Effects of different extenders on epigenetic patterns and functional parameters of bull sperm during cryopreservation process

The cryopreservation process induces alterations in cellular parameters and epigenetic patterns in bull sperm, which can be prevented by adding cryoprotectants in the freezing extenders. The purpose of this study was to compare the protective effects of two extenders based on soybean lecithin (SLE) and egg yolk (EYE) on epigenetic patterns and quality parameters of sperm such as motility parameters, mitochondrial membrane integrity, DNA fragmentation, viability, and apoptotic-like changes of bull sperm after cryopreservation. Results demonstrated that cryopreservation significantly (p < .05) reduced the level of DNA global methylation, H3K9 histone acetylation, and H3K4 histone methylation in both frozen groups compared to the fresh sperm. Also, the level of H3K9 acetylation was lower in the frozen SLE group (21.2 ± 1.86) compared to EYE group (15.2 ± 1.86). In addition, the SLE frozen group had a higher percentage of viability, progressive motility, and linearity (LIN) in SLE frozen group compared to EYE frozen group. However, no difference was observed in mitochondrial membrane integrity and DNA fragmentation between SLE and EYE frozen groups. While soybean-lecithin-based extender showed some initial positive impacts of epigenetics and semen parameters, further investigations can provide useful information for better freezing.

The effect of peroxisome proliferator-activated receptor gamma (PPARγ) as a mediator of dietary fatty acids and thiazolidinedione in pulmonary arterial hypertension induced by cold stress of broilers

The objective of this experiment was to evaluate the effects of dietary fish oil and pioglitazone as peroxisome proliferators-activated receptor gamma (PPARγ) activating ligands on the reduction of cold-induced ascites in broiler chickens. A total of 480 one-day-old (Ross 308) male chicks were randomly allocated to four treatment groups with eight replicates of 15 birds each. The following treatments were used: 1) ambient temperature (negative control), with basal diet; 2) cold-induced ascites (positive control), with basal diet; 3) cold-induced ascites, with basal diet +10 mg/kg/day pioglitazone and 4) cold-induced ascites, with basal diet +1% of fish oil. When compared with the positive control, body weight gain was higher (P ≤ 0.05) for broilers fed diets containing fish oil and pioglitazone at 28, 42, and 0-42 d. Broilers under cold-induced ascites had the highest blood pressure at 21 and 42 d, while fish oil and pioglitazone treatment reduced the blood pressure (P ≤ 0.05). Red blood cells, white blood cells, hematocrit, erythrocyte osmotic fragility, bursa of Fabricius and spleen weights were improved (P ≤ 0.05) for chickens fed fish oil diets and pioglitazone compared to the cold-induced ascites (positive control). Exposure to cold temperature resulted in an increase in plasma T3 and T3/T4 ratio and decline in plasma T4 (P ≤ 0.05). In conclusion, PPARγ agonist pioglitazone and fish oil as source of omega-3 polyunsaturated fatty acid could be used as a strategy to reduce the negative effects of pulmonary arterial hypertension and ascites in broiler chickens.

Investigating the expression of fertility-regulating LncRNAs in multiparous and uniparous Shal ewe's ovaries

Sheep is the primary source of animal protein in Iran. Birth type is one of the significant features that determine total meat output. Little is known about how long non-coding RNAs (LncRNAs) affect litter size. The purpose of this research is to investigate the DE-LncRNAs in ovarian tissue between multiparous and uniparous Shal ewes. Through bioinformatics analyses, LncRNAs with variable expression levels between ewes were discovered. Target genes were annotated using the DAVID database, and STRING and Cytoscape software were used to evaluate their interactions. The expression levels of 148 LncRNAs were different in the multiparous and uniparous ewe groups (false discovery rate (FDR) < 0.05). Eight biological process terms, nine cellular component terms, 10 molecular function terms, and 38 KEGG pathways were significant (FDR < 0.05) in the GO analysis. One of the most significant processes impacting fertility is mitogen-activated protein kinase (MAPK) signaling pathway, followed by oocyte meiosis, gonadotropin-releasing hormone signaling pathway, progesterone-mediated oocyte maturation, oxytocin signaling pathway, and cAMP signaling pathway. ENSOARG00000025710, ENSOARG00000025667, ENSOARG00000026034, and ENSOARG00000026632 are LncRNAs that may affect litter size and fertility. The most crucial hub genes include MAPK1, BRD2, GAK, RAP1B, FGF2, RAP1B, and RAP1B. We hope that this study will encourage researchers to further investigate the effect of LncRNAs on fertility.

