Unique Patterns in Amino Acid Sequences of Aging-Related Proteins

Aging has strong genetic components and the list of genes that may regulate the aging process is collected in the GenAge database. There may be characteristic patterns in the amino acid sequences of aging-related proteins that distinguish them from other proteins and this information will lead to a better understanding of the aging process. To test this hypothesis, human protein sequences are extracted from the UniProt database and the relative frequency of every amino acid residue in aging-related proteins and the remaining proteins is calculated. The main observation is that the mean relative frequency of aspartic acid (D) is consistently higher, while the mean relative frequencies of tryptophan (W) and leucine (L) are consistently lower in aging-related proteins compared to the non-aging-related proteins for the human and four examined model organisms. It is also observed that the mean relative frequency of aspartic acid is higher, while the mean relative frequency of tryptophan is lower in pro-longevity proteins compared to anti-longevity proteins in model organisms. Finally, it is found that aging-related proteins tend to be longer than non-aging-related proteins. It is hoped that this analysis initiates further computational and experimental research to explore the underlying mechanisms of these findings.

Intercomparison on the measurement of the thoron exhalation rate from building materials

Thoron (²²⁰Rn) exhalation from building materials has become increasingly recognized as a potential source for radiation exposure in dwellings. However, contrary to radon (²²²Rn), limited information on thoron exposure is available. As a result no harmonized test procedures for determining thoron exhalation from building materials are available at present. This study is a first interlaboratory comparison of different test methods to determine the thoron exhalation and a pre-step to a harmonized standard. The purpose of this study is to compare the experimental findings from a set of three building materials that are tested, and to identify future challenges in the development of a harmonized standard.

Preparation and characterisation of ceramic-based thoron sources for thoron calibration chamber

The aim of this study is to explore the correlations between the properties of the source's material and the thoron flux produced. This means a complex procedure that involves morphological characterisation (the determination of specific surface area and pore size distribution) and thoron emanation and exhalation measurements as well. In this work, the preparation of 27 thoron sources has been carried out. Three types of ceramics with different morphological properties were used as a matrix material with three different thorium contents. Spheres were formed from the dollop, and they were fired at different temperatures (200, 600 and 900°C). The phase analysis of the samples was performed by powder X-ray diffraction. The pore size distribution was determined by mercury penetration. The thoron emanation was measured using an accumulation chamber; the measured thoron emanation coefficients were from 0.34 ± 0.03 to 7.69 ± 0.13 %. Based on the results, the preparation parameters of the thoron source optimised for the calibration procedure have been given.

Preliminary results of indoor radon survey in V4 countries

The measurements of radon activity concentration carried out in residential houses of V4 countries (Hungary, Poland and Slovakia) show that radon levels in these countries considerably exceed the world average. Therefore, the new radon data and statistical analysis are required from these four countries. Each partner chose a region in their own country, where radon concentration in residential buildings was expected to be higher. The results of the survey carried out in the period from March 2012 to May 2012 show that radon concentrations are <200 Bq m(-3) in ∼87% of cases. However, dwellings with radon concentration ∼800 Bq m(-3) were found in Poland and Slovakia. It was also found that the distribution of radon frequency follows that of houses according to the year of their construction.

Calibration of CR-39-based thoron progeny device

Radon isotopes and their progenies have proven significant role in respiratory tumour formation. In most cases, the radiological effect of one of the radon isotopes (thoron) and its progenies has been neglected together with its measurement technique; however, latest surveys proved that thoron's existence is expectable in flats and in workplace in Europe. Detectors based on different track detector measurement technologies have recently spread for measuring thoron progenies; however, the calibration is not yet completely elaborated. This study deals with the calibration of the track detector measurement method suitable for measuring thoron progenies using different devices with measurement techniques capable of measuring several progenies (Pylon AB5 and WLx, Sarad EQF 3220). The calibration factor values related to the thoron progeny monitors, the measurement uncertainty, reproducibility and other parameters were found using the calibration chamber. In the future, the effects of the different parameters (aerosol distribution, etc.) will be determined.

Preliminary results from an indoor radon thoron survey in Hungary

More than half of the radiation dose of natural origin comes from radon. However, according to some surveys in certain cases, the radiation dose originating from thoron may be considerable. Among the factors disturbing the measurement of radon, the presence of thoron may also influence the measured radon value, making the estimated radiation exposure imprecise. Thoron has previously been surveyed, mainly in Asia; however, recent surveys for some European locations have found that significant thoron concentrations also need to be considered. In this survey, several types of commercially available SSNTDs (solid-state nuclear track detectors) capable of measuring both radon and thoron were placed at the same time in 73 houses and 7 workplaces in Hungary with 3-month exposition periods. In order to measure thoron, the distance of the detector sets was fixed as 15-20 cm from the walls. The radon concentration was measured with five types of SSNTDs: NRPB, NRPB SSI, Raduet, DTPS and DRPS. The first four types had relatively good accordance (within ± 10 %), but the results of the DRPS detectors were considerably lower when compared with other detectors for radon concentrations over 100 Bq m(-3). The thoron averages were provided by two different types of detectors: Raduet and DTPS. The difference between their average results was more than 30 % and was six times the maximum values. Therefore, the thoron measurement results were judged to be erroneous, and their measurement protocol should be clearly established for future work.

