Benchmarking of Two Peptide Clean-Up Protocols: SP2 and Ethyl Acetate Extraction for Sodium Dodecyl Sulfate or Polyethylene Glycol Removal from Plant Samples before LC-MS/MS.

The success of bottom-up proteomic analysis frequently depends on the efficient removal of contaminants from protein or peptide samples before LC-MS/MS. For a peptide clean-up workflow, single-pot solid-phase-enhanced peptide sample preparation on carboxylate-modified paramagnetic beads (termed SP2) was evaluated for sodium dodecyl sulfate or polyethylene glycol removal from Arabidopsis thaliana tryptic peptides. The robust and efficient 40-min SP2 protocol, tested for 10-ng, 250-ng, and 10-µg peptide samples, was proposed and benchmarked thoroughly against the ethyl acetate extraction protocol. The SP2 protocol on carboxylated magnetic beads proved to be the most robust approach, even for the simultaneous removal of massive sodium dodecyl sulfate (SDS) and polyethylene glycol (PEG) contaminations from AT peptide samples in respect of the LC-MS/MS data outperforming ethyl acetate extraction.

Current possibilities and risks of donating some tissues, cells, and organs from living donors.

Transfusion, transplantation, and regenerative medicine are rapidly developing fields. The authors of the text want to inform about upcoming legislative changes at the EU level and briefly describe and compare the difficulty of some donation procedures from the point of view of a living donor, as well as their risks, including psychosocial risks. The study is based on a qualitative expert investigation. Comparing the complexity of procedures from the perspective of donors is important, for example, for setting compensations. The tables show that the current compensations are disproportionate.

SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS.

Quantitative protein extraction from biological samples, as well as contaminants removal before LC-MS/MS, is fundamental for the successful bottom-up proteomic analysis. Four sample preparation methods, including the filter-aided sample preparation (FASP), two single-pot solid-phase-enhanced sample preparations (SP3) on carboxylated or HILIC paramagnetic beads, and protein suspension trapping method (S-Trap) were evaluated for SDS removal and protein digestion from Arabidopsis thaliana (AT) lysate. Finally, the optimized carboxylated SP3 workflow was benchmarked closely against the routine FASP. Ultimately, LC-MS/MS analyses revealed that regarding the number of identifications, number of missed cleavages, proteome coverage, repeatability, reduction of handling time, and cost per assay, the SP3 on carboxylated magnetic particles proved to be the best alternative for SDS and other contaminants removal from plant sample lysate. A robust and efficient 2-h SP3 protocol for a wide range of protein input is presented, benefiting from no need to adjust the amount of beads, binding and rinsing conditions, or digestion parameters.

Proteomic characterization and antifungal activity of potato tuber proteins isolated from starch production waste under different temperature regimes.

Proteins were obtained from effluent of a starch manufacture by using different isolation temperatures (40, 60, 80, and 100 °C). The proteins, remaining in effluent after treatment of potato juice at 80 and 100 °C differed significantly in composition and in structural stability as well as in trypsin inhibitory and antifungal activities in comparison with the variants of 40 and 60 °C. The protein samples of 80 °C exhibited the highest antifungal activity and its average value of IC50 against five strains of two Fusarium species was determined in average at 0.18 mg ml-1. The 80 °C protein samples consisted predominantly of low-molecular proteins (7-17 kDa) identified as potato tuber protease inhibitors I and II. Predominantly, protease inhibitors II were identified for the protein samples obtained by 100 °C and here we identified 7 spots in comparison with 12 identified for the 80 °C samples. Samples of 40 and 60 °C with low antifungal activities represent high variability of detected and identified proteins. We identified various representatives of aspartic, cysteine, and serine protease inhibitors in both types of samples. These samples also contained Kunitz-type protease inhibitors that were not found in the 80 and 100 °C samples which documented thermal unstableness of Kunitz-type protease inhibitors. Functional stability at high temperatures and antifungal activity of isolated potato protease inhibitors I and II support the potential of this fraction usage in food, feed, pharmaceutical, or agricultural industry and offer new products for starch manufactures. At the same time, utilization of the stable protein fraction of waste deproteinized potato water promotes exploitation of potato starch production resources.

