Project description:In mammals, microbial colonization of the digestive tract (GIT) occurs right after birth by several bacterial phyla. Numerous human and mouse studies have reported the importance of early gut microbial inhabitants on host health. However, few attempts have been undertaken to directly interrogate the role of early gut/rumen microbial colonization on GIT development or host health in neonatal ruminants through artificial manipulation of the rumen microbiome. Thus, the molecular changes associated with bacterial colonization are largely unknown in cattle. In this study, we dosed young calves with exogenous rumen fluid obtained from an adult donor cow, starting at birth, and repeated every other week until six weeks of age. Eight Holstein bull calves were included in this study and were separated into two groups of four: the first group was treated with rumen content freshly extracted from an adult cow, and the second group was treated with sterilized rumen content. Using whole-transcriptome RNA-sequencing, we investigated the transcriptional changes in the host liver, which is a major metabolic organ and vital to the calf's growth performance. Additionally, the comparison of rumen epimural microbial communities between the treatment groups was performed using the rRNA reads generated by sequencing. Liver transcriptome changes were enriched with genes involved in cell signaling and protein phosphorylation. Specifically, up-regulation of SGPL1 suggests a potential increase in the metabolism of sphingolipids, an essential molecular signal for bacterial survival in digestive tracts. Notably, eight genera, belonging to four phyla, had significant increases in abundance in treated calves. Our study provides insight into host liver transcriptome changes associated with early colonization of the microbial communities in neonatal calves. Such knowledge provides a foundation for future probiotics-based research in microbial organism mediated rumen development and nutrition in ruminants.
Project description:We investigated miRNA expression in Holstein dairy cow of mammary gland with different producing quality milk using high-throughput sequence and qRT-PCR techniques. miRNA libraries were constructed from mammary gland tissues taken from a high producing quality milk and a low producing quality milk Holstein dairy cow, the small RNA digitalization analysis based on HiSeq high-throughput sequencing takes the SBS-sequencing by synthesis.The libraries included 4732 miRNAs. A total of 124 miRNAs in the high producing quality milk mammary gland showed significant differences in expression compared to low producing quality milk mammary gland (P<0.05). Conclusion: Our study provides a broad view of the bovine mammary gland small RNA expression profile characteristics. Differences in types and expression levels of miRNAs were observed between high producing quality milk and a low producing quality milk Holstein dairy cow Overall design: Examination of 3 group of different producing quality milk mammary gland of Holstein dairy cow,each group has 3 sample
Project description:Milk can mediate maternal-neonatal signal transmission by the bioactive component extracellular vesicles (EVs), which select specific types of miRNA to encapsulate. The miRNA profiling of sheep milk EVs was characterized by sequencing and compared with that of cow milk. Nanoparticle tracking analysis revealed that the concentration of sheep milk EVs was 1.3 ± 0.09 × 1012 particles/mL and the diameter was peaked at 131.2 ± 0.84 nm. Sheep milk EVs contained various small RNAs, including tRNA, Cis-regulatory element, rRNA, snRNA, other Rfam RNA, and miRNA, which held about 36% of all the small RNAs. In total, 84 types of miRNA were annotated with Ovis aries by miRBase (version 22.0) in sheep milk EVs, with 75 shared types of miRNAs in all samples. The miR-26a, miR-191, let-7f, let-7b and miR-10b were highly expressed both in cow and sheep milk EVs, and 14 sheep milk EV-miRNAs in the top 20, occupying 98% of the total expression, were immune-related. Although pathway analysis showed different potential functions of cow and sheep milk EV-miRNAs, there were still some shared points: lipid metabolism (phospholipase D, glycerophospholipid and glycosylphosphatidylinositol), calcium metabolism, and nerve conduction (axon guidance and synapse). This study provides reference for the bioactive components in the milk of different species.
