Predicting feed intake in confined beef cows.

Six existing equations (three for nonlactating and three for lactating; NRC, 1987, Predicting feed intake of food-producing animals. Washington, DC: The National Academies Press, National Academy of Science; doi: 10.17226/950; NRC, 1996, Nutrient requirements of beef cattle, 7th Revised Edition: Update 1996. Washington, DC: The National Academies Press; doi: 10.17226/9791; Hibberd and Thrift, 1992. Supplementation of forage-based diets. J. Anim. Sci. 70:181. [Abstr]) were evaluated for predicting feed intake in beef cows. Each of the previously published equations are sensitive to cow-shrunk BW and feed energy concentration. Adjustments in feed intake prediction are provided for level of milk yield in NRC (1987. Predicting feed intake of food-producing animals. Washington, DC: The National Academies Press, National Academy of Science; doi: 10.17226/950) and NRC (1996 Nutrient requirements of beef cattle, 7th Revised Edition: Update 1996. Washington, DC: The National Academies Press; doi: 10.17226/9791) equations. The equation published in 1996 used data generated between 1979 and 1993. Our objectives were to validate the accuracy of the published equations using more recent data and to propose alternative prediction models. Criteria for inclusion in the evaluation dataset included projects conducted or published since 2002, direct measurement of feed intake, adequate protein supply, and pen feeding (no metabolism crate data). After removing outliers, the dataset included 53 treatment means for nonlactating cows and 32 treatment means for lactating cows. Means for the nonlactating dataset were dry matter intake (DMI) = 13.2 ±â€…2.9 kg/d, shrunk body weight (SBW) = 578 ±â€…83.9 kg, body condition score = 5.7 ±â€…0.73, and Mcal net energy for maintenance (NEm)/kg of feed = 1.27 ±â€…0.15 Mcal/kg. Means for the lactating dataset were DMI = 14.6 ±â€…2.24 kg/d, SBW = 503 ±â€…73.4 kg, body condition score = 4.7 ±â€…0.58, and Mcal NEm/kg feed = 1.22 ±â€…0.16. Simple linear regression was used to determine slope, intercept, and bias when observed DMI (y) was regressed against predicted DMI (x). The NRC (1996. Nutrient requirements of beef cattle, 7th Revised Edition: Update 1996. Washington, DC: The National Academies Press; doi: 10.17226/9791) nonlactating equation underestimated feed intake in diets moderate to high in energy density with intercept differing from 0 and slope differing from one (P ≤ 0.01). Average deviation from observed values was 2.4 kg/d. Similarly, when the NRC (1996. Nutrient requirements of beef cattle, 7th Revised Edition: Update 1996. Washington, DC: The National Academies Press; doi: 10.17226/9791) equation was used to predict DMI in lactating cows, the slope differed from one (P < 0.01) with average deviation from observed values of 3.0 kg/d. New models were developed by pooling the two datasets and including a categorical variable for stage of production (0 = nonlactating and 1 = lactating). Continuous variables included study-average SBW0.75 and diet NEm, Mcal/kg. The best-fit empirical model accounted for 68% of the variation in daily feed intake with standard error of the estimate Sy root mean squared error = 1.31. The proposed equation needs to be validated with independent data.

Diet and monensin influence the temporal dynamics of the rumen microbiome in stocker and finishing cattle.

BACKGROUND: Stocker cattle diet and management influence beef cattle performance during the finishing stage, but knowledge of the dynamics of the rumen microbiome associated with the host are lacking. A longitudinal study was conducted to determine how the feeding strategy from the stocker to the finishing stages of production affects the temporal dynamics of rumen microbiota. During the stocker phase, either dry hay or wheat pasture were provided, and three levels of monensin were administrated. All calves were then transported to a feedlot and received similar finishing diets with or without monensin. Rumen microbial samples were collected on d 0, 28, 85 during the stocker stage (S0, S28 and S85) and d 0, 14, 28, 56, 30 d before slaughter and the end of the trial during the finishing stage (F0, F14, F28, F56, Pre-Ba, and Final). The V4 region of the bacterial 16S rRNA gene of 263 rumen samples was sequenced. RESULTS: Higher alpha diversity, including the number of observed bacterial features and the Shannon index, was observed in the stocker phase compared to the finishing phase. The bacterial amplicon sequence variants (ASVs) differentiating different sampling time points were identified. Dietary treatments during the stocker stage temporally impact the dynamics of rumen microbiota. For example, shared bacteria, including Bacteroidales (ASV19) and Streptococcus infantarius (ASV94), were significantly higher in hay rumen on S28, S85, and F0, while Bacteroidaceae (ASV11) and Limivicinus (ASV15) were more abundant in wheat. Monensin affected rumen microbial composition at a specific time. Transportation to feedlot significantly influenced microbiome structure and diversity in hay-fed calves. Bacterial taxa associated with body weight were classified, and core microbiotas interacted with each other during the trial. CONCLUSIONS: In summary, the temporal dynamics of the rumen microbiome in cattle at the stocker and finishing stage are influenced by multiple factors of the feeding strategy. Diet at the stocker phase may temporarily affect the microbial composition during this stage. Modulating the rumen microbiome in the steers at the stocker stage affects the microbial interactions and performance in the finishing stage.

