Computational pharmacogenotype extraction from clinical next-generation sequencing

Background

Next-generation sequencing (NGS), including whole genome sequencing (WGS) and whole exome sequencing (WES), is increasingly being used for clinic care. While NGS data have the potential to be repurposed to support clinical pharmacogenomics (PGx), current computational approaches have not been widely validated using clinical data. In this study, we assessed the accuracy of the Aldy computational method to extract PGx genotypes from WGS and WES data for 14 and 13 major pharmacogenes, respectively.

Methods

Germline DNA was isolated from whole blood samples collected for 264 patients seen at our institutional molecular solid tumor board. DNA was used for panel-based genotyping within our institutional Clinical Laboratory Improvement Amendments- (CLIA-) certified PGx laboratory. DNA was also sent to other CLIA-certified commercial laboratories for clinical WGS or WES. Aldy v3.3 and v4.4 were used to extract PGx genotypes from these NGS data, and results were compared to the panel-based genotyping reference standard that contained 45 star allele-defining variants within CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, CYP4F2, DPYD, G6PD, NUDT15, SLCO1B1, TPMT, and VKORC1.

Results

Mean WGS read depth was >30x for all variant regions except for G6PD (average read depth was 29 reads), and mean WES read depth was >30x for all variant regions. For 94 patients with WGS, Aldy v3.3 diplotype calls were concordant with those from the genotyping reference standard in 99.5% of cases when excluding diplotypes with additional major star alleles not tested by targeted genotyping, ambiguous phasing, and CYP2D6 hybrid alleles. Aldy v3.3 identified 15 additional clinically actionable star alleles not covered by genotyping within CYP2B6, CYP2C19, DPYD, SLCO1B1, and NUDT15. Within the WGS cohort, Aldy v4.4 diplotype calls were concordant with those from genotyping in 99.7% of cases. When excluding patients with CYP2D6 copy number variation, all Aldy v4.4 diplotype calls except for one CYP3A4 diplotype call were concordant with genotyping for 161 patients in the WES cohort.

Conclusion

Aldy v3.3 and v4.4 called diplotypes for major pharmacogenes from clinical WES and WGS data with >99% accuracy. These findings support the use of Aldy to repurpose clinical NGS data to inform clinical PGx.

Sequential Sampling Models in Cognitive Neuroscience: Advantages, Applications, and Extensions

Sequential sampling models assume that people make speeded decisions by gradually accumulating noisy information until a threshold of evidence is reached. In cognitive science, one such model--the diffusion decision model--is now regularly used to decompose task performance into underlying processes such as the quality of information processing, response caution, and a priori bias. In the cognitive neurosciences, the diffusion decision model has recently been adopted as a quantitative tool to study the neural basis of decision making under time pressure. We present a selective overview of several recent applications and extensions of the diffusion decision model in the cognitive neurosciences.

Expression and regulation of the Na+-K+-2Cl- cotransporter NKCC1 in the normal and CFTR-deficient murine colon

Defective regulation and/or reduced expression of the Na+-K+-2Cl- cotransporter NKCC1 may contribute to the severe secretory defect that is observed in cystic fibrosis, but data concerning the expression and function of NKCC1 in cystic fibrosis transmembrane conductance regulator (CFTR)-deficient cells are equivocal. We therefore investigated NKCC1 mRNA expression, Na+-K+-2Cl- cotransport activity and regulation by cAMP in crypts isolated from the proximal colon of CFTR-containing (CFTR (+/+)) and CFTR-deficient (CFTR (-/-)) mice. mRNA expression levels were determined by semiquantitative PCR, transport rates were measured fluorometrically in 2',7'-bis(carboxyethyl)-5(6)-carboxyfluorescein acetomethylester (BCECF)-loaded crypts, cytoplasmic volume changes were assessed by confocal microscopy, and [Cl-]i changes were examined by N-(ethoxycarbonylmethyl)-6-methoxyquinolinium bromide (MQAE) quenching. NKCC1 mRNA expression levels were not significantly reduced in CFTR (-/-) crypts compared to controls. Azosemide-sensitive NH4+ influx (used as a measure of Na+-K+-2Cl- cotransport) was 2.23 +/- 0.72 vs. 1.56 +/- 0.16 mM min-1, and increased by 63.6 % in (+/+) and 87.3 % in (-/-) crypts upon stimulation for 5 min with forskolin. After 20 min of stimulation with forskolin, the Na+-K+-2Cl- cotransport rates in (-/-) and (+/+) crypts were identical. Crypt cross-sectional area and [Cl-]i decreased only in (+/+) crypts upon stimulation. In conclusion, normal NKCC1 expression levels, somewhat reduced Na+-K+-2Cl- cotransport rates, but preserved activation by cAMP were found in colonic crypts from CFTR (-/-) mice, ruling out a severe dysfunction of the Na+-K+-2Cl- cotransporter in the CF intestine. Furthermore, these studies establish the existence of a direct, cell-volume- and [Cl-]i-independent activation of colonic NKCC1 by an increase in intracellular cAMP.

cAMP-mediated regulation of murine intestinal/pancreatic Na+/HCO3- cotransporter subtype pNBC1