The attitudes of IVF patients treated in the Czech Republic towards informing children born after gamete donation.

BACKGROUND: In recent decades gamete donation has received growing attention. Data from the Czech National Registry of Assisted Reproduction show that the number of cycles using donated oocytes has been increasing every year. According to Czech law, gamete donation is anonymous. Since 2011, some members of the Czech parliament have repeatedly made requests to revoke the anonymity but anonymity is one of the preconditions for such donation in this country. The aim of this study was to find out how the gamete recipients feel towards informing their child about the circumstances of their conception and their access to the identity of the donor. METHODS: A total of 195 recipients (122 women undergoing treatment - 43 Czechs, 79 foreigners (Western Europe and the USA) and 73 male partners - 28 Czechs, 45 foreigners) participated in this survey. The data were obtained by anonymous questionnaire. RESULTS: A significant difference between the attitude of the future Czech and foreign parents regarding disclosing the mode of conception was found (P = 0.003). The vast majority of Czechs were against disclosure. The foreign recipients were somewhat more divided. Regarding the donor's identity, there was no difference in atttitude between the groups. Recipients rarely consider that the knowledge of the donor's identity will be important for their child. The recipients overall, were convinced that the psychological aspects of parenting are far more important to the child than genetics, and see no reasons for disclosing the donor´s identity. CONCLUSION: While the the foreign recipients were less adamant about non-disclosure, the overall finding was in accord with the current Czech law on anonymity and not in agreement with the proposed abolition. The recipient's attitudes towards disclosing were also culturally determined. The fact that some countries have revised their rules towards open idendity is not a rationale for such change in the Czech Republic.

Deep coverage of the beer proteome.

We adopted an approach based on peptide immobilized pH gradient-isoelectric focusing (IPG-IEF) separation, coupled with LC-MS/MS, in order to maximize coverage of the beer proteome. A lager beer brewed using traditional Czech technology was degassed, desalted and digested. Tryptic peptides were separated by isoelectric focusing on an immobilized pH gradient strip and, after separation, the gel strip was divided into seven equally sized parts. Peptides extracted from gel fractions were analyzed by LC-MS/MS. This approach resulted in a three-fold increase in the number of proteins identified (over 1700) when compared to analysis of unfractionated beer processed by a filter-aided sample preparation (FASP). Over 1900 protein groups (PGs) in total were identified by both approaches. SIGNIFICANCE: The study significantly extends knowledge about the beer proteome and demonstrates its complexity. Detailed knowledge of the protein content, especially gluten proteins, will enhance the evaluation of potential health risks related to beer consumption (coeliac disease) and will contribute to improving beer quality.

Complete genome analysis of two new bacteriophages isolated from impetigo strains of Staphylococcus aureus.

Exfoliative toxin A (ETA)-coding temperate bacteriophages are leading contributors to the toxic phenotype of impetigo strains of Staphylococcus aureus. Two distinct eta gene-positive bacteriophages isolated from S. aureus strains which recently caused massive outbreaks of pemphigus neonatorum in Czech maternity hospitals were characterized. The phages, designated ϕB166 and ϕB236, were able to transfer the eta gene into a prophageless S. aureus strain which afterwards converted into an ETA producer. Complete phage genome sequences were determined, and a comparative analysis of five designed genomic regions revealed major variances between them. They differed in the genome size, number of open reading frames, genome architecture, and virion protein patterns. Their high mutual sequence similarity was detected only in the terminal regions of the genome. When compared with the so far described eta phage genomes, noticeable differences were found. Thus, both phages represent two new lineages of as yet not characterized bacteriophages of the Siphoviridae family having impact on pathogenicity of impetigo strains of S. aureus.

How old is too old? A contribution to the discussion on age limits for assisted reproduction technique access.

In 2012, the Czech Republic established the women's age limit for access to assisted reproduction techniques at age 49 years. In this paper, the acceptability of this age limit from the children's perspective in the Czech Republic is assessed. Although the necessity of balancing the interests of parents and children is acknowledged, little research has taken children's interests into account. We have attempted to map out 'children's interests', asking older children and adolescents (aged 11-25 years) how old they would prefer their parents to be: Czech respondents would prefer to have younger parents. This finding is consistent with the optimal biological childbearing age rather than with the current postponement to a later age. So far, assisted reproduction techniques have been largely regarded as a medical treatment justifying the current women's age limit of 49 years. Had the children's perspective been taken into account, this age limit might have been lower than 49 years. We propose that reproductive health policy should adequately reflect multiple perspectives as an integral part of a multi-layered support system of a society.

