Screening for phenotypic outliers identifies an unusually low concentration of a ß-lactoglobulin B protein isoform in bovine milk caused by a synonymous SNP.

BACKGROUND: Milk samples from 10,641 dairy cattle were screened by a mass spectrometry method for extreme concentrations of the A or B isoforms of the whey protein, ß-lactoglobulin (BLG), to identify causative genetic variation driving changes in BLG concentration. RESULTS: A cohort of cows, from a single sire family, was identified that produced milk containing a low concentration of the BLG B protein isoform. A genome-wide association study (GWAS) of BLG B protein isoform concentration in milk from AB heterozygous cows, detected a group of highly significant single nucleotide polymorphisms (SNPs) within or close to the BLG gene. Among these was a synonymous G/A variation at position + 78 bp in exon 1 of the BLG gene (chr11:103256256G > A). The effect of the A allele of this SNP (which we named B') on BLG expression was evaluated in a luciferase reporter assay in transfected CHO-K1 and MCF-7 cells. In both cell types, the presence of the B' allele in a plasmid containing the bovine BLG gene from -922 to + 898 bp (relative to the transcription initiation site) resulted in a 60% relative reduction in mRNA expression, compared to the plasmid containing the wild-type B sequence allele. Examination of a mammary RNAseq dataset (n = 391) identified 14 heterozygous carriers of the B' allele which were homozygous for the BLG B protein isoform (BB'). The level of expression of the BLG B' allele was 41.9 ± 1.0% of that of the wild-type BLG B allele. Milk samples from three cows, homozygous for the A allele at chr11:103,256,256 (B'B'), were analysed (HPLC) and showed BLG concentrations of 1.04, 1.26 and 1.83 g/L relative to a mean of 4.84 g/L in milk from 16 herd contemporaries of mixed (A and B) BLG genotypes. The mechanism by which B' downregulates milk BLG concentration remains to be determined. CONCLUSIONS: High-throughput screening and identification of outliers, enabled the discovery of a synonymous G > A mutation in exon 1 of the B allele of the BLG gene (B'), which reduced the milk concentration of ß-lactoglobulin B protein isoform, by more than 50%. Milk from cows carrying the B' allele is expected to have improved processing characteristics, particularly for cheese-making.

Genome-wide association analysis reveals QTL and candidate mutations involved in white spotting in cattle.

BACKGROUND: White spotting of the coat is a characteristic trait of various domestic species including cattle and other mammals. It is a hallmark of Holstein-Friesian cattle, and several previous studies have detected genetic loci with major effects for white spotting in animals with Holstein-Friesian ancestry. Here, our aim was to better understand the underlying genetic and molecular mechanisms of white spotting, by conducting the largest mapping study for this trait in cattle, to date. RESULTS: Using imputed whole-genome sequence data, we conducted a genome-wide association analysis in 2973 mixed-breed cows and bulls. Highly significant quantitative trait loci (QTL) were found on chromosomes 6 and 22, highlighting the well-established coat color genes KIT and MITF as likely responsible for these effects. These results are in broad agreement with previous studies, although we also report a third significant QTL on chromosome 2 that appears to be novel. This signal maps immediately adjacent to the PAX3 gene, which encodes a known transcription factor that controls MITF expression and is the causal locus for white spotting in horses. More detailed examination of these loci revealed a candidate causal mutation in PAX3 (p.Thr424Met), and another candidate mutation (rs209784468) within a conserved element in intron 2 of MITF transcripts expressed in the skin. These analyses also revealed a mechanistic ambiguity at the chromosome 6 locus, where highly dispersed association signals suggested multiple or multiallelic QTL involving KIT and/or other genes in this region. CONCLUSIONS: Our findings extend those of previous studies that reported KIT as a likely causal gene for white spotting, and report novel associations between candidate causal mutations in both the MITF and PAX3 genes. The sizes of the effects of these QTL are substantial, and could be used to select animals with darker, or conversely whiter, coats depending on the desired characteristics.

Widespread cis-regulation of RNA editing in a large mammal.

Post-transcriptional RNA editing may regulate transcript expression and diversity in cells, with potential impacts on various aspects of physiology and environmental adaptation. A small number of recent genome-wide studies in Drosophila, mouse, and human have shown that RNA editing can be genetically modulated, highlighting loci that quantitatively impact editing of transcripts. The potential gene expression and physiological consequences of these RNA-editing quantitative trait loci (edQTL), however, are almost entirely unknown. Here, we present analyses of RNA editing in a large domestic mammal (Bos taurus), where we use whole-genome and high-depth RNA sequencing to discover, characterize, and conduct genetic mapping studies of novel transcript edits. Using a discovery population of nine deeply sequenced cows, we identify 2413 edit sites in the mammary transcriptome, the majority of which are adenosine to inosine edits (98.6%). Most sites are predicted to reside in double-stranded secondary structures (85.1%), and quantification of the rates of editing in an additional 355 cows reveals editing is negatively correlated with gene expression in the majority of cases. Genetic analyses of RNA editing and gene expression highlight 152 cis-regulated edQTL, of which 15 appear to cosegregate with expression QTL effects. Trait association analyses in a separate population of 9989 lactating cows also shows 12 of the cis-edQTL coincide with at least one cosegregating lactation QTL. Together, these results enhance our understanding of RNA-editing dynamics in mammals, and suggest mechanistic links by which loci may impact phenotype through RNA editing mediated processes.

