A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency.

BACKGROUND: Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation challenging because it is an allotetraploid, likely arising from hybridisation between diploid N. sylvestris and N. tomentosiformis ancestors. A draft assembly was recently published for N. tabacum, but because of the aforementioned genome complexities it was of limited utility due to a high level of fragmentation. RESULTS: Here we report an improved tobacco genome assembly, which, aided by the application of optical mapping, achieves an N50 size of 2.17 Mb and enables anchoring of 64% of the genome to pseudomolecules; a significant increase from the previous value of 19%. We use this assembly to identify two homeologous genes that explain the differentiation of the burley tobacco market class, with potential for greater understanding of Nitrogen Utilization Efficiency and Nitrogen Use Efficiency in plants; an important trait for future sustainability of agricultural production. CONCLUSIONS: Development of an improved genome assembly for N. tabacum enables what we believe to be the first successful map-based gene discovery for the species, and demonstrates the value of an improved assembly for future research in this model and commercially-important species.

Characterizing dilute combustion instabilities in a multi-cylinder spark-ignited engine using symbolic analysis.

Spark-ignited internal combustion engines have evolved considerably in recent years in response to increasingly stringent regulations for emissions and fuel economy. One new advanced engine strategy ustilizes high levels of exhaust gas recirculation (EGR) to reduce combustion temperatures, thereby increasing thermodynamic efficiency and reducing nitrogen oxide emissions. While this strategy can be highly effective, it also poses major control and design challenges due to the large combustion oscillations that develop at sufficiently high EGR levels. Previous research has documented that combustion instabilities can propagate between successive engine cycles in individual cylinders via self-generated feedback of reactive species and thermal energy in the retained residual exhaust gases. In this work, we use symbolic analysis to characterize multi-cylinder combustion oscillations in an experimental engine operating with external EGR. At low levels of EGR, intra-cylinder oscillations are clearly visible and appear to be associated with brief, intermittent coupling among cylinders. As EGR is increased further, a point is reached where all four cylinders lock almost completely in phase and alternate simultaneously between two distinct bi-stable combustion states. From a practical perspective, it is important to understand the causes of this phenomenon and develop diagnostics that might be applied to ameliorate its effects. We demonstrate here that two approaches for symbolizing the engine combustion measurements can provide useful probes for characterizing these instabilities.

Pharmacokinetic interaction of abacavir (1592U89) and ethanol in human immunodeficiency virus-infected adults.

While in vitro results at clinically relevant concentrations do not predict abacavir (1592U89) interactions with drugs highly metabolized by cytochrome P450, the potential does exist for a pharmacokinetic interaction between abacavir and ethanol, as both are metabolized by alcohol dehydrogenase. Twenty-five subjects were enrolled in an open-label, randomized, three-way-crossover, phase I study of human immunodeficiency virus-infected male subjects. The three treatments were administration of (i) 600 mg of abacavir, (ii) 0.7 g of ethanol per kg of body weight, and (iii) 600 mg of abacavir and 0.7 g of ethanol per kg. Twenty-four subjects completed the study with no unexpected adverse events reported. Ethanol pharmacokinetic parameters were unchanged with abacavir coadministration. The geometric least squares mean area under the concentration curve extrapolated to infinite time for abacavir increased 41% (from 11.07 to 15.62 microg. h/ml), and the half-life increased 26% (from 1.42 to 1.79 h) in the presence of ethanol (mean ethanol maximum concentration in plasma of 498 microg/ml). The percentages of abacavir dose recovered in urine as abacavir and its two major metabolites were each altered in the presence of ethanol, but there was no change in the total percentage ( approximately 50%) of administered dose recovered in the 12-h collection interval. In conclusion, while a single 600-mg dose of abacavir does not alter blood ethanol concentration, ethanol does increase plasma abacavir concentrations.

Abacavir: absolute bioavailability, bioequivalence of three oral formulations, and effect of food.

