Determination of bovine fetal sex by PCR using fetal fluid aspirated by transvaginal ultrasound-guided amniocentesis

A rapid approach for sex assignment by RAD-seq using a reference genome

Sex identification is a common objective in molecular ecology. While many vertebrates display sexual dimorphism, determining the sex can be challenging in certain situations, such as species lacking clear sex-related phenotypic characteristics or in studies using non-invasive methods. In these cases, DNA analyses serve as valuable tools not only for sex determination but also for validating sex assignment based on phenotypic traits. In this study, we developed a bioinformatic framework for sex assignment using genomic data obtained through GBS, and having an available closely related genome assembled at the chromosome level. Our method consists of two ad hoc indexes that rely on the different properties of the mammalian heteromorphic sex chromosomes. For this purpose, we mapped RAD-seq loci to a reference genome and then obtained missingness and coverage depth values for the autosomes and X and Y chromosomes of each individual. Our methodology successfully determined the sex of 165 fur seals that had been phenotypically sexed in a previous study and 40 sea lions sampled in a non-invasive way. Additionally, we evaluated the accuracy of each index in sequences with varying average coverage depths, with Index Y proving greater reliability and robustness in assigning sex to individuals with low-depth coverage. We believe that the approach presented here can be extended to any animal taxa with known heteromorphic XY/ZW sex chromosome systems and that it can tolerate various qualities of GBS sequencing data.

Sexing of cattle embryos using RNA-sequencing data or polymerase chain reaction based on a complete sequence of cattle chromosome Y

When necessary, RNA-sequencing data or polymerase chain reaction (PCR) assays can be used to determine the presence of the chromosome Y (ChrY) in samples. This information allows for biological variation due to sexual dimorphism to be studied. A prime example is when researchers conduct RNA-sequencing of single embryos, or conceptuses, prior to the development of gonads. A recent publication of a complete sequence of the ChrY has removed limitations for the development of these procedures in cattle, otherwise imposed by the absence of a ChrY in the reference genome. Using the sequence of the cattle ChrY and transcriptome data, we conducted a systematic search for genes in the ChrY that are exclusively expressed in male tissues. The genes ENSBIXG00000029763, ENSBIXG00000029774, ENSBIXG00000029788, and ENSBIXG00000029892 were consistently expressed across male tissues and lowly expressed or absent in female samples. We observed that the cumulative values of counts per million were 2688-fold greater in males than the equivalent values in female samples. Thus, we deemed these genes suitable for the sexing of samples using RNA-sequencing data. We successfully used this set of genes to infer the sex of 22 cattle blastocysts (8 females and 14 males). Additionally, the completed sequence of the cattle ChrY has segments in the male-specific region that are not repeated. We designed a pair of oligonucleotides that targets one of these non-repeated regions in the male-specific sequence of the ChrY. Using this pair of oligonucleotides, in a multiplexed PCR assay with oligonucleotides that anneal to an autosome chromosome, we accurately identified the sex of cattle blastocysts. We developed efficient procedures for the sexing of samples in cattle using either transcriptome data or their DNA. The procedures using RNA-sequencing will greatly benefit researchers who work with samples limited in cell numbers which are only sufficient to produce transcriptome data. The oligonucleotides used for the accurate sexing of samples using PCR are transferable to other cattle tissue samples.

Protective and Therapeutic Effects of Bovine Amniotic Fluids Collected in Different Trimesters on the Epidural Fibrosis After Experimental Laminectomy in Rats

BACKGROUND

The aim of this study was to investigate the protective and therapeutic effects of bovine amniotic fluid (BAF) on the inhibition of epidural fibrosis (EF) after experimental laminectomy.

METHODS

Forty female Sprague Dawley rats were used. The amniotic fluids were collected from each trimester of a pregnant cow. The rats were divided into 5 groups. Whereas no laminectomy was applied to the control group, animals in the sham group underwent laminectomy. Laminectomy was performed in the animals in other groups and the operation area was closed by dripping 1 mL of BAF collected in 3 trimesters of pregnancy. Animals were killed 28 days after the operation.