Vitamin and Trace Element Nutrition of Stocker Cattle on Small Grain and Winter Annual Pastures.

This article reviews the trace mineral and macro mineral content of small grain forages and the potential role in the health of cattle grazing the forages. Reasons for the variability of trace mineral content in small grain forages are discussed, as well as the role of antagonists, such as sulfur and molybdenum, in creating trace mineral deficiencies. The sampling of cattle for the determination of trace mineral statues is described, including which samples to collect for analysis, as well as sample handling. The authors offer a useful discussion on the vitamin content of small grain forages, and conclude that vitamin supplementation is not necessary.

Immune phenotype is differentially affected by changing the type of bovine respiratory disease vaccine administered at revaccination in beef heifers.

During preconditioning, modified-live vaccines are frequently administered to beef calves before weaning. In this study, we began to characterize the immune phenotype of calves that received a modified-live vaccination at 3-4 months of age and then either received the same modified-live or an inactivated vaccine upon arrival at the feedlot (weaning) and 28 days post-arrival (booster). Innate and adaptive immune measures were assessed before revaccination and 14 and 28 days post. Heifers that received three doses of the modified-live vaccine exhibited a relatively balanced immune response based on increases in mean cytokine concentrations (IL-17, IL-21) and total immunoglobulin-G (IgG) and subsets IgG1 and IgG2, which are related to both arms of the adaptive immune system. Conversely, heifers that received one dose of modified live and two doses of the inactivated vaccine had a more robust neutrophil chemotactic response and greater serum-neutralizing antibody titers, resulting in an enhanced innate immune and a skewed proinflammatory response. These results indicate that the revaccination protocol used after initial vaccination with a modified-live vaccine differentially influences the immune phenotype of beef calves, with three doses of modified live inducing potentially immune homeostasis and a combination of modified live and inactivated vaccines inducing a skewed immune phenotype. However, more research is needed to determine the protective efficacy of these vaccination protocols against disease.

The Effects of Respiratory Vaccine Type and Timing on Antibody Titers, Immunoglobulins, and Growth Performance in Pre- and Post-Weaned Beef Calves.

In order to examine the effects of vaccine type and timing of crossbred beef calves (n = 151) were assigned to one of three BRD vaccination protocols stratified by breed of sire, sex, and date of birth, which included: (1) KM-a pentavalent killed viral (KV) vaccine at 2 to 3 months of age (D 0) and a pentavalent modified-live viral (MLV) vaccine at weaning (D 127); (2) MM-MLV on D 0 and revaccinated on D 127 or (3) WN-MLV at weaning and D 140. Vaccination treatment did not affect performance nor BRSV serum-neutralizing antibody titers. Serum-neutralizing antibody titers to BVDV-1 were greatest for the MM through D 154. However, following booster (KM) or initial vaccination (WN) at D 127, titers increased for the other treatment groups to higher values (KM) by the end of the study. Delay of initial vaccination until weaning may have delayed specific antibody response in the WN group and skewed the immune response towards a Th-1 or cell-mediated response. Overall, the inclusion of an MLV in the vaccine protocol resulted in a more robust antibody response, and the timing of vaccination may affect the onset of efficacious and robust vaccine responses.

Association of maternal temperament and offspring disposition on growth performance.

