High-throughput analysis suggests differences in journal false discovery rate by subject area and impact factor but not open access status.

BACKGROUND: A low replication rate has been reported in some scientific areas motivating the creation of resource intensive collaborations to estimate the replication rate by repeating individual studies. The substantial resources required by these projects limits the number of studies that can be repeated and consequently the generalizability of the findings. We extend the use of a method from Jager and Leek to estimate the false discovery rate for 94 journals over a 5-year period using p values from over 30,000 abstracts enabling the study of how the false discovery rate varies by journal characteristics. RESULTS: We find that the empirical false discovery rate is higher for cancer versus general medicine journals (p = 9.801E-07, 95% CI: 0.045, 0.097; adjusted mean false discovery rate cancer = 0.264 vs. general medicine = 0.194). We also find that false discovery rate is negatively associated with log journal impact factor. A two-fold decrease in journal impact factor is associated with an average increase of 0.020 in FDR (p = 2.545E-04). Conversely, we find no statistically significant evidence of a higher false discovery rate, on average, for Open Access versus closed access journals (p = 0.320, 95% CI - 0.015, 0.046, adjusted mean false discovery rate Open Access = 0.241 vs. closed access = 0.225). CONCLUSIONS: Our results identify areas of research that may need additional scrutiny and support to facilitate replicable science. Given our publicly available R code and data, others can complete a broad assessment of the empirical false discovery rate across other subject areas and characteristics of published research.

Pollen-mediated gene flow in flax (Linum usitatissimum L.): can genetically engineered and organic flax coexist?

Coexistence allows growers and consumers the choice of producing or purchasing conventional or organic crops with known standards for adventitious presence of genetically engineered (GE) seed. Flax (Linum usitatissimum L.) is multipurpose oilseed crop in which product diversity and utility could be enhanced for industrial, nutraceutical and pharmaceutical markets through genetic engineering. If GE flax were released commercially, pollen-mediated gene flow will determine in part whether GE flax could coexist without compromising other markets. As a part of pre-commercialization risk assessment, we quantified pollen-mediated gene flow between two cultivars of flax. Field experiments were conducted at four locations during 2006 and 2007 in western Canada using a concentric donor (20 × 20 m) receptor (120 × 120 m) design. Gene flow was detected through the xenia effect of dominant alleles of high α-linolenic acid (ALA; 18:3(cisΔ9,12,15)) to the low ALA trait. Seeds were harvested from the pollen recipient plots up to a distance of 50 m in eight directions from the pollen donor. High ALA seeds were identified using a thiobarbituric acid test and served as a marker for gene flow. Binomial distribution and power analysis were used to predict the minimum number of seeds statistically required to detect the frequency of gene flow at specific α (confidence interval) and power (1-ß) values. As a result of the low frequency of gene flow, approximately 4 million seeds were screened to derive accurate quantification. Frequency of gene flow was highest near the source: averaging 0.0185 at 0.1 m but declined rapidly with distance, 0.0013 and 0.00003 at 3 and 35 m, respectively. Gene flow was reduced to 50% (O50) and 90% (O90) between 0.85 to 2.64 m, and 5.68 to 17.56 m, respectively. No gene flow was detected at any site or year > 35 m distance from the pollen source, suggesting that frequency of gene flow was ≤ 0.00003 (P = 0.95). Although it is not possible to eliminate all adventitious presence caused by pollen-mediated gene flow, through harvest blending and the use of buffer zones between GE and conventional flax fields, it could be minimized. Managing other sources of adventitious presence including seed mixing and volunteer populations may be more problematic.

Cloning, localization, and permanent expression of a Drosophila octopamine receptor.

A cDNA for a member of the G protein-coupled receptor family was isolated from Drosophila using a probe derived from a human beta 2-adrenergic receptor cDNA. This Drosophila receptor gene is localized at 99A10-B1 on the right arm of chromosome 3 and is preferentially expressed in Drosophila heads. The insect octopamine receptor has been permanently expressed in mammalian cells, where it mediates the attenuation of adenylate cyclase activity and exhibits a pharmacological profile consistent with an octopamine type 1 receptor. Sequence and pharmacological comparisons indicate that the octopamine receptor is unique but closely related to mammalian adrenergic receptors, perhaps as an evolutionary precursor.

Development of extended-spectrum activity in TEM beta-lactamases in hyper-mutable, mutS Escherichia coli.