STUDY OBJECTIVES: Study A: to determine the absolute bioavailability of a single 300-mg abacavir hemisulfate tablet. Study B: to determine the bioequivalence of two oral abacavir formulations (300-mg hemisulfate tablet, 100-mg succinate caplet), the effect of food on the bioavailability of the 300-mg hemisulfate tablet, and the bioavailability of the hemisulfate tablet relative to the hemisulfate solution. DESIGN: Phase I, randomized, open-label, balanced two- (study A) and three- or four-period (study B), crossover studies. SETTING: Two clinical research centers. SUBJECTS: Six men infected with the human immunodeficiency virus (HIV), aged 27-39 years (study A), and 18 HIV-infected men and women, aged 21-50 years (study B). INTERVENTIONS: In study A, all subjects received a single, oral 300-mg tablet of abacavir hemisulfate or a single, intravenous infusion of abacavir hemisulfate 150 mg over 60 minutes. In study B, all subjects received each of three single-dose treatments: three 100-mg abacavir succinate caplets in a fasted state, one 300-mg abacavir hemisulfate tablet in a fasted state, and one 300-mg abacavir hemisulfate tablet with a high-fat breakfast. Twelve subjects in study B also received a fourth treatment of abacavir hemisulfate 300 mg as an oral solution in a fasted state. Plasma samples collected for 24 hours (study A) or 12 hours (study B), and urine samples collected for 12 hours (study A) were analyzed by validated high-performance liquid chromatographic methods. MEASUREMENTS AND MAIN RESULTS: Abacavir pharmacokinetic parameters were calculated using standard, noncompartmental methods. In study A, the geometric least square (GLS) mean absolute bioavailability of oral abacavir was 83% (range 65-107%). In study B, the hemisulfate tablet was bioequivalent to the succinate caplet, but its time to maximum concentration (Tmax) occurred 30 minutes earlier. Administration of the abacavir hemisulfate tablet with food had no effect on area under the curve from time zero to infinity (AUC0-infinity), decreased maximum concentration (Cmax) by 26%, and delayed Tmax by 38 minutes. The relative bioavailability (GLS mean AUC0-infinity ratio) of the 300-mg abacavir hemisulfate tablet to solution was 101%, Cmax was 11% lower, and Tmax was unchanged. The most common drug-related adverse events associated with abacavir were nausea, vomiting, abdominal pain, and headache, all of which were mild. CONCLUSION: Based on our results, abacavir is safe and well tolerated and can be administered with or without meals.

Pharmacokinetics and disposition of the lipid-lowering drug acifran in normal subjects and in patients with renal failure.

The pharmacokinetics and metabolic fate of the antihyperlipidemic drug acifran were assessed after a single oral dose of the 14C-labeled drug to healthy male volunteers. Peak serum acifran and radioactivity concentrations were attained 1 to 2 hours after dosing, and the drug was eliminated with a half-life of 1.6 hours. Virtually all of the recovered dose was excreted in the urine. All of the serum and urinary radioactivity was caused by unconjugated acifran. In patients with moderate chronic renal failure, the binding of acifran to plasma proteins was decreased, and the plasma concentrations of total and unbound drug were greater than those of healthy subjects. Renal failure substantially reduced the plasma and renal clearance of total and particularly of unbound acifran, moderately reduced its volume of distribution, and increased its elimination half-life from 1.4 to 1.7 hours to 5.7 hours. The results show that acifran is very well absorbed, is rapidly eliminated, is excreted in the urine, and does not undergo any detectable biotransformation in healthy human subjects.

Acifran: a double-blind, randomized, placebo-controlled efficacy study in type IIa hyperlipoproteinemic patients.

The antihyperlipoproteinemic agent acifran (AY-25,712) was administered double-blind to 14 Type IIa hyperlipoproteinemic patients for 12 weeks in dosages of 100 mg t.i.d. or 300 mg t.i.d. An additional seven patients received placebo. Fasting plasma lipid and lipoprotein concentrations were determined at baseline (mean of 3 values), Week 8 (mean of 6- and 8-Week values), and Week 12 (mean of 10- and 12-Week values). At Week 8, patients receiving acifran 100 mg t.i.d. showed low-density lipoprotein (LDL) cholesterol levels which were 13% lower than pretreatment baseline (p less than 0.01) and 14% lower than patients given placebo (p less than 0.05); high-density lipoprotein (HDL) cholesterol levels were 11% higher compared with either baseline or the placebo group (p less than 0.05); the LDL/HDL ratio was 20% lower than baseline (p less than 0.001) and 21% lower than the placebo group (p less than 0.05); total cholesterol was 8% lower than that of the placebo group (p less than 0.05). There was no apparent relationship between changes in plasma lipid concentrations and acifran dose or treatment duration except for triglycerides, which at Week 12 were 25% lower than baseline (p less than 0.001) and 35% lower than the placebo group (p less than 0.05) only in the acifran 300 mg t.i.d. group, in which HDL-cholesterol was concurrently 18% higher compared with placebo (p less than 0.05). In this 12-week study acifran provided safe and effective treatment for Type IIa hyperlipoproteinemia.

Controlled trial of acifran in type II hyperlipoproteinemia.