MitoWheel, visualizing the human mitochondrial genome

So far researchers, web users were restricted to non-intuitive and visually poor text based databases every time they wanted to take a look on the mitochondrial DNA and find a region of interest. But with MitoWheel the situation is about to change. MitoWheel is a graphical representation of the circular human mitochondrial genome available on the web at "http://mitowheel.org":http://mitowheel.org.The human mitochondrial DNA is a 16569 basepair long, circular molecule and this very circularity is the basic idea behind MitoWheel. The mitochondrial genome can be represented with a wheel and by spinning this wheel users can quickly scan through, browse and identify the particular regions. The spinning is via click-and-drag or by using the left and right arrows in the sequence bar.The sequence used is the standard Revised Cambridge Reference Sequence. The main components of the application are a search box, a sequence bar and the wheel itself.The most important feature of the MitoWheel is its versatile search function. As an output of a query the wheel and the sequence bar stops at the searched nucleotide position or sequence and additional information (whether the nucleotide or the sequence is part of a gene or other specific region) can be seen on a pop-up window. People can search for a nucleotide position or sequence in the search box with numbers (15450, 8366-8572), with nucleotides (ATGCTAAAA), search for an encoded gene or specific region by abbreviations (atp8), genes (complex III, cytochrome b) and sequence features, even mutations (12276A) with the possible functional effects of the mutation. Selected sequences or their reverse complementary sequences can be send to the clipboard and saved.MitoWheel incorporates data on fully sequenced human mitochondrial genomes that have been deposited in the GenBank nucleotide database by different research groups. The sequence bar contains information not only about the function of specific nucleotides, but also about allele frequencies at polymorphic positions.MitoWheel was developed by human mitochondrial geneticist Gábor Zsurka, the wheel was made with Flash Professional 8.0 and the code harnessed the power of Actionscript, a scripting language designed specially for Flash. Attila Csordás is the other member of the developer group. The web application can be useful for anybody interested in human mitochondrial genetics and its biological, medical consequences.

Rapid 'glycaemic swings' induce nitrosative stress, activate poly(ADP-ribose) polymerase and impair endothelial function in a rat model of diabetes mellitus

AIM/HYPOTHESIS

Postpandrial hyperglycaemia is a significant risk factor for the development of macrovascular diseases. There is no clear agreement in the field whether these alterations result from hyperglycaemic episodes or from exaggerated alterations ('glycaemic swings') in blood glucose. We compared the effect of stable high glucose with a model of poorly maintained insulin-controlled diabetes (on average lower glucose, but with large glycaemic swings) on the development of endothelial dysfunction in rats.

METHODS

Intermediate- or long-acting insulin was used to reduce mean blood glucose levels. One group of animals had stable low glucose levels, while animals in the other group exhibited rapid changes ('swings') in their blood glucose concentration. Acetylcholine-induced endothelium-dependent vascular relaxation of the thoracic aorta was measured. Immunohistochemistry, western blot analysis and flow cytometry were used to determine nitrotyrosine formation and poly(ADP-ribose) accumulation in the aorta, in circulating leucocytes and in bone marrow cells.

RESULTS

Steady normalisation of blood glucose levels (a model of well-controlled diabetes) protected against the development of endothelial dysfunction, poly(ADP-ribose) polymerase (PARP) activation and nitrotyrosine production. However, impairment of endothelium-dependent relaxation was found in the animals undergoing glycaemic swings, even though the fructosamine levels in these animals were lower than in the untreated diabetic rats. This was associated with elevated PARP activation in the aorta and in bone marrow cells that was similar to or even more pronounced than that seen in the untreated diabetic animals.

CONCLUSIONS/INTERPRETATION

Large glycaemic swings exert deleterious cardiovascular effects in diabetes mellitus, in part via enhanced activation of the PARP pathway.

Mitochondrial transfer between eukaryotic animal cells and its physiologic role

Experiments recently reported by the Prockop laboratory show that some form of mitochondrial transfer can occur among cells in vitro and can have a physiologic role by rescuing the respiration of respiration-deficient cells. However, these results do not establish whether it was only mtDNA or whole functional mitochondria that were transferred, or if the latter, whether the mitochondria were transferred through direct cytoplasmic transport or as discrete vesicles. Two hypotheses are discussed here concerning the physiologic role of mitotransfer (the first is preferred): (a) respiration-competent mitochondria transfer from respiration-competent cells to respiration-deficient cells with damaged mitochondria (the "entropy" scenario); and (b) respiration-competent mitochondria transfer from predominantly respiration-deficient cells to respiration-competent cells, which provide a more favorable host environment (the "selfish" scenario).

