Do Viruses Exchange Genes across Superkingdoms of Life?

Viruses can be classified into archaeoviruses, bacterioviruses, and eukaryoviruses according to the taxonomy of the infected host. The host-constrained perception of viruses implies preference of genetic exchange between viruses and cellular organisms of their host superkingdoms and viral origins from host cells either via escape or reduction. However, viruses frequently establish non-lytic interactions with organisms and endogenize into the genomes of bacterial endosymbionts that reside in eukaryotic cells. Such interactions create opportunities for genetic exchange between viruses and organisms of non-host superkingdoms. Here, we take an atypical approach to revisit virus-cell interactions by first identifying protein fold structures in the proteomes of archaeoviruses, bacterioviruses, and eukaryoviruses and second by tracing their spread in the proteomes of superkingdoms Archaea, Bacteria, and Eukarya. The exercise quantified protein structural homologies between viruses and organisms of their host and non-host superkingdoms and revealed likely candidates for virus-to-cell and cell-to-virus gene transfers. Unexpected lifestyle-driven genetic affiliations between bacterioviruses and Eukarya and eukaryoviruses and Bacteria were also predicted in addition to a large cohort of protein folds that were universally shared by viral and cellular proteomes and virus-specific protein folds not detected in cellular proteomes. These protein folds provide unique insights into viral origins and evolution that are generally difficult to recover with traditional sequence alignment-dependent evolutionary analyses owing to the fast mutation rates of viral gene sequences.

Effect of feeding 25-hydroxyvitamin D3 with a negative cation-anion difference diet on calcium and vitamin D status of periparturient cows and their calves.

Holstein cows (>1 gestation) were fed 1 of 3 diets during the last 13 d of gestation (ranged from 22 to 7 d). The control diet (16 cows) was formulated to provide 18,000 IU/d of vitamin D3 and had a dietary cation-anion difference (DCAD) of 165mEq/kg (DCAD=Na + K - Cl - S). The second diet (DCAD + D) provided the same amount of vitamin D3 but had a DCAD of -139mEq/kg (17 cows). The third diet (DCAD + 25D) had no supplemental vitamin D3 but provided 6mg/d of 25-(OH) vitamin D3 [25-(OH)D3] with a DCAD of -138mEq/kg (20 cows). Diets were fed until parturition and then all cows were fed a common lactation diet that contained vitamin D3. Negative DCAD diets reduced urine pH, with the greatest decrease occurring with the DCAD + D treatment. Urinary Ca excretion was greatest for cows fed DCAD + 25D followed by cows fed DCAD + D. Urinary pH was negatively correlated with urinary excretion of Ca for cows fed DCAD + D. No such correlation was observed with the DCAD + 25D treatment because substantial excretion of urinary Ca occurred at moderate urinary pH values for that treatment. Cows fed DCAD + 25D had greater serum concentrations of 25-(OH)D3 than other treatments from 5 d after supplementation started through 7 d in milk. Concentrations of 1,25-(OH)2D3 in serum were greatest in DCAD + 25D cows starting at 2 d before calving and continued through 7 d in milk. Serum Ca concentrations 5 d before calving were greatest for cows fed DCAD + 25D, but at other time points before and after parturition treatment did not affect serum Ca. Incidence of clinical hypocalcemia was not statistically different between treatments, but cows fed DCAD + 25 had the highest incidence rate (12.5, 0, and 20% for control, DCAD + D, and DCAD + 25D). Calves born from cows fed DCAD + 25D had greater concentrations of 25-(OH)D3 in serum at birth than calves from other treatments (before colostrum consumption), but concentrations were similar by 3 d of age. Concentrations of 25-(OH)D3 in colostrum and transition milk were increased by feeding DCAD + 25D, but by 28 d in milk treatment effects no longer existed. Overall, feeding 25-OH vitamin D with a negative DCAD diet increased vitamin D status of the cow and her newborn calf but had minimal effects on calcium status and did not have positive effects on the incidence of hypocalcemia.

Effects of dietary amylase and sucrose on productivity of cows fed low-starch diets.

