Classification of Amyloidosis by Model-Assisted Mass Spectrometry-Based Proteomics

Amyloidosis is a rare disease caused by the misfolding and extracellular aggregation of proteins as insoluble fibrillary deposits localized either in specific organs or systemically throughout the body. The organ targeted and the disease progression and outcome is highly dependent on the specific fibril-forming protein, and its accurate identification is essential to the choice of treatment. Mass spectrometry-based proteomics has become the method of choice for the identification of the amyloidogenic protein. Regrettably, this identification relies on manual and subjective interpretation of mass spectrometry data by an expert, which is undesirable and may bias diagnosis. To circumvent this, we developed a statistical model-assisted method for the unbiased identification of amyloid-containing biopsies and amyloidosis subtyping. Based on data from mass spectrometric analysis of amyloid-containing biopsies and corresponding controls. A Boruta method applied on a random forest classifier was applied to proteomics data obtained from the mass spectrometric analysis of 75 laser dissected Congo Red positive amyloid-containing biopsies and 78 Congo Red negative biopsies to identify novel “amyloid signature” proteins that included clusterin, fibulin-1, vitronectin complement component C9 and also three collagen proteins, as well as the well-known amyloid signature proteins apolipoprotein E, apolipoprotein A4, and serum amyloid P. A SVM learning algorithm were trained on the mass spectrometry data from the analysis of the 75 amyloid-containing biopsies and 78 amyloid-negative control biopsies. The trained algorithm performed superior in the discrimination of amyloid-containing biopsies from controls, with an accuracy of 1.0 when applied to a blinded mass spectrometry validation data set of 103 prospectively collected amyloid-containing biopsies. Moreover, our method successfully classified amyloidosis patients according to the subtype in 102 out of 103 blinded cases. Collectively, our model-assisted approach identified novel amyloid-associated proteins and demonstrated the use of mass spectrometry-based data in clinical diagnostics of disease by the unbiased and reliable model-assisted classification of amyloid deposits and of the specific amyloid subtype.     

Effect of Oligothienyl Chain Length on Tuning the Solar Cell Performance in Fluorene‐Based Polyplatinynes

A series of solution‐processable and strongly visible‐light absorbing polyplatinynes containing oligothienyl–fluorene ring hybrids were synthesized and characterized. These rigid‐rod organometallic materials are soluble in polar organic solvents and show intense absorptions in the visible spectral region, rendering them excellent candidates for bulk heterojunction polymer solar cells. The photovoltaic behavior depends significantly on the number of thienyl rings along the polymer chain, and some of these polymer solar cells show high power conversion efficiencies (PCEs) of up to 2.9% and a peak external quantum efficiency to 83% under AM1.5 simulated solar illumination. The effect of oligothienyl chain length on improving the polymer solar cell efficiency and on their optical and charge transport properties is elucidated in detail. At the same blend ratio of 1:5, the light‐harvesting capability and PCE increase markedly with increasing number of thienyl rings. The power dependencies of the solar cell parameters (including the short‐circuit current density, open‐circuit voltage, fill‐factor, and PCE) were also examined. The present work opens up an attractive avenue to developing conjugated metallopolymers with broad and strong solar energy absorptions and tunable solar cell efficiency and supports the potential of metalated conjugated polymers for efficient power generation.     

Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on Paphiopedilum Pfitz. (Orchidaceae)

The phylogeny of the genus Paphiopedilum based on the plastome is consistent with morphological analysis. However, to date, none of the analyzed nuclear markers has confirmed this. Topology incongruence among the trees of different nuclear markers concerns entire sections of the subgenus Paphiopedilum. The low-copy nuclear protein-coding gene PHYC was obtained for 22 species representing all sections and subgenera of Paphiopedilum. The nuclear-based phylogeny is supported by morphological characteristics and plastid data analysis. We assumed that an incongruence in nuclear gene trees is caused by ancestral homoploid hybridization. We present a model for inferring the phylogeny of the species despite the incongruence of the different tree topologies. Our analysis, based on six low-copy nuclear genes, is congruent with plastome phylogeny and has been confirmed by phylogenetic network analysis.     

The Periplasmic Oxidoreductase DsbA Is Required for Virulence of the Phytopathogen Dickeya solani

In bacteria, the DsbA oxidoreductase is a crucial factor responsible for the introduction of disulfide bonds to extracytoplasmic proteins, which include important virulence factors. A lack of proper disulfide bonds frequently leads to instability and/or loss of protein function; therefore, improper disulfide bonding may lead to avirulent phenotypes. The importance of the DsbA function in phytopathogens has not been extensively studied yet. Dickeya solani is a bacterium from the Soft Rot Pectobacteriaceae family which is responsible for very high economic losses mainly in potato. In this work, we constructed a D. solani dsbA mutant and demonstrated that a lack of DsbA caused a loss of virulence. The mutant bacteria showed lower activities of secreted virulence determinants and were unable to develop disease symptoms in a potato plant. The SWATH-MS-based proteomic analysis revealed that the dsbA mutation led to multifaceted effects in the D. solani cells, including not only lower levels of secreted virulence factors, but also the induction of stress responses. Finally, the outer membrane barrier seemed to be disturbed by the mutation. Our results clearly demonstrate that the function played by the DsbA oxidoreductase is crucial for D. solani virulence, and a lack of DsbA significantly disturbs cellular physiology.     

