Use of genotyping by sequencing data to develop a high‐throughput and multifunctional SNP panel for conservation applications in Pacific lamprey

Next‐generation sequencing data can be mined for highly informative single nucleotide polymorphisms (SNPs) to develop high‐throughput genomic assays for nonmodel organisms. However, choosing a set of SNPs to address a variety of objectives can be difficult because SNPs are often not equally informative. We developed an optimal combination of 96 high‐throughput SNP assays from a total of 4439 SNPs identified in a previous study of Pacific lamprey (Entosphenus tridentatus) and used them to address four disparate objectives: parentage analysis, species identification and characterization of neutral and adaptive variation. Nine of these SNPs are F_ST outliers, and five of these outliers are localized within genes and significantly associated with geography, run‐timing and dwarf life history. Two of the 96 SNPs were diagnostic for two other lamprey species that were morphologically indistinguishable at early larval stages and were sympatric in the Pacific Northwest. The majority (85) of SNPs in the panel were highly informative for parentage analysis, that is, putatively neutral with high minor allele frequency across the species’ range. Results from three case studies are presented to demonstrate the broad utility of this panel of SNP markers in this species. As Pacific lamprey populations are undergoing rapid decline, these SNPs provide an important resource to address critical uncertainties associated with the conservation and recovery of this imperiled species.     

Assessment of arbovirus vector infection rates using variable size pooling

Pool testing of vector samples for arboviruses is widely used in surveillance programmes. The proportion of infected mosquitoes (Diptera: Culicidae) is often estimated from the minimum infection rate (MIR), based on the assumption of only one infected mosquito per positive pool. This assumption becomes problematic when pool size is large and/or infection rate is high. By relaxing this constraint, maximum likelihood estimation (MLE) is more useful for a wide range of infection levels that may be encountered in the field. We demonstrate the difference between these two estimation approaches using West Nile virus (WNV) surveillance data from vectors collected by gravid traps in Chicago during 2002. MLE of infection rates of Culex mosquitoes was as high as 60 per 1000 at the peak of transmission in August, whereas MIR was less than 30 per 1000. More importantly, we demonstrate roles of various pooling strategies for better estimation of infection rates based on simulation studies with hypothetical mosquito samples of 18 pools. Variable size pooling (with a serial pool sizes of 5, 10, 20, 30, 40 and 50 individuals) performed consistently better than a constant size pooling of 50 individuals. We conclude that variable pool size coupled with MLE is critical for accurate estimates of mosquito infection rates in WNV epidemic seasons.     

Exercise testing and training in patients with peripheral vascular disease and lower extremity amputation.

Patients with peripheral vascular disease have a high risk of coronary artery disease. The risk is even greater when the peripheral vascular disease leads to lower extremity amputation. Exercise testing using lower extremity exercise has been the "gold standard" for screening for coronary artery disease, but many patients with peripheral vascular disease and those with amputations have difficulty doing this type of exercise. Arm exercise ergometry has been shown to be a safe and effective alternative for the detection of coronary artery disease in patients who cannot do leg exercise. This test has also been used to determine safe exercise levels and may be able to predict the ultimate level of prosthetic use in amputees. Exercise training with arm ergometry also improves cardiovascular efficiency and upper body strength in poorly conditioned patients. Studies are needed to appreciate fully the role of exercise testing and training in the recovery of these patients after amputation.     

Occurrence of pathogens in Pacific lamprey (Entosphenus tridentatus)

Reviews in Fish Biology and Fisheries - Pacific lamprey (Entosphenus tridentatus) is a First Food of Native Americans. Declines in lamprey abundance due to dam construction and habitat loss have...     

Primary sequence of two regions of mouse pro-adrenocorticotropin/endorphin

The amino acid sequences of two previously uncharacterized regions of the mouse anterior pituitary common precursor to adrenocorticotropin (ACTH) and beta-endorphin (pro-ACTH/endorphin) were determined. Portions of the NH2-terminal region of pro-ACTH/endorphin (called the 16K fragment) and the region between ACTH and beta-endorphin (called gamma-lipotropin) were sequenced by Edman degradations of biosynthetically labeled immunoprecipitated proteins and by Edman degradations of purified 16K fragment and beta-lipotropin. With a combination of these two approaches, 29 of the first 34 residues at the NH2-terminal end of the mouse 16K fragment were determined. The NH2-terminal region of the mouse 16K fragment was found to be nearly identical with the homologous porcine and bovine molecules. The complete amino acid sequence of the NH2-terminal region of gamma-lipotropin was determined. In contrast to the highly conserved nature of the 16K fragment, mouse gamma-lipotropin was found to differ substantially from the gamma-lipotropins of other species. Although the NH2-terminal and beta-melanotropin-like regions of the mouse gamma-lipotropin are similar to the corresponding regions of other gamma-lipotropins, the intervening region of mouse gamma-lipotropin is substantially shorter than it is in other gamma-lipotropins. In addition, mouse gamma-lipotropin lacks the pair of basic amino acids that normally mark the proteolytic cleavage site used to produce beta-melanotropin from gamma-lipotropin.     

Primary structure of macromomycin, an antitumor antibiotic protein

The antitumor protein macromomycin is a single chain polypeptide of 112 amino acid residues cross-linked by two intramolecular disulfide bonds. The protein was reduced and S-alkylated with 2-mercaptoethanol in 8 M urea followed by treatment with iodoacetic acid. Tryptic digestion of tetra-S-carboxymethyl macromomycin gave four tryptic peptides which were fractionated by gel permeation on Sephadex G-50. The amino acid sequence of the tryptic peptides and the overlap sequences were determined by a combination of automated Edman degradation analysis, gas chromatographic mass spectrometry, and fast atom bombardment mass spectrometry. A comparison of the structures of macromomycin, actinoxanthin, and neocarzinostatin suggests that they belong to a family of related proteins.     

New respiratory gas valve support for graded exercise studies.

We describe a new support structure for respiratory gas valves for use in exercise studies. Use of this structure largely avoids problems of large inertial reactions and feelings of confinement on the part of the subject which have characterized previous systems. The support mechanism consists of a spring-reacted, pivoted boom carried on the end of a counterbalanced swinging beam. This device was designed for use on an adjustable slope motor-driven treadmill, but may be adapted to a variety of other experimental arrangements.     

Papillary mechanics and cardiac morphology of infarcted rat hearts after training

Infarction of the left ventricle was induced by ligation of the coronary artery in male Sprague-Dawley rats under ketamine-xylazine anesthesia. Three weeks after surgery, animals were assigned to a trained (n = 21; running at 20 m/min, 10% grade, 1 h/day, 5 days/wk) or nontrained group (n = 23) for an additional 8 wk. A third, sham-operated control group (n = 16) remained cage sedentary for 11 wk. Ventricular mass was greater in the trained and nontrained infarct groups [1,335 +/- 57.3 and 1,414 +/- 56.1 mg, respectively (mean +/- SE)] compared with the control group (1,155 +/- 50.9 mg) (P less than or equal to 0.05). The diameter of septal fibers was 13% greater in the trained and 17% greater in the nontrained infarct groups compared with control. The specific peak developed force and maximum rate of force development of left ventricular papillary muscle in vitro were 75 and 62% greater in both infarcted groups compared with the control group; these variables were unaffected by training. Myofibrillar adenosine triphosphatase activity of septum was 20% lower in both infarct groups compared with sham-operated animals. We conclude that exercise training did not alter the magnitude of morphological and physiological adaptations to infarction.