Factors Influencing Compact–Extended Structure Equilibrium in Oligomers of Aβ1–40 Peptide—An Ion Mobility Mass Spectrometry Study

Oligomers formed by amyloid β (Aβ) peptide are widely believed to be the main neurotoxic agent in Alzheimer's disease. Studies discovered a broad variety of oligomeric forms, which display different levels of toxicity. Some of these forms may further assemble into mature fibrils, while other might be off-pathway from conversion to fibrils and assemble into alternative forms. To better understand a relationship between the structure and toxicity of Aβ oligomers, we require systematic characterization and classification of all possible forms, facilitating rational design of the beneficial modifiers of their activity. In previous ion mobility analysis of Aβ1–40 oligomers, we have detected the coexistence of two alternative structural forms (compact and extended) in a pool of low-order Aβ1–40 oligomers. These forms may represent two pathways of the oligomer evolution, leading either to fibrils or to off-pathway oligomers, which are potential candidates for the neurotoxic species. Here, we have analyzed the impact of incubation time, the presence of selected metal ions and the effect of a series of point mutations on mutual population of alternative forms. We have shown that a salt bridge D23K28 provides stabilization of the compact form whereas G25 is required for the existence of the extended form. We have found that binding of metal ions also stabilizes the compact form. These results improve our understanding of the possible molecular mechanism of the bifurcation of structural evolution of non-monomeric Aβ species into an off-fibril pathway, ultimately leading to the formation of potentially neurotoxic species.     

Common variants of xeroderma pigmentosum genes and prostate cancer risk

The genetic basis of prostate cancer (PC) is complex and appears to involve multiple susceptibility genes. A number of studies have evaluated a possible correlation between several NER gene polymorphisms and PC risk, but most of them evaluated only single SNPs among XP genes and the results remain inconsistent. Out of 94 SNPs located in seven XP genes (XPA–XPG) a total of 15 SNPs were assayed in 720 unselected patients with PC and compared to 1121 healthy adults. An increased risk of disease was associated with the XPD SNP, rs1799793 (Asp312Asn) AG genotype (OR = 2.60; p < 0.001) and with the AA genotype (OR = 531; p < 0.0001) compared to the control population. Haplotype analysis of XPD revealed one protective haplotype and four associated with an increased disease risk, which showed that the A allele (XPD rs1799793) appeared to drive the main effect on promoting prostate cancer risk. Polymorphism in XPD gene appears to be associated with the risk of prostate cancer.     

Active creatine kinase is present in matrix vesicles isolated from femurs of chicken embryo: Implications for bone mineralization

Proteomic analysis of matrix vesicles (MVs) isolated from 17-day-old chicken embryo femurs revealed the presence of creatine kinase. In this report we identified the enzyme functionally and suggest that the enzyme may participate in the synthesis of ATP from ADP and phosphocreatine within the lumen of these organelles. Then, ATP is converted by nucleotide hydrolyzing enzymes such as Na⁺, K⁺-ATPase, protein kinase C, or alkaline phosphatase to yield inorganic phosphate (P_i), a substrate for mineralization. Alternatively, ATP can be hydrolyzed by a nucleoside triphosphate pyrophosphatase phosphodiesterase 1 producing inorganic pyrophosphate (PP_i), a mineralization inhibitor. In addition, immunochemical evidence indicated that VDAC 2 is present in MVs that may serve as a transporter of nucleotides from the extracellular matrix. We discussed the implications of ATP production and hydrolysis by MVs as regulatory mechanisms for mineralization.     