The hypolipidemic effects of acifran were evaluated in a randomized, double-blind, placebo-controlled study of 30 patients with type IIa hyperlipoproteinemia. Plasma lipid and lipoprotein values were determined at baseline (mean of three values), again after a 2-week single-blind period of acifran dosing, and at 2-week intervals during a 10-week period of double-blind drug dosing. At week 8, subjects who received the lower dose of acifran (100 mg t.i.d.) showed significantly lower levels of total and low-density lipoprotein cholesterol and triglycerides compared with their baseline levels (P less than 0.01) or the placebo group (P less than 0.05). At week 12, subjects who received the higher dose of acifran (300 mg t.i.d.) had an increase in high-density lipoprotein levels of 16% (P less than 0.01) and a decrease in the ratio of low- to high-density lipoproteins of 22% compared with their baseline levels (P less than 0.01). There were no significant differences in lipid responses between the two groups receiving acifran. Transient mild flushing and pruritus were experienced by some subjects, but no subject failed to complete the study because of drug intolerance or side effects. The safety and efficacy demonstrated in this short-term therapeutic trial justify additional long-term studies with acifran.

Dietary influences on the hepatic mixed-function oxidase system in the rat after portacaval anastomosis.

Studies were undertaken to determine the influence of diet on the hepatic mixed-function oxidase system in rats after portacaval anastomosis. Male rats fed either a cereal-based or purified diet underwent portacaval anastomosis. Weight gain after surgery was highly dependent on the diet. Because rats fed the cereal-based diet weighed 50% less at 4-5 wk after portacaval shunt surgery than unoperated controls fed the same diet, pair-fed unoperated controls were also studied. Rats fed the purified diet grew normally after shunting and therefore studies with this diet did not require pair-fed controls. Shunted rats fed the cereal-based diet had lower liver weights, hepatic microsomal protein concentrations, ethylmorphine N-demethylase, aniline hydroxylase, and cytochromes P450 and b5 when compared with corresponding values in unoperated controls fed the same diet ad libitum; comparisons with pair-fed controls indicated that decreased intake of the cereal-based diet could account for part but not all of the changes seen after portacaval anastomosis. It was shown in rats fed the purified diet that sham operation had no effect on the mixed-function oxidase system, whereas portacaval anastomosis resulted in reduced liver weight, microsomal protein, ethylmorphine N-demethylase, aniline hydroxylase, and cytochrome P450. In comparing shunted rats fed the two types of diet, in contrast with the effects of these diets in normal rats, these hepatic microsomal mixed-function oxidase system components were generally lower in the shunted rats fed the cereal diet. It is concluded that although decreased mixed-function oxidase activity occurs after portacaval anastomosis in the rat, the diet can have an additional substantial influence. Dietary influences on drug oxidations may be an important consideration in drug therapy after portacaval anastomosis.

Cholesterol homeotasis in rats fed a purified diet.

The rate of whole bodyb cholesterol synthesis was measured in male Sprague-Dawley rats fed either a standard chow, cereal-based diet or a semi-synthetic purified diet consisting of casein, sucrose and lard. The purified diet significantly decreased daily fecal excretion of neutral and acidic sterols, the specific acitvity of hepatic 3-hydroxy-3-methylglutaryl coenzyme A reductase, the bile acid pool size, and total daily cholesterol synthesis in the rat, while increasing plasma cholesterol concentrations and the total body content of cholesterol. The increased body content of cholesterol occurred primarily in muscle and connective tissue and not in the liver. The data demonstrate the importance of quantitating the net tissue accumulatin of cholesterol for accurate measurement of daily sterol synthesis in growing animals when sterol balance measurements are used. Tissue accumulation accounted for 7% of total daily cholesterol synthesis in rats fed the cereal diet, and 20% of daily synthesis in animals fed the purified diet.

Changes in glomerulotubular dimensions, single nephron glomerular filtration rates and the renin-angiotensin system in hypothyroid rats.

Glomerular diameters (GD) and lengths of attached proximal convoluted tubules (TPL) were measured in nephrons dissected from the superficial (S), intermediate and juxtamedullary (JM) cortex (7-15 each) of acid-macerated kidneys of weight-matched (E) euthyroid and (H) hypothyroid (2-6 months after radioiodine treatment or thyroidectomy) male Sherman-Wistar rats. Incoordination of growth in H rats was evident in a more marked retardation in kidney than in total body growth. A similar incoordination of microstructural growth was evident in maintenance or GD within normal limits with respect to body weight while attached TPL fell 23% on the average below control values relative to body weight. These changes affected the total nephron population uniformly. As a result, GD/TPL in all nephrons increased significantly (p less than 0.01), by 27% in S and by 29% in JM nephrons. The glomerulotubular dimensional imbalance was associated with a marked and uniformly distributed reduction in single nephron glomerular filtration rate (ferrocyanide method), by 36% in S and JM nephrons. Plasma renin activity fell within normal limits while plasma renin substrate was decreased to 56% of control values. These findings are construed as evidence that growth retardation in hypothyroid rats affects the parenchyma of the kidney (and perhaps other viscera) more than the vasculature.