RESULTS

Compared with control, VEGF gene expression levels were downregulated approximately 5-fold in BAF-2. Whereas IL-6 was upregulated approximately 8-fold in the sham, it was downregulated 5-fold and 3-fold in BAF-1 and BAF-2, respectively. There was downregulation in BAF-2 and BAF-3 in terms of CD105 gene expression levels. TGFβ1 was upregulated approximately 2-fold in the sham group and downregulated in BAF-1 and BAF-2. Although histopathologic alterations including EF grade and fibroblast cell density were found to increase in the sham group, all BAF treatment decreased those of alterations. The highest CD105 immunoreactivity was detected in the sham group. All BAF treatment markedly aggravated fibrosis via decreasing CD105 immunoreactivity. In terms of grading parameters, almost the closest grades to the control were determined in the BAF-2. BAF collected in the second trimester is most effective in healing of scar tissue and preventing fibrosis via decreasing microvessel and fibroblast densities.

CONCLUSIONS

The results indicate that BAF may be used as a potential protective agent to prevent EF.

Evaluation of serum anti-Müllerian hormone (AMH) and equine chorionic gonadotrophin (eCG) concentrations in pregnant mares in relation to foetal sex

The aim of this study was to investigate the foetal sex related difference and progression in maternal serum anti-Müllerian hormone (AMH) and equine chorionic gonadotrophin (eCG) concentrations during different points of time in pregnant Arabian mares. The study groups formed by 12 healthy male offspring- and 12 healthy female offspring-foaling mares, designated as group MFM and group FFM, respectively. Peripheral blood samples were collected on the day of natural mating and then monthly until the 6th month (mo) of gestation. Serum AMH was measured in all serum samples; eCG was measured in samples collected from 2 to 5 months Of gestation. Serum AMH concentrations of group FFM at mo 4 and mo 5 (3.89 ± 0.49 ng/ml; 2.89 ± 0.32 ng/ml), were significantly higher than in group MFM (2.11 ± 0.46 ng/ml; 1.87 ± 0.32 ng/ml), (P < 0.05). The mo of gestation (mo 1–6) had no effect on serum AMH concentrations of either group MMF or FFM (P > 0.05). Serum eCG concentrations of group FFM at mo 2 (359.73 ± 41.51 mIU/ml), were significantly higher than in group MFM (255 ± 21.18 mIU/ml) (P < 0.05). Group-time interaction for eCG concentrations at mo 2–4 was non-significant (P > 0.05). Concentrations of serum AMH showed no relationship with corresponding eCG levels at mo 2–4 (P > 0.05). Individual variations in AMH and eCG concentrations and the inability to determine a cut-off point for determination of foetal sex make these hormones unlikely candidates for determining foetal sex in the mare.

Antimicrobial prophylaxis post-amniocentesis procedures in cattle: A randomized controlled equivalence study

Amniocentesis is a routine procedure utilized on several species including human, equine, and bovine patients. Early assessment and discovery of new genetic traits in the cattle industry are highly desirable in order to accelerate genetic gain by shortening generational intervals. One of the main concerns from this procedure is the introduction of pathogenic bacterial contamination into the amniotic cavity thereby increasing the risks of spontaneous pregnancy losses post procedure. In this randomized controlled equivalence study, we have tested the effect of antimicrobial prophylaxis on the incidence of spontaneous abortions and contrasted it to untreated individuals post amniocentesis. On the treated group (n = 67) all heifers remained pregnant whereas 1 of the untreated group (n = 65) resulted in a spontaneous abortion during the study period. The latter represents 1.54% of pregnancy losses attributed to the risk associated to the amniocentesis procedure. However, the probability of inducing spontaneous abortion from the technique itself is not different to that of the contemporaneous population (n = 694) not undergoing amniocentesis viz., 1.59%. Following a two-tailed distribution, statistical analyses showed no significant differences across treatments (Fisher's exact test P = 0.49). The current prospective study indicates that performing amniocenteses on cattle have resulted in similar spontaneous pregnancy losses comparable to those of pregnant heifers without undergoing amniocentesis and regardless of antimicrobial use. In conclusion, prophylactic antimicrobials may not be applicable within the cattle amniocentesis framework.

