Genomes2Drugs: Identifies Target Proteins and Lead Drugs from Proteome Data

Background: Genome sequencing and bioinformatics have provided the full hypothetical proteome of many pathogenic organisms. Advances in microarray and mass spectrometry have also yielded large output datasets of possible target proteins/genes. However, the challenge remains to identify new targets for drug discovery from this wealth of information. Further analysis includes bioinformatics and/or molecular biology tools to validate the findings. This is time consuming and expensive, and could fail to yield novel drugs if protein purification and crystallography is impossible. To pre-empt this, a researcher may want to rapidly filter the output datasets for proteins that show good homology to proteins that have already been structurally characterised or proteins that are already targets for known drugs. Critically, those researchers developing novel antibiotics need to select out the proteins that show close homology to any human proteins, as future inhibitors are likely to cross-react with the host protein, causing off-target toxicity effects later in clinical trials. Methodology/Principal Findings: To solve many of these issues, we have developed a free online resource called Genomes2Drugs which ranks sequences to identify proteins that are (i) homologous to previously crystallized proteins or (ii) targets of known drugs, but are (iii) not homologous to human proteins. When tested using the Plasmodium falciparum malarial genome the program correctly enriched the ranked list of proteins with known drug target proteins. Conclusions/Significance: Genomes2Drugs rapidly identifies proteins that are likely to succeed in drug discovery pipelines

fac-Tris(4-amino­benzohydroxamato)iron(III) ethanol solvate

In the structure of the title compound, [Fe(C7H7N2O2)3]·CH3CH2OH, the FeIII atom is in a distorted octa­hedral O6 environment with the three hydroxamate O atoms (and the three carbonyl O atoms) arranged in a fac configuration and one of the hydroxamate ligands being puckered. The methyl C atom of the ethanol solvent mol­ecule is disordered over two positions with occupancies of 0.626 (13) and 0.374 (13), respectively. The cocrystallized ethanol mol­ecule is hydrogen bonded to one of the hydroxamate O atoms. O—H⋯O and N—H⋯O inter­actions generate infinite three-dimensional networks along [100], [010] and [001]

Preparation and Crystal Structure of a Platinum(II) Complex of [CH2N(CH2COOH)CH2CONH2]2, the Hydrolysis Product of an Anti-Tumour Bis(3,5-Dioxopiperazin-1-YL)Alkane

The synthesis and crystal and molecular structures of the platinum(II) complex Pt(HL)Cl where H2L is the diacid diamide –[CH2N(CH2COOH)CH2CONH2]2, a hydrolytic metabolite of an antitumour active bis(3,5-dioxopiperazin-1-yl)alkane are reported. The complex is square planar and contains HL– as a tridentate 2N (amino), O (carboxylate) donor. The metal to ligand bond distances are Pt-Cl 2.287(1) Å, Pt-O 2.002 (1) Å, Pt-Ntrans Cl 2.014(1) Å and Pt-Ntrans O 2.073 Å. There is extensive hydrogen bonding, each molecule of Pt(HL)Cl being intermolecularly hydrogen bonded to ten others giving a 3-dimensional network. There is also one intramolecular H-bond

