Dry matter intake and feed efficiency of heifers from 4 dairy breed types grazing organic grass and grass-birdsfoot trefoil mixed pastures.

Insufficient dry matter intake (DMI) of pasture by dairy cattle is a major factor limiting growth and milk production; however, it has been hypothesized that some dairy breeds may be more efficient grazers than others. This study was conducted to determine whether dairy breed types differ in DMI and feed efficiency when grazing either grass monoculture or grass-legume mixed pastures. The experiment compared 4 different dairy breed types (Jersey, Holstein, Holstein-Jersey crossbreds, and Montbéliarde-Swedish Red-Holstein 3-breed crossbreds) and 2 levels of pasture type [grass monoculture (MONO) and grass-birdsfoot trefoil (BFT) mixture (MX)] for a total of 8 treatments. Pastures were rotationally stocked with groups of 4 prepubertal heifers for 105 d for 3 yr, and DMI was determined from herbage disappearance. Feed conversion efficiency (FCE) and residual feed intake (RFI) were then derived from DMI, and heifer body weights (BW) and normalized to animal units (AU) as 40% metabolic mature BW of the corresponding dairy breed type to account for inherent differences in size and growth rates. We observed differences in DMI and feed efficiency among breed types and between pasture types. On average, Holsteins had the greatest overall DMI (4.4 kg/AU), followed by intermediate DMI by the crossbreds (4.0 kg/AU), and Jerseys had the least DMI (3.6 kg/AU). Heifers grazing MX pastures had on average 22% greater DMI than those grazing MONO, but heifers on grass monocultures were more efficient in converting DMI to BW gain (i.e., RFI/AU of 0.27 and -0.27, respectively; more negative RFI numbers indicate less DMI to achieve the expected gains). Overall, Jerseys had the most favorable feed efficiency; however, ranking of Holsteins and crossbreds depended upon the feed efficiency metric. This study is one of the first to compare the interaction of dairy breed and pasture quality on grazing efficiency. However, the lack of a breed type × pasture type interaction for DMI, FCE, or RFI indicated that none of these dairy breed types were better adapted than another breed type to pastures with contrasting levels of nutritive value.

In-situ characterization of porcine fibroblasts in response to silver ions by Raman spectroscopy and liquid scanning transmission electron microscopy.

Since silver ion is known for its antimicrobial function, most of the research has focused mainly on toxicity effects rather than the role of silver ion in general biology and the behind mechanism of actions of silver ion in mammalian cells. Moreover, a conventional in vitro approach to estimate the effects of silver ion on cells does not provide information about the biochemical changes and might accompany artifacts due to invasive and destructive sample preparation processes. In the present study, in-situ real time approaches were applied to evaluate the impact of silver ion (0.57, 1.34, 1.96, 2.33 mg/L) on fibroblast cells. Raman spectroscopy analysis showed that Raman peak intensities of proteins and nucleic acids significantly increased in the cells after exposure to silver ion for 21 h, especially at relatively higher levels 1.34, 1.96, and 2.33 mg/L. Raman peak at 1585 cm-1 and liquid scanning transmission electron microscopy energy-dispersive x-ray spectroscopy (STEM-EDS) analysis revealed the fate of silver ion that was taken up by the cell and reduced into metallic silver accumulating in the cell as silver nanoparticles. These results suggest cells were undergoing different activities such as enhanced metabolic activities rather than cell apoptosis or cell death. Additionally, Raman spectroscopy predicted the level of silver ion exposed to the cell at 2.11 ± 0.38 and 1.73 ± 0.26 mg/L by the PLS prediction model, compared with the results measured by inductively coupled plasma mass spectrometry (ICP-MS), 2.14 ± 0.07 and 1.87 ± 0.07 mg/L respectively, suggesting Raman spectroscopy can provide a new and fast approach to determine and measure the concentration of silver ion or probably other tested molecules treated to the cell for the future research.

The effects of organic grass and grass-birdsfoot trefoil pastures on Jersey heifer development: Heifer growth, performance, and economic impact.