Utility and Applicability of a Universal Set of Primers in Identifying the Sex of South and Southeast Asian Mammals

Sex identification of individuals is an important task in wildlife forensics as well as in conservation biology. It helps scientists understand population sex ratios with respect to maintaining genetic diversity, managing inbreeding depression and preventing the demographic consequences of sex-biased poaching. The literature on the use of mammalian molecular sex markers indicates that the success of accurate sex identification is variable across species. Very little is known about the effectiveness of such markers on the mammals of South and Southeast Asia. Therefore, we selected and tested three sets of universal primers for low-cost gel-based sex identification of mammals. We amplified different sets of markers-SRY (157 bp) and 12S rRNA (384 bp); Y-53-SRY (225 bp) and ZFX/ZFY (P1/P2; 445); SRY (157 bp) and 12S rRNA (151 bp)-to be used with different types (tissue, hair and skin) of samples from 20 mammalian species. All three sets of primers amplified the sex-specific fragment in a range of samples from hair to tissue. With an increasing number of field studies using non-invasively collected samples, this proposed low-cost gel- based method of molecular sexing may be applied in various aspects of the ecology and biology of South and Southeast Asian mammals, their conservation and forensics. We suggest that at least two sets of primers be used for any biological samples to avoid ambiguity.

Use of trichostatin A alters the expression of HDAC3 and KAT2 and improves in vitro development of bovine embryos cloned using less methylated mesenchymal stem cells

The aim of this work was to investigate the methylation and hydroxymethylation status of mesenchymal stem cells (MSC) from amniotic fluid (MSC-AF), adipose tissue (MSC-AT) and fibroblasts (FIB-control) and to verify the effect of trichostatin A (TSA) on gene expression and development of cloned bovine embryos produced using these cells. Characterization of MSC from two animals (BOV1 and BOV2) was performed by flow cytometry, immunophenotyping and analysis of cellular differentiation genes expression. The cells were used in the nuclear transfer in the absence or presence of 50 nM TSA for 20 hr in embryo culture. Expression of HDAC1, HDAC3 and KAT2A genes was measured in embryos by qRT-PCR. Methylation results showed difference between animals, with MSC from BOV2 demonstrating lower methylation rate than BOV1. Meanwhile, MSC-AF were less hydroxymethylated for both animals. MSC-AF from BOV2 produced 44.92 ± 8.88% of blastocysts when embryos were exposed to TSA and similar to embryo rate of MSC-AT also treated with TSA (37.96 ± 15.80%). However, when methylation was lower in FIB compared to MSC, as found in BOV1, the use of TSA was not sufficient to increase embryo production. MSC-AF embryos expressed less HDAC3 when treated with TSA, and expression of KAT2A was higher in embryos produced with all MSC and treated with TSA than embryos produced with FIB. The use of MSC less methylated and more hydroxymethylated in combination with embryo incubation with TSA can induce lower expression of HDAC3 and higher expression of KAT2A in the embryos and consequently improve bovine embryo production.

Production of Bovine Embryos and Calves Cloned by Nuclear Transfer Using Mesenchymal Stem Cells from Amniotic Fluid and Adipose Tissue

The less differentiated the donor cells are used in nuclear transfer (NT), the more easily are they reprogrammed by the recipient cytoplasm. In this context, mesenchymal stem cells (MSCs) appear as an alternative to donor nuclei for NT. The amniotic fluid and adipose tissue are sources of MSCs that have not been tested for the production of cloned embryos in cattle. The objective of this study was to isolate, characterize, and use MSCs derived from amniotic fluid (MSC-AF) and adipose tissue (MSC-AT) to produce cloned calves. Isolation of MSC-AF was performed using in vivo ultrasound-guided transvaginal amniocentesis, and MSC-AT were isolated by explant culture. Cellular phenotypic and genotypic characterization by flow cytometry, immunohistochemistry, and RT-PCR were performed, as well as induction in different cell lineages. The NT was performed using MSC-AF and MSC-AT as nuclear donors. The mesenchymal markers of MSC were expressed in bovine MSC-AF and MSC-AT cultures, as evidenced by flow cytometry, immunohistochemistry, and RT-PCR. When induced, these cells differentiated into osteocytes, chondrocytes, and adipocytes. Embryo production was similar between the cell types, and two calves were born. The calf from MSC-AT was born healthy, and this fact opens a new possibility of using this type of cell to produce cloned cattle by NT.