Tight Junction Protein Abundance and Apoptosis During Involution of Rat Mammary Glands.

To examine tight junction protein abundance and apoptosis of epithelial cells at the onset of involution in rodent mammary glands, milk accumulation and mammary engorgement were induced by teat-sealing with an adhesive for 0, 6, 12, 18, 24, and 36 h (n = 6 per group) at peak lactation. In non-sealed control glands, histological analysis confirmed a lactating phenotype, indicating suckling by pups throughout the experiment. In contrast, alveoli of teat-sealed glands were distended within 6 h, with maximal luminal size observed by 12 h of non-suckling. By 18 h following teat-sealing, an involuting phenotype was observed, indicated by alveolar lumina engorged with milk vesicles and increased leukocytes. Relative to non-sealed glands, mammary apoptosis was increased in engorged glands 18 h following teat-sealing. The abundance of ZO-1 and occludin proteins was decreased in engorged glands by 12 and 18 h, respectively, following teat-sealing. In contrast, the claudin-1 22 kDa band was increased by 6 h and peaked at 12-18 h, whereas the 28 kDa band declined by 36 h, relative to controls. There were no temporal changes in ZO-1, occludin, and claudin-1 22 kDa proteins within control glands, although there were minor differences in claudin-1 28 kDa. These data indicate that intramammary milk accumulation due to cessation of milk removal is associated with mammary apoptosis. The apoptotic event is preceded by a rapid loss of abundance of ZO-1, occludin and an initial increase in claudin-1. The loss of cell-cell communication may initiate involution and apoptosis of mammary epithelial cells and is a localized intramammary event, occurring only in non-suckled glands. J. Cell. Physiol. 232: 2075-2082, 2017. © 2016 Wiley Periodicals, Inc.

Immune components of colostrum and milk--a historical perspective.

Key developments in the understanding of the immune functions of milk and colostrum are reviewed, focusing on their proteinaceous components. The topics covered include the immunoglobulins, immune cells, immunomodulatory substances, and antimicrobial proteins. The contributions of new technologies and the introduction of fresh approaches from other fields are highlighted, as are the contributions that mammary biology research has made to the development of other fields. Finally, a summary of some current outstanding questions and likely future directions of the field are given.

An overview of the antifungal properties of allicin and its breakdown products--the possibility of a safe and effective antifungal prophylactic.

Reports about the safe and successful intravenous (i.v.) use of garlic derivatives in China against invasive fungal infections have been made, but little has been done to seriously investigate the in vivo use of these derivatives in the West. Laboratories have demonstrated impressive in vitro MICs using allitridium, one of these derivatives, against a range of medically important fungi. In addition, it has been demonstrated that allitridium shows in vitro synergy with amphotericin B, one of the main i.v. antifungal agents. Some of the breakdown products of allicin, the main parent antifungal compound in garlic, have been investigated for their general antimicrobial, anticancer and anticholesterol properties, and it appears that there is a common mode of action that underlies these activities. It appears that these small molecules have the ability to cross cell membranes and combine with sulfur-containing molecular groups in amino acids and proteins, thus interfering with cell metabolism. It has been suggested that the reason human cells are not poisoned by allicin derivatives is that they contain glutathione, a sulfur-containing amino acid that combines with the allicin derivative, thus preventing cell damage. In addition to their biochemical mechanism, these derivatives appear to stimulate cellular immunity, an important ability lacking in conventional antifungal chemotherapy. These derivatives appear to be safe, cheap, wide-spectrum and immunostimulatory, as well as possibly synergistic with conventional antifungal therapy, making them ideal candidates for investigation into their use as prophylactic antifungal agents.

Decreased expression of beta1-integrin and focal adhesion kinase in epithelial cells may initiate involution of mammary glands.

The mechanisms regulating involution of mammary glands after weaning are not clear, but engorgement with milk is a key trigger. Many cell types require to be anchored to an extracellular matrix (ECM) as a prerequisite for survival and this is achieved via intregrins binding to specific motifs and signalling their attachment, intracellularly, via focal adhesion kinase (FAK). We sought to determine firstly, if expression of beta1-integrin and FAK is reduced during the first stage of involution. Expression of beta1-integrin and FAK was significantly reduced at 6 h after sealing teats and this was accompanied with a decreased abundance of cytochrome C in mitochondria. Secondly, we sought to determine if expression of beta1-integrin and FAK was restored during the first, partially reversible stage of involution (at 24 h), but not during the second irreversible stage, which occurs after 72 h. Re-suckling restored full expression of the 80 kDa fragment of FAK, but not of the 125 kDa protein or beta1-integrin at 24 h after weaning. Re-suckling did not restore expression of either peptide after 72 h. Changes in expression of cytochrome C and pro-caspase-3 (apoptotic markers) were similar to that of the 80 kDa fragment of FAK. These data suggest that epithelial cells can restore partial contact with their basement membrane during the first, reversible stage, but not during the second irreversible stage of involution. We speculate that decreased contact between epithelial cells and their basement membrane initiates apoptosis in mammary glands at weaning. This process begins within 6 h of pup withdrawal.