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Biomedical subjects

Petr Novák

Publications and source records attributed to Petr Novák.

17 recordsLinked to original sources
PubMed2006

Preparation of highly substituted 6-arylpurine ribonucleosides by Ni-catalyzed cyclotrimerization. Scope of the reaction.

Transition metal complex catalyzed cocyclotrimerization of protected alkynylpurine ribonucleosides 1 with various diynes 2 gave rise to a series of 6-arylpurine nucleosides 3 that were further deprotected to free nucleosides 4. Generally, the best yields of cyclotrimerizations were obtained with a catalytic system Ni(cod)2/2PPh(3). On the other hand, CoBr(PPh(3))3 proved to be a superior catalyst for cyclotrimerization of 1 with dipropargyl ether 2g. In addition, Ni catalysis is also suitable for direct cyclotrimerization of unprotected alkynylpurine ribonucleosides 5 to the corresponding 6-arylpurinylribosides 4.

Catalysis↗
PubMed2006

Demonstrating oxygen loss and associated structural reorganization in the lithium battery cathode Li[Ni0.2Li0.2Mn0.6]O2.

The cathode in rechargeable lithium-ion batteries operates by conventional intercalation; Li+ is extracted from LiCoO2 on charging accompanied by oxidation of Co3+ to Co4+; the process is reversed on discharge. In contrast, Li+ may be extracted from Mn4+-based solids, e.g., Li2MnO3, without oxidation of Mn4+. A mechanism involving simultaneous Li and O removal is often proposed. Here, we demonstrate directly, by in situ differential electrochemical mass spectrometry (DEMS), that O2 is evolved from such Mn4+ -containing compounds, Li[Ni(0.2)Li(0.2)Mn(0.6)]O2, on charging and using powder neutron diffraction show that O loss from the surface is accompanied by diffusion of transition metal ions from surface to bulk where they occupy vacancies created by Li removal. The composition of the compound moves toward MO(2). Understanding such unconventional Li extraction is important because Li-Mn-Ni-O compounds, irrespective of whether they contain Co, can, after O loss, store 200 mAhg(-1) of charge compared with 140 mAhg(-1) for LiCoO(2).

Journal Article↗
PubMed2006

Rechargeable LI2O2 electrode for lithium batteries.

Rechargeable lithium batteries represent one of the most important developments in energy storage for 100 years, with the potential to address the key problem of global warming. However, their ability to store energy is limited by the quantity of lithium that may be removed from and reinserted into the positive intercalation electrode, Li(x)CoO(2), 0.5 < x < 1 (corresponding to 140 mA.h g(-1) of charge storage). Abandoning the intercalation electrode and allowing Li to react directly with O(2) from the air at a porous electrode increases the theoretical charge storage by a remarkable 5-10 times! Here we demonstrate two essential prerequisites for the successful operation of a rechargeable Li/O(2) battery; that the Li(2)O(2) formed on discharging such an O(2) electrode is decomposed to Li and O(2) on charging (shown here by in situ mass spectrometry), with or without a catalyst, and that charge/discharge cycling is sustainable for many cycles.

Journal Article↗
PubMed2006

Molecular dynamics study of major urinary protein-pheromone interactions: a structural model for ligand-induced flexibility increase.

Recently, two independent (15)N NMR relaxation studies indicated that in contrast to the decreased flexibility expected for induced-fit interactions, the backbone flexibility of major urinary protein isoform I (MUP-I) slightly increased upon complex formation with its natural pheromone 2-sec-butyl-4,5-dihydrothiazol. We have investigated the subtle details of molecular interactions by molecular dynamics simulations in explicit solvent. The calculated order parameters S(2) for a free- and ligand-bound protein supply evidence that mobility in various regions of MUP-I can be directly related to small conformational changes of the free- and complexed protein resulting from modifications of the hydrogen bonding network.

Computer Simulation↗
PubMed2006

Separation of nuclear protein complexes by blue native polyacrylamide gel electrophoresis.