Genetic variants in the TAC1 transcriptional regulatory region affect on trainability and excitability levels in Belgian Malinois dogs

BACKGROUND

Trainability in dogs is affected by learning aptitude and memory capacity. While this trait has a heritable basis in canines, the specific genetic loci responsible for it remain unknown. Our previous results suggested that the BDNF, CCK and TAC1 genes are associated with learning and memory in canines. Experimental validation is crucial to confirm the effects of these candidate genes on trainability. Understanding the genetic foundation of this trait would offer insight into the inheritance pattern of complex behavioural characteristics.

OBJECTIVE

This study aimed to assess the genetic variations within candidate genes and explore their potential associations with behavioural phenotypes in dogs.

METHODS

The behavioural characteristics of 123 male Belgian Malinois dogs were assessed using a customised questionnaire. Target regions of candidate genes were screened for genetic variation by single-strand conformational polymorphism (SSCP). Following that, SSCP banding patterns were sequenced, and putative transcription factor binding sites were predicted using bioinformatics tools. Quantitative association analysis between identified genetic variants and behavioural trait scores was performed using the general linear model (GLM).

RESULTS

Sequencing the coding and flanking regions revealed three mutations (c.-89C>T, c.-162G>C and c.*33T>A) in the dog TAC1 gene. Bioinformatics analysis predicted two single nucleotide polymorphisms (SNPs) were located within the putative TAC1 promoter and could disrupt transcription factor binding sites. Statistical tests revealed that the c.-89C>T was significantly associated with excitability (p < 0.01), while the c.-162G>C was significantly associated with trainability level (p < 0.05).

CONCLUSION

In summary, we identified two regulatory SNPs in the 5'-UTR promoter region of the TAC1 gene that are associated with excitability and trainability in Belgian Malinois dogs. These genetic variations have the potential to alter the binding sites of transcription factors NRF1 and OTX1, consequently influencing TAC1 expression and related behavioural characteristics. Our findings implicate TAC1 polymorphisms as candidates influencing breed-specific behavioural characteristics in canines. Further studies on diverse breeds of dogs are necessary to validate these SNPs' effects.

Influence of optical property contrast on the critical distribution of electrostatic torques in double-beam torsional Casimir actuators: Non-linear actuation toward chaotic motion

Here, we discuss how to achieve the stable actuation of a double beam torsional micro-actuator over the largest possible displacement of the moving component under the influence of Casimir and electrostatic torques, when the rotating component is constructed from different materials. The main part of this study is devoted to finding the optimal distribution of the electrostatic torque between the left and right sides of the micro-actuator to reach the maximum stable operation of the device. The latter is manifested by switching from homoclinic to heteroclinic orbits in the phase portraits. Indeed, the bifurcation curves and the phase portraits have been employed to show the sensitivity of the critical distribution of the electrostatic torque, beyond which the device does show stable performance, on the contrast of the optical properties of the moving component and the applied voltage in a conservative autonomous system. Moreover, for driven systems, the Melnikov function approach and the Poincaré portraits are used to study the presence of chaotic motion, which eventually leads to stiction. It is shown that the application of the optimal distribution of the electrostatic torque can significantly decrease the possibility of chaotic motion, and at this optimal level, the threshold curves reveal less difference between systems with different optical contrast.

