Combining proteomics and lipid analysis to unravel Confidor stress response in Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae is a useful model for studying the influence of different stress factors on eukaryotic cells. In this work we used the pesticide imidacloprid, in the Confidor formulation, as the stress factor and analyzed its influence on the metabolic activity, proteome and lipid content and composition of Saccharomyces cerevisiae yeast. During the cultivation of yeast, the lowest recommended application dose of Confidor (0.025%, v/v) was added to the growth media and its influence on the mitochondria, cytosol with microsomes, and the whole yeast cells was monitored. The results show that under the stress provoked by the toxic effects of Confidor, yeast cells density significantly decreased and the percentage of metabolically disturbed cells significantly increased comparing with untreated control. Also, there was a downregulation of majority of glycolytic, gluconeogenesis, and TCA cycle enzymes (Fba1, Adh1, Hxk2, Tal1, Tdh1,Tdh3, Eno1) thus providing enough acetyl‐CoA for the lipid restructuring and accumulation mechanism since we have found the changes in the cell and mitochondrial lipid content and FA composition. This data suggest that lipids could be the molecules that orchestrate the answer of the cells in the stress response to the Confidor treatment.     

Effects of non-thermal atmospheric plasma treatment on dentin wetting and surface free energy for application of universal adhesives

Objectives

The study aims to evaluate the effects of non-thermal atmospheric plasma (NTAP) treatments on dentin wetting and surface free energy (SFE) and compare the effects of NTAP treatment, etch-and-rinse, and self-etch protocols for application of universal adhesives.

Materials and methods

Mid-coronal dentin of intact third molars was used to measure contact angles of distilled water, ethylene-glycol, and diiodomethane and calculate SFE following different NTAP preset treatments (feeding gas consisting of pure He, He + 1% O₂, He + 1.5% O₂), power input (1 or 3 W), and tip-to-surface distance (2, 4, or 8 mm). Contact angles of reference liquids and SFE of dentin following He + 1.5% O₂ at 3-W and 4-mm treatment was compared to phosphoric acid etching. Contact angles of Single Bond Universal (SBU; 3M ESPE) and Clearfil Universal Bond (CUB; Kuraray Noritake) were measured following NTAP, etch-and-rinse, and self-etch protocols.

Results

NTAP significantly reduced contact angles of reference liquids and increased dentin SFE compared to untreated dentin (p < 0.05). O₂ intensified the effect of He NTAP (p < 0.05). NTAP and phosphoric acid increased dentin polarity and Lewis base surface characteristics. Phosphoric acid increased contact angles of adhesives compared to the self-etch protocol (p < 0.05). NTAP resulted in lower adhesive contact angles than phosphoric acid, the difference being statistically significant for CUB (p < 0.05). Compared to the self-etch protocol, NTAP slightly reduced CUB contact angle but not that of SBU (p > 0.05).

Conclusions

He NTAP with and without O₂ increased dentin wetting and SFE, surpassing the effect of phosphoric acid and lowering adhesive contact angles. NTAP produced no apparent micro-morphological changes on dentin surface comparable to acid etching.

Clinical significance

NTAP treatment of dentin prior to adhesive application increases dentin wetting and surface free energy facilitating better adhesive distribution on dentin surface compared to phosphoric acid etching and similar to the “self-etch” application protocol.

     

Protective effect of interferon-α on the DNA- and RNA-degrading pathway in anti-Fas-antibody induced apoptosis

Aim: Fas membrane-associated polypeptide antigen is a receptor molecule responsible for apoptosis-mediated signals. In animal models of acute viral hepatitis, apoptosis of hepatocytes is mediated by Fas-death receptors; therefore, the aim of this study was to evaluate the effect of interferon (IFN)-alpha on apoptotic markers and nuclease activity against different coding and non-coding single and double stranded RNAs during Fas-induced liver apoptosis. Methods: An in vivo experiment was performed with simultaneous administration of anti-Fas (CD95) antibodies and IFN-alpha, and an in vitro experiment was performed in hepatocyte cultures treated with anti-Fas antibodies and IFN-alpha. Results: Detection of apoptosis using Annexin V-FITC/propidium iodide, Bcl-2 and Bax expression in hepatocyte cultures confirmed the appearance of early apoptotic events and progression toward late apoptosis after anti-Fas antibody treatment. IFN-alpha had a tendency to retard the apoptosis process in Fas-induced apoptosis by increasing the number of viable cells and decreasing the number of cells in late apoptosis, by increasing the percentage of Bcl-2 positive cells, by decreasing the percentage of Bax positive cells, and by decreasing the nuclease activity compared to the anti-Fas antibody treated group. Total DNA and RNA concentration was much reduced in the Fas group and DNA fragmentation assay provided evidence for increased DNA degradation. Enhanced nuclease activity against DNA, rRNA, poly(A), poly(C), poly(U), poly(I:C), and poly(A:U) was manifested in the anti-Fas antibody treated group, except for the inhibitory-bound alkaline RNase. Conclusions: The results demonstrate that the RNA-degrading pathway in Fas-induced apoptosis can accelerate the liberation of the latent enzyme from the inhibitor complex. IFN-alpha prevented enormous, Fas-ligand induced degradation of all the substrates used in this experimental study, most probably due to similarities in the signal transduction pathways. Investigations of death receptor-induced apoptosis may lead to novel treatment combinations for patients with acute or chronic liver diseases.     

