Non-invasive assessment of phosphate metabolism and oxidative capacity in working skeletal muscle in healthy young Chinese volunteers using 31P Magnetic Resonance Spectroscopy
Background. Generally, males display greater strength and muscle capacity than females while performing a task. Muscle biopsy is regarded as the reference method of evaluating muscle functions; however, it is invasive and has sampling errors, and is not practical for longitudinal studies and dynamic measurement during excise. In this study, we built an in-house force control and gauge system for quantitatively applying force to quadriceps while the subjects underwent 31P Magnetic Resonance Spectroscopy (31P-MRS); our aim was to investigate if there is a sex difference of phosphate metabolite change in working muscles in young heathy Chinese volunteers. Methods. Volunteers performed knee-extending excises using a force control and gauge system while lying prone in a Philips 3T Magnetic Resonance (MR) scanner. The 31P-MRS coil was firmly placed under the middle of the quadriceps . 31P-MRS measurements of inorganic phosphate (Pi), phosphocreatine (PCr) and adenosine triphosphate (ATP) were acquired from quadriceps while subjects were in a state of pre-, during- and post-exercise. The PCr, Pi, PCr/Pi, PCr/ATP, pH, work/energy cost ratio (WE), kPCr and oxidative capacity were compared between males and females. Results. A total of 17 volunteers underwent the study. Males: N = 10, age = 23.30 ± 1.25years; females: N = 7, age = 23.57 ± 0.79 years. In this study, males had significantly greater WE (16.33 ± 6.46 vs. 7.82 ± 2.16, p = 0.002) than females. Among PCr, Pi, PCr/Pi, PCr/ATP, pH, kPCr and oxidative capacity at different exercise status, only PCr/Pi (during-exercise, males = 5.630 ± 1.647, females = 4.014 ± 1.298, p = 0.047), PCr/ATP (during-exercise, males =1.273 ± 0.219, females = 1.523 ± 0.167, p = 0.025), and ATP (post-exercise, males = 24.469 ± 3.911 mmol/kg, females = 18.353 ± 4.818 mmol/kg, p = 0.035) had significant sex differences. Males had significantly greater PCr/Pi, but less PCr/ATP than females during exercise, suggesting males had higher energy transfer efficiency than females. At the post-exercise status, the recovery of PCr did not show sex difference. Conclusions. Our in-house force control and gauge system quantitatively applied force during the exercise for 31P-MRS experiments, and a sex difference of higher energy transfer efficiency and WE was detected in males with mild loaded exercising quadriceps. This noninvasive technology allows us to further study and understand the sex difference of high energy phosphate metabolism in the future.
Li et al. (2016) Non-invasive assessment of phosphate metabolism and oxidative capacity in working skeletal muscle in healthy young Chinese volunteers using 31P Magnetic Resonance Spectroscopy. PeerJ 4:e2259 https://doi.org/10.7717/peerj.2259
Impact of agricultural management on bacterial laccase-encoding genes with possible implications for soil carbon storage in semi-arid Mediterranean olive farming
Background: In this work, we aimed to gain insights into the contribution of soil bacteria to carbon sequestration in Mediterranean habitats. In particular, we aimed to use bacterial laccase-encoding genes as molecular markers for soil organic C cycling. Using rainfed olive farming as an experimental model, we determined the stability and accumulation levels of humic substances and applied these data to bacterial laccase-encoding gene expression and diversity in soils under four different agricultural management systems (bare soils under tillage/no tillage and vegetation cover under chemical/mechanical management). Materials and Methods: Humic C (> 104 Da) was subjected to isoelectric focusing. The GC-MS method was used to analyze aromatic hydrocarbons. Real-Time PCR quantification and denaturing gradient gel electrophoresis (DGGE) for functional bacterial laccase-like multicopper oxidase (LMCO)-encoding genes and transcripts were also carried out. Results: Soils under spontaneous vegetation, eliminated in springtime using mechanical methods for more than 30 years, showed the highest humic acid levels as well as the largest bacterial population rich in laccase genes and transcripts. The structure of the bacterial community based on LMCO genes also pointed to phylogenetic differences between these soils due to the impact of different management systems. Soils where herbicides were used to eliminate spontaneous vegetation once a year and those where pre-emergence herbicides resulted in bare soils clustered together for DNA-based DGGE analysis, which indicated a certain amount of microbial selection due to the application of herbicides. When LMCO-encoding gene expression was studied, soils where cover vegetation was managed either with herbicides or with mechanical methods showed less than 10% similarity, suggesting that the type of weed management strategy used can impact weed community composition and consequently laccase substrates derived from vegetation decay. Conclusions: We suggest that the low humic acid content retrieved in the herbicide-treated soils was mainly related to the type (due to vegetal cover specialization) and smaller quantity (due to lower vegetal biomass levels) of phenolic substrates for laccase enzymes involved in humification processes. We also found that spontaneous vegetal cover managed using mechanical methods could be the best option for achieving C stabilization in rainfed Mediterranean agroecosystems.