Peroxisome proliferator-activated receptor gamma (PPARγ) activation: a potential treatment for ascites syndrome in broiler chickens

Ascites (serous fluid accumulation in the abdominal cavity) has been observed worldwide in fast growing broilers. Pulmonary vascular remodeling is an important pathological feature of broiler ascites syndrome. Peroxisome proliferators-activated receptor gamma (PPARγ) and peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) are expressed in pulmonary vascular endothelial cells and vascular smooth muscle cells (VSMC) where they participate in the regulation of normal pulmonary vascular function. The objective of the present study was to investigate the effects of omega-3 fatty acids (found in fish oil) and pioglitazone (PIO) as natural and synthetic PPARγ ligands supplementation on PPARγ and PGC-1α expression in the prevention of pulmonary arterial hypertension (PAH) syndrome in broiler chickens. The experiment was conducted with 4 treatment groups: 1) negative control, normal temperature conditions with basal diet; 2) positive control, low-temperature conditions with basal diet; 3) positive control + 10 mg PIO/kg of weight/d and 4) positive control + 1% FO. Each treatment had 5 replicates. Ascites heart index (RV/TV) was significantly (P < 0.05) reduced in chickens receiving FO (0.20) and PIO (0.21) compared to the positive control group (0.26). The addition of PIO in broilers under cold-induced ascites significantly increased the expression of PPARγ (9.44) and PGC-1α (5.81) genes in lung tissue compared to the negative control group (1.03, P < 0.05). Proliferative indexes of VSMC in pulmonary arteries such as PMT, PIT, and percentage wall thickness were significantly elevated in positive control group, indicating that pulmonary vascular remodeling occurred following VSMC proliferation in ascites. The vessel internal diameter was increased in FO and PIO groups. Based on these results, activation and expression of PPARγ and PGC-1α genes as a critical regulator of pulmonary artery smooth muscle cell using ligands, especially PIO, can be effective in reducing the incidence of PAH in broiler chickens.

Trade-off between feed efficiency and immunity in specialized high-performing chickens

Based on resource allocation theory, ignoring importance of immunity, and focus on growth and feed efficiency (FE) traits in breeding plans may lead to serious weakness in immune system performance. However, in poultry the adverse effects of selection for FE on the immune system are unclear. Therefore, an experiment was conducted to study the trade-off between FE and immunity using a total of 180 high-performing specialized male chickens from a commercial broiler line which were selected over 30 generations for growth (body weight gain, BWG) and FE (residual feed intake, RFI). Birds were reared for 42 d and 5 FE-related traits of the birds in the last week were considered including daily feed intake (DFI), feed conversion ratio (FCR), residual feed intake (RFI), residual BW gain (RG), and residual intake and gain (RIG). For all 180 chickens, immune system performance including humoral immune response, cell-mediated immunity (CMI), and the activity of lysozyme enzyme (L. activity) as innate immunity was measured. After ascending sort of each FE records, 10% of higher records (H-FE: N = 18) and 10% of lower records (L-FE: N = 18) were determined, and immunity between L-FE and H-FE groups were compared. Moreover, L-BWG and H-BWG were analyzed because BWG is one of components in the FE formula. Performance of the immune system was not statistically different for CMI in none of the studied FE groups. Moreover, high and low groups for DFI and BWG were not different regarding the immunity of the birds. Antibody titers against Newcastle disease virus (NDV) were different between low and high groups of FCR, RG, and RIG. Likewise, SRBC-derived antibodies were significantly different between RFI groups. Rather than humoral immunity, RIG had adversely effect on the innate immunity. Results of the present study showed that although RIG is a more appropriate indicator for FE, choosing for high RIG can weaken the performance of the both humoral and innate immune systems, while RFI had fewer adverse effects.

Gene expression pattern and molecular mechanisms involved in Shal and Sangsari sheep fertility using RNA-Seq

