Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains

Quantitative structures are obtained at 30 degrees C for the fully hydrated fluid phases of palmitoyloleoylphosphatidylcholine (POPC), with a double bond on the sn-2 hydrocarbon chain, and for dierucoylphosphatidylcholine (di22:1PC), with a double bond on each hydrocarbon chain. The form factors F(qz) for both lipids are obtained using a combination of three methods. (1) Volumetric measurements provide F(0). (2) X-ray scattering from extruded unilamellar vesicles provides /F(qz)/ for low q(z). (3) Diffuse X-ray scattering from oriented stacks of bilayers provides /F(qz)/ for high q(z). Also, data using method (2) are added to our recent data for dioleoylphosphatidylcholine (DOPC) using methods (1) and (3); the new DOPC data agree very well with the recent data and with (4) our older data obtained using a liquid crystallographic X-ray method. We used hybrid electron density models to obtain structural results from these form factors. The result for area per lipid (A) for DOPC 72.4 +/- 0.5 A(2) agrees well with our earlier publications, and we find A = 69.3 +/- 0.5 A2 for di22:1PC and A = 68.3 +/- 1.5 A2 for POPC. We obtain the values for five different average thicknesses: hydrophobic, steric, head-head, phosphate-phosphate and Luzzati. Comparison of the results for these three lipids and for our recent dimyristoylphosphatidylcholine (DMPC) determination provides quantitative measures of the effect of unsaturation on bilayer structure. Our results suggest that lipids with one monounsaturated chain have quantitative bilayer structures closer to lipids with two monounsaturated chains than to lipids with two completely saturated chains.     

Codon bias in actin multigene families and effects on the reconstruction of phylogenetic relationships

Codon usage patterns and phylogenetic relationships in the actin multigene family have been analyzed for three dipteran species—Drosophila melanogaster, Bactrocera dorsalis, and Ceratitis capitata. In certain phylogenetic tree reconstructions, using synonymous distances, some gene relationships are altered due to a homogenization phenomenon. We present evidence to show that this homogenization phenomenon is due to codon usage bias. A survey of the pattern of synonymous codon preferences for I I actin genes from these three species reveals that five out of the six Drosophila actin genes show high degrees of codon bias as indicated by scaled ² values. In contrast to this, four out of the five actin genes from the other species have low codon bias values. A Monte Carlo contingency test indicates that for those Drosophila actin genes which exhibit codon bias, the patterns of codon usage are different compared to actin genes from the other species. In addition, the genes exhibiting codon bias also appear to have reduced rates of synonymous substitution. The homogenization phenomenon seen in terms of synonymous substitutions is not observed for nonsynonymous changes. Because of this homogenization phenomenon, trees constructed based on synonymous substitutions will be affected. These effects can be overt in the case of multigene families, but similar distortions may underlie reconstructions based on single-copy genes which exhibit codon usage bias.Correspondence to: M. He     

Perils of parsimony: properties of reduced-rank estimates of genetic covariance matrices

Eigenvalues and eigenvectors of covariance matrices are important statistics for multivariate problems in many applications, including quantitative genetics. Estimates of these quantities are subject to different types of bias. This article reviews and extends the existing theory on these biases, considering a balanced one-way classification and restricted maximum-likelihood estimation. Biases are due to the spread of sample roots and arise from ignoring selected principal components when imposing constraints on the parameter space, to ensure positive semidefinite estimates or to estimate covariance matrices of chosen, reduced rank. In addition, it is shown that reduced-rank estimators that consider only the leading eigenvalues and -vectors of the "between-group" covariance matrix may be biased due to selecting the wrong subset of principal components. In a genetic context, with groups representing families, this bias is inverse proportional to the degree of genetic relationship among family members, but is independent of sample size. Theoretical results are supplemented by a simulation study, demonstrating close agreement between predicted and observed bias for large samples. It is emphasized that the rank of the genetic covariance matrix should be chosen sufficiently large to accommodate all important genetic principal components, even though, paradoxically, this may require including a number of components with negligible eigenvalues. A strategy for rank selection in practical analyses is outlined.     

