Interaction of 13C-enriched folate with dihydrofolate reductase studied by carbon magnetic resonance spectroscopy

In the presence of dihydrofolate reductase the carbon magnetic resonance spectrum of folate labeled at the benzoylcarbonyl carbon with ¹³C contains two broadened peaks arising from free and enzyme-bound folate, the latter appearing over 2 ppm upfield from free folate. Addition of TPN⁺ causes sharpening of both peaks indicating formation of a single folate-TPN⁺-enzyme ternary complex. Methotrexate specifically displaces folate from the ternary complex regenerating a single sharp resonance at 170.4 ppm characteristic of free folate. Line width changes show that folate is bound more tightly in the ternary than in the binary complex. Increased shielding of this carbonyl upon binding is inconsistent with its participation in a H-bond.     

Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter

Thousands of new phages have recently been discovered thanks to viral metagenomics. These phages are extremely diverse and their genome sequences often do not resemble any known phages. To appreciate their ecological impact, it is important to determine their bacterial hosts. CRISPR spacers can be used to predict hosts of unknown phages, as spacers represent biological records of past phage–bacteria interactions. However, no guidelines have been established to standardize host prediction based on CRISPR spacers. Additionally, there are no tools that use spacers to perform host predictions on large viral datasets. Here, we developed a set of tools that includes all the necessary steps for predicting the hosts of uncharacterized phages. We created a database of >11 million spacers and a program to execute host predictions on large viral datasets. Our host prediction approach uses biological criteria inspired by how CRISPR–Cas naturally work as adaptive immune systems, which make the results easy to interpret. We evaluated the performance using 9484 phages with known hosts and obtained a recall of 49% and a precision of 69%. We also found that this host prediction method yielded higher performance for phages that infect gut-associated bacteria, suggesting it is well suited for gut-virome characterization.     

Benefits of long-term beta-blockade in experimental chronic aortic regurgitation

The objective of this study was to assess the long-term effects of beta-blockade on survival and left ventricular (LV) remodeling in rats with aortic valve regurgitation (AR). The pharmacological management of chronic AR remains controversial. No drug has been definitively proven to delay the need for valve replacement or to affect morbidity and/or mortality. Our group has reported that the adrenergic system is activated in an animal model of AR and that adrenergic blockade may help maintain normal LV function. The effects of prolonged treatment with a beta-blocker are unknown. Forty Wistar rats with severe AR were divided into 2 groups of 20 animals each and treated with metoprolol (Met, 25 mg.kg(-1).day(-1)) or left untreated for 1 yr. LV remodeling was evaluated by echocardiography. Survival was assessed by Kaplan-Meir curves. Hearts were harvested for tissue analysis. All Met-treated animals were alive after 6 mo vs. 70% of untreated animals. After 1 yr, 60% of Met-treated animals were alive vs. 35% of untreated animals (P = 0.028). All deaths, except one, were sudden. There were no differences in LV ejection fraction (all >50%) or LV dimensions. LV mass tended to be lower in the Met-treated group. There was less subendocardial fibrosis in this group, as well as lower LV filling pressures (LV end-diastolic pressure). beta-Adrenergic receptor ratio (beta(1)/beta(2)) was improved. One year of treatment with Met was well tolerated. Met improved 1-yr survival, minimized LV hypertrophy, improved LV filling pressures, decreased LV subendocardial fibrosis, and helped restore the beta-adrenergic receptor ratio.     

Microbial and plant-derived compounds both contribute to persistent soil organic carbon in temperate soils

Our study tests the emerging paradigm that biochemical recalcitrance does not affect substantially long-term (50 years) SOC persistence. We analyzed the molecular composition of SOC in archived soils originating from four European long-term bare fallow experiments (Askov, Rothamsted, Versailles and Ultuna). The soils had been collected after various periods (up to 53 years) under bare fallow. With increasing duration of bare fallow without new organic inputs, the relative abundance of cutin- and suberin-derived compounds declined substantially, and the abundance of lignin-derived compounds was close to zero. Conversely, the relative abundance of plant-derived long-chain alkanes remained almost constant or increased during the bare fallow period. The relative abundance of N-containing compounds, considered to be abundant in SOC derived from microbial activity, increased consistently illustrating that microbial turnover of SOC continues even when plant inputs are stopped. The persistence of the different families of plant-derived compounds differed markedly over the scale of half a century, which may be ascribed to their contrasting chemical characteristics and recalcitrance, or to differences in their interactions with the soil mineral matrix, and likely some combination since chemical composition drives the degree of mineral association. Using soil from this unique set of long-term bare fallow experiments, we provide direct evidence that multi-decadal scale persistent SOC is enriched in microbe-derived compounds but also includes a substantial fraction of plant-derived compounds.     

Detection of QTL for milk production on Chromosomes 1 and 6 of Holstein cattle

Seventy to 75 sons of each of six Holstein sires were assayed for genotypes at a number of microsatellite loci spanning Chromosomes (Chrs) 1 and 6. The number of informative loci varied from three to eight on each chromosome in different sire families. Linkage order and map distance for microsatellite loci were estimated using CRI-MAP. Estimates of QTL effect and location were made by using a least squares interval mapping approach based on daughter yield deviations of sons for 305-d milk, fat, protein yield, and fat and protein percentage. Thresholds for statistical significance of QTL effects were determined from interval mapping of 10,000 random permutations of the data across the bull sire families and within each sire family separately. Across-sire analyses indicated a significant QTL for fat and protein yield, and fat percentage on Chr 1, and QTL effects on milk yield and protein percentage that might represent one or two QTL on Chr 6. Analyses within each sire family indicated significant QTL effects in five sire families, with one sire possibly being heterozygous for two QTLs. Statistically significant estimates of QTL effects on breeding value ranged from 340 to 640 kg of milk, from 15.6 to 28.4 kg of fat, and 14.4 to 17.6 kg of protein. Received: 19 November 1999 / Accepted: 31 August 2000     

Ustilago maydis Mating Hyphae Orient Their Growth toward Pheromone Sources

Snetselaar, K. M., Bolker, M., and Kahmann, R. 1996. Ustilago maydis mating hyphae orient their growth toward pheromone sources. Fungal Genetics and Biology 20, 299-312. When small drops of Ustilago maydis sporidia were placed 100-200 μm apart on agar surfaces and covered with paraffin oil, sporidia from one drop formed thin hyphae that grew in a zig-zag fashion toward the other drop if it contained sporidia making the appropriate pheromone. For example, a2b2 mating hyphae grew toward a1b1 and a1b2 mating hyphae, and the filaments eventually fused tip to tip. Time-lapse photography indicated that the mating hyphae can rapidly change orientation in response to nearby compatible sporidia. When exposed to pheromone produced by cells in an adjacent drop, haploid sporidia with the a2 allele began elongating before sporidia with the a1 allele. Sporidia without functional pheromone genes responded to pheromone although they did not induce a response, and sporidia without pheromone receptors induced formation of mating hyphae although they did not form mating hyphae. Diploid sporidia heterozygous at b but not at a formed straight, rigid, aerial filaments when exposed to pheromone produced by the appropriate haploid sporidia. Again, the a2a2b1b2 strain formed filaments more quickly than the a1a1b1b2 strain. Taken together, these results suggest that the a2 pheromone diffuses less readily or is degraded more quickly than the a1 pheromone.