TEM-1 and TEM(pUC19)beta-lactamases can gain activity against ceftazidime and other expanded-spectrum cephalosporins via point mutation. The frequency of emergent resistance to ceftazidime at 4 x MIC was elevated >or= 250-fold in hyper-mutable, MutS-deficient Escherichia coli harbouring these beta-lactamase genes on high- or low-copy plasmids. Moreover, although ceftazidime-resistant mutants, or those with reduced susceptibility, were selected in both the wild-type and mutS hosts, many more mutants in the mutS host showed ceftazidimase-type extended-spectrum beta-lactamase (ESBL) activity. This correlated with a G-A point mutation at position 484 in the bla(TEM-1) and bla(TEM-pUC19) genes, conferring the Arg164His amino-acid substitution found in the TEM-29 ESBL. Non-ESBL mutants lacked changes in bla(TEM).

Decrease in creatine kinase in human prostatic carcinoma compared to benign prostatic hyperplasia.

Many previous studies have shown that a proportion of patients with carcinoma of the prostate have increased activity of the creatine kinase (E.C. 2.7.3.2) isoenzyme designated BB in sera from their peripheral blood. We have analyzed tissues from prostatic hyperplasia of 22 patients and from prostatic carcinoma of 23 additional patients. Prostatic carcinomas contain less (p less than 0.001) creatine kinase activity (units/g) than do prostates with benign prostatic hyperplasia. The facts that (a) histochemical studies that we performed confirmed the observation reported previously by others that creatine kinase activity is found primarily in the epithelial elements of hyperplastic prostates and prostatic carcinomas, (b) the carcinomas that we examined had, on the average, a somewhat larger epithelial component than the hyperplastic prostates that we examined, and (c) prostate cancer was found to contain less creatine kinase activity than hyperplastic prostates suggest that the epithelial cells in prostate cancers contain less creatine kinase activity per cell than do those from hyperplastic prostates. The BB form of creatine kinase accounts for 98% of the activity in prostatic carcinoma and in prostates without cancer. Creatine kinase has been discussed as a possible marker for prostatic carcinoma, and we had hoped that it might be useful for the assay of tumor burden. Our data suggest that, if creatine kinase is to be useful in the monitoring of tumor burden, it will be useful only in the contexts of particular patients studied longitudinally since the creatine kinase activity varies enormously among different prostatic carcinomas.

Saxitoxin binding to sodium channels in head extracts from wild-type and tetrodotoxin-sensitive strains of Drosophila melanogaster.

Extracts prepared from heads of Drosophila melanogaster show high-affinity binding (KD = 1.9 nM) of [3H]saxitonin, a compound known to bind to and block voltage-sensitive sodium channels in other organisms. The interaction between saxitoxin and the Drosophila saxitoxin receptor is non-cooperative and reversible with a half-life of 18.3 s for binding at 4 degrees C. The saturable binding is specifically inhibited by tetrodotoxin with a K1 = 0.30 nM. The number of saturable binding sites in the extract is 97 fmol/mg protein. Since approx. 50% of the binding activity is recovered in the extract, the number of binding sites in the head is estimated to be 6.4 fmol/mg head. Nerve conduction in Drosophila larvae is completely blocked after 20 min in a bathing solution containing 200 nM tetrodotoxin. A comparison between the binding and the electrophysiological studies in Drosophila and other organisms suggests that the Drosophila saxitoxin receptor is part of the voltage-sensitive sodium channel involved in the propagation of action potentials. A mutant (ttxs), which is abnormally sensitive to dietary tetrodotoxin, is shown to be indistinguishable from wild type with respect to [3H]saxitonin-binding properties and physiological sensitivity to tetrodotoxin. These studies provide techniques which can be used to identify mutants with defects in the saxitoxin-binding component of the sodium channel.

Adenosine diphosphate inhibits the serotonin transporter.

