Targeted imputation of sequence variants and gene expression profiling identifies twelve candidate genes associated with lactation volume,composition and calving interval in dairy cattle

Dairy cattle are an interesting model for gaining insights into the genes responsible for the large variation between and within mammalian species in the protein and fat content of their milk and their milk volume. Large numbers of phenotypes for these traits are available, as well as full genome sequence of key founders of modern dairy cattle populations. In twenty target QTL regions affecting milk production traits, we imputed full genome sequence variant genotypes into a population of 16,721 Holstein and Jersey cattle with excellent phenotypes. Association testing was used to identify variants within each target region, and gene expression data were used to identify possible gene candidates. There was statistical support for imputed sequence variants in or close to BTRC, MGST1, SLC37A1, STAT5A, STAT5B, PAEP, VDR, CSF2RB, MUC1, NCF4, and GHDC associated with milk production, and EPGN for calving interval. Of these candidates, analysis of RNA-Seq data demonstrated that PAEP, VDR, SLC37A1, GHDC, MUC1, CSF2RB, and STAT5A were highly differentially expressed in mammary gland compared to 15 other tissues. For nine of the other target regions, the most significant variants were in non-coding DNA. Genomic predictions in a third dairy breed (Australian Reds) using sequence variants in only these candidate genes were for some traits more accurate than genomic predictions from 632,003 common SNP on the Bovine HD array. The genes identified in this study are interesting candidates for improving milk production in cattle and could be investigated for novel biological mechanisms driving lactation traits in other mammals.     

Pulsed-field electrophoresis indicates larger-than-expected sizes for mycoplasma genomes.

The sizes of large DNA fragments produced from genomes of members of the Mycoplasmataceae by digestion with restriction endonucleases having infrequent (1 to 3) cleavage sites within the genome were estimated from their mobility in contour-clamped homogeneous electric field (CHEF) agarose gel electrophoresis by comparison with yeast chromosomal DNA markers. The estimates of total genome size for 7 strains of 6 species ranged from approximately 900 kilo base pairs (kb) for Ureaplasma urealyticum 960T to 1330 kb for M. mycoides subsp. mycoides, GC-1176. The values derived from this new method are considerably higher than those of approximately 500 Mdaltons or 750 kb previously reported for genome sizes in members of the Mycoplasmataceae.     

Mate choice copying and conspecific cueing in Japanese quail, Coturnix coturnix japonica

In four experiments, we examined the effects on the affiliative preferences of 'focal' female Japanese quail given the opportunity to watch a conspecific male interact with a 'model' female. Experiments were conducted in three, 10-min phases: (1) a pretest, during which a 'focal' female chose between two males; (2) an observation phase, when each focal female watched the male she had spent less time near during the pretest (her 'nonpreferred' male) interact with a 'model' quail; and (3) a post-test, during which each focal female again chose between her nonpreferred and preferred males. Focal females increased their preferences for nonpreferred males after seeing them together with a model female (but not a model male), even if the nonpreferred male and model female were separated by an opaque barrier that prevented them from interacting. A focal female's preference for the end of the enclosure containing her nonpreferred male was not increased when she either watched him court a concealed model female or watched a model female that was being courted by him. Taken together, the present results suggest that a simple tendency for females to approach areas where they have previously seen a male and female quail, in preference to locations where they have seen only a male quail, can explain some of the effect of watching a nonpreferred male mate on a female's tendency to affiliate with him. However, focal females also showed enhanced preferences for nonpreferred males they had seen mating after we both moved those males and controlled for effects of transposition. Thus, processes akin to both 'mate choice copying' and 'conspecific cueing' remain viable explanations for the increase in a focal female quail's tendency to affiliate with a male she watched mate with another female. Copyright 1999 The Association for the Study of Animal Behaviour.     

