R/qtl: high-throughput multiple QTL mapping

MOTIVATION: R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10,000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis-trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets. AVAILABILITY: R/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R/qtl can be installed from http://www.rqtl.org/. R/qtl queries should be directed at the mailing list, see http://www.rqtl.org/list/. CONTACT: kbroman@biostat.wisc.edu.     

Mechanism of rescue of common p53 cancer mutations by second-site suppressor mutations

The core domain of p53 is extremely susceptible to mutations that lead to loss of function. We analysed the stability and DNA-binding activity of such mutants to understand the mechanism of second-site suppressor mutations. Double-mutant cycles show that N239Y and N268D act as 'global stability' suppressors by increasing the stability of the cancer mutants G245S and V143A-the free energy changes are additive. Conversely, the suppressor H168R is specific for the R249S mutation: despite destabilizing wild type, H168R has virtually no effect on the stability of R249S, but restores its binding affinity for the gadd45 promoter. NMR structural comparisons of R249S/H168R and R249S/T123A/H168R with wild type and R249S show that H168R reverts some of the structural changes induced by R249S. These results have implications for possible drug therapy to restore the function of tumorigenic mutants of p53: the function of mutants such as V143A and G245S is theoretically possible to restore by small molecules that simply bind to and hence stabilize the native structure, whereas R249S requires alteration of its mutant native structure.     

ATPase inhibitory factor 1 protects the heart from acute myocardial ischemia/reperfusion injury through activating AMPK signaling pathway

Rationale: Myocardial ischemia/reperfusion (I/R) injury is a common clinic scenario that occurs in the context of reperfusion therapy for acute myocardial infarction (AMI). The mitochondrial F1Fo-ATPase inhibitory factor 1 (IF1) blocks the reversal of the F1Fo-ATP synthase to prevent detrimental consumption of cellular ATP and associated demise. In the present study, we study the role and mechanism of IF1 in myocardial I/R injury.Methods: Mice were ligated the left anterior descending coronary artery to build the I/R model in vivo. Rat hearts were isolated and perfused with constant pressure according to Langendorff. Also, neonatal cardiomyocytes hypoxia-reoxygenation (H/R) model was also used. Myocardial infarction area, cardiac function, cellular function, and cell viability was conducted and compared.Results: Our data revealed that IF1 is upregulated in hearts after I/R and cardiomyocytes with hypoxia/re-oxygenation (H/R). IF1 delivered with adenovirus and adeno-associated virus serotype 9 (AAV9) ameliorated cardiac dysfunction and pathological development induced by I/R ex vivo and in vivo. Mechanistically, IF1 stimulates glucose uptake and glycolysis activity and stimulates AMPK activation during in vivo basal and I/R and in vitro OGD/R conditions, and activation of AMPK by IF1 is responsible for its cardioprotective effects against H/R-induced injury.Conclusions: These results suggest that increased IF1 in the I/R heart confer cardioprotective effects via activating AMPK signaling. Therefore, IF1 can be used as a potential therapeutic target for the treatment of pathological ischemic injury and heart failure.     

OntologyTraverser: an R package for GO analysis

SUMMARY: Gene Ontology (GO) annotations have become a major tool for analysis of genome-scale experiments. We have created OntologyTraverser--an R package for GO analysis of gene lists. Our system is a major advance over previous work because (1) the system can be installed as an R package, (2) the system uses Java to instantiate the GO structure and the SJava system to integrate R and Java and (3) the system is also deployed as a publicly available web tool. AVAILABILITY: Our software is academically available through http://franklin.imgen.bcm.tmc.edu/OntologyTraverser/. Both the R package and the web tool are accessible. CONTACT: cashaw@bcm.tmc.edu     

Loss of seven-up from Drosophila R1/R6 photoreceptors reveals a stochastic fate choice that is normally biased by Notch

Recent evidence suggests that stochasticism is important for generating cell type diversity. We have identified a novel stochastic fate choice as part of the mechanism by which Delta/Notch (Dl/N) signaling specifies R7 fate in the Drosophila eye. The equivalence of R1/R6/R7 precursors is normally broken by the activation of N, which specifies the R7 fate. The orphan nuclear hormone receptor Seven-up (Svp) is necessary and sufficient to direct R1/R6/R7 precursors to adopt the R1/R6 fate. A simple model, therefore, is that N represses Svp, which otherwise prevents adoption of the R7 fate. However, we have found that R1/R6s lacking svp stochastically adopt either the R7 or the R8 fate with equal likelihood. We show that N specifies the R7 fate by a novel branched pathway: N represses Svp expression, thereby exposing an underlying stochastic choice between the R7 and R8 fates, and then tips this choice towards the R7 fate.     