Population-specific gender-biased hybridization between Dryopteris intermedia and D. carthusiana: evidence from chloroplast DNA

As has been shown for many kinds of organisms, barriers to interspecific hybridization may differ in strength between reciprocal crosses, resulting in a bias in the probability that one or the other species may be the maternal or paternal parent of hybrids. The fern Dryopteris Xtriploidea, the "backcross" hybrid between the diploid D. intermedia and the tetraploid D. carthusiana, occurs in large numbers in nature, providing an opportunity to investigate whether such a bias exists. Differences in the chloroplast genome distinguishing the two parental species were discovered in the sequence of the trnL region following amplification by polymerase chain reaction (PCR), including a Mse I restriction site. This allowed rapid identification of the donor of the chloroplast genome, and therefore the maternal parent of each hybrid, assuming chloroplast DNA to be maternally inherited in Dryopteris. Analysis was carried out on 127 hybrids, shown to be of independent origin using allozymes, occurring at three localities in Virginia and West Virginia. When samples from all localities were pooled, 91 possessed the D. carthusiana trnL genotype and 36 possessed the D. intermedia genotype, a ratio that is significantly different (P < 0.001) from the null hypothesis of no gender bias. The strength of the bias differed significantly among the three sites, however, with bias at the West Virginia site much stronger (5.6:1 carthusiana:intermedia; P < 0.001) than at either Virginia site (1.55:1 and 1.43:1 carthusiana:intermedia, respectively; P > 0.05 in both cases). The cause of the strong bias in the West Virginia sample is unknown, as is the cause of the population differences. Causes of bias could include differences between the parental species related to their ploidy difference, including sizes of gametes and/or gametangia, sperm motility, breeding system (D. intermedia is outcrossing while D. carthusiana is selfing), or the nature and strength of interspecific isolating mechanisms.     

Systematic Review of the Empirical Evidence of Study Publication Bias and Outcome Reporting Bias — An Updated Review

Background

The increased use of meta-analysis in systematic reviews of healthcare interventions has highlighted several types of bias that can arise during the completion of a randomised controlled trial. Study publication bias and outcome reporting bias have been recognised as a potential threat to the validity of meta-analysis and can make the readily available evidence unreliable for decision making.

Methodology/Principal Findings

In this update, we review and summarise the evidence from cohort studies that have assessed study publication bias or outcome reporting bias in randomised controlled trials. Twenty studies were eligible of which four were newly identified in this update. Only two followed the cohort all the way through from protocol approval to information regarding publication of outcomes. Fifteen of the studies investigated study publication bias and five investigated outcome reporting bias. Three studies have found that statistically significant outcomes had a higher odds of being fully reported compared to non-significant outcomes (range of odds ratios: 2.2 to 4.7). In comparing trial publications to protocols, we found that 40–62% of studies had at least one primary outcome that was changed, introduced, or omitted. We decided not to undertake meta-analysis due to the differences between studies.

Conclusions

This update does not change the conclusions of the review in which 16 studies were included. Direct empirical evidence for the existence of study publication bias and outcome reporting bias is shown. There is strong evidence of an association between significant results and publication; studies that report positive or significant results are more likely to be published and outcomes that are statistically significant have higher odds of being fully reported. Publications have been found to be inconsistent with their protocols. Researchers need to be aware of the problems of both types of bias and efforts should be concentrated on improving the reporting of trials.     

Testing the relationship between morphological and molecular rates of change along phylogenies

Abstract.— Molecular evolution has been considered to be essentially a stochastic process, little influenced by the pace of phenotypic change. This assumption was challenged by a study that demonstrated an association between rates of morphological and molecular change estimated for "total-evidence" phylogenies, a finding that led some researchers to challenge molecular date estimates of major evolutionary radiations. Here we show that Omland's (1997) result is probably due to methodological bias, particularly phylogenetic nonindependence, rather than being indicative of an underlying evolutionary phenomenon. We apply three new methods specifically designed to overcome phylogenetic bias to 13 published phylogenetic datasets for vertebrate taxa, each of which includes both morphological characters and DNA sequence data. We find no evidence of an association between rates of molecular and morphological rates of change.     

