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971.
Proskurnin MA Zhidkova TV Volkov DS Sarimollaoglu M Galanzha EI Mock D Nedosekin DA Zharov VP 《Cytometry. Part A》2011,79(10):834-847
Recently, photoacoustic (PA) flow cytometry (PAFC) has been developed for in vivo detection of circulating tumor cells and bacteria targeted by nanoparticles. Here, we propose multispectral PAFC with multiple dyes having distinctive absorption spectra as multicolor PA contrast agents. As a first step of our proof-of-concept, we characterized high-speed PAFC capability to monitor the clearance of three dyes (Indocyanine Green [ICG], Methylene Blue [MB], and Trypan Blue [TB]) in an animal model in vivo and in real time. We observed strong dynamic PA signal fluctuations, which can be associated with interactions of dyes with circulating blood cells and plasma proteins. PAFC demonstrated enumeration of circulating red and white blood cells labeled with ICG and MB, respectively, and detection of rare dead cells uptaking TB directly in bloodstream. The possibility for accurate measurements of various dye concentrations including Crystal Violet and Brilliant Green were verified in vitro using complementary to PAFC photothermal (PT) technique and spectrophotometry under batch and flow conditions. We further analyze the potential of integrated PAFC/PT spectroscopy with multiple dyes for rapid and accurate measurements of circulating blood volume without a priori information on hemoglobin content, which is impossible with existing optical techniques. This is important in many medical conditions including surgery and trauma with extensive blood loss, rapid fluid administration, and transfusion of red blood cells. The potential for developing a robust clinical PAFC prototype that is safe for human, and its applications for studying the liver function are further highlighted. 相似文献
972.
Structural knowledge about protein-protein interactions can provide insights to the basic processes underlying cell function. Recent progress in experimental and computational structural biology has led to a rapid growth of experimentally resolved structures and computationally determined near-native models of protein-protein interactions. However, determining whether a protein-protein interaction is physiological or it is the artifact of an experimental or computational method remains a challenging problem. In this work, we have addressed two related problems. The first problem is distinguishing between the experimentally obtained physiological and crystal-packing protein-protein interactions. The second problem is concerned with the classification of near-native and inaccurate docking models. We first defined a universal set of interface features and employed a support vector machines (SVM)-based approach to classify the interactions for both problems, with the accuracy, precision, and recall for the first problem classifier reaching 93%. To improve the classification, we next developed a semi-supervised learning approach for the second problem, using transductive SVM (TSVM). We applied both classifiers to a commonly used protein docking benchmark of 124 complexes. We found that while we reached the classification accuracies of 78.9% for the SVM classifier and 80.3% for the TSVM classifier, improving protein-docking methods by model re-ranking remains a challenging problem. 相似文献
973.
Ziganshin R Arapidi G Azarkin I Zaryadieva E Alexeev D Govorun V Ivanov V 《Journal of Proteomics》2011,74(5):595-606
This report describes a new method for desorption of low-molecular weight (LMW) peptides from abundant blood proteins for use in subsequent mass spectrometry analyses. Heating of diluted blood serum to 98°C for 15min resulted in dissociation of LMW peptides from the most abundant blood proteins. Application of blood plasma/serum fractionation using magnetic beads with a functionalized surface followed by heating of the resultant fractions significantly increases the number of LMW peptides detected by MALDI-TOF MS, enhances the general reproducibility of mass spectrometry profiles and considerably increases the number of identified blood serum peptides by LC-MS/MS using an Agilent 6520 Accurate-Mass Q-TOF. 相似文献
974.
ten Hove CA de Jong M Lapin D Andel A Sanchez-Perez GF Tarutani Y Suzuki Y Heidstra R van den Ackerveken G 《PloS one》2011,6(4):e19028
Receptor-like kinases (RLKs) constitute a large family of signal perception molecules in Arabidopsis. The largest group of RLKs is the leucine-rich repeat (LRR) class that has been described to function in development and defense. Of these, CLAVATA1 (CLV1) and ERECTA (ER) receptors function in maintaining shoot meristem homeostasis and organ growth, but LRR RLKs with similar function in the root remain unknown. For the interaction of Arabidopsis with the oomycete pathogen Hyaloperonospora arabidopsidis the involvement of LRR RLKs has not been demonstrated. A set of homozygous T-DNA insertion lines mutated in LRR RLKs was investigated to assess the potential role of these receptors in root meristem maintenance and compatibility. One mutant line, rlk902, was discovered that showed both reduced root growth and resistance to downy mildew in a recessive manner. The phenotypes of this mutated line could not be rescued by complementation, but are nevertheless linked to the T-DNA insertion. Microarray studies showed that gene expression spanning a region of approximately 84 kb upstream of the mutated gene was downregulated. The results suggest T-DNA mediated trans-repression of multiple genes upstream of the RLK902 locus links both phenotypes. 相似文献
975.
Jeanguenin L Lara-Núñez A Rodionov DA Osterman AL Komarova NY Rentsch D Gregory JF Hanson AD 《Functional & integrative genomics》2012,12(1):25-34
The transporter(s) that mediate uptake of nicotinate and its N-methyl derivative trigonelline are not known in plants, and certain mammalian nicotinate transporters also remain unidentified.
