DNA aptamers detecting generic amyloid epitopes

Amyloids are fibrillar protein aggregates resulting from non-covalent autocatalytic polymerization of various structurally and functionally unrelated proteins. Previously we have selected DNA aptamers, which bind specifically to the in vitro assembled amyloid fibrils of the yeast prionogenic protein Sup35. Here we show that such DNA aptamers can be used to detect SDS-insoluble amyloid aggregates of the Sup35 protein, and of some other amyloidogenic proteins, including mouse PrP, formed in yeast cells. The obtained data suggest that these aggregates and the Sup35 amyloid fibrils assembled in vitro possess common conformational epitopes recognizable by aptamers. The described DNA aptamers may be used for detection of various amyloid aggregates in yeast and, presumably, other organisms.     

Precursors of HLDF differentiation factor and ribosomal protein RPS21 have a common N-terminal sequence

The mature differentiation factor HLDF, isolated from culture fluid, comprises 54 aa, whereas the open reading frame of mRNA encodes a 97-aa protein. We presumed that the protein translation begins from the first ATG codon, whose environment mostly meets the requirements for the initiation point. Two more ATG triplets are localized in positions 48-50 and 100-102, i.e., in the area preceding the cDNA fragment that encodes the N-terminal fragment of the mature protein. The mRNAs of HLDF and the S21 ribosomal protein have previously been shown to be highly homologous, and, therefore, their differences appear to be derived from two point deletions in the cDNA of the HLDF-encoding sequence (a G residue in position 112 and a C residue in position 224). As a result, the mature differentiation factor and RPS21 may be the products of translation from different open reading frames, the differentiation factor may be synthesized in the cell as a precursor, and its N-terminal sequence may be identical to that of RPS21. To test this hypothesis, we prepared recombinant RPS21 and the polyclonal antibodies to HLDF, full-size RPS21, and the C-terminal RPS21 peptide. Immunochemical staining by specially produced antibodies of native HL-60 cells and the same cells brought into apoptosis or differentiation confirmed that the precursor of the differentiation factor and the ribosomal S21 protein have a common N-terminal sequence and different cellular localizations. Neither an intron-containing gene nor a pseudogene with the nucleotide sequence corresponding to the HLDF cDNA was detected in the human genome or in the HL-60 cell line genome. On the basis of these facts, we propose a hypothesis of the molecular mechanism of the HLDF mRNA biosynthesis by means of posttranslational modifications of pre-mRNA of RPS21. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 2; see also http://www.maik.ru.     

The Effects of Acute and Chronic Infusions of Dexamethasone on Audiogenic Seizures and Catalepsy in Rats of Krushinsky–Molodkina and “0” Strains

Journal of Evolutionary Biochemistry and Physiology - Dexamethasone is a synthetic glucocorticosteroid with anti–inflammatory and immunosuppressive effects. In order to identify new targets...     

State of protein B23/nucleophosmin in brain cells

Protein B23/nucleophosmin is a polyfunctional protein existing in cells in numerous structural forms. In this work, for the immunochemical analysis of nucleophosmin we used the antibodies specific to different forms of nucleophosmin, namely, antibodies selectively revealing monomers of all the known forms of this protein and antibodies specific only to isoform B23.1. Homogenates of different rat tissues such as the brain, liver, kidney, lung and heart were used, as well as nuclei from liver and brain cells. For the first time, we show that the structural state of nucleophosmin in brain differs from its state in other tissues, including the liver that is enriched with nucleophosmin. It was revealed that on immunoblots of brain homogenates not only monomeric form of nucleophosmin but also unique SDS-resistant oligomeric forms were detected in the SDS-PAGE. Analysis of nucleophosmin in the cerebellum, cortex, amygdala, brainstem, and hippocampus showed that most enriched with nucleophosmin were hippocampus and cerebellum; on their immunoblots SDS-resistant oligomeric forms of nucleophosmin dominated. Using immunochemical analysis of the protein in primary cultures of cerebellum glial cells and neurons, significant structural differences of nucleophosmin in proliferating glial cells and non-proliferating neurons were revealed for the first time. It was found also that the nucleophosmin content in glial cells is much higher than in neurons and that the main forms of protein B23 in glial cells on immunoblots are the SDS-resistant oligomers, while a monomeric form was present in much smaller quantities. In contrast to glial cells, neurons did not contain such oligomers. In neurons, only trace amounts of a monomeric form of nucleophosmin were found, which were undetectable by the antibodies specific to isoform B23.1.     

Heat-shock responsive genes identified and validated in Atlantic cod (Gadus morhua) liver, head kidney and skeletal muscle using genomic techniques

Background

The Mongolian gerbils are a good model to mimic the Helicobacter pylori -associated pathogenesis of the human stomach. In the current study the gerbil-adapted strain B8 was completely sequenced, annotated and compared to previous genomes, including the 73 supercontigs of the parental strain B128.

