A clone-free, single molecule map of the domestic cow (Bos taurus) genome.

BackgroundThe cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two cattle genome sequence assemblies (UMD3.1 and Btau4.6) from groups using dissimilar assembly algorithms, which were complemented by genetic and physical map resources. However, past comparisons between these assemblies revealed substantial differences. Consequently, such discordances have engendered ambiguities when using reference sequence data, impacting genomic studies in cattle and motivating construction of a new optical map resource--BtOM1.0--to guide comparisons and improvements to the current sequence builds. Accordingly, our comprehensive comparisons of BtOM1.0 against the UMD3.1 and Btau4.6 sequence builds tabulate large-to-immediate scale discordances requiring mediation.ResultsThe optical map, BtOM1.0, spanning the B. taurus genome (Hereford breed, L1 Dominette 01449) was assembled from an optical map dataset consisting of 2,973,315 (439 X; raw dataset size before assembly) single molecule optical maps (Rmaps; 1 Rmap = 1 restriction mapped DNA molecule) generated by the Optical Mapping System. The BamHI map spans 2,575.30 Mb and comprises 78 optical contigs assembled by a combination of iterative (using the reference sequence: UMD3.1) and de novo assembly techniques. BtOM1.0 is a high-resolution physical map featuring an average restriction fragment size of 8.91 Kb. Comparisons of BtOM1.0 vs. UMD3.1, or Btau4.6, revealed that Btau4.6 presented far more discordances (7,463) vs. UMD3.1 (4,754). Overall, we found that Btau4.6 presented almost double the number of discordances than UMD3.1 across most of the 6 categories of sequence vs. map discrepancies, which are: COMPLEX (misassembly), DELs (extraneous sequences), INSs (missing sequences), ITs (Inverted/Translocated sequences), ECs (extra restriction cuts) and MCs (missing restriction cuts).ConclusionAlignments of UMD3.1 and Btau4.6 to BtOM1.0 reveal discordances commensurate with previous reports, and affirm the NCBI's current designation of UMD3.1 sequence assembly as the "reference assembly" and the Btau4.6 as the "alternate assembly." The cattle genome optical map, BtOM1.0, when used as a comprehensive and largely independent guide, will greatly assist improvements to existing sequence builds, and later serve as an accurate physical scaffold for studies concerning the comparative genomics of cattle breeds

Steroids and miRNAs in assessment of ovarian tissue damage following cryopreservation

Ovarian cortical tissue cryopreservation is a relatively novel approach to preserving fertility in women diagnosed with cancer. However, the effects of freezing-thawing are not fully understood, mainly due to the lack of suitable methods to assess tissue’s survival after thawing. Disparities in steroid production have been associated with ovarian failure by disrupting folliculogenesis, ovulation and oocyte apoptosis. Moreover, specific miRNAs, identified in human ovarian follicles, are thought to play a fundamental role in folliculogenesis. In this study, we investigated the possible interplay between the ovariansteroidal production and miRNA expression patterns in spent culture media, as potential non-invasive markers for ovarian tissue damage after cryopreservation. Cryopreservation of ovarian cortical tissue decreased (P < 0.05) both steroid production (oestradiol and progesterone) and expression of miRNA-193b and 320A in spent culture media over 5 days; however, expression of miRNA-24 increased (P < 0.05). The number of primordial follicles was also reduced (P < 0.05) in fresh-cultured and cryopreserved-cultured cortical tissues when compared with fresh tissues. Downregulation of miRNA-193b and miRNA-320A together with upregulation of miRNA-24 could have a synergistic role in cell apoptosis, and consequently leading to reduced oestradiol and progesterone production.Thus, there appears to be an interplay between these miRNAs, ov arian steroid production and cell damage, which can be further explored as novel non-invasive markers of cell damage following cryopreservation

Low protein intake during the preconception period in beef heifers affects offspring and maternal behaviour

Maternal low protein diets prior to conception alter embryo and fetal development and are associated with detrimental outcomes in the offspring in many species. The aim of this study in beef cattle was to investigate the effect of preconception dietary protein upon maternal and offspring behaviour at birth concomitant with the associated hormonal profile. Sixty days prior to conception, nulliparous yearling heifers (n = 85) were fed either a High (PreH: 18%; n = 43) or Low (PreL: 10%; n = 42) crude protein diet, followed by a control diet throughout gestation. After calving, each cow-calf pair was penned individually, accelerometers fitted, and each pen observed continuously via video recordings. Cows fed on the low protein diet during preconception showed an increase in standing time (P [less than] 0.01); while calves born to heifers receiving the PreL diet showed an increase in suckling time (P = 0.04). These calves were also heavier at birth than calves from PreH mothers (P [less than] 0.01). In conclusion, low maternal dietary protein prior to conception in beef heifers modifies both offspring feeding behaviour and birth weight, and cow’s standing times

Regulatory mechanisms for natriuretic peptide signalling in sheep granulosa cells

