corresponding mRNA and microRNA data, novel microRNAs associated with a poor prognosis and their relationship to cisplatin resistance was elucidated. Results: In the discovery cohort of 154 patients with early stage disease, activation of oncogenic pathways associated with wound healing (angiogenesis), chromosomal instability, and STAT signaling were associated with an increased risk of recurrence (p<0.001). Utilizing the extremes of survival to identify cohorts of patients as high and low risk phenotypes, using bayesian regression, a 100 gene signature (‘metagene') that captured the diversity of signaling pathways unique to patients at increased risk of recurrence was identified and validated in an independent cohort (n = 364) of lung ADC samples with 78.3% accuracy. Kaplan Meier survival analysis and multivariate analysis further confirmed the independent prognostic value of the 100 gene signature (p= 0.007). Using in vitro cell proliferation assays, predicted high risk lung ADC cell lines were identified as being more resistant to cisplatin therapy than those predicted to be low risk (p=0.001). In a novel manner, we also identified several microRNAs (miR-215, miR-98, miR- 643, let-7b, miR-665, miR-629) associated with a high risk of recurrence and more importantly cisplatin resistance. Conclusions: mRNA and microRNA profiles reflect unique aspects of individual tumors and may characterize histology-specific tumor heterogeneity in lung ADC, providing an opportunity to better characterize the oncogenic process and refine therapeutic options.

No significant financial relationships to disclose.

Inhibition requirements of the human apical sodium-dependent bile acid transporter (hASBT) using aminopiperidine conjugates of glutamyl-bile acids

PURPOSE

Synthesize aminopiperidine conjugates of glutamyl-bile acids (glu-BAs) and develop a hASBT inhibition model using the conformationally sampled pharmacophore (CSP) approach.

METHODS

glu-BAs aminopiperidine conjugates were synthesized. hASBT inhibition was measured as K(i). A CSP-SAR model was built using structural and physico-chemical descriptors and evaluated via cross-validation.

RESULTS

Twenty-nine aminopiperidine conjugates were synthesized. All inhibited hASBT, with K(i) ranging from 0.95 to 31.8 muM. Amidation of the piperidine nitrogen slightly decreased activity, while replacement by a carbon increased potency. Esterification of the glutamic acid linker had a minor impact, suggesting that a negative charge around C-24 is not required for binding. Three quantitative CSP-SAR models were developed. The best model (r (2) = 0.813, Q (2) = 0.726) included two descriptors: angle between 7-OH, alpha-substituent and centroid of rings B and C, and electrostatic contribution to the solvation free-energy. The model successfully distinguished between compounds with K(i) < 16muM and K(i) > 16muM. Models indicated that hydrophobicity, alpha substituent orientation, and partially compacted side chain conformation promote inhibitory potency. Qualitative CSP-SAR analysis indicated that the presence of an internal salt bridge, resulting in a locked conformation of the side chain, yielded weaker inhibitors.

CONCLUSIONS

Aminopiperidine conjugates of glu-BAs were potent hASBT inhibitors. A predictive and robust CSP-SAR model was developed.

Uranium sequestration by a marine cyanobacterium, Synechococcus elongatus strain BDU/75042

A marine, unicellular cyanobacterium, Synechococcus elongatus strain BDU/75042 was found to sequester uranium from aqueous systems at pH 7.8. The organism could remove 72% (53.5 mg U g(-1) dry weight) of uranium from test solutions containing 100 microM uranyl carbonate within 1h. The equilibrium data fitted well in the Langmuir isotherm thus suggesting a monolayer adsorption of uranium on the cyanobacterial biomass and predicted the maximum adsorption capacity of 124 mg U g(-1) dry weight. Light and scanning electron microscopy coupled with energy dispersive X-ray fluorescence (EDXRF) spectroscopy confirmed the uranyl adsorption by this organism. Most of the bound uranium was found to be associated with the extracellular polysaccharides (EPS) suggesting its interaction with the surface active ligands. Fourier transform infrared (FT-IR) spectroscopy suggested the amide groups and the deprotonated carboxyl groups on the cyanobacterial cell surface were likely to be involved in uranyl adsorption. The cell bound uranium could be released by washing with ethylene diamine tetraacetic acid (EDTA) or 0.1N HCl. The X-ray diffraction (XRD) analyses revealed the identity of uranium deposits associated with the cell biomass as uranyl carbonate hydrate. The study revealed the potential of this cyanobacterium for harvesting uranium from natural aquatic environments.