Basolateral Na(+)-HCO(3)(-) cotransport is essential for intestinal anion secretion, and indirect evidence suggests that it may be stimulated by a rise of intracellular cAMP. We therefore investigated the expression, activity, and regulation by cAMP of the Na(+)-HCO(3)(-) cotransporter isoforms NBC1 and NBCn1 in isolated murine colonic crypts. Na(+)-HCO(3)(-) transport rates were measured fluorometrically in BCECF-loaded crypts, and mRNA expression levels and localization were determined by semiquantitative PCR and in situ hybridization. Acid-activated Na(+)-HCO(3)(-) cotransport rates were 5.07 +/- 0.7 mM/min and increased by 62% after forskolin stimulation. NBC1 mRNA was more abundant in colonic crypts than in surface cells, and crypts expressed far more NBC1 than NBCn1. To investigate whether the cAMP-induced Na(+)-HCO(3)(-) cotransport activation was secondary to secretion-associated changes in HCO(3)(-) or cell volume, we measured potential forskolin-induced changes in intracellular pH and assessed Na(+)-HCO(3)(-) transport activity in CFTR -/- crypts (in which no forskolin-induced cell shrinkage occurs). We found 30% reduced Na(+)-HCO(3)(-) transport rates in CFTR -/- compared with CFTR +/+ crypts but similar Na(+)-HCO(3)(-) cotransport activation by forskolin. These studies establish the existence of an intracellular HCO(3)(-) concentration- and cell volume-independent activation of colonic NBC by an increase in intracellular cAMP.

A novel approach to pathogen reduction in biosolids: the enzymic hydrolyser

Revision of the Sludge (Use in Agriculture) Regulations in the UK has resulted in the requirement of a final product standard in terms of E. coli per gram of dry solids. Conventional mesophilic digestion including 14-day secondary storage should normally provide adequate treatment to meet the Treated Sludge Standard. Any process capable of greater pathogen reduction would ensure more process security and compliance comfort. Such a process would be a welcome alternative to extra secondary storage where an existing works does not have sufficient capacity, particularly if the differences in costs between the options are small. Enzymic hydrolysis was found to be up to ten-fold more effective in E. coli reduction than conventional secondary digestion. A two-stage digestion process based on this technique has been developed by United Utilities and Montgomery Watson Harza (termed the enzymic hydrolyser, patent pending). Studies showed that the mean numbers of E. coli were significantly lower in the enzymic hydrolyser systems (P > 0.05; t = 13.19) compared to conventional digesters. Increased stability was a secondary benefit of the system (foam was eliminated or greatly reduced in the enzymic hydrolyser units). Another benefit of the system for retrofit to existing assets is the decreased tankage volumes required compared to secondary digestion to achieve more than twice the log kill of pathogens.

A comparison of four methods for simulating the diffusion process

Four methods for the simulation of the Wiener process with constant drift and variance are described. These four methods are (1) approximating the diffusion process by a random walk with very small time steps; (2) drawing directly from the joint density of responses and reaction time by means of a (possibly) repeated application of a rejection algorithm; (3) using a discrete approximation to the stochastic differential equation describing the diffusion process; and (4) a probability integral transform method approximating the inverse of the cumulative distribution function of the diffusion process. The four methods for simulating response probabilities and response times are compared on two criteria: simulation speed and accuracy of the simulation. It is concluded that the rejection-based and probability integral transform method perform best on both criteria, and that the stochastic differential approximation is worst. An important drawback of the rejection method is that it is applicable only to the Wiener process, whereas the probability integral transform method is more general.

A multinomial model for short-term priming in word identification

A simple multinomial model for short-term priming in perceptual word identification is presented. In the experiments to which the model is applied, prime words are presented just prior to a flashed target word, and subjects must decide which of 2 alternative words matches the target. The model assumes that on some proportion of trials, confusion among the words leads to the decision being based on 1 of the prime words instead of the target. In addition, it is assumed that subjects sometimes discount a prime that matches 1 of the test alternatives and so choose the alternative that does not match. With these assumptions, the model fits the data from 5 experiments (including 4 used to develop the model known as ROUSE [responding optimally with unknown sources of evidence]; D. E. Huber, R. Shiffrin, K. Lyle, & K. Ruys, 2001). The multinomial model fits the data about as well as the ROUSE model and so should lead to further development and critical testing of both models.

Counter model for word identification: reply to Bowers (1999)

The counter model (R. Ratcliff & G. McKoon, 1997) was designed to explain the normal processes of word identification and how they are influenced by a prior encounter with a word. The model accounts for the findings of word identification experiments in which words are flashed briefly. A crucial finding is that prior encounters with words typically lead to biases such that a previously encountered word is more likely to be given as a response. However, for low-frequency words, a prior encounter can improve overall performance (J. S. Bowers, 1999; E. M. Wagenmakers, R. Zeelenberg, & J. G. W. Raaijmakers, 2000). The authors show how the model can explain this result. Also, J. S. Bowers (1999) has claimed that some earlier data concerning dissimilar alternatives in forced-choice experiments that support the counter model are spurious, but the authors show that his claims are incorrect. In sum, the authors argue for a theoretical approach that offers a detailed description of the cognitive processes of word identification and explains performance across tasks, measures, and independent variables.

The effects of aging on reaction time in a signal detection task

The effects of aging on response time are examined in 2 simple signal detection tasks with young and older subjects (age 60 years and older). Older subjects were generally slower than young subjects, and standard Brinley plot analyses of response times showed typical results: slopes greater than 1 and (mostly) negative intercepts. R. Ratcliff, D. Spieler, and G. McKoon (2000) showed that the slopes of Brinley plots measure the relative standard deviations of the distributions of response times for older versus young subjects. Applying R. Ratcliff's (1978) diffusion model to fit the response times, their distributions, and response accuracy, it was found that the larger spread in older subjects' response times and their slowness relative to young subjects comes from a 50-ms slowing of the nondecision components of response time and more from conservative settings of response criteria.