Results

The complete genome of H. pylori B8 was manually curated gene by gene, to assign as much function as possible. It consists of a circular chromosome of 1,673,997 bp and of a small plasmid of 6,032 bp carrying nine putative genes. The chromosome contains 1,711 coding sequences, 293 of which are strain-specific, coding mainly for hypothetical proteins, and a large plasticity zone containing a putative type-IV-secretion system and coding sequences with unknown function. The cag -pathogenicity island is rearranged such that the cag A-gene is located 13,730 bp downstream of the inverted gene cluster cag B- cag 1. Directly adjacent to the cag A-gene, there are four hypothetical genes and one variable gene with a different codon usage compared to the rest of the H. pylori B8-genome. This indicates that these coding sequences might be acquired via horizontal gene transfer. The genome comparison of strain B8 to its parental strain B128 delivers 425 unique B8-proteins. Due to the fact that strain B128 was not fully sequenced and only automatically annotated, only 12 of these proteins are definitive singletons that might have been acquired during the gerbil-adaptation process of strain B128.

Conclusion

Our sequence data and its analysis provide new insight into the high genetic diversity of H. pylori -strains. We have shown that the gerbil-adapted strain B8 has the potential to build, possibly by a high rate of mutation and recombination, a dynamic pool of genetic variants (e.g. fragmented genes and repetitive regions) required for the adaptation-processes. We hypothesize that these variants are essential for the colonization and persistence of strain B8 in the gerbil stomach during inflammation.     

Formation of amyloid-like fibrillar structures and destruction of fibroblasts of the Tenon’s capsule in progressive myopia due to resistance of the pigment epithelium-derived factor to restricted proteolysis

We have previously shown that, normally, two forms of the pigment epithelium-derived factor (PEDF) with molecular weights of 50 and 45 kDa are present in the Tenon??s capsule in equal amounts. These forms represent the full-length protein and a product of restricted proteolysis of PEDF. In persons with myopia, the full-length uncleaved factor was predominantly detected, which correlated with the disturbance of collagen fiber formation. An immunohistochemical study of the Tenon??s capsule using polyclonal antibodies to PEDF showed that, in the control group, the factor is localized solely inside fibroblasts, whereas in patients with myopia, PEDF is distributed outside the cell as a halo around destroyed fibroblasts. It was shown in the present work using atomic force microscopy and immunodot assay with antibodies specific to amyloid fibrils that only the full-length PEDF is capable of forming amyloid-like fibrillar structures. The accumulation of fibrils leads to the destruction of fibroblasts and is a cause of changes in the biochemical composition and morphological structure of the Tenon??s capsule in myopia.     

Laboratory rat selection for the trait “the absence of audiogenic seizure proneness”

The hybrids between Krushinsky-Molodkina (KM) inbred strain, selected for high predisposition to audiogenic epilepsy (AE), and Wistar rats non-prone to audiogenic seizure were the initial population for selection. Rats were selected for the trait ??the absence of audiogenic seizure proneness??. The creation of such strain in which the significant proportion of animals develop no AE in response to sound and share partly the genetic background of the KM strain is very important for the correct use of KM strain as the laboratory model of seizure states. As alleles which determine the AE proneness are recessive the selection for the ??opposite?? trait proceeds necessarily slow.     

The Impact of Power on Humanity: Self-Dehumanization in Powerlessness

Power gives people the ability to control themselves and their environment, and this control is considered a fundamental human need. We investigated whether experiencing powerlessness induces the experience of self-dehumanization using three methods: priming, role-playing, and cueing. People in a position of low power viewed themselves (Experiments 1–3) as less human relative to people in a position of high power; furthermore, people with low power believed that they were viewed as less human by others as well (Experiments 2–3). In all of the experiments, human nature traits were most negatively affected by powerlessness in self-perception judgments, and uniquely human traits were most negatively affected by powerlessness in meta-perception judgments. Furthermore, the powerless believed they were viewed as less human not only by the powerful people but also the outside observers of the power dynamic. Self-dehumanization also appears to be a consequence of powerlessness rather than an incidental result of a change in mood or a negative self-view. Our findings are an important extension of previous work on the adverse effects of powerlessness and dehumanization.     

Synthetic peptides -- analogs of biologically active fragment of the differentiation factor from HL-60 cells show radioprotective and adaptogenic activities

It was shown that the addition of synthetic six-membered peptide (HLDF-6) and its Tyr-analog (HLDF-Y) to cultural medium significantly increased the survival of cells HL-60, treated by cold shock. The prophylactic administration of HDLF-Y (1 mg/kg, 4 hours prior to applied actions) decreased the response of hypothalamushypophysis-adrenal glands system and sympathicoadrenal system of rat males on supercooling and also increased the resistance of mouse males to supercooling and X-irradiation. In the experiences with females HDLF-Y did not show the similar biological activity.     

Intermale aggression in mice,selected for the cognitive trait

The data are presented on intermale aggression in mice which were selected for high scores of cognitive trait (the ability for extrapolation of movement direction) in comparison to the data of control mice performance. The changes in aggression level in the course of selection are presumably connected with anxiety level which also changed during selection generations.