Improving Retention of Very Old Participants in Longitudinal Research: Experiences from the Newcastle 85+ Study

Background

People aged 85 and over are often excluded from research on the grounds of being difficult to recruit and problematic to retain. The Newcastle 85+ study successfully recruited a cohort of 854 85-year-olds to detailed health assessment at baseline and followed them up over 3 phases spanning 5 years. This paper describes the effectiveness of its retention strategies.

Methods

Primary retention strategies involved meticulous management of contact information and active maintenance of contact with participants between research visits and between phases of the study. For statistical analysis, data on post-inclusion attrition over the 3 follow-up phases was separated into ‘death’ and ‘withdrawal’ categories, with sub-categories ‘health’ and ‘non-health’ reasons created for ‘withdrawal’. Multinomial logistic regression was used to determine if particular socio-demographic and health characteristics were associated with post-inclusion attrition due to withdrawal at each of the 3 phase-to-phase transition points.

Results

For both sexes, at successive follow-up phases there was a decrease in attrition due to withdrawal and an increase due to death. Withdrawal was most prevalent between baseline and phase 2. Across the 5 years of the study total post-inclusion (post-baseline) attrition due to death accounted for a 40% (344/854) loss to cohort and total post-inclusion attrition due to withdraw a 19% (166/854) loss to cohort, with health reasons for withdrawal becoming more dominant over time. Adjusting for sex, parsimonious modelling showed only occupational class (National Statistics Socio-economic Classification) to be associated with withdrawal and only between baseline and phase 2 (routine/manual compared to managerial (OR 3.41; 95% CI [1.23 to 9.44]).

Conclusion

Following successful recruitment, we retained a high proportion of participants from a very old age group over 5 years of longitudinal research. No strong predictors of post-inclusion attrition due to withdrawal were found, suggesting the general effectiveness of our retention strategies.     

Treadmill experience alters treadmill effects on perceived visual motion

Information on ongoing body movements can affect the perception of ambiguous visual motion. Previous studies on "treadmill capture" have shown that treadmill walking biases the perception of ambiguous apparent motion in backward direction in accordance with the optic flow during normal walking, and that long-term treadmill experience changes the effect of treadmill capture. To understand the underlying mechanisms for these phenomena, we conducted Experiment 1 with non-treadmill runners and Experiment 2 with treadmill runners. The participants judged the motion direction of the apparent motion stimuli of horizontal gratings in front of their feet under three conditions: walking on a treadmill, standing on a treadmill, and standing on the floor. The non-treadmill runners showed the presence of downward bias only under the walking condition, indicating that ongoing treadmill walking but not the awareness of being on a treadmill biased the visual directional discrimination. In contrast, the treadmill runners showed no downward bias under any of the conditions, indicating that neither ongoing activity nor the awareness of spatial context produced perception bias. This suggests that the long-term repetitive experience of treadmill walking without optic flow induced the formation of a treadmill-specific locomotor-visual linkage to perceive the complex relationship between self and the environment.     

Sleep-induced periodic breathing and apnea: a theoretical study

To elucidate the mechanisms that lead to sleep-disordered breathing, we have developed a mathematical model that allows for dynamic interactions among the chemical control of respiration, changes in sleep-waking state, and changes in upper airway patency. The increase in steady-state arterial PCO2 accompanying sleep is shown to be inversely related to the ventilatory response to CO2. Chemical control of respiration becomes less stable during the light stage of sleep, despite a reduction in chemoresponsiveness, due to a concomitant increase in "plant gain" (i.e., responsiveness of blood gases to ventilatory changes). The withdrawal of the "wakefulness drive" during sleep onset represents a strong perturbation to respiratory control: higher magnitudes and rates of withdrawal of this drive favor instability. These results may account for the higher incidence of periodic breathing observed during light sleep and sleep onset. Periodic ventilation can also result from repetitive alternations between sleep onset and arousal. The potential for instability is further compounded if the possibility of upper airway occlusion is also included. In systems with high controller gains, instability is mediated primarily through chemoreflex overcompensation. However, in systems with depressed chemoresponsiveness, rapid sleep onset and large blood gas fluctuations trigger repetitive episodes of arousal and hyperpnea alternating with apneas that may or may not be obstructive. Between these extremes, more complex patterns can arise from the interaction between chemoreflex-mediated oscillations of shorter-cycle-duration (approximately 36 s) and longer-wavelength (approximately 60-80 s) state-driven oscillations.     