Project description:MicroRNA (miRNA) and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small RNAs characterized in mammals and to examine relationship between host miRNA expression and viral infection we used Illumina's ultrahigh throughput sequencing approach. We sequenced three small RNA libraries prepared from cell line derived from the adult bovine kidney under normal conditions and upon infection of the cell line with Bovine herpesvirus 1. We used a bioinformatics approach to distinguish authentic mature miRNA sequences from other classes of small RNAs and short RNA fragments represented in the sequencing data. Using this approach we detected 219 out of 356 known bovine miRNAs and 115 respective miRNA* sequences. In addition we identified five new bovine orthologs of known mammalian miRNAs and discovered 268 new cow miRNAs many of which are not identifiable in other mammalian genomes and thus might be specific to the ruminant lineage. In addition we found seven new bovine mirtron candidates. We also discovered 10 small nucleolar RNA (snoRNA) loci that give rise to small RNA with possible miRNA-like function. Results presented in this study extend our knowledge of the biology and evolution of small regulatory RNAs in mammals and illuminate mechanisms of small RNA biogenesis and function. New miRNA sequences and the original sequencing data have been submitted to miRNA repository (miRBase) and NCBI GEO archive respectively. We envisage that these resources will facilitate functional annotation of the bovine genome and promote further functional and comparative genomics studies of small regulatory RNA in mammals.
Project description:Given that different diets could alter cow milk yield and composition, the effects of different feed formula on milk extracellular vesicle (EV) miRNAs were detected. Cow milk EVs contained various small RNAs, including miRNAs, snRNAs, tiRNAs, Cis-regulatory elements, and piRNAs. Two hundred and seventy-six known bos taurus miRNAs were identified by sequencing in bovine milk EVs. There were 13 immune-related miRNAs in the top 20 miRNAs in milk EVs. Nine differently expressed known miRNAs were detected in responding to different feed formulations. Cow milk EVs are abundant of small RNAs, especially miRNAs, which might be closely related to the development of maternal mammary gland and neonatal immune maturity. Overall design: Exploration the EV-miRNA profiling changes of bovine milk responding to two different diets
Project description:We evaluated liver transcriptome throughout gestation and early lactation of purebred and crossbred beef cows (Angus, Hereford and their F1 crossbreeds, CR), grazing high or low herbage allowances (HA) of native grasslands (4 and 2.5 kg DM/kg BW annual mean; n = 16) using an Agilent 4x44k bovine array. A total of 4,661 transcripts were affected by days (272 M-bM-^IM-% 2.5-fold difference, FDR M-bM-^IM-$ 0.10) and 47 pathways were altered during winter gestation (-165 to -15 days relative to calving, d). Gluconeogenesis and fatty acid oxidation pathways were substantially upregulated, while cell growth, DNA replication and transcription pathways were downregulated (FDR M-bM-^IM-$ 0.25). We observed only small changes in the liver transcriptome during the early lactation period (+15 to +60 d). A total of 225 genes were differentially expressed (47 M-bM-^IM-% 2-fold difference, FDR M-bM-^IM-$ 0.10) between HA. The majority of those were related to glucose and pyruvate metabolism and were upregulated in high HA, reflecting their better metabolic status. Two genes were upregulated in CR cows, but 148 transcripts (74 M-bM-^IM-% 2-fold change difference, FDR M-bM-^IM-$ 0.10) were affected by the HA and cow genotype interaction. The transcriptional changes observed indicates a complex and previously unrecognized adaptive program in beef cow liver. We report novel candidate genes, metabolic pathways, and regulatory mechanisms, which can be used as targets of future studies. Complete randomized block design with two spatial replications and a factorial arrangement of herbage allowance (HA) and cow genotype (CG). Herbage allowance treatments represented 4 and 2.5 kg DM/kg BW of annual mean (HI and LO, respectively). Four purebred (PU M-bM-^@M-^S Hereford, H and Angus, A) and four crossbred (CR - F1, HA and AH) multiparous pregnant cows (5 to 6 year-old), were evaluated per treatment (HI-CR, HI-PU, LO-CR, and LO-PU) throughout the gestation and lactation period (-165 to +60 days relative to parturition, days). Cows belonged to or were descendants of experimental animals generated as part of a diallel crossbreeding experiment carried out for 10 years at the Experimental Station and were assigned to the same forage allowance (HI or LO) since May 2007 and gestated and lactated one calf every year from 2007 to 2009.
Project description:The raw data from a genome sequencing project sometimes contains DNA from contaminating organisms, which may be introduced during sample collection or sequence preparation. In some instances, these contaminants remain in the sequence even after assembly and deposition of the genome into public databases. As a result, searches of these databases may yield erroneous and confusing results. We used efficient microbiome analysis software to scan the draft assembly of domestic cow, Bos taurus, and identify 173 small contigs that appeared to derive from microbial contaminants. In the course of verifying these findings, we discovered that one genome, Neisseria gonorrhoeae TCDC-NG08107, although putatively a complete genome, contained multiple sequences that actually derived from the cow and sheep genomes. Our findings illustrate the need to carefully validate findings of anomalous DNA that rely on comparisons to either draft or finished genomes.