Studies of the Influence of Temperature and the Energy State of the Surface Layer of Adsorbents on Wall Effects in Soap-Based Greases

This paper presents the results of studies of wall effects in commercial soap-based greases LT4-S2 and HUTPLEX EP-2, thickened with, respectively, lithium 12-hydroxystearate and overbased calcium sulfonate. The studies were conducted in the presence of five different materials: copper alloy C11000, bronze B476, EPDM rubber and PTFE and PU thermoplastics. The influence of the energy state of the surface layer of the adsorbents and temperature (ranging from ?20 to 60 °C) on the intensity of wall effects was investigated. Changes in the structural viscosity and shear stress in the boundary layer area in the greases and the soap-based thickener’s ability to adsorb on the surfaces of the adsorbents were determined by evaluating the rheological parameter plateau modulus.     

The role of MCM-41 composition in the creation of basicity by alkali metal impregnation

Three types of mesoporous molecular sieves (silicate MCM-41, niobosilicate NbMCM-41, and aluminosilicate AlMCM-41) were impregnated with alkali metal acetates. The textural stability of the samples was estimated on the basis of XRD measurements and nitrogen adsorption/desorption methods. The acidic–basic properties of the obtained materials were tested in the cyclization of acetonylacetone and studied by FTIR spectroscopy after adsorption of methylacetylene (propyne) and pyridine. Two types of chemical reactions between mesoporous matrix and alkali metal salt/oxide were observed: the reaction between alkali metal salt and silica/silicate and the reaction between basic oxide and silanol groups or Na⁺ cations. In the first one the alkali metal silicate formation decreases from Li to Cs species and leads to the destruction of the material. The second reaction places alkali metal cations in extra framework positions, which increases from Li to Cs species and is only observed in the case of AlMCM-41 and NbMCM-41 materials. As a result of the second reaction Lewis acidity is generated. The average effect of these two interactions leads to the volcanic curve for basicity of M/AlMCM-41 and M/NbMCM-41 with the maximum for K-samples. In contrast, basicity of M/MCM-41 systematically increases from Li to Cs form since the second type of interaction does not occur for these samples.     

Adaptive perceptual color-texture image segmentation.

We propose a new approach for image segmentation that is based on low-level features for color and texture. It is aimed at segmentation of natural scenes, in which the color and texture of each segment does not typically exhibit uniform statistical characteristics. The proposed approach combines knowledge of human perception with an understanding of signal characteristics in order to segment natural scenes into perceptually/semantically uniform regions. The proposed approach is based on two types of spatially adaptive low-level features. The first describes the local color composition in terms of spatially adaptive dominant colors, and the second describes the spatial characteristics of the grayscale component of the texture. Together, they provide a simple and effective characterization of texture that the proposed algorithm uses to obtain robust and, at the same time, accurate and precise segmentations. The resulting segmentations convey semantic information that can be used for content-based retrieval. The performance of the proposed algorithms is demonstrated in the domain of photographic images, including low-resolution, degraded, and compressed images.     

Double-Headed Cationic Lipopeptides: An Emerging Class of Antimicrobials

Antimicrobial peptides (AMPs) constitute a promising tool in the development of novel therapeutic agents useful in a wide range of bacterial and fungal infections. Among the modifications improving pharmacokinetic and pharmacodynamic characteristics of natural AMPs, an important role is played by lipidation. This study focuses on the newly designed and synthesized lipopeptides containing multiple Lys residues or their shorter homologues with palmitic acid (C₁₆) attached to the side chain of a residue located in the center of the peptide sequence. The approach resulted in the development of lipopeptides representing a model of surfactants with two polar headgroups. The aim of this study is to explain how variations in the length of the peptide chain or the hydrocarbon side chain of an amino acid residue modified with C₁₆, affect biological functions of lipopeptides, their self-assembling propensity, and their mode of action.     

Influence of Soft Cocoa Butter Equivalents on Color and Other Physical Attributes of Chocolate

The physical characteristics and color of chocolate depend on the physical properties and crystallization behavior of the fat phase. In this study, the fat phase of chocolate samples contains cocoa butter from Ghana and soft cocoa butter equivalent (CBE). The laboratory-made chocolate samples were tempered at three different precrystallization temperatures (25, 27 and 29 °C), using three different concentrations of CBE (3, 5 and 7%), calculated as percentage of the chocolate. Physical characteristics of chocolate, namely thermoreographic parameters and solid fat content (SFC), were measured. The color of the chocolate was determined instrumentally, before and after thermo-cycle testing at 32/20 °C. It was found that CBE changed the melting properties of chocolate produced with cocoa butter from Ghana, which is of moderate hardness. It was determined that the optimum precrystallization temperature for chocolate mass with addition of CBE in the given conditions of measurement was 27 °C, the temperature that resulted in the best fat bloom resistance.     

Proteomic Analysis of Embryogenesis and the Acquisition of Seed Dormancy in Norway Maple (Acer platanoides L.)

The proteome of zygotic embryos of Acer platanoides L. was analyzed via high-resolution 2D-SDS-PAGE and MS/MS in order to: (1) identify significant physiological processes associated with embryo development; and (2) identify changes in the proteome of the embryo associated with the acquisition of seed dormancy. Seventeen spots were identified as associated with morphogenesis at 10 to 13 weeks after flowering (WAF). Thirty-three spots were associated with maturation of the embryo at 14 to 22 WAF. The greatest changes in protein abundance occurred at 22 WAF, when seeds become fully mature. Overall, the stage of morphogenesis was characterized by changes in the abundance of proteins (tubulins and actin) associated with the growth and development of the embryo. Enzymes related to energy supply were especially elevated, most likely due to the energy demand associated with rapid growth and cell division. The stage of maturation is crucial to the establishment of seed dormancy and is associated with a higher abundance of proteins involved in genetic information processing, energy and carbon metabolism and cellular and antioxidant processes. Results indicated that a glycine-rich RNA-binding protein and proteasome proteins may be directly involved in dormancy acquisition control, and future studies are warranted to verify this association.