Animal behavior is complex and varies in definition, depending upon specific traits under observation. Temperament is one component of behavior, that in cattle, is described as the level of fearfulness to a novel or threatening environment. Temperament is a heritable trait which is important since aggressiveness and docility contribute to reproductive success, growth, and carcass quality. We observed maternal temperament at calving and the subsequent influence, if any, on offspring disposition at weaning and their effects collectively on growth performance and carcass traits. Maternal behaviors at calving were observed at four locations within the University of Arkansas system. Cows were assigned a maternal disposition score (MDS) at calving; a scale from 1 to 5 in which aggression decreases. At weaning, calves were assigned a chute score (CS); a scale from 1 to 6 in which aggression increases. Both scoring systems have been previously established. Blood was collected during the 56-d backgrounding period postweaning for blood glucose analysis. Data were analyzed using GLIMMIX procedures of SAS (α = 0.05). The relationship between the two scoring systems was determined with a Pearson correlation (P = 0.22). Animal was the experimental unit and blocked by location for all dependent variables. Location, sex, diet, and MDS were included in the class as covariables for all growth performance and carcass data related to CS. Cows that were more aggressive birthed heavier calves (P < 0.01) compared to indifferent cows. Calves born to cows with either very aggressive or very attentive (MDS of 2 or 3, respectively) scores were heavier upon feedlot entry (P = 0.03) compared to those from indifferent or apathetic cows (MDS of 4 or 5, respectively). Calves defined as nervous and restless (CS of 3 and 2, respectively) were heavier at weaning compared to docile calves (P < 0.01). Restless calves were heavier compared to nervous calves upon arrival and exiting the feedlot (P ≤ 0.01). Calves that were docile at weaning had greater marbling compared to calves that were restless (P ≤ 0.01). Calves that were restless at weaning had greater lean muscle area compared to calves that were nervous (P = 0.05). No definitive relationship was determined between dam and calf temperament. However, the results suggest temperament does impact growth performance and carcass traits but whether the influence comes from the dam or calf temperament, specifically, remains unanswered.

Presence of higenamine in beetroot containing 'foodstuffs' and the implication for WADA-relevant anti-doping testing.

Higenamine is an alkaloid found within plant species including some that are used in traditional Asian and Chinese herbal medicines. Identified as having mixed mode adrenergic receptor activity, higenamine is present within some nutritional supplements marketed for stimulant and/or weight loss. Its inclusion within nutritional supplements can be via its natural presence within botanical ingredients or as a synthetic additive, often added in mg amounts. The World Anti-doping Agency (WADA) prohibited list has contained higenamine since 2017 as banned at all times in the beta-2 agonist (S3) category, with a reporting level of 10 ng/ml for the free parent form in urine. In this study, an investigation into the content of beetroot or beetroot-containing foodstuffs and supplement products was conducted. Higenamine was confirmed as present within the majority of foodstuffs and supplements, with experimental evidence that higenamine can arise within beetroot extracts through heating. The results in this paper demonstrate the first reported evidence of a link between beetroot and this WADA prohibited substance. To investigate the link between intake and excretion, concentrated beetroot drinks were consumed by six individuals and higenamine quantified in their urine. Free higenamine was detected in the urine of all individuals, with maximum measured concentration in samples of less than 1% of the current WADA reporting limit. Although the risk of an inadvertent doping violation by consumption of the foodstuffs and products investigated in this study is low, beetroot as a source of higenamine should be considered by athletes.

Strain level and comprehensive microbiome analysis in inflammatory bowel disease via multi-technology meta-analysis identifies key bacterial influencers of disease.

Objective: Inflammatory bowel disease (IBD) is a heterogenous disease in which the microbiome has been shown to play an important role. However, the precise homeostatic or pathological functions played by bacteria remain unclear. Most published studies report taxa-disease associations based on single-technology analysis of a single cohort, potentially biasing results to one clinical protocol, cohort, and molecular analysis technology. To begin to address this key question, precise identification of the bacteria implicated in IBD across cohorts is necessary. Methods: We sought to take advantage of the numerous and diverse studies characterizing the microbiome in IBD to develop a multi-technology meta-analysis (MTMA) as a platform for aggregation of independently generated datasets, irrespective of DNA-profiling technique, in order to uncover the consistent microbial modulators of disease. We report the largest strain-level survey of IBD, integrating microbiome profiles from 3,407 samples from 21 datasets spanning 15 cohorts, three of which are presented for the first time in the current study, characterized using three DNA-profiling technologies, mapping all nucleotide data against known, culturable strain reference data. Results: We identify several novel IBD associations with culturable strains that have so far remained elusive, including two genome-sequenced but uncharacterized Lachnospiraceae strains consistently decreased in both the gut luminal and mucosal contents of patients with IBD, and demonstrate that these strains are correlated with inflammation-related pathways that are known mechanisms targeted for treatment. Furthermore, comparative MTMA at the species versus strain level reveals that not all significant strain associations resulted in a corresponding species-level significance and conversely significant species associations are not always re-captured at the strain level. Conclusion: We propose MTMA for uncovering experimentally testable strain-disease associations that, as demonstrated here, are beneficial in discovering mechanisms underpinning microbiome impact on disease or novel targets for therapeutic interventions.