Intra- and interspecific DNA variation and codon bias of the alcohol dehydrogenase (Adh) locus in Arabis and Arabidopsis species

Sequence variation at the alcohol dehydrogenase (Adh) locus was analyzed for six species each of the genera Arabis and Arabidopsis. Phylogenetic analysis showed that investigated species were grouped into three clusters, and the generic classification did not correspond to the clusterings. The results indicated that the genera could not be distinguished on the basis of the Adh variation. A significant difference in the ratio of silent to replacement sites was detected by MK test in two comparisons, with Arabidopsis thaliana polymorphism due to excess silent divergence. Silent changes were predominant in the evolution of the Adh locus in Arabis and Arabidopsis. To infer evolutionary significance of silent substitutions, codon bias was studied. The degree of codon bias of the Adh region was relatively constant over Arabis and Arabidopsis species. "Preferred" codons of A. thaliana were determined. No evidence of natural selection on codon change was detected in the Adh regions of A. thaliana and Arabis gemmifera.     

Statistical analysis of fluorescence correlation spectroscopy: the standard deviation and bias

We present a detailed statistical analysis of fluorescence correlation spectroscopy for a wide range of timescales. The derivation is completely analytical and can provide an excellent tool for planning and analysis of FCS experiments. The dependence of the signal-to-noise ratio on different measurement conditions is extensively studied. We find that in addition to the shot noise and the noise associated with correlated molecular dynamics there is another source of noise that appears at very large lag times. We call this the "particle noise," as its behavior is governed by the number of particles that have entered and left the laser beam sample volume during large dwell times. The standard deviations of all the points on the correlation function are calculated analytically and shown to be in good agreement with experiments. We have also investigated the bias associated with experimental correlation function measurements. A "phase diagram" for FCS experiments is constructed that demonstrates the significance of the bias for any given experiment. We demonstrate that the value of the bias can be calculated and added back as a first-order correction to the experimental correlation function.     

Assessment of Bias Associated with Incomplete Extraction of Microbial DNA from Soil

DNA extraction bias is a frequently cited but poorly understood limitation of molecular characterizations of environmental microbial communities. To assess the bias of a commonly used soil DNA extraction kit, we varied the cell lysis protocol and conducted multiple extractions on subsamples of clay, sand, and organic soils. DNA, as well as bacterial and fungal ribosomal gene copies as measured by quantitative PCR, continued to be isolated in successive extractions. When terminal restriction fragment length polymorphism was used, a significant shift in community composition due to extraction bias was detected for bacteria but not for fungi. Pyrosequencing indicated that the relative abundances of sequences from rarely cultivated groups such as Acidobacteria, Gemmatimonades, and Verrucomicrobia were higher in the first extraction than in the sixth but that the reverse was true for Proteobacteria and Actinobacteria. This suggests that the well-known phylum-level bacterial cultivation bias may be partially exaggerated by DNA extraction bias. We conclude that bias can be adequately reduced in many situations by pooling three successive extractions, and additional measures should be considered when divergent soil types are compared or when comprehensive community analysis is necessary.The vast majority of soil bacteria (1, 7, 27) and fungi (13, 29) cannot be cultured via traditional laboratory techniques and must be identified using molecular methods. Successful characterization of microbial communities is therefore often dependent on DNA that is extracted from the environment. However, extraction of high-quality DNA from soil can be problematic (8, 11, 22, 26). Commercial DNA extraction kits are now commonly used in the assessment of taxonomic and functional diversity, community composition, and population abundance (e.g., references 19, 21, 23, 25, and 31). Studies comparing various kits (18, 32) or comparing commercial kits to other methods (2, 10, 24) have shown that DNA yield and purity vary depending on methodology and soil type. While these comparative studies are valuable, it is still unclear to what extent these protocols yield genomic DNA representative of the microbial community found within soil.Our objective in this study was to optimize and assess the bias of a widely used commercial soil DNA extraction kit. We hypothesized that cell lysis would be enhanced and DNA would be removed from adsorption sites by conducting multiple extractions on a single sample, thereby increasing genomic DNA yield and obtaining a more complete survey of microbial taxa. This hypothesis was tested by (i) varying the extraction protocol and measuring DNA yield for three soils with differing characteristics and (ii) examining extraction bias in the genomic DNA obtained from successive extractions by using an improved method. Analytical replicates rather than biological replicates were used in order to focus strictly on variation and bias introduced through methodology, although multiple soil types were analyzed to determine whether biases detected were consistent.     