Dairy heifers developed in certified organic programs, especially those utilizing pasture-based management schemes, have lower rates of gain than heifers raised in nonorganic confinement production systems in temperate climates, such as in the Intermountain West region of the United States. This study investigates the effects that different forages in a rotational grazing system have on development of organically raised Jersey heifers. Over 3 years, 210 yearling Jersey heifers were randomly assigned to one of 9 treatments, including a conventional confinement control where animals were fed a total mixed ration or one of 8 pasture treatments: Cache Meadow bromegrass (Bromus riparius Rehmann), QuickDraw orchard grass (Dactylis glomerata L.), Amazon perennial ryegrass (Lolium perenne L.), or Fawn tall fescue (Schendonorus arundinaceus [Schreb.] Dumort) and each individual grass interseeded with birdsfoot trefoil (Lotus corniculatus L., BFT). Each treatment had 3 blocks/yr over the 3-yr period, with each block having a 0.4 ha pasture of each treatment. Every 35 d, over a 105-d period, heifers were weighed and measured for hip height, and blood samples were collected to determine serum insulin-like growth factor-1 and blood urea nitrogen concentrations. Fecal egg counts were also assessed. Heifer body weight (BW), blood urea nitrogen, and insulin-like growth factor-1 concentrations were affected by treatment when analyzed over time. Heifers on grass-BFT pastures had increased BW compared with heifers on monoculture grass pastures. Heifers receiving a total mixed ration or perennial ryegrass+BFT had increased BW gain over the 105-d period compared with heifers grazing tall fescue+BFT, orchard grass, perennial ryegrass, meadow bromegrass, or tall fescue. Individually for all grass species, heifers grazing +BFT pastures had greater ending BW and weight gain than heifers grazing the respective grass monocultures. Furthermore, weight gain for heifers on perennial ryegrass+BFT, meadow bromegrass+BFT, and orchard grass+BFT were not different from those on a total mixed ration. Heifers grazing grass-BFT pastures had increased blood urea nitrogen compared with heifers grazing monoculture grass pastures. Heifer hip height and fecal egg counts were not affected by treatment. These results show that the addition of BFT to organic pasture improves growth of grazing replacement heifers. Economic analyses also demonstrate that interseeding grass pastures with BFT results in an increased economic return compared with grazing monoculture grass pastures. Grass pastures interseeded with BFT may be a sustainable option to achieve adequate growth of Jersey heifers raised in an organic pasture scenario in a temperate climate.

The effects of organic grass and grass-birdsfoot trefoil pastures on Jersey heifer development: Herbage characteristics affecting intake.

Low dietary energy and decreased intake of herbage have been attributed to the reduced performance of grazing dairy cattle. We hypothesized that grasses with inherently greater energy would interact in a complementary way with condensed tannins (CT) in birdsfoot trefoil to increase herbage intake by grazing dairy heifers. Eight pasture treatments comprising high-sugar perennial ryegrass (Lolium perenne L.), orchardgrass (Dactylis glomerata L.), meadow bromegrass (Bromus riparius Rehmann), and tall fescue [Schendonorus arundinaceus (Schreb.) Dumort] were established in Lewiston, Utah as monocultures and binary mixtures with birdsfoot trefoil (Lotus corniculatus L.; BFT). Pasture treatments were rotationally stocked by Jersey heifers for 105 d in 2017 and 2018, and herbage samples were collected pre- and postgrazing for each 7-d grazing period and analyzed for herbage mass, nutritive value, and apparent herbage intake. We observed differences among pasture treatments in herbage quantity and nutritive value, as well as differences in herbage intake by grazing Jersey heifers. On average, grass-BFT mixtures had greater herbage intake than grass monocultures, and every grass-BFT treatment individually had greater herbage intake than their respective grass monocultures. Using multivariate analyses, we determined that approximately 50% of the variation in herbage intake was due to nutritive and physical herbage characteristics, with the most explanatory being characteristics related to fiber and energy, followed by those related to the percent of BFT in the herbage. Grass monocultures exhibited a range of inherent dietary energy, but there was indication that an imbalance of energy to crude protein (e.g., protein deficient) reduced intake of grass monocultures. Moreover, there was some evidence of a complementary effect between increased dietary energy and CT; however, low CT levels made it impossible to determine the effect of CT on herbage intake per se. This study confirmed that chemical and physical characteristics inherent to different pasture species have a large effect on herbage intake by grazing cattle. Pastures planted to binary mixtures of nutritious grasses and birdsfoot trefoil increase herbage intake of temperate pastures by grazing Jersey heifers.