Ovulation rate and litter size are the main reproductive traits with high economic value in the sheep breeding industry. In this study, three Shal ewes (multiparous) and three Sangsari ewes (uniparous) at the age of 5 were used. The live weight was between 45 and 50 kg at an extremely body condition score of 3. These breeds are marked seasonal reproduction activity and are often bred in semi-closed breeding systems. Total RNAs were extracted from the ovarian tissues, and RNA sequencing was carried out. The DAVID (Database for Annotation, Visualization and Integrated Discovery) database was then used to annotate genes, and the string database and the Cytoscape software were used to investigate their interactions. Then path-act network analysis and gene-act network analysis were investigated. The results indicated that 19,932 genes were differentially expressed. The 5968 differentially expressed genes were identified in Shal ewe's ovarian tissue compared to Sangsari ewes (FDR < 0.05), of which 2921 genes were up-regulated and 3047 genes were down-regulated. Bioinformatics analysis exhibited that most of the biological processes and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways associated with significant DEGs (Differentially Expressed Genes) in the two studied breeds are associated with oocyte maturation and metabolism. MAPK signalling pathways and Ubiquitin-mediated proteolysis are the most important biological pathways associated with reproductive and fertility traits in the Shal breed. AKT3, MAPK8, MAPK9 and RELA genes are also important genes related to the fertility of multiparous sheep. Analysis of ovarian RNA-seq data identified that most of the differentially expressed genes were involved in various reproductive processes including folliculogenesis, ovulation, ovarian and embryonic development. The MAPK signalling pathway had the most interaction with other pathways, and the AKT3 gene could be a powerful candidate gene in the reproduction and fertility of Shal sheep. These results could pave the way for future efforts to address sheep prolificacy barriers.

Nonlinear actuation of micromechanical Casimir oscillators with topological insulator materials toward chaotic motion: Sensitivity on magnetization and dielectric properties

We have investigated the dynamical actuation of micro-electromechanical systems under the influence of attractive and repulsive Casimir forces between topological insulator plates as a function of their dielectric function and coating magnetization. The analysis of the Casimir force in the limit of strong and weak magnetization shows that the attractive force, which is produced for plate magnetizations in the same direction, is greater than the repulsive force that is produced for opposite magnetizations. However, both forces remain comparable for intermediate magnetizations. Moreover, for weak magnetization, the attractive force becomes stronger for an increasing dielectric function, while the opposite occurs for the repulsive force. On the other hand, increasing magnetization decreases the influence of the dielectric function on both the repulsive and attractive forces. Furthermore, for conservative systems, bifurcation and phase portrait analysis revealed that increasing magnetization decreases the regime of stable operation for devices with attractive forces, while their operation remains always stable under the presence of repulsive forces. Finally, for non-conservative periodically driven systems, the Melnikov function and Poincaré portrait analysis show that for magnetizations in the same direction leading to strong attractive Casimir forces, chaotic motion toward stiction is highly likely to occur preventing the long-term prediction of actuating dynamics. A remedy for this situation is obtained by the application of any magnetization in opposite directions between the interacting surfaces since the repulsive force makes it possible to prevent stiction.

Identification of differentially expressed long noncoding RNAs in the ovarian tissue of ewes Shal and Sangsari using RNA-seq

Background

The ovary has an important role in reproductive function. Animal reproduction is dominated by numerous coding genes and noncoding elements. Although long noncoding RNAs (LncRNAs) are important in biological activity, little is known about their role in the ovary and fertility.

Methods

Three adult Shal ewes and three adult Sangsari ewes were used in this investigation. LncRNAs in ovarian tissue from two breeds were identified using bioinformatics analyses, and then target genes of LncRNAs were discovered. Target genes were annotated using the DAVID database, and their interactions were examined using the STRING database and Cytoscape software. The expression levels of seven LncRNAs with their target genes were assessed by real‐time PCR to confirm the RNA‐seq.

Results

Among all the identified LncRNAs, 124 LncRNAs were detected with different expression levels between the two breeds (FDR < 0.05). According to the DAVID database, target genes were discovered to be engaged in one biological process, one cellular component, and 21 KEGG pathways (FDR < 0.05). The PES1, RPS9, EF‐1, Plectin, SURF6, CYC1, PRKACA MAPK1, ITGB2 and BRD2 genes were some of the most crucial target genes (hub genes) in the ovary.

Conclusion

These results could pave the way for future efforts to address sheep prolificacy barriers.

