It Could Not Be Seen Because It Could Not Be Believed on June 30, 2013

Nineteen Prescott Fire Department, Granite Mountain Hot Shot (GMHS) wildland firefighters (WF) perished in Arizona in June 2013 Yarnell Hill Fire, an inexplicable wildland fire disaster. In complex wildland fires, sudden, dynamic changes in human factors and fire conditions can occur, thus mistakes can be unfortunately fatal. Individual and organizational faults regarding the predictable, puzzling, human failures that will result in future WF deaths are addressed. The GMHS were individually, then collectively fixated with abandoning their Safety Zone to reengage, committing themselves at the worst possible time, to relocate to another Safety Zone - a form of collective tunnel vision. Our goal is to provoke meaningful discussion toward improved wildland firefighter safety with practical solutions derived from a long-established wildland firefighter expertise/performance in a fatality-prone profession. Wildfire fatalities are unavoidable, hence these proposals, applied to ongoing training, can significantly contribute to other well-thought-out and validated measures to reduce them

A Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8, Bound to DNA Gyrase

Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets

Enhancement by postfiltering for speech and audio coding in ad-hoc sensor networks

Enhancement algorithms for wireless acoustics sensor networks~(WASNs) are indispensable with the increasing availability and usage of connected devices with microphones. Conventional spatial filtering approaches for enhancement in WASNs approximate quantization noise with an additive Gaussian distribution, which limits performance due to the non-linear nature of quantization noise at lower bitrates. In this work, we propose a postfilter for enhancement based on Bayesian statistics to obtain a multidevice signal estimate, which explicitly models the quantization noise. Our experiments using PSNR, PESQ and MUSHRA scores demonstrate that the proposed postfilter can be used to enhance signal quality in ad-hoc sensor networks

PIASy-dependent SUMOylation regulates DNA topoisomerase IIα activity

SUMOylation of TopoIIα inhibits its decatenation activity, preventing resolution of tangled DNA at centromeres before anaphase onset

MULTIPLE CURRENT SHEET SYSTEMS IN THE OUTER HELIOSPHERE: ENERGY RELEASE AND TURBULENCE

Accepted for publication in The Astrophysical Journal, March 21, 201

A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function

DNA topoisomerases manage chromosome supercoiling and organization in all forms of life. Gyrase, a prokaryotic heterotetrameric type IIA topo, introduces negative supercoils into DNA by an ATP-dependent strand passage mechanism. All gyrase orthologs rely on a homologous set of catalytic domains for function; however, these enzymes also can possess species-specific auxiliary regions. The gyrases of many gram-negative bacteria harbor a 170-amino acid insertion of unknown architecture and function in the metal- and DNA-binding TOPRIM domain of the GyrB subunit. We have determined the structure of the 212 kDa Escherichia coli gyrase DNA binding and cleavage core containing this insert to 3.1 Å resolution. We find that the insert adopts a novel, extended fold that braces the GyrB TOPRIM domain against the coiled-coil arms of its partner GyrA subunit. Structure-guided deletion of the insert greatly reduces the DNA binding, supercoiling and DNA-stimulated ATPase activities of gyrase. Mutation of a single amino acid at the contact point between the insert and GyrA more modestly impairs supercoiling and ATP turnover, and does not affect DNA binding. Our data indicate that the insert has two functions, acting as a steric buttress to pre-configure the primary DNA-binding site, and serving as a relay that may help coordinate communication between different functional domains

Structural Insights into the Quinolone Resistance Mechanism of Mycobacterium tuberculosis DNA Gyrase

Mycobacterium tuberculosis DNA gyrase, an indispensable nanomachine involved in the regulation of DNA topology, is the only type II topoisomerase present in this organism and is hence the sole target for quinolone action, a crucial drug active against multidrug-resistant tuberculosis. To understand at an atomic level the quinolone resistance mechanism, which emerges in extensively drug resistant tuberculosis, we performed combined functional, biophysical and structural studies of the two individual domains constituting the catalytic DNA gyrase reaction core, namely the Toprim and the breakage-reunion domains. This allowed us to produce a model of the catalytic reaction core in complex with DNA and a quinolone molecule, identifying original mechanistic properties of quinolone binding and clarifying the relationships between amino acid mutations and resistance phenotype of M. tuberculosis DNA gyrase. These results are compatible with our previous studies on quinolone resistance. Interestingly, the structure of the entire breakage-reunion domain revealed a new interaction, in which the Quinolone-Binding Pocket (QBP) is blocked by the N-terminal helix of a symmetry-related molecule. This interaction provides useful starting points for designing peptide based inhibitors that target DNA gyrase to prevent its binding to DNA

Structural Basis of Gate-DNA Breakage and Resealing by Type II Topoisomerases

Type II DNA topoisomerases are ubiquitous enzymes with essential functions in DNA replication, recombination and transcription. They change DNA topology by forming a transient covalent cleavage complex with a gate-DNA duplex that allows transport of a second duplex though the gate. Despite its biological importance and targeting by anticancer and antibacterial drugs, cleavage complex formation and reversal is not understood for any type II enzyme. To address the mechanism, we have used X-ray crystallography to study sequential states in the formation and reversal of a DNA cleavage complex by topoisomerase IV from Streptococcus pneumoniae, the bacterial type II enzyme involved in chromosome segregation. A high resolution structure of the complex captured by a novel antibacterial dione reveals two drug molecules intercalated at a cleaved B-form DNA gate and anchored by drug-specific protein contacts. Dione release generated drug-free cleaved and resealed DNA complexes in which the DNA gate instead adopts an unusual A/B-form helical conformation with a Mg2+ ion repositioned to coordinate each scissile phosphodiester group and promote reversible cleavage by active-site tyrosines. These structures, the first for putative reaction intermediates of a type II topoisomerase, suggest how a type II enzyme reseals DNA during its normal reaction cycle and illuminate aspects of drug arrest important for the development of new topoisomerase-targeting therapeutics

A Symmetric Dual Feedback System Provides a Robust and Entrainable Oscillator

Many organisms have evolved molecular clocks to anticipate daily changes in their environment. The molecular mechanisms by which the circadian clock network produces sustained cycles have extensively been studied and transcriptional-translational feedback loops are common structures to many organisms. Although a simple or single feedback loop is sufficient for sustained oscillations, circadian clocks implement multiple, complicated feedback loops. In general, different types of feedback loops are suggested to affect the robustness and entrainment of circadian rhythms