Recent studies have observed positive effects of both sucrose and exogenous amylase on the productivity of dairy cattle. Our objective was to evaluate direct effects and interactions of amylase and sucrose on dry matter intake (DMI), milk production, and milk components. Forty-eight multiparous Holstein cows between 70 and 130 d in milk were randomly assigned to each of 4 pens (12 cows/pen). Pens were randomly assigned to treatment sequence in a 4 × 4 Latin square design, balanced for carryover effects. Treatment periods were 28 d, with 24 d for diet adaptation and 4d for sample and data collection. The treatments were a control diet (36% NDF and 21% starch), the control diet with amylase [0.5 g/kg of DM; Ronozyme RumiStar 600 (CT); DSM Nutritional Products Ltd., Basel, Switzerland], a diet with sucrose replacing corn grain at 2% of DM, and the sucrose diet with amylase (0.5 g/kg of DM). All data were analyzed with mixed models, including the fixed effects of sugar, amylase, and their interaction, and the random effects of period and pen. Milk data included the random effects of cow nested within pen and pen × period to provide the error term for the pen-level analysis. Dry matter intake was not affected by treatments. Milk yield and milk composition were not altered by the inclusion of sucrose or amylase; however, a tendency for an amylase × sucrose interaction was observed for milk protein content, reflecting slightly lower milk protein concentrations for amylase and sucrose treatments (3.00 and 2.99 ± 0.03%) compared with the control and amylase + sucrose treatments (3.02 and 3.03 ± 0.03%). Solids-corrected and fat-corrected milk yields were not significantly altered by treatment, although the direct effect of amylase approached significance for both variables, suggesting possible small increases with amylase supplementation (~0.5 kg/d). Feed efficiency (energy-corrected milk divided by dry matter intake) numerically increased with either amylase (1.57 ± 0.12) or sucrose (1.60 ± 0.12) treatment, but the combination of the 2 resulted in feed efficiency similar to the control treatment (both 1.50 ± 0.12). The inclusion of amylase or sucrose did not affect DMI, productivity, or feed efficiency in mid-lactation cows fed low-starch, high-fiber diets.

The effect of an exogenous amylase on performance and total-tract digestibility in lactating dairy cows fed a high-byproduct diet.

The objective of this experiment was to determine the performance and digestibility response of lactating dairy cows fed a reduced-starch diet containing a commercial amylase product. Treatments consisted of a normal-starch total mixed ration (NS-), a reduced-starch total mixed ration (RS-), and a reduced-starch total mixed ration with exogenous amylase (RS+) added to the concentrate. Treatments were assigned according to a replicated 3 × 3 Latin square design with 28-d periods. Twenty-three cows completed the study. Starch concentrations in NS-, RS-, and RS+ total mixed rations were 27.7, 23.5, and 22.7%, respectively. Effects of treatment on intake, milk production, milk composition, and total-tract apparent nutrient digestibility were evaluated during the last week of each period. Effects of amylase on in vitro starch digestibility of the NS- and RS- grain mixes were also measured. We hypothesized that the reduction in dietary starch in the RS- ration would decrease diet digestibility and limit milk production compared with NS- due to a decrease in available energy, and that RS+ would alleviate some of this decrease by increasing nutrient digestibility. Contrary to this hypothesis, the RS- diet did not affect intake or milk production relative to the NS- diet, except for increased milk urea nitrogen and a tendency for a decrease in milk protein yield. This lack of response is attributed to both low milk fat concentrations across treatments and greater than predicted dietary energy content preventing the energy deficit that was intended to occur with the reduced-starch rations. Cows fed the RS+ ration had the lowest production performance, with reduced milk, fat-corrected milk, protein, and lactose yields relative to cows fed NS-. Cows fed RS+ also had reduced lactose yield and tended to have reduced milk and fat-corrected milk relative to cows fed RS-. Despite the negative effects of the RS+ treatment on performance, exogenous amylase did increase both in vitro and in vivo measurements of digestibility. Although amylase increased nutrient digestibility, this did not translate into improved milk performance, likely due to the relatively high energy content of experimental diets compared with cow requirements.

The degradation of arabinoxylan-rich cell walls in digesta obtained from piglets fed wheat-based diets varies depending on digesta collection site, type of cereal, and source of exogenous xylanase.