Preventing the mixed detergent micelle effect in two-dimensional electrophoresis on Tris-Tricine gels.

Application of Tris-N-[Tris(hydroxymethyl)methyl]glycine gels for 2DE is hampered by formation of mixed CHAPS-SDS micelles resulting in typical swirling pattern in the low mass range, which makes reliable quantitative and qualitative gel evaluation impossible. Modification of 2DE strip equilibration procedure prevented the direct interaction between both detergents during equilibration process, thus substantially improving gel separation.

A combined approach for the study of histone deacetylase inhibitors.

Overexpression of histone deacetylases (HDACs), with consequent hypoacetylation of histones, is reportedly associated with transcriptional repression of tumour suppressor genes. Thus, inhibition of HDACs has emerged as a promising strategy in cancer therapy. In order to monitor the effects of potential HDAC inhibitors, a multi-level approach consisting of preliminary screening (measurement of HDAC activity and semi-quantitative evaluation of histone H4 modification profile by MALDI-TOF MS) and detailed analysis of histone modification forms (using 2-D AUT/AU PAGE and LC-ESI-IT MS) has been used in this study. The data obtained provide a global insight into the effects of HDAC inhibitors on the histone acetylation status that participates in gene transcription control. Using two example inhibitors, valproic acid sodium salt and entinostat, we show that similar levels of HDAC inhibition induced by different agents can lead to distinct rates of histone hyperacetylation, suggesting that except for the direct inhibition of HDACs, additional molecular mechanisms amplifying the response are likely to be involved in the inhibitory process. The approach used in our study makes it possible not only to follow the dynamics of individual histone modification forms, but also of their combined occurrence in the N-terminal fragment.

Exploration of beer proteome using OFFGEL prefractionation in combination with two-dimensional gel electrophoresis with narrow pH range gradients.

Two-dimensional gel electrophoresis in combination with mass spectrometry has already been applied successfully to study beer proteome. Due to the abundance of protein Z in beer samples, prefractionation techniques might help to improve beer proteome coverage. Proteins from four lager beers of different origins were separated by two-dimensional electrophoresis (2-DE) followed by tandem mass spectrometric analysis. Initially 52 proteins mostly from Hordeum vulgare (22 proteins) and Saccharomyces species (25 proteins) were identified. Preparative isoelectric focusing by OFFGEL Fractionator was applied prior to 2-DE to improve its resolution power. As a result of this combined approach, a total of 70 beer proteins from Hordeum vulgare (30 proteins), from Saccharomyces species (31 proteins), and from other sources (9 proteins) were identified. Of these, 37 proteins have not been previously reported in beer samples.

Cytokinin-induced photomorphogenesis in dark-grown Arabidopsis: a proteomic analysis.

High concentrations of cytokinins (CKs) in the cultivation medium can induce partial photomorphogenesis in dark-grown Arabidopsis seedlings. However, no significant increases in endogenous CK levels have been found in de-etiolated mutants, suggesting that either parallel pathways are involved in the light and CK responses, or changes in the sensitivity to CKs occur during photomorphogenesis. Here it is shown that even modest increases in endogenous CK levels induced by transgenic expression of the CK biosynthetic gene, ipt, can lead to many typical features of light-induced de-etiolation, including inhibition of hypocotyl elongation and partial cotyledon opening. In addition, significant changes in expression of 37 proteins (mostly related to chloroplast biogenesis, a major element of light-induced photomorphogenesis) were detected by image and mass spectrometric analysis of two-dimensionally separated proteins. The identified chloroplast proteins were all up-regulated in response to increased CKs, and more than half are up-regulated at the transcript level during light-induced photomorphogenesis according to previously published transcriptomic data. Four of the up-regulated chloroplast proteins identified here have also been shown to be up-regulated during light-induced photomorphogenesis in previous proteomic analyses. In contrast, all differentially regulated mitochondrial proteins (the second largest group of differentially expressed proteins) were down-regulated. Changes in the levels of several tubulins are consistent with the observed morphological alterations. Further, 10 out of the 37 differentially expressed proteins detected have not been linked to either photomorphogenesis or CK action in light-grown Arabidopsis seedlings in previously published transcriptomic or proteomic analyses.

