Monika Piwowar

Autologous muscle-derived cells for the treatment of female stress urinary incontinence: A 2-year follow-up of a polish investigation

We evaluated the safety, feasibility and initial effects of therapy with muscle‐derived cells (MDCs) for women with stress urinary incontinence (SUI).

In silico Structural Study of Random Amino Acid Sequence Proteins Not Present in Nature

The three‐dimensional structures of a set of ‘never born proteins’ (NBP, random amino acid sequence proteins with no significant homology with known proteins) were predicted using two methods: Rosetta and the one based on the ‘fuzzy‐oil‐drop’ (FOD) model. More than 3000 different random amino acid sequences have been generated, filtered against the non redundant protein sequence data base, to remove sequences with significant homology with known proteins, and subjected to three‐dimensional structure prediction. Comparison between Rosetta and FOD predictions allowed to select the ten top (highest structural similarity) and the ten bottom (the lowest structural similarity) structures from the ranking list organized according to the RMS‐D value. The selected structures were taken for detailed analysis to define the scale of structural accordance and discrepancy between the two methods. The structural similarity measurements revealed discrepancies between structures generated on the basis of the two methods. Their potential biological function appeared to be quite different as well. The ten bottom structures appeared to be ‘unfoldable’ for the FOD model. Some aspects of the general characteristics of the NBPs are also discussed. The calculations were performed on the EUChinaGRID grid platform to test the performance of this infrastructure for massive protein structure predictions.

Breakfast and Other Meal Consumption in Adolescents from Southern Poland

The aim of the study was to evaluate the frequency of breakfast and other meal consumption by adolescents and to assess the relationship between the first and the last meal consumption and sex, body mass index (BMI), and middle school and high school students’ education level. The study was conducted in 2013–2014 among 3009 students (1658 girls and 1351 boys) from middle s and high schools in Krakow and Silesia (Poland). The data was obtained from questionnaires that were analyzed with a logistic regression model for measurable and dichotomous variables. Breakfast consumers were seen to eat other meals (second breakfast, lunch, dessert, supper) significantly more often than breakfast skippers. The main meal consumption habits depend on sex and change as adolescents age. Being a girl and a high school student predisposed participants to skip breakfast and supper more often. The BMI of breakfast consumers does not differ significantly from the BMI of breakfast skippers, so BMI might thus not be a sufficient marker of breakfast consumption regularity and dietary habits in an adolescent group. The importance of regularly eaten meals, especially breakfast, together with adequate daily dietary energy intake are beneficial for physical and psychological development and cannot be overestimated in nutritional education and it is necessary to promote healthy eating behavior for well-being in later adult life.

Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes

The presented analysis concerns the inter-domain and inter-protein interface in protein complexes. We propose extending the traditional understanding of the protein domain as a function of local compactness with an additional criterion which refers to the presence of a well-defined hydrophobic core. Interface areas in selected homodimers vary with respect to their contribution to share as well as individual (domain-specific) hydrophobic cores. The basic definition of a protein domain, i.e., a structural unit characterized by tighter packing than its immediate environment, is extended in order to acknowledge the role of a structured hydrophobic core, which includes the interface area. The hydrophobic properties of interfaces vary depending on the status of interacting domains—In this context we can distinguish: (1) Shared hydrophobic cores (spanning the whole dimer); (2) Individual hydrophobic cores present in each monomer irrespective of whether the dimer contains a shared core. Analysis of interfaces in dystrophin and utrophin indicates the presence of an additional quasi-domain with a prominent hydrophobic core, consisting of fragments contributed by both monomers. In addition, we have also attempted to determine the relationship between the type of interface (as categorized above) and the biological function of each complex. This analysis is entirely based on the fuzzy oil drop model.

Loss of CYLD expression unleashes Wnt signaling in multiple myeloma and is associated with aggressive disease

Deletion or mutation of the gene encoding the deubiquitinating enzyme CYLD is a common genomic aberration in multiple myeloma (MM). However, the functional consequence of CYLD loss and the mechanism underlying its putative role as a tumor suppressor gene in the pathogenesis of MM has not been established. Here, we show that CYLD expression is highly variable in myeloma cell lines and primary MMs and that low CYLD expression is associated with disease progression from monoclonal gammopathy of undetermined significance to MM, and with poor overall and progression free-survival of MM patients. Functional assays revealed that CYLD represses MM cell proliferation and survival. Furthermore, CYLD acts as a negative regulator of NF-κB and Wnt/β-catenin signaling and loss of CYLD sensitizes MM cells to NF-κB-stimuli and Wnt ligands. Interestingly, in primary MMs, low CYLD expression strongly correlated with a proliferative and Wnt signaling-gene expression signature, but not with an NFκB target gene signature. Altogether, our findings identify CYLD as a negative regulator of NF-κB and Wnt/β-catenin signaling in MM and indicate that loss of CYLD enhances MM aggressiveness through Wnt pathway activation. Thus, targeting the Wnt pathway could be a promising therapeutic strategy in MM with loss of CYLD activity.