Natriuretic peptides (NPs) have been reported to have critical roles in follicular development and oocyte maturation in rodents. This study aimed to extend our current understanding of NP-mediated signalling pathways and mechanisms of action in the follicles of a monovulatory species. Ovine granulosa cells (GCs) and theca cells (TCs) were cultured under conditions designed to allow gonadotrophin-stimulated cell differentiation. Gene expression analysis was performed by qualitative (q)PCR for NPs and NPRs (between 16 and 96 h of culture) and VEGF120 and VEGF164 (between 16 and 144 h of culture). A qualitative analysis of the production of NP/NPR family members and NP ligand/receptor associations was carried out utilising a highly sensitive immunological approach known as ‘proximity ligation assay’ (PLA). All NPRs were observed in GCs, while NPRA was absent in TCs. In GCs, gene expression of NPRA, NPRB and NPRC was apparent but only active BNP and CNP and not ANP, were detected. Also in GCs, ANP but not CNP was able to significantly (P [less than] 0.05) reduce oestradiol and increase (P [less than] 0.05) progesterone. Inhibition of VEGF164 by ANP and CNP (P [less than] 0.01) after 48 h of culture preceded up-regulation of VEGF120 by ANP (P [less than] 0.01) after 144 h, but not CNP. Taken together, these findings appear to demonstrate that NP responsiveness in the GC compartment of sheep follicles is multi-facilitated, utilising both autocrine and paracrine stimulation pathways

Evaluating the influence of progesterone concentration and time of exposure on in vitro endometrial decidualisation

This study aimed to evaluate the influence of progesterone (concentration and time of exposure) on endometrial decidualisation using an in vitro model cell line: Human Endometrial Stromal Cells (HESCs). HESCs exposed to progesterone (1 and 10 μM) had higher percentages of decidualised cells and higher expression of the decidual marker (Insulin Like Growth Factor Binding Protein 1 (IGFBP1)) compared with those exposed to (0.1 μM). Among those HESCs cultured with 1 μM progesterone for 11 days, the highest rate of morphological differentiation (40–50%) occurred between days 7–9 and IGFBP1 peaked on day 7. The cell-cycle pathway was significantly down-regulated in HESCs exposed to at least 1 μM progesterone regardless of the incubation period. We conclude that exposure to high progesterone concentration for 7–9 days is essential to maximise the process of decidualisation

Bovine sperm defects are affected by breed, age, season and region

This study reports the distribution of sperm morphology defects by breed, age, season and region of 11,387 bulls in 500 herds in Australia and near Pacific Islands during annual BBSE. Bull location was divided into 4 broad climatic regions based upon temperature, vegetation and climatic risk. Taking into account the impact of age, season, region, and breed there were differences between breeds in both percent morphologically normal sperm and in some individual categories of sperm abnormality (P < 0.001). Independent of breed, season and region, proximal droplets were significantly increased in bulls less than 20 months of age. This is the first study to comprehensively collect data from this wide geographical area and compare sperm morphology profiles among the Bos indicus and Bos taurus breeds. The findings of this study will act as a guide for veterinary practitioners and cattle breeders in the proportion of bulls that can be expected to pass the PNS test, by breed, age and region, based on a robust data set

Suboptimal mid-luteal progesterone concentrations are associated with aberrant endometrial gene expression, potentially resulting in implantation failure

Research questionWhat is the difference in endometrial transcriptomics between women with normal and with low mid-luteal progesterone during the implantation window?DesignAn endometrial biopsy and serum progesterone concentration were taken from participants during the mid-luteal phase (LH+7 to LH+9). A total of 12 participants were recruited and categorized into two groups based on their progesterone concentrations: normal progesterone (>15 ng/ml, n = 6) and low progesterone ([less than] 15 ng/ml, n = 6). Global endometrial gene expression between the two groups was compared by microarray techniques. Principal component analysis was used to display the gene's expression pattern. Pathway and gene ontology enrichment analysis were performed to determine the biological mechanism of progesterone on the endometrium.ResultsSeveral key genes related to endometrial receptivity were found to be regulated by progesterone. With regard to gene ontology and pathway analysis, progesterone was shown to be mainly involved in structure morphogenesis predominantly during a process of decidualization, extracellular matrix–receptor interaction and cell adhesion. Distinct differences were observed in the transcriptomic profiles between the two groups, indicating potential impairment of endometrial receptivity in women with suboptimal progesterone concentrations. There was a relatively similar pattern of gene expression between endometrial samples with progesterone concentrations approximately 10 ng/ml and >15 ng/ml. Thus, a progesterone concentration of between 10 and 15 ng/ml appears to be sufficient to induce endometrial receptivity.ConclusionsAbnormally low progesterone below the threshold of 10–15 ng/ml during the implantation window results in aberrant endometrial gene expression that may affect implantation potential

Detrimental Effects of Non-Functional Spermatozoa on the Freezability of Functional Spermatozoa from Boar Ejaculate

