BackgroundThe recent emergence of COVID-19, rapid worldwide spread, and incomplete knowledge of molecular mechanisms underlying SARS-CoV-2 infection have limited development of therapeutic strategies. Our objective was to systematically investigate molecular regulatory mechanisms of COVID-19, using a combination of high throughput RNA-sequencing-based transcriptomics and systems biology approaches.MethodsRNA-Seq data from peripheral blood mononuclear cells (PBMCs) of healthy persons, mild and severe 17 COVID-19 patients were analyzed to generate a gene expression matrix. Weighted gene co-expression network analysis (WGCNA) was used to identify co-expression modules in healthy samples as a reference set. For differential co-expression network analysis, module preservation and module-trait relationships approaches were used to identify key modules. Then, protein-protein interaction (PPI) networks, based on co-expressed hub genes, were constructed to identify hub genes/TFs with the highest information transfer (hub-high traffic genes) within candidate modules.ResultsBased on differential co-expression network analysis, connectivity patterns and network density, 72% (15 of 21) of modules identified in healthy samples were altered by SARS-CoV-2 infection. Therefore, SARS-CoV-2 caused systemic perturbations in host biological gene networks. In functional enrichment analysis, among 15 non-preserved modules and two significant highly-correlated modules (identified by MTRs), 9 modules were directly related to the host immune response and COVID-19 immunopathogenesis. Intriguingly, systemic investigation of SARS-CoV-2 infection identified signaling pathways and key genes/proteins associated with COVID-19’s main hallmarks, e.g., cytokine storm, respiratory distress syndrome (ARDS), acute lung injury (ALI), lymphopenia, coagulation disorders, thrombosis, and pregnancy complications, as well as comorbidities associated with COVID-19, e.g., asthma, diabetic complications, cardiovascular diseases (CVDs), liver disorders and acute kidney injury (AKI). Topological analysis with betweenness centrality (BC) identified 290 hub-high traffic genes, central in both co-expression and PPI networks. We also identified several transcriptional regulatory factors, including NFKB1, HIF1A, AHR, and TP53, with important immunoregulatory roles in SARS-CoV-2 infection. Moreover, several hub-high traffic genes, including IL6, IL1B, IL10, TNF, SOCS1, SOCS3, ICAM1, PTEN, RHOA, GDI2, SUMO1, CASP1, IRAK3, HSPA5, ADRB2, PRF1, GZMB, OASL, CCL5, HSP90AA1, HSPD1, IFNG, MAPK1, RAB5A, and TNFRSF1A had the highest rates of information transfer in 9 candidate modules and central roles in COVID-19 immunopathogenesis.ConclusionThis study provides comprehensive information on molecular mechanisms of SARS-CoV-2-host interactions and identifies several hub-high traffic genes as promising therapeutic targets for the COVID-19 pandemic.

The objectives of this study were to determine the relationships between milk urea N and days in milk, parity, and season in Iranian Holstein cows. Twelve Iranian commercial dairy herds participated in a 13-mo study from December 1, 2008, to December 31, 2009. All cows were milked 3 times daily, housed in freestalls, and fed a total mixed ration twice a day. Mean milk urea N over the study period was 16.0mg/dL. Mean milk urea N, categorized by 30-d increments of days in milk, paralleled changes in milk values and followed a curvilinear shape. However, milk urea N concentration reached a maximum at the fifth month of days in milk, but milk production reached a maximum at the third month. The concentration of milk urea N was lower during the first 30 d in milk category compared with all other days in milk categories. Overall mean milk urea N concentration of Holstein cows in the third and greater lactations was lower than in the first or second lactation. Milk urea N was at its lowest level in December (13 mg/dL), increased in the spring and summer months, and reached a maximum in July (18.8 mg/dL). From that point, milk urea N concentration progressively diminished to the autumn-winter level. In this study, milk urea N concentration was positively correlated with monthly temperature mean and may be a reason for the lower reproductive performance during the summer months. It has been recommended that milk urea N concentration should be evaluated in association with parity, days in milk, and season (or month). These variables should be considered potential sources of misinterpretation when exploring the relationship between milk urea N and nutritional management or measures of performance.

