Evolution and functional impact of rare coding variation from deep sequencing of human exomes

As a first step toward understanding how rare variants contribute to risk for complex diseases, we sequenced 15,585 human protein-coding genes to an average median depth of 111× in 2440 individuals of European (n = 1351) and African (n = 1088) ancestry. We identified over 500,000 single-nucleotide variants (SNVs), the majority of which were rare (86% with a minor allele frequency less than 0.5%), previously unknown (82%), and population-specific (82%). On average, 2.3% of the 13,595 SNVs each person carried were predicted to affect protein function of ~313 genes per genome, and ~95.7% of SNVs predicted to be functionally important were rare. This excess of rare functional variants is due to the combined effects of explosive, recent accelerated population growth and weak purifying selection. Furthermore, we show that large sample sizes will be required to associate rare variants with complex traits.     

Olfactory and endocrine response to steroids in an African cichlid fish, Haplochromis burtoni

A cichlid (Haplochromis burtoni) detects conjugated steroids through five olfactory receptor mechanisms, and increases serum testosterone in response to a mixture of detected steroids.     

First application in Turkey of the European Non‐native Species in Aquaculture Risk Analysis Scheme to evaluate the farmed non‐native fish,striped catfish Pangasianodon hypophthalmus

The European Non‐native Species in Aquaculture Risk Analysis Scheme (ENSARS) was used to assess one of the most popular aquaculture species in the world, the striped catfish Pangasianodon hypophthalmus (Sauvage, 1878), in two locations of southern Anatolia (Turkey). The overall mean risk score generated for P. hypophthalmus by the ENSARS Organism module (which assesses the risks of introduction, establishment, dispersal and impact) indicated that the species poses a medium risk under current climatic conditions. All other ENSARS modules rendered scores that indicated a moderately low risk under current climatic conditions. However, the risks of introducing novel diseases and the actual use (e.g. deliberate introduction to the natural habitats or food market) of the species both attracted scores indicating a medium risk. Confidence levels were medium or high for all modules except the Socio‐economic, with low confidence values also attributed to the risks for farming process of the organism, and its overall risk of spread into the wild during farming procedures and to marketing impacts. Recommendations are provided for further use of the ENSARS scheme, especially for a a priori assessment of potential aquaculture species in Turkey, where the sector has been remarkably developing in the last decades.     

Dexamethasone, melphalan, actinomycin D, cytosine arabinoside (DMAC) protocol for dogs with relapsed lymphoma

BACKGROUND: In general, treatment of relapsed lymphoma is associated with a lower probability of response and shorter duration of remission. The purpose of this study was to evaluate the efficacy of the combination chemotherapy protocol DMAC (dexamethasone, melphalan, actinomycin D, and cytosine arabinoside) for reinduction of remission in dogs with relapsed lymphoma. HYPOTHESIS: That DMAC would be an effective reinduction protocol for dogs with relapsed lymphoma. ANIMALS: Fifty-four dogs. RESULTS: Seventy-two percent of the dogs achieved remission (44% complete remission [CR] and 28% partial remission [PR]), 11% had stable disease (SD), and 17% had progressive disease (PD). The median remission duration was 61 days (range, 2-467+ days). The median remission durations for dogs with CR, PR, and SD were 112, 44, and 27 days, respectively. Factors that affected the response rate were previous treatment with doxorubicin and an inability to achieve remission with the previous protocol. Thrombocytopenia occurred in 56% of the dogs (grade 1 in 3 dogs, grade 2 in 6 dogs, grade 3 in 7 dogs, and grade 4 in 7 dogs) and neutropenia in 17% of the dogs (grade 2 in 1 dog, grade 3 in 2 dogs, and grade 4 in 4 dogs). Gastrointestinal toxicosis occurred in 22% of the dogs (grades 1 in 5 dogs, grade 2 in 3 dogs, and grade 3 in 1 dog). CONCLUSIONS AND CLINICAL IMPORTANCE: The DMAC protocol is an effective rescue protocol for dogs with relapsed multicentric lymphoma. Although thrombocytopenia is a common manifestation of toxicity, in general, the protocol is well tolerated.     

Chemical Control of Sand Sagebrush: Implications for Lesser Prairie-Chicken Habitat

Traditional management of sand sagebrush (Artemisia filifolia) rangelands has emphasized sagebrush control to increase forage for livestock. Since the 1950s shrub removal has been primarily achieved with herbicides. Concerns over declining lesser prairie-chicken (Tympanuchus pallidicinctus; LPC) populations have led to increased scrutiny over the use of herbicides to control shrubs. The objective of our research was to describe changes to LPC habitat qualities following chemical control of sand sagebrush in northwest Oklahoma. Study pastures ranged in size from 10 to 21 ha. Five pastures were sprayed with 2,4-dichlorophenoxyacetic acid (2,4-D) in 2003 (RECENT), five were sprayed with 2,4-D in 1984 (OLD), and four received no treatment (SAGE). We measured habitat structure (sagebrush cover, sagebrush density, visual obstruction [VO], and basal grass cover), and dietary resources (forb density, forb richness, and grasshopper density) in all pastures from 2003 to 2006. OLD and RECENT pastures had less sagebrush (cover and density) and VO than SAGE pastures. OLD pastures produced more annual forbs than either SAGE or RECENT pastures. SAGE pastures had more perennial forbs than RECENT pastures. Herbicide application reduced protective cover while providing no increase in forb abundance in RECENT pastures. Our results indicated that it may take several years to realize increases in annual forbs following application of 2,4-D. However, loss of protective cover may persist for multiple years (20+ yr), and removal of sagebrush did not increase forb richness or grasshopper abundance. Thus, 2,4-D may have limited use as a habitat management tool because it takes numerous years to reap the benefit of increased forb abundance while reducing habitat structure in the long term.     