Modeling the effects of repetition and word frequency in perceptual identification

The counter model for word identification (Ratcliff & McKoon, 1997) has been challenged by recent empirical findings that performance on low-frequency words improves as the result of repetition of the words. We show that the model can accommodate this learning effect, and that it can do so without jeopardizing its explanations of the effects on word identification of a large number of other variables.

Explicitly modeling the effects of aging on response time

Research into the effects of aging on response time has focused on Brinley plots. Brinley plots are constructed by plotting mean response times for older subjects against those for young subjects for a set of experimental conditions. The typical result is a straight line with a slope greater than 1 and a negative intercept. This linear function has been interpreted as showing that aging leads to a general slowing of cognitive processes. In this article, we show that the slope of the Brinley plot is actually a measure of the relative standard deviations of older versus young subjects' response times; it is not a measure of general slowing. We examine current models of the effects of aging on mean response time and show how they might be reinterpreted. We also show how a more comprehensive model, Ratcliff's diffusion model (1978), can account for Brinley plot regularities and, at the same time, provide an account of accuracy rates, the shapes of response time distributions, and the relative speeds of error and correct response times, aspects of the data about which models designed to account for Brinley plots are mute. We conclude by endorsing a research approach that applies explicit models to response time data in aging in order to use the parameters of the model to interpret the effects of aging.

A diffusion model account of masking in two-choice letter identification

The diffusion model developed by R. Ratcliff (1978, 1981, 1985, 1988) for 2-choice decisions was applied to data from 2 letter identification experiments. In the experiments, stimulus letters were displayed and then masked, and the stimulus onset asynchrony between letter and mask was manipulated to vary accuracy from near chance to near ceiling. A standard reaction time procedure was used in one experiment and a deadline procedure in the other. Two hypotheses about the effect of masking on the information provided to the decision process were contrasted: (a) The output of perception to the decision process varies with time, so that the information used by the decision process rises and falls, reflecting the stimulus onset and mask onset. (b) The output of perception to the decision is constant over time, reflecting information integrated over the time between the stimulus and mask onsets. The data were well fit by the diffusion model only with the assumption of constant information over time.

Sodium channel blockers and uridine triphosphate: effects on nasal potential difference in cystic fibrosis mice

Sodium channel inhibitors block the enhanced Na+ reabsorption in cystic fibrosis (CF). Extracellular nucleotides facilitate Cl- secretion via Ca2+ gated Cl- channels. A combination of these effects may produce less viscid secretions in CF which are easier to expectorate. This study examined the effects of combining sodium channel blockers with uridine triphosphate (UTP) on nasal membrane potential difference (PD) in CF insertional null mutant mice (cftr(tm1HGU)), deltaF508 homozygous mice (cftr(tm1Cam)) and matched control animals. Median basal PD in the insertional CF mice and deltaF508 CF mice were -28 and -34 mV respectively. These values were significantly different to the control animals (-20 mV). Amiloride and loperamide reduced the PD in cftr(tm1HGU) CF mice (deltaPD 13 mV & 15 mV respectively) suggesting Na+ blockade. The subsequent addition of UTP in a chloride-free vehicle increased the PD (deltaPD -8- -12.5 mV). DeltaF508 mice showed significantly greater responses compared with CF insertional null mutant mice (p<0.05). The action of UTP was brief and not prolonged by the addition alpha-beta-methylene-adenosine 5' diphosphate. Suramin, a competitive antagonist of P2 purinoceptors blocked the action of UTP. In conclusion, this study demonstrated dose dependant nasal membrane potential changes in differences mice with uridine triphosphate in the presence of sodium channel blockers suggestive of chloride secretion. More stable analogues of uridine triphosphate in combination with long acting sodium channel blockers such as loperamide may have therapeutic potential in cystic fibrosis.

A neural network model of implicit memory for object recognition

People name well-known objects shown in pictures more quickly if they have studied them previously. The most common interpretation of this priming effect is that processing is facilitated by an implicit memory trace in a perceptual representation system. We show that object priming can be explained instead as a bias in information processing, without recourse to an implicit memory system. Assumptions about psychological decision-making processes and bias were added to a neural network model for object identification, and the model accounted for performance both qualitatively and quantitatively in four object identification experiments.

Connectionist and diffusion models of reaction time

Two connectionist frameworks, GRAIN (J. L. McClelland, 1993) and brain-state-in-a-box (J. A. Anderson, 1991), and R. Ratcliff's (1978) diffusion model were evaluated using data from a signal detection task. Dependent variables included response probabilities, reaction times for correct and error responses, and shapes of reaction-time distributions. The diffusion model accounted for all aspects of the data, including error reaction times that had previously been a problem for all response-time models. The connectionist models accounted for many aspects of the data adequately, but each failed to a greater or lesser degree in important ways except for one model that was similar to the diffusion model. The findings advance the development of the diffusion model and show that the long tradition of reaction-time research and theory is a fertile domain for development and testing of connectionist assumptions about how decisions are generated over time.