Meta-analysis of the effects of monensin on performance of beef replacement heifers and beef cows.

Although performance benefits of monensin have been extensively studied in finishing cattle, growing cattle, and dairy cows, considerably less published work is available evaluating response to monensin supplementation in cow-calf production systems. This meta-analysis investigated the impacts of monensin on performance of beef cows and developing replacement heifers. The replacement heifer analysis was conducted using data from 18 different peer-reviewed publications and experiment station reports. The mature cow analysis included 21 different publications and experiment station reports. The metaphor package (version 2.4-0; Viechtbauer, 2010) for R (version 4.0.3; www.r-project.org) was used to determine the overall effect size of monensin compared to a negative control. Each study's n, means, and SEM or P value was used to calculate the mean difference and estimate of within study variance for responses of interest. In replacement heifers, monensin treatment increased (P < 0.01); average daily gain (+0.03 ± 0.008 kg/d), feed efficiency (+0.013 ± 0.008 gain:feed), and percentage cycling before the breeding season (+15.9 ± 5.13%); while decreasing (P < 0.01): dry matter intake (0.293 ± 0.081 kg), and age at puberty (-8.9 ± 1.48 d). Six studies reporting ad libitum forage intake for mature cows showed decreased (P = 0.008) DMI by 0.85 ± 0.32 kg/d. Six studies reported milk yield and revealed an increase (P = 0.01) of 0.39 ± 0.15 kg/d when cows were supplemented with monensin. Monensin supplementation resulted in a reduction (P = 0.02) in days to first estrus by 18 ± 8.2 d and percentage of cows exhibiting estrus prior to the breeding season was increased by 19 ± 8% (P = 0.03). There were no differences in artificial insemination pregnancy nor total pregnancy for either the heifer or mature cow data sets. This analysis indicates potential for use of monensin in heifer development and beef cow production systems. Further research is needed to elucidate the effects on reproductive efficiency, DMI, milk production, weight, and body composition change.

Meta-analysis of the effects of monensin on growth and bloat of cattle on pasture.

Monensin has been part of the beef production landscape for over 45 years. Although first approved for use in finishing cattle, it has since been approved for cattle in extensive production systems and has been an economical way to increase performance of forage-fed animals. This meta-analysis investigated the impacts of monensin on performance of stocker cattle on high-forage diets. The stocker performance analysis resulted from 38 experiments with 73 mean comparisons; bloat analysis was conducted with 12 experiments with 23 mean comparisons. The metaphor package (version 2.4-0) for R (version 4.0.3; www.r-project.org) was used to determine the overall effect size of monensin compared to a negative control. Each study's n, means, and SEM or P-value was used to calculate the mean difference and estimate of within-study variance for responses of interest. Moderators of monensin response considered in the analysis were delivery method, dose, study duration, initial calf BW, diet ME and CP, and forage category. Initial BW and basal ADG averaged 236 ± 45.9 kg and 0.72 ± 0.28 kg, respectively. In the ADG analysis, the only significant moderator of those considered was length of the study (P < 0.01); as duration of the study increased, the ADG response to monensin decreased by 0.0007 kg/day. For the average 112-day length of study, the average monensin response was estimated to be 0.0784 kg/day increase in ADG, approximately 10% above controls. Sufficient information was presented in 18 citations representing 40 mean comparisons for determining the effect of monensin on BW at the end of the experiment. The response model (P < 0.01) for ending BW, kg = 22.3-0.05 (initial calf BW, kg). Thus, for the average initial BW of 235 kg the average monensin response was estimated to be 10.6 kg increase in average ending BW. The incidence (-20%) and severity (-0.7 bloat score) of bloat was found to be reduced in bloat-prone pastures. There is ample evidence that monensin increases performance of growing calves on high forage diets along with reducing the incidence and severity of bloat.

Effects of supplementation rate of an extruded dried distillers' grains cube fed to growing heifers on voluntary intake and digestibility of bermudagrass hay.

