Sperm morphology and fertility of progeny-tested AI dairy bulls in Sweden

Use of bull semen with high levels of sperm abnormalities, reflecting genital dysfunction, is not recommended for artificial insemination (AI) since it would most likely lead to subfertility. Sperm quality, including sperm morphology, may deteriorate with increasing age of the bull thus becoming a source of concern when using older, progeny-tested AI bull sires. Although a relationship between sperm morphology and fertility after AI in progeny-tested bull sires has been reported, it is yet unclear which sperm abnormalities are most critical. This constituted the core aim of a 22-month long retrospective study in proven (aged 60-84 months at the start of the study) AI sires of the Swedish Red (SR, n=8) and Swedish Holstein (SLB, n=4) breeds where their semen (107 freezing batches in total, built by a single ejaculate (n=3) or pooling two consecutive ejaculates (n=104) collected at 1-3 months interval), were subjected to detailed morphological examinations on wet- and dry, stained smears. Attention was paid to between- and within-bull variations with regard to presence and level of sperm abnormalities. Sperm morphology differed significantly between sires and ejaculates, with 6/12 sires having ejaculates containing >10% of morphologically deviating sperm head shapes, a commonly used threshold for young AI bulls in Sweden. However, with the exception of pear-shaped or narrow-at-the-base anomalies, the mean values for individual defects were always within the limits expected for a normal bull sire, and were therefore considered acceptable. The percentage of morphologically normal spermatozoa was positively related to fertility, whose output differed significantly among bulls. Among sperm abnormalities, the proportion of morphologically deviating sperm head shapes were negatively correlated with fertility, pear-shaped sperm heads in particular. In conclusion, the relationship between sperm morphology and fertility after AI calls for frequent (2-3 months interval) detailed assessments of sperm morphology in AI stud bull sires.     

Comparison of different normalization assumptions for analyses of DNA methylation data from the cancer genome

Nowadays, some researchers normalized DNA methylation arrays data in order to remove the technical artifacts introduced by experimental differences in sample preparation, array processing and other factors. However, other researchers analyzed DNA methylation arrays without performing data normalization considering that current normalizations for methylation data may distort real differences between normal and cancer samples because cancer genomes may be extensively subject to hypomethylation and the total amount of CpG methylation might differ substantially among samples. In this study, using eight datasets by Infinium HumanMethylation27 assay, we systemically analyzed the global distribution of DNA methylation changes in cancer compared to normal control and its effect on data normalization for selecting differentially methylated (DM) genes. We showed more differentially methylated (DM) genes could be found in the Quantile/Lowess-normalized data than in the non-normalized data. We found the DM genes additionally selected in the Quantile/Lowess-normalized data showed significantly consistent methylation states in another independent dataset for the same cancer, indicating these extra DM genes were effective biological signals related to the disease. These results suggested normalization can increase the power of detecting DM genes in the context of diagnostic markers which were usually characterized by relatively large effect sizes. Besides, we evaluated the reproducibility of DM discoveries for a particular cancer type, and we found most of the DM genes additionally detected in one dataset showed the same methylation directions in the other dataset for the same cancer type, indicating that these DM genes were effective biological signals in the other dataset. Furthermore, we showed that some DM genes detected from different studies for a particular cancer type were significantly reproducible at the functional level.     

The Scent of Symmetry: A Human Sex Pheromone that Signals Fitness?

A previous study by the authors showed that the body scent of men who have greater body bilateral symmetry is rated as more attractive by normally ovulating (non-pill-using) women during the period of highest fertility based on day within the menstrual cycle. Women in low-fertility phases of the cycle and women using hormone-based contraceptives do not show this pattern. The current study replicated these findings with a larger sample and statistically controlled for men's hygiene and other factors that were not controlled in the first study. The current study also examined women's scent attractiveness to men and found no evidence that men prefer the scent of symmetric women. We propose that the scent of symmetry is an honest signal of phenotypic and genetic quality in the human male, and chemical candidates are discussed. In both sexes, facial attractiveness (as judged from photos) appears to predict body scent attractiveness to the opposite sex. Women's preference for the scent associated with men's facial attractiveness is greatest when their fertility is highest across the menstrual cycle. The results overall suggest that women have an evolved preference for sires with good genes.     