Salmonella typhi uses CFTR to enter intestinal epithelial cells

Homozygous mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) cause cystic fibrosis (CF). In the heterozygous state, increased resistance to infectious diseases may maintain mutant CFTR alleles at high levels in selected populations. Here we investigate whether typhoid fever could be one such disease. The disease is initiated when Salmonella typhi enters gastrointestinal epithelial cells for submucosal translocation. We found that S. typhi, but not the related murine pathogen S. typhimurium, uses CFTR for entry into epithelial cells. Cells expressing wild-type CFTR internalized more S. typhi than isogenic cells expressing the most common CFTR mutation, a phenylalanine deleted at residue 508 (delta508). Monoclonal antibodies and synthetic peptides containing a sequence corresponding to the first predicted extracellular domain of CFTR inhibited uptake of S. typhi. Heterozygous deltaF508 Cftr mice translocated 86% fewer S. typhi into the gastrointestinal submucosa than wild-type Cftr mice; no translocation occurred in deltaF508 Cftr homozygous mice. The Cftr genotype had no effect on the translocation of S. typhimurium. Immunoelectron microscopy revealed that more CFTR bound to S. typhi in the submucosa of Cftr wild-type mice than in deltaF508 heterozygous mice. We conclude that diminished levels of CFTR in heterozygotes may decrease susceptibility to typhoid fever.

Basal chloride currents in murine airway epithelial cells: modulation by CFTR

We have isolated ciliated respiratory cells from the nasal epithelium of wild-type and cystic fibrosis (CF) null mice and used the patch-clamp technique to investigate their basal conductances. Current-clamp experiments on unstimulated cells indicated the presence of K+ and Cl- conductances and, under certain conditions, a small Na+ conductance. Voltage-clamp experiments revealed three distinct Cl- conductances. Itv-indep was time and voltage independent with a linear current-voltage (I-V) plot; Iv-act exhibited activation at potentials greater than +/- 50 mV, giving an S-shaped I-V plot; and Ihyp-act was activated by hyperpolarizing potentials and had an inwardly rectified I-V plot. The current density sequence was Ihyp-act = Iv-act >> Itv-indep. These conductances had Cl(-)-to-N-methyl-D-glucamine cation permeability ratios of between 2.8 and 10.3 and were unaffected by tamoxifen, flufenamate, glibenclamide, DIDS, and 5-nitro-2-(3-phenylpropylamino) benzoic acid but were inhibited by Zn2+ and Gd3+. Itv-indep and Iv-act were present in wild-type and CF cells at equal density and frequency. However, Ihyp-act was detected in only 3% of CF cells compared with 26% of wild-type cells, suggesting that this conductance may be modulated by cystic fibrosis transmembrane conductance regulator (CFTR).

Memory-based language processing: psycholinguistic research in the 1990s

There are two main domains of research in psycholinguistics: sentence processing, concerned with how the syntactic structures of sentences are computed, and text processing, concerned with how the meanings of larger units of text are understood. In recent sentence processing research, a new and controversial theme is that syntactic computations may rely heavily on statistical information about the relative frequencies with which different syntactic structures occur in the language. In text processing, recent research has focused on what information the words and ideas of a text evoke from long-term memory quickly, passively, and at low processing cost. Research in both domains has begun to use the information that can be obtained from large corpora of naturally occurring texts.

A functional CFTR protein is required for mouse intestinal cAMP-, cGMP- and Ca(2+)-dependent HCO3- secretion

1. Most segments of the gastrointestinal tract secrete HCO3-, but the molecular nature of the secretory mechanisms has not been identified. We had previously speculated that the regulator for intestinal electrogenic HCO3- secretion is the cystic fibrosis transmembrane regulator (CFTR) channel. To prove this hypothesis, we have now measured HCO3- secretion by pH-stat titration, and recorded the electrical parameters of in vitro duodenum, jejunum and ileum of mice deficient in the gene for the CFTR protein ('CF-mice') and their normal littermates. 2. Basal HCO3- secretory rates were reduced in all small intestinal segments of CF mice. Forskolin, PGE2, 8-bromo-cAMP and VIP (cAMP-dependent agonists), heat-stable enterotoxin of Escherichia coli (STa), guanylin and 8-bromo-cGMP (cGMP-dependent agonists) and carbachol (Ca2+ dependent) stimulated both the short-circuit current (Isc) and the HCO3- secretory rate (JHCO3-) in all intestinal segments in normal mice, whereas none of these agonists had any effect on JHCO3- in the intestine of CF mice. 3. To investigate whether Cl(-)-HCO3- exchangers, which have been implicated in mediating the response to some of these agonists in the intestine, were similarly active in the small intestine of normal and CF mice, we studied Cl- gradient-driven 36Cl- uptake into brush-border membrane (BBM) vesicles isolated from normal and CF mouse small intestine. Both the time course and the peak value for 4,4'-diisothiocyanostilbene-2',2-disulphonic acid (DIDS)-inhibited 36Cl- uptake was similar in normal and CF mice BBM vesicles. 4. In summary, the results demonstrate that the presence of the CFTR channel is necessary for agonist-induced stimulation of electrogenic HCO3- secretion in all segments of the small intestine, and all three intracellular signal transduction pathways stimulate HCO3- secretion exclusively via activation of the CFTR channel.