Moreno et al. (2016) Impact of agricultural management on bacterial laccase-encoding genes with possible implications for soil carbon storage in semi-arid Mediterranean olive farming. PeerJ 4:e2257 https://doi.org/10.7717/peerj.2257
Detection of methylation, acetylation and glycosylation of protein residues by monitoring 13C chemical-shift changes: A quantum-chemical study
Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here the feasibility of using 13C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the 13C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a proof-of-concept, we used 13C chemical shifts, computed at the DFT-level of theory, to test this hypothesis. Moreover, as a validation test of this approach, we compare our theoretical computations of the 13Cε chemical-shift values against existing experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ∼1 ppm. Then, further use of this approach to select the most suitable 13C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.
Garay et al. (2016) Detection of methylation, acetylation and glycosylation of protein residues by monitoring 13C chemical-shift changes: A quantum-chemical study. PeerJ 4:e2253 https://doi.org/10.7717/peerj.2253
Simultaneous bilateral laser therapy accelerates recovery after noise-induced hearing loss in a rat model
Noise-induced hearing loss is a common type of hearing loss. The effects of laser therapy have been investigated from various perspectives, including in wound healing, inflammation reduction, and nerve regeneration, as well as in hearing research. A promising feature of the laser is its capability to penetrate soft tissue; depending on the wavelength, laser energy can penetrate into the deepest part of the body without damaging non-target soft tissues. Based on this idea, we developed bilateral transtympanic laser therapy, which uses simultaneous laser irradiation in both ears, and evaluated the effects of bilateral laser therapy on cochlear damage caused by noise overexposure. Thus, the purpose of this research was to assess the benefits of simultaneous bilateral laser therapy compared with unilateral laser therapy and a control. Eighteen Sprague-Dawley rats were exposed to narrow-band noise at 115 dB SPL for 6 h. Multiple auditory brainstem responses were measured after each laser irradiation, and cochlear hair cells were counted after the 15th such irradiation. The penetration depth of the 808 nm laser was also measured after sacrifice. Approximately 5% of the laser energy reached the contralateral cochlea. Both bilateral and unilateral laser therapy decreased the hearing threshold after noise overstimulation in the rat model. The bilateral laser therapy group showed faster functional recovery at all tested frequencies compared with the unilateral laser therapy group. However, there was no difference in the endpoint ABR results or final hair cell survival, which was analyzed histologically.
Lee et al. (2016) Simultaneous bilateral laser therapy accelerates recovery after noise-induced hearing loss in a rat model. PeerJ 4:e2252 https://doi.org/10.7717/peerj.2252
Neural and endocranial anatomy of Triassic phytosaurian reptiles and convergence with fossil and modern crocodylians
Phytosaurs are a clade of large, carnivorous pseudosuchian archosaurs from the Late Triassic with a near cosmopolitan distribution. Their superficial resemblance to longirostrine (long-snouted) crocodylians, such as gharials, has often been used in the past to infer ecological and behavioural convergence between the two groups. Although more than thirty species of phytosaur are currently recognised, little is known about the endocranial anatomy of this clade. Here, we describe the endocranial anatomy (including the brain, inner ear, neurovascular structures and sinus systems) of the two non-mystriosuchine phytosaurs Parasuchus angustifrons (=“Paleorhinus angustifrons”) and Ebrachosuchus neukami from the Late Triassic of Germany based on digital reconstructions. Results show that the endocasts of both taxa are very similar to each other in their rostrocaudally elongate morphology, with long olfactory tracts, weakly demarcated cerebral regions and dorsoventrally short endosseous labyrinths. In addition, several sinuses, including large antorbital sinuses and prominent dural venous sinuses, were reconstructed. Comparisons with the endocranial anatomy of derived phytosaurs indicate that Phytosauria is united by the presence of elongate olfactory tracts and longitudinally arranged brain architecture—characters which are also shared with Crocodyliformes. However, a substantial morphological variability is observed in the cephalic and pontine flexure and the presence of a pineal organ across the different phytosaur species. These results suggest that the endocranial anatomy in Phytosauria generally follows a plesiomorphic pattern, with moderate variation within the clade likely resulting from divergent sensory and behavioural adaptations.