Effects of electrical biostimulation and silver ions on porcine fibroblast cells.

The medical applications of electrical biostimulation and silver ions have been evaluated in laboratory experiments and clinical studies for more than two decades. Their effects on preventing infection and promoting wound healing have been described. However, little is known about the role of electrical biostimulation and/or silver ion on changes in cellular transcriptome dynamics. To our knowledge, few studies have been conducted to investigate the potential of electrical biostimulation and silver ions in cell reprogramming. Besides, it is essential to assess any possible adverse effects or potential benefits of the silver ions on mammalian cells to address its safety concerns and to improve silver medical products. In this study, we investigated transcriptomic changes in porcine fibroblast cells in response to electrical biostimulation in the presence of silver ions. Exposed cells presented distinct morphological changes after treatment, which was mainly due to the exposure of silver ions rather than the electrical current itself. Gene expression analyses suggested that electrical biostimulation and silver ions did not increase the expression of pluripotency genes. Interestingly, a set of genes related to cellular metabolic processes were differentially expressed after cells were exposed to electrically generated silver ions for 21 hours. We found that 2.00 mg/L of electrically generated silver ion caused an increase of ATP generation and an increase of the total pool of NAD+ and NADH, while ROS production did not change. Aside from toxic effects, the results reported herein demonstrate the alternative effects of silver ions on mammalian cells, especially an oxidative phosphorylation burst. To our knowledge, this response of mammalian cells to silver ions has not been described previously. Although the function of this burst is not understood, it may lead to alterations in cellular activities such as metabolic remodeling and cell reprogramming, and/or serve an as-yet unknown function in neutralization or detoxification of the silver ions within the cells.

Association between fear of hypoglycemia and physical activity in youth with type 1 diabetes: The SEARCH for diabetes in youth study.

BACKGROUND: Youth with type 1 diabetes (T1D) are encouraged to participate in physical activity (PA). Studies have identified fear of hypoglycemia (FOH) as a barrier to participating in PA. OBJECTIVES: To examine (a) PA patterns in youth with T1D by age group and (b) the relationship between both parental and youth FOH and youth PA. METHODS: A cross-sectional analysis from the SEARCH cohort study visit of youth ages 10 to 17 years with T1D (n = 1129) was conducted. Linear regression models estimated the association between self-reported number of days of vigorous PA (VPA) and moderate PA (MPA) and both youth- and parent-reported FOH. Multivariable models were adjusted for age, sex, race, duration of T1D, HbA1c, use of continuous glucose monitoring (CGM), recent severe hypoglycemia, primary insulin regimen, and BMI. RESULTS: Participants were 52% female, had mean (sd) age 14.4 (4.2) years, diabetes duration 7.5 years (1.8), HbA1c 9.2% (1.7). Older youth were less likely to engage in VPA (P < .01), or sports teams (P < .01), but more likely to engage in MPA (P < .01). Higher youth FOH (behavior subscale) was associated with increased levels of VPA (ß (se) 0.30 (0.11), P = .01) but not significantly associated with MPA (P = .06). There was no statistically significant association between parental FOH and youth PA. CONCLUSIONS: In SEARCH participants with T1D, VPA, and team sports participation declined with age, while MPA increased. We observed that higher scores on the youth FOH behavioral subscale were associated with increased VPA levels, suggesting that FOH may be less of a barrier to PA than previously thought.