The nucleus is a highly structured organelle with distinct compartmentalization of specific functions. To understand the functions of these nuclear compartments, detailed description of protein complexes which form these structures is of crucial importance. We explored therefore the potential of blue native PAGE (BN-PAGE) method for the separation of nuclear protein complexes. We focused on (i) solubility and stability of nuclear complexes under conditions prerequisite for the separation by BN-PAGE, (ii) improved separation of native nuclear protein complexes using 2-D colorless native/blue native PAGE (CN-/BN-PAGE), and (iii) mass spectrometric analysis of protein complexes which were isolated directly from native 1-D or from 2-D CN/BN-PAGE gels. The suitability of BN-PAGE for nuclear proteomic research is demonstrated by the successful separation of polymerase I and polymerase II complexes, and by mass spectrometric determination of U1 small nuclear ribonucleoprotein particle composition. Moreover, practical advice for sample preparation is provided.

Amino Acid Sequence↗
PubMed2005

Cloning and molecular analysis of the regulatory factor HlMyb1 in hop (Humulus lupulus L.) and the potential of hop to produce bioactive prenylated flavonoids.

The concentrations of prenylated chalcones and bitter acids were analyzed in Czech hop varieties. The highest levels of (xanthohumol + desmethylxanthohumol) (0.97%, m/m) and of total bitter acids (17.19%, m/m) were observed for cv. Agnus. The concentration ratios of bitter acids to prenylated chalcones varied depending on the genotype, thereby suggesting genetic determination by different set(s) of structural and regulatory genes. Promoter elements of the chs_H1 gene encoding a "true"chalcone synthase, a candidate gene to co-determine the biosynthesis of prenylated chalcones, were analyzed, and several boxes for cis-regulatory elements including Myb transcription factors were discovered. A cDNA library was established from glandular tissue-enriched cones of cv. Osvald's clone 72 and used to screen for Myb regulatory elements. The cDNA of the first Myb regulatory factor from hop, called HlMyb1, was cloned and analyzed. The HlMyb1 open reading frame encodes 272 amino acids (29.8 kDa), and the protein showed highest homology to the light-regulated factor AtMyb68 from Arabidopsis thaliana within the Myb domain, whereas there was no significant homology with known MYB proteins outside this domain. Unlike AtMyb68, which is expressed in mature leaves, HlMyb1 is strongly expressed in hop inflorescences and could participate in the regulation of developmental processes involved in the production of hop cones and bioactive secondary metabolites.

Acyltransferases↗
PubMed2005

Mass spectrometric analysis of the glycosphingolipid-enriched microdomains of rat natural killer cells.

Glycosphingolipid-enriched microdomains (GEM) are membrane entities that concentrate glycosylphosphatiolylinositol(GPI)-anchored, acylated and membrane proteins important for immune receptor signaling. Using rat leukemic cell line RNK-16 we have initiated proteomic studies of microdomains in natural killer (NK) cells. Isolated plasma membranes were treated with Brij 58, or Nonidet-P40, or sodium carbonate. Extracts were separated by sucrose density gradient centrifugation into very light membrane, medium light membrane and heavy fractions, and a complete protein profile was analyzed by tandem mass spectrometry. Up to 250 proteins were unambiguously identified in each analyzed fraction. The first study of the proteome of NK cell GEM revealed several new aspects including identification of molecules not expected to be expressed in rat NK cells (e.g., NAP-22) or associated with GEM (e.g., NKR-P1, CD45, CD2). Moreover, it provided clear data consolidating controversial views concerning the occurrence of major histcompatibility complex glycoproteins and RT6.1/CD73/CD38 complex in NK cells. Our results also identified a large number of receptors as candidates for future functional studies.

Animals↗
PubMed2005

SURLAS: a new clinical grade ultrasound system for sequential or concomitant thermoradiotherapy of superficial tumors: applicator description.

A new ultrasound applicator with three-dimensional power distribution control was developed for simultaneous thermoradiotherapy. The system was named SURLAS for Scanning Ultrasound Reflector Linear Arrays System. In this paper, the hardware of the first clinical grade SURLAS applicator is described with emphasis on clinically important static acoustic characteristics and on construction aspects not reported before. Functionally, the SURLAS applicator consists of two parallel opposed ultrasound linear arrays aiming their acoustic beams to a V-shape scanning ultrasound reflector, which deflects the beams coming from opposite directions toward the treatment area. The reciprocating motion of the reflector in-between the arrays spreads the ultrasonic energy over the target area scanned. Control of power deposition over the 16 cm by 16 cm treatment window area is achieved by adjusting the power input into the transducer elements of the arrays as a function of the position of the scanning reflector. Furthermore, the arrays operate at significantly different frequencies (1.9 and 4.9 MHz) so that intensity modulation of beams of different frequencies can be exploited to adjust the depth of energy penetration. With this design, external electron or photon beams can be concurrently delivered with hyperthermia by irradiating through the applicator's body. Safety features were implemented into the applicator's design to monitor its performance during operation. A detailed description of the applicator including impedance matching circuits/filters, radiation force balance power measurements, hydrophone pressure field distribution measurements, as well as safety test results are reported.