Adenosine 5'-diphosphate (ADP) caused rapid and significant reductions in the rates of [3H]serotonin uptake observed for human platelets, human platelet vesicles, and rat brain synaptic vesicles. Estimated Vmax values in platelets (N = 15). platelet vesicles (N = 3), and synaptic vesicles (N = 3) exposed to 100 microM ADP were 42.3 +/- 11.4%, 78.8 +/- 1.4%, and 56.8 +/- 9.9% of control values, respectively. The EC50 values observed for ADP in platelets and platelet vesicles were 10-24 microM. Exposure to 100 microM ADP had small, inconsistent effects on KM values observed for the platelet transporter. ADP (100 microM) caused only a slight competitive inhibition of the platelet membrane binding of [3H]citalopram, a ligand for the 5HT uptake site of the transporter (5.0% displacement of 1.0 nM [3H]citalopram, 13% increase in apparent KD). The ADP analogue 2-methylthioADP caused similar decreases in the rates of platelet [3H]serotonin uptake, while a number of other related compounds had little or no effect on rates of platelet uptake. The ADP-effect on uptake was rapid, occurring in less than 2.5 s. and was additive with reductions produced by protein kinase C (PKC) activation. The ADP-induced decreases in uptake did not appear to occur through the ADP receptor or known platelet second messenger systems. The exact mechanism of the ADP-effect and its functional significance remain to be determined.

Transcripts, genes and bands in 315,000 base-pairs of Drosophila DNA.

We have mapped transcripts arising from 315,000 base-pairs of DNA from chromosome region 87D,E of Drosophila melanogaster. The DNA is represented in a series of overlapping recombinant phages; it constitutes about 14 bands in the polytene chromosome from 87D5,6 to 87E5,6 and contains the essential sequences for at least 12 complementation groups. We have defined 20 discrete polyadenylated RNA species transcribed from non-repetitive DNA in the region at various developmental stages. There is a generally good correlation between the position of transcription units, chromomeric units and complementation groups but with some significant exceptions. In particular, the two large bands in the region (E1,2 and E5,6) each contain several transcription units. We also find that a major part of a large band (E1,2) has no detectable transcripts and is apparently genetically silent.

Drosophila melanogaster acetylcholinesterase gene. Structure, evolution and mutations.

Acetylcholinesterase is a key component of cholinergic neurotransmission. In Drosophila melanogaster, acetylcholinesterase is encoded by the Ace locus. We have determined the complete organization of the locus. The transcription unit is 34 kb (1 kb = 10(3) bases) long and encompasses ten exons. We have mapped the 5' end of the transcript, sequenced all the intron/exon boundaries, as well as the 3' end of the transcript. The deduced mature transcript is 4291 nucleotides long without poly(A). Sequencing of the promoter region reveals a potential TATA box and (GA)n motives. The Drosophila coding sequence is more split than its vertebrate counterparts, but the splicing sites of the two last exons are precisely conserved among Drosophila and vertebrate cholinesterases, and intriguingly also with the bovine thyroglobulin gene. Finally, a number of the mutations isolated in earlier genetic work are precisely placed on our molecular map in introns, exons and promoter regions. Among them, for example, a short deletion known to affect acetylcholinesterase level and tissue distribution removes promoter regions and the first non-coding exon.

Crystal structure of the cyanobacterial metallothionein repressor SmtB: a model for metalloregulatory proteins.

SmtB from Synechococcus PCC7942 is a trans-acting dimeric repressor that is required for Zn(2+)-responsive expression of the metallothionein SmtA. The structure of SmtB was solved using multiple isomorphous replacement techniques and refined at 2.2 A resolution by simulated annealing to an R-factor of 0.218. SmtB displays the classical helix-turn-helix motif found in many DNA-binding proteins. It has an alpha + beta topology, and the arrangement of the three core helices and the beta hairpin is similar to the HNF-3/fork head, CAP and diphtheria toxin repressor proteins. Although there is no zinc in the crystal structure, analysis of a mercuric acetate derivative suggests a total of four Zn2+ binding sites in the dimer. Two of these putative sites are at the opposite ends of the dimer, while the other two are at the dimer interface and are formed by residues contributed from each monomer. The structure of the dimer is such that simultaneous binding for both recognition helices to DNA would require either a bend in the DNA helix or a conformational change in the dimer. The structure of Synechococcus SmtB is the first in this family of metal-binding DNA repressors.

Molecular Genetics of the ROSY-ACE Region of DROSOPHILA MELANOGASTER.

Three hundred and fifteen kilobases of DNA from the rosy-Ace region on chromosome 3R of D. melanogaster have previously been cloned and extensively characterized. We describe the isolation of nine new deficiency mutants that break within the 315-kb interval. The position of these breakpoints on the DNA map was determined by in situ and Southern hybridization. Further, we more precisely mapped the breakpoints of several deletions previously analyzed. The results permit us to delimit sequences essential to the known complementation groups in the region within approximately 20 kb in most cases. However, one gene, B16-1, is shown to contain essential sequences that span about 50 kb. Also, we demonstrate by overlapping deficiencies that a 45-kb DNA segment from the region, which includes one known complementation group, allows limited survival when deleted.