Dorsal noradrenergic bundle lesions fail to alter opiate withdrawal or suppression of opiate withdrawal by clonidine

Previous work has shown that clonidine effectively supresses many of the signs of opiate withdrawal. The present study was designed to test the hypothesis that the supression of opiate withdrawal by clonidine is mediated by forebrain noradrenergic projections of the locus coeruleus. Two groups of 24 rats each were subjected to either a 6-hydroxydopamine lesion of the dorsal noradrenergic bundle (Lesion group) or a sham, vehicle injection (Sham group). All rats were made dependent on morphine by subcutaneous implantation of one 75 mg silastic morphine pellet for three days followed by 3 more days with two additional 75 mg pellets. Following removal of the morphine pellet, withdrawal was precipitated in all rats by subcutaneous injection of 4 mg/kg of naloxone. Pretreatment 10 min. before withdrawal with clonidine (0.1 or 0.2 mg/kg) produced a significant attenuation of withdrawal signs as compared to saline injected rats; this effect was equally significant in both sham and lesion groups. Lesions of the locus coeruleus had no effect on withdrawal, nor did they affect the ameliorating action of clonidine. These results substantiate the observation that clonidine can effectively attenuate signs of opiate withdrawal in the rat, but fail to support the hypothesis that these effects are mediated by the forebrain projections of the locus coeruleus.     

Modification of the effects of naloxone in morphine-dependent mice

Mice were rendered dependent on morphine by mixing morphine with their food (2 mg/g) for three days. Increasing doses of naloxone precipitated dose-dependent withdrawal reactions such as weight loss and jumping. These withdrawal reactions were antagonized by morphine pretreatment. Effects of morphine, such as increased locomotor activity, inhibition of intestinal transport, and analgesia were antagonized by naloxone in both non-dependent and dependent subjects. The antagonist actions of naloxone were increased in dependent subjects; lower doses of naloxone were sufficient to antagonize effects of morphine. The present results confirm earlier studies indicating that precipitation of withdrawal can be antagonized by morphine pretreatment suggesting that withdrawal reactions are due to actions of naloxone at the same receptor at which opioid agonists act. The increased antagonist potency of naloxone in dependent subjects extends earlier results obtained with analgesic effects to several other agonist effects of morphine and is consistent with the interpretation that exposure to an opioid agonist induces a change in the conformation of opioid receptors.     

Mortality associated with withdrawal of life-sustaining therapy for patients with severe traumatic brain injury: a Canadian multicentre cohort study

Background:

Severe traumatic brain injury often leads to death from withdrawal of life-sustaining therapy, although prognosis is difficult to determine.

Methods:

To evaluate variation in mortality following the withdrawal of life-sustaining therapy and hospital mortality in patients with critical illness and severe traumatic brain injury, we conducted a two-year multicentre retrospective cohort study in six Canadian level-one trauma centres. The effect of centre on hospital mortality and withdrawal of life-sustaining therapy was evaluated using multivariable logistic regression adjusted for baseline patient-level covariates (sex, age, pupillary reactivity and score on the Glasgow coma scale).

Results:

We randomly selected 720 patients with traumatic brain injury for our study. The overall hospital mortality among these patients was 228/720 (31.7%, 95% confidence interval [CI] 28.4%–35.2%) and ranged from 10.8% to 44.2% across centres (χ² test for overall difference, p < 0.001). Most deaths (70.2% [160/228], 95% CI 63.9%–75.7%) were associated with withdrawal of life-sustaining therapy, ranging from 45.0% (18/40) to 86.8% (46/53) (χ² test for overall difference, p < 0.001) across centres. Adjusted odd ratios (ORs) for the effect of centre on hospital mortality ranged from 0.61 to 1.55 (p < 0.001). The incidence of withdrawal of life-sustaining therapy varied by centre, with ORs ranging from 0.42 to 2.40 (p = 0.001). About one half of deaths that occurred following the withdrawal of life-sustaining therapies happened within the first three days of care.