Fort Collins Flood 1997: lessons from an extreme event

Includes bibliographical references.The July 28, 1997 flood disaster in Fort Collins, Colorado is generally called a "500-year event" and offers insight into the causes and impacts of extreme urban flooding. Although it hurt and traumatized many people, the flood provided valuable lessons for civil engineers, managers of government agencies, political leaders, counselors, and citizens. Representing several disciplines and entities, the authors present a cross-cutting view of the flood emergency and its lessons. The paper also includes a synthesis of a post-flood conference at Colorado State University which featured reports from all major entities involved in the flood. The remarkable storm that caused the flood produced the heaviest rains ever documented to have fallen over an urbanized area in this state in the recorded history of Colorado. The storm occurred in stages, and dropped 10 to 14 inches in 31 hours in a large area around Fort Collins. The heaviest hourly precipitation occurred at the storm's end, which is different from most storms, and may have exacerbated the flooding. Runoff was dramatic and some peak discharges greatly exceeded projected 100-year and 500-year flows. The City Manager's report showed five people dead, 54 people injured, loss of about 200 homes, and 1500 homes and businesses damaged throughout the City. Fort Collins was more prepared than most cities because it has a nationally-recognized Stormwater Utility and good emergency response capabilities, but it still learned much from the event. Damages at Colorado State University were unusually severe, totaling in the range of $100 million, including building damages, about 425,000 library volumes inundated, loss of a semester's textbooks in the bookstore, and many other losses-both personal and professional. Although the university was surprisingly vulnerable, it responded well with no delay in opening school a month later, but only as a result of tremendous efforts. Emergency response in the City by the Poudre Fire Authority was outstanding, and although the flood had tremendous impacts on the community, not one firefighter or police officer was injured. Within three months after the flood, the local paper, the Coloradoan, had published 282 stories about the flood, and the event received broad coverage in the United States and abroad. After the flood, Fort Collins has tried to focus beyond the physical issues to recognize the multi-faceted losses and the ensuing grief experienced by many people. Lessons are presented in the paper about complacency, protecting vulnerable areas, flood frequency analysis, stress and trauma, the importance of organizational mobilization, the vulnerability of universities, growth management in a hazardous environment, mitigation versus response, communicating risk to officials and the public, and handling large influxes of donations

Monohydroxamic acids and bridging dihydroxamic acids as chelators to ruthenium(III) and as nitric oxide donors: syntheses, speciation studies and nitric oxide releasing investigations.

The synthesis and spectroscopic characterisation of novel mononuclear Ru(III)(edta)(hydroxamato) complexes of general formula [Ru(H2edta)(monoha)] (where monoha = 3- or 4-NH2, 2-, 3- or 4-C1 and 3-Me-phenylhydroxamato), as well as the first example of a Ru(III)-N-aryl aromatic hydroxamate, [Ru(H2edta)(N-Me-bha)].H2O (N-Me-bha = N-methylbenzohydroxamato) are reported. Three dinuclear Ru(III) complexes with bridging dihydroxamato ligands of general formula [{Ru(H2edta)}2(mu-diha)] where diha = 2,6-pyridinedihydroxamato and 1,3- or 1,4-benzodihydroxamato, the first of their kind with Ru(III), are also described. The speciation of all of these systems (with the exception of the Ru-1,4-benzodihydroxamic acid and Ru-N-methylbenzohydroxamic systems) in aqueous solution was investigated. We previously proposed that nitrosyl abstraction from hydroxamic acids by Ru(III) involves initial formation of Ru(III)-hydroxamates. Yet, until now, no data on the rate of nitric oxide (NO) release from hydroxamic acids has been published. We now describe a UV-VIS spectroscopic study, where we monitored the decrease in the ligand-to-metal charge-transfer band of a series of Ru(III)-monohydroxamates with time, with a view to gaining an insight into the NO-releasing properties of hydroxamic acids

School Psychologists\u27 Self-Perceptions of Multicultural Competence: The Relevance of Experience and Training

A national survey of 216 school psychologists\u27 perceptions of multicultural competence indicated that multicultural competence significantly increases as a function of hours of training and frequency of experience working with individuals from cultures different from their own. Results are discussed in the context of measurement limitations for multicultural competence and implications for trainers of school psychologists

Soluble extract from the nematode Strongyloides stercoralis induces CXCR2 dependent/IL-17 independent neutrophil recruitment.