Activation of the bgl operon by adaptive mutation

In growing Escherichia coli K12 cells, the cryptic bgl operon is activated 98% of the time by insertions of IS1 or IS5 into the control region, designated bglR. The activated bgl operon permits utilization of the beta-glucoside sugar arbutin as a sole carbon and energy source. The bgl operon is also activated by late-occurring mutations during prolonged selection on arbutin. The late-occurring mutations that occurred during prolonged carbon starvation in the presence of arbutin were "adaptive mutations" because they were specific to the presence of arbutin, and they did not occur during prolonged starvation in the absence of arbutin. The spectrum of late-arising mutations differed from that of early-arising, growth-dependent mutations in that 20% of the late-arising mutants resulted from mutations at the hns locus. This provides the first direct evidence for adaptive mutagenesis mediated by the insertion of IS elements. Because no special genetic background is required to select Bgl+ mutants, this affords the opportunity to study IS-element-mediated adaptive mutagenesis in a variety of genetic backgrounds, including the backgrounds of natural isolates of E. coli.      

Inhibition of L- and P-selectin by a rationally synthesized novel core 2-like branched structure containing GalNAc-Lewisx and Neu5Acalpha2- 3Galbeta1-3GalNAc sequences

The selectins interact in important normal and pathological situations with certain sialylated, fucosylated glycoconjugate ligands containing sialyl Lewisx(Neu5Acalpha2-3Galbeta1-4(Fucalpha1-3)GlcN Ac). Much effort has gone into the synthesis of sialylated and sulfated Lewisxanalogs as competitive ligands for the selectins. Since the natural selectin ligands GlyCAM-1 and PSGL-1 carry sialyl Lewisxas part of a branched Core 2 O-linked structure, we recently synthesized Galbeta1-4(Fucalpha1-3)GlcNAcbeta1-6(SE-3Galbeta1++ +-3)GalNAc1alphaOMe and found it to be a moderately superior ligand for L and P-selectin (Koenig et al. , Glycobiology 7, 79-93, 1997). Other studies have shown that sulfate esters can replace sialic acid in some selectin ligands (Yeun et al. , Biochemistry, 31, 9126-9131, 1992; Imai et al. , Nature, 361, 555, 1993). Based upon these observations, we hypothesized that Neu5Acalpha2-3Galbeta1-3GalNAc might have the capability of interacting with L- and P-selectin. To examine this hypothesis, we synthesized Galbeta1-4(Fucalpha1-3)GlcNAcbeta1-6(Neu5Acalpha2++ +-3Galbeta1-3)- GalNAc alpha1-OB, which was found to be 2- to 3-fold better than sialyl Lexfor P and L selectin, respectively. We also report the synthesis of an unusual structure GalNAcbeta1-4(Fucalpha1- 3)GlcNAcbeta1-OMe (GalNAc- Lewisx-O-methyl glycoside), which also proved to be a better inhibitor of L- and P-selectin than sialyl Lewisx-OMe. Combining this with our knowledge of Core 2 branched structures, we have synthesized a molecule that is 5- to 6-fold better at inhibiting L- and P-selectin than sialyl Lewisx-OMe, By contrast to unbranched structures, substitution of a sulfate ester group for a sialic acid residue in such a molecule resulted in a considerable loss of inhibition ability. Thus, the combination of a sialic acid residue on the primary (beta1-3) arm, and a modified Lexunit on the branched (beta1-6) arm on an O-linked Core 2 structure generated a monovalent synthetic oliogosaccharide inhibitor superior to SLexfor both L- and P-selectin.      