Interpretation:

We observed significant variation in mortality across centres. This may be explained in part by regional variations in physician, family or community approaches to the withdrawal of life-sustaining therapy. Considering the high proportion of early deaths associated with the withdrawal of life-sustaining therapy and the limited accuracy of current prognostic indicators, caution should be used regarding early withdrawal of life-sustaining therapy following severe traumatic brain injury.Traumatic brain injury is the leading cause of death and disability among patients younger than 45 years of age, with mortality rates ranging from 30% to 40%.^1–3 Moreover, the impact of traumatic brain injury on quality of life among survivors is tremendous, with up to 30% of patients acquiring major neurologic sequelae.Although few studies have compared mortality among centres in global trauma populations,^4,5 overall mortality and variation in mortality, specifically for patients with critical illness and traumatic brain injury, are less well described. Because patients with severe traumatic brain injury lack capacity for making medical decisions, relatives and medical teams must frequently estimate patients’ preferences for treatment, including life support. Decisions to withdraw life-sustaining therapies are usually based on perceptions of unfavourable prognosis for meaningful neurologic recovery.^6–8 However, there are relatively few accurate and useful prediction tools to inform such estimates of prognosis. Therefore, prognostication is often based on clinicians’ impressions and past experiences. The subjective nature of neuroprognostication may lead to variability in the incidence of death associated with the withdrawal of life-sustaining therapy. With the recent advent of programs for organ donation following cardiovascular death, potential variability in mortality and withdrawal of life-sustaining therapy among patients with severe traumatic brain injury would be of major importance from a medicolegal perspective. The ethical debate surrounding organ donation following cardiovascular death having recently reached a public hearing⁹ highlights the need to improve our understanding of withdrawal of life-sustaining therapy for this specific population of patients.We hypothesized that hospital mortality varies across centres and that this may be explained, at least in part, by variability in the rate of withdrawal of life-sustaining therapy. We conducted a multicentre cohort study in six Canadian level-one trauma centres to investigate and compare rates of death associated with withdrawal of life-sustaining therapy among patients with severe traumatic brain injury.     

Bias of heritability estimates from twin data in presence of errors of zygosity determination

Simple heritability estimators of continuous as well as discrete traits from twin data are known to overestimate the degree of genetic determination of the measured traits for several reasons. Errors of zygosity determination will, however, underestimate the true heritability. The bias due to wrong assignment of dizygous twin pairs into monozygous type is evaluated here, and the results indicate that this negative bias has a compensatory effect on the estimate of the degree of genetic determination when other factors of similarity between twin pairs are taken into account. It is shown that when an estimate of zygosity error is available, the bias due to this factor can be evaluated quantitatively, and hence the adjustment for zygosity error can be incorporated in the estimation of the degree of genetic determination of a trait. Although this theory is explicitly developed here for twin studies, the general principle also applies for other types of errors of determining the degree of biological relationships for estimation of heritability, in which case this type of error may be more important than the simple zygosity error.     

Methyl-Deficient Transfer Ribonucleic Acid and Macromolecular Synthesis in Methionine-Starved Saccharomyces cerevisiae

Haploid methionine auxotrophs of Saccharomyces cerevisiae continue to multiply for several hours after withdrawal of a required amino acid from the medium. Macro-molecular synthesis continues during this period of residual growth, although the net ribonucleic acid (RNA) and protein content is constant during the later part of this period. In this study, growth after withdrawal of methionine was in some cases accompanied by accumulation of transfer RNA (tRNA), which was shown by methylation in vitro to be deficient in methyl groups. This phenomenon was shown by only four of nine methionine auxotrophs tested, but no evidence could be found that these four strains had "relaxed" control of RNA synthesis. The nine methionine-requiring strains represent mutations in five different positions in the methionine biosynthesis pathway, and only mutants blocked at two of these five positions accumulated methyl-deficient tRNA. This accumulation therefore appears to be correlated with the position of the strain's block in the pathway of methionine biosynthesis.     