Genome-wide profiling of sperm DNA methylation in relation to buffalo (Bubalus bubalis) bull fertility

The DNA methylation pattern in spermatozoa of buffalo bulls of different fertility status was investigated. Spermatozoa isolated DNA from two groups of buffalo bulls (n = 5), selected based on their artificial insemination–generated conception rate data followed by IVF efficiency, were studied for global methylation changes using a custom-designed 180 K buffalo (Bubalus bubalis) CpG island/promoter microarray. A total of 96 individual genes with another 55 genes covered under CpG islands were found differentially methylated in sperm of high-fertile and subfertile buffalo bulls. Important genes associated with biological processes, cellular components, and functions were identified to be differentially methylated in buffalo bulls with differential fertility status. The identified differentially methylated genes were found to be involved in germ cell development, spermatogenesis, capacitation, and embryonic development. The observations hint that methylation defects of sperm DNA may play a crucial role in determining the fertility of breeding bulls. This growing field of sperm epigenetics will be of great benefit in understanding the graded fertility conditions of breeding bulls in commercial livestock production system.     

Genome-wide association study identifies candidate markers for bull fertility in Holstein dairy cattle

The decline in the reproductive efficiency of dairy cattle has become a challenging problem worldwide. Female fertility is now taken into account in breeding goals while generally less attention is given to male fertility. The objective of this study was to perform a genome-wide association study in Holstein bulls to identify genetic variants significantly related to sire conception rate (SCR), a new phenotypic evaluation of bull fertility. The analysis included 1755 sires with SCR data and 38,650 single nucleotide polymorphisms (SNPs) spanning the entire bovine genome. Associations between SNPs and SCR were analyzed using a mixed linear model that included a random polygenic effect and SNP genotype either as a linear covariate or as a categorical variable. A multiple testing correction approach was used to account for the correlation between SNPs because of linkage disequilibrium. After genome-wide correction, eight SNPs showed significant association with SCR. Some of these SNPs are located close to or in the middle of genes with functions related to male fertility, such as the sperm acrosome reaction, chromatin remodeling during the spermatogenesis, and the meiotic process during male germ cell maturation. Some SNPs showed marked dominance effects, which provide more evidence for the relevance of non-additive effects in traits closely related to fitness such as fertility. The results could contribute to the identification of genes and pathways associated with male fertility in dairy cattle.     

Body odor attractiveness as a cue of impending ovulation in women: evidence from a study using hormone-confirmed ovulation

Scent communication plays a central role in the mating behavior of many nonhuman mammals but has often been overlooked in the study of human mating. However, a growing body of evidence suggests that men may perceive women's high-fertility body scents (collected near ovulation) as more attractive than their low-fertility body scents. The present study provides a methodologically rigorous replication of this finding, while also examining several novel questions. Women collected samples of their natural body scent twice--once on a low-fertility day and once on a high-fertility day of the ovulatory cycle. Tests of luteinizing hormone confirmed that women experienced ovulation within two days of their high-fertility session. Men smelled each woman's high- and low-fertility scent samples and completed discrimination and preference tasks. At above-chance levels, men accurately discriminated between women's high- and low-fertility scent samples (61%) and chose women's high-fertility scent samples as more attractive than their low-fertility scent samples (56%). Men also rated each scent sample on sexiness, pleasantness, and intensity, and estimated the physical attractiveness of the woman who had provided the sample. Multilevel modeling revealed that, when high- and low-fertility scent samples were easier to discriminate from each other, high-fertility scent samples received even more favorable ratings compared with low-fertility scent samples. This study builds on a growing body of evidence indicating that men are attracted to cues of impending ovulation in women and raises the intriguing question of whether women's cycling hormones influence men's attraction and sexual approach behavior.     

Vocal cues of ovulation in human females

Recent research has documented a variety of ovulatory cues in humans, and in many nonhuman species, the vocal channel provides cues of reproductive state. We collected two sets of vocal samples from 69 normally ovulating women: one set during the follicular (high-fertility) phase of the cycle and one set during the luteal (low-fertility) phase, with ovulation confirmed by luteinizing hormone tests. In these samples we measured fundamental frequency (pitch), formant dispersion, jitter, shimmer, harmonics-to-noise ratio and speech rate. When speaking a simple introductory sentence, women's pitch increased during high- as compared with low-fertility, and this difference was the greatest for women whose voices were recorded on the two highest fertility days within the fertile window (the 2 days just before ovulation). This pattern did not occur when the same women produced vowels. The high- versus low-fertility difference in pitch was associated with the approach of ovulation and not menstrual onset, thus representing, to our knowledge, the first research to show a specific cyclic fertility cue in the human voice. We interpret this finding as evidence of a fertility-related enhancement of femininity consistent with other research documenting attractiveness-related changes associated with ovulation.     

