Overcoming sequence misalignments with weighted structural superposition

An appropriate structural superposition identifies similarities and differences between homologous proteins that are not evident from sequence alignments alone. We have coupled our Gaussian‐weighted RMSD (wRMSD) tool with a sequence aligner and seed extension (SE) algorithm to create a robust technique for overlaying structures and aligning sequences of homologous proteins (HwRMSD). HwRMSD overcomes errors in the initial sequence alignment that would normally propagate into a standard RMSD overlay. SE can generate a corrected sequence alignment from the improved structural superposition obtained by wRMSD. HwRMSD's robust performance and its superiority over standard RMSD are demonstrated over a range of homologous proteins. Its better overlay results in corrected sequence alignments with good agreement to HOMSTRAD. Finally, HwRMSD is compared to established structural alignment methods: FATCAT, secondary‐structure matching, combinatorial extension, and Dalilite. Most methods are comparable at placing residue pairs within 2 Å, but HwRMSD places many more residue pairs within 1 Å, providing a clear advantage. Such high accuracy is essential in drug design, where small distances can have a large impact on computational predictions. This level of accuracy is also needed to correct sequence alignments in an automated fashion, especially for omics‐scale analysis. HwRMSD can align homologs with low‐sequence identity and large conformational differences, cases where both sequence‐based and structural‐based methods may fail. The HwRMSD pipeline overcomes the dependency of structural overlays on initial sequence pairing and removes the need to determine the best sequence‐alignment method, substitution matrix, and gap parameters for each unique pair of homologs. Proteins 2012. © 2012 Wiley Periodicals, Inc.     

Microwave characterization of low-molecular-weight antioxidant specific biomarkers

Antioxidants play a crucial role in the life sciences, as the regulators of biochemical reactions. We studied the dielectric properties of the low-molecular weight antioxidant specific biomarkers sodium ascorbate and glutathione in solutions of different concentrations. The biomarkers are multifunctional metabolites relevant to the reactive oxygen species (ROS) scavenging system of cells. The newly developed high-Q microwave whispering-gallery-mode (WGM) dielectric resonator based technique was applied. The technique allows investigation of liquids of nanoliter volumes filled in microfluidic channel within several milliseconds. The revealed peculiarities in the dependence of permittivity on concentrations of the sodium ascorbate and glutathione solutions are explained by differences in relaxation times and loses introduced by molecules of different shapes. We suggest that this novel approach offers the potential for the detection and characterization of ROS-relevant biomarkers with millisecond-time resolution.     

Features of lettuce transgenic plants with ifn-alpha2b gene regenerated after Agrobacterium rhizogenes-mediated transformation

"Hairy" roots of lettuce Lactuca sativa and regenerated plants with interferon-alpha2b gene had been obtained via Agrobacterium rhizogenes-mediated transformation. According to the results of PCR and rt-PCR analyses the studied plants had ifn-alpha2b gene. The regenerated plants differed from the plants of wild type by elongated internodes, early flower-bearing stem formation and purple coloration of leaves in artificial illumination conditions.     

Oligomeric BAX induces mitochondrial permeability transition and complete cytochrome c release without oxidative stress

In the present study, we investigated the mechanism of cytochrome c release from isolated brain mitochondria induced by recombinant oligomeric BAX (BAX(oligo)). We found that BAX(oligo) caused a complete release of cytochrome c in a concentration- and time-dependent manner. The release was similar to those induced by alamethicin, which causes maximal mitochondrial swelling and eliminates barrier properties of the OMM. BAX(oligo) also produced large amplitude mitochondrial swelling as judged by light scattering assay and transmission electron microscopy. In addition, BAX(oligo) resulted in a strong mitochondrial depolarization. ATP or a combination of cyclosporin A and ADP, inhibitors of the mPT, suppressed BAX(oligo)-induced mitochondrial swelling and depolarization as well as cytochrome c release but did not influence BAX(oligo) insertion into the OMM. Both BAX(oligo)- and alamethicin-induced cytochrome c releases were accompanied by inhibition of ROS generation, which was assessed by measuring mitochondrial H(2)O(2) release with an Amplex Red assay. The mPT inhibitors antagonized suppression of ROS generation caused by BAX(oligo) but not by alamethicin. Thus, BAX(oligo) resulted in a complete cytochrome c release from isolated brain mitochondria in the mPT-dependent manner without involvement of oxidative stress by the mechanism requiring mitochondrial remodeling and permeabilization of the OMM.     

Dynamics of nitrite metabolism in the blood of irradiated rats

Studies of sodium nitrite metabolism and correlation between NaNO2 metabolism and methemoglobin formation in the blood of rats exposed to radiation have been carried out. It has been shown that, along with radiation-induced damage of OHb----MHb dynamic system, an increase in NaNO2 uptake rate by the blood is the factor causing intensification of methemoglobin formation in irradiated animals.     