A second dose of a CFTR cDNA-liposome complex is as effective as the first dose in restoring cAMP-dependent chloride secretion to null CF mice trachea

Phase I clinical trials have provided encouraging data suggesting that gene transfer could provide a treatment for cystic fibrosis (CF). However, for all the current viral and nonviral vectors used to deliver the cystic fibrosis transmembrane conductance regulator (CFTR) gene, the duration of CFTR expression is limited, necessitating a repeat dosing regimen to provide a long-term treatment. This study was performed to determine whether a second delivery of a CFTR cDNA-liposome complex could result in a similar level of functional CFTR expression observed after a single delivery and to assess whether the deliveries produced adverse inflammatory responses. CFTR functional expression was assessed by short circuit current measurements of tracheas taken from CF null mice (Cftrtm1Cam) treated with a CFTR cDNA-liposome complex in the upper airways. Mice receiving two deliveries of this complex, the second after the response to the first had declined, showed cAMP-stimulated chloride currents which were not significantly different from normal tracheas or tissues assayed after a single dose of the complex. This double treatment was well tolerated with no discernible inflammation of lung tissue.

Phenotypic and molecular characterization of three clinical isolates of Mycobacterium interjectum

Introduction of molecular biology-based technology into an Australian mycobacterial reference laboratory has resulted in the identification of three isolates of Mycobacterium interjectum in the past 12 months. Conventional phenotypic methods failed to identify the species of these isolates, and high-performance liquid chromatography found that only one of the three isolates had a mycolic acid pattern similar to that of the type strain. In contrast, all three isolates were rapidly identified as M. interjectum by 16S rRNA gene sequence analysis. Two isolates were recovered from the lymph nodes of children with cervical lymphadenitis, confirming the pathogenicity of this organism. However, the third isolate was obtained from the sputum of an elderly male with chronic lung disease without evidence of clinical or radiological progression, suggesting that isolation of M. interjectum should not imply disease. With the increasing use of molecular biology-based technology in mycobacterial laboratories, M. interjectum may be recognized more frequently as a pathogen or commensal organism.

The intrinsic Cl- conductance of mouse kidney cortex brush-border membrane vesicles is not related to CFTR

Brush-border membrane vesicles (BBMV) were prepared from whole Balb/c mice kidneys by a Mg2+ precipitation technique. The presence of an intrinsic Cl- conductance co-expressed with Na+/glucose cotransport was inferred by the anion dependence of [14C]glucose uptake and overshoot with inward Na(+)-anion gradients. In Na(+)-equilibrated conditions, an inside-negative membrane potential difference (p.d.) produced by an inward Cl- gradient alone was capable of driving intravesicular [14C]glucose accumulation. The apparent anion conductance had a selectivity of Br- = I- = Cl- > F- > > gluconate, was inhibited by 0.5 mM 5-nitro-2-(3-phenylpropylamino)-benzoic acid (NPPB) but was unaffected by 0.5 mM 4,4'-diisothiocyanatostilbene 2,2'-disulphonate (DIDS). BBMV were isolated from mice in which the CFTR gene had been disrupted by a termination mutation (-/-) and compared with normal litter mates (+/+) and heterozygotes (-/+)[18]. [14C]Glucose uptake in NaCl media was significantly greater than glucose uptake in Na gluconate media for all three genotypes measured at 20 s: for homozygous -/- animals [14C]glucose uptake was increased by 2.80 +/- 0.53 fold in Cl- media compared to gluconate media, n = 6; for wild-type +/+, by 2.16 +/- 0.53 fold, n = 8; and for heterozygous +/- animals, by 2.17 +/- 0.45 fold, n = 8. The observation of a Cl-(-)dependent component in BBMV isolated from homozygous -/- mutant animals shows that the chloride conductance in these vesicles cannot be due to CFTR expression.

Co-ordinate regulation of the cystic fibrosis and multidrug resistance genes in cystic fibrosis knockout mice

The cystic fibrosis (Cftr and multidrug resistance (Mdr1) genes encode structurally similar proteins which are members of the ABC transporter superfamily. These genes exhibit complementary patterns of expression in vivo, suggesting that the regulation of their expression may be co-ordinated. We have tested this hypothesis in vivo by examining Cftr and Mdr1 expression in cystic fibrosis knockout transgenic mice (Cftr(tm1CAM)). Cftr mRNA expression in Cftr(tm1CAM)/Cftr(tm1CAM) mice was 4-fold reduced in the intestine, as compared with littermate wild-type mice. All other Cftr(tm1CAM)/Cftr(tm1CAM) mouse tissues examined showed similar reductions in Cftr expression. In contrast, we observed a 4-fold increase in Mdr1 mRNA expression in the intestines of neonatal and 3- to 4-week-old Cftr(tm1CAM)/Cftr(tm1CAM) mice, as compared with age-matched +/+ mice, and an intermediate level of Mdr1 mRNA in heterozygous Cftr(tm1CAM) mice. In 10-week-old, Cftr(tm1CAM)/Cftr(tm1CAM) mice and in contrast to the younger mice, Mdr1 mRNA expression was reduced, by 3-fold. The expression of two control genes, Pgk-1 and Mdr2, was similar in all genotypes, suggesting that the changes in Mdr1 mRNA levels observed in the Cftr(tm1CAM)/Cftr(tm1CAM) mice are specific to the loss of Cftr expression and/or function. These data provide further evidence supporting the hypothesis that the regulation Cftr and Mdr1 expression is co-ordinated in vivo, and that this co-ordinate regulation is influenced by temporal factors.