Computational model for predicting chemical substituent effects on passive drug permeability across parallel artificial membranes

Drug permeability is often a limiting step in drug action, requiring chemical optimization of a drug candidate to improve this property. Such optimization is typically performed in the context of a congeneric series, where substituents are varied to optimize the target property. Motivated by this need the present work examines the influence of chemical substituents on passive permeability (log P pass) across parallel artificial membranes (PAMPA) undertaken for three congeneric series of compounds; benzoic acids, pyridines and quinolines. PAMPA showed pyridine and quinoline to have high permeability and chemical substituents to typically reduce the permeability. On the contrary, benzoic acid showed poor permeability and chemical substituents typically increased the permeability. To quantitate these effects with respect to physical properties, models were built to explain and predict the permeability of these classes of compounds based on computed molecular descriptors. Models for the benzoic acid series in the ionized state indicated the solvent accessible surface area, cavity dispersion and the free energy of solvation in hexane as well as in water to dominate permeability. However, when the acid group is treated as neutral, the free energy of solvation in water, the fraction polar surface area, the polar surface area and difference in the free energy of solvation between hexane and water were important; these terms, among others, were also important for the neutral pyridine-quinoline series. Considering that the permeability of the benzoic acid series is about 2 orders of magnitude lower than the pyridines and quinolines and that a shift of approximately two pH units in the p K a of the acid group of benzoic acid will allow for the neutral species of the molecule to dominate under experimental conditions (pH = 6.5), these results suggest that the additional energy barrier associated with permeation of the benzoic acid series is associated with the need to protonate the acidic group, thereby forming the neutral species which may then cross the hydrophobic region of the membrane.

Pharmacogenomic strategies provide a rational approach to the treatment of cisplatin-resistant patients with advanced non- small cell lung cancer (NSCLC)

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Background: Standard treatment for advanced non-small lung cancer (NSCLC) includes platinum-based therapy. Response is however suboptimal and unpredictable. Newer agents, such as pemetrexed, have shown significant activity in the second-line setting, but their role in the first-line setting is unknown. Methods: Using in vitro drug sensitivity data, coupled with Affymetrix microarray data, gene expression signatures predicting sensitivity to cisplatin and pemetrexed were developed, using methods previously described (Nature Medicine, 2006). Signatures were validated with response data from 32 independent ovarian and lung cancer cell lines as well as 59 patient samples. Results: Genomic-derived signatures of cisplatin and pemetrexed sensitivity were shown to accurately predict response in vitro and, in the case of cisplatin, in 59 samples obtained from advanced disease patients previously treated with cisplatin. The accuracy of the cisplatin predictor, using clinical response as the endpoint, was 83.1% (Sensitivity: 100%, Specificity: 57%). In comparison, determination of ERCC1 status (IHC) had a predictive accuracy of 62% (Sensitivity: 82.8%, Specificity: 33.3%). Interestingly, a significant inverse correlation (p = 0.004) was found between the likelihood of cisplatin and pemetrexed sensitivity in the NSCLC cell lines. This relationhip was further validated in another indepedent cohort of 91 patients with NSCLC (p < 0.01). Finally, using novel cell proliferation experiments, we show that tumors from cisplatin refractory patients that are initially sensitive to pemetrexed, if treated with a taxane (docetaxel or paclitaxel) prior to pemetrexed therapy, develop resistance to subsequent pemetrexed therapy. Conclusions: The use of gene expression signatures that predict cisplatin and pemetrexed sensitivity can be incorporated into strategies to refine the selection of chemotherapeutic drugs chosen as first-line therapy in advanced NSCLC. It is critical for future prospective studies to validate the use of pharmacogenomic predictors of chemosensitivity in NSCLC, to optimize response rates and survival benefit.

No significant financial relationships to disclose.

Treatment of high-strength pet food wastewater using two-stage membrane bioreactors

A two-stage membrane bioreactor was used to treat dissolved-air-flotation pretreated, high-strength pet food wastewater characterized by oil and grease concentrations of 50 000 to 82 000 mg/L and total chemical oxygen demand (COD) and five-day biochemical oxygen demand (BOD5) concentrations of 100 000 and 80 000 mg/L, respectively, to meet stringent surface discharge criteria (i.e., BOD5, total suspended solids [TSS], and ammonium-nitrogen [NH4(+)-N] of < 10 mg/L at an overall hydraulic retention time of 6.3 days). Organic contaminants were removed primarily in the first stage, followed by almost complete removal of ammonia in the second stage. Despite a rise in poorly biodegradable COD in the second stage, overall removal of TSS, BOD5, COD, and ammonia was 100, 99.9, 95.2, and 99.7%, respectively, thus readily achieving the required criteria. Consistent nitrite accumulation over a period of more than 100 days, even at dissolved oxygen concentrations of more than 2.5 mg/L, was remarkable. A residual alkalinity requirement for nitrification was quantified. Membrane performance was extensively studied in this work.

