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This study evaluated the infuence of feeding low and high preweaning allowances of unpasteurized whole milk (MA) on intake, selected blood metabolites, antibody response, mammary gland growth, and growth of New Zealand (NZ) dairy heifers to 7 mo of age. At 10 ± 2 d of age (study day 0), group-housed (six·pen−1) heifer calves (Holstein-Friesian × Jersey) were allocated to low (4 L whole milk·calf−1·d−1; n = 7 pens) or high (8 L whole milk·calf−1·d−1; n = 7 pens) MA for the next 63 d. Calves were gradually weaned between days 63 ± 2 and 73 ± 2. Calves in each pen had ad-libitum access to clean water, pelleted calf starter, and chopped grass hay from day 1 to 91 ± 2 d. At 92 ± 2 d, all calves were transferred to pasture, grazed in a mob, and their growth and selected blood metabolites were measured until day 209. All animals were weighed weekly during the indoor period (to day 91) and then at days 105, 112, 128, 162, 184, and 209. Skeletal growth measurements and blood samples to analyze selected metabolites were collected at the start of the experiment, weaning, and then postweaning on day 91, and day 201. Specifc antibodies against Leptospira and Clostridia were quantifed in weeks 7, 13, and 27. Mammary glands were scanned using ultrasonography at the start of the experiment, weaning, and day 201. Feeding high vs. low amounts of MA increased the preweaning growth in heifer calves (P = 0.02) without negatively affecting postweaning average daily gain (ADG) (P = 0.74). Compared with heifers fed with low MA, high MA fed heifers had a greater increase in antibodies against Leptospira and Clostridia by 13 wk of age (P = 0.0007 and P = 0.06, respectively). By 27 wk of age, the antibody response was the same in heifers offered low or high MA. There was no effect of MA on the total size of the mammary gland, measured by ultrasonography, at weaning and 7 mo of age. However, the greater MA was associated with more mammary parenchyma (P = 0.01) and less mammary fat pad (P = 0.03) in back glands at 7 mo of age compared with heifers fed lower MA. In conclusion, feeding a high vs. a low amount of unpasteurized whole milk increased the preweaning growth of New Zealand replacement heifers without negatively affecting their ADG during postweaning under grazing conditions. Feeding more (8 vs. 4 L·d−1) unpasteurized whole milk positively affected antibody responses early in life and mammary gland composition by 7 mo of age in dairy heifers reared for pasture-based dairy systems. [ABSTRACT FROM AUTHOR]

Modulation of the immune system is known to be important for successful pregnancy but how immune function might differ between the lymph nodes draining the reproductive tract and peripheral lymph nodes is not well understood. Additionally, if immune system changes in response to the presence of an embryo during early pregnancy, and if this response differs in local versus peripheral immune tissue, has not been well characterized. To address these questions, we examined expression of genes important for immune function using Nano-String technology in the ampulla and isthmus of the oviduct, endometrium, lymph nodes draining the reproductive tract (lumbo-aortic and medial iliac) as well as a peripheral lymph node (axillary), the spleen, and circulating immune cells from ewes on day 5 of the estrous cycle or pregnancy. Concentrations of estradiol and progesterone in plasma were also determined. Principal component analysis revealed separation of the local from the peripheral lymph nodes (MANOVA P = 3.245e-08, R2 = 0.3) as well as separation of tissues from pregnant and nonpregnant animals [lymph nodes (MANOVA P = 2.337e-09, R2 = 0.5), reproductive tissues (MANOVA P = 2.417e-14, R2 = 0.47)]. Nine genes were differentially (FDR < 0.10) expressed between lymph node types, with clear difference in expression of these genes between the lumbo-aortic and axillary lymph nodes. Expression of these genes in the medial iliac lymph node was not consistently different to either the axillary or the lumbo-aortic lymph node. Expression of IL10RB was increased (FDR < 0.05) by 24% in the reproductive tissue of the pregnant animals compared to nonpregnant animals. Analysis of gene categories revealed that expression of genes of the T-cell receptor pathway in reproductive tract tissues was associated (P < 0.05) with pregnancy status. In conclusion, assessment of gene expression of reproductive and immune tissue provides evidence for a specialization of the local immune system around the reproductive tract potentially important for successful establishment of pregnancy. Additionally, differences in gene expression patterns in reproductive tissue from pregnant and nonpregnant animals could be discerned as early as day 5 of pregnancy. This was found to be associated with expression of genes important for T-cell function and thus highlights the important role of these cells in early pregnancy. [ABSTRACT FROM AUTHOR]

