Ambient Light Promotes Selective Subcellular Proteotoxicity after Endogenous and Exogenous Porphyrinogenic Stress

Hepatic accumulation of protoporphyrin-IX (PP-IX) in erythropoietic protoporphyria (EPP) or X-linked-dominant protoporphyria (XLP) cause liver damage. Hepatocyte nuclear lamin aggregation is a sensitive marker for PP-IX-mediated liver injury. We tested the hypothesis that extracellular or intracellular protoporphyria cause damage to different subcellular compartments, in a light-triggered manner. Three hepatoma cell lines (HepG2, Hepa-1, and Huh-7) were treated with exogenous PP-IX (mimicking XLP extrahepatic protoporphyria) or with the iron chelator deferoxamine and the porphyrin precursor 5-aminolevulinic acid (ALA) (mimicking intracellular protoporphyrin accumulation in EPP). Exogenous PP-IX accumulated predominantly in the nuclear fraction and caused nuclear shape deformation and cytoplasmic vacuoles containing electron-dense particles, whereas ALA+deferoxamine treatment resulted in higher PP-IX in the cytoplasmic fraction. Protein aggregation in the nuclear and cytoplasmic fractions paralleled PP-IX levels and, in cell culture, the effects were exclusively ambient light-mediated. PP-IX and ALA caused proteasomal inhibition, whereas endoplasmic reticulum protein aggregation was more prominent in ALA-treated cells. The enhanced ALA-related toxicity is likely due to generation of additional porphyrin intermediates including uroporphyrin and coproporphyrin, based on HPLC analysis of cell lysates and the culture medium, as well as cell-free experiments with uroporphyrin/coproporphyrin. Mouse livers from drug-induced porphyria phenocopied the in vitro findings, and mass spectrometry of liver proteins isolated in light/dark conditions showed diminished (as compared with light-harvested) but detectable aggregation under dark-harvested conditions. Therefore, PP-IX leads to endoplasmic reticulum stress and proteasome inhibition in a manner that depends on the source of porphyrin buildup and light exposure. Porphyrin-mediated selective protein aggregation provides a potential mechanism for porphyria-associated tissue injury.     

Comparison of Bayesian models to estimate direct genomic values in multi-breed commercial beef cattle

Background

While several studies have examined the accuracy of direct genomic breeding values (DGV) within and across purebred cattle populations, the accuracy of DGV in crossbred or multi-breed cattle populations has been less well examined. Interest in the use of genomic tools for both selection and management has increased within the hybrid seedstock and commercial cattle sectors and research is needed to determine their efficacy. We predicted DGV for six traits using training populations of various sizes and alternative Bayesian models for a population of 3240 crossbred animals. Our objective was to compare alternate models with different assumptions regarding the distributions of single nucleotide polymorphism (SNP) effects to determine the optimal model for enhancing feasibility of multi-breed DGV prediction for the commercial beef industry.

Results

Realized accuracies ranged from 0.40 to 0.78. Randomly assigning 60 to 70% of animals to training (n ≈ 2000 records) yielded DGV accuracies with the smallest coefficients of variation. Mixture models (BayesB95, BayesCπ) and models that allow SNP effects to be sampled from distributions with unequal variances (BayesA, BayesB95) were advantageous for traits that appear or are known to be influenced by large-effect genes. For other traits, models differed little in prediction accuracy (~0.3 to 0.6%), suggesting that they are mainly controlled by small-effect loci.

Conclusions

The proportion (60 to 70%) of data allocated to training that optimized DGV accuracy and minimized the coefficient of variation of accuracy was similar to large dairy populations. Larger effects were estimated for some SNPs using BayesA and BayesB95 models because they allow unequal SNP variances. This substantially increased DGV accuracy for Warner-Bratzler Shear Force, for which large-effect quantitative trait loci (QTL) are known, while no loss in accuracy was observed for traits that appear to follow the infinitesimal model. Large decreases in accuracy (up to 0.07) occurred when SNPs that presumably tag large-effect QTL were over-regressed towards the mean in BayesC0 analyses. The DGV accuracies achieved here indicate that genomic selection has predictive utility in the commercial beef industry and that using models that reflect the genomic architecture of the trait can have predictive advantages in multi-breed populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0106-8) contains supplementary material, which is available to authorized users.     

Speed adaptation in a powered transtibial prosthesis controlled with a neuromuscular model

Control schemes for powered ankle-foot prostheses would benefit greatly from a means to make them inherently adaptive to different walking speeds. Towards this goal, one may attempt to emulate the intact human ankle, as it is capable of seamless adaptation. Human locomotion is governed by the interplay among legged dynamics, morphology and neural control including spinal reflexes. It has been suggested that reflexes contribute to the changes in ankle joint dynamics that correspond to walking at different speeds. Here, we use a data-driven muscle-tendon model that produces estimates of the activation, force, length and velocity of the major muscles spanning the ankle to derive local feedback loops that may be critical in the control of those muscles during walking. This purely reflexive approach ignores sources of non-reflexive neural drive and does not necessarily reflect the biological control scheme, yet can still closely reproduce the muscle dynamics estimated from biological data. The resulting neuromuscular model was applied to control a powered ankle-foot prosthesis and tested by an amputee walking at three speeds. The controller produced speed-adaptive behaviour; net ankle work increased with walking speed, highlighting the benefits of applying neuromuscular principles in the control of adaptive prosthetic limbs.     