Our objectives were to 1) investigate the difference in chemical composition and disappearance kinetics between loose dried distillers' grains (DDG) and extruded DDG cubes and 2) evaluate the effects of supplementation rate of extruded DDG cubes on voluntary dry matter intake (DMI), rate and extent of digestibility, and blood parameters of growing beef heifers offered ad libitum bermudagrass (Cynodon dactylon) hay. To characterize the changes in chemical composition during the extrusion process, loose and extruded DDG were evaluated via near-infrared reflectance spectroscopy, and dry matter (DM) disappearance kinetics were evaluated via time point in situ incubations. Extruded DDG cubes had greater (P ≤ 0.01) contents of fat, neutral detergent insoluble crude protein, and total digestible nutrients, but lower (P ≤ 0.01) neutral and acid detergent fiber than loose DDG. Additionally, the DM of extruded DDG cubes was more immediately soluble (P < 0.01), had greater (P < 0.01) effective degradability and lag time, and tended (P = 0.07) to have a greater disappearance rate than loose DDG. In the 29-d supplementation rate study, 23 Charolais-cross heifers were randomly assigned to one of four supplemental treatments: 1) control, no supplement; 2) low, 0.90 kg DDG cubes per d; 3) intermediate, 1.81 kg DDG cubes per d; or 4) high, 3.62 kg DDG cubes per d. Titanium dioxide was used as an external marker to estimate fecal output and particulate passage rate (Kp). Blood was collected from each animal to determine supplementation effects on blood metabolites. Indigestible neutral detergent fiber was used as an internal marker to assess the rate and extent of hay and diet DM digestibility (DMD). Increasing supplementation rate increased Kp and total diet DMI linearly (P < 0.01), yet linearly decreased (P < 0.01) hay DMI. Hay DMD decreased quadratically (P < 0.01), while total diet DMD increased linearly (P < 0.01) with increased DDG cube inclusion. Supplemented heifers had greater (P = 0.07) blood urea nitrogen concentrations than control animals 4 h post-supplementation. Intermediate and high rates of supplementation resulted in lower (P < 0.01) serum nonesterified fatty acid concentrations post-supplementation than control heifers. Concentrations of serum glucose and lactate were greatest (P ≤ 0.06) 8 h post-supplementation. Our results suggest that extruded DDG cubes may be an adequate supplement for cattle consuming moderate-quality forage, and further research is warranted.

Growing cattle are oftentimes provided supplemental concentrate as a source of protein and energy in order to meet performance goals when consuming low-quality forages. The effects of supplemental concentrate on forage intake vary, which may be related to the quality of forage and the characteristics of the supplement being evaluated. Dried distillers' grains (DDG) are a by-product of ethanol production and have become a common supplement for growing cattle due to the increased energy and rumen undegradable protein content. A stable DDG cube made via a novel extrusion process may be advantageous for pasture supplementation due to the reduced risk of loss of product from wind and soil mixing that is common with loose DDG. The effects of supplementation rate of traditional concentrate sources on forage intake are abundant, but research regarding extruded DDG cubes is almost nonexistent. Thus, our objective was to evaluate extruded DDG cube supplementation rate (0, 0.90, 1.81, or 3.62 kg DDG cubes per d) for growing cattle on voluntary intake and digestibility of moderate-quality forage. Although increasing supplementation rate reduced forage intake and digestibility, total diet intake and digestibility were increased. Our results suggested that extruded DDG cubes have potential as a supplement for cattle consuming moderate-quality forage.

Association of Circulating Fibrocytes With Fibrostenotic Small Bowel Crohn's Disease.

BACKGROUND: Fibrocytes are hematopoietic cells with features of mesenchymal cells found in the circulation and inflammatory sites implicated in promoting fibrosis in many fibroinflammatory diseases. However, their role(s) in the development of intestinal fibrosis is poorly understood. Here, we investigated a potential role of fibrocytes in the development of fibrosis in Crohn's disease (CD) and sought factors that may impact their development and function. METHODS: Plasma and mononuclear cells were collected from patients with and without fibrostenotic CD. Fibrocytes defined as CD11b+, CD34+, and Collagen 1+ were correlated with clinical assessments of fibrosis, including evaluation using intestinal ultrasound. We measured the levels of relevant circulating molecules via Luminex and studied the effect of patient plasma proteins on fibrocyte differentiation. RESULTS: Fibrocyte numbers were increased in CD patients with stricturing Crohn's disease compared with patients with an inflammatory phenotype (P = .0013), with strong correlation between fibrocyte numbers and acoustic radiation force impulse (ARFI), a measure of bowel elasticity on intestinal ultrasound (R = .8383, P = .0127). Fibrostenotic plasma was a more potent inducer of fibrocyte differentiation in both primary human monocytes and cell line and contained increased levels of cytokines implicated in fibrocyte differentiation compared with plasma from inflammatory patients. Interestingly, increased fibrocyte numbers at time of ultrasound were associated with escalation of medical therapy and endoscopic/surgical management of small bowel strictures at 30 months follow-up. CONCLUSIONS: Circulating fibrocytes strongly correlate with fibrostenotic disease in CD, and they may serve as predictors for escalation of medical +/- surgical therapy.