The influence of R:FR ratio on the growth, photosynthesis and rooting ability of Terminalia spinosa Engl. and Triplochiton scleroxylon K. Schum

Stockplants of the tropical hardwoods Terminalia spinosa Engl, and Triplochiton scleroxylon K. Schum were grown in a controlled environment under red:far-red (R:FR) ratios ranging from 0.5-3.1. In both species, rates of shoot height increment were higher (P < 0.05) under the low R:FR ratios as a result of increased internode elongation. In Terminalia spinosa , specific leaf area (SLA) was also significantly higher under lower R:FR ratios, values ranging from 175 to 210 cm² g^-1 in the 3.1 and 0.9 treatments respectively. No effect of R:FR ratio on SLA was recorded in Triplochiton scleroxylon. Pre-severance photo-synthetic rate, stomatal conductance and water-use efficiency were increased under the higher R:FR ratios in Terminalia spinosa , rates of photosynthesis ranging between 2.68-4.59 μmol m^-2 s^-1 in the 0.5 and 3.1 R:FR treatments respectively. Gas exchange rates of Triplochiton scleroxylon were unaffected by R:FR treatment. These contrasting responses to variation in R:FR ratio were associated with differences in rooting ability. In Terminalia spinosa , significantly higher percentage rooting was recorded in the cuttings from the 3.1 R:FR treatment than from 0.5, with values of 93.7% and 77.5% recorded respectively. R:FR ratio also affected rooting percentages of Triplochiton scleroxylon , but in this case, higher rooting percentages were recorded in the lower R:FR ratios, values ranging from 31.1–54.1% in the 3.0 and 0.5 R.FR treatments respectively. This difference in rooting response is attributed to the contrasting effects of R:FR ratio on the leaf and stem morphology of the two species. The implications of these results for stockplant management are discussed.     

Lung volume and spirometric standards for healthy female lifetime nonsmokers

The FRC, RV, VC, TLC, RV/TLC (%), FVC, FEV1.0, FEF25-75%, and FEV1.0/FVC (%) were measured in 161 South Australian females aged 18.4-81.2 yr using a Stead-Wells spirometer and helium analyzer. Multiple regression equations were generated to predict these lung volume and spirometric parameters from the best weighted combination of age, mass, standing height, and various other anthropometric variables (FRC: R = 0.715, SEE = 387 ml; RV: R = 0.684, SEE = 256 ml; VC: R = 0.815, SEE = 383 ml; TLC: R = 0.754, SEE = 468 ml; RV/TLC: R = 0.780, SEE = 4.2%; FVC: R = 0.839, SEE = 375 ml; FEV1.0: R = 0.869, SEE = 326 ml; FEV1.0/FVC: R = 0.644, SEE = 5.7%; FEF25-75%: R = 0.753, SEE = 802 ml/s). The range of normality for the lung volumes was defined as the predicted value plus or minus the 95% confidence interval (two-tailed test), and the lower limit of normality for the spirometric variables was designated as the predicted value minus the 95% confidence interval (one-tailed test). Cross-validation of other equations in the literature indicates that they are of limited use for the sample and instrumentation used in this study.     

