The Isolation and Characterization of Glycosylated Phosphoproteins from Herring Fish Bones

Past studies of bone extracellular matrix phosphoproteins such as osteopontin and bone sialoprotein have yielded important biological information regarding their role in calcification and the regulation of cellular activity. Most of these studies have been limited to proteins extracted from mammalian and avian vertebrates and nonvertebrates. The present work describes the isolation and purification of two major highly glycosylated and phosphorylated extracellular matrix proteins of 70 and 22 kDa from herring fish bones. The 70-kDa phosphoprotein has some characteristics of osteopontin with respect to amino acid composition and susceptibility to thrombin cleavage. Unlike osteopontin, however, it was found to contain high levels of sialic acid similar to bone sialoprotein. The 22-kDa protein has very different properties such as very high content of phosphoserine (∼270 Ser(P) residues/1000 amino acid residues), Ala, and Asx residues. The N-terminal amino acid sequence analysis of both the 70-kDa (NPIMA(M)ETTS(M)DSKVNPLL) and the 22-kDa (NQDMAMEASSDPEAA) fish phosphoproteins indicate that these unique amino acid sequences are unlike any published in protein databases. An enzyme-linked immunosorbent assay revealed that the 70-kDa phosphoprotein was present principally in bone and in calcified scales, whereas the 22-kDa phosphoprotein was detected only in bone. Immunohistological analysis revealed diffusely positive immunostaining for both the 70- and 22-kDa phosphoproteins throughout the matrix of the bone. Overall, this work adds additional support to the concept that the mechanism of biological calcification has common evolutionary and fundamental bases throughout vertebrate species.     

Effects of aminoglutethimide on ovarian histology in the rat

Aminoglutethimide, a corticosteroid inhibitor, administered at a daily dose of 150 mg per kg body weight, showed a dramatic interference with ovarian histology in the rat. The drug caused thinning of the germinal epithelium and disruption of the layers of the follicular cells. It also resulted in the appearance of cytoplasmic vacuoles and distortion of follicle cell nuclei. In the corpus luteum, it caused shrinkage of the lutein cells, resulting in large spaces between the cords of cells. It also arrested immature follicles at various stages of their development. Our results indicate that aminoglutethimide, by modifying ovarian structure in the rat, interferes with the ovulation process.     

Modeling Response of N Addition on C and N Allocation in Scandinavian Norway Spruce Stands

Because nitrogen is considered to be the major growth-limiting element in boreal forests, the increasing nitrogen availability from deposition should lead to increasing growth. We have tested this assumption by simulating, with a simple model, carbon and nitrogen development in seven long-term fertilization experiments in three Nordic countries. The only differences between sites in the model are climate, the ambient nitrogen deposition, nitrogen fertilization regimes, and the initial conditions at the start of the experiment. The model simulates the observed stand development well as long as nitrogen remains the limiting factor. The simulated retention of deposited nitrogen is in general low (less than 50%), whereas retention of fertilizer nitrogen is higher. This seems to imply that the higher production in the fertilized stands will not be maintained once the fertilization is stopped. The model results also indicate that the major effect of climate on site productivity is through soil processes, not tree physiology.     

Strong nucleosomes reside in meiotic centromeres of C. elegans

Recently discovered strong nucleosomes (SNs) are characterized by strongly periodical DNA sequence, with visible rather than hidden sequence periodicity. In a quest for possible functions of the SNs, it has been found that the SNs concentrate within centromere regions of A. thaliana chromosomes . They, however, have been detected in Caenorhabditis elegans as well, although the holocentric chromosomes of this species do not have centromeres. Scrutinizing the SNs of C. elegans and their distributions along the DNA sequences of the chromosomes, we have discovered that the SNs are located mainly at the ends of the chromosomes of C. elegans. This suggests that, perhaps, the ends of the chromosomes fulfill some function(s) of centromeres in this species, as also indicated by the cytogenetic studies on meiotic chromosomes in spermatocytes of C. elegans, where the end-to-end association is observed. The centromeric involvement of the SNs, also found in A. thaliana, opens new horizons for the chromosome and centromere structure studies.     

Sequence-directed Mapping of Nucleosome Positions

Abstract

A nucleosome DNA sequence probe is designed that combines recently derived RR/YY counter-phase and AA/TT in-phase periodical patterns. A simple nucleosome mapping procedure is introduced for prediction of the nucleosome positions in the sequence of interest, to serve as a guide for experimental studies of the chromatin structure.     

Immunohistochemistry in the evaluation of neovascularization in tumor xenografts

Angiogenesis, or neovascularization, is known to play an important role in the neoplastic progression leading to metastasis. CD31 or Factor VIII-related antigen (F VIII RAg) immunohistochemistry is widely used in experimental studies for quantifying tumor neovascularization in immunocompromised animal models implanted with transformed human cell lines. Quantification, however, can be affected by variations in the methodology used to measure vascularization including antibody selection, antigen retrieval (AR) pretreatment, and evaluation techniques. To examine this further, we investigated the microvessel density (MVD) and the intensity of microvascular staining among five different human tumor xenografts and a mouse syngeneic tumor using anti-CD31 and F VIII RAg immunohistochemical staining. Different AR methods also were evaluated. Maximal retrieval of CD31 was achieved using 0.5 M Tris (pH 10) buffer, while maximum retrieval of F VIII RAg was achieved using 0.05% pepsin treatment of tissue sections. For each optimized retrieval condition, anti-CD31 highlighted small vessels better than F VIII RAg. Furthermore, the MVD of CD31 was significantly greater than that of F VIII RAg decorated vessels (p<0.001). The choice of antibody and AR method has a significant affect on immunohistochemical findings when studying angiogenesis. One also must use caution when comparing studies in the literature that use different techniques and reagents.     