Transfer from paediatric to adult care for young adults with Type 2 diabetes: the SEARCH for Diabetes in Youth Study.

AIM: To describe factors associated with transfer from paediatric to adult care and poor glycaemic control among young adults with Type 2 diabetes, using the SEARCH for Diabetes in Youth study. METHODS: Young adults with Type 2 diabetes were included if they had a baseline SEARCH visit while in paediatric care at < 18 years and ≥ 1 follow-up SEARCH visit thereafter at 18-25 years. At each visit, HbA1c , BMI, self-reported demographic and healthcare provider data were collected. Associations of demographic factors with transfer of care and poor glycaemic control (HbA1c ≥ 75 mmol/mol; 9.0%) were explored with multivariable logistic regression. RESULTS: 182 young adults with Type 2 diabetes (36% male, 75% minority, 87% with obesity) were included. Most (n = 102, 56%) reported transfer to adult care at follow-up; a substantial proportion (n = 28, 15%) reported no care and 29% did not transfer. Duration of diabetes [odds ratio (OR) 1.4, 95% confidence interval (95% CI) 1.1, 1.8] and age at diagnosis (OR 1.8, 95% CI 1.4, 2.4) predicted leaving paediatric care. Transfer to adult or no care was associated with a higher likelihood of poor glycaemic control at follow-up (adult: OR 4.5, 95% CI 1.8, 11.2; none: OR 4.6, 95% CI 1.4, 14.6), independent of sex, age, race/ethnicity or baseline HbA1c level. CONCLUSIONS: Young adults with Type 2 diabetes exhibit worsening glycaemic control and loss to follow-up during the transfer from paediatric to adult care. Our study highlights the need for development of tailored clinical programmes and healthcare system policies to support the growing population of young adults with youth-onset Type 2 diabetes.

Biochemical, biophysical, and genetic changes of porcine trophoblast-derived stem-like cells during differentiation as evaluated using Raman microspectroscopy, Atomic force microscopy, and quantitative polymerase chain reaction.

Porcine trophoblast-derived stem-like cells grown into serum medium start to differentiate and become senescent within 30 days. However, trophoblast-derived cells, cultured in vitro in a defined and non-serum medium, have the regenerative properties, such as indefinite passage and foreign DNA receptivity, similar to stem cells. To evaluate the biochemical, biophysical, and genetic changes of the terminal differentiation of trophoblast derived cells, Raman microspectroscopy, atomic force microscopy, and qPCR were applied. It was found that Raman spectral intensities of characteristic peaks, cell morphology, and Young's modulus can be used to distinguish differentiated and undifferentiated trophoblast cells. In addition, 17 cytoskeleton and extracellular matrix-related genes were significantly impacted by medium type (non-serum versus serum). Our findings suggest that Raman microspectroscopy and atomic force microscopy-both considered as label-free, non-invasive techniques-can be applied to distinguish differentiated trophoblast cells, and cellular biochemical information and biophysical properties can be indicative of cellular differences during cell differentiation. In addition, most of cytoskeleton-related genes exhibit similar pattern to that of Young's modulus during trophoblast cell differentiation, indicating the potential connection between cytoskeleton-related genes and cellular stiffness.

A phase II clinical trial of weekly paclitaxel and carboplatin in combination with panitumumab in metastatic triple negative breast cancer.