Comparison of endotracheal intubation techniques in llamas

This study evaluated a retrograde orotracheal intubation technique and compared it to the traditional normograde intubation technique used in llamas. Oral anatomical features, which can impair visualization of the epiglottis and laryngeal structures, and the production of excessive salivary secretions make it difficult to establish an airway under emergency conditions. Normograde intubation involves placing a stylet through the mouth into the trachea and advancing the endotracheal tube over the stylet into the trachea. For retrograde intubation, a nested trochar with cannula is placed into the cervical trachea and a stylet is advanced through the cannula and out the mouth. The endotracheal tube is advanced over the stylet back into the trachea. Our evaluation of both techniques found no statistical difference in time to place the stylet or endotracheal tube; however, fewer attempts were needed to place the tube using the retrograde technique. We found the retrograde technique to be a viable option for intubating llamas.     

Bovine intelectins: cDNA sequencing and expression in the bovine intestine

Intelectins (Itlns) are lectins with potential roles in innate immunity, capable of binding bacteria via galactofuranose residues. Itlns also function as intestinal receptors for the antimicrobial glycoprotein lactoferrin (Lf). Since Lf binds strongly to enterohemorrhagic Escherichia coli O157:H7 (EHEC), we aimed to determine the expression of Lf receptor in terminal rectum, the site of predilection of EHEC in cattle. We sequenced two bovine intelectins (Itln1 and Itln2) and showed that both were expressed in abomasum and rectum, but expression appeared minimal in the jejunum. There was significantly higher expression of Itln2 in terminal rather than proximal rectum. Lactoferrin was expressed in all samples examined. Thus, we have demonstrated two novel bovine Itlns and shown that they are expressed along with Lf in the gastrointestinal tract, where they may interact with microbial pathogens.     

Assessment of three variations of the 1,9-dimethylmethylene blue assay for measurement of sulfated glycosaminoglycan concentrations in equine synovial fluid

OBJECTIVE: To determine whether 3 variations of the 1,9-dimethylmethylene blue (DMMB) assay yield comparable results when measuring sulfated glycosaminoglycan (sGAG) concentrations in equine synovial fluid (SF). SAMPLE POPULATION: 25 samples of SF collected from affected joints of 13 horses and 13 samples of SF collected from nonaffected (control) joints of 4 horses. PROCEDURE: Sulfated glycosaminoglycan concentrations were measured by the direct spectrophotometric (ie, Farndale), microplate, and indirect DMMB assays in samples of SF collected from normal and affected joints and in samples digested with nucleases, papain, and hyaluronidase. RESULTS: All 3 assays reacted similarly to standard solutions of sGAGs and digestion of SF samples with nucleases, papain, and hyaluronidase. Nucleic acids were not important interfering substances, and papain and hyaluronidase could not be used interchangeably to digest SE All 3 assays proved to have satisfactory precision (SD < 10%), but each DMMB assay resulted in significantly different measures of sGAG in equine SF. CONCLUSIONS AND CLINICAL RELEVANCE: Samples of SF should be digested with papain or hyaluronidase prior to measurement via DMMB assay. Researchers currently are unable to compare clinical information when variations of the DMMB assay are used, because each DMMB assay yields substantially different sGAG concentrations in SF. Of the 3 assays examined here, we recommend use of the direct spectrophotometric DMMB assay.     

Efficacy and safety of once versus twice daily administration of methimazole in cats with hyperthyroidism

OBJECTIVE: To determine whether once daily administration of methimazole was as effective and safe as twice daily administration in cats with hyperthyroidism. DESIGN: Randomized, nonblinded, clinical trial. ANIMALS: 40 cats with newly diagnosed hyperthyroidism. PROCEDURE: Cats were randomly assigned to receive 5 mg of methimazole, PO, once daily (n = 25) or 2.5 mg of methimazole, PO, twice daily (15). A complete physical examination, including measurement of body weight; CBC; serum biochemical analyses, including measurement of serum thyroxine concentration; and urinalysis were performed, and blood pressure was measured before and 2 and 4 weeks after initiation of treatment. RESULTS: Serum thyroxine concentration was significantly higher in cats given methimazole once daily, compared with cats given methimazole twice daily, 2 weeks (3.7 vs 2.0 micro +/- g/dL) and 4 weeks (3.2 vs 1.7 microg/dL) after initiation of treatment. In addition, the proportion of cats that were euthyroid after 2 weeks of treatment was lower for cats receiving methimazole once daily (54%) than for cats receiving methimazole twice daily (87%). Percentages of cats with adverse effects (primarily gastrointestinal tract upset and facial pruritus) were not significantly different between groups. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggest that once daily administration of methimazole was not as effective as twice daily administration in cats with hyperthyroidism and cannot be recommended for routine use.