Intestinal strictures are thought to result from excessive deposition of extracellular matrix by activated mesenchymal cells. In this study, we provide evidence that supports a potential role of fibrocytes (bone marrow­derived mesenchymal precursors) in collagen deposition in Crohn's disease strictures. Inasmuch as fibrocyte numbers correlate with sonographic measures of bowel stiffness, fibrocyte numbers may predict the need for therapy escalation.

Water and forage intake, diet digestibility, and blood parameters of beef cows and heifers consuming water with varying concentrations of total dissolved salts.

The objective of this study was to investigate the effects of water quality on water intake (WI), forage intake, diet digestibility, and blood constituents in beef cows and growing beef heifers. This was a replicated 5 × 5 Latin square with five drinking water treatments within each square: 1) fresh water (Control); 2) brackish water (100 BRW treatment) with approximately 6,000 mg/kg total dissolved solids (TDS); 3) same TDS level as 100 BRW achieved by addition of NaCl to fresh water (100 SLW); 4) 50% brackish water and 50% fresh water to achieve approximately 3,000 mg/kg TDS (50 BRW); and 5) same TDS level as 50 BRW achieved by addition of NaCl to fresh water (50 SLW). Each of the five 21-d periods consisted of 14 d of adaptation and 5 d of data collection. Animals were housed individually and fed mixed alfalfa (Medicago sativa) grass hay cubes. Feed and WI were recorded daily. Data were analyzed with animal as the experimental unit. Age, treatment, and age × treatment were fixed effects, and animal ID within age was the random variable for intake, digestibility, and blood parameter data. Water and feed intake were greater than expected, regardless of age or water treatment. No treatment × age interactions were identified for WI (P = 0.71), WI expressed as g/kg body weight (BW; P = 0.70), or dry matter intake (DMI; P = 0.21). However, there was an age × treatment tendency for DMI when scaled to BW (P = 0.09) in cows consuming 100 BRW compared with fresh water. No differences were found for the other three treatments. Heifers provided 50 SLW water consumed less (P < 0.05) feed (g/kg BW) compared with heifers provided fresh water and 100 BRW. No differences (P > 0.05) in water, DMI, feed intake, or diet digestibility were found due to water quality treatment. In conclusion, under these conditions, neither absolute WI, absolute DMI, nor diet digestibility was influenced by the natural brackish or saline water used in this experiment. These results suggest that further research is necessary to determine thresholds for TDS or salinity concentration resulting in reduced water and/or feed intake and diet digestibility.

Differential Effect of Genetic Burden on Disease Phenotypes in Crohn's Disease and Ulcerative Colitis in a Canadian Cohort.

BACKGROUND AND AIMS: Crohn's disease (CD) and ulcerative colitis (UC) demonstrate considerable phenotypic heterogeneity and course. Accurate predictors of disease behaviour are lacking. The contribution of genetics and specific polymorphisms is widely appreciated; however, their cumulative effect(s) upon disease behaviour remains poorly understood. Here, we investigate the relationship between genetic burden and disease phenotype in a Canadian inflammatory bowel disease (IBD) Cohort. METHODS: We retrospectively examined a cohort of CD and UC patients recruited from a single tertiary referral center genotyped using a Goldengate Illumina platform. A genetic risk score (GRS) incorporating strength of association (log odds ratio) and allele dose for 151 IBD-risk loci was calculated and evaluated for phenotypic associations. RESULTS: Among CD patients, higher GRS was associated with earlier onset of disease (regression coefficient -2.19, 95% confidence interval [CI] -3.77 to -0.61, P = 0.007), ileal disease (odds ratio [OR] 1.45), stricturing/penetrating disease (OR 1.72), perianal disease (OR 1.57) and bowel resection (OR 1.66). Higher GRS was associated with use of anti-tumor necrosis factor (TNF) (P < 0.05) but not immunomodulators. Interestingly, we could not demonstrate an association between higher GRS and family history of IBD (OR 1.27, P = 0.07). Onset of disease remained statistically significant for never smokers (P = 0.03) but not ever smokers (P = 0.13). For UC, having a higher GRS did not predict the age of diagnosis nor was it predictive of UC disease extent (P = 0.18), the need for surgery (P = 0.74), nor medication use (immunomodulators P = 0.53, anti-TNF P = 0.49). We could not demonstrate an association between increased GRS and having a family history of IBD in the UC group. CONCLUSIONS: Increasing genetic burden is associated with early age of diagnosis in CD and may be useful in predicting disease behaviour in CD but not UC.