Construction of efficient bioelectrochemical devices: Improved electricity production from cyanobacteria (Leptolyngbia sp.) based on π-conjugated conducting polymer/gold nanoparticle composite interfaces

In this study, gold electrodes (GE) were coated with conducting polymers to obtain a high photocurrent using cyanobacteria from a novel bioelectrochemical fuel cell. For this purpose, 4-(4H-ditiheno[3,2-b:2',3'-d]pyrol-4-yl) aniline and 5-(4H-dithieno[3,2-b:2',3'-d]pyrol-4-yl) napthtalane-1-amine monomers were coated on GE by performing an electropolymerization process. After that, gold nanoparticles (AuNP) were specifically modified by 2-mercaptoethane sulfonic acid and p-aminothiophenol to attach to the electrode surface. The conducting polymers GE coat was modified with functionalized AuNP using a cross-linker. The resulting electrode structures were characterized by cyclic voltammetry and chronoamperometry under on-off illumination using a fiber optic light source. Cyanobacteria Leptolyngbia sp. was added to the GE/conducting polymer/AuNP electrode surface and stabilized by using a cellulose membrane. During the illumination, water was oxidized by the photosynthesis, and oxygen was released. The released oxygen was electrocatalytically reduced at the cathode surface and a 25 nA/cm ² photocurrent was observed in GE/ Leptolyngbia sp. After the electrode modifications, a significant improvement in the photocurrent up to 630 nA/cm ² was achieved.     

Chemical composition effects onto antimicrobial and antioxidant activities of propolis collected from different regions of Turkey

Chrysin, apigenin, flavonoids, flavanones, naringenin, ethyl oleate, 3-4-dimethoxy-cinnamic acid and 9-octadecenoic acid were the predominant components of propolis samples collected from different regions of Turkey. The extracts of P3 from Denizli-Ba?karci, P5 from Denizli and P7 from Tekirda? had effective antibacterial activities on Gram-negatives. Chrysin, which has antibacterial activity, was found to be high concentration. The extracts of P3, P2B from Aydin and P6 from Konya had much more effective antibacterial activities on Gram-positives. The total antioxidant activity increased with the increasing amount of extracts added to linoleic acid emulsion. All doses of propolis ethanol extract displayed antioxidant activity.     

Automated identification of diseases related to lymph system from lymphography data using artificial immune recognition system with fuzzy resource allocation mechanism (fuzzy-AIRS)

Artificial immune recognition system (AIRS) classification algorithm, which has an important place among classification algorithms in the field of artificial immune systems, has showed an effective and intriguing performance on the problems it was applied. AIRS was previously applied to some medical classification problems including breast cancer, Cleveland heart disease, diabetes and it obtained very satisfactory results. So, AIRS proved to be an efficient artificial intelligence technique in medical field. In this study, the resource allocation mechanism of AIRS was changed with a new one determined by fuzzy-logic. This system, named as fuzzy-AIRS was used as a classifier in the diagnosis of lymph diseases, which is of great importance in medicine. The classifications of lymph diseases dataset taken from University of California at Irvine (UCI) Machine Learning Repository were done using 10-fold cross-validation method. Reached classification accuracies were evaluated by comparing them with reported classifiers in UCI web site in addition to other systems that are applied to the related problems. Also, the obtained classification performances were compared with AIRS with regard to the classification accuracy, number of resources and classification time. While only AIRS algorithm obtained 83.138% classification accuracy, fuzzy-AIRS classified the lymph diseases dataset with 90.00% accuracy. For lymph diseases dataset, fuzzy-AIRS obtained the highest classification accuracy according to the UCI web site. Beside of this success, fuzzy-AIRS gained an important advantage over the AIRS by means of classification time. By reducing classification time as well as obtaining high classification accuracies in the applied datasets, fuzzy-AIRS classifier proved that it could be used as an effective classifier for medical problems.     

Fullerene‐based inhibitors of HIV‐1 protease

A series of Fmoc‐Phe(4‐aza‐C₆₀)‐OH of fullerene amino acid derived peptides have been prepared by solid phase peptide synthesis, in which the terminal amino acid, Phe(4‐aza‐C₆₀)‐OH, is derived from the dipolar addition to C₆₀ of the Fmoc‐Nα‐protected azido amino acids derived from phenylalanine: Fmoc‐Phe(4‐aza‐C₆₀)‐Lys₃‐OH ( 1 ), Fmoc‐Phe(4‐aza‐C₆₀)‐Pro‐Hyp‐Lys‐OH ( 2 ), and Fmoc‐Phe(4‐aza‐C₆₀)‐Hyp‐Hyp‐Lys‐OH ( 3 ). The inhibition constant of our fullerene aspartic protease PRIs utilized FRET‐based assay to evaluate the enzyme kinetics of HIV‐1 PR at various concentrations of inhibitors. Simulation of the docking of the peptide Fmoc‐Phe‐Pro‐Hyp‐Lys‐OH overestimated the inhibition, while the amino acid PRIs were well estimated. The experimental results show that C₆₀‐based amino acids are a good base structure in the design of protease inhibitors and that their inhibition can be improved upon by the addition of designer peptide sequences. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.