The chemical genomic portrait of yeast: uncovering a phenotype for all genes

Genetics aims to understand the relation between genotype and phenotype. However, because complete deletion of most yeast genes ( approximately 80%) has no obvious phenotypic consequence in rich medium, it is difficult to study their functions. To uncover phenotypes for this nonessential fraction of the genome, we performed 1144 chemical genomic assays on the yeast whole-genome heterozygous and homozygous deletion collections and quantified the growth fitness of each deletion strain in the presence of chemical or environmental stress conditions. We found that 97% of gene deletions exhibited a measurable growth phenotype, suggesting that nearly all genes are essential for optimal growth in at least one condition.     

A selective activity-dependent requirement for dynamin 1 in synaptic vesicle endocytosis

Dynamin 1 is a neuron-specific guanosine triphosphatase thought to be critically required for the fission reaction of synaptic vesicle endocytosis. Unexpectedly, mice lacking dynamin 1 were able to form functional synapses, even though their postnatal viability was limited. However, during spontaneous network activity, branched, tubular plasma membrane invaginations accumulated, capped by clathrin-coated pits, in synapses of dynamin 1-knockout mice. Synaptic vesicle endocytosis was severely impaired during strong exogenous stimulation but resumed efficiently when the stimulus was terminated. Thus, dynamin 1-independent mechanisms can support limited synaptic vesicle endocytosis, but dynamin 1 is needed during high levels of neuronal activity.     

The genomic sequence of the accidental pathogen Legionella pneumophila

We present the genomic sequence of Legionella pneumophila, the bacterial agent of Legionnaires' disease, a potentially fatal pneumonia acquired from aerosolized contaminated fresh water. The genome includes a 45-kilobase pair element that can exist in chromosomal and episomal forms, selective expansions of important gene families, genes for unexpected metabolic pathways, and previously unknown candidate virulence determinants. We highlight the genes that may account for Legionella's ability to survive in protozoa, mammalian macrophages, and inhospitable environmental niches and that may define new therapeutic targets.     

Shade coffee in Hawai‘i – Exploring some aspects of quality,growth, yield,and nutrition

In a harsh (Kunia) and an ideal (Kona) growing region of Hawai‘i, sun grown Coffea arabica L. was compared to coffee shaded with varying degrees of black and aluminized shade cloth, macadamia trees, and a novel, spray-on shade composed mostly of kaolin. Shading did not appreciably affect organoleptic quality. Shading resulted in statistically different yields in the macadamia (16% of sun) and kaolin (199% of sun) treatments in the second year compared to full sun treatments in their respective locations, although a negative, linear trend was observed with increased shading. The lack of significant differences in yields between the shade cloth and sun treatments was likely a result of large yield variation among replicates. Bean sizes differed little between shade treatments and the percentage of defects and broken beans were generally not significantly different among the treatments in Kunia. Kona bean sizes and characteristics were not different. Shading reduced surface leaf temperatures and increased specific leaf area but generally did not affect lateral nodal growth. Leaf nutrient concentration differed between treatments.     

Significant increases in pulping efficiency in C4H-F5H-transformed poplars: improved chemical savings and reduced environmental toxins

The gene encoding ferulate 5-hydroxylase (F5H) was overexpressed in poplar (Populus tremula x Populus alba) using the cinnamate-4-hydroxylase (C4H) promoter to drive expression specifically in cells involved in the lignin biosynthetic pathway and was shown to significantly alter the mole percentage of syringyl subunits in the lignin, as determined by thioacidolysis. Analysis of poplar transformed with a C4H-F5H construct demonstrated significant increases in chemical (kraft) pulping efficiency from greenhouse-grown trees. Compared to wild-type wood, decreases of 23 kappa units and increases of >20 ISO brightness units were observed in trees exhibiting high syringyl monomer concentrations. These changes were associated with no significant modification in total lignin content and no observed phenotypic differences. C4H-F5H-transformed trees could increase pulp throughputs at mills by >60% while concurrently decreasing chemicals employed during processing (chemical pulping and bleaching) and, consequently, the amount of deleterious byproducts released into the environment.     