PURPOSE: Women with metastatic triple negative breast cancer (TNBC) can have a poor prognosis with treatment limited to cytotoxic chemotherapy. The identification of effective therapies that may limit exposure to cytotoxic chemotherapy and lead to prolonged survival is an unmet medical need. We tested an inhibitor of the epidermal growth factor receptor, panitumumab in combination with chemotherapy. METHODS: We conducted a single arm clinical trial in women with metastatic or locally advanced TNBC to paclitaxel 80 mg/m2 and carboplatin AUC of 2 on days 1, 8, and 15 and panitumumab 6 mg/kg on days 1 and 15 for a cycle length of 28 days. The objectives were to evaluate the response rate and safety of the combination in comparison to historical controls. RESULTS: Fourteen patients with TNBC were enrolled with a median age of 53 years. The majority of women were African American (64.3%) with visceral metastasis (64.2%). Hematologic toxicities, particularly neutropenia and thrombocytopenia, were a major cause of missed chemotherapy and delayed treatment in this study. The overall response rate (complete and partial response) of the 13 evaluable patients was 46%. The median time to best response was 2.4 months and the median time to disease progression was 3.6 months. We were able to perform the PAM50 analysis on tumors from 7 of our subjects. All the samples tested clustered within the basal-like subtype. CONCLUSIONS: In our experience the response rate of carboplatin, paclitaxel and panitumumab was consistent with other reports of response for cytotoxic chemotherapy in metastatic TNBC.

Expression profiles of select genes in cumulus-oocyte complexes from young and aged mares.

There is compelling evidence that oocytes from mares >18 years of age have a high incidence of inherent defects that result in early embryonic loss. In women, an age-related decrease in oocyte quality is associated with an increased incidence of aneuploidy and it has recently been determined that the gene expression profile of human oocytes is altered with advancing age. We hypothesised that similar age-related aberrations in gene expression occur in equine oocytes. Therefore, the aim of the present study was to compare gene expression profiles of individual oocytes and cumulus cells from young and aged mares, specifically evaluating genes that have been identified as being differentially expressed with advancing maternal age and/or aneuploidy in human oocytes. Expression of 48 genes was compared between 14 cumulus-oocyte complexes (COCs) from mares aged 3-12 years and 10 COCs from mares ≥18 years of age. Three genes (mitochondrial translational initiation factor 3 (IF3), heat shock transcription factor 5 (HSF5) and Y box binding protein 2 (YBX2)) were differentially expressed in oocytes, with all being more abundant in oocytes from young mares. Three genes (ADP-ribosylation factor-like 6 interacting protein 6 (ARL6IP6), BCL2-associated X protein (BAX) and hypoxia upregulated 1 (HYOU1)) were differentially expressed in cumulus cells, with all being more abundant in aged mares. The results of the present study confirm there are age-related differences in gene expression in equine COCs, which may be associated with the lower quality and decreased developmental competence of oocytes from aged mares.

Isolation and characterization of trophoblast-derived stem-like cells from peri-implantation porcine embryos.

In mammals, the trophoblast lineage of the embryo is specified before attachment/implantation to become the fetal portion of the placenta. Trophoblast-derived cells were isolated and cultured from day 10 and day 13 porcine embryos and were grown in vitro in a defined, serum-free culture medium for over 2 years without showing any signs of senescence. However, trophoblast-derived cells placed into serum-containing medium rapidly senesce and fail to proliferate. Semiquantitative and quantitative gene expression analyses of cells in culture from 0 to 30 days confirmed the presence (and relative abundance) of mRNA transcripts from genes involved in trophoblast function (CDX2, TEAD4, CYP17A1, HSD17B1, FGFR2, PLET, HAND1) as well as some genes known to mediate pluripotency (POU5F1, KLF4, CMYC). Protein immunolocalization demonstrated expression of both trophoblast and mesenchymal cell markers. DNA methylation patterns in promoters of three critical developmental genes (HAND1, KLF4, TEAD4) did not change appreciably over 4 months of culture in vitro. It was demonstrated that these trophoblast-derived cells are easily stably transfected with an exogenous transgene (eGFP) by a variety of methods, and show the ability to survive and to be passaged repeatedly after transfection. In summary, early embryonic porcine trophoblast-derived cells have demonstrated unique characteristics, which means they could be used as valuable tools for laboratory work. Anticipated applications include the study of trophoblast physiology as well as possible solutions for improving efficiency of transgenesis by somatic cell nuclear transfer and for pluripotency reprogramming of cells.

Effects of heat stress on carbohydrate and lipid metabolism in growing pigs.