Structural analysis of human and macaque mAbs 2909 and 2.5B: implications for the configuration of the quaternary neutralizing epitope of HIV-1 gp120

The quaternary neutralizing epitope (QNE) of HIV-1 gp120 is preferentially expressed on the trimeric envelope spikes of intact HIV virions, and QNE-specific monoclonal antibodies (mAbs) potently neutralize HIV-1. Here, we present the crystal structures of the Fabs of human mAb 2909 and macaque mAb 2.5B. Both mAbs have long beta hairpin CDR H3 regions >20 ? in length that are each situated at the center of their respective antigen-binding sites. Computational analysis showed that the paratopes include the whole CDR H3, while additional CDR residues form shallow binding pockets. Structural modeling suggests a way to understand the configuration of QNEs and the antigen-antibody interaction for QNE mAbs. Our data will be useful in designing immunogens that may elicit potent neutralizing QNE Abs.     

Design and initial characterization of the SC-200 proteomics standard mixture

High-throughput (HTP) proteomics studies generate large amounts of data. Interpretation of these data requires effective approaches to distinguish noise from biological signal, particularly as instrument and computational capacity increase and studies become more complex. Resolving this issue requires validated and reproducible methods and models, which in turn requires complex experimental and computational standards. The absence of appropriate standards and data sets for validating experimental and computational workflows hinders the development of HTP proteomics methods. Most protein standards are simple mixtures of proteins or peptides, or undercharacterized reference standards in which the identity and concentration of the constituent proteins is unknown. The Seattle Children's 200 (SC-200) proposed proteomics standard mixture is the next step toward developing realistic, fully characterized HTP proteomics standards. The SC-200 exhibits a unique modular design to extend its functionality, and consists of 200 proteins of known identities and molar concentrations from 6 microbial genomes, distributed into 10 molar concentration tiers spanning a 1,000-fold range. We describe the SC-200's design, potential uses, and initial characterization. We identified 84% of SC-200 proteins with an LTQ-Orbitrap and 65% with an LTQ-Velos (false discovery rate?=?1% for both). There were obvious trends in success rate, sequence coverage, and spectral counts with protein concentration; however, protein identification, sequence coverage, and spectral counts vary greatly within concentration levels.     

Effects of different elastic cord assistance levels on vertical jump

Tran, TT, Brown, LE, Coburn, JW, Lynn, SK, Dabbs, NC, Schick, MK, Schick, EE, Khamoui, AV, Uribe, BP, and Noffal, GJ. Effects of different elastic cord assistance levels on vertical jump. J Strength Cond Res 25(12): 3472-3478, 2011-Currently, little research has been conducted using body weight reduction (BWR) as a means to enhance vertical jump. The purpose of this study was to determine the effects of different elastic cord assistance levels on vertical jump height (JH), takeoff velocity (TOV), relative ground reaction force (rGRF), relative impact force (RIF), and descent velocity (DV). Thirty recreationally trained college men and women (M = 15, W = 15) completed 3 testing sessions consisting of 5 conditions: 0, 10, 20, 30, and 40% BWR. In all BWR conditions, the subjects wore a full body harness while being attached to 2 elastic cords suspended from the ceiling and a linear velocity transducer. They then performed 3 maximal countermovement jumps with arm swing on a force plate. The results indicated no interaction of condition by sex for any variable; however, there was a significant (p < 0.05) main effect for condition for each variable. The JH significantly increased across all conditions (0%: 43.73 ± 1.62 cm, 40%: 64.77 ± 2.36 cm). The TOV at 30% (2.73 ± 0.34 m·s) was significantly greater than that at 0% (2.59 ± 0.39 m·s) and 10% (2.63 ± 0.34 m·s), whereas that at 40% (2.79 ± 0.43 m·s) was significantly greater than that at >0, 10, and 20%. The rGRF at 30% (18.62 ± 4.35 N·kg) was significantly greater than that at >0, 10, and 20%, whereas that at 40% (21.38 ± 5.21 N·kg) was significantly greater than in all conditions. The RIF at 20, 30, and 40% (40%: 61.60 ± 18.53 N·kg) was significantly greater than that at 0% (44.46 ± 9.12 N·kg). The DV at 20% (2.61 ± 0.31 m·s) was significantly greater than at 10%, whereas those at 30 and 40% (2.8 ± 0.41 m·s) were significantly greater than at 0, 10, and 20%. These results demonstrate that using different elastic cord levels to reduce body weight appears effective for increasing ascent and descent force and velocity variables. Future research should investigate greater BWR% and chronic training.     

Time course of the effects of static stretching on cycling economy

Stretching has been implemented as part of the warm-up before physical events and widely thought to promote increased sport performance and decreased injury risk. However, recent research has concluded that static stretching before many exercises inhibits acute power, strength, and sprinting performance. There is little research examining the time course of these effects on moderate intensity cycling. The purpose of this study was to examine the time course of static stretching on cycling economy. The subjects consisted of 5 men and 5 women highly trained endurance cyclists. The first of 3 visits was baseline testing of their cycling VO2max. The second and third visits were either stretching or no stretching before a 30-minute stationary ride at 65% of their VO2max. The stretching condition consisted of four 30-second repetitions of 5 stretches with an average total stretching time of 16 minutes. VO2 demonstrated a significant condition by time interaction with the 5-minute time point being significantly less in the nonstretching condition (32.66 ± 5.35 ml·kg(-1)·min(-1)) than stretching (34.39 ± 5.39 ml·kg(-1)·min(-1)). No other time points were different. Our results demonstrate that static stretching yielded an acute increase in submaximal VO2; therefore, coaches and highly trained endurance cyclists should exclude static stretching immediately before moderate intensity cycling because it reduces acute cycling economy.