Lautenschlager et al. (2016) Neural and endocranial anatomy of Triassic phytosaurian reptiles and convergence with fossil and modern crocodylians. PeerJ 4:e2251 https://doi.org/10.7717/peerj.2251
Percentile curves for skinfold thickness for Canadian children and youth
Background. Skinfold thickness (SFT) measurements are a reliable and feasible method for assessing body fat in children but their use and interpretation is hindered by the scarcity of reference values in representative populations of children. The objective of the present study was to develop age- and sex-specific percentile curves for five SFT measures (biceps, triceps, subscapular, suprailiac, medial calf) in a representative population of Canadian children and youth. Methods. We analyzed data from 3,938 children and adolescents between 6 and 19 years of age who participated in the Canadian Health Measures Survey cycles 1 (2007/2009) and 2 (2009/2011). Standardized procedures were used to measure SFT. Age- and sex-specific centiles for SFT were calculated using the GAMLSS method. Results. Percentile curves were materially different in absolute value and shape for boys and girls. Percentile girls in girls steadily increased with age whereas percentile curves in boys were characterized by a pubertal centered peak. Conclusions. The current study has presented for the first time percentile curves for five SFT measures in a representative sample of Canadian children and youth.
Kuhle et al. (2016) Percentile curves for skinfold thickness for Canadian children and youth. PeerJ 4:e2247 https://doi.org/10.7717/peerj.2247
Emotional intelligence and depressive symptoms in Spanish institutionalized elders: does emotional self-efficacy act as a mediator?
Background. This work examines the relationship between emotional intelligence (EI) and depressive symptomatology in institutionalized older adults, delving into the mechanisms underlying this relationship. Considering that previous evidence of the variation of the EI-depression relationship depending on whether the emotional ability or the perception of that ability is evaluated, a model of multiple mediation was tested in which the dimensions of emotional self-efficacy (ESE) act as mediators in the relationship between ability EI and depressive symptomatology. Methods. The sample consisted of 115 institutionalized older adults (47.82% women; 80.3 ± 7.9 years of age) from the province of Jaén (Spain) who completed a test of ESE, a measure of ability EI, and a self-administered questionnaire of depressive symptoms. Results. The results showed a positive association between older adults’ emotional performance and depressive symptomatology, finding stronger associations with ESE than with EI abilities. In addition, multiple mediation analyses showed that two of the four dimensions of ESE fully mediated the relationship between ability EI and depressive symptoms. Discussion. These findings suggest that older adults’ high levels of emotional competence generate a feeling of ESE which can protect them against depressive symptoms. This work supports the predictive validity of emotional abilities and ESE for the mental health of a group that is particularly vulnerable to depression, institutionalized older adults. The limitations of the work are discussed, and future lines of research were considered.
Luque-Reca et al. (2016) Emotional intelligence and depressive symptoms in Spanish institutionalized elders: does emotional self-efficacy act as a mediator?. PeerJ 4:e2246 https://doi.org/10.7717/peerj.2246
Fast men slow more than fast women in a 10 kilometer road race
Background. Previous studies have demonstrated that men are more likely than women to slow in the marathon (footrace). This study investigated whether the sex difference in pacing occurs for a shorter race distance. Materials & Methods. Data were acquired from the Bolder Boulder 10 km road race for the years 2008–2013, which encompassed 191,693 performances. There were two pacing measures, percentage change in pace of the first 3 miles relative to the final 3.2 miles and percentage change in pace of the first mile relative to the final 5.2 miles. Pacing was analyzed as a continuous variable and as two categorical variables, as follows: “maintain the pace,” defined as slowing <5% and “marked slowing,” defined as slowing ≥10%. Results. Among the fastest (men < 48:40; women < 55:27) and second fastest (men < 53:54; women < 60:28) sex-specific finishing time sextiles, men slowed significantly more than women with both pacing measures, but there were no consistently significant sex differences in pacing among the slower four sextiles. For the fastest sextile, the odds for women were 1.96 (first pacing measure) and 1.36 (second measure) times greater than men to maintain the pace. For the fastest sextile, the odds for women were 0.46 (first measure) and 0.65 (second measure) times that of men to exhibit marked slowing. Multiple regression indicated that being older was associated with lesser slowing, but the sex difference among faster runners persisted when age was controlled. Conclusions. There was a sex difference in pacing during a 10 km race where glycogen depletion is not typically relevant. These results support the hypothesis that the sex difference in pacing partly reflects a sex difference in decision making.