The objective of the present study was to compare the ability of experimental and commercial xylanases to degrade, in vitro, the arabinoxylan (AX) fraction in digesta from 28-d-old piglets fed a wheat (Triticum aestivum)-based diet (49% wheat). Pigs were euthanized at 1, 2, 3, or 4 h after feeding; stomach and ileum contents were isolated and frozen and later used for the in vitro studies. Xylan solubilization provided information regarding the ability of the enzymes to degrade AX during the harsh in vivo conditions prevailing in the gastrointestinal tract. The hydrolytic capacity of a commercial xylanase was compared with that of an experimental xylanase using stomach digesta (pH 1.8) obtained at 4 h after feeding. Relative to the control, both enzymes increased (P < 0.001) xylan solubilization 3-fold. In the ileal digesta (1 h), xylan solubilization was increased by 36% (P < 0.001). Inclusion of arabinofuranosidases (Ara f) with xylanases increased xylan solubilization in stomach samples (P = 0. 007 and P = 0. 030) but not in ileal samples (P = 0.873 and P = 0.997). Our results illustrate clearly the importance of using different conditions and substrates when enzyme performance is studied in vitro as a prescreening tool for setting up in vivo trials.

Influence of the combination of 25-hydroxyvitamin D3 and a diet negative in cation-anion difference on peripartal calcium homeostasis of dairy cows.

Around parturition, many dairy cows experience varying degrees of hypocalcemia, which increases the incidence of several diseases in early lactation. In the current study, an established concept of feeding a diet negative in cation-anion difference (DCAD) was combined with oral supplementation of 25-hydroxyvitamin D(3) (25-OHD(3)) from d 270 of gestation until parturition. Fifty-six dairy cows were divided into 2 feeding groups (low DCAD and control). Fourteen animals of each group received a daily dosage of 3mg of 25-OHD(3). From the beginning of the treatment to d 10 after parturition, plasma samples for analysis of 25-OHD(3), 1,25-dihydroxyvitamin D(3), parathyroid hormone (PTH), Ca(2+), phosphate, the bone resorption marker CrossLaps, and osteocalcin were collected every other day, at calving, and at 6, 12, and 24h after calving. Urine samples for determination of macrominerals and measures of acid-base status were collected on d 6 of treatment and on d 6 after calving. The induction of a compensated metabolic acidosis by the animals on the DCAD diet could be demonstrated by decreased urinary pH. A linear correlation between treatment duration and the plasma concentration of 25-OHD(3) indicated effective absorption of 25-OHD(3) in supplemented animals. The mean plasma concentrations of Ca(2+) from d -4 prepartum to d 4 postpartum were significantly higher in animals treated with the combination of the low DCAD diet and 25-OHD(3) supplementation (1.24±0.02 mmol/mL) compared with the 3 other groups (low DCAD: 1.17±0.02 mmol/mL; control diet plus 25-OHD(3): 1.16±0.02 mmol/mL; control diet: 1.18±0.02 mmol/mL). We postulate that the increased tissue responsiveness to parathyroid hormone induced by the low DCAD is crucial for the observed positive effects of the 25-OHD(3) treatment.

Evaluation of a rapid-format antibody test and the tuberculin skin test for diagnosis of tuberculosis in two contrasting endemic settings.

OBJECTIVE AND SETTING: We evaluated a rapid-format antibody card test and the tuberculin skin test for diagnosis of active tuberculosis (TB) in high (Cairo, Egypt) and low (St. Louis, USA) prevalence areas. DESIGN: Prospective study of hospitalized TB patients and controls with other chest diseases. RESULTS: Test performance varied significantly in the two study sites. The antibody test detected 87% of 71 smear-positive pulmonary TB cases (86% of smear-negative pulmonary cases and 48% of TB meningitis cases) in Egypt; specificity was 82%. The tuberculin test was highly sensitive in Egypt in subjects with pulmonary TB (100%) but not in those with meningitis (23%); specificity was 70%. The sensitivity and specificity of the antibody test in St. Louis were 29% and 79%, respectively; 50% of St. Louis TB cases and 15% of controls had positive tuberculin tests. CONCLUSIONS: This convenient antibody card test may have value for diagnosis of patients suspected of having TB in high prevalence areas like Egypt. However, the specificity of the test is too low for it to be useful as a screening test. Our results suggest that neither the antibody test nor the tuberculin test have much diagnostic utility in low prevalence settings like St. Louis.