Aeroecology: probing and modeling the aerosphere

Aeroecology is a discipline that embraces and integrates thedomains of atmospheric science, ecology, earth science, geography,computer science, computational biology, and engineering. Theunifying concept that underlies this emerging discipline isits focus on the planetary boundary layer, or aerosphere, andthe myriad of organisms that, in large part, depend upon thisenvironment for their existence. The aerosphere influences bothdaily and seasonal movements of organisms, and its effects haveboth short- and long-term consequences for species that usethis environment. The biotic interactions and physical conditionsin the aerosphere represent important selection pressures thatinfluence traits such as size and shape of organisms, whichin turn facilitate both passive and active displacements. Theaerosphere also influences the evolution of behavioral, sensory,metabolic, and respiratory functions of organisms in a myriadof ways. In contrast to organisms that depend strictly on terrestrialor aquatic existence, those that routinely use the aerosphereare almost immediately influenced by changing atmospheric conditions(e.g., winds, air density, precipitation, air temperature),sunlight, polarized light, moon light, and geomagnetic and gravitationalforces. The aerosphere has direct and indirect effects on organisms,which often are more strongly influenced than those that spendsignificant amounts of time on land or in water. Future advancesin aeroecology will be made when research conducted by biologistsis more fully integrated across temporal and spatial scalesin concert with advances made by atmospheric scientists andmathematical modelers. Ultimately, understanding how organismssuch as arthropods, birds, and bats aloft are influenced bya dynamic aerosphere will be of importance for assessing, andmaintaining ecosystem health, human health, and biodiversity.     

Evaluation of anthropogenic dose distribution amongst building walls at the Metlino area of the upper Techa River region

This paper presents the results of an effort to evaluate anthropogenic doses in bricks from old buildings located on the banks of the Techa River. The river area was contaminated in 1949–1956 as a result of radioactive waste releases by the Mayak plutonium facility (Southern Urals, Russia). Absorbed doses were determined by luminescence measurements of quartz extracted from the near-surface layers of bricks sampled in 1991–1997 from three remained buildings (a mill, a granary and a church). These buildings are located in the former residence area of Metlino, which was the settlement located closest to the release site (residents of Metlino were relocated from the contaminated river in 1956). The measured anthropogenic dose in the three buildings was found to be comparable: minimum values were equal to 0.5–0.9 Gy and maximum values amounted to about 3–4 Gy. Unfortunately, the geometry of gamma-exposure of the brick samples changed significantly in 1956 as a result of creation of an artificial reservoir downstream of the Metlinsky pond. Since luminescence data provide absorbed dose in the investigated samples accumulated over the whole period of irradiation, for interpretation of the data obtained it is important to know the exposure geometry for the period of maximal exposure, which was in the early 1950s. In 2005, archival data describing configuration of contaminated water streams and shorelines (which were the main sources of gamma-irradiation) were published. Comparison of these data with the results of the luminescence study presented here showed that the bricks with the highest thermoluminescence (TL)-based doses faced contaminated shores and were located close to them. In contrast, the bricks with lower values of measured dose were opposite to contaminated shores and/or being shielded. This demonstrates that the luminescence method allowed reconstruction of the anthropogenic dose distribution in the former settlement center. The obtained results suggest new options for further luminescence studies in Metlino aimed at the reconstruction of the external exposures of the affected population.     

Calcium-induced cytochrome c release from CNS mitochondria is associated with the permeability transition and rupture of the outer membrane

The mechanisms of Ca2+-induced release of Cytochrome c (Cyt c) from rat brain mitochondria were examined quantitatively using a capture ELISA. In 75 or 125 mm KCl-based media 1.4 micromol Ca2+/mg protein caused depolarization and mitochondrial swelling. However, this resulted in partial Cyt c release only in 75 mm KCl. The release was inhibited by Ru360, an inhibitor of the Ca2+ uniporter, and by cyclosporin A plus ADP, a combination of mitochondrial permeability transition inhibitors. Transmission electron microscopy (TEM) revealed that Ca2+-induced swelling caused rupture of the outer membrane only in 75 mm KCl. Koenig's polyanion, an inhibitor of mitochondrial porin (VDAC), enhanced swelling and amplified Cyt c release. Dextran T70 that is known to enhance mitochondrial contact site formation did not prevent Cyt c release. Exposure of cultured cortical neurons to 500 microM glutamate for 5 min caused Cyt c release into the cytosol 30 min after glutamate removal. MK-801 or CsA inhibited this release. Thus, the release of Cyt c from CNS mitochondria induced by Ca2+ in vitro as well as in situ involved the mPT and appeared to require the rupture of the outer membrane.