Deaner et al. (2016) Fast men slow more than fast women in a 10 kilometer road race. PeerJ 4:e2235 https://doi.org/10.7717/peerj.2235
Computer-assisted initial diagnosis of rare diseases
Introduction. Most documented rare diseases have genetic origin. Because of their low individual frequency, an initial diagnosis based on phenotypic symptoms is not always easy, as practitioners might never have been exposed to patients suffering from the relevant disease. It is thus important to develop tools that facilitate symptom-based initial diagnosis of rare diseases by clinicians. In this work we aimed at developing a computational approach to aid in that initial diagnosis. We also aimed at implementing this approach in a user friendly web prototype. We call this tool Rare Disease Discovery. Finally, we also aimed at testing the performance of the prototype. Methods. Rare Disease Discovery uses the publicly available ORPHANET data set of association between rare diseases and their symptoms to automatically predict the most likely rare diseases based on a patient’s symptoms. We apply the method to retrospectively diagnose a cohort of 187 rare disease patients with confirmed diagnosis. Subsequently we test the precision, sensitivity, and global performance of the system under different scenarios by running large scale Monte Carlo simulations. All settings account for situations where absent and/or unrelated symptoms are considered in the diagnosis. Results. We find that this expert system has high diagnostic precision (≥80%) and sensitivity (≥99%), and is robust to both absent and unrelated symptoms. Discussion. The Rare Disease Discovery prediction engine appears to provide a fast and robust method for initial assisted differential diagnosis of rare diseases. We coupled this engine with a user-friendly web interface and it can be freely accessed at http://disease-discovery.udl.cat/. The code and most current database for the whole project can be downloaded from https://github.com/Wrrzag/DiseaseDiscovery/tree/no_classifiers.
Alves et al. (2016) Computer-assisted initial diagnosis of rare diseases. PeerJ 4:e2211 https://doi.org/10.7717/peerj.2211
A century of ecosystem change: human and seabird impacts on plant species extirpation and invasion on islands
We used 116 years of floral and faunal records from Mandarte Island, British Columbia, Canada, to estimate the indirect effects of humans on plant communities via their effects on the population size of a surface-nesting, colonial seabird, the Glaucous-winged gull (Larus glaucescens). Comparing current to historical records revealed 18 extirpations of native plant species (32% of species historically present), 31 exotic species introductions, and one case of exotic introduction followed by extirpation. Contemporary surveys indicated that native species cover declined dramatically from 1986 to 2006, coincident with the extirpation of ‘old-growth’ conifers. Because vegetation change co-occurred with an increasing gull population locally and regionally, we tested several predictions from the hypothesis that the presence and activities of seabirds help to explain those changes. Specifically, we predicted that on Mandarte and nearby islands with gull colonies, we should observe higher nutrient loading and exotic plant species richness and cover than on nearby islands without gull colonies, as a consequence of competitive dominance in species adapted to high soil nitrogen and trampling. As predicted, we found that native plant species cover and richness were lower, and exotic species cover and richness higher, on islands with versus without gull colonies. In addition, we found that soil carbon and nitrogen on islands with nesting gulls were positively related to soil depth and exotic species richness and cover across plots and islands. Our results support earlier suggestions that nesting seabirds can drive rapid change in insular plant communities by increasing nutrients and disturbing vegetation, and that human activities that affect seabird abundance may therefore indirectly affect plant community composition on islands with seabird colonies.
Lameris et al. (2016) A century of ecosystem change: human and seabird impacts on plant species extirpation and invasion on islands. PeerJ 4:e2208 https://doi.org/10.7717/peerj.2208