An association of CEP78, MEF2C, VPS13A and ARRDC3 genes with survivability to heat stress in an F2 chicken population

Heat stress is a serious problem in the poultry industry. An effective tool for improving heat tolerance can be genomic selection based on single nucleotide polymorphisms. This study was performed to identify genomic regions controlling survivability to heat stress in a population of F₂ chickens that accidentally experienced acute heat stress, using Illumina 60K Chicken SNP Bead Chip. After quality control in markers, 47,730 SNPs remained for genome-wide association study (GWAS). The GWAS results indicated that markers Gga_rs16111480 (p = 8.503e-08), GGaluGA354375 (p = 5.99e-07) and Gga_rs14748694 (p = 7.085e-07) located on Z chromosome showed significant association with heat stress tolerance trait. The Gga_rs16111480 marker was located inside the CEP78 gene. The marker GGaluGA354375 was located inside the LOC101752071 gene and next to the MEF2C gene. The Gga_rs14748694 marker was adjacent to LOC101752071 and MEF2C genes. Moreover, the SNP maker of Gga_rs16111480 was located on 243 kb downstream of the VPS13A gene, and the GGaluGA354375 and Gga_rs14748694 SNPs were located on 947 kb and 888 kb downstream of the ARRDC3 gene, respectively. The results of this study suggest that apart from the gene LOC101752071, which its function was unknown, each of the two MEF2C and CEP78 genes were found to be closely related to heat stress resistance in bird.

One-pot synthesis of 1,8-dioxodecahydroacridines by using Ag-TiO2 nanocomposite as a mild and heterogeneous catalytic system

Abstract:

Ag-TiO2 nanocomposite was displayed to be an efficient, active, and benign recyclable catalyst for the highly efficient synthesis of 1,8-dioxodecahydroacridine derivatives from dimedone, aromatic aldehydes, and several anilines or ammonium acetate in ethanol as a solvent at room temperature in short reaction time and suitable yield. This catalyst was effortlessly recycled by simple filtration and was reused up to five times with only a negligible loss in its catalytic effectiveness. This process showed substantial advantages containing low loading of the catalyst, cost-effectively mild conditions, purification of target molecules by non-chromatographic technique, worthy atom economy, informal process, application of cheaply available nanocomposite catalyst, use of economical and recyclability of the catalyst. AFM analysis was also attained to confirm the structure topography and morphology of Ag-TiO2 nanocomposite. Natural significance 1,8dioxodecahydroacridine derivatives have a wide range of pharmacological activities for instance antibacterial, antimalarial, anticancer, and mutagenic properties. This method achieves has a varied scope regarding the difference in the aldehydes and anilines.

New insights into genetics underlying of plumage color

Plumage color can be considered as a social signal in chickens and a breeding identification tool among breeders. The relationship between plumage color and trait groups of immunity, growth and fertility is still a controversial issue. This research aimed to determine the genome-wide additive and epistatic variants affecting plumage color variation in chickens using the chicken Illumina 60k high-density SNP array. Two scenarios of genome-wide additive association studies using all SNPs and independent SNPs were carried out. To perform epistatic association analysis, the LD pruning approach was used to reduce the complexity of the analysis. We detected seven novel significant loci using all of the SNPs in the model and 14 SNPs using the LD pruning approach associated with plumage color. Moreover, 89 significantly associated SNP-SNP interactions (P-value <10^-6 ) distributed in 25 chromosomes were identified, indicating that all of the signals together putatively influence the quantitative variation of plumage color. By annotating genes relevant to top SNPs, we have distinguished 18 potential candidate genes comprising HNF4beta, CKMT1B, TBC1D22A, RPL8, CACNA2D1, FZD4, SGMS1, IRF8, OPTN, LOC420362, TRABD, OvoDA1, DAD1, USP6, RBM12B, MIR1772, MIR1709 and MIR6696 and also 89 putative gene-gene combinations responsible for plumage color variation in chickens. Furthermore, several KEGG pathways including metabolic pathway, cytokine-cytokine receptor interaction, focal adhesion, melanogenesis, glycosaminoglycan biosynthesis-keratan sulfate and sphingolipid metabolism were enriched in the gene-set analysis. The results indicated that plumage color is a highly polygenic trait which, in turn, can be affected by multiple coding genes, regulatory genes and gene-gene epistasis interactions. In addition to genes with additive effects, epistatic genes with tiny individual effect sizes but significant effects in a pair have the potential to control plumage coloration in chickens.