Respiration of 14CO2 by intact animals of various species given L-[1-14C]fucose or D-[1-14C]arabinose.

The production of 14CO2 from L-[1-14C]fucose and D-[1-14C]arabinose been studied in five mammalian species. Cats, guinea pigs, mice, and rabbits respired about 22% of the label of L-[1-14C]fucose or of D-[1-14C]arabinose within 6 h after intraperitoneal injection of the sugar. Rats respired only 1.5% of the L-fucose label and 5% of the D-arabinose label in the same time period. Liver homogenates from cat, guinea pig, and rabbit produced significantly more 14CO2 from L-[1-14C]fucose or D-[1-14C]arabinose than mouse or liver homogenates. Unlike those of the other species, guinea pig liver homogenates had very low L-fucose dehydrogenase activity. The results suggest that substantial catabolism of L-fucose and D-arabinose occurs in the tissues of some animal species. Investigators wishing to employ L-fucose as a tracer of glycoprotein metabolism must, therefore, ensure that the species that they employ does not metabolize L-fucose to products interfering with their studies.

Cholesterol homeostasis in the rat with a portacaval anastomosis.

Studies were undertaken to determine the effect of portacaval anastomosis on cholesterol homeostasis in rats fed sucrose/lard under conditions of normal body growth. Four to 6 weeks after portacaval shunt surgery, we found decreases in plasma cholesterol and triglyceride concentrations, total liver weight, and hepatic microsomal protein concentration. Measurements oof hepatic 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase (EC 1.1.1.34) activity showed decreases in specific activity and total liver activity in portacaval shunt rats, but the enzyme diurnal rhythm remained. Decreased reductase activity in shunted rats was not due to an altered Km for D-HMG-COA, nor was an enzyme inhibitor found in the livers of the portacaval shunt animals. Sterol balance measurements in rats with shunts showed a 22% decrease in whole body cholesterol synthesis rate compared to controls. These metabolic studies, coupled with postmortem data, showed diminished bile acid synthesis, unchanged fecal neutral steroid excretion, and decreased net tissue accumulation of cholesterol during growth. The decreased whole body cholesterol synthesis rate ultimately led to a diminished total carcass cholesterol concentration in the rats with shunts.

Lowering of blood pressure, plasma renin substrate, cholesterol and triglyceride by portacaval anastomosis in rats fed on a 60% sucrose/5% lard diet.

1. Portacaval anastomosis was carried out in ten rats fed on a 60% sucrose/5% lard diet, which induced moderate hypertriglyceridaemia, mild hypercholesterolaemia and normotension. 2. Plasma triglyceride was decreased to 45% of concentrations observed in ten pair-weighed control rats. 3. Plasma cholesterol concentrations were reduced to 58%, renin substrate to 70% and aortic blood pressure to 80% of control values by portacaval shunt surgery. 4. Individual blood pressures were directly related to plasma renin substrate concentrations.

A third dipeptide carrier system typified by l-prolyl-lhydroxyproline and independent of l-leucyl and beta-alanyl dipeptides in rat gut loops.

1. The intestinal transport of L-prolyl-L-hydroxyproline (10 mmol/l) was investigated in rat small gut loops in vivo under pentobarbitone anaesthesia. Osmolality of test solutions was adjusted to eliminate any positive effect of solvent drag on disappearance of solutes from the lumen. 2. L-Leucylglycine and beta-alanyl-L-histidine (carnosine), representative members of two distinctly different dipeptide transport groups previously delineated, were tested for competitive action on L-prolyl-L-hydroxyproline uptake at ten times equimolar concentration (100 mmol/l), but were found to have no effect on the carrier system. 3. L-Prolyl-L-hydroxyproline uptake was markedly blocked by other L-prolyl dipeptides, indicating that they shared a common carrier system. Disappearance of L-prolyl-L-hydroxyproline from the gut lumen was reduced from 48% 15 min-1 10 cm-1 (control, containing 70 mmol/l mannitol) to 11% or 20% in the presence of L-prolylglycine (100 mmol/l) or L-prolyl-L-leucine (25 mmol/l), respectively. 4. It was concluded that at least three separate dipeptide carrier protein systems exist in the rat small gut, the disappearance of L-prolyl-L-hydroxyproline from the gut lumen being inhibited by two other L-prolyl dipeptides but not by L-leucyl or beta-alanyl dipeptides.