The divergence entropy characterizing the internal force field in proteins

Abstract: This chapter deals with the characterization of the distribution of nonbonding interactions (including hydrophobic interactions) in the protein body. We establish that in most proteins, the hydrophobic interactions can be modeled by a 3D Gaussian function (the “fuzzy oil drop” model), while the electrostatic interactions follow a random distribution. A method for quantitative measurement of the degree of accordance between the expected and observed distributions is introduced and applied. From the point of view of optimizing nonbonding interactions, it is important to note that the non-Gaussian distributions observed in actual proteins approach the idealized Gaussian model when the residues involved in specific activities (enzymatic activity, ligand binding, protein complexation, etc.) are disregarded. It is concluded that pairwise (atom–atom) optimization is sufficient for modeling van der Waals forces and electrostatic interactions, whereas the optimization of hydrophobic interactions must reflect the tertiary structure of the molecule as a whole. It is shown that mismatches in the location of residues responsible for interaction with external molecules distort the protein’s hydrophobicity field, which would otherwise agree with the “fuzzy oil drop” model. The biological function of many proteins (enzymatic activity) is strongly related to deformations in their hydrophobic cores, which can be expressed quantitatively by the degree of structural divergence from the idealized “fuzzy oil drop” model. The deformations identified seem to be specific to specific biological functions.

ExonVisualiser - application for visualization exon units in 2D and 3D protein structures.

The web application oriented on identification and visualization of protein regions encoded by exons is presented. The Exon Visualiser can be used for visualisation on different levels of protein structure: at the primary (sequence) level and secondary structures level, as well as at the level of tertiary protein structure. The programme is suitable for processing data for all genes which have protein expressions deposited in the PDB database. The procedure steps implemented in the application: I) loading exons sequences and theirs coordinates from GenBank file as well as protein sequences: CDS from GenBank and aminoacid sequence from PDB II) consensus sequence creation (comparing amino acid sequences form PDB file with the CDS sequence from GenBank file) III) matching exon coordinates IV) visualisation in 2D and 3D protein structures. Presented web-tool among others provides the color-coded graphical display of protein sequences and chains in three dimensional protein structures which are correlated with the corresponding exons. Availability http://149.156.12.53/ExonVisualiser/

DNA microarray integromics analysis platform

BackgroundThe study of interactions between molecules belonging to different biochemical families (such as lipids and nucleic acids) requires specialized data analysis methods. This article describes the DNA Microarray Integromics Analysis Platform, a unique web application that focuses on computational integration and analysis of “multi-omics” data. Our tool supports a range of complex analyses, including – among others – low- and high-level analyses of DNA microarray data, integrated analysis of transcriptomics and lipidomics data and the ability to infer miRNA-mRNA interactions.ResultsWe demonstrate the characteristics and benefits of the DNA Microarray Integromics Analysis Platform using two different test cases. The first test case involves the analysis of the nutrimouse dataset, which contains measurements of the expression of genes involved in nutritional problems and the concentrations of hepatic fatty acids. The second test case involves the analysis of miRNA-mRNA interactions in polysaccharide-stimulated human dermal fibroblasts infected with porcine endogenous retroviruses.ConclusionsThe DNA Microarray Integromics Analysis Platform is a web-based graphical user interface for “multi-omics” data management and analysis. Its intuitive nature and wide range of available workflows make it an effective tool for molecular biology research. The platform is hosted at https://lifescience.plgrid.pl/.

Quality of life assessment in female patients 2 and 4 years after muscle-derived cell transplants for stress urinary incontinence treatment

INTRODUCTION Regenerative medicine for the treatment of urinary incontinence has become a popular area of focus in the search for therapies for this disease. The paper focused on womens quality of life assessment who were subjected to transplantation of MDSC (autologous muscle derived stem cells) to the urethral sphincter. METHODS The procedure was conducted in 16 female patients who completed the observation stage. Assessment of quality of life before and after the treatment (two and four years post-operation) was conducted based on the validated I-QOL questionnaire (the Polish language version). RESULTS The questionnaire study showed that autologous cell therapy significantly improves quality of life in female patients suffering from stress urinary incontinence (SUI). The total I-QOL score increased from 49 (SD ± 7.7) before therapy to 77 (SD ± 5.4) two years post-operation. Four years after the procedure, quality of life remained at a higher level than before therapy, although quality of life decreased by several points when compared with the results from the two-year follow-up - 63 (SD ± 7.2). Patients reported significantly less concern related to their ability to reach the toilet to avoid incontinence, improved sleep at night, a higher level of satisfaction with life, and more satisfaction with their sexual lives (p<0.05). CONCLUSION The MDSC injection procedure for SUI treatment has significant improved quality of life in the majority of our patients in 2 and 4 year follow-up.

Simulation of the Protein Folding Process

This chapter introduces a novel protein folding simulation model which involves several stages. In particular, it distinguishes the so-called early stage (ES) and late state (LS) intermediates, though it can also account for a greater number of intermediates or — alternatively — using ES as the sole intermediate. The early stage intermediate is generated by geometric modeling of polypeptide bond chains, expressed as pairs of their relative binding angles (V-angle) and radii of curvature (R - which is dependent on V). Results of this process point to a limited conformational subspace, providing a convenient set of starting structures for subsequent free internal energy optimization algorithms. The late stage folding model acknowledges the influence of water on the folding process, with hydrophobic residues directed toward the center of the emerging protein body and hydrophilic residues exposed on its surface. Overall, the structure of the protein’s hydrophobic core can be modeled with a 3D Gauss function (hence the “fuzzy oil drop” designation). The presented algorithm reflects the influence of the aqueous environment on the protein’s structure as addition to the optimization of its internal free energy components.