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.     

Successful management of suspected acorn (Quercus petraea) toxicity in a dog

A 7-year-old neutered male Labrador retriever dog was referred to a tertiary care veterinary hospital because of gastrointestinal signs and icterus. The dog developed a hepatopathy and acute kidney injury after ingesting acorns (Quercus petraea) 4 days prior to referral. The dog required hospitalization in an intensive care unit but made a full clinical recovery and was discharged after 6 days. This report documents that dogs can be affected by this toxicity and highlights the need for veterinarians to consider acorns as a potential cause of acute hepatotoxicity and renal injury. To the authors’ knowledge, this is the first reported case of acorn toxicity in a dog.     

Digestion and metabolism of low and high residual feed intake Nellore bulls

Understanding the reasons why animals of similar performances have different feed requirements is important to increase profits for cattle producers and to decrease the environmental footprint of beef cattle production. This study was carried out aiming to identify the associations between residual feed intake (RFI) and animal performance, nutrient digestibility, and blood metabolites related to energy balance of young Nellore bulls during the finishing period. Animals previously classified as low (n?=?13) and high RFI (n?=?12), with average initial body weight of 398 kg and age of 503 days were used. Cattle were fed a high energy diet and were slaughtered when rib fat thickness measured by ultrasound between the 12th and 13th ribs reached the minimum of 4 mm. A completely randomized design was adopted, being data analyzed with a mixed model that included the random effect of slaughter group, the fixed effect of RFI class, and linear effect of the covariate feedlot time. No differences were found (p?>?0.10) between RFI classes for performance, dry matter, and nutrients intake. However, dry (p?=?0.0911) and organic matter (p?=?0.0876) digestibility tended to be lower, and digestibility of neutral detergent fiber corrected for ash and protein (p?=?0.0017), and total digestible nutrients (p?=?0.0657) were lower for high RFI animals, indicating lesser capacity of food utilization. Difference between low and high RFI animals was also found for blood cortisol at the end of the trial (p?=?0.0044), having low RFI animals lower cortisol concentrations. Differences in the ability to digest food can affect the efficiency of transforming feed into meat by Nellore cattle.     

Understanding foot-and-mouth disease virus transmission biology: identification of the indicators of infectiousness

The control of foot-and-mouth disease virus (FMDV) outbreaks in non-endemic countries relies on the rapid detection and removal of infected animals. In this paper we use the observed relationship between the onset of clinical signs and direct contact transmission of FMDV to identify predictors for the onset of clinical signs and identify possible approaches to preclinical screening in the field. Threshold levels for various virological and immunological variables were determined using Receiver Operating Characteristic (ROC) curve analysis and then tested using generalized linear mixed models to determine their ability to predict the onset of clinical signs. In addition, concordance statistics between qualitative real time PCR test results and virus isolation results were evaluated. For the majority of animals (71%), the onset of clinical signs occurred 3–4 days post infection. The onset of clinical signs was associated with high levels of virus in the blood, oropharyngeal fluid and nasal fluid. Virus is first detectable in the oropharyngeal fluid, but detection of virus in the blood and nasal fluid may also be good candidates for preclinical indicators. Detection of virus in the air was also significantly associated with transmission. This study is the first to identify statistically significant indicators of infectiousness for FMDV at defined time periods during disease progression in a natural host species. Identifying factors associated with infectiousness will advance our understanding of transmission mechanisms and refine intra-herd and inter-herd disease transmission models.     

Symbiosis of Trifolium subterraneum with mycorrhizal fungi and Rhizobium trifolii as affected by ammonium sulphate and nitrification inhibitors

The symbioses between Trifolium subterraneum, mycorrhizal fungi and Rhizohium are affected by (NH₄)₂SO₄ and by the nitrification inhibitors 2-chloro-6 (trichloromethyl) pyridine (N-Serve) and 2-trichloromethyl pyridine (2TMP). At 50 μg · g^?1 soil N-Serve and 2TMP had toxic effects on plant growth, measured as leaf expansion, root length and dry weight. Lower concentrations of N-Serve also produced some toxic symptoms. The addition of (NH₄)₂SO₄ to the soil at 2 and 6 m-equiv NH⁺₄ per pot, resulted in reduced root length and nodulation. Shoot dry weight was reduced at 6 m-equiv NH⁺₄ per pot. In the presence of (NH₄)₂SO₄ the toxic effects of the nitrification inhibitors on plant growth were less.Both nitrification inhibitors reduced development of mycorrhizal entry-points and extent of root colonization (% infection). Percentage infection of the root system was also reduced by (NH₄)₂SO₄. Development of nodules on the lateral roots was increased in the presence of N-Serve at 5 and 15 μ · g^?1. This effect, however, was accompanied by a marked reduction in N₂ase activity. Smaller increases in nodulation were apparent with 2TMP and were associated with variable N₂ase activity.     