Increased prevalence of coronary heart disease in analgesic nephropathy: relation to hypertension, hypertriglyceridemia and combined hyperlipidemia.

The prevalence of coronary heart disease (58%) in 43 patients with analgesic nephropathy with moderate to severe chronic renal failure was significantly higher than in the general population of the same age and sex. Mean serum triglyceride concentration and mean diastolic blood pressure were significantly higher in the group with coronary heart disease (214 mg/dl and 102 mm Hg, respectively) than in the group without it (162 and 94). Serum triglyceride values correlated inversely with GFR, indicating that hypertriglyceridemia was largely due to associated chronic renal failure; a specific effect of analgesic abuse on prevalence of heart disease, noted by others, could not be assessed in the absence of GFR-matched controls. The prevalence of coronary heart disease was significantly higher (81%) in the group with combined hyperlipidemia (hypertriglyceridemia and hypercholesteremia) compared to the groups without it or with normal serum triglyceride concentrations (44 and 41%, respectively). Hypotryptophanemia (a possible cause of hyperlipidemia in the nephrotic syndrome) was present in 77% of patients.

Efficacy and interactions of oxandrolone, halo-fenate and clofibrate in a factorial study on experimental acute nephrotic hyperlipidemia.

Nephrotic mixed hyperlipidemia may be associated with accelerated coronary artery disease. To investigate the response of experimental nephrotic hyperlipidemia to therapy, a 2(4) factorial study of sodium clofibrate and beta-benzalbutyrate, halofenate and oxandrolone (250, 150, 100 and 10 mg/kg/day, respectively) was carried out. Nephrotic syndrome was induced by a single i.p. injection of puromycin aminonucleoside (90 mg/kg) in 80 female white rats of average weight 160 g. Oxandrolone proved to be significantly hypotriglyceridemic in combined therapy (average fall, 38%; P less than .05), and also lowered serum total cholesterol and phospholipid concentrations (23% and 21% falls, P less than .01) and less than .05), due largely to synergistic interactions with clofibrate-like drugs. Hypocholesteremic effects (23 and 22% average falls) were also significant for halofenate (P less than .01) and clofibrate (P less than .05) . Serum triglyceride levels actually rose significantly (P less than .05) with drug combinations containing beta-benzalbutyrate. Clofibrate and its analogs (halofenate and beta-benzalbutyrate) produced significant hepatomegaly (mean responses of +18, +18 and +10%, respectively) whereas oxandrolone produced significant hepatic shrinkage (-10%)(P less than .05). Secondary effects (drug interactions) were also found; hypotriglyceridemic synergism (effects more than additive) occurred between oxandrolone and clofibrate or its analogs (P less than .05), whereas antagonism (effects less than additive) was observed within the clofibrate-like group (P less than .01 or less .05).

A study of serum and myocardial digitoxin concentrations in man during cardiac arrest.

In 22 digitalized (of a total of 39) patients studied at random by radioimmunoassay during cardiac arrest, the mean serum digoxin concentration was 2.6 (+/- 1.86, range 0.6-8.2) ng/ml, significantly higher (P less than 0.001) than the "eudigitalized" concentration (1.3 +/- 0.52, range 0.5-2.3 ng/ml) determined under carefully standardized conditions in a non-toxic population. Half of the arrest patients had serum digoxin levels in the toxic range (2.4 ng/ml or above), mainly due to significant renal failure (mean serum creatinine concentration 2.9 +/- 2.66 v. 1 +/- 0.26 mg/dl for non-toxic subjects, P less than 0.001), partly due to a higher mean daily digoxin dose (0.40 v 0.31 mg/day, P less than 0.05) and frequently associated with potent diuretic therapy (73 v 54%). A smaller fraction of digitalized patients survived, both short- (27%) and long-term (14%), than did non-digitalized subjects (35% and 26%, respectively). The mean myocardial digoxin concentration was 150 (+/- 63.3, range 52-252) ng/g with an average myocardial/serum ratio of 62.5 (range 38-91). There were significant positive correlations between the serum digoxin and left-ventricular myocardial digoxin concentration (r=0.8107, P less than 0.01) or serum creatinine concentration (r=0.4637, P less than 0.001).