Application of Metabolomics to Identify Hepatic Biomarkers of Foie Gras Qualities in Duck

Foie gras is a traditional dish in France that contains 50 to 60% of lipids. The high-fat content of the liver improves the organoleptic qualities of foie gras and reduces its technological yield at cooking (TY). As the valorization of the liver as foie gras products is strongly influenced by the TY, classifying the foie gras in their potential technological quality before cooking them is the main challenge for producers. Therefore, the current study aimed to identify hepatic biomarkers of foie gras qualities like liver weight (LW) and TY. A group of 120 male mule ducks was reared and overfed for 6–12 days, and their livers were sampled and analyzed by proton nuclear magnetic resonance (¹H-NMR). Eighteen biomarkers of foie gras qualities were identified, nine for LW and TY, five specific to LW, and four specific to TY. All biomarkers were strongly negatively correlated to the liver weights and positively correlated to the technological yield, except for the lactate and the threonine, and also for the creatine that was negatively correlated to foie gras technological quality. As a result, in heavy livers, the liver metabolism was oriented through a reduction of carbohydrate and amino acid metabolisms, and the plasma membrane could be damaged, which may explain the low technological yield of these livers. The detected biomarkers have been strongly discussed with the metabolism of the liver in nonalcoholic steatohepatitis.

Identification of Plasmatic Biomarkers of Foie Gras Qualities in Duck by Metabolomics

The foie gras is an emblematic product of French gastronomy composed of waterfowl fatty liver. The organoleptic qualities of this product depend on the liver characteristics such as liver weight (LW) and technological yield (TY) at cooking. One of the main issues for producers is to classify the foie gras with high or low technological quality before cooking them. Thus the study aims at identifying biomarkers of these characteristics with non-invasive biomarkers in duck. ¹H-NMR (nuclear magnetic resonance of the proton) analyses were performed on plasma of male mule ducks at different time points during the overfeeding period to obtain a large range of liver characteristics so as to identify plasmatic biomarkers of foie gras. We used two methods, one based on bucket data from the ¹H-NMR spectra and another one based on the fingerprints of several metabolites. PLS analyses and Linear models were performed to identify biomarkers. We identified 18 biomarkers of liver weight and 15 biomarkers of technological yield. As these two quality parameters were strongly correlated (−0.82), 13 biomarkers were common. The lactate was the most important biomarker, the other were mainly amino acids. Contrary to the amino acids, the lactate increased with the liver weight and decreased with the technological yield. We also identified 5 biomarkers specific to LW (3 carbohydrates: glucuronic acid, mannose, sorbitol and 2 amino acids: glutamic acid and methionine) that were negatively correlated to liver weight. It was of main interest to identify 2 biomarkers specific to the technological yield. Contrary to the isovaleric acid, the valine was negatively correlated to the technological yield.

Genome-wide association study of shank length and diameter at different developmental stages in chicken F2 resource population

In order to find SNPs and genes affecting shank traits, we performed a GWAS in a chicken F2 population of eight half-sib families from five hatches derived from reciprocal crosses between an Arian fast-growing line and an Urmia indigenous slow-growing chicken. A total of 308 birds were genotyped using a 60K chicken SNP chip. Shank traits including shank length and diameter were measured weekly from birth to 12 weeks of age. A generalized linear model and a compressed mixed linear model (CMLM) were applied to achieve the significant regions. The value of the average genomic inflation factor (λ statistic) of the CMLM model (0.99) indicated that the CMLM was more effective than the generalized linear model in controlling the population structure. The genes surrounding significant SNPs and their biological functions were identified from NCBI, Ensembl and UniProt databases. The results indicated that 12 SNPs at 12 different ages passed the LD-adjusted 5% Bonferroni significant threshold. Two SNPs were significant for shank length and nine SNPs were significant for shank diameter. The significant SNPs were located near to or inside 11 candidate genes. The results showed that a number of significant SNPs in the middle ages were higher than the rest. The MXRA8 gene was related to the significant SNP at week 1 that promotes proliferation of growth plate chondrocytes. A unique SNP of Gga_rs16689511 located on chicken Z chromosome within the LOC101747628 gene was related to shank length at three different ages of birds (weeks 8, 9 and 11). The significant SNPs for shank diameter were found at weeks 4 and 7 (four and five SNPs respectively). The identifications of SNPs and genes here could contribute to a better understanding of the genetic control of shank traits in chicken.

