Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

Targeted capture combined with massively parallel exome sequencing is a promising approach to identify genetic variants implicated in human traits. We report exome sequencing of 200 individuals from Denmark with targeted capture of 18,654 coding genes and sequence coverage of each individual exome at an average depth of 12-fold. On average, about 95% of the target regions were covered by at least one read. We identified 121,870 SNPs in the sample population, including 53,081 coding SNPs (cSNPs). Using a statistical method for SNP calling and an estimation of allelic frequencies based on our population data, we derived the allele frequency spectrum of cSNPs with a minor allele frequency greater than 0.02. We identified a 1.8-fold excess of deleterious, non-syonomyous cSNPs over synonymous cSNPs in the low-frequency range (minor allele frequencies between 2% and 5%). This excess was more pronounced for X-linked SNPs, suggesting that deleterious substitutions are primarily recessive.     

The prevalence of Echinococcus granulosus and other taeniid cestodes in sheep dogs of central Utah

Fifty-one of 62 sheep dogs in central Utah were successfully purged for diagnosis of cestodes in 1981. Tapeworms were identified in the purged fecal samples of 33 (64.7 percent) animals. Minimum infection rates in the dogs which were purged were; 9.8 percent for Echinococcus granulosus , 29.4 percent for Taenia pisiformis , 27.5 percent for T. ovis krabbei , 27.5 percent for T. hydatigena , and 2.0 percent for T. serialis . The prevalence of E. granulosus decreased from 27 percent in 1971 to 9.8 percent in 1981.     

Ribulose diphosphate carboxylase activities in cold-resistant common mallow, Malva neglecta Wallr. and a cold-sensitive tomato, Lycopersicon esculentum L., Ace 55 var.

Common mallow ( Malva neglecta Wallr.) and tomato ( Lycopersicon esculentum L. var. Ace 55) were compared as to certain characteristics: Co 2 fixation properties, ribulose diphosphate carboxyl activities, (RuDPCase) photosynthesis, respiration, and compensation points. Significant differences in these factors were observed in all cases except dark respiration. Mallow enzyme (RuDPCase) activities were higher per unit of enzyme than those of tomato. The Mallow RuDPCase exhibited slightly higher activity at 5 to 25 C. Mallow leaves retained their capacity for photosynthesis and respiration after long periods of exposure to subfreezing temperature. The cold adapted mallow had a higher CO 2 compensation point, suggesting a lower efficiency for CO 2 fixation. The results suggest that cold acclimation in common mallow affects photosynthesis but has little effect on respiration.     

Effect of irrigation on survival of third-stage Haemonchus contortus larvae (Nematoda: Trichostrongylidae)

During May through October 1976, samples of sheep pellets containing laboratory - reared, thirdstage Haemonchus contortus larvae were placed on irrigated and nonirrigated pasture plots at Provo, Utah. Periodically thereafter, grass clippings, soil scrapings, and remaining pellets were collected and baermannized to determine their comparative survival from the two environments. Water was added to the irrigated plots in accordance with a weekly sprinkling regime designed to furnish sufficient moisture to maintain pasture grass in this semiarid region. Meteorologic measurements were collected daily from both irrigated and nonirrigated sections.   During the year the nonirrigated section received a total of 131 mm of precipitation, whereas an additional 979 mm of water were added via sprinkling to the irrigated section. The monthly mean maximum temperature at soil surface under grass cover for the six - month study period on the irrigated section averaged 17.7 C less than on the nonirrigated section, and the corresponding soil moisture content remained 14.4 percent higher. A bioclimatograph of conditions on the nonirrigated section showed that none of the months during the year had levels of temperature and moisture which fell within the prescribed limits for optimum pasture transmission of H. contortus; on the irrigated section only October of the six - month study period failed to have suitable conditions for optimum pasture transmission. Larvae placed on the plots survived significantly longer and also in significantly greater numbers on the irrigated section, and irrigation enhanced the ability of larvae to migrate from pellets onto vegetation.     

Winter survival of Northern Pintails in the Middle Rio Grande Valley, New Mexico

In response to continued low population numbers of Northern Pintail ( Anas acuta ) in North America and to increase knowledge of the geographic variation in pintail survival rates, we estimated 126-day (27 October–2 March) survival for male and female pintails wintering in the Middle Rio Grande Valley, New Mexico, during 2001–2002 (SY1) and 2002–2003 (SY2). Sixty-nine adult male and female pintails were marked with radio-transmitters and tracked throughout the study period. Weekly relocation data in relation to study year, sex, time (week), body condition at capture, and hunting seasons were modeled using the known-fate procedure in Program MARK. Year, sex, time, and body condition covariates did not improve model performance in estimating survival, so we used the most parsimonious model to produce an overall winter survival estimate of 0.597 ± 0.077 (95% C.I. = 0.442–0.735). Weekly survival estimates did not differ between hunting and nonhunting seasons. Male and female point estimates did not differ (χ 1 2 = 0.209, P = 0.65). Our adult female survival estimate of 0.639 ± 0.117 (95% C.I. = 0.396–0.827) was 5.5%–28.6% lower than published estimates for adult female pintails in 5 other geographic regions. No winter survival estimates for males in other geographic regions were available for direct comparison with our study. Although relatively small sample sizes may have contributed to the lack of statistical differences in weekly survival between years, sexes, and hunting seasons, as well as to the lack of influence of body condition, relatively abundant water and food resources and absence of hunting in a refuge setting contributed to consistent survival probabilities. Because our low survival estimates, relative to other geographic regions, cannot be attributed to hunting, we postulate that natural causes of mortality play a larger role in pintail survival in our study region than in other wintering regions.     

A simple technique for the measurement of 3H- and 14C-radioactivity per microgram DNA in fixed tissue

A simple, rapid and versatile technique for scintillation counting of double labelled fixed tissue is described. Furthermore, DNA determination can be performed on the same tissue digest.