Osteogenic differentiation of human bone marrow stromal cells on partially demineralized bone scaffolds in vitro

Tissue engineering has been used to enhance the utility of biomaterials for clinical bone repair by the incorporation of an osteogenic cell source into a scaffold followed by the in vitro promotion of osteogenic differentiation before host implantation. In this study, three-dimensional, partially demineralized bone scaffolds were investigated for their ability to support osteogenic differentiation of human bone marrow stromal cells (BMSCs) in vitro. Dynamic cell seeding resulted in homogeneous cell attachment and infiltration within the matrix and produced significantly higher seeding efficiencies when compared with a conventional static seeding method. Dynamically seeded scaffolds were cultured for 7 and 14 days in the presence of dexamethasone and evaluated on biochemical, molecular, and morphological levels for osteogenic differentiation. Significant elevation in alkaline phosphatase activity was observed versus controls over the 14-day culture, with a transient peak indicative of early mineralization on day 7. On the basis of RT-PCR, dexamethasone-treated samples showed elevations in alkaline phosphatase and osteocalcin expression levels at 7 and 14 days over nontreated controls, while bone sialoprotein was produced only in the presence of dexamethasone at 14 days. Scanning electron microscopy evaluation of dexamethasone-treated samples at 14 days revealed primarily cuboidal cells indicative of mature osteoblasts, in contrast to nontreated controls displaying a majority of cells with a fibroblastic cell morphology. These results demonstrate that partially demineralized bone can be successfully used with human BMSCs to support osteogenic differentiation in vitro. This osseous biomaterial may offer new potential benefits as a tool for clinical bone replacement.     

Applying spatial distribution analysis techniques to classification of 3D medical images

OBJECTIVE: The objective of this paper is to classify 3D medical images by analyzing spatial distributions to model and characterize the arrangement of the regions of interest (ROIs) in 3D space. METHODS AND MATERIAL: Two methods are proposed for facilitating such classification. The first method uses measures of similarity, such as the Mahalanobis distance and the Kullback-Leibler (KL) divergence, to compute the difference between spatial probability distributions of ROIs in an image of a new subject and each of the considered classes represented by historical data (e.g., normal versus disease class). A new subject is predicted to belong to the class corresponding to the most similar dataset. The second method employs the maximum likelihood (ML) principle to predict the class that most likely produced the dataset of the new subject. RESULTS: The proposed methods have been experimentally evaluated on three datasets: synthetic data (mixtures of Gaussian distributions), realistic lesion-deficit data (generated by a simulator conforming to a clinical study), and functional MRI activation data obtained from a study designed to explore neuroanatomical correlates of semantic processing in Alzheimer's disease (AD). CONCLUSION: Performed experiments demonstrated that the approaches based on the KL divergence and the ML method provide superior accuracy compared to the Mahalanobis distance. The later technique could still be a method of choice when the distributions differ significantly, since it is faster and less complex. The obtained classification accuracy with errors smaller than 1% supports that useful diagnosis assistance could be achieved assuming sufficiently informative historic data and sufficient information on the new subject.     