Bacterial species belonging to the genus Pseudobutyrivibrio are important members of the rumen microbiome contributing to the degradation of complex plant polysaccharides. Pseudobutyrivibrio xylanivorans MA3014 was selected for genome sequencing to examine its ability to breakdown and utilize plant polysaccharides. The complete genome sequence of MA3014 is 3.58 Mb, consists of three replicons (a chromosome, chromid, and plasmid), has an overall G + C content of 39.6%, and encodes 3,265 putative protein-coding genes (CDS). Comparative pan-genomic analysis of all cultivated and currently available P. xylanivorans genomes has revealed a strong correlation of orthologous genes within this rumen bacterial species. MA3014 is metabolically versatile and capable of growing on a range of simple mono- or oligosaccharides derived from complex plant polysaccharides such as pectins, mannans, starch, and hemicelluloses, with lactate, butyrate, and formate as the principal fermentation end products. The genes encoding these metabolic pathways have been identified and MA3014 is predicted to encode an extensive range of Carbohydrate-Active enZYmes with 78 glycoside hydrolases, 13 carbohydrate esterases, and 54 glycosyl transferases, suggesting an important role in solubilization of plant matter in the rumen. [ABSTRACT FROM AUTHOR]

Internal parasitic nematodes are a global animal health issue causing drastic losses in livestock. Here, we report a H. contortus representative draft genome to serve as a genetic resource to the scientific community and support future experimental research of molecular mechanisms in related parasites. A de novo hybrid assembly was generated from PCR-free whole genome sequence data, resulting in a chromosome-level assembly that is 465 Mb in size encoding 22,341 genes. The genome sequence presented here is consistent with the genome architecture of the existing Haemonchus species and is a valuable resource for future studies regarding population genetic structures of parasitic nematodes. Additionally, comparative pan-genomics with other species of economically important parasitic nematodes have revealed highly open genomes and strong collinearities within the phylum Nematoda. [ABSTRACT FROM AUTHOR]

Non-semantic approaches to bioinformatic data analysis have potential relevance where semantic resources such as annotated finished reference genomes are lacking, such as in the analysis and utilisation of growing amounts of sequence data from non-model organisms, often associated with sequence-based agricultural, aqua-cultural and environmental sampling studies and commercial services. Even where rich semantic resources are available, semantic approaches to problems such as contrasting and comparing reference assemblies, and utilising multiple references in parallel to avoid reference bias, are costly and difficult to fully automate. We introduce and discuss a non-semantic data representation approach intended mainly for bioinformatic data called non-semantic labelling. Non-semantic labelling involves tensorially combining multiple kinds of model-based entropy-reducing data representation, with multiple representation models, so as to map both data and models into dual metric representation spaces, with goals of both reducing the statistical complexity of the data, and highlighting latent structure via machine learning and statistical analyses conducted within the dual representation spaces. As part of the framework, we introduce a novel algebraic abstraction of data representation mappings, and present four proof-of-concept examples of its application, to problems such as comparing and contrasting sequence assemblies, utilisation of multiple references for annotation and development of quality control diagnostics in a variety of high-throughput sequencing contexts. Database URL : https://github.com/AgResearch/data_prism [ABSTRACT FROM AUTHOR]