Synthesis and reactivity of coordinatively unsaturated osmium and ruthenium stannyl complexes

Treatment of MHCl(CO)(PPh₃)₃ (M=Ru, Os) with (CH₂=CH)SnR₃ is a good general route to the coordinatively unsaturated osmium and ruthenium stannyl complexes M(SnR₃)Cl(CO)(PPh₃)₂ (1: M=Ru, R=Me; 2: M=Ru, R = n-butyl; 3: M=Ru, R = p-tolyl; 4: M=Os, R=Me). These coordinatively unsaturated complexes readily add CO and CN-p-tolyl to form the coordinatively saturated compounds M(SnR₃)Cl(CO)L(PPh₃)₂ (5: M=Ru, R=Me, L=CO; 6: M=;Ru, R = n-butyl, L=CO; 7: M=Ru, R = p-tolyl, L=CO; 8: M=Os, R=Me, L=CO; 9: M=Ru, R=Me, L=CN-p-tolyl; 10: M=Ru, R = n-butyl, L=CN-p-tolyl; 11: M=Os, R=Me, L=CN-p-tolyl). In addition, the chloride ligand in Ru(SnR₃)Cl(CO)(PPh₃)₂ proves to be labile and treatment with the potentially bidentate anionic ligands, dimethyldithiocarbamate or diethyldithiocarbamate, affords the coordinatively saturated compounds Ru(SnR₃)(η²-S₂CNR′₂)(CO)(PPh₃)₂ (12: R=Me, R′ = Me; 13: R=Me, R′ = Et; 14: R = n-butyl, R′ = Me; 15: R = p-tolyl, R′ = Me; 16: R = p-tolyl, R′ = Et). Chloride is also displaced by carboxylates forming the six-coordinate compounds Ru(SnR₃)(η²-O₂CR′)(CO)(PPh₃)₂ (17: R=Me, R′ = H; 18: R=Me, R′ = Me; 19: R=Me, R′ = Ph; 20: R = n-butyl, R′ = Me; 21: R = p-tolyl, R′ = Me). IR and ¹H NMR spectral data for all the new compounds and ³¹P and ¹¹⁹Sn NMR spectral data for selected compounds are reported.     

Site-directed mutagenesis of Arginine282 suggests how protons and peptides are co-transported by rabbit PepT1

The mammalian proton-coupled peptide transporter PepT1 is the major route of uptake for dietary nitrogen, as well as the oral absorption of a number of drugs, including beta-lactam antibiotics and angiotensin-converting enzyme inhibitors. Here we have used site-directed mutagenesis to investigate further the role of conserved charged residues in transmembrane domains. Mutation of rabbit PepT1 arginine282 (R282, transmembrane domain 7) to a positive (R282K) or physiologically titratable residue (R282H), resulted in a transporter with wild-type characteristics when expressed in Xenopus laevis oocytes. Neutral (R282A, R282Q) or negatively charged (R282D, R282E) substitutions gave a transporter that was not stimulated by external acidification (reducing pH(out) from 7.4 to 5.5) but transported at the same rate as the wild-type maximal rate (pH(out) 5.5); however, only the R282E mutation was unable to concentrate substrate above the extracellular level. All of the R282 mutants showed trans-stimulation of efflux comparable to the wild-type, except R282E-PepT1 which was faster. A conserved negatively charged residue, aspartate341 (D341) in transmembrane domain 8 was implicated in forming a charge pair with R282, as R282E/D341R- and R282D/D341R-PepT1 had wild-type transporter characteristics. Despite their differences in ability to accumulate substrate, both R282E- and R282D-PepT1 showed an increased charge:peptide stoichiometry over the wild-type 1:1 ratio for the neutral dipeptide Gly-l-Gln, measured using two-electrode voltage clamp. This extra charge movement was linked to substrate transport, as 4-aminobenzoic acid, which binds but is not translocated, did not induce membrane potential depolarisation in R282E-expressing oocytes. A model is proposed for the substrate binding/translocation process in PepT1.     

Reactive oxygen species mediate modification of glycocalyx during ischemia-reperfusion injury