In the present study, the impact of non-functional spermatozoa on the cryopreservation success of functional boar spermatozoa was evaluated. Fifteen sperm-rich ejaculate fractions collected from five fertile boars were frozen with different proportions of induced non-functional sperm (0 –native semen sample-, 25, 50 and 75% non-functional spermatozoa). After thawing, the recovery of motile and viable spermatozoa was assessed, and the functional of the spermatozoa was evaluated from plasma membrane fluidity and intracellular reactive oxygen species (ROS) generation upon exposure to capacitation conditions. In addition, the lipid peroxidation of the plasma membrane was assessed by the indirect measurement of malondialdehyde (MDA) generation. The normalized (with respect to a native semen sample) sperm motility (assessed by CASA) and viability (cytometrically assessed after staining with Hoechst 33342, propidium iodide and fluorescein-conjugated peanut agglutinin) decreased (p<0.01) as the proportion of functional spermatozoa in the semen samples before freezing decreased, irrespective of the semen donor. However, the magnitude of the effect differed (p<0.01) among boars. Moreover, semen samples with the largest non-functional sperm subpopulation before freezing showed the highest (p<0.01) levels of MDA after thawing. The thawed viable spermatozoa of semen samples with a high proportion of non-functional spermatozoa before freezing were also functionally different from those of samples with a low proportion of non-functional spermatozoa. These differences consisted of higher (p<0.01) levels of intracellular ROS generation (assessed with 5-(and-6) chloromethyl-20,70-dichlorodihydrofluorescein diacetate acetyl ester; CM-H2DCFDA) and increased (p<0.01) membrane fluidity (assessed with Merocyanine 540). These findings indicate that non-functional spermatozoa in the semen samples before freezing negatively influence the freezability of functional spermatozoa

The environmental costs and benefits of high-yield farming

How we manage farming and food systems to meet rising demand is pivotal to the future of biodiversity. Extensive field data suggest impacts on wild populations would be greatly reduced through boosting yields on existing farmland so as to spare remaining natural habitats. High-yield farming raises other concerns because expressed per unit area it can generate high levels of externalities such as greenhouse gas (GHG) emissions and nutrient losses. However, such metrics underestimate the overall impacts of lower-yield systems, so here we develop a framework that instead compares externality and land costs per unit production. Applying this to diverse datasets describing the externalities of four major farm sectors reveals that, rather than involving trade-offs, the externality and land costs of alternative production systems can co-vary positively: per unit production, land-efficient systems often produce lower externalities. For GHG emissions these associations become more strongly positive once forgone sequestration is included. Our conclusions are limited: remarkably few studies report externalities alongside yields; many important externalities and farming systems are inadequately measured; and realising the environmental benefits of high-yield systems typically requires additional measures to limit farmland expansion. Yet our results nevertheless suggest that trade-offs among key cost metrics are not as ubiquitous as sometimes perceived. There is an author correction to this article. See: https://doi.org/10.1038/s41893-018-0138-5We are grateful for funding from the Cambridge Conservation Initiative Collaborative Fund and Arcadia, the Grantham Foundation for the Protection of the Environment, the Kenneth Miller Trust the UK-China Virtual Joint Centre for Agricultural Nitrogen (CINAg, 780 BB/N013468/1, financed by the Newton Fund via BBSRC and NERC), BBSRC (BBS/E/C/000I0330), DEVIL (NE/M021327/1), U-GRASS (NE/M016900/1), Soils-R-GRREAT (NE/P019455/1), N-Circle (BB/N013484/1), BBSRC Soil to Nutrition (S2N) strategic programme (BBS/E/C/000I0330), UNAM-PAPIIT (IV200715), the Belmont Forum/FACEE-JPI (NE/M021327/1 ‘DEVIL’), and the Cambridge Earth System Science NERC DTP (NE/L002507/1); AB is supported by a Royal Society Wolfson Research Merit award

A ferrous oxalate mediated photo-Fenton system: Toward an increased biodegradability of indigo dyed wastewaters

This study assessed the applicability of a ferrous oxalate mediated photo-Fenton pretreatment for indigo-dyed wastewaters as to produce a biodegradable enough effluent, likely of being derived to conventional biological processes. The photochemical treatment was performed with ferrous oxalate and hydrogen peroxide in a Compound Parabolic Concentrator (CPC) under batch operation conditions. The reaction was studied at natural pH conditions (5–6) with indigo concentrations in the range of 6.67–33.33 mg L−1, using a fixed oxalate-to-iron mass ratio (C2O42−/Fe2+ = 35) and assessing the system's biodegradability at low (257 mg L−1) and high (1280 mg L−1) H2O2 concentrations. In order to seek the optimal conditions for the treatment of indigo dyed wastewaters, an experimental design consisting in a statistical surface response approach was carried out. This analysis revealed that the best removal efficiencies for Total Organic Carbon (TOC) were obtained for low peroxide doses. In general it was observed that after 20 kJ L−1, almost every treated effluent increased its biodegradability from a BOD5/COD value of 0.4. This increase in the biodegradability was confirmed by the presence of short chain carboxylic acids as intermediate products and by the mineralization of organic nitrogen into nitrate. Finally, an overall decrease in the LC50 for Artemia salina indicated a successful detoxification of the effluent