Twenty-four Holstein male calves (BW ¼ 320 ± 48kg) were used to evaluate the effects of vinasse supplementation on growth, carcase and meat chemical composition and total-tract digestibility in a randomised complete block design. The calves were divided into four groups and allocated to four diets: a maize/barley-based diet with no added vinasse (C); a diet containing 5% (DM basis) vinasse (LV); a diet containing 10% (DM basis) vinasse (MV) and a diet containing 15% (DM basis) vinasse (HV). Amount of feed offered was recorded daily and the calves were weighed monthly and slaughtered after 4 months of trial. Dry matter intake was not affected significantly by treatments. Calves fed with C and LV diets had higher live slaughter weight, ADG, longissimus muscle area and lower feed efficiency than calves fed the MV and HV diets (p < .001). Digestibility of OM, EE and NDF were not different between C and LV diets (p > .05), but it was decreased as the level of vinasse increased to the level of 15% in HV diet (p < .05). No differences were detected in the NH 3 -N and molar proportion of rumen VFAs except for propionate, in which calves were fed the C and LV diets had higher concentration of propionate and total VFAs compare to those fed the MV and HV diets (p < .05). These results showed that vinasse can be included in the growing calves ration around 5% without adverse effects and would promote carcase composition. ARTICLE HISTORY

Background: Bovine respiratory disease (BRD) is the most common disease in the beef and dairy cattle industry. BRD is a multifactorial disease resulting from the interaction between environmental stressors and infectious agents. However, the molecular mechanisms underlying BRD are not fully understood yet. Therefore, this study aimed to use a systems biology approach to systematically evaluate this disorder to better understand the molecular mechanisms responsible for BRD.Methods: Previously published RNA-seq data from whole blood of 18 healthy and 25 BRD samples were downloaded from the Gene Expression Omnibus (GEO) and then analyzed. Next, two distinct methods of weighted gene coexpression network analysis (WGCNA), i.e., module–trait relationships (MTRs) and module preservation (MP) analysis were used to identify significant highly correlated modules with clinical traits of BRD and non-preserved modules between healthy and BRD samples, respectively. After identifying respective modules by the two mentioned methods of WGCNA, functional enrichment analysis was performed to extract the modules that are biologically related to BRD. Gene coexpression networks based on the hub genes from the candidate modules were then integrated with protein–protein interaction (PPI) networks to identify hub–hub genes and potential transcription factors (TFs).Results: Four significant highly correlated modules with clinical traits of BRD as well as 29 non-preserved modules were identified by MTRs and MP methods, respectively. Among them, two significant highly correlated modules (identified by MTRs) and six nonpreserved modules (identified by MP) were biologically associated with immune response, pulmonary inflammation, and pathogenesis of BRD. After aggregation of gene coexpression networks based on the hub genes with PPI networks, a total of 307 hub–hub genes were identified in the eight candidate modules. Interestingly, most of these hub–hub genes were reported to play an important role in the immune response and BRD pathogenesis. Among the eight candidate modules, the turquoise (identified by MTRs) and purple (identified by MP) modules were highly biologically enriched in BRD. Moreover, STAT1, STAT2, STAT3, IRF7, and IRF9 TFs were suggested to play an important role in the immune system during BRD by regulating the coexpressed genes of these modules. Additionally, a gene set containing several hub–hub genes was identified in the eight candidate modules, such as TLR2, TLR4, IL10, SOCS3, GZMB, ANXA1, ANXA5, PTEN, SGK1, IFI6, ISG15, MX1, MX2, OAS2, IFIH1, DDX58, DHX58, RSAD2, IFI44, IFI44L, EIF2AK2, ISG20, IFIT5, IFITM3, OAS1Y, HERC5, and PRF1, which are potentially critical during infection with agents of bovine respiratory disease complex (BRDC).Conclusion: This study not only helps us to better understand the molecular mechanisms responsible for BRD but also suggested eight candidate modules along with several promising hub–hub genes as diagnosis biomarkers and therapeutic targets for BRD.

An experiment was conducted to quantify the effects of incremental levels of heat-moisture-treated canola meal (TCM) fed to dairy cows on the relationship between ruminal nutrient digestion and milk production. Experimental diets were fed to 4 multiparous rumen-cannulated Nordic Red cows, averaging (mean ± standard deviation) 681 ± 54.8 kg of body weight, 111 ± 16 d in milk, and 29.1 ± 9.1 kg of milk/d at the start of the study, in a Latin square design with four 21-d periods. The 4 experimental dietary treatments consisted of a basal diet of grass silage and crimped barley, and 3 diets in which the crimped barley was replaced with TCM, giving 3 incremental levels of protein supplementation. Nutrient flow was quantified by the omasal sampling technique using 3 markers (Cr, Yb, and indigestible neutral detergent fiber). Continuous infusion of N was used to label bacterial crude protein. Additionally, ruminal sampling and evacuations and measurements of total-tract digestibility were conducted. The experimental diets provided 132, 148, 164, and 180 g of crude protein/kg of dry matter. The increased level of TCM linearly increased dry matter intake from 15.1 to 16.6 kg/d and energy-corrected milk yield from 21.0 to 25.6 kg/d. The increased proportion of TCM when substituting barley with TCM was associated with greater total-tract digestibility of neutral detergent fiber and potentially digestible neutral detergent fiber, which could be explained by increased digestion rate of potentially digestible neutral detergent fiber. Omasal flow of nonammonia N naturally increased with greater dietary TCM inclusion, but the increased intestinal supply of rumen-undegradable protein was partly offset by diminished microbial protein synthesis when feeding more TCM. This was also reflected in a decreased proportion of milk protein from ruminal bacterial protein when TCM supplementation increased.