Acoustics↗
PubMed2005

Treatment delivery software for a new clinical grade ultrasound system for thermoradiotherapy.

A detailed description of a clinical grade Scanning Ultrasound Reflector Linear Array System (SURLAS) applicator was given in a previous paper [Med. Phys. 32, 230-240 (2005)]. In this paper we concentrate on the design, development, and testing of the personal computer (PC) based treatment delivery software that runs the therapy system. The SURLAS requires the coordinated interaction between the therapy applicator and several peripheral devices for its proper and safe operation. One of the most important tasks was the coordination of the input power sequences for the elements of two parallel opposed ultrasound arrays (eight 1.5 cm x 2 cm elements/array, array 1 and 2 operate at 1.9 and 4.9 MHz, respectively) in coordination with the position of a dual-face scanning acoustic reflector. To achieve this, the treatment delivery software can divide the applicator's treatment window in up to 64 sectors (minimum size of 2 cm x 2 cm), and control the power to each sector independently by adjusting the power output levels from the channels of a 16-channel radio-frequency generator. The software coordinates the generator outputs with the position of the reflector as it scans back and forth between the arrays. Individual sector control and dual frequency operation allows the SURLAS to adjust power deposition in three dimensions to superficial targets coupled to its treatment window. The treatment delivery software also monitors and logs several parameters such as temperatures acquired using a 16-channel thermocouple thermometry unit. Safety (in particular to patients) was the paramount concern and design criterion. Failure mode and effects analysis (FMEA) was applied to the applicator as well as to the entire therapy system in order to identify safety issues and rank their relative importance. This analysis led to the implementation of several safety mechanisms and a software structure where each device communicates with the controlling PC independently of the others. In case of a malfunction in any part of the system or a violation of a user-defined safety criterion based on temperature readings, the software terminates treatment immediately and the user is notified. The software development process consisting of problem analysis, design, implementation, and testing is presented in this paper. Once the software was finished and integrated with the hardware, the therapy system was extensively tested. Results demonstrated that the software operates the SURLAS as intended with minimum risk to future patients.

Algorithms↗
PubMed2004

Heat shock protein 90 recognized as an iron-binding protein associated with the plasma membrane of HeLa cells.

Heat shock protein 90 (Hsp90) is a molecular chaperone abundant in eukaryotic cells. However, its exact role is not completely understood yet. Employing an iron-binding assay and mass spectrometric analysis, we have identified human Hsp90 as an iron-binding protein in membrane protein preparations of human HeLa cells. Western blot analysis and confocal microscopy confirmed that a portion of cellular Hsp90 is associated with the plasma membrane, but it does not seem to be expressed on the cell surface. The iron-binding assay with purified human Hsp90 confirmed iron binding by Hsp90. Thus we suggest that Hsp90 is an iron-binding protein associated with the plasma membrane.

Cell Membrane↗
PubMed2002

Non-T cell activation linker (NTAL): a transmembrane adaptor protein involved in immunoreceptor signaling.