A counter model for implicit priming in perceptual word identification

A model for the identification of briefly presented words is presented. The model accounts for data from naming and forced-choice experiments in which factors such as similarity of alternatives and stimulus presentation time are varied. The model assumes that counts are accumulated in counters that correspond to words and that a word is chosen as a response when the number of counts in its counter exceeds the maximum of the numbers of counts in other counters by a criterial value. Prior exposure to a word causes its counter to attract more counts than it otherwise would, and this yields priming effects. Ten experiments are presented, and the model provides correct predictions for the data. Implications of the model for research in implicit memory are considered.

Chloride secretion in the trachea of null cystic fibrosis mice: the effects of transfection with pTrial10-CFTR2

1. An improved novel plasmid backbone, pTrial10, has been developed. We have used this vector to deliver the cDNA for the cystic fibrosis transmembrane conductance regulator (CFTR) to cells, both in vitro and in vivo, complexed with cationic liposomes. 2. Human 293 kidney epithelial cells (HEK 293) showed expression of an immunoprecipitable 165 kDa protein corresponding to CFTR when transfected in vitro with pTrial10-CFTR2, but not when the vector pTrial10 was used. 3. HEK 293 cells transfected with pTrial10-CFTR2, but not pTrial10, demonstrated a cAMP-dependent anion conductance, measured by fluorescence microscopy using a halide-sensitive probe, SPQ. 4. The CFTR-dependent, cAMP-sensitive chloride secretory response in murine tracheal epithelium could be measured if the calcium-dependent chloride secretory process was first maximally stimulated with a mixture of the Ca(2+)-ATPase inhibitor, TBHQ, and the calcium ionophore, A23187. With these conditions wild-type and CF-null (transgenic animals in which the cystic fibrosis (CF) gene has been disrupted so that no CFTR is produced) murine tracheas could be distinguished. The difference between the current elicited by forskolin in wild-type and CF tracheas was highly significantly different (P < 0.001), giving a CFTR-dependent current of 11.2 microA cm-2. 5. Transfection of the airways with pTrial10-CFTR2, but not pTrial10, significantly (P < 0.01) increased the CFTR-dependent chloride secretory current in CF tracheas. The degree of correction was greater when intra-tracheal installation rather than nasal insufflation was used to deliver the plasmids.

A placebo-controlled study of liposome-mediated gene transfer to the nasal epithelium of patients with cystic fibrosis

Cystic fibrosis (CF) is a common, serious, inherited disease. The major cause of mortality in CF is lung disease, due to the failure of airway epithelial cells to express a functional product of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. A potential treatment for CF lung disease is the expression of CFTR in the airways following gene transfer. We have undertaken a double-blinded, placebo-controlled, clinical study of the transfer of the CFTR cDNA to the nasal epithelium of 12 CF patients. Cationic liposomes complexed with plasmid containing the human CFTR cDNA were administered to eight patients, whilst four patients received placebo. Biopsies of the nasal epithelium taken 7 days after dosing were normal. No significant changes in clinical parameters were observed. Functional expression of CFTR assessed by in vivo nasal potential difference measurements showed transient correction of the CF chloride transport abnormality in two patients (15 days after dosing in one patient). Fluorescence microscopy demonstrated CFTR function ex vivo. In cells from nasal brushings. In total, evidence of functional CFTR gene transfer was obtained in six out of the eight treated patients. These results provide proof of concept for liposome-mediated CF gene transfer.

Cystic fibrosis transmembrane conductance regulator mediates the cyclic adenosine monophosphate-induced fluid secretion but not the inhibition of resorption in mouse gallbladder epithelium

We have studied the physiological role of the cystic fibrosis (CF) gene product (cystic fibrosis transmembrane conductance regulator [CFTR]) in gallbladder epithelium using a knockout mouse model for CF. We found that normal mouse gallbladder epithelium expresses functional CFTR as shown by reverse-transcription polymerase chain reaction (RT-PCR) analysis and Ussing chamber experiments. Gallbladders from Cftr -/- mice were structurally intact as shown by microscopic and physiological parameters but lacked the cyclic adenosine monophosphate (cAMP)-induced chloride current observed in normal gallbladders. In fluid transport measurements, normal and Cftr -/- gallbladders were equally active in basal resorption. The addition of forskolin, which activates CFTR anion channel activity through the cAMP system, resulted in net fluid secretion in normal gallbladders. In contrast, Cftr -/- gallbladders were unable to secrete fluid while a complete inhibition of resorption by forskolin was observed. We conclude that, in normal mouse gallbladder epithelium, cAMP-induced fluid secretion involves simultaneous inhibition of apical sodium chloride resorption and activation of CFTR. Our data support the hypothesis that gallbladder disease in CF is at least in part caused by a deficient secretory response to the endogenous cAMP-linked hormones VIP and secretin.

Bias in auditory priming

Priming for previously studied words in an implicit auditory memory task has been interpreted as evidence for a presemantic perceptual representation system that encodes acoustic representations of words (B. A. Church & D. L. Schacter, 1994). In this article, 3 experiments provided evidence that such priming may result instead from a bias to respond with studied words. In forced-choice identification with similar alternative choices, there was no overall improvement in performance due to prior study. Benefits for studied test words were offset by costs for similar but nonstudied test words. Prior study had no effect when forced-choice alternatives were dissimilar. The data are discussed in relation to current models of auditory information processing and a new model (R. Ratcliff & G. McKoon, in press) for priming in visual word identification.