Human heart mitochondria do not produce physiologically relevant quantities of nitric oxide

Previous studies raised the possibility that nitric oxide synthase is present in heart mitochondria (mtNOS) and the existence of such an enzyme became generally accepted. However, original experimental evidence is rather scarce and positive identification of the enzyme is lacking. We aimed to detect an NOS protein in human and mouse heart mitochondria and to measure the level of NO released from the organelles. Western blotting with 7 different anti-NOS antibodies failed to detect a NOS-like protein in mitochondria. Immunoprecipitation or substrate-affinity purification of the samples concentrated NOS in control preparations but not in mitochondria. Release of NO from live respiring human mitochondria was below 2 ppb after 45 min of incubation. In a bioassay system, mitochondrial suspension failed to cause vasodilation of human mammary artery segments. These results indicate that mitochondria do not produce physiologically relevant quantities of NO in the heart and are unlikely to have any physiological importance as NO donors, nor do they contain a recognizable mtNOS enzyme.

Mitochondria produce reactive nitrogen species via an arginine-independent pathway

We measured the contribution of mitochondrial nitric oxide synthase (mtNOS) and respiratory chain enzymes to reactive nitrogen species (RNS) production. Diaminofluorescein (DAF) was applied for the assessment of RNS production in isolated mouse brain, heart and liver mitochondria and also in a cultured neuroblastoma cell line by confocal microscopy and flow cytometry. Mitochondria produced RNS, which was inhibited by catalysts of peroxynitrite decomposition but not by nitric oxide (NO) synthase inhibitors. Disrupting the organelles or withdrawing respiratory substrates markedly reduced RNS production. Inhibition of complex I abolished the DAF signal, which was restored by complex II substrates. Inhibition of the respiratory complexes downstream from the ubiquinone/ubiquinol cycle or dissipating the proton gradient had no effect on DAF fluorescence. We conclude that mitochondria from brain, heart and liver are capable of significant RNS production via the respiratory chain rather than through an arginine-dependent mtNOS.

Graft derived cells with double nuclei in the penumbral region of experimental brain trauma

Recent in vitro studies showed that stem cells might fuse with mature cells or each other; however, there is no in vivo evidence for this phenomenon in the cerebral cortex. Our goal was to find evidence for cell fusion in a model of traumatic brain injury followed by grafting of embryonic cortical cells. Cold lesion protocol was applied to induce lesion of the motor cortex in adult male rats. Six days later we grafted a suspension of freshly isolated rat brain cortical cells of early embryonic stage (E14) into the penumbra area of the lesion. The grafted cell nuclei were labelled with bromodeoxyuridine (BrDU). Six days after transplantation 4,328 BrDU positive cells were observed in nine animals. 89.5% of these cells had cytoplasmic staining probably representing dead or phagocyted grafted cells. Ten percent of surviving BrDU positive cells had only one BrDU positive nucleus and negative cytoplasm, while 0.5% had two distinct nuclei, one was unlabelled and one was BrDU positive. These cells were similar in appearance and size to the astrocytes in the vicinity and expressed the astocyte specific glial fibrillaly acidic protein. Thus, these cells showed a possible sign of cell fusion in the penumbral region of the injured brain.

Mitochondrial NO and reactive nitrogen species production: Does mtNOS exist?

It is more than 10 years now that mitochondria are suspected to be sources of nitric oxide (NO). This hypothesis is intriguing since NO has multiple targets within the organelle and it is even suggested that mitochondria are the primary targets of NO in the cell. Most remarkably, nanomolar concentrations of NO can inhibit mitochondrial respiration, so even a small amount of NO in the mitochondrial matrix may regulate ATP synthesis. Therefore, the idea that mitochondria themselves are capable of NO production is an important concept in several physiological and pathological mechanisms. However, this field of research generates surprisingly few original papers and the published studies contain conflicting results. The reliability of the results is frequently questioned since they are seldom reproduced by independent investigators. Until 2003, all papers published in this field showed affirmative results but since then several studies directly challenged the existence of a mitochondrial nitric oxide synthase. The present review aims to summarize the most recent developments in mitochondrial NO production, highlights a few unsolved questions, and proposes new directions for future work in this research area.

The novel red-fluorescent probe DAR-4M measures reactive nitrogen species rather than NO

INTRODUCTION

Several fluorescent probes were designed for the measurement of nitric oxide (NO), however, questions arose regarding their specificity and sensitivity in biological samples. In the present study we tested the reaction of a novel rhodamine-based chromophore diaminorhodamine-4M (DAR-4M) with NO and other reactive nitrogen and oxygen species.