Potential candidates for these missing transporters include proteins from the ubiquitous NiaP family. In bacteria, niaP genes often belong to NAD-related regulons, and genetic evidence supports a role for Bacillus subtilis and Acinetobacter baumannii NiaP proteins in uptake of nicotinate or nicotinamide. Other bacterial niaP genes are, however, not in NAD-related regulons but cluster on the chromosome with choline-related (e.g., Ralstonia solanacearum and Burkholderia xenovorans) or thiamin-related (e.g., Thermus thermophilus) genes, implying that they might encode transporters for these compounds. Radiometric uptake assays using Lactococcus lactis cells expressing NiaP proteins showed that B. subtilis, R. solanacearum, and B. xenovorans NiaP transport nicotinate via an energy-dependent mechanism. Likewise, NiaP proteins from maize (GRMZM2G381453, GRMZM2G066801,
and GRMZM2G081774), Arabidopsis (At3g13050), and mouse (SVOP) transported nicotinate; the Arabidopsis protein also transported trigonelline. In contrast, T. thermophilus NiaP transported only thiamin. None of the proteins tested transported choline or the thiazole and pyrimidine products of
thiamin breakdown. The maize and Arabidopsis NiaP proteins are the first nicotinate transporters reported in plants, the Arabidopsis protein is the first trigonelline transporter, and mouse SVOP appears to represent a novel type of mammalian nicotinate transporter.
More generally, these results indicate that specificity for nicotinate is conserved widely, but not absolutely, among pro-
and eukaryotic NiaP family proteins. 相似文献
976.
977.
Permyakov SE Zernii EY Knyazeva EL Denesyuk AI Nazipova AA Kolpakova TV Zinchenko DV Philippov PP Permyakov EA Senin II 《Amino acids》2012,42(4):1435-1442
Recoverin belongs to the family of intracellular Ca2+-binding proteins containing EF-hand domains, neuronal calcium sensors (NCS). In photoreceptor outer segments, recoverin is
involved into the recovery of visual cycle via Ca2+-dependent interaction with disk membranes and inhibition of rhodopsin kinase. The function of a conservative within NCS family
Cys residue in the inactive EF-loop 1 remains unclear, but previous study has shown its vulnerability to oxidation under mild
oxidizing conditions. To elucidate the influence of oxidation of the conservative Cys39 in recoverin the properties of its
C39D mutant, mimicking oxidative conversion of Cys39 into sulfenic, sulfinic or sulfonic acids have been studied using intrinsic
fluorescence, circular dichroism, and equilibrium centrifugation methods. The C39D substitution results in essential changes
in structural, physico-chemical and physiological properties of the protein: it reduces α-helical content, decreases thermal
stability and suppresses protein affinity for photoreceptor membranes. The latter effect precludes proper functioning of the
Ca2+-myristoyl switch in recoverin. The revealed significance of oxidation state of Cys39 for maintaining the protein functional
status shows that it may serve as redox sensor in vision and suggests an explanation of the available data on localization
and light-dependent translocation of recoverin in rod photoreceptors. 相似文献
978.
Falk M Andoralov V Blum Z Sotres J Suyatin DB Ruzgas T Arnebrant T Shleev S 《Biosensors & bioelectronics》2012,37(1):38-45
Here we present unequivocal experimental proof that microscale cofactor- and membrane-less, direct electron transfer based enzymatic fuel cells do produce significant amounts of electrical energy in human lachrymal liquid (tears). 100 μm diameter gold wires, covered with 17 nm gold nanoparticles, were used to fashion three-dimensional nanostructured microelectrodes, which were biomodified with Corynascus thermophilus cellobiose dehydrogenase and Myrothecium verrucaria bilirubin oxidase as anodic and cathodic bioelements, respectively. The following characteristics of miniature glucose/oxygen biodevices operating in human tears were registered: 0.57 V open-circuit voltage, about 1 μW cm(-2) maximum power density at a cell voltage of 0.5 V, and more than 20 h operational half-life. Theoretical calculations regarding the maximum recoverable electrical energy can be extracted from the biofuel and the biooxidant, glucose and molecular oxygen, each readily available in human lachrymal liquid, fully support our belief that biofuel cells can be used as electrical power sources for so called smart contact lenses. 相似文献
979.
Jeffrey A. Deskus Douglas D. Dischino Ronald J. Mattson Jonathan L. Ditta Michael F. Parker Derek J. Denhart Dmitry Zuev Hong Huang Richard A. Hartz Vijay T. Ahuja Henry Wong Gail K. Mattson Thaddeus F. Molski James E. Grace Larisa Zueva Julia M. Nielsen Heidi Dulac Yu-Wen Li Mary Guaraldi Michael Azure John E. Macor 《Bioorganic & medicinal chemistry letters》2012,22(21):6651-6655
Based on a favorable balance between CRF-R1 affinity, lipophilicity and metabolic stability, compound 10 was evaluated for potential development as PET radioligand. Compound [18F]10 was prepared with high radiochemical purity and showed promising binding properties in rat brain imaging experiments. 相似文献
980.
Guryanov SG Selivanova OM Nikulin AD Enin GA Melnik BS Kretov DA Serdyuk IN Ovchinnikov LP 《PloS one》2012,7(5):e36969
YB-1, a multifunctional DNA- and RNA-binding nucleocytoplasmic protein, is involved in the majority of DNA- and mRNA-dependent events in the cell. It consists of three structurally different domains: its central cold shock domain has the structure of a β-barrel, while the flanking domains are predicted to be intrinsically disordered. Recently, we showed that YB-1 is capable of forming elongated fibrils under high ionic strength conditions. Here we report that it is the cold shock domain that is responsible for formation of YB-1 fibrils, while the terminal domains differentially modulate this process depending on salt conditions. We demonstrate that YB-1 fibrils have amyloid-like features, including affinity for specific dyes and a typical X-ray diffraction pattern, and that in contrast to most of amyloids, they disassemble under nearly physiological conditions. 相似文献