Biomedical applications of ovarian transvaginal ultrasonography in cattle

Ovarian transvaginal ultrasonography (OTU) has been used world-wide for commercial ovum pick-up programs for in vitro embryo production in elite herds, providing an excellent model for the elucidation of factors controlling bovine oocyte developmental competence. Noninvasive sampling and treatment of ovarian structures is easily accomplished with bovine OTU techniques providing a promising system for in vivo delivery of transgenes directly into the ovary. The current review summarizes existing bovine OTU models and provides prospective applications of bovine OTU to undertake research in reproductive topics of biomedical relevance, with special emphasis on the development of in vivo gene transfer strategies.

Manual rupture versus transvaginal ultrasound-guided aspiration of allanto-amniotic fluid in multiple pregnancies: a clinical approach to embryo reduction in dairy cattle

To avoid the problems associated with twinning in dairy cattle, one of the embryos may be eliminated. This study compares the effect on pregnancy maintenance of two embryo reduction techniques, manual rupture (MR) and transvaginal ultrasound-guided aspiration (TUGA) of allanto-amniotic fluid, in Holstein-Friesian cows with multiple pregnancies. In the first experiment, 61 lactating cows bearing unilateral twins (n=27), bilateral twins (n=30) or triplets/quadruplets (n=4) were subjected to MR (n=45) or TUGA using a 17-G neddle (n=16) on day 28-34 of gestation. In 21 and 10 cows undergoing MR and TUGA embryo reduction, respectively, pregnancy loss occurred before day 90 (46.7 vs. 62.5%, P= 0.28). Through binary logistic regression, the type of pregnancy was identified as the only variable significantly affecting pregnancy maintenance (P=0.03). Based on the odds ratio, the risk of pregnancy loss was 4.1 times higher for unilateral twins than for bilateral twins (70.4 vs. 36.7%, respectively, P=0.01). No effect was detected on pregnancy maintenance of the technique used (P=0.17) or of the interaction technique by type of pregnancy (P=0.22). In the second experiment, a 22-G needle was used to perform TUGA on 22 lactating cows. The pregnancy loss rates were 44.4% (4/9), 18.2% (2/11) and 50% (1/2) for cows bearing unilateral twins, bilateral twins and triplets, respectively. The total pregnancy loss rate following TUGA using the 22-G needle tended to be lower than that using the 17-G needle (31.8 vs. 62.5%; P=0.06). Our results suggest that TUGA using a 22-G needle could be the method of choice to perform embryo reduction in cows carrying multiple pregnancies.

Zinc-finger intron 7: a new locus for sex identification of giant panda (Ailuropoda melanoleuca)

We developed a single-reaction test for identifying the sex of giant panda (Ailuropoda melanoleuca) targeted to co-amplify homologous fragments with size polymorphism that located at zinc-finger (ZF) intron 7 by using one pair of primers. This assay produced one sex-specific fragment in females (XX genotypes) whereas two fragments were produced in males (XY genotypes). Indels (insertion/deletion) in intron 7 of Y-linked allele provide a significant discrimination between ZFX and ZFY, thus the amplification products can be simply distinguished by agarose gel electrophoresis, exhibiting sex-specific banding patterns (female, 354 bp; male, 354 bp, 135 bp). The new primer set was successfully tested on known-sex giant pandas by using template DNA extracted from both blood and fecal samples. Cross-species test was also performed, revealing that this assay could be applied to other Ursidae species.