I read this book the same weekend that the Packers took on the Rams, and the experience of the latter event, obviously, colored my judgment. Although I abhor anything that smacks of being a handbook (like, \"How to Earn a Merit Badge in Neurosurgery\") because too many volumes in biomedical science already evince a boyscout-like approach, I must confess that parts of this volume are fast, scholarly, and significant, with certain reservations. I like parts of this well-illustrated book because Dr. Sj6strand, without so stating, develops certain subjects on technique in relation to the acquisition of judgment and sophistication. And this is important! So, given that the author (like all of us) is somewhat deficient in some areas, and biased in others, the book is still valuable if the uninitiated reader swallows it in a general fashion, realizing full well that what will be required from the reader is a modulation to fit his vision, propreception, adaptation and response, and the kind of problem he is undertaking. A major deficiency of this book is revealed by comparison of its use of physics and of chemistry to provide understanding and background for the application of high resolution electron microscopy to problems in biology. Since the volume is keyed to high resolution electron microscopy, which is a sophisticated form of structural analysis, but really morphology in a modern guise, the physical and mechanical background of The instrument and its ancillary tools are simply and well presented. The potential use of chemical or cytochemical information as it relates to biological fine structure , however, is quite deficient. I wonder when even sophisticated morphol-ogists will consider fixation a reaction and not a technique; only then will the fundamentals become self-evident and predictable and this sine qua flon will become less mystical. Staining reactions (the most inadequate chapter) ought to be something more than a technique to selectively enhance contrast of morphological elements; it ought to give the structural addresses of some of the chemical residents of cell components. Is it pertinent that auto-radiography gets singled out for more complete coverage than other significant aspects of cytochemistry by a high resolution microscopist, when it has a built-in minimal error of 1,000 A in standard practice? I don't mean to blind-side (in strict football terminology) Dr. Sj6strand's efforts for what is \"routinely used in our laboratory\"; what is done is usually well done. It's just that …

Methods in Enzymology.

This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix. There is now a complete MolProbity mirror site at http://molprobity.manchester.ac.uk. GitHub serves our open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria. Coordinate output after Asn/Gln/His "flip" correction is now more idealized, since the post-refinement step has apparently often been skipped in the past. Two distinct sets of heavy-atom-to-hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron-cloud-center positions suitable for X-ray crystallography and one for nuclear positions. New validations include messages at input about problem-causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality-filtered residues in a new reference dataset, the CaBLAM Cα-CO virtual-angle analysis of backbone and secondary structure for cryoEM or low-resolution X-ray, and flagging of the very rare cis-nonProline and twisted peptides which have recently been greatly overused. Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity's unique all-atom clashscore.

/pdf/molprobity-more-and-better-reference-data-for-improved-all-3pdc7vb80p.pdf

MolProbity: More and better reference data for improved all-atom structure validation.

Microbes play key geoactive roles in the biosphere, particularly in the areas of element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, and soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic associations with each other and 'higher organisms', can contribute actively to geological phenomena, and central to many such geomicrobial processes are transformations of metals and minerals. Microbes have a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Such mechanisms are important components of natural biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences in a human context. Bioremediation is the application of biological systems to the clean-up of organic and inorganic pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline or colloidal forms, and these are relevant to the development of novel biomaterials for technological and antimicrobial purposes. On the negative side, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social and economic consequences. The ubiquity and importance of microbes in biosphere processes make geomicrobiology one of the most important concepts within microbiology, and one requiring an interdisciplinary approach to define environmental and applied significance and underpin exploitation in biotechnology.

http://dzumenvis.nic.in/Physiology/pdf/Metals,%20minerals%20and%20microbes.pdf

Metals, minerals and microbes: geomicrobiology and bioremediation

The X-ray structure of the heterodimeric Ni–Fe hydrogenase from Desulfovibrio gigas, the enzyme responsible for the metabolism of molecular hydrogen, has been solved at 2.85 A resolution. The active site, which appears to contain, besides nickel, a second metal ion, is buried in the 60K subunit. The 28K subunit, which coordinates one [3Fe–4S] and two [4Fe–4S] clusters, contains an amino-terminal domain with similarities to the redox protein flavodoxin. The structure suggests plausible electron and proton transfer pathways.