Heat stress (HS) jeopardizes human and animal health and reduces animal agriculture productivity; however, its pathophysiology is not well understood. Study objectives were to evaluate the direct effects of HS on carbohydrate and lipid metabolism. Female pigs (57 ± 5 kg body weight) were subjected to two experimental periods. During period 1, all pigs remained in thermoneutral conditions (TN; 20°C) and were ad libitum fed. During period 2, pigs were exposed to: (1) constant HS conditions (32°C) and fed ad libitum (n = 7), or (2) TN conditions and pair-fed (PFTN; n = 10) to minimize the confounding effects of dissimilar feed intake. All pigs received an intravenous glucose tolerance test (GTT) and an epinephrine challenge (EC) in period 1, and during the early and late phases of period 2. After 8 days of environmental exposure, all pigs were killed and tissue samples were collected. Despite a similar reduction in feed intake (39%), HS pigs tended to have decreased circulating nonesterified fatty acids (NEFA; 20%) and a blunted NEFA response (71%) to the EC compared to PFTN pigs. During early exposure, HS increased basal circulating C-peptide (55%) and decreased the insulinogenic index (45%) in response to the GTT. Heat-stressed pigs had a reduced T3 to T4 ratio (56%) and hepatic 5'-deiodinase activity (58%). After 8 days, HS decreased or tended to decrease the expression of genes involved in oxidative phosphorylation in liver and skeletal muscle, and ATGL in adipose tissue. In summary, HS markedly alters both lipid and carbohydrate metabolism independently of nutrient intake.

Label-free and non-invasive monitoring of porcine trophoblast derived cells: differentiation in serum and serum-free media.

Traditional approaches to characterize stem cell differentiation are time-consuming, lengthy and invasive. Here, Raman microspectroscopy (RM) and atomic force microscopy (AFM) - both considered as non-invasive techniques - are applied to detect the biochemical and biophysical properties of trophoblast derived stem-like cells incubated up to 10 days under conditions designed to induce differentiation. Significant biochemical and biophysical differences between control cells and differentiated cells were observed. Quantitative real time PCR was also applied to analyze gene expression. The relationship between cell differentiation and associated cellular biochemical and biomechanical changes were discussed. Monitoring trophoblast cells differentiation.

A shortcut for multiple testing on the directed acyclic graph of gene ontology.

BACKGROUND: Gene set testing has become an important analysis technique in high throughput microarray and next generation sequencing studies for uncovering patterns of differential expression of various biological processes. Often, the large number of gene sets that are tested simultaneously require some sort of multiplicity correction to account for the multiplicity effect. This work provides a substantial computational improvement to an existing familywise error rate controlling multiplicity approach (the Focus Level method) for gene set testing in high throughput microarray and next generation sequencing studies using Gene Ontology graphs, which we call the Short Focus Level. RESULTS: The Short Focus Level procedure, which performs a shortcut of the full Focus Level procedure, is achieved by extending the reach of graphical weighted Bonferroni testing to closed testing situations where restricted hypotheses are present, such as in the Gene Ontology graphs. The Short Focus Level multiplicity adjustment can perform the full top-down approach of the original Focus Level procedure, overcoming a significant disadvantage of the otherwise powerful Focus Level multiplicity adjustment. The computational and power differences of the Short Focus Level procedure as compared to the original Focus Level procedure are demonstrated both through simulation and using real data. CONCLUSIONS: The Short Focus Level procedure shows a significant increase in computation speed over the original Focus Level procedure (as much as ~15,000 times faster). The Short Focus Level should be used in place of the Focus Level procedure whenever the logical assumptions of the Gene Ontology graph structure are appropriate for the study objectives and when either no a priori focus level of interest can be specified or the focus level is selected at a higher level of the graph, where the Focus Level procedure is computationally intractable.

Transcriptional profiling by RNA-Seq of peri-attachment porcine embryos generated by a variety of assisted reproductive technologies.