Enzymes of intermediary carbohydrate metabolism in Ureaplasma urealyticum and Mycoplasma mycoides subsp. mycoides

Cell extracts of Ureaplasma urealyticum and Mycoplasma mycoides were examined for enzymes of intermediary carbohydrate metabolism using a sensitive radiochemical assay procedure. For M. mycoides, the enzyme activities detected were supporting evidence for the existence of a glycolytic pathway giving lactate anaerobically and acetate aerobically. U. urealyticum also had activities of many glycolytic enzymes. Enzymes of the pentose phosphate pathway occurred in both M. mycoides and U. urealyticum. Their presence allowed the proposal of a sequence for the synthesis from glycolytic pathway intermediates of ribose 5-phosphate, and hence phosphoribosyl diphosphate, for the synthesis of nucleotides. Pathways for the further metabolism of deoxyribose 1-phosphate and ribose 1-phosphate produced from nucleoside phosphorylase reactions operated in extracts from both organisms.     

Study of 100 patients injured by London underground trains 1981-6.

One hundred patients who were injured by London underground trains during 1981-6 were studied; 43 of them died. Deliberate self harm was probable in roughly three quarters. Alcohol intoxication was thought to play an important part in a further tenth of cases. Thirteen were psychiatric inpatients at the time of the incident, and a further two had recently been discharged. Early warning of a potential suicide attempt was given during the 24 hours preceding the incident in 15 of the cases. Some of the deaths in the psychiatric patients may have been preventable.     

Global diversity and endemism in Early Silurian (Aeronian) brachiopods

Silurian brachiopods of Middle Llandovery (Aeronian) ages are reviewed, and 215 genera are identified here, compared with 109 in the preceding Early Llandovery (Rhuddanian), indicating a recovery‐radiation interval after the end‐Ordovician mass extinction. The chief regions in which they are found are the continents of South China, Avalonia‐Baltica, Laurentia and Siberia, which were all at tropical latitudes with the exception of Avalonia. In addition, the very large superterrane of Gondwana, although with patchy brachiopod distribution, included temperate faunas, as well as subtropical faunas (in Iran and Afghanistan). Aeronian brachiopods greatly increased in diversity, with dominance of four major groups: orthides and strophomenides (which had flourished previously in the Rhuddanian), pentamerides and atrypides (which became dominant in the Aeronian), and many newly evolved taxa, and occupied deeper water and wider ecological niches (level bottom and reef) than those in the Rhuddanian. Each of the continents has some endemic genera, but there is a greater proportion of them in South China, where some groups (such as the pentamerides and atrypides) are more diverse and others, such as the orthides, are much less common than elsewhere. Affinity indices (AI) show that two megaunits can be recognized: South China and Avalonia‐Baltica‐Laurentia (ABL); Siberia seems to have been loosely connected with ABL and even more loosely to South China presumably because of its geographical separation in the Northern Hemisphere. The separation of South China from the other megaunits is further supported by cluster analysis.     

Genetic variants in mammary development,prolactin signalling and involution pathways explain considerable variation in bovine milk production and milk composition

Background

The maintenance of lactation in mammals is the result of a balance between competing signals from mammary development, prolactin signalling and involution pathways. Dairy cattle are an interesting case study to investigate the effect of polymorphisms that affect the function of genes in these pathways. In dairy cattle, lactation yields and milk composition (for example protein percentage and fat percentage) are routinely recorded, and these vary greatly between individuals. In this study, we test 8058 single nucleotide polymorphisms in or close to genes in these pathways for association with milk production traits and determine the proportion of variance explained by each pathway, using data on 16 812 dairy cattle, including Holstein-Friesian and Jersey bulls and cows.

Results

Single nucleotide polymorphisms close to genes in the mammary development, prolactin signalling and involution pathways were significantly associated with milk production traits. The involution pathway explained the largest proportion of genetic variation for production traits. The mammary development pathway also explained additional genetic variation for milk volume, fat percentage and protein percentage.

Conclusions

Genetic variants in the involution pathway explained considerably more genetic variation in milk production traits than expected by chance. Many of the associations for single nucleotide polymorphisms in genes in this pathway have not been detected in conventional genome-wide association studies. The pathway approach used here allowed us to identify some novel candidates for further studies that will be aimed at refining the location of associated genomic regions and identifying polymorphisms contributing to variation in lactation volume and milk composition.