Crystal structure of the nickel–iron hydrogenase from Desulfovibrio gigas

The design of advanced, nanostructured materials at the molecular level is of tremendous interest for the scientific and engineering communities because of the broad application of these materials in the biomedical field. Among the available techniques, the layer-by-layer assembly method introduced by Decher and co-workers in 1992 has attracted extensive attention because it possesses extraordinary advantages for biomedical applications: ease of preparation, versatility, capability of incorporating high loadings of different types of biomolecules in the films, fine control over the materials’ structure, and robustness of the products under ambient and physiological conditions. In this context, a systematic review of current research on biomedical applications of layer-by-layer assembly is presented. The structure and bioactivity of biomolecules in thin films fabricated by layer-by-layer assembly are introduced. The applications of layer-bylayer assembly in biomimetics, biosensors, drug delivery, protein and cell adhesion, mediation of cellular functions, and implantable materials are addressed. Future developments in the field of biomedical applications of layer-by-layer assembly are also discussed.

/pdf/biomedical-applications-of-layer-by-layer-assembly-from-1i20r8iian.pdf

Biomedical Applications of Layer‐by‐Layer Assembly: From Biomimetics to Tissue Engineering

The buildup of layer-by-layer assemblies onto gold surfaces from water-soluble charged polyelectrolytes and proteins is examined using quartz crystal microgravimetry (QCM) and electrochemical techniques. Polyelectrolytes such as poly(styrenesulfonate) and poly(ester sulfonic acid) (Eastman AQ-29D polymer) adsorb spontaneously onto gold, contrary to poly(ethyleneimine). From the modification of the gold surface with a thiol and specific adsorption of polymers under polarization conditions, it is concluded that the hydrophobicity of the gold surface seems to be a determining factor in the adsorption process. Alternate adsorption onto gold resonators first coated with AQ-29D polymer gives stable multilayer films in the case of positively charged lysozyme (pI = 11) or polyheme Desulfovibrio vulgaris Hildenborough cytochrome c3 (pI = 10.5). QCM frequency changes with the number of adsorption steps suggest that a linear increase in film mass occurs. Desulfomicrobium norvegicum polyheme cytochrome c3 (pI = 7), w...

Buildup of polyelectrolyte-protein multilayer assemblies on gold electrodes. Role of the hydrophobic effect.

Current—potential responses for a tetrahemic protein: a method of determining the individual half-wave potentials of cytochrome c3 from desulfovibrio desulfuricans strain Norway

Electrochemical behavior of c-type cytochromes at clay-modified carbon electrodes: a model for the interaction between proteins and soils

Hydrogen uptake and evolution reactions have been electrochemically measured using a glassy carbon electrode modified by a coating made of whole Desulfovibrio vulgaris Hildenborough cells. High cathodic and anodic catalytic currents have been obtained using methyl viologen as a mediator, which are reflecting hydrogenase activity inside the bacterial cell, in the production and uptake of hydrogen, respectively. The influence of various parameters, such as pH, ionic strength and nature of the mediator on the catalytic current values has been studied. An original strategy has been proposed in order to specify and understand the location of the hydrogenase activity. CV experiments have been performed using cell fractions of Desulfovibrio vulgaris Hildenborough, i. e., periplasmic, membrane and cytoplasmic fractions, respectively. Comparison has been made between the hydrogenase activities obtained from the electrochemical data in each cellular fraction and those measured using the pure isolated hydrogenases located in the different spaces of the cell.

Hydrogenase Activity Control at Desulfovibrio vulgaris Cell‐Coated Carbon Electrodes: Biochemical and Chemical Factors Influencing the Mediated Bioelectrocatalysis

Pierre Bianco

Papers

Buildup of polyelectrolyte-protein multilayer assemblies on gold electrodes. Role of the hydrophobic effect.

Current—potential responses for a tetrahemic protein: a method of determining the individual half-wave potentials of cytochrome c3 from desulfovibrio desulfuricans strain Norway

Electrochemical behavior of c-type cytochromes at clay-modified carbon electrodes: a model for the interaction between proteins and soils

Hydrogenase Activity Control at Desulfovibrio vulgaris Cell‐Coated Carbon Electrodes: Biochemical and Chemical Factors Influencing the Mediated Bioelectrocatalysis

Correlations studies between structural and redox properties of cytochromes C3