Efficacy of Allogeneic Hematopoietic Cell Transplantation for Autoimmune Diseases.

Allogeneic hematopoietic cell transplantation (HCT) may be efficacious for autoimmune diseases (AIDs), but its efficacy for individual AIDs is unknown. Factors influencing the likelihood of relapse for each AID are also unknown. This study aimed to determine the likelihood of relapse for each common AID and to generate hypotheses about factors influencing the likelihood of relapse. We reviewed charts of adult patients with nonhematologic AIDs who had undergone HCT in Alberta (n = 21) and patients described in the literature (n = 67). We used stringent inclusion criteria to minimize the inclusion of patients whose AID may have been cured before transplantation. We also used stringent definitions of AID relapse and remission. AID relapsed in 2 of 9 patients (22%) with lupus, in 4 of 12 (33%) with rheumatoid arthritis (RA), in 0 of 4 (0%) with systemic sclerosis (SSc), in 3 of 16 (19%) with psoriasis, in 1 of 12 (8%) with Behçet's disease (BD), in 1 of 15 (7%) with Crohn's disease (CD), in 0 of 5 (0%) with ulcerative colitis (UC), in 4 of 8 (50%) with multiple sclerosis (MS), and in 3 of 3 (100%) with type 1 diabetes mellitus (T1DM). Among highly informative patients (followed for >1 year after discontinuation of immunosuppressive therapy if no relapse, or donor AID status known if relapse), relapse occurred in 0 of 3 patients with lupus, in 2 of 7 with RA, in 0 of 2 with SSc, in 3 of 6 with psoriasis, in 0 of 3 with BD, in 0 of 10 with CD, in 0 of 3 with UC, in 2 of 3 with MS, and in 2 of 2 with T1DM. There appeared to be no associations between AID relapse and low intensity of pretransplantation chemoradiotherapy, multiple lines of AID therapy (surrogate for AID refractoriness) except perhaps for lupus, absence of serotherapy for graft-versus-host disease (GVHD) prophylaxis, lack of GVHD except perhaps for lupus, or incomplete donor chimerism. Even though remission commonly occurs after HCT in lupus, RA, SSc, psoriasis, BD, CD, and UC, HCT is efficacious for only a subset of patients. The efficacy appears to be unrelated to pretransplantation therapy, GVHD, or chimerism. Large studies are needed to determine the characteristics of patients likely to benefit from HCT for each AID.

Analysis of supplements available to UK consumers purporting to contain selective androgen receptor modulators.

Selective androgen receptor modulators (SARMs) are compounds with specific androgenic properties investigated for the treatment of conditions such as muscle wasting diseases. The reported androgenic properties have resulted in their use by athletes, and consequently they have been on the World Anti-Doping Agency prohibited list for more than a decade. SARMs have been investigated by pharmaceutical companies as potential drug candidates, but to date no SARM has demonstrated sufficient safety and efficacy to gain clinical approval by either the European Medicines Agency or the U.S. Food and Drug Administration. Despite their lack of safety approval, SARMs are often illegally marketed as dietary supplements, available for consumers to buy online. In this study, a range of supplement products marketed as SARMs were purchased and analyzed using high resolution accurate mass - mass spectrometry to evaluate the accuracy of product claims and content labeling. This study found discrepancies ranging from a supplement in which no active ingredients were found, to supplements containing undeclared prohibited analytes. Where SARMs were detected, discrepancies were observed between the concentrations measured and those detailed on the product packaging. The outcome of this experiment highlights the high risk of such supplement products to consumers. The inaccurate product claims give rise to uncertainty over both the dose taken and the identity of any of these unapproved drugs. Even for supplements for which the product labeling is correct, the lack of complete toxicity data, especially for combinations of SARMs taken as stacks, means that the safety of these supplements is unknown.