A proteomic analysis of protein variations during differentiation of v-myb-transformed monoblasts.

v-myb oncogene of avian myeloblastosis virus (AMV) transforms myelomonocytic cells in vitro and induces acute monoblastic leukemia in vivo. The transforming effect of the v-myb can be suppressed using phorbol ester (TPA) or histone deacetylase inhibitor trichostatin A (TSA), the inducers of cell differentiation that are in clinical trials. In this study, we used proteomics-based approach to identify proteins with variable expression in differentiated BM2 cells. Proteome variations induced by TPA and TSA were compared to examine the mechanism of differentiation-promoting effects of these drugs. We found that expression of several proteins participating in cell cytoskeleton rearrangement, heat shock response, proteosynthesis and cell signaling was altered in TPA- or TSA-treated cells. We present here the first comparative proteome analysis of v-myb-transformed monoblasts BM2 focused on identification of proteins involved in their terminal differentiation.

Structural protein analysis of the polyvalent staphylococcal bacteriophage 812.

Phage 812 is a polyvalent phage with a very broad host range in the genus Staphylococcus, which makes it a suitable candidate for phage therapy of staphylococcal infections. This proteomic study, combining the results of both 1-DE and 2-DE followed by PMF, led to the identification of 24 virion proteins. Twenty new proteins, not yet identified by proteome analysis of closely related staphylococcal phages K and G1 were identified using this approach. Fifteen proteins were assigned unambiguously to the head-tail genome module; the remaining nine proteins are encoded by genes of the left or right arms of the phage genome. As expected, the most abundant proteins in the electrophoretic patterns are the major capsid protein, the major tail sheath protein and proteins identical to ORF 50 and ORF 95 of phage K, although their function is only putative. Identification of these 20 new proteins contributes substantially to a detailed characterization of phage virions, knowledge of which is necessary for rational phage therapy.

The identification of catalytic pentad in the haloalkane dehalogenase DhmA from Mycobacterium avium N85: reaction mechanism and molecular evolution.

Haloalkane dehalogenase DhmA from Mycobacterium avium N85 showed poor expression and low stability when produced in Escherichia coli. Here, we present expression DhmA in newly constructed pK4RP rhodococcal expression system in a soluble and stable form. Site-directed mutagenesis was used for the identification of a catalytic pentad, which makes up the reaction machinery of all currently known haloalkane dehalogenases. The putative catalytic triad Asp123, His279, Asp250 and the first halide-stabilizing residue Trp124 were deduced from sequence comparisons. The second stabilizing residue Trp164 was predicted from a homology model. Five point mutants in the catalytic pentad were constructed, tested for activity and were found inactive. A two-step reaction mechanism was proposed for DhmA. Evolution of different types of catalytic pentads and molecular adaptation towards the synthetic substrate 1,2-dichloroethane within the protein family is discussed.

Role of vimentin in regulation of monocyte/macrophage differentiation.

Maturation of blood cells depends on dramatic changes of expression profiles of specific genes. Although these changes have been extensively studied, their functional outcomes often remain unclear. In this study, we explored the identity and function of an unknown protein that was greatly overexpressed in v-myb-transformed BM2 monoblasts undergoing differentiation to macrophage-like cells. We identified this protein as vimentin, the intermediate filament protein. We show that an increased level of vimentin protein results from activation of the vimentin gene promoter occurring in monoblastic cells induced to differentiate by multiple agents. Furthermore, our studies reveal that the vimentin gene promoter is stimulated by Myb and Jun proteins, the key transcriptional regulators of myeloid maturation. Silencing of vimentin gene expression using siRNA markedly suppressed the ability of BM2 cells to form macrophage polykaryons active in phagocytosis and producing reactive oxygen species. Taken together, these findings document that up-regulation of vimentin gene expression is important for formation of fully active macrophage-like cells and macrophage polykaryons.