A novel two-stage MBR denitrification process for the treatment of high strength pet food wastewater

A novel paradigm using pre-denitrification process is presented to optimize an existing system of two-stage MBRs treating high strength pet food wastewater. Successive reduction of organics in the 1st stage and almost complete nitrification in the 2nd stage generated effluent meeting stringent surface discharge criteria i.e. BOD5, TSS and NH4+ -N of < 10 mg/L at an overall HRT of 6.3 days. Pre-anoxic zone was created by a submerged coil in the path of influent to the 1st stage. Final effluent and the 1st stage mixed liquor were recirculated to the coil. With prevailing high denitrification rates, more than 94% of the recirculated nitrates were denitrified in less than 15 min of effective anoxic residence time. At a recycle ratio of 3:1, total nitrogen was reduced by 84%, aeration energy by 25% and the external alkalinity requirement by 65%, enhancing economical viability of the system.

Conventional and thermophilic aerobic treatability of high strength oily pet food wastewater using membrane-coupled bioreactors

Although thermophilic treatment systems have recently gained considerable interest, limited information exists on the comparative performances of membrane-coupled bioreactors (MBR) at thermophilic and conventional conditions. In this study aerobic MBRs operating at room temperature (20 degrees C) and at lower thermophilic range (45 degrees C) were investigated for the treatment of dissolved air flotation (DAF) pretreated pet food wastewater. The particular wastewater is characterized by oil and grease (O & G) concentrations as high as 6 g/L, COD of 51 g/L, BOD of 16 g/L and volatile fatty acid (VFA) of 8.3 g/L. The performances of the two systems in terms of COD, BOD and O & G removal at varying hydraulic retention time (HRT) are compared. COD removal efficiencies in the thermophilic MBR varied from 75% to 98% and remained constant at 94% in the conventional MBR. The O & G removal efficiencies were 66-86% and 98% in the thermophilic and conventional MBR, respectively. Interestingly, high concentrations of VFA were recorded, equivalent to 50-73% of total COD, in the thermophilic MBR effluent. The observed yield in the thermophilic MBR was 40% of that observed in the conventional MBR.

Microbial Desulfurization of Different Coals

Coal is the most important nonrenewable energy source of fossil origin. It is also the most common fuel in thermal power plants. However, during coal incineration in power plants, high sulfur content of coal poses serious environmental problems owing to sulfur dioxide emission. We studied the application of microbial methods for removal of sulfur from three types of high sulfur coals-two samples collected from Assam and Rajasthan in India and one from Libiaz, Poland. These coal samples were desulfurized using indigenous Acidithiobacillus sp. After investigation of the effect of various parameters, the conditions optimized for the maximum removal of total sulfur (91.87% for lignite, 63.13% for Polish coal, and only 9.44% for Assam coal) were as follows: initial pH of 1.5 (2.5 in the case of Assam coal), particle size of 45 micro, pulp density of 2% (w/v), incubation period of 30 d at -35 degrees C in presence of 44.2 g/L of ferrous sulfate in the media with shaking at 140 rpm. Poor removal of sulfur in the case of Assam coal was owing to extensive precipitation of jarosites. In addition, the sulfur in Assam coal is mostly found in organic form, which is difficult to remove with Acidithiobacillus sp. The removal of sulfur from the three coal samples was demonstrated with photomicrographic studies.

Activation of cytochrome P450 gene expression in the rat brain by phenobarbital-like inducers

Oxidative biotransformation, coupled with genetic variability in enzyme expression, has been the focus of hypotheses interrelating environmental and genetic factors in the etiology of central nervous system disease processes. Chemical modulation of cerebral cytochrome P450 (P450) monooxygenase expression character may be an important determinant of in situ metabolism, neuroendocrine homeostasis, and/or central nervous system toxicity resulting from exposure to neuroactive drugs and xenobiotic substances. To examine the capacity of the rat brain to undergo phenobarbital (PB)-mediated induction, we developed reverse transcription-polymerase chain reaction methods and evaluated the effects of several PB-like inducers on P450 and microsomal epoxide hydrolase gene expression. Animals treated i.p. with four daily doses of PB demonstrated markedly induced levels of CYP2B1, CYP2B2, and CYP3A1 mRNA in the striatum and cerebellum. In contrast, 1 or 2 days of PB treatment resulted in unchanged or even slightly decreased levels of CYP2B1 and CYP2B2 in the brain, although the latter treatments produced marked induction of the corresponding genes in the liver. Only slight increases in epoxide hydrolase RNA levels resulted in brains of PB-treated animals. Substantial activation of cerebral CYP2B1, CYP2B2, and CYP3A1 mRNA levels also resulted when animals were treated with the neuroactive drugs diphenylhydantoin and amitryptiline, and with the potential PB-like xenobiotic inducers trans-stilbene oxide and diallyl sulfide, whereas dichlorodiphenyltrichloroethane was less efficacious. Although the time course of the induction response is delayed in brain relative to that required for the liver, these results clearly establish that brain P450s are markedly PB inducible.