Linear parameters of normal and abnormal cava septi pellucidi: a post-mortem study

Anatomical variations in the dimensions of different brain structures have been correlated with clinical syndromes. This study on the parameters of normal and abnormal cavum septi pellucidi (CSP) can be of clinical significance. We obtained 479 brains from autopsied persons (310 males and 169 females, 377 normal or asymptomatic and 102 abnormal or symptomatic persons, aged 22-89 years) and observed that 110 brains (75 males and 35 females) had CSP. These cava were classified into two groups depending on the past medical histories of the autopsied person: 40 asymptomatic and 70 symptomatic cava. We have defined symptomatic cava as those in autopsied persons who had known past medical history of psychiatric or neurological disease. Asymptomatic cava were in autopsied persons who had no known past medical history of psychiatric or neurological disease. The CSP parameters (length, width, depth) of the symptomatic and asymptomatic groups were measured and were statistically analyzed. Analysis showed that the cava in the symptomatic group were significantly longer and wider. Discriminant function analysis was used to derive a mathematical formula to classify CSP into an asymptomatic or symptomatic group based on length and width measurements of the cavum.     

Large B-cell lymphomas: fine-needle aspiration plays an important role in initial diagnosis of cases which are falsely negative by flow cytometry

Large B-cell lymphomas (LBCLs) have significant false-negative results when immunophenotyped by flow cytometry (FC). To clarify the role fine-needle aspiration (FNA) in reducing this false-negative rate, 28 cases ultimately diagnosed as LBCL that had FNA as part of the workup and a negative FC were identified. We examined their clinical and cytologic features, in comparison with cases of LBCL with FNAs that were positive by FC. In 24/28 FC-negative cases (86%) a cytologic diagnosis of suspicious or positive for malignancy was rendered. We conclude that cytologic analysis is more sensitive than FC in the diagnosis of malignancy in FNA of LBCL, particularly in aspirates with low cellularity and/or low viability. Examination of cytospin preparations of the actual material analyzed by FC may provide an indication that an FC result is falsely negative. It is important to recognize the potential of false-negativity by FC of LBCLs when interpreting FNAs with features suggesting lymphoma.     

Differential effects of growth factors on tissue-engineered cartilage

The effects of four regulatory factors on tissue-engineered cartilage were examined with specific focus on the ability to increase construct growth rate and concentrations of glycosaminoglycans (GAG) and collagen, the major extracellular matrix (ECM) components. Bovine calf articular chondrocytes were seeded onto biodegradable polyglycolic acid (PGA) scaffolds and cultured in medium with or without supplemental insulin-like growth factor (IGF-I), interleukin-4 (IL-4), transforming growth factor-beta1 (TGF-beta1) or platelet-derived growth factor (PDGF). IGF-I, IL-4, and TGF-beta1 increased construct wet weights by 1.5-2.9-fold over 4 weeks of culture and increased amounts of cartilaginous ECM components. IGF-I (10-300 ng/mL) maintained wet weight fractions of GAG in constructs seeded at high cell density and increased by up to fivefold GAG fractions in constructs seeded at lower cell density. TGF-beta1 (30 ng/mL) increased wet weight fractions of total collagen by up to 1.4-fold while maintaining a high fraction of type II collagen (79 plus minus 11% of the total collagen). IL-4 (1-100 ng/mL) minimized the thickness of the GAG-depleted region at the construct surfaces. PDGF (1-100 ng/mL) decreased construct growth rate and ECM fractions. Different regulatory factors thus elicit significantly different chondrogenic responses and can be used to selectively control the growth rate and improve the composition of engineered cartilage.     

Identifying the nature and extent of public and donor concern about the commercialisation of biobanks for genomic research

Various forms of private investment are considered necessary for the sustainability of biobanks, yet pose significant challenges to public trust. To manage this tension, it is vital to identify the concerns of relevant stakeholders to ensure effective and acceptable policy and practice. This research examines the aspects of commercialisation that are of most concern to the Australian public (n = 800) and patients who had donated their tissue to two large disease specific (cancer) public biobanks (n = 564). Overall, we found a commercialisation effect (higher support for public relative to private) in relation to funding, research location and access to stored biospecimens. The effect was strongest for research locations and access compared to funding. A latent class analysis revealed the pattern of concern differed, with the majority (34.1%) opposing all aspects of commercialisation, a minority supporting all (15.7%), one quarter (26.8%) opposing some (sharing and selling tissue) but not others (research locations and funding), and a group who were unsure about most aspects but opposed selling tissue (23.5%). Patient donors were found to be more accepting of and unsure about most aspects of commercialisation. Members of the (general) public who were motivated to participate in biobanking were more likely to oppose some aspects while supporting others, while those who indicated they would not donate to a biobank were more likely to oppose all aspects of commercialisation. The results suggest that approaches to policy, engagement and awareness raising need to be tailored for different publics and patient groups to increase participation.Subject terms: Genetics research, Ethics