Bias in auditory priming

Priming for previously studied words in an implicit auditory memory task has been interpreted as evidence for a presemantic perceptual representation system that encodes acoustic representations of words (B. A. Church & D. L. Schacter, 1994). In this article, 3 experiments provided evidence that such priming may result instead from a bias to respond with studied words. In forced-choice identification with similar alternative choices, there was no overall improvement in performance due to prior study. Benefits for studied test words were offset by costs for similar but nonstudied test words. Prior study had no effect when forced-choice alternatives were dissimilar. The data are discussed in relation to current models of auditory information processing and a new model (R. Ratcliff & G. McKoon, in press) for priming in visual word identification.

Sentential context effects on lexical decisions with a cross-modal instead of an all-visual procedure

J. L. Nicol and D. Swinney (1989) reported facilitation in a cross-modal lexical-decision task as evidence that implicit objects of verbs (WH-traces) are reinstated during comprehension. G. McKoon and R. Ratcliff (1994) found the same priming effects in the absence of implicit objects, suggesting that the effects are attributable to some factor other than a syntactic process that would fill in implicit objects. J. L. Nicol, J. D. Fodor, and D. Swinney (1994) questioned the relevance of McKoon and Ratcliff's findings because they were obtained with all-visual rather than cross-modal presentation. In 2 experiments, the authors replicated McKoon and Ratcliff's results using cross-modal lexical decision.

Separating implicit from explicit retrieval processes in perceptual identification

Light and Kennison (this issue) proposed that bias effects in the forced-choice perceptual identification of words result from a strategy engaged in by subjects to retrieve explicit information about the words. This article enumerates several problems with this proposal and presents new experimental data against it. It is concluded that subjects do not ordinarily employ an explicit retrieval strategy. The data are discussed in the context of the general problem of separating implicit from explicit influences on performance.

Bias effects in implicit memory tasks

A major focus of recent research in memory has been performance on implicit tasks. The phenomenon of most interest has been repetition priming, the effect that prior exposure to a stimulus has on later perception of the stimulus or on a later decision about the stimulus. Picture naming, word identification, and word production in stem- and fragment-completion tasks all show repetition priming effects. The separation of implicit from explicit memory systems provides one account of this data, but a different theoretical view is proposed here: Repetition-priming effects come about because the processes that perform a task are biased products, temporary modifications of the processes, which influence later processing. The aim of this article is to demonstrate the potential of this view for developing new theories and for prompting new empirical questions.

CFTR expression and mucin secretion in cultured mouse gallbladder epithelial cells

Dysfunction of the cystic fibrosis transmembrane conductance regulator (CFTR) in humans is frequently associated with progressive liver disease, which appears to result from obstruction of biliary ducts with mucous material. CFTR in the liver is expressed in the biliary epithelium. With the use of a mouse model for cystic fibrosis (CF) we have studied the relationship between CFTR expression and glycoprotein secretion in primary culture of mouse gallbladder epithelial cells (MGBC) MGBC in culture maintain a well-differentiated phenotype as shown by microscopy. The cells produce CFTR mRNA to levels comparable to the intact tissue. With patch-clamp analysis we could frequently observe a linear protein kinase A-regulated Cl- channel that shows all the major characteristics of human CFTR, although its conductance is lower (5 pS compared with 8 pS). MGBC in culture produce and secrete high molecular weight glycoproteins (HMG) in a time-dependent and temperature-sensitive manner. Secretion of HMG was not stimulated significantly by either adenosine 3',5'-cyclic monophosphate (cAMP), Ca2+, or protein kinase C agonists in this system. High concentrations (3 mM) of extracellular ATP stimulated secretion threefold, but low concentrations (0.3 mM) had no effect. Approximately one-third of the HMG produced and secreted consisted of mucin. Cultured MGBC from CFTR-deficient mice produced and secreted mucin to a similar extent as normal cells. We conclude that cultured mouse gallbladder cells are a convenient model to study both CFTR function and mucin secretion. In this system, we found no evidence for a direct link between mucin secretion and CFTR activity, as has been suggested for other cell types.

Sentential context effects on lexical decisions with a cross-modal instead of an all-visual procedure

J. L. Nicol and D. Swinney (1989) reported facilitation in a cross-modal lexical-decision task as evidence that implicit objects of verbs (WH-traces) are reinstated during comprehension. G. McKoon and R. Ratcliff (1994) found the same priming effects in the absence of implicit objects, suggesting that the effects are attributable to some factor other than a syntactic process that would fill in implicit objects. J. L. Nicol, J. D. Fodor, and D. Swinney (1994) questioned the relevance of McKoon and Ratcliff's findings because they were obtained with all-visual rather than cross-modal presentation. In 2 experiments, the authors replicated McKoon and Ratcliff's results using cross-modal lexical decision.

Sequential effects in lexical decision: tests of compound-cue retrieval theory

According to compound-cue retrieval theories, responses in lexical decision are determined by a passive process that matches a compound of the items in short-term memory against all of the information in long-term memory. Because responses depend on other items in short-term memory in addition to the target item about which a lexical decision is required, compound-cue theories must predict sequential effects and priming effects. For example, a nonword preceding a target should slow responses to the target, and a prime word related to a target word can affect responses to the target even when another item intervenes between them. In this article, the results of 4 experiments are presented and sequential effects are shown to be in accord with compound-cue theory.