Complete genomic sequence and analysis of the prion protein gene region from three mammalian species

The prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single exon of a single-copy chromosomal gene. In addition to the protein-coding exon, PrP genes in mammals contain one or two 5'-noncoding exons. To learn more about the genomic organization of regions surrounding the PrP exons, we sequenced 10(5) bp of DNA from clones containing human, sheep, and mouse PrP genes isolated in cosmids or lambda phage. Our findings are as follows: (1) Although the human PrP transcript does not include the untranslated exon 2 found in its mouse and sheep counterparts, the large intron of the human PrP gene contains an exon 2-like sequence flanked by consensus splice acceptor and donor sites. (2) The mouse Prnpa but not the Prnpb allele found in 44 inbred lines contains a 6593 nucleotide retroviral genome inserted into the anticoding strand of intron 2. This intracisternal A-particle element is flanked by duplications of an AAGGCT nucleotide motif. (3) We found that the PrP gene regions contain from 40% to 57% genome-wide repetitive elements that independently increased the size of the locus in all three species by numerous mutations. The unusually long sheep PrP 3'-untranslated region contains a "fossil" 1.2-kb mariner transposable element. (4) We identified sequences in noncoding DNA that are conserved between the three species and may represent biologically functional sites.

Automated determination of urine and cerebrospinal fluid proteins with Coomassie Brilliant Blue and the Abbott ABA-100

We have evaluated the use of Coomassie Brilliant Blue (CBB) dye to measure the protein of urine and cerebral spinal fluid. The method was automated and compared with the turbidimetric method and with Ponceau S dye. With both the manual and automated procedures the CBB method could be used to protein concentrations of 160 mg/dl. Comparing this method to the method measuring the turbidity produced by trichloracetic acid (TCA) we found a correlation coefficient (r) of 0.96. The regression line was CBB = 0.84 TCA + 4.97. A similar comparison to the method using Ponceau S (PS) produced an r = 0.98 and the regression line, CBB = 0.91 P-S + 3.2. The CBB method was not as affected by turbidity in the samples or by xanthochromia as was the TCA Method. It is simpler to perform than the P-S method, since it does not require decantation. With the manual method, the coefficient of variation (CV) at 40 mg/dl for within-day determinations was less than 2% and, for between-day determinations, less than 4%. While the CV was somewhat higher with the ABA than with the manual method at 40 mg/dl, it was below 5% for both within-day and between-day determinations at the concentrations between 70 and 170 mg/dl. The method using CBB is useful as both a manual and automated procedure to measure protein in urine and cerebral spinal fluid.

Immunologic parameters of children with urinary tract infection: effects of trimethoprim-sulfamethoxazole

In order to determine whether a deficiency in immunologic response predisposes certain children to recurrent infections of the urinary tract, four groups of children were investigated: a control group; children with extraurinary infections; children with urinary tract infections; and a group of children treated with trimethoprim-sulfamethoxazole (TMP-SMX). In none of the groups were there changes in humoral immunoglobulins, peripheral neutrophil counts, serum complement concentrations or urinary excretion of IgG, IgA, or IgM that might might predispose to infection. However, children with urinary tract infections were more likely to belong to blood group A (66.6%; expected frequency, 45%) and had a blunted thymidine uptake of their stimulated lymphocytes (RLB) when compared with children with extraurinary infection. As well, their nitroblue tetrazolium reduction (NBT) was significantly lowered and this paralleled their RLB response. We postulated a shared antigenic feature of either their renal-urinary tissue or bacterial antigen with blood group A antigen; this prevents the mounting of an effective immunologic defence. If TMP-SMX further depresses the lymphocyte response, it may be considered contraindicated in urinary tract infection. In 11 children treated with this drug we found no significant difference between their RLB and NBT responses and those of children with infections of the urinary system treated with other drugs. We conclude that TMP-SMX does not alter the immune responses in children.