Neutrophil recruitment via CXCR2 is required for innate and adaptive protective immunity to the larvae of Strongyloides stercoralis in mice. The goal of the present study was to determine the mechanism of CXCR2-mediated neutrophil recruitment to S. stercoralis. Mice deficient in the receptor for IL-17A and IL-17F, upstream mediators of CXCR2 ligand production, were infected with S. stercoralis larvae; there was no difference in larval survival, neutrophil recruitment, or production of CXCR2 ligands compared with wild type mice. In vivo and in vitro stimulation of neutrophils with S. stercoralis soluble extract resulted in significant neutrophil recruitment. In vitro assays demonstrated that the recruitment functioned through both chemokinesis and chemotaxis, was specific for CXCR2, and was a G protein-coupled response involving tyrosine kinase and PI3K. Finally, neutrophil stimulation with S. stercoralis soluble extract induced release of the CXCR2 ligands MIP-2 and KC from neutrophils, thereby potentially enhancing neutrophil recruitment

Single circulating-tumor-cell-targeted sequencing to identify somatic variants in liquid biopsies in non-small-cell lung cancer patients

Non-small-cell lung cancer (NSCLC) accounts for most cancer-related deaths worldwide. Liquid biopsy by a blood draw to detect circulating tumor cells (CTCs) is a tool for molecular profiling of cancer using single-cell and next-generation sequencing (NGS) technologies. The aim of the study was to identify somatic variants in single CTCs isolated from NSCLC patients by targeted NGS. Thirty-one subjects (20 NSCLC patients, 11 smokers without cancer) were enrolled for blood draws (7.5 mL). CTCs were identified by immunofluorescence, individually retrieved, and DNA-extracted. Targeted NGS was performed to detect somatic variants (single-nucleotide variants (SNVs) and insertions/deletions (Indels)) across 65 oncogenes and tumor suppressor genes. Cancer-associated variants were classified using OncoKB database. NSCLC patients had significantly higher CTC counts than control smokers

Canadian Hydrogen Intensity Mapping Experiment (CHIME) Pathfinder

A pathfinder version of CHIME (the Canadian Hydrogen Intensity Mapping Experiment) is currently being commissioned at the Dominion Radio Astrophysical Observatory (DRAO) in Penticton, BC. The instrument is a hybrid cylindrical interferometer designed to measure the large scale neutral hydrogen power spectrum across the redshift range 0.8 to 2.5. The power spectrum will be used to measure the baryon acoustic oscillation (BAO) scale across this poorly probed redshift range where dark energy becomes a significant contributor to the evolution of the Universe. The instrument revives the cylinder design in radio astronomy with a wide field survey as a primary goal. Modern low-noise amplifiers and digital processing remove the necessity for the analog beamforming that characterized previous designs. The Pathfinder consists of two cylinders 37\,m long by 20\,m wide oriented north-south for a total collecting area of 1,500 square meters. The cylinders are stationary with no moving parts, and form a transit instrument with an instantaneous field of view of $\sim$100\,degrees by 1-2\,degrees. Each CHIME Pathfinder cylinder has a feedline with 64 dual polarization feeds placed every $\sim$30\,cm which Nyquist sample the north-south sky over much of the frequency band. The signals from each dual-polarization feed are independently amplified, filtered to 400-800\,MHz, and directly sampled at 800\,MSps using 8 bits. The correlator is an FX design, where the Fourier transform channelization is performed in FPGAs, which are interfaced to a set of GPUs that compute the correlation matrix. The CHIME Pathfinder is a 1/10th scale prototype version of CHIME and is designed to detect the BAO feature and constrain the distance-redshift relation.Comment: 20 pages, 12 figures. submitted to Proc. SPIE, Astronomical Telescopes + Instrumentation (2014

Calibrating CHIME, A New Radio Interferometer to Probe Dark Energy

The Canadian Hydrogen Intensity Mapping Experiment (CHIME) is a transit interferometer currently being built at the Dominion Radio Astrophysical Observatory (DRAO) in Penticton, BC, Canada. We will use CHIME to map neutral hydrogen in the frequency range 400 -- 800\,MHz over half of the sky, producing a measurement of baryon acoustic oscillations (BAO) at redshifts between 0.8 -- 2.5 to probe dark energy. We have deployed a pathfinder version of CHIME that will yield constraints on the BAO power spectrum and provide a test-bed for our calibration scheme. I will discuss the CHIME calibration requirements and describe instrumentation we are developing to meet these requirements