Comparative Efficacy of Anesthetics for the Freshwater Prawn Macrobrachiurn rosenbergii

Abstract— The freshwater prawn Macrobrachiurn rosenbergii is a commercially important culture species in the South Central United States. Two major constraints in the commercial culture of the freshwater prawn in the U.S. are poor survival during live transportation of seed‐stock to growout ponds, and live transportation of pond harvested prawn to distant live markets due to the territorial and cannibalistic nature of prawn. The use of anesthetics could possibly improve transport survival; however, to date anesthetic agents have not been evaluated for use with prawn. Two trials were conducted with juvenile freshwater prawn to compare the efficacy of anesthetics commonly used on fish. The first trial was designed to identify the most promising candidates. In Study 1, tricaine methanesulfonate (MS‐222), 2‐phenoxyethanol, quinaldine sulfate (quinaldine), clove oil, and Aqui‐S^TM were evaluated at 25 and 100 mg/L for 1 h in three replicate 10‐L glass containers, containing five juvenile prawn each. Relative sedation level was determined every 3 min for 1 h, then recovery time and survival were measured. In Study 1, MS‐222 and 2‐phenoxyethanol were determined to be ineffective on prawn at all rates tested. Based on their performance in Study 1, quinaldine, clove oil, and AquiS^TM were evaluated at 100, 200, and 300 mg/L in Study 2. Observations were determined as in Study 1. Clove oil and Aqui‐S^TM induced anesthesia faster and at lower concentrations than quinaldine. At the highest treatment rate (300 mg/L) prawn suffered 60% mortality in the Aqui‐S^TM treatment, 13% mortality in the quinaldine treatment, and 0% mortality in the clove oil treatment and control following a 1‐h exposure to these concentrations. Based on these data, Aqui‐S^TM and clove oil applied at 100 mg/L may be suitable anesthetic treatments for prawn. Additional research is needed to determine optimal time and dose relationships to minimize stress during holding, handling, and transportation of prawn.     

Simulating the spatial dynamics of foot and mouth disease outbreaks in feral pigs and livestock in Queensland, Australia, using a susceptible-infected-recovered cellular automata model

We describe an approach to modelling the spatio-temporal spread of foot and mouth disease through feral animal and unfenced livestock populations. We used a susceptible-infected-recovered model, implemented in a cellular automata framework, to assess the spread of FMD across two regions of Queensland, Australia. Following a sensitivity analysis on the infectious states, scenario analyses were conducted using feral pigs only as the susceptible population, and then with the addition of livestock, and initiated in the wet season and in the dry season. The results indicate that, depending on the season the outbreak is initiated, and without the implementation of control measures, an outbreak of Foot and Mouth Disease around Winton could continue unchecked, while an outbreak around Cape York may die out naturally. The approach explicitly incorporates the spatial relationships between the populations through which the disease spreads and provides a framework by which the spread of disease outbreaks can be explored through varying the model parameters. It highlights the emergence and importance of spatio-temporal patterns, something that previous modelling of FMD in feral animal and unfenced livestock populations has lacked.     

Intraosseous gentamicin perfusion of the distal metacarpus in standing horses

OBJECTIVE: To report tissue gentamicin concentrations after intraosseous (IO) perfusion in standing horses. STUDY DESIGN: In vivo study. ANIMALS OR SAMPLE POPULATION: Twelve horses. METHODS: Sedated horses had a cannulated cortical bone screw inserted into the dorsolateral aspect of the treated metacarpus and a tourniquet applied proximally. Gentamicin (2.2 mg/kg) diluted in sterile saline solution (0.1 mL/kg) was infused through the screw. Two horses were euthanatized at each time interval: 0, 2, 6, 12, 24, and 36 hours. Synovial fluid and bone samples were collected distal to the screw from both forelimbs. Gentamicin concentrations were measured using fluorescence polarization immunoassay. RESULTS: The highest synovial fluid gentamicin concentrations were 385+/-273 microg/mL (mean+/-SD) in the metacarpophalangeal joint, 225+/-205 microg/mL in the proximal interphalangeal joint, 215+/-205 microg/mL in the distal interphalangeal joint, 382+/-195 microg/mL in the digital flexor tendon sheath, and 206+/-161 microg/mL in the navicular bursa. The highest bone concentrations of gentamicin were 55+/-30 microg/g in the distal metacarpus, 34+/-27 microg/g in the proximal, 16+/-15 microg/g in the middle, and 16+/-2.2 microg/g in the distal phalanges, and 27+/-17 microg/g in the proximal and 24+/-11 microg/g in the distal sesamoid bones. CONCLUSION: Standing IO perfusion of gentamicin resulted in local antibiotic concentrations in the synovial structures and bones of the distal aspect of the limb that exceed the reported minimum inhibitory concentration of pathogens commonly implicated in equine orthopedic infections. CLINICAL RELEVANCE: Standing IO perfusion of gentamicin in the distal aspect of the limb should be considered for treatment of orthopedic infections of this region in horses.