Enhancer of seizure: a new genetic locus in Drosophila melanogaster defined by interactions with temperature-sensitive paralytic mutations.

Mutations in the enhancer of seizure (e(sei] locus have been isolated on the basis of their ability to cause temperature-induced paralysis of alleles at the seizure (sei) locus at temperatures at which these mutations ordinarily do not paralyze. This enhancer is specific to the seizure locus and is without effect on other temperature-sensitive paralytic mutants including para, nap, tip-E and shi. This suggests that the enhancer responds specifically to the mechanism of paralysis mediated by the seizure mutations. The e(sei) is a recessive mutation which maps to 39.0 on the left arm of chromosome 3. Deficiency mapping has placed it at 69A4-B5 on the salivary gland polytene chromosome map. When a new enhancer allele was isolated following P-M hybrid dysgenesis, there was a concomitant P-element insertion at 69B. In the absence of seizure mutations, the enhancer mutation causes non-temperature dependent hyperactivity when agitated and interferes with the climbing response. Electrophysiological studies examined the effects of increasing temperature on electrical activity in the adult giant fiber/flight muscle system. Neuronal hyperactivity was seen in both e(sei) and sei single mutant homozygotes, but not in wild type. The hyperactivity was more severe in the sei;e(sei) double mutants. The correlation between the physiological effects and the mutant behavior suggests that both sei and e(sei) cause membrane excitability defects. Since previous work has shown that seizure mutants affect [3H]saxitoxin binding to the voltage-sensitive sodium channel, e(sei) may code for a gene product which interacts with this channel.

Genetic and developmental characterization of Dmca1D, a calcium channel alpha1 subunit gene in Drosophila melanogaster.

To begin unraveling the functional significance of calcium channel diversity, we identified mutations in Dmca1D, a Drosophila calcium channel alpha1 subunit cDNA that we recently cloned. These mutations constitute the l(2)35Fa lethal locus, which we rename Dmca1D. A severe allele, Dmca1D(X10), truncates the channel after the IV-S4 transmembrane domain. These mutants die as late embryos because they lack vigorous hatching movements. In the weaker allele, Dmca1D(AR66), a cysteine in transmembrane domain I-S1 is changed to tyrosine. Dmca1D(AR66) embryos hatch but pharate adults have difficulty eclosing. Those that do eclose have difficulty in fluid-filling of the wings. These studies show that this member of the calcium channel alpha1 subunit gene family plays a nonredundant, vital role in larvae and adults.

Cytogenetic and molecular localization of tipE: a gene affecting sodium channels in Drosophila melanogaster.

Voltage-sensitive sodium channels play a key role in nerve cells where they are responsible for the increase in sodium permeability during the rising phase of action potentials. In Drosophila melanogaster a subset of temperature-sensitive paralytic mutations affect sodium channel function. One such mutation is temperature-induced paralysis locus E (tipE), which has been shown by electrophysiology and ligand binding studies to reduce sodium channel numbers. Three new gamma-ray-induced tipE alleles associated with either visible deletions in 64AB or a translocation breakpoint within 64B2 provide landmarks for positional cloning of tipE. Beginning with the flanking cloned gene Ras2, a 140-kb walk across the translocation breakpoint was completed. Germline transformation using a 42-kb cosmid clone and successively smaller subclones localized the tipE gene within a 7.4-kb genomic DNA segment. Although this chromosome region is rich in transcripts, only three overlapping mRNAs (5.4, 4.4, and 1.7 kb) lie completely within the smallest rescuing construct. The small sizes of the rescuing construct and transcripts suggest that tipE does not encode a standard sodium channel alpha-subunit with four homologous repeats. Sequencing these transcripts will elucidate the role of the tipE gene product in sodium channel functional regulation.

QSAR modeling based on structure-information for properties of interest in human health.