The glycocalyx (Gcx) is a complex and poorly understood structure covering the luminal surface of endothelial cells. It is known to be a determinant of vascular rheology and permeability and may be a key control site for the vascular injuries caused by ischemia-reperfusion (I/R). We used intravital-microscopy to evaluate the effects of I/R injury on two properties of Gcx in mouse cremasteric microvessels: exclusion of macromolecules (anionic-dextrans) and intracapillary distribution of red blood cells (RBC). In this model, the Gcx is rapidly modified by I/R injury with an increase in 70-kDa anionic-dextran penetration without measurable effect on the penetration of 580-kDa anionic-dextran or on RBC exclusion. The effects of I/R injury appear to be mediated by the rapid production of reactive oxygen species (ROS) because they are ameliorated by the addition of exogenous superoxide dismutase-catalase. Intravenous application of allopurinol or heparin also inhibited the effects of I/R injury, and we interpret efficacy of allopurinol as evidence for a role for xanthine-oxidoreductase (XOR) in the response to I/R injury. Heparin, which is hypothesized to displace XOR from a heparin-binding domain in the Gcx, reduced the effects of I/R. The effects of I/R injury were also partially prevented or fully reversed by the intravascular infusion of exogenous hyaluronan. These data demonstrate: 1) the liability of Gcx during I/R injury; 2) the importance of locally produced ROS in the injury to Gcx; and 3) the potential importance of heparin-binding sites in modulating the ROS production. Our findings further highlight the relations between glycosaminoglycans and the pathophysiology of Gcx in vivo.     

APE: Analyses of Phylogenetics and Evolution in R language

Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. AVAILABILITY: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.     

R/qtl: QTL mapping in experimental crosses

SUMMARY: R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental populations derived from inbred lines. It is implemented as an add-on package for the freely-available statistical software, R, and includes functions for estimating genetic maps, identifying genotyping errors, and performing single-QTL and two-dimensional, two-QTL genome scans by multiple methods, with the possible inclusion of covariates. AVAILABILITY: The package is freely available at http://www.biostat.jhsph.edu/~kbroman/qtl.     

Tissue transglutaminase contributes to disease progression in the R6/2 Huntington's disease mouse model via aggregate-independent mechanisms

Huntington's disease (HD) is caused by an expansion of CAG repeats within the huntingtin gene and is characterized by intraneuronal mutant huntingtin protein aggregates. In order to determine the role of tissue transglutaminase (tTG) in HD aggregate formation and disease progression, we cross-bred the R6/2 HD mouse model with a tTG knockout mouse line. R6/2 mice that were tTG heterozygous knockouts (R6/2 : tTG+/-) and tTG homozygous knockouts (R6/2 : tTG-/-) showed a very similar increase in aggregate number within the striatum compared with R6/2 mice that were wild-type with respect to tTG (R6/2 : tTG+/+). Interestingly, a significant delay in the onset of motor dysfunction and death occurred in R6/2 : tTG-/- mice compared with both R6/2 : tTG+/+ and R6/2 : tTG+/- mice. As aggregate number was similarly increased in the striatum of both R6/2 : tTG+/- and R6/2 : tTG-/- mice, whereas only R6/2 : tTG-/- mice showed delayed disease progression, these data suggest that the contribution of tTG towards motor dysfunction and death in the R6/2 mouse is independent of its ability to negatively regulate aggregate formation. Moreover, the combined results from this study suggest that the formation of striatal huntingtin aggregates does not directly influence motor dysfunction or death in this HD mouse model.     

Ammonia removal from anaerobically digested dairy manure by struvite precipitation

Ammonia is one of the most important contaminants impairing the quality of water resources. When this is considered along with the fact that the global demand for nitrogenous fertilizers is in constant rise, the need for recovery as well as removal of nitrogen is well justified. Crystallization of N and P in the form of struvite (MgNH₄PO₄·6H₂O), which is a slow releasing and valuable fertilizer, is one possible technique for this purpose. This study investigated the removal of NH₄⁺ through struvite precipitation from the effluents of one- (R1) and two-phase (R2) anaerobic reactors digesting dairy manure. To force the formation of struvite in the anaerobic reactor effluents, Mg²⁺ ion was added by using both Mg(OH)₂ and MgCl₂·6H₂O. To prevent the effect of different total phosphorus (TP) concentration in the effluents of R1 and R2, as well as to not limit the formation of struvite, an excess amount of PO₄³⁻ (0.14 M) was added in the form of Na₂HPO₄. Different stoichiometric Mg²⁺:NH₄⁺:PO₄³⁻ ratios were tested to determine the required Mg²⁺ concentrations for maximum NH₄⁺ removal by keeping NH₄⁺:PO₄³⁻ ratio constant for the effluents of reactors R1 and R2. The results revealed that very high NH₄⁺ removal efficiencies (above 95%) were possible by adding Mg²⁺ ions higher than 0.06 M concentration in the effluents from reactors R1 and R2. It was also observed that the initial pH adjustment to 8.50 using NaOH did not result in any significant increase in the removal of NH₄⁺ and the removal of NH₄⁺ in the reactors treated with MgCl₂·6H₂O was higher than those treated with Mg(OH)₂ for the same Mg²⁺ concentration.     

