[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.

/pdf/cell-biology-and-molecular-basis-of-denitrification-red4l5iffz.pdf

Cell biology and molecular basis of denitrification.

基礎講座 電気泳動(Electrophoresis)

Nanomaterials, such as metal or semiconductor nanoparticles and nanorods, exhibit similar dimensions to those of biomolecules, such as proteins (enzymes, antigens, antibodies) or DNA. The integration of nanoparticles, which exhibit unique electronic, photonic, and catalytic properties, with biomaterials, which display unique recognition, catalytic, and inhibition properties, yields novel hybrid nanobiomaterials of synergetic properties and functions. This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of 2D and 3D ordered structures in solutions and on surfaces. Particular emphasis is directed to the use of biomolecule-nanoparticle (metallic or semiconductive) assemblies for bioanalytical applications and for the fabrication of bioelectronic devices.

Integrated Nanoparticle–Biomolecule Hybrid Systems: Synthesis, Properties, and Applications

Triangular silver nanoparticles (∼100 nm wide and 50 nm high) have remarkable optical properties. In particular, the peak extinction wavelength, λmax of their localized surface plasmon resonance (LSPR) spectrum is unexpectedly sensitive to nanoparticle size, shape, and local (∼10−30 nm) external dielectric environment. This sensitivity of the LSPR λmax to the nanoenvironment has allowed us to develop a new class of nanoscale affinity biosensors. The essential characteristics and operational principles of these LSPR nanobiosensors will be illustrated using the well-studied biotin−streptavidin system. Exposure of biotin-functionalized Ag nanotriangles to 100 nM streptavidin (SA) caused a 27.0 nm red-shift in the LSPR λmax. The LSPR λmax shift, ΔR/ΔRmax, versus [SA] response curve was measured over the concentration range 10-15 M < [SA] < 10-6 M. Comparison of the data with the theoretical normalized response expected for 1:1 binding of a ligand to a multivalent receptor with different sites but invariant af...

A nanoscale optical biosensor: sensitivity and selectivity of an approach based on the localized surface plasmon resonance spectroscopy of triangular silver nanoparticles.

The merging of silicon microfabrication techniques with surface functionalization biochemistry offers new exciting opportunities in developing microscopic biomedical analysis devices with unique characteristics. Micro-mechanical transducers for chemical and biosensing applications represent one possibility. Microcantilevers can transduce a chemical signal into a mechanical motion with high sensitivity. In this review we summarize how cantilever-based sensors can be operated, and their working principle is presented in few selected biosensing experiments which have been performed recently in our groups in the study of biotin–streptavidin and antigen–antibody interactions, and specific surface charge development of organic molecules. We also discuss the advantages of this novel technique as well as its potentials.

Micromechanical cantilever-based biosensors

We review the progress achieved during the recent five years in immunochemical biosensors (immunosensors) combined with nanoparticles for enhanced sensitivity. The initial part introduces antibodies as classic recognition elements. The optical sensing part describes fluorescent, luminescent, and surface plasmon resonance systems. Amperometry, voltammetry, and impedance spectroscopy represent electrochemical transducer methods; electrochemiluminescence with photoelectric conversion constitutes a widely utilized combined method. The transducing options function together with suitable nanoparticles: metallic and metal oxides, including magnetic ones, carbon-based nanotubes, graphene variants, luminescent carbon dots, nanocrystals as quantum dots, and photon up-converting particles. These sources merged together provide extreme variability of existing nanoimmunosensing options. Finally, applications in clinical analysis (markers, tumor cells, and pharmaceuticals) and in the detection of pathogenic microorganisms, toxic agents, and pesticides in the environmental field and food products are summarized.

Nanoparticle-Based Immunochemical Biosensors and Assays: Recent Advances and Challenges

Hippo effectors YAP/TAZ act as on-off mechanosensing switches by sensing modifications in extracellular matrix (ECM) composition and mechanics. The regulation of their activity has been described by a hierarchical model in which elements of Hippo pathway are under the control of focal adhesions (FAs). Here we unveil the molecular mechanism by which cell spreading and RhoA GTPase activity control FA formation through YAP to stabilize the anchorage of the actin cytoskeleton to the cell membrane. This mechanism requires YAP co-transcriptional function and involves the activation of genes encoding for integrins and FA docking proteins. Tuning YAP transcriptional activity leads to the modification of cell mechanics, force development and adhesion strength, and determines cell shape, migration and differentiation. These results provide new insights into the mechanism of YAP mechanosensing activity and qualify this Hippo effector as the key determinant of cell mechanics in response to ECM cues.

/pdf/yap-regulates-cell-mechanics-by-controlling-focal-adhesion-32l3cvez9b.pdf

YAP regulates cell mechanics by controlling focal adhesion assembly

Electrochemical biosensors - principles and applications

Popularity of graphene oxide (GO) became ballistic in the last few years – in short, it almost seems that now everyone wants to work with graphene. However, as the number of electrochemical papers about graphene grows, so is the amount of misinterpretations. Our work was mostly focused on preparation of GO and its electrochemical properties, namely catalysis. Our results show, that chemical preparation of GO by strong oxidation is very tricky. Several approaches were tested, such as different sizes of graphite particles, oxidation mixtures, even repetitive preparations under the same conditions usually resulted in different products. Another big topic are impurities which are present due to natural occurrence in graphite and some of them might be also introduced during purification processes of GO. This could also lead to often observed catalytic activity of graphene. From our observations neither selectivity nor significant electrocatalytic abilities of the reduced graphene oxide modified electrodes towards H2O2 were observed. Moreover, our results suggest that GO does not need linking molecules in order to be deposited onto the surface of the electrodes, since it attaches spontaneously and keeps its electrochemical properties. Graphene is usually reported as a superior material, but its proper description and characterization should not be underestimated.

Petr Skládal

Papers

Micromechanical cantilever-based biosensors

Nanoparticle-Based Immunochemical Biosensors and Assays: Recent Advances and Challenges

YAP regulates cell mechanics by controlling focal adhesion assembly

Electrochemical biosensors - principles and applications

About graphene oxide