Bead-based multiplex immuno-assays for cytokines, chemokines, growth factors and other analytes: Median fluorescence intensities versus their derived absolute concentration values for statistical analysis

Within the scientific literature, analyses of data from bead based multiplex immunoassays are based on either median fluorescence intensities (MFI) or derived absolute concentration values (ACV) but no consideration of which set of data is the most appropriate for analysis has been published. Here we look at the variance of MFI versus their ACV from the expression of 14 analytes in plasma, using 6 commercially available kits, across 177 patients, recorded at two time points and the associated analyte standards. In total 60 micro titre plates were used resulting in 4965 MFI. In doing so we develop a new background subtraction procedure that reduced by 50% the number of out-of-range values observed in our data set. Using a linear mixed-effect model, which normalizes for assay-to-assay variation, MFI produced similar significant differences than that observed using absolute concentration values. We show that subtracting analyte blanks produces 15% negative MFI resulting in uncertainty of the data being analysed. We argue for analysis of protein expression values MFI are generally a better choice than absolute concentration values. It is argued that analyte standards are not required on each plate, or not at all, in multi-plate experiments, but knowledge of the concentration curve and the range of MFI values that fall within the limits of this curve for each analyte is required. The significance of using MFI over concentration values for the life scientist means higher statistical power and lower costs

Why We Should Invest Money in Child Care.

Prepared for the Alliance of Early Childhood Professionals

Profiling of the secretome of human cancer cells: Preparation of supernatant for proteomic analysis

Secretomic analysis requires removal of serum proteins from cell-culture media. We evaluate the proteins washed from cells prepared in bovine serum-supplemented medium. PBS and serum-free-medium (SFM) were the washing solutions. A Bradford assay was used for total protein concentration and a 1D gel and LC-MS/MS, to assign the protein to human or bovine origin. For both wash solutions, all bovine protein had been removed by the third wash, without compromising the number of living cells. Further washes reduced the number of living cells, especially when using PBS. Proteomic analysis of wash supernatant showed that SFM induced greater lysis of dead cells. Three washes were sufficient to minimize the effects on cell viability, while still removing serum proteins. Washing in SFM resulted in contamination of the wash supernatant with lysed dead cell proteins. Washed cells were incubated in SFM and exposed to ionizing radiation. Analysis of the supernatant showed an increase in human cytoplasmic, plasma membrane, and nuclear protein following irradiation. Secreted proteins were also detected, but in smaller quantities. The significance of these findings extend to in vitro studies of bystander phenomena, since the proteins of lysed dead cells may participate in driving bystander responses

Alice in Wonderland: The effects of body size and movement on children’s size perception and body representation in virtual reality

Previous work shows that in adults, illusory embodiment of a virtual avatar can be induced using congruent visuomotor cues. Furthermore, embodying different-sized avatars influences adults’ perception of their environment’s size. This study (N = 92) investigated whether children are also susceptible to such embodiment and size illusions. Adults and 5-year-old children viewed a first-person perspective of different-sized avatars moving either congruently or incongruently with their own body. Participants rated their feelings of embodiment over the avatar and also estimated the sizes of their body and objects in the environment. Unlike adults, children embodied the avatar regardless of visuomotor congruency. Both adults and children freely embodied different-sized avatars, and this affected their size perception in the surrounding virtual environment; they felt that objects were larger in a small body and vice versa in a large body. In addition, children felt that their body had grown in the large body condition. These findings have important implications for both our theoretical understanding of own-body representation, and our knowledge of perception in virtual environments

Extreme downsizing of spin crossover nanoparticles towards stable colloids in water: a detailed nano-topographic study