Bio3d: an R package for the comparative analysis of protein structures

An automated procedure for the analysis of homologous protein structures has been developed. The method facilitates the characterization of internal conformational differences and inter-conformer relationships and provides a framework for the analysis of protein structural evolution. The method is implemented in bio3d, an R package for the exploratory analysis of structure and sequence data. AVAILABILITY: The bio3d package is distributed with full source code as a platform-independent R package under a GPL2 license from: http://mccammon.ucsd.edu/~bgrant/bio3d/     

Epinephrine and Norepinephrine Act as Potent Agonists at the Recombinant Human Dopamine D4 Receptor

Abstract: The catecholamines dopamine (DA), epinephrine (EP), and norepinephrine (NE) play important roles in learning and memory, emotional states, and control of voluntary movement, as well as cardiovascular and kidney function. They activate distinct but overlapping neuronal pathways through five distinct DA receptors (D1R–D5R) and at least 10 different adrenergic receptors (α1a/b/c, α2a/b/c-1/c-2, and β1/β2/β3). The D4R, which is localized to mesolimbic areas of the brain implicated in affective and emotional behavior, has a deduced amino acid sequence with homology to both adrenergic and dopaminergic receptor subtypes. We report here that DA, EP, and NE all show binding in the nanomolar range to three isoforms of the recombinant human D4R (hD4R): D4.2, D4.4, and D4.7. Submicromolar concentrations of DA, EP, and NE were sufficient to activate hD4R isoforms in two different functional assays: agonist-induced guanosine 5'- O -(3-[³⁵S]thiotriphosphate) binding and modulation of adenylyl cyclase activity. DA was approximately fivefold more potent than EP and NE at the D4R, whereas activation of the human D2R required at least 100-fold higher catecholamine concentrations. Functional activation of the D4R by multiple neurotransmitters may provide a novel mechanism for integration of catecholamine signaling in the brain and periphery.     

参麦注射液对肠缺血/再灌注肺损伤大鼠肺组织p38MAPK及凋亡相关基因表达的影响

目的:观察参麦注射液(SM)对肠缺血/再灌注(I/R)肺损伤大鼠肺组织p38MAPK和凋亡相关基因Bax、Bcl-2蛋白表达的影响,探讨其保护机制。方法:采用夹闭肠系膜上动脉(SMA)方法建立大鼠肠I/R损伤模型。24只SD大鼠随机分为对照组(Control组)、肠缺血/再灌注组(I/R组)、参麦注射液组(SM+I/R组),每组8只。比较各组大鼠肺湿/干比(W/D)、肺表面活性物质主要成分卵磷脂(PC)及总磷脂(TPL)含量的变化;同时免疫组织化学法检测各组大鼠肺组织中p38MAPK、Bax及Bcl-2蛋白的表达水平。结果:与对照组比较,I/R组肺组织W/D明显升高,而PC和TPL的含量显著降低,肺组织p38MAPK、Bcl-2和Bax蛋白表达明显增强(P均＜0.01),其中Bax的增强比Bcl-2的增强更为明显,Bcl-2/Bax比值降低(P＜0.01);与I/R组比较,SM+I/R组大鼠肺组织W/D明显降低,PC和TPL的含量增加,肺组织p38MAPK和Bax蛋白表达下降(P均＜0.01),Bcl-2的表达增强,Bcl-2/Bax比值明显升高(P＜0.01)。相关分析显示,肠I/R时肺组织p38MAPK蛋白表达水平与肺表面活性物质主要功能成分PC含量及凋亡基因Bcl-2/Bax比值呈负相关(r分别为-0.787,-0.731,P均＜0.01)。结论:SM可能通过抑制p38MAPK信号通路的激活,提高Bcl-2/Bax比值来阻抑细胞凋亡,从而减轻肠I/R时的肺损伤。