Gel-free mass spectrometry-based high throughput proteomics: tools for studying biological response of proteins and proteomes

Revolutionary advances in biological mass spectrometry (MS) have provided a basic tool to make possible comprehensive proteomic analysis. Traditionally, two-dimensional gel electrophoresis has been used as a separation method coupled with MS to facilitate analysis of complex protein mixtures. Despite the utility of this method, the many challenges of comprehensive proteomic analysis has motivated the development of gel-free MS-based strategies to obtain information not accessible using two-dimensional gel separations. These advanced strategies have enabled researchers to dig deeper into complex proteomes, gaining insights into the composition, quantitative response, covalent modifications and macromolecular interactions of proteins that collectively drive cellular function. This review describes the current state of gel-free, high throughput proteomic strategies using MS, including (i) the separation approaches commonly used for complex mixture analysis; (ii) strategies for large-scale quantitative analysis; (iii) analysis of post-translational modifications; and (iv) recent advances and future directions. The use of these strategies to make new discoveries at the proteome level into the effects of disease or other cellular perturbations is discussed in a variety of contexts, providing information on the potential of these tools in electromagnetic field research.     

Differential effects of strength training leading to failure versus not to failure on hormonal responses, strength, and muscle power gains.

The purpose of this study was to examine the efficacy of 11 wk of resistance training to failure vs. nonfailure, followed by an identical 5-wk peaking period of maximal strength and power training for both groups as well as to examine the underlying physiological changes in basal circulating anabolic and catabolic hormones. Forty-two physically active men were matched and then randomly assigned to either a training to failure (RF; n = 14), nonfailure (NRF; n = 15), or control groups (C; n = 13). Muscular and power testing and blood draws to determine basal hormonal concentrations were conducted before the initiation of training (T0), after 6 wk of training (T1), after 11 wk of training (T2), and after 16 wk of training (T3). Both RF and NRF resulted in similar gains in 1-repetition maximum bench press (23 and 23%) and parallel squat (22 and 23%), muscle power output of the arm (27 and 28%) and leg extensor muscles (26 and 29%), and maximal number of repetitions performed during parallel squat (66 and 69%). RF group experienced larger gains in the maximal number of repetitions performed during the bench press. The peaking phase (T2 to T3) after NRF resulted in larger gains in muscle power output of the lower extremities, whereas after RF it resulted in larger gains in the maximal number of repetitions performed during the bench press. Strength training leading to RF resulted in reductions in resting concentrations of IGF-1 and elevations in IGFBP-3, whereas NRF resulted in reduced resting cortisol concentrations and an elevation in resting serum total testosterone concentration. This investigation demonstrated a potential beneficial stimulus of NRF for improving strength and power, especially during the subsequent peaking training period, whereas performing sets to failure resulted in greater gains in local muscular endurance. Elevation in IGFBP-3 after resistance training may have been compensatory to accommodate the reduction in IGF-1 to preserve IGF availability.     

Quantitative comparison of bacterial communities in two Mediterranean sponges

Marine sponges can host in their tissues abundant and diverse bacterial communities. Lack of truly quantitative data on bacterial abundance and dynamics limits our understanding of the organization and functioning of these endobiotic communities. In this technical note, we describe a quantitative polymerase chain reaction approach to quantify the relative abundance of multiple clades of three major sponge-associated bacterial phyla: Chloroflexi, Acidobacteria, and Actinobacteria. To test our approach we used the Mediterranean sponges Spongia lamella and Aplysina aerophoba. We designed five out of the six primer sets used in our study. We tested the new primer sets for specificity and optimized their conditions. Our preliminary data showed that Spongia lamella had larger bacterial abundance than Aplysina aerophoba, except for one clade of Chloroflexi. The two Chloroflexi clades investigated in our study amplified a fraction of the Chloroflexi present in Spongia lamella and most of what is present in Aplysina aerophoba, suggesting a more diverse Chloroflexi population in Spongia lamella than in Aplysina aerophoba. This quantitative technique has a great potential to provide a rapid and robust assessment of sponge microbial target and could contribute to deciphering the complexity of these largely unknown host-symbiont interactions.     

New insights into and novel applications for platelet-rich fibrin therapies

The therapeutic use of autologous platelet-rich plasma constitutes a relatively new biotechnology that has been a breakthrough in the stimulation and acceleration of soft-tissue and bone healing. The efficiency of this process lies in the local and continuous delivery of a wide range of growth factors and proteins, mimicking the needs of the physiological wound healing and reparative tissue processes. Consequently, the application of platelet-rich plasma has been extended to many different fields, including orthopedics, sports medicine, dentistry, cosmetic and periodontal medicine and cosmetic, plastic and maxillofacial surgery. This article highlights the use of this technology and discusses some of the obstacles and challenges that need to be addressed to maintain progress in this field.     