Random amplified polymorphic DNA (RAPD) variation among native little bluestem [Schizachyrium scoparium (Michx.) Nash] populations from sites of high and low fertility in forest and grassland biomes

Random amplified polymorphic DNA (RAPD) markers were used to provide estimates of the comparative genetic variation within and among four native populations of Schizachyrium scoparium . Genotypes were collected from high- and low-fertility sites in both New Jersey (forest biome) and in Oklahoma (grassland biome), USA, and propagated in the greenhouse. Four oligonucleotide primers, 10 bp in length, produced a total of 60 RAPD markers, with the minimum marker difference between any two individuals being 14 markers. Euclidean metric distances were calculated among all individuals, and the analysis of molecular variance ( AMOVA ) technique was used to apportion the total genetic variation among individuals within populations, populations within fertility levels, populations within biomes, fertility levels, and biomes. Even though most genetic variation resided within populations, statistically significant differences were detected between populations within each biome. Furthermore, genetic distances between high and low fertility levels within biomes were equal to or greater than biome distances. Therefore, in this wide-ranging and highly variable species, RAPD analysis suggests that local site differences in fertility and ecological history can promote genetic differentiation equal to or greater than geographical differentiation.     

Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing

We have developed a method that enriches for methylated cytosines by capturing the fraction of bisulfite-treated DNA with unconverted cytosines. The method, called streptavidin bisulfite ligand methylation enrichment (SuBLiME), involves the specific labeling (using a biotin-labeled nucleotide ligand) of methylated cytosines in bisulfite-converted DNA. This step is then followed by affinity capture, using streptavidin-coupled magnetic beads. SuBLiME is highly adaptable and can be combined with deep sequencing library generation and/or genomic complexity-reduction. In this pilot study, we enriched methylated DNA from Csp6I-cut complexity-reduced genomes of colorectal cancer cell lines (HCT-116, HT-29 and SW-480) and normal blood leukocytes with the aim of discovering colorectal cancer biomarkers. Enriched libraries were sequenced with SOLiD-3 technology. In pairwise comparisons, we scored a total of 1,769 gene loci and 33 miRNA loci as differentially methylated between the cell lines and leukocytes. Of these, 516 loci were differently methylated in at least two promoter-proximal CpG sites over two discrete Csp6I fragments. Identified methylated gene loci were associated with anatomical development, differentiation and cell signaling. The data correlated with good agreement to a number of published colorectal cancer DNA methylation biomarkers and genomic data sets. SuBLiME is effective in the enrichment of methylated nucleic acid and in the detection of known and novel biomarkers.     

Influence of interactions between semen extender and number of spermatozoa on nonreturn rate estimates of fertility for individual Holstein bulls

The aim of the present study was to investigate the possibility of adapting sperm cell concentration per insemination unit to the intrinsic fertility of a given bull. For this purpose, split ejaculates of seven proven Holstein sires of unknown fertility were diluted in TRIS or in Laiciphos extenders. TRIS diluted doses contained either 8.12 or 16 million total sperm cells (T8, T12, T16 respectively), while the routinely-used Laiciphos units contained 16 million sperm (L16). A total of 18.068 first artificial inseminations were performed by three different AI centers. No difference in the average fertility occurred between T16 and L16 (69.2 vs 69%), but the individual bull results varied; L16 displayed lower inter-bull variability. The nonreturn rates (60 to 90 days) obtained with T8 and T12 (65.7 and 66.8%, respectively) were significantly lower than with T16 and L16 (P < 0.02). The effect of AI center was also significant (P < 0.05). Despite a highly significant effect of the sire (P < 0.001), no interaction was found between the bull and cell concentration or the AI center. The bull effect indicates that it may be worthwile especially for the bulls of the highest genetic merit to test for the appropriate lowest number of spermatozoa per unit to allow wider commercial and genetic diffusion without compromising the average nonreturn rate of the sire.     

Is apoptosis in bovine in vitro produced embryos related to early developmental kinetics and in vivo bull fertility?

Although several studies have indicated a paternal effect on bovine embryo development, no conclusive data exist on the effect of in vivo bull fertility on apoptosis. Therefore, it was the main objective of this study to compare the apoptotic cell ratio (ACR) in embryos originating from bulls with different in vivo fertility. However, since it is has been demonstrated before that bulls with different in vivo fertility differ in timing of first cleavage, it was necessary to investigate first the effect of timing of development on apoptosis in vitro in order to get an unbiased insight in the contribution of in vivo bull fertility on apoptosis in bovine blastocysts. In the first experiment, bovine embryos (n = 939) were allocated to different groups according to cleavage rate at 30, 36 and 48 hpi and blastocysts were selected at 7 and 8 dpi. The blastocyst rate at 7 dpi was significantly lower in embryos which had first cleaved at 48 hpi than in embryos from the 30 and 36 hpi group (P < 0.05). The ACR after TUNEL in day 7 blastocyst was significantly lower in the 30 hpi group in comparison with the 36 and 48 hpi group (P < 0.05) and lower in day 7 blastocysts than in day 8 blastocysts. In the second experiment, sperm of eight bulls with different non return rates was used for in vitro bovine embryo production (n = 3820 oocytes). Cleavage rates (30, 36 and 48 hpi) and blastocyst rate (7 dpi) were determined. Only very low negative correlations could be found between in vivo and in vitro bull fertility and ACR did not differ between groups derived from sires with either low or normal fertility (P > 0.05). Further research in serum free conditions is needed to confirm that the lower ACR in early cleaved embryos could be mediated by the cooperative interaction of embryos of good quality cultured in group. In vivo bull fertility could hardly be correlated with in vitro blastocyst yield and could not be correlated with appearance of apoptosis.     