16S rDNA Pyrosequencing Analysis of Bacterial Community in Heavy Metals Polluted Soils

Soil contamination with heavy metals is a widespread problem, especially prominent on grounds lying in the vicinity of mines, smelters, and other industrial facilities. Many such areas are located in Southern Poland; they are polluted mainly with Pb, Zn, Cd, or Cu, and locally also with Cr. As for now, little is known about most bacterial species thriving in such soils and even less about a core bacterial community—a set of taxa common to polluted soils. Therefore, we wanted to answer the question if such a set could be found in samples differing physicochemically and phytosociologically. To answer the question, we analyzed bacterial communities in three soil samples contaminated with Pb and Zn and two contaminated with Cr and lower levels of Pb and Zn. The communities were assessed with 16S rRNA gene fragments pyrosequencing. It was found that the samples differed significantly and Zn decreased both diversity and species richness at species and family levels, while plant species richness did not correlate with bacterial diversity. In spite of the differences between the samples, they shared many operational taxonomic units (OTUs) and it was possible to delineate the core microbiome of our sample set. The core set of OTUs comprised members of such taxa as Sphingomonas, Candidatus Solibacter, or Flexibacter showing that particular genera might be shared among sites ~40 km distant.     

More than just tails: intrinsic disorder in histone proteins

Many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions are very common in nature, abundantly found in all organisms, where they carry out important biological functions. The functions of these proteins complement the functional repertoire of "normal" ordered proteins, and many protein functional classes are heavily dependent on intrinsic disorder. Among these disorder-centric functions are interactions with nucleic acids and protein complex assembly. In this study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 2007 histones from 746 species. We show that all the members of the histone family are intrinsically disordered proteins. Furthermore, intrinsic disorder is not only abundant in histones, but is absolutely necessary for various histone functions, starting from heterodimerization to formation of higher order oligomers, to interactions with DNA and other proteins, and to posttranslational modifications.     

Ultrastructure of the spermatozoa of the flatworms Phaenocelis peleca and Boninia divae (Platyhelminthes, Polycladida)

The ultrastructure of spermatozoa of the acotylean Phaenocelis peleca and the cotylean Boninia divae is described. All spermatozoa are filiform and biflagellate with a 9+"1" microtubular pattern in the axoneme. Sperm characters in P. peleca follow the morphologies described for other acotyleans, with axonemes exiting the sperm shaft at the distal end and remaining in close contact with the sperm membrane. The nucleus occupies the proximal region of the shaft, and two types of dense bodies and mitochondria are located at the distal end. Unlike other members of the Cotylea, the axonemes of B. divae spermatozoa are incorporated into the sperm shaft, leaving the shaft at some distance from the distal end and then remaining free. This type of morphology is characteristic for acotyleans. Additionally, the spermatozoa of B. divae contain only one type of dense bodies plus a unique structure, which we call a central core. The nucleus in this species is unique as well; it shows periodic constrictions and rings of electron-dense granules, characters that further contribute to the distinct status of Boniniidae.     

Structure and Ultrastructure of the Endodermal Region of the Alimentary Tract in the Freshwater Shrimp Neocaridina heteropoda (Crustacea,Malacostraca)

The freshwater shrimp Neocaridina heteropoda (Crustacea, Malacostraca, Decapoda) originates from Asia and is one of the species that is widely available all over the world because it is the most popular shrimp that is bred in aquaria. The structure and the ultrastructure of the midgut have been described using X-ray microtomography, transmission electron microscopy, light and fluorescence microscopes. The endodermal region of the alimentary system in N. heteropoda consists of an intestine and a hepatopancreas. No differences were observed in the structure and ultrastructure of males and females of the shrimp that were examined. The intestine is a tube-shaped organ and the hepatopancreas is composed of two large diverticles that are divided into the blind-end tubules. Hepatopancreatic tubules have three distinct zones – proximal, medial and distal. Among the epithelial cells of the intestine, two types of cells were distinguished – D and E-cells, while three types of cells were observed in the epithelium of the hepatopancreas – F, B and E-cells. Our studies showed that the regionalization in the activity of cells occurs along the length of the hepatopancreatic tubules. The role and ultrastructure of all types of epithelial cells are discussed, with the special emphasis on the function of the E-cells, which are the midgut regenerative cells. Additionally, we present the first report on the existence of an intercellular junction that is connected with the E-cells of Crustacea.     

Transmission vs. Diffuse Transmission in Circular Dichroism: What to Choose for Probing Solid‐State Samples?