Moderate volume of high relative training intensity produces greater strength gains compared with low and high volumes in competitive weightlifters

The purpose of this study was to examine the effect of 3 volumes of heavy resistance, average relative training intensity (expressed as a percentage of 1 repetition maximum that represented the absolute kilograms lifted divided by the number of repetitions performed) programs on maximal strength (1RM) in Snatch (Sn), Clean & Jerk (C&J), and Squat (Sq). Twenty-nine experienced (>3 years), trained junior weightlifters were randomly assigned into 1 of 3 groups: low-intensity group (LIG; n = 12), moderate-intensity group (MIG; n = 9), and high-intensity group (HIG; n = 8). All subjects trained for 10 weeks, 4-5 days a week, in a periodized routine using the same exercises and training volume (expressed as total number of repetitions performed at intensities equal to or greater than 60% of 1RM), but different programmed total repetitions at intensities of >90-100% of 1RM for the entire 10-week period: LIG (46 repetitions), MIG (93 repetitions), and HIG (184 repetitions). During the training period, MIG and LIG showed a significant increase (p < 0.01-0.05) for C&J (10.5% and 3% for MIG and LIG, respectively) and Sq (9.5% and 5.3% for MIG and LIG, respectively), whereas in HIG the increase took place only in Sq (6.9%, p < 0.05). A calculation of effect sizes revealed greater strength gains in the MIG than in HIG or LIG. There were no significant differences between LIG and HIG training volume-induced strength gains. All the subjects in HIG were unable to fully accomplish the repetitions programmed at relative intensities greater than 90% of 1RM. The present results indicate that short-term resistance training using moderate volumes of high relative intensity tended to produce higher enhancements in weightlifting performance compared with low and high volumes of high relative training intensities of equal total volume in experienced, trained young weightlifters. Therefore, for the present population of weightlifters, it may be beneficial to use the MIG training protocol to improve the weightlifting program at least in a short-term (10 weeks) cycle of training.     

Cerebrospinal fluid space alterations in melancholic depression

Melancholic depression is a biologically homogeneous clinical entity in which structural brain alterations have been described. Interestingly, reports of structural alterations in melancholia include volume increases in Cerebro-Spinal Fluid (CSF) spaces. However, there are no previous reports of CSF volume alterations using automated whole-brain voxel-wise approaches, as tissue classification algorithms have been traditionally regarded as less reliable for CSF segmentation. Here we aimed to assess CSF volumetric alterations in melancholic depression and their clinical correlates by means of a novel segmentation algorithm ('new segment', as implemented in the software Statistical Parametric Mapping-SPM8), incorporating specific features that may improve CSF segmentation. A three-dimensional Magnetic Resonance Image (MRI) was obtained from seventy patients with melancholic depression and forty healthy control subjects. Although imaging data were pre-processed with the 'new segment' algorithm, in order to obtain a comparison with previous segmentation approaches, tissue segmentation was also performed with the 'unified segmentation' approach. Melancholic patients showed a CSF volume increase in the region of the left Sylvian fissure, and a CSF volume decrease in the subarachnoid spaces surrounding medial and lateral parietal cortices. Furthermore, CSF increases in the left Sylvian fissure were negatively correlated with the reduction percentage of depressive symptoms at discharge. None of these results were replicated with the 'unified segmentation' approach. By contrast, between-group differences in the left Sylvian fissure were replicated with a non-automated quantification of the CSF content of this region. Left Sylvian fissure alterations reported here are in agreement with previous findings from non-automated CSF assessments, and also with other reports of gray and white matter insular alterations in depressive samples using automated approaches. The reliable characterization of CSF alterations may help in the comprehensive characterization of brain structural abnormalities in psychiatric samples and in the development of etiopathogenic hypotheses relating to the disorders.     

Multiple SNP Markers Reveal Fine-Scale Population and Deep Phylogeographic Structure in European Anchovy (Engraulis encrasicolus L.)

Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian-Atlantic coast appear to have been founded by secondary waves of migrants from a southern refuge.     

Mapping of Genomic Regions (Quantitative Trait Loci) Controlling Production and Quality in Industrial Cultures of the Edible Basidiomycete Pleurotus ostreatus

Industrial production of the edible basidiomycete Pleurotus ostreatus (oyster mushroom) is based on a solid fermentation process in which a limited number of selected strains are used. Optimization of industrial mushroom production depends on improving the culture process and breeding new strains with higher yields and productivities. Traditionally, fungal breeding has been carried out by an empirical trial and error process. In this study, we used a different approach by mapping quantitative trait loci (QTLs) controlling culture production and quality within the framework of the genetic linkage map of P. ostreatus. Ten production traits and four quality traits were studied and mapped. The production QTLs identified explain nearly one-half of the production variation. More interestingly, a single QTL mapping to the highly polymorphic chromosome VII appears to be involved in control of all the productivity traits studied. Quality QTLs appear to be scattered across the genome and to have less effect on the variation of the corresponding traits. Moreover, some of the new hybrid strains constructed in the course of our experiments had production or quality values higher than those of the parents or other commercial strains. This approach opens the possibility of marker-assisted selection and breeding of new industrial strains of this fungus.     

The distribution of nuclear mass, volume and dimensions

Our own measurements and a review of measurements presented in the literature showed that the mass, volume and dimensions of cell nuclei are distributed with a skew towards higher values, a distribution that can best be described as lognormal. The practical consequences of this finding suggest that the measurements of mass and of size should be plotted on a logarithmic scale while DNA values are appropriately presented on a linear scale. The distribution of DNA values of normal cells represents errors introduced by random disturbances in preparations and measurements.