The objective of the present study was to evaluate the effect of different levels of ground oak acorn on growth performance, blood parameters and carcass characteristics. Twenty-four goat kids averaging 16.93 ± 1.25 kg initial bodyweight were randomly assigned to four experimental diets in a completely randomised design for 90 days. The experimental diets consisted of (1) 0% oak acorn (control), (2) 8% oak acorn, (3) 17% oak acorn and (4) 25% oak acorn on a DM basis. The goats were slaughtered after 105 days of feeding and carcass characteristics were measured. DM intake increased linearly in small amounts as the level of acorn in the diet increased (P < 0.004). The results showed that average daily gain, water intake and feed conversion ratio were unaffected by levels of ground oak acorn (P > 0.05). There were no significant differences in blood parameters (P > 0.05). Carcass fat depth and abdominal fat weight decreased with increasing ground oak acorn in the diet. Other carcass characteristics were not affected by different levels of ground oak acorn. On the basis of the results of the present study, it may be concluded that ground oak acorn can be used up to 25% in the diets of young goats without any adverse effects on growth performance and carcass characteristics. At this level of acorns, the goats received low concentrations of hydrolysable tannins (11 g/kg DM) in their diet.

The objective of this study was to develop and compare techniques for determining nutrient flow based on digesta samples collected from the reticulum or rumen of lactating dairy cows with estimates generated by the omasal sampling technique. Pre-experimental method development suggested, after comparing with the particle size distribution of feces, application of primary sieving of ruminal and reticular digesta from lactating cows through an 11.6-mm sieve, implying that digesta particles smaller than this were eligible to flow out of the rumen. For flow measurements at the different sampling sites 4 multiparous, lactating Nordic Red cows fitted with ruminal cannulas were used in a Latin square design with 4 dietary treatments, in which crimped barley was replaced with 3 incremental levels of protein supplementation of canola meal. Digesta was collected from the rumen, reticulum, and omasum to represent a 24-h feeding cycle. Nutrient flow was calculated using the reconstitution system based on Cr, Yb, and indigestible neutral detergent fiber and using (15)N as microbial marker. Large and small particles and the fluid phase were recovered from digesta collected at all sampling sites. Bacterial samples were isolated from the digesta collected from the omasum. Several differences existed for digesta composition, nutrient flows, and estimates of ruminal digestibility among the 3 different sampling sites. Sampling site × diet interactions were not significant. The estimated flows of DM, potentially digestible neutral detergent fiber, nonammonia N, and microbial N were significantly different between all sampling sites. However, the difference between DM flow based on sampling from the reticulum and the omasum was small (0.13kg/d greater in the omasum). The equality between the reticulum and the omasum as sampling sites was supported by the following regression: omasal DM flow=0.37 (±0.649) + 0.94 (±0.054) reticular DM flow (R(2)=0.96 and root mean square error=0.438kg/d). More deviating nutrient-flow estimates when sampling digesta from the rumen than the reticulum compared with the omasum suggested that sampling from the reticulum is the most promising alternative to the omasal sampling technique. To definitively promote sampling from the reticulum as an alternative to the omasal sampling technique, more research is needed to determine selection criteria of reticular digesta for accurate and precise flow estimates across a range of diets.

This study was carried out to evaluate the effects of replacing alfalfa hay with ensiled mixed tomato and apple pomace (EMTAP) on ruminal fermentation, blood metabolites, chewing activity and apparent digestibility of diets. Six multiparous mid-lactating Holstein dairy cows were used in 3×3 Latin square design. The animals were fed with a control (0%EMTAP) and two different levels of EMTAP (15, 30%) containing diets. Results showed significant differences between treatments. The substitution of EMTAP in dairy cow’s diet was associated with a reduction of chewing activity, better DM and OM digestibility and higher blood metabolites concentration. Feeding EMTAP resulted in a significant higher concentration of acetic, propionic acids, and total volatile fatty acids in rumen, and lower rumen pH. It was concluded that, EMTAP might efficiently comprise up to 30% of the diets. The nutritive value of tomato and apple pomace could be improved when they are used together (50:50) in dairy cows diet