Project description:MicroRNAs (miRNAs) are a class of small non-coding, endogenous regulatory RNAs that function by controlling gene expression at the post-transcriptional level. Using small RNA sequencing and qRT-PCR techniques, we found that the expression of miR-152 was significantly increased during lactation in the mammary glands of dairy cows producing high quality milk compared with that in cows producing low quality milk. Furthermore, DNA methyltransferase 1 (DNMT1), which is a target of miR-152, was inversely correlated with the expression levels of miR-152 in the mammary glands of dairy cows. Dairy cow mammary epithelial cells (DCMECs) were used as in vitro cell models to study the function of miR-152. The forced expression of miR-152 in DCMECs resulted in a marked reduction of DNMT1 at both mRNA and protein levels. This in turn led to a decrease in global DNA methylation and increased the expression of two lactation-related genes, serine/threonine protein kinase Akt (Akt) and peroxisome proliferator-activated receptor gamma (Ppar?). In contrast, inhibition of miR-152 showed the opposite results. By using an electronic Coulter counter (CASY-TT) and flow cytometer, we discovered that miR-152 enhanced the viability and multiplication capacity of DCMECs. In conclusion, miR-152 plays an important role in the development and lactation processes in the mammary glands of dairy cows. Our data provide insights into dairy cow mammary gland development and lactation.
Project description:MicroRNAs are conserved, endogenous small RNAs with critical post-transcriptional regulatory functions throughout eukaryota, including prominent roles in development and disease. Despite much effort, microRNA annotations still contain errors and are incomplete due especially to challenges related to identifying valid miRs that have small numbers of reads, to properly locating hairpin precursors and to balancing precision and recall. Here, we present miRWoods, which solves these challenges using a duplex-focused precursor detection method and stacked random forests with specialized layers to detect mature and precursor microRNAs, and has been tuned to optimize the harmonic mean of precision and recall. We trained and tuned our discovery pipeline on data sets from the well-annotated human genome, and evaluated its performance on data from mouse. Compared to existing approaches, miRWoods better identifies precursor spans, and can balance sensitivity and specificity for an overall greater prediction accuracy, recalling an average of 10% more annotated microRNAs, and correctly predicts substantially more microRNAs with only one read. We apply this method to the under-annotated genomes of Felis catus (domestic cat) and Bos taurus (cow). We identified hundreds of novel microRNAs in small RNA sequencing data sets from muscle and skin from cat, from 10 tissues from cow and also from human and mouse cells. Our novel predictions include a microRNA in an intron of tyrosine kinase 2 (TYK2) that is present in both cat and cow, as well as a family of mirtrons with two instances in the human genome. Our predictions support a more expanded miR-2284 family in the bovine genome, a larger mir-548 family in the human genome, and a larger let-7 family in the feline genome.
Project description:The ruminant liver has multiple roles in the dairy cow and many of these are crucial in nutrient supply during lactation. Reduced feed intake alters the expression of many genes and pathways in the liver, inducing a period of negative energy balance. Once-daily milking is a management strategy to reduce the effects of periods of negative energy balance so the objective of this study was to determine if once-daily milking altered hepatic gene transcription during a period of negative energy balance induce by caloric restriction. Multiparous Holstein-Friesian and Holstein-Friesian x Jersey cows (n = 120) were grazed on pasture and milked twice daily (2X) from calving until 34 ± 6 days in milk (mean ± standard deviation). Cows were then allocated to one of four treatments in a 2 x 2 factorial arrangement. Treatments consisted of two milking frequencies (2X or once daily; 1X) and two feeding levels for three weeks: adequately fed (AF), consuming 14.3 kg dry matter intake/cow per d, or underfed (UF) consuming 8.3 kg dry matter intake /cow per d. After the treatment period, all cows were fed to target grazing residuals ? 1600 kg DM/cow per d and milked 2X for 20 wk. Liver tissue was collected from 12 cows per treatment by subcutaneous biopsy at 3 wk relative to treatment start, RNA extracted and transcript abundance of genes quantified. 48 animals were enrolled in this study, a liver sample from 45 animals was used for microarray analysis. A reference design was used for hybridisation, whereby each of the 46 samples were hybridised to individual microarrays along with a pooled reference sample. The reference sample was generated by taking equal concentrations of each of the experimental samples.