Whole-genome shotgun sequencing of mitochondria from ancient hair shafts

Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.     

Effect of soil characteristics, seeding depth, operating speed, and opener design on draft force during direct seeding

Direct seeding practices that promote soil and water conservation and reduce input costs have become an increasingly accepted alternative to conventional tillage systems in western Canada. The objective of the present study was to determine the relative importance of soil characteristics, seeding depth, operating speed, and opener design on draft forces during direct seeding in central Saskatchewan. Draft was measured for nine different openers operated at 1–5 cm seeding depths and three ground speeds in four untilled Chernozemic soils that differed in soil moisture and/or texture. The average increase in opener draft for all fields was 4% for each km h⁻¹ increase in speed. Although the range in soil consistency was small, there was a 24% increase in draft in heavy clay compared to sandy loam soil. Draft force of the average opener increased by nearly 20% for each centimeter increase in seeding depth. However, highly significant interactions among most of the variables investigated indicated that the relative performance of openers was not consistent for the range of conditions evaluated. Large differences among the draft forces of different openers operated at different depths in soils with different consistencies were particulary noteworthy. For example, a 4.5-fold increase in the draft of a low versus a high draft opener operated at 1.25 versus 5.0 cm seeding depth at 7.5 km h⁻¹ in moist, heavy clay soil emphasized the large influence that opener design and seeding depth have on tractor power requirements and direct seeding input costs.     

Effects of L-lysine and L-arginine on in vitro replication of feline herpesvirus type-1

OBJECTIVE: To determine the effects of various concentrations of L-lysine and L-arginine on in vitro replication of feline herpesvirus type-1 (FHV-1). SAMPLE POPULATION: Cultured Crandell-Reese feline kidney (CRFK) cells and FHV-1 strain 727. PROCEDURE: Uninfected CRFK cells or CRFK cells infected with FHV-1 were cultured in Dulbecco's modified Eagle's medium or in 1 of 7 test media containing various concentrations of lysine and arginine. Viral titer and CRFK growth rate were assessed in each medium. RESULTS: Media depleted of arginine almost completely inhibited viral replication, whereas 2.5 or 5.0 microg of arginine/ml of media was associated with a significant increase in FHV-1 replication. In media with 2.5 microg of arginine/ml, supplementation with 200 or 300 microg of lysine/ml reduced viral replication by 34.2 and 53.9%, respectively. This effect was not seen in media containing 5.0 microg of arginine/ml. Growth rates of CRFK cells also were suppressed in media containing these concentrations of amino acids, but they were not significantly different from each other. CONCLUSIONS AND CLINICAL RELEVANCE: Arginine exerts a substantial growth-promoting effect on FHV-1. Supplementation of viral culture medium with lysine attenuates this growth-promoting effect in media containing low concentrations of arginine. Analysis of data from this study indicates that high concentrations of lysine reduce in vitro replication of FHV-1 but only in media containing low concentrations of arginine. Clinical trials will be necessary to determine whether supplemental administration of lysine, with or without arginine restriction, will be useful in the management of cats with FHV-1 infections.     

Accumulation of amino acids,proline, and carbohydrates in response to aluminum and manganese stress in maize

Synthesis of amino acids, proline, and carbohydrates was studied in roots and shoots of 5 maize accessions, differing in aluminum (Al) and manganese (Mn) tolerance, in response to Al and Mn stress at the seedling stage in solution culture. The concentrations of these metabolites increased in roots and shoots of the seedlings in the nutrient solution with added Al (0.22 mM), and Mn (2.0 mM). Both Al and/or Mn tolerant and non‐tolerant accessions accumulated more metabolites under stress than control. Generally, the tolerant accessions accumulated more solutes than the non‐tolerant maize accessions examined.     

Evaluation of conventional and radiometric fecal culture and a commercial DNA probe for diagnosis of Mycobacterium paratuberculosis infections in cattle.

Radiometric (RCM) and conventional fecal culture (HEY) and a commercial polymerase chain reaction/DNA probe were evaluated as diagnostic tests for subclinical paratuberculosis in dairy cattle using fecal specimens from a repository of paratuberculosis specimens. The case definition of subclinical bovine paratuberculosis was isolation of Mycobacterium paratuberculosis, by conventional or radiometric culture, from fecal samples or internal organs of dairy cattle without diarrhea or chronic weight loss. Animals designated as free of the disease originated exclusively from certified paratuberculosis-free herds in Wisconsin. Among 182 infected cattle, RCM and HEY fecal culture and the DNA probe had test sensitivities of 54.4%, 45.1% and 33.5%, respectively. Fecal samples from only 111 of the M. paratuberculosis-infected cows tested positive by at least one of the three tests and these cows were designated as fecal shedders; the remaining 71 were considered to have prepatent infections. Among the 111 M. paratuberculosis fecal shedders, RCM, HEY and the probe detected the organism in 89.2%, 73.8% and 55.0% of the fecal specimens, respectively. Herd prevalence significantly affected the sensitivity of all three diagnostic tests (p less than 0.05) but only affected the fecal shedder detection efficiency of the DNA probe (p less than 0.01). No positive DNA probe results were found on 100 randomly selected fecal samples from cows in four certified paratuberculosis-free herds, thus the DNA probe was 100% specific. Probe analyses could be performed in 24 h or less. Time to complete the culture-based tests was 12 wk for HEY and 7 wk for RCM.(ABSTRACT TRUNCATED AT 250 WORDS)