A key molecule necessary for activation of T lymphocytes through their antigen-specific T cell receptor (TCR) is the transmembrane adaptor protein LAT (linker for activation of T cells). Upon TCR engagement, LAT becomes rapidly tyrosine phosphorylated and then serves as a scaffold organizing a multicomponent complex that is indispensable for induction of further downstream steps of the signaling cascade. Here we describe the identification and preliminary characterization of a novel transmembrane adaptor protein that is structurally and evolutionarily related to LAT and is expressed in B lymphocytes, natural killer (NK) cells, monocytes, and mast cells but not in resting T lymphocytes. This novel transmembrane adaptor protein, termed NTAL (non-T cell activation linker) is the product of a previously identified WBSCR5 gene of so far unknown function. NTAL becomes rapidly tyrosine-phosphorylated upon cross-linking of the B cell receptor (BCR) or of high-affinity Fcgamma- and Fc epsilon -receptors of myeloid cells and then associates with the cytoplasmic signaling molecules Grb2, Sos1, Gab1, and c-Cbl. NTAL expressed in the LAT-deficient T cell line J.CaM2.5 becomes tyrosine phosphorylated and rescues activation of Erk1/2 and minimal transient elevation of cytoplasmic calcium level upon TCR/CD3 cross-linking. Thus, NTAL appears to be a structural and possibly also functional homologue of LAT in non-T cells.

Adaptor Proteins, Signal Transducing↗
PubMed2002

Nuclear DNA helicase II is recruited to IFN-alpha-activated transcription sites at PML nuclear bodies.

It is known that nuclear DNA helicase II (NDH II) links CREB-binding protein directly to RNA polymerase II holoenzyme, and that this interaction is essential for gene activation by CREB. Here, we report for the first time that some NDH II/RNA helicase A is a component of promyelocytic leukemia nuclear bodies (PML NBs). An autoimmune serum specific for PML NBs was identified and used in immunoprecipitation experiments. NDH II was present in the immunoprecipitates as shown by mass spectrometry and by immunoblotting. Immunofluorescence and ultrastructural studies showed that NDH II colocalizes with a small subset of PML NBs in control cells, however, colocalizes with practically all bodies in interferon-alpha-stimulated cells. After interferon stimulation, more PML NBs were found to contain newly synthesized RNA, as indicated by bromouridine incorporation. PML NBs also contain RNA polymerase II. The association of NDH II with PML NBs was transcriptionally dependent, and NDH II was present in all bodies with nascent RNA. Blocking of mRNA synthesis caused NDH II relocalization from nucleoplasm to nucleoli. Based on the data, we suggest that NDH II recruitment to PML NBs is connected with transcriptional regulation of interferon-alpha-inducible genes attached to PML NBs.

Adenosine Triphosphatases↗
PubMed2002

Monitoring of in vitro deamidation of gliadin peptic fragment by mass spectrometry may reflect one of the molecular mechanisms taking place in celiac disease development.

Celiac disease, a chronic disorder of the small intestine, is caused by dietary gluten and is characterized by villous atrophy and local inflammation associated with infiltration of B and T lymphocytes and/or macrophages into the intestinal wall. In genetically predisposed individuals, the infiltrating cells are activated by gluten, gliadin and their proteolytic fragments and produce chemokines, cytokines and reactive radicals. The sequence of one of the macrophage-stimulatory gliadin peptic fragment was determined by mass spectrometry (MS) as VSFQQPQQQYPSSQ. The role of tissue transglutaminase (tTG) in innate immunity stimulation was studied by mass spectrometric monitoring of sequence changes in this active peptide. Two sites of glutamine deamidation in this peptide were localized by high-resolution scanning in MS/MS mode in an ion trap. A single deamidation in the parent peptide led to the complete loss of its stimulatory effect on macrophages.

Amino Acid Sequence↗
PubMed2002

Activation of macrophages by gliadin fragments: isolation and characterization of active peptide.

Celiac disease, induced by dietary gluten, is characterized by mucosal atrophy and local inflammation associated with cell infiltration and activation. Unlike other food proteins, gluten and its proteolytic fragments, besides inducing a specific immune response, were shown to activate components of innate immunity and cause, e.g., direct stimulation of TNF-alpha and IL-10 and a significant rise in NO production by peritoneal macrophages. The identity of the active fragments was established by separating the peptic digest of gliadin by RP-HPLC chromatography. The purest fraction with the highest activity was analyzed by mass spectrometry, and the gliadin peptide sequence was identified as VSFQQPQQQYPSSQ. This peptide (T) and its N- and C-terminally shortened forms (A, B, C and D, E, F) were synthesized. Peptide B (FQQPQQQYPSSQ) elicited the highest TNF-alpha, IL-10, and RANTES secretion and increase in IFN-gamma-primed NO production by mouse macrophages. In contrast, C-terminally shortened peptides had a lower ability to stimulate macrophages than the native form.

Animals↗