Temperate agroforestry research: considering multifunctional woody polycultures and the design of long-term field trials

The many benefits of agroforestry are well-documented, from ecological functions such as biodiversity conservation and water quality improvement, to cultural functions including aesthetic value. In North American agroforestry, however, little emphasis has been placed on production capacity of the woody plants themselves, taking into account their ability to transform portions of the landscape from annual monoculture systems to diversified perennial systems capable of producing fruits, nuts, and timber products. In this paper, we introduce the concept of multifunctional woody polycultures (MWPs) and consider the design of long-term experimental trials for supporting research on agroforestry emphasizing tree crops. Critical aspects of long-term agroforestry experiments are summarized, and two existing well-documented research sites are presented as case studies. A new long-term agroforestry trial at the University of Illinois, “Agroforestry for Food,” is introduced as an experiment designed to test the performance of increasingly complex woody plant combinations in an alley cropping system with productive tree crops. This trial intends to address important themes of food security, climate change, multifunctionality, and applied solutions. The challenges of establishing, maintaining, and funding long-term agroforestry research trials are discussed.     

Cation exchange capacity of density fractions from paired conifer/grassland soils

The cation exchange capacity (CEC) of a soil depends on the type and amount of both mineral and organic surfaces. Previous studies that have sought to determine the relative contribution of organic matter to total soil CEC have not addressed differences in soil organic matter (SOM) composition that could lead to differences in CEC. The objectives of this study were (1) to compare the CEC of two distinct SOM pools, the “light fraction (LF)” composed of particulate plant, animal, and microbial debris, and the “heavy fraction (HF)” composed of mineral-bound organic matter; and (2) to examine the effects of differences in aboveground vegetation on CEC. Soil samples were collected from four paired grassland/conifer sites within a single forested area and density fractionated. LF CEC was higher in conifer soils than in grassland soils, but there was no evidence of an effect of vegetation on CEC for the HF or bulk soil. LF CEC (but not HF CEC) correlated well with the C concentration in the fraction. The mean CEC of both fractions (per kg fraction) exceeded that of the bulk soil; thus, when the LF and HF CEC were combined mathematically by weighting values for each fraction in proportion to dry mass, the resulting value was nearly twice the measured CEC of bulk soil. On a whole soil basis, the HF contributed on average 97% of the CEC of the whole soil, although this conclusion must be tempered given the inflation of CEC values by the density fractionation procedure.     

Diagnosis of trichomoniasis in 'virgin' bulls by culture and polymerase chain reaction

The diagnostic test for Tritrichomonas foetus in bulls is microscopic examination of cultured preputial samples. Trichomonads other than T. foetus can be present in a preputial sample. Both a staining technique and a polymerase chain reaction assay were useful in differentiating between T. foetus and another trichomonad observed in samples from virgin bulls.     

Effect of Dimethyl sulfoxide (DMSO) and egg yolk on sperm motility,fertility and hatching rates of depik Rasbora tawarensis (Pisces: Cyprinidae) eggs after short‐term cryopreservation

Cryoprotectant is the crucial factor in the cryopreservation process. In general, there are two types of cryoprotectant, permeating and non‐permeating cryoprotectants. Dimethyl sulfoxide (DMSO) and egg yolk are common permeating and non‐permeating cryoprotectants respectively. Hence, the objective of the present study was to determine the best proportion of DMSO and egg yolk for the cryopreservation of Rasbora tawarensis sperm. A completely randomized experimental design was used in this study which involves two types of cryoprotectant and their combination at different concentrations, namely 5% DMSO, 5% egg yolk, 5% DMSO + 5% egg yolk and 2.5% DMSO + 2.5% egg yolk. Every treatment was conducted in three replicates. Combination of 5% DMSO + 5% egg yolk gave the best results cryoprotectant treatment had significant effects on sperm motility, fertilization and hatching rate of the R. tawarensis eggs (p < .05). It is concluded that the best proportion of cryoprotectants for sperm cryopreservation in this species is 5% DMSO + 5% egg yolk.