Deeper into the maize: new insights into genomic imprinting in plants

Current models for regulation of parent-specific gene expression in plants have been based on a small number of imprinted genes in Arabidopsis. These present repression as the default state, with expression requiring targeted activation. In general, repression is associated with maintenance methylation of cytosines, while no role has been found in Arabidopsis imprinting for de novo methylation--unlike the case in mammals. A recent paper both reinforces and challenges the model drawn from Arabidopsis. Methylation patterns of two imprinted loci in maize were tracked from gametes to offspring, enabling an exploration of the timing of imprinting. For one gene, fie1, the results were as expected: parent-specific methylation patterns were inherited from the three types of gamete: egg, central cell and sperm. The behaviour of fie2, however, was a surprise: no alleles were methylated in the gametes, although paternally contributed fie2 is methylated and silent in the endosperm, indicating that, in some cases, plant imprinting requires de novo DNA methylation. This work significantly broadens our understanding of plant imprinting and points to a greater diversity in imprinting mechanisms than has previously been appreciated.     

Principal component analysis- and tensor decomposition-based unsupervised feature extraction to select more suitable differentially methylated cytosines: Optimization of standard deviation versus state-of-the-art methods

In contrast to RNA-seq analysis, which has various standard methods, no standard methods for identifying differentially methylated cytosines (DMCs) exist. To identify DMCs, we tested principal component analysis and tensor decomposition-based unsupervised feature extraction with optimized standard deviation, which has been shown to be effective for differentially expressed gene (DEG) identification. The proposed method outperformed certain conventional methods, including those that assume beta-binomial distribution for methylation as the proposed method does not require this, especially when applied to methylation profiles measured using high throughput sequencing. DMCs identified by the proposed method also significantly overlapped with various functional sites, including known differentially methylated regions, enhancers, and DNase I hypersensitive sites. The proposed method was applied to data sets retrieved from The Cancer Genome Atlas to identify DMCs using American Joint Committee on Cancer staging system edition labels. This suggests that the proposed method is a promising standard method for identifying DMCs.     

Bisulphite sequencing reveals dynamic DNA methylation under desiccation and salinity stresses in rice cultivars

DNA methylation governs gene regulation in plants in response to environmental conditions. Here, we analyzed role of DNA methylation under desiccation and salinity stresses in three (IR64, stress-sensitive; Nagina 22, drought-tolerant and Pokkali, salinity-tolerant) rice cultivars via bisulphite sequencing. Methylation in CG context within gene body and methylation in CHH context in distal promoter regions were positively correlated with gene expression. Hypomethylation in Nagina 22 and hypermethylation in Pokkali in response to desiccation and salinity stresses, respectively, were correlated with higher expression of few abiotic stress response related genes. Most of the differentially methylated and differentially expressed genes (DMR-DEGs) were cultivar-specific, suggesting an important role of DNA methylation in abiotic stress responses in rice in cultivar-specific manner. DMR-DEGs harboring differentially methylated cytosines due to DNA polymorphisms between the sensitive and tolerant cultivars in their promoter regions and/or coding regions were identified, suggesting the role of epialleles in abiotic stress responses.     

Synthesis of universal unmethylated control DNA by nested whole genome amplification with phi29 DNA polymerase

Optimization of highly sensitive methods to detect methylation of CpG islands in gene promoter regions requires adequate methylated and unmethylated control DNA. Whereas universal methylated control DNA is available, universal unmethylated control (UUC) DNA has not been made because demethylase is not available to remove methyl groups from all methylated cytosines. On the basis that DNA synthesized by DNA polymerase does not contain methylated cytosines, we developed a method to create UUC DNA by nested whole genome amplification (WGA) with phi29 DNA polymerase. Contamination of the template genomic DNA in UUC was only 3.1 x 10(-7), below the detection limit of sensitive methods used for methylation studies such as methylation-specific PCR. Assessment of microsatellite markers demonstrated that even nested phi29 WGA achieves highly accurate and homogeneous amplification with very low amounts of genomic DNA as an initial template. The UUC DNA created by nested phi29 WGA is practically very useful for methylation analysis.