Dipeptide frequency/bias analysis identifies conserved sites of nonrandomness shared by cysteine-rich motifs.

This report describes the application of a simple computational tool, AAPAIR.TAB, for the systematic analysis of the cysteine-rich EGF, Sushi, and Laminin motif/sequence families at the two-amino acid level. Automated dipeptide frequency/bias analysis detects preferences in the distribution of amino acids in established protein families, by determining which "ordered dipeptides" occur most frequently in comprehensive motif-specific sequence data sets. Graphic display of the dipeptide frequency/bias data revealed family-specific preferences for certain dipeptides, but more importantly detected a shared preference for employment of the ordered dipeptides Gly-Tyr (GY) and Gly-Phe (GF) in all three protein families. The dipeptide Asn-Gly (NG) also exhibited high-frequency and bias in the EGF and Sushi motif families, whereas Asn-Thr (NT) was distinguished in the Laminin family. Evaluation of the distribution of dipeptides identified by frequency/bias analysis subsequently revealed the highly restricted localization of the G(F/Y) and N(G/T) sequence elements at two separate sites of extreme conservation in the consensus sequence of all three sequence families. The similar employment of the high-frequency/bias dipeptides in three distinct protein sequence families was further correlated with the concurrence of these shared molecular determinants at similar positions within the distinctive scaffolds of three structurally divergent, but similarly employed, motif modules.     

Systematic bias in high-throughput sequencing data and its correction by BEADS

Genomic sequences obtained through high-throughput sequencing are not uniformly distributed across the genome. For example, sequencing data of total genomic DNA show significant, yet unexpected enrichments on promoters and exons. This systematic bias is a particular problem for techniques such as chromatin immunoprecipitation, where the signal for a target factor is plotted across genomic features. We have focused on data obtained from Illumina's Genome Analyser platform, where at least three factors contribute to sequence bias: GC content, mappability of sequencing reads, and regional biases that might be generated by local structure. We show that relying on input control as a normalizer is not generally appropriate due to sample to sample variation in bias. To correct sequence bias, we present BEADS (bias elimination algorithm for deep sequencing), a simple three-step normalization scheme that successfully unmasks real binding patterns in ChIP-seq data. We suggest that this procedure be done routinely prior to data interpretation and downstream analyses.     

Opiate Modulation of Striatal Dopamine and Hippocampal Norepinephrine Release Following Morphine Withdrawal

When opiates are abruptly withdrawn after chronic treatment, increases in hippocampal noradre-nergic function are observed which are accompanied by decreases in striatal dopamine release. The latter effects have to shown to persist for several weeks following the onset of opiate withdrawal. We examined the long-term effects of opiate withdrawal on 4-aminopyridine and potassium stimulated release of striatal dopamine and hippocampal norepinephrine. Tissue samples were obtained either from rats that had been exposed to opiate withdrawal following a seven day morphine infusion or sham treated control subjects. At 48 hours after the onset of withdrawal (cessation of morphine infusions), slices were loaded with [³H] neurotransmitter, washed extensively, and exposed to different drug treatments. 4-aminopyridine induced concentration related increases in striatal dopamine release, which was 36% calcium independent. Similar values for fractional release of striatal dopamine were obtained in morphine withdrawn and control subjects, for both potassium and 4-aminopyridine induced release. In addition, thresholds for 4-aminopyridine or potassium induced release of striatal dopamine did not differ between control and morphine withdrawn subjects. Treatment with 1.0 M morphine sulfate potentiated potassium evoked release of norepinephrine to an equal extent in both morphine withdrawn and sham treated hippocampal tissue. Exposure to a threshold concentration of potassium (8.0 mM), stimulated increased release of hippocampal norepinephrine in a significantly greater fraction of tissue samples obtained from morphine withdrawn animals. Although these results do not support changes in striatal dopamine release following opiate withdrawal, opiate mechanisms appear to be important determinants of in vitro hippocampal norepinephrine release.