Latent Class Analysis for the Diagnosis of Clostridioides difficile Infection.

BACKGROUND: Clostridioides difficile infection (CDI) is an opportunistic disease that lacks a gold-standard test. Nucleic acid amplification tests such as real-time polymerase chain reaction (PCR) demonstrate an excellent limit of detection (LOD), whereas antigenic methods are able to detect protein toxin. Latent class analysis (LCA) provides an unbiased statistical approach to resolving true disease. METHODS: A cross-sectional study was conducted in patients with suspected CDI (N = 96). Four commercial real-time PCR tests, toxin antigen detection by enzyme immunoassay (EIA), toxigenic culture, and fecal calprotectin were performed. CDI clinical diagnosis was determined by consensus majority of 3 experts. LCA was performed using laboratory and clinical variables independent of any gold standard. RESULTS: Six LCA models were generated to determine CDI probability using 4 variables including toxin EIA, toxigenic culture, clinical diagnosis, and fecal calprotectin levels. Three defined zones as a function of real-time PCR cycle threshold (Ct) were identified using LCA: CDI likely (>90% probability), CDI equivocal (<90% and >10%), CDI unlikely (<10%). A single model comprising toxigenic culture, clinical diagnosis, and toxin EIA showed the best fitness. The following Ct cutoffs for 4 commercial test platforms were obtained using this model to delineate 3 CDI probability zones: GeneXpert®: 24.00, 33.61; Simplexa®: 28.97, 36.85; Elite MGB®: 30.18, 37.43; and BD Max™: 27.60, 34.26. CONCLUSIONS: The clinical implication of applying LCA to CDI is to report Ct values assigned to probability zones based on the commercial real-time PCR platform. A broad range of equivocation suggests clinical judgment is essential to the confirmation of CDI.

Tissue-selective alternate promoters guide NLRP6 expression.

The pryin domain (PYD) domain is involved in protein interactions that lead to assembly of immune-sensing complexes such as inflammasomes. The repertoire of PYD-containing genes expressed by a cell type arms tissues with responses against a range of stimuli. The transcriptional regulation of the PYD gene family however is incompletely understood. Alternative promoter utilization was identified as a mechanism regulating the tissue distribution of human PYD gene family members, including NLRP6 that is translationally silenced outside of intestinal tissue. Results show that alternative transcriptional promoters mediate NLRP6 silencing in mice and humans, despite no upstream genomic synteny. Human NLRP6 contains an internal alternative promoter within exon 2 of the PYD, resulting in a truncated mRNA in nonintestinal tissue. In mice, a proximal promoter was used that expanded the 5' leader sequence restricting nuclear export and abolishing translational efficiency. Nlrp6 was dispensable in disease models targeting the kidney, which expresses noncanonical isoforms. Thus, alternative promoter use is a critical mechanism not just for isoform modulation but for determining expression profile and function of PYD family members.

A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data.

Metabolomic analyses of human gut microbiome samples can unveil the metabolic potential of host tissues and the numerous microorganisms they support, concurrently. As such, metabolomic information bears immense potential to improve disease diagnosis and therapeutic drug discovery. Unfortunately, as cohort sizes increase, comprehensive metabolomic profiling becomes costly and logistically difficult to perform at a large scale. To address these difficulties, we tested the feasibility of predicting the metabolites of a microbial community based solely on microbiome sequencing data. Paired microbiome sequencing (16S rRNA gene amplicons, shotgun metagenomics, and metatranscriptomics) and metabolome (mass spectrometry and nuclear magnetic resonance spectroscopy) datasets were collected from six independent studies spanning multiple diseases. We used these datasets to evaluate two reference-based gene-to-metabolite prediction pipelines and a machine-learning (ML) based metabolic profile prediction approach. With the pre-trained model on over 900 microbiome-metabolome paired samples, the ML approach yielded the most accurate predictions (i.e., highest F1 scores) of metabolite occurrences in the human gut and outperformed reference-based pipelines in predicting differential metabolites between case and control subjects. Our findings demonstrate the possibility of predicting metabolites from microbiome sequencing data, while highlighting certain limitations in detecting differential metabolites, and provide a framework to evaluate metabolite prediction pipelines, which will ultimately facilitate future investigations on microbial metabolites and human health.