Recent advances in equipment enabled the collection of solid‐state electronic circular dichroism (ECD) spectra using the commercially available integrating sphere attachment for a regular ECD spectrometer. This accessory was designed to reduce negative factors occurring in solid‐state ECD measurements, and is, thereby, very useful for recording diffuse transmittance CD (DTCD) spectra using the pellet technique. In the present article, the operating principle of the integrating sphere and utility of the DTCD method in recording solid‐state ECD spectra is demonstrated. Based on illustrative examples, i.e., 10‐camphorsulfonic acid ammonium, cholest‐4‐en‐3‐one, (3R,4R,5S)‐oseltamivir, and (S)‐linezolid, ECD solid‐state measurements were performed by means of both transmission and diffusion methods and later compared. Selection of these compounds as models for comparative studies was made in view of their different chromophoric systems and the profound importance in the pharmaceutical industry. During the course of this work the benefits and limitations of the use of integrating sphere are presented. The final conclusion is that more relevant solid‐state spectra can be obtained by means of the DTCD method. Chirality 27:441–448, 2015. © 2015 Wiley Periodicals, Inc.     

The arterial circle of the brain,its branches and connections in selected representatives of the Antilopinae

The arterial circle of the brain, that is, the circle of Willis, and its branches in ruminants have been chiefly described in farm animals and only in selected wild species. In view of the deficit of information about this vascular region in numerous other species of the Ruminantia, the arteries of the encephalic base were analyzed in five antelope species representing different genera of the Bovidae, Antilopinae. Specimens of the following species were examined: springbuck (Antidorcas marsupialis), blackbuck (Antilope cervicapra), dik‐dik (Madoqua kirkii), saiga (Saiga tatarica), and oribi (Ourebia ourebi). Post‐autopsy material received from domestic zoological gardens was used to inject the bilateral common carotid arteries with a stained acetone solution of vinyl superchloride. When the material was polymerized, the specimens were macerated enzymatically. The process resulted in casts of arteries of the head and encephalic base on a skeletal scaffold. The investigations revealed that the bilateral components of the arterial circle of the brain, that is, the rostral cerebral artery and caudal communicating artery, arose from the division of the intracranial segment of the internal carotid artery, which emerges from the rostral epidural rete mirabile. The extracranial segment of the internal carotid artery was obliterated. In consequence of this process, the blood reaches the brain chiefly from the maxillary artery. The research proved that the arteries of the encephalic base in the Antilopinae are most similar to the vessels described in antelopes of Tragelaphus, Taurotragus, and Boselaphus genera and small domestic ruminants. However, they are different from the arterial pattern of the encephalic base in bovines and other species classified as the Bovini. J. Morphol. 276:766–771, 2015. © 2015 Wiley Periodicals, Inc.     

The SpoIIQ‐SpoIIIAH complex of Clostridium difficile controls forespore engulfment and late stages of gene expression and spore morphogenesis

Engulfment of the forespore by the mother cell is a universal feature of endosporulation. In Bacillus subtilis, the forespore protein SpoIIQ and the mother cell protein SpoIIIAH form a channel, essential for endosporulation, through which the developing spore is nurtured. The two proteins also form a backup system for engulfment. Unlike in B. subtilis, SpoIIQ of Clostridium difficile has intact LytM zinc‐binding motifs. We show that spoIIQ or spoIIIAH deletion mutants of C. difficile result in anomalous engulfment, and that disruption of the SpoIIQ LytM domain via a single amino acid substitution (H120S) impairs engulfment differently. SpoIIQ and SpoIIQ^H120S interact with SpoIIIAH throughout engulfment. SpoIIQ, but not SpoIIQ^H120S, binds Zn²⁺, and metal absence alters the SpoIIQ‐SpoIIIAH complex in vitro. Possibly, SpoIIQ^H120S supports normal engulfment in some cells but not a second function of the complex, required following engulfment completion. We show that cells of the spoIIQ or spoIIIAH mutants that complete engulfment are impaired in post‐engulfment, forespore and mother cell‐specific gene expression, suggesting a channel‐like function. Both engulfment and a channel‐like function may be ancestral functions of SpoIIQ‐SpoIIIAH while the requirement for engulfment was alleviated through the emergence of redundant mechanisms in B. subtilis and related organisms.