Testing models of decision making using confidence ratings in classification

Classification implies decision making (or response selection) of some kind. Studying the decision process using a traditional signal detection theory analysis is difficult for two reasons: (a) The model makes a strong assumption about the encoding process (normal noise), and (b) the two most popular decision models, optimal and distance-from-criterion models, can mimic each other's predictions about performance level. In this article, the authors show that by analyzing certain distributional properties of confidence ratings, a researcher can determine whether the decision process is optimal, without knowing the form of the encoding distributions. Empirical results are reported for three types of experiments: recognition memory, perceptual discrimination, and perceptual categorization. In each case, the data strongly favored the distance-from-criterion model over the optimal model.

Reliability of prosodic cues for resolving syntactic ambiguity

Although previous research has shown that listeners can use prosody to resolve syntactic ambiguities in spoken sentences, it is not clear whether naive, untrained speakers in experimental situations ordinarily produce the prosodic cues necessary for disambiguating such sentences. In a series of experiments, the authors found that neither professional nor untrained speakers consistently produced such prosodic cues when simply reading ambiguous sentences in a disambiguating discourse context. Speakers who were aware of the ambiguities and were told to intentionally pronounce the sentences with one meaning of the other, however, did produce sufficient prosodic cues for listeners to identify the intended meanings.

Testing models of decision making using confidence ratings in classification

Classification implies decision making (or response selection) of some kind. Studying the decision process using a traditional signal detection theory analysis is difficult for two reasons: (a) The model makes a strong assumption about the encoding process (normal noise), and (b) the two most popular decision models, optimal and distance-from-criterion models, can mimic each other's predictions about performance level. In this article, the authors show that by analyzing certain distributional properties of confidence ratings, a researcher can determine whether the decision process is optimal, without knowing the form of the encoding distributions. Empirical results are reported for three types of experiments: recognition memory, perceptual discrimination, and perceptual categorization. In each case, the data strongly favored the distance-from-criterion model over the optimal model.

Reliability of prosodic cues for resolving syntactic ambiguity

Although previous research has shown that listeners can use prosody to resolve syntactic ambiguities in spoken sentences, it is not clear whether naive, untrained speakers in experimental situations ordinarily produce the prosodic cues necessary for disambiguating such sentences. In a series of experiments, the authors found that neither professional nor untrained speakers consistently produced such prosodic cues when simply reading ambiguous sentences in a disambiguating discourse context. Speakers who were aware of the ambiguities and were told to intentionally pronounce the sentences with one meaning of the other, however, did produce sufficient prosodic cues for listeners to identify the intended meanings.

Process dissociation, single-process theories, and recognition memory

According to the assumptions of L. L. Jacoby's (1991) process dissociation method, performance in recognition memory is determined by the combination of an unconscious familiarity process and a conscious intentional recollection process. The process dissociation method is used to produce estimates of the contributions of the 2 components to recognition performance. This article investigates whether the method provides the correct estimates of components if performance actually depends on only a single process or on 2 processes different from those assumed by the method. The SAM model (G. Gillund & R. M. Shiffrin, 1984) was used to produce simulated data based on a single process. Variants of SAM with 2 processes and R. C. Atkinson and J. F. Juola's (1973) 2-process model were used to produce data based on 2 processes.

Process dissociation, single-process theories, and recognition memory

According to the assumptions of L. L. Jacoby's (1991) process dissociation method, performance in recognition memory is determined by the combination of an unconscious familiarity process and a conscious intentional recollection process. The process dissociation method is used to produce estimates of the contributions of the 2 components to recognition performance. This article investigates whether the method provides the correct estimates of components if performance actually depends on only a single process or on 2 processes different from those assumed by the method. The SAM model (G. Gillund & R. M. Shiffrin, 1984) was used to produce simulated data based on a single process. Variants of SAM with 2 processes and R. C. Atkinson and J. F. Juola's (1973) 2-process model were used to produce data based on 2 processes.

Sequential effects in lexical decision: tests of compound-cue retrieval theory

According to compound-cue retrieval theories, responses in lexical decision are determined by a passive process that matches a compound of the items in short-term memory against all of the information in long-term memory. Because responses depend on other items in short-term memory in addition to the target item about which a lexical decision is required, compound-cue theories must predict sequential effects and priming effects. For example, a nonword preceding a target should slow responses to the target, and a prime word related to a target word can affect responses to the target even when another item intervenes between them. In this article, the results of 4 experiments are presented and sequential effects are shown to be in accord with compound-cue theory.

The application of Fourier deconvolution to reaction time data: a cautionary note

The Fourier transform method in conjunction with frequency domain smoothing techniques has been suggested as a powerful tool for examining components in a serial, additive reaction time model (P. L. Smith, 1990). Robustness and sensitivity to violations of the assumptions of serial model of this method are evaluated. When an incorrect distribution was used in recovering an unobserved component, results gave no information to show that an incorrect distribution was used, and the results were just as interpretable as those obtained using the correct distribution. These results demonstrate that the assumptions underlying the method cannot be assessed by the result of deconvolution, and the method cannot show that the purported component is actually from the serial combination.

Bias in the priming of object decisions

Seven experiments examined priming effects for 3-dimensional line drawings in the object decision task. One of the most important previous findings about object decisions has been that the decision about a possible object is primed by previous presentation of the object, but the decision about an impossible object is not. Through the use of manipulations that can eliminate processes that retrieve episodic information (response time deadlines, memory load, forced choice, and similarity), equal size effects on impossible and possible objects were obtained. This is interpreted to mean that priming effects reflect a bias to respond "possible," which can be opposed for impossible objects by episodic information so as to yield the approximately null priming effect for impossible objects found in past experiments.