Substantial mortality of in vitro manipulated porcine embryos is observed during peri-attachment development. Herein we describe our efforts to characterize the transcriptomes of embryonic disc (ED) and trophectoderm (TE) cells from porcine embryos derived from in vivo fertilization, in vitro fertilization (IVF), parthenogenetic oocyte activation (PA), and somatic cell nuclear transfer (SCNT) on days 10, 12, and 14 of gestation. The IVF, PA, and SCNT embryos were generated with in vitro matured oocytes and were cultured overnight in vitro before being transferred to recipient females. Sequencing of cDNA from the resulting embryonic samples was accomplished with the Genome Analyzer IIx platform from Illumina. Reads were aligned to a custom-built swine transcriptome. A generalized linear model was fit for ED and TE samples separately, accounting for embryo type, gestation day, and their interaction. Those genes with significant differences between embryo types were characterized in terms of gene ontologies and KEGG pathways. Transforming growth factor-ß signaling was downregulated in the EDs of IVF embryos. In TE cells from IVF embryos, ubiquitin-mediated proteolysis and ErbB signaling were aberrantly regulated. Expression of genes involved in chromatin modification, gene silencing by RNA, and apoptosis was significantly disrupted in ED cells from SCNT embryos. In summary, we have used high-throughput sequencing technologies to compare gene expression profiles of various embryo types during peri-attachment development. We expect that these data will provide important insight into the root causes of (and possible opportunities for mitigation of) suboptimal development of embryos derived from assisted reproductive technologies.

Targeted DNA methylation analysis by high throughput sequencing in porcine peri-attachment embryos.

The purpose of this experiment was to implement and evaluate the effectiveness of a next-generation sequencing-based method for DNA methylation analysis in porcine embryonic samples. Fourteen discrete genomic regions were amplified by PCR using bisulfite-converted genomic DNA derived from day 14 in vivo-derived (IVV) and parthenogenetic (PA) porcine embryos as template DNA. Resulting PCR products were subjected to high-throughput sequencing using the Illumina Genome Analyzer IIx platform. The average depth of sequencing coverage was 14,611 for IVV and 17,068 for PA. Quantitative analysis of the methylation profiles of both input samples for each genomic locus showed distinct differences in methylation profiles between IVV and PA samples for six of the target loci, and subtle differences in four loci. It was concluded that high throughput sequencing technologies can be effectively applied to provide a powerful, cost-effective approach to targeted DNA methylation analysis of embryonic and other reproductive tissues.

Timing of first embryonic cleavage is a positive indicator of the in vitro developmental potential of porcine embryos derived from in vitro fertilization, somatic cell nuclear transfer and parthenogenesis.

Evidence in many species has suggested that those embryos that cleave earliest after fertilization are more developmentally competent than those that cleave relatively later after fertilization. Herein we document this phenomenon in porcine in vitro-fertilized (IVF), somatic cell nuclear transfer (SCNT), and parthenogenetic (PA) embryos. In vitro-matured pig oocytes were used to generate IVF, SCNT, and PA embryos. At 24 hr post-activation (or insemination; hpa/hpi), embryos were visually assessed, and cleaved embryos were moved into a new culture well. This process was repeated at 30 and 48 hpa/hpi. All embryos were allowed to develop 7 days in culture. For IVF embryos, 39.9%, 24.6%, and 10.5% of fast-, intermediate-, or slow-cleaving embryos, respectively, developed into blastocysts by day 7. For SCNT embryos, 31.8% of fast-, 5.7% of intermediate-, and 2.9% of late-cleaving embryos achieved the blastocyst stage of development. For PA embryos, the percentages of those cleaved embryos that developed to blastocyst were 59.3%, 36.7%, and 7.5% for early-, intermediate-, and late-cleaving embryos, respectively. Using RNA collected from early-, intermediate-, and late-cleaving embryos, real-time PCR was performed to assess the transcript levels of 14 different genes of widely varied function. The qPCR results suggest that maternal mRNA degradation may not proceed in an appropriate pattern in slow-cleaving embryos. These findings (1) confirm that, as observed in other species, earlier-cleaving porcine embryos are more successful at developing in culture than are slower-cleaving embryos, and (2) implicate mechanisms of maternal transcript destruction as potential determinants of oocyte/embryo quality.