The investigation and elaboration of the Spin-Crossover (SCO) phenomenon in Two – Dimensional (2D) Hofmann-type nanosized SCO materials and the size-reduction effect on cooperativity and thermodynamic properties of the nanoparticle are still in progress. Liquid Phase Exfoliation (LPE) as a top-down experimental protocol for the fabrication of 2D SCO atomically thin nanosheets is also an underexplored area of research. Given the increasing scientific interest for 2D nanosheets and their unique thickness-dependent electronic properties the above-mentioned study is of outmost importance. In this context, we present a detailed nano-synthetic study based on the reverse-micellar synthesis of [FeII(2-mpz)2Ni(CN)4] and a further rationalization of this method followed by LPE experimental protocols in order to synthesize nanoparticles with well-controlled size and shape. The role of concentration and reaction’s temperature is investigated in relation to the size, dispersion, morphology and magnetic properties of the nanoparticles. It was found that for specific values of these parameters the synthesis of nanoparticles is controlled and the final products are nanoparticles with an agglomerated architecture. According to an extensive Atomic Force Microscopy (AFM) Nano-topographic study, this agglomeration is best described as right truncated thick prisms of [FeII(2-mpz)2Ni(CN)4] stacked in a vertical position on a rectangular base plate. During the LPE procedure and by prolonging the sonication period the thick prisms are detached and, eventually, exfoliated to atomically thin right prism of height ~1 nm. Magnetic measurements revealed that the size reduction leads to the progressive downshift of abrupt thermal hysteresis with two-step SCO transition temperatures of the bulk [FeII(2-mpz)2Ni(CN)4] material to a gradual incomplete SCO behavior of an almost single layer 2D [FeII(2-mpz)2Ni(CN)4] nanosheet

A systematic analysis of the effects of increasing degrees of serum immunodepletion in terms of depth of coverage and other key aspects in top-down and bottom-up proteomic analyses

Immunodepletion of clinical fluids to overcome the dominance by a few very abundant proteins has been explored but studies are few, commonly examining only limited aspects with one analytical platform. We have systematically compared immunodepletion of 6, 14, or 20 proteins using serum from renal transplant patients, analysing reproducibility, depth of coverage, efficiency, and specificity using 2-D DIGE (‘top-down’) and LC-MS/MS (‘bottom-up’). A progressive increase in protein number (≥2 unique peptides) was found from 159 in unfractionated serum to 301 following 20 protein depletion using a relatively high-throughput 1-D-LC-MS/MS approach, including known biomarkers and moderate–lower abundance proteins such as NGAL and cytokine/growth factor receptors. On the contrary, readout by 2-D DIGE demonstrated good reproducibility of immunodepletion, but additional proteins seen tended to be isoforms of existing proteins. Depletion of 14 or 20 proteins followed by LC-MS/MS showed excellent reproducibility of proteins detected and a significant overlap between columns. Using label-free analysis, greater run-to-run variability was seen with the Prot20 column compared with the MARS14 column (median %CVs of 30.9 versus 18.2%, respectively) and a corresponding wider precision profile for the Prot20. These results illustrate the potential of immunodepletion followed by 1-D nano-LC-LTQ Orbitrap Velos analysis in a moderate through-put biomarker discovery process

High Abundance Proteins Depletion vs Low Abundance Proteins Enrichment: Comparison of Methods to Reduce the Plasma Proteome Complexity

BACKGROUND: To date, the complexity of the plasma proteome exceeds the analytical capacity of conventional approaches to isolate lower abundance proteins that may prove to be informative biomarkers. Only complex multistep separation strategies have been able to detect a substantial number of low abundance proteins (<100 ng/ml). The first step of these protocols is generally the depletion of high abundance proteins by the use of immunoaffinity columns or, alternatively, the enrichment of by the use of solid phase hexapeptides ligand libraries. METHODOLOGY/PRINCIPAL FINDINGS: Here we present a direct comparison of these two approaches. Following either approach, the plasma sample was further fractionated by SCX chromatography and analyzed by RP-LC-MS/MS with a Q-TOF mass spectrometer. The depletion of the 20 most abundant plasma proteins allowed the identification of about 25% more proteins than those detectable following low abundance proteins enrichment. The two datasets are partially overlapping and the identified proteins belong to the same order of magnitude in terms of plasma concentration. CONCLUSIONS/SIGNIFICANCE: Our results show that the two approaches give complementary results. However, the enrichment of low abundance proteins has the great advantage of obtaining much larger amount of material that can be used for further fractionations and analyses and emerges also as a cheaper and technically simpler approach. Collectively, these data indicate that the enrichment approach seems more suitable as the first stage of a complex multi-step fractionation protocol