METHODS

We performed fluorometry in 96-well plates in a cell-free buffer with similar ion concentrations as the cytoplasm. Dose-response curves were generated using various NO donors and reactive nitrogen and oxygen species. The effects were compared between the red-fluorescent DAR-4M and its green-fluorescent counterpart 4-amino-5-methylamino-2',7'-difluorofluorescein (DAF-FM).

RESULTS

DAR-4M had a markedly higher fluorescence yield to NO donors than DAF-FM, while both probes had a comparable threshold of sensitivity (in the range of 0.1 mM nitroprusside). Both dyes reacted with various NO donors in a dose-dependent manner, while superoxide, hydrogen peroxide, peroxynitrite, or nitroxyl failed to change the fluorescence intensity of the probes. DAR-4M was potentiated in the presence of peroxynitrite to react with low levels of NO donors in a similar manner to DAF-FM.

DISCUSSION

We conclude that DAR-4M is a suitable red-fluorescent probe for the qualitative assessment of reactive nitrogen species production, but not specific for NO. Quantitative comparisons among samples is inappropriate since the fluorescent yield is affected by the presence of other oxidants in the sample.

?Dark? (compacted) neurons may not die through the necrotic pathway

"Dark" neurons were produced in the cortex of the rat brain by hypoglycemic convulsions. In the somatodendritic domain of each affected neuron, the ultrastructural elements, except for disturbed mitochondria, were remarkably preserved during the acute stage, but the distances between them were reduced dramatically (ultrastructural compaction). Following a 1-min convulsion period, only a few neurons were involved and their environment appeared undamaged. In contrast, 1-h convulsions affected many neurons and caused swelling of astrocytic processes and neuronal dendrites (excitotoxic neuropil). A proportion of "dark" neurons recovered the normal structure in 2 days. The non-recovering "dark" neurons were removed from the brain cortex through two entirely different pathways. In the case of 1-h convulsions, their organelles swelled, then disintegrated and finally dispersed into the neuropil through large gaps in the plasma membrane (necrotic-like removal). Following a 1-min convulsion period, the non-recovering "dark" neurons fell apart into membrane-bound fragments that retained the compacted interior even after being engulfed by astrocytes or microglial cells (apoptotic-like removal). Consequently, in contrast to what is generally accepted, the "dark" neurons produced by 1-min hypoglycemic convulsions do not die as a consequence of necrosis. As regards the case of 1-h convulsions, it is assumed that a necrotic-like removal process is imposed, by an excitotoxic environment, on "dark" neurons that previously died through a non-necrotic pathway. Apoptotic neurons were produced in the hippocampal dentate gyrus by intraventricularly administered colchicine. After the biochemical processes had been completed and the chromatin condensation in the nucleus had reached an advanced phase, the ultrastructural elements in the somatodendritic cytoplasm of the affected cells became compacted. If present in an apparently undamaged environment such apoptotic neurons were removed from the dentate gyrus through the apoptotic sequence of morphological changes, whereas those present in an impaired environment were removed through a necrotic-like sequence of morphological changes. This suggests that the removal pathway may depend on the environment and not on the death pathway, as also assumed in the case of the "dark" neurons produced by hypoglycemic convulsions.

Recovery versus death of "dark" (compacted) neurons in non-impaired parenchymal environment: light and electron microscopic observations

The formation of massively shrunken, hyperbasophilic, hyperargyrophilic and hyper-electron-dense but not apoptotic ("dark") neurons was initiated in rat brains by means of an electric-shock and two mechanical-injury paradigms that do not cause considerable parenchymal damage in the areas investigated. The rats were killed by perfusion fixation either immediately after these instantaneous initiating insults or after a survival period ranging from 40 min to 6 days. The formation of "dark" neurons was complete in less than a few minutes. In the somatodendritic domain of each "dark" neuron, all ultrastructural elements were remarkably preserved during the acute stage, apart from a dramatic reduction of the distances between them. This ultrastructural compaction was accompanied by a marked shift of cell fluid through seemingly intact plasma membrane, mainly into surrounding astrocytic elements. The majority of the "dark" neurons regained their normal morphology and staining properties (recovery) in 4 h. Thereafter, only solitary mitochondrion-derived membranous whorls in the cytoplasm reminded of a previous morphological disturbance. The dead "dark" neurons fell apart into membrane-bound fragments that retained their sharp outlines and compacted interior even after being engulfed by astrocytes or microglial cells. The latter sequence of morphological changes can not be harmonized with the prevailing assumption, according to which "dark" neurons die through the necrotic pathway. The fate of the "dark" neurons appeared to depend on the presence or absence of serious post-insult pathophysiological circumstances in their surroundings.