The development of QSAR models based on topological structure description is presented for problems in human health. These models are based on the structure-information approach to quantitative biological modeling and prediction, in contrast to the mechanism-based approach. The structure-information approach is outlined, starting with basic structure information developed from the chemical graph (connection table). Information explicit in the connection table (element identity and skeletal connections) leads to significant (implicit) structure information that is useful for establishing sound models of a wide range of properties of interest in drug design. Valence state definition leads to relationships for valence state electronegativity and atom/group molar volume. Based on these important aspects of molecules, together with skeletal branching patterns, both the electrotopological state (E-state) and molecular connectivity (chi indices) structure descriptors are developed and described. A summary of four QSAR models indicates the wide range of applicability of these structure descriptors and the predictive quality of QSAR models based on them: aqueous solubility (5535 chemically diverse compounds, 938 in external validation), percent oral absorption (%OA, 417 therapeutic drugs, 195 drugs in external validation testing), AMES mutagenicity (2963 compounds including 290 therapeutic drugs, 400 in external validation), fish toxicity (92 substituted phenols, anilines and substituted aromatics). These models are established independent of explicit three-dimensional (3-D) structure information and are directly interpretable in terms of the implicit structure information useful to the drug design process.

Expression of a foreign gene in Chlamydomonas reinhardtii.

Genomic transformation of Chlamydomonas reinhardtii exposed to glass-bead abrasion was accomplished with a chimeric neomycin phosphotransferaseII (NPTII)-encoding gene (nos::npt) flanked by the nopaline synthase promoter and polyadenylation sequences obtained from the Ti plasmid of Agrobacterium tumefaciens. These sequences were in a plasmid (pGA482) which also contained gene nit1 encoding nitrate reductase of C. reinhardtii. Transformants were selected by their ability to grow on medium containing nitrate, and 52% of these was also resistant to kanamycin. Evidence for nos::npt expression includes: (1) hybridization with probes specific for npt, (2) demonstration of NPTII activity after electrophoresis of extracts, and (3) chromatographic identification of the reaction product of NPTII, kanamycin phosphate. The highly biased codon usage in Chlamydomonas does not preclude expression.

Cloning, sequence analysis and chromosome localization of a Drosophila muscarinic acetylcholine receptor.

Two cDNA clones (3.7 kb and 4.8 kb) encoding a Drosophila muscarinic acetylcholine receptor were isolated from a Drosophila head cDNA library and characterized by automated DNA sequence analysis. The Drosophila muscarinic receptor contains 788 amino acids with a calculated Mr of 84,807 and displays greater than 60% homology with mammalian muscarinic receptors. The muscarinic receptor maps to the tip of the right arm of the second chromosome of the Drosophila genome.

Association of enzyme inhibition with methods of museum skin preparation.

Enzyme inhibition is commonly encountered when using molecular biological techniques on museum-prepared animal skin samples, and this problem is exacerbated by a lack of information on how particular skins have been prepared for preservation. This report: (i) demonstrates that while some methods of museum preparation inhibit both proteinase K digestion and the PCR, others do not; (ii) describes a change in buffer conditions that reduces proteinase K enzyme inhibition during tissue digestion: and (iii) uses electron-dispersive X-ray microanalysis (EDXA) to show that the preparation methods for museum-preserved skin are often more complex than the treatment description provided with samples and also suggests that some of these descriptions are incorrect.

Muscarinic acetylcholine receptors in invertebrates: comparisons with homologous receptors from vertebrates.

The pharmacology, physiology and molecular biology of invertebrate muscarinic acetylcholine receptors are compared with current knowledge concerning vertebrate muscarinic acetylcholine receptors. Evidence for the existence of multiple receptor subtypes in invertebrates is examined, emphasizing what is presently known about the sensitivity of invertebrate preparations to subtype selective ligands previously defined in vertebrate studies. Other evidence for muscarinic receptor subtypes which is examined includes: heterogeneous responses to classical muscarinic ligands and evidence for coupling of invertebrate muscarinic receptors to several different classes of second messenger systems. Clues regarding possible functions for invertebrate muscarinic receptors are discussed, including evidence from both physiological studies and in situ localization studies which reveal patterns of receptor protein and mRNA expression. A detailed analysis of the structural similarities between a cloned Drosophila muscarinic receptor and vertebrate muscarinic receptors is also presented. Regions of the receptors that may be involved in ligand binding, effector coupling and receptor regulation are identified in this comparison. Future directions for invertebrate muscarinic receptor research are considered including: methods for cloning other receptor subtypes, methods for cloning homologous receptors from other species and genetic approaches for determining the physiological roles of muscarinic receptors.