Use of Opuntia ficus-indica (L.) Mill extracts from Brazilian Caatinga as an alternative of natural moisturizer in cosmetic formulations

ABSTRACT The aim of this work was the obtainment of Opuntia fícus-indica (L.) Mill extract for the development of cosmetic formulations and in vivo evaluation of its moisturizing effects. The formulations were tested for preliminary and accelerated stability. Organoleptic characteristics, pH values and rheological behavior were assessed. The evaluation of moisturizing efficacy of the emulsions formulated with 3.0% of Polyacrylamide (and) C13-14 Isoparaffin (and) Laureth-7 containing 1.0 and 3.0% of O. ficus-indica hydroglycolic extract (EHG001) was performed using the capacitance method (Corneometer(r)) and the transepidermal water loss - TEWL evaluation (Tewameter(r)). The emulsions formulated were stable, exhibiting pseudoplastic and thixotropic behavior. The results of evaluation of moisturizing efficacy showed increased skin hydration after five hours by mainly increasing the skin barrier effect. The formulations containing 1.0 and 3.0% of EHG001 enhanced the skin barrier effect by reducing TEWL up to four hours after application. The results observed suggest that O. ficus-indica hydroglycolic extract may act through a humectant and occlusion mechanism

Berry Flesh and Skin Ripening Features in Vitis vinifera as Assessed by Transcriptional Profiling

Background Ripening of fleshy fruit is a complex developmental process involving the differentiation of tissues with separate functions. During grapevine berry ripening important processes contributing to table and wine grape quality take place, some of them flesh- or skin-specific. In this study, transcriptional profiles throughout flesh and skin ripening were followed during two different seasons in a table grape cultivar ‘Muscat Hamburg’ to determine tissue-specific as well as common developmental programs. Methodology/Principal Findings Using an updated GrapeGen Affymetrix GeneChip® annotation based on grapevine 12×v1 gene predictions, 2188 differentially accumulated transcripts between flesh and skin and 2839 transcripts differentially accumulated throughout ripening in the same manner in both tissues were identified. Transcriptional profiles were dominated by changes at the beginning of veraison which affect both pericarp tissues, although frequently delayed or with lower intensity in the skin than in the flesh. Functional enrichment analysis identified the decay on biosynthetic processes, photosynthesis and transport as a major part of the program delayed in the skin. In addition, a higher number of functional categories, including several related to macromolecule transport and phenylpropanoid and lipid biosynthesis, were over-represented in transcripts accumulated to higher levels in the skin. Functional enrichment also indicated auxin, gibberellins and bHLH transcription factors to take part in the regulation of pre-veraison processes in the pericarp, whereas WRKY and C2H2 family transcription factors seems to more specifically participate in the regulation of skin and flesh ripening, respectively. Conclusions/Significance A transcriptomic analysis indicates that a large part of the ripening program is shared by both pericarp tissues despite some components are delayed in the skin. In addition, important tissue differences are present from early stages prior to the ripening onset including tissue-specific regulators. Altogether, these findings provide key elements to understand berry ripening and its differential regulation in flesh and skin.This study was financially supported by GrapeGen Project funded by Genoma España within a collaborative agreement with Genome Canada. The authors also thank The Ministerio de Ciencia e Innovacion for project BIO2008-03892 and a bilateral collaborative grant with Argentina (AR2009-0021). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewe