Bioinorganic Chemistry

This book covers material that could be included in a one-quarter or one-semester course in bioinorganic chemistry for graduate students and advanced undergraduate students in chemistry or biochemistry. We believe that such a course should provide students with the background required to follow the research literature in the field. The topics were chosen to represent those areas of bioinorganic chemistry that are mature enough for textbook presentation. Although each chapter presents material at a more advanced level than that of bioinorganic textbooks published previously, the chapters are not specialized review articles. What we have attempted to do in each chapter is to teach the underlying principles of bioinorganic chemistry as well as outlining the state of knowledge in selected areas. We have chosen not to include abbreviated summaries of the inorganic chemistry, biochemistry, and spectroscopy that students may need as background in order to master the material presented. We instead assume that the instructor using this book will assign reading from relevant sources that is appropriate to the background of the students taking the course. For the convenience of the instructors, students, and other readers of this book, we have included an appendix that lists references to reviews of the research literature that we have found to be particularly useful in our courses on bioinorganic chemistry

Positive regulation of meiotic DNA double-strand break formation by activation of the DNA damage checkpoint kinase Mec1(ATR)

During meiosis, formation and repair of programmed DNA double-strand breaks (DSBs) create genetic exchange between homologous chromosomes-a process that is critical for reductional meiotic chromosome segregation and the production of genetically diverse sexually reproducing populations. Meiotic DSB formation is a complex process, requiring numerous proteins, of which Spo11 is the evolutionarily conserved catalytic subunit. Precisely how Spo11 and its accessory proteins function or are regulated is unclear. Here, we use Saccharomyces cerevisiae to reveal that meiotic DSB formation is modulated by the Mec1(ATR) branch of the DNA damage signalling cascade, promoting DSB formation when Spo11-mediated catalysis is compromised. Activation of the positive feedback pathway correlates with the formation of single-stranded DNA (ssDNA) recombination intermediates and activation of the downstream kinase, Mek1. We show that the requirement for checkpoint activation can be rescued by prolonging meiotic prophase by deleting the NDT80 transcription factor, and that even transient prophase arrest caused by Ndt80 depletion is sufficient to restore meiotic spore viability in checkpoint mutants. Our observations are unexpected given recent reports that the complementary kinase pathway Tel1(ATM) acts to inhibit DSB formation. We propose that such antagonistic regulation of DSB formation by Mec1 and Tel1 creates a regulatory mechanism, where the absolute frequency of DSBs is maintained at a level optimal for genetic exchange and efficient chromosome segregation

Long-range electron transfer in structurally engineered pentaammineruthenium (histidine-62) cytochrome c

In many biological processes, long-range electron transfer (ET) plays a key role. When the three-dimensional structures of proteins are accurately known, use of modified proteins and protein-protein complexes provides an experimental approach to study ET rates between two metal centers. For Ru(His)- modified proteins, the introduction of histidine residues at any desired surface location by site-directed mutagenesis opens the way for systematic investigations of ET pathways

Automatic detection of change in address blocks for reply forms processing

In this paper, an automatic method to detect the presence of on-line erasures/scribbles/corrections/over-writing in the address block of various types of subscription and utility payment forms is presented. The proposed approach employs bottom-up segmentation of the address block. Heuristic rules based on structural features are used to automate the detection process. The algorithm is applied on a large dataset of 5,780 real world document forms of 200 dots per inch resolution. The proposed algorithm performs well with an average processing time of 108 milliseconds per document with a detection accuracy of 98.96%

SeaNet -- Towards A Knowledge Graph Based Autonomic Management of Software Defined Networks

Automatic network management driven by Artificial Intelligent technologies has been heatedly discussed over decades. However, current reports mainly focus on theoretic proposals and architecture designs, works on practical implementations on real-life networks are yet to appear. This paper proposes our effort toward the implementation of knowledge graph driven approach for autonomic network management in software defined networks (SDNs), termed as SeaNet. Driven by the ToCo ontology, SeaNet is reprogrammed based on Mininet (a SDN emulator). It consists three core components, a knowledge graph generator, a SPARQL engine, and a network management API. The knowledge graph generator represents the knowledge in the telecommunication network management tasks into formally represented ontology driven model. Expert experience and network management rules can be formalized into knowledge graph and by automatically inferenced by SPARQL engine, Network management API is able to packet technology-specific details and expose technology-independent interfaces to users. The Experiments are carried out to evaluate proposed work by comparing with a commercial SDN controller Ryu implemented by the same language Python. The evaluation results show that SeaNet is considerably faster in most circumstances than Ryu and the SeaNet code is significantly more compact. Benefit from RDF reasoning, SeaNet is able to achieve O(1) time complexity on different scales of the knowledge graph while the traditional database can achieve O(nlogn) at its best. With the developed network management API, SeaNet enables researchers to develop semantic-intelligent applications on their own SDNs

Fundamental Behavior of Electric Field Enhancements in the Gaps Between Closely Spaced Nanostructures

We demonstrate that the electric field enhancement that occurs in a gap between two closely spaced nanostructures, such as metallic nanoparticles, is the result of a transverse electromagnetic waveguide mode. We derive an explicit semianalytic equation for the enhancement as a function of gap size, which we show has a universal qualitative behavior in that it applies irrespective of the material or geometry of the nanostructures and even in the presence of surface plasmons. Examples of perfect electrically conducting and Ag thin-wire antennas and a dimer of Ag spheres are presented and discussed.Comment: 9 pages and 4 figure