Porcine skin-derived progenitor (SKP) spheres and neurospheres: Distinct "stemness" identified by microarray analysis.

Skin-derived progenitors (SKP) are neural crest derived and can generate neural and mesodermal progeny in vitro, corresponding to the multipotency of neural crest stem cells. Likewise, neural stem/progenitor cells (displaying as neurospheres) have the capacity of self-renewing, and can produce most phenotypes in the nervous system. Both form spheres when cultured with epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF). Although the "stemness" of neural stem/progenitor cells has been extensively investigated, the molecular comparison of SKP spheres and neurospheres has not been elucidated. Here, SKP spheres and neurospheres from the same individual porcine fetuses were isolated with the same culture medium, and the multipotency was tested by in vitro differentiation assays. Microarray analysis was used to illustrate the "stemness" of SKP spheres and neurospheres. The upregulated genes that were in common in the SKP spheres and neurospheres are involved in ribosome, tight junction, gap junction, cell communication, calcium signaling, ErbB signaling, JAK-STAT signaling, MAPK signaling, etc. The differentially expressed genes between SKP spheres and neurospheres are mainly involved in ECM-receptor interaction and the transforming growth factor-beta (TGF-b) signaling pathway. Finally, treatment with leukemia inhibitory factor (LIF) or MEK inhibitor results in a distinctive impact on the "stemness" and differentiation genes of SKP spheres and neurospheres. Thus, the cell-intrinsic genetic program may contribute to the innate "stemness" of SKP spheres and neurospheres in a similar local microenvironment.

Transcriptional profiling of day 12 porcine embryonic disc and trophectoderm samples using ultra-deep sequencing technologies.

cDNA derived from trophectoderm (TE) and embryonic disc (ED) of a single day 12 porcine embryo was subjected to next-generation sequencing using the Illumina platform. The short sequencing reads from triplicate sequencing runs were aligned to a custom database designed to represent the known porcine transcriptome. As expected, genes involved in epithelial cell function and steroid biosynthesis were more abundant in cells from the TE; genes involved in maintenance of pluripotency and chromatin remodeling were more highly expressed in cells from the ED. Quantitative real-time PCR was used to confirm the validity of the approach. We conclude that gene expression profiles of even extremely small samples (

Transcriptional profiling by deep sequencing identifies differences in mRNA transcript abundance in in vivo-derived versus in vitro-cultured porcine blastocyst stage embryos.

In vitro embryo culture systems promote development at rates lower than in vivo systems. The goal of this project was to discover transcripts that may be responsible for a decrease of embryo competency in blastocyst-stage embryos cultured in vitro. Gilts were artificially inseminated on the first day of estrus, and on Day 2, one oviduct and the tip of a uterine horn were flushed and the recovered embryos were cultured in porcine zygote medium 3 for 4 days. On Day 6, the gilts were euthanized and the contralateral horn was flushed to obtain in vivo derived embryos. Total RNA was extracted from three pools of 10 blastocysts from each treatment. First and second strand cDNA was synthesized and sequenced using Illumina sequencing. The reads generated were aligned to a custom-built database designed to represent the known porcine transcriptome. A total of 1170 database members were different between the two groups (P < 0.05), and 588 of those had at least a 2-fold difference. Eleven transcripts were subjected to real-time PCR that validated the sequencing. There was an overall decrease in inner cell mass (ICM) and trophectodermal (TE) cell numbers in embryos cultured in vitro; however, no difference in the ICM:TE ratio was found. Interestingly, the transcript SLC7A1 was higher in the in vitro cultured group. This difference disappeared after addition of arginine to the 4-day culture. Illumina sequencing and alignment to a custom transcriptome identified a large number of genes that yield clues on ways to manipulate the culture media to mimic the in vivo environment.