Chaotic motion due to lateral Casimir forces during nonlinear actuation dynamics

We investigated here the influence of the lateral Casimir force on the dynamical actuation of devices with interacting materials covering a broad range of optical properties ranging from poor to good conductors, such as, for example, nitrogen doped SiC and Au, respectively. The conservative actuating system shows a central heteroclinic orbit surrounded by a finite number of homoclinic orbits, because at higher periods, an increased lateral Casimir force will be necessary to counterbalance the restoring force. As a result, the conservative system reaches stable operation sooner for the higher conductivity materials (Au-Au), indicating the significant impact of the material optical properties on the lateral Casimir force. Furthermore, for the non-conservative driven systems, the decrement of the Melnikov parameter α leads to a faster disappearance of the satellite homoclinic orbits in the Poincaré portraits, followed by a strong shrinkage of the central heteroclinic orbit toward unstable chaotic motion. The latter is more pronounced for the lower conductivity materials since comparison shows the Au-Au system to be significantly more stable than the SiC-SiC system. Therefore, in actuating systems where the lateral Casimir force could play a significant role, the higher conductivity materials appear to be a better choice to ensure stable operation against a chaotic motion.

Electron scattering in a superlattice of line defects on the surface of topological insulators

The electron scattering from periodic line defects on the surface of topological insulators with hexagonal warping effect is investigated theoretically by means of a transfer matrix method. The influence of surface line defects, acting as structural ripples on propagation of electrons are studied in two perpendicular directions due to the asymmetry of warped energy contour under momentum exchange. The transmission profiles and the details of resonant peaks which vary with the number of defects and the strength of their potentials are strongly dependent on the direction in which the line defects extend. At low energies, the quantum interference between the incident and reflected propagating electrons has the dominant contribution in transmission resonances, while at high energies the multiple scattering processes on the constant-energy contour also appear because of the strong warping effect. By increasing the spatial separation between the line defects, the minimum value of electrical conductance remains significantly high at low incident energies, while the minimum value may approach zero at high energies as the number of defects is increased. Our findings suggest that the potential ripples on the surface of topological insulators can be utilized to control the local electronic properties of these materials.

Sensitivity of nonequilibrium Casimir forces on low frequency optical properties toward chaotic motion of microsystems: Drude vs plasma model

Here, we investigate the sensitivity of nonequilibrium Casimir forces to optical properties at low frequencies via the Drude and plasma models and the associated effects on the actuation of microelectromechanical systems. The stability and chaotic motion for both autonomous conservative and nonconservative driven systems were explored assuming good, e.g., Au, and poor, e.g., doped SiC, interacting conductors having large static conductivity differences. For both material systems, we used the Drude and plasma methods to model the optical properties at low frequencies, where measurements are not feasible. In fact, for the conservative actuating system, bifurcation and phase space analysis show that the system motion is strongly influenced by the thermal nonequilibrium effects depending on the modeling of the optical properties at low frequencies, where also the presence of residual electrostatic forces can also drastically alter the actuating state of the system, depending strongly on the material conductivity. For nonconservative systems, the Melnikov function approach is used to explore the presence of chaotic motion rendering predictions of stable actuation or malfunction due to stiction on a long-term time scale rather impossible. In fact, the thermal effects produce the opposite effect for the emerging chaotic behavior for the Au-Au and SiC-SiC systems if the Drude model is used to model the low optical frequencies. However, using the plasma model, only for the poor conducting SiC-SiC system, the chance of chaotic motion is enhanced, while for the good conducting Au-Au system, the chaotic behavior will remain unaffected at relatively short separations (<2 μm).

Plant extract supplementation as a strategy for substituting dietary antibiotics in broiler chickens exposed to low ambient temperature

The present study was conducted to investigate the effects of two plant extracts as alternatives to dietary antibiotics in broiler chickens exposed to low ambient temperature. A total of 300 one-day-old male broiler chickens were randomly assigned to four dietary treatments (5 replicate pens; 15 broiler chickens each) which consisted of starter (d 0 to 10), and grower (d 10 to 28) diets. Dietary treatments included a basal diet (negative control, NC) and three similar diets that were either supplemented with 200 mg/kg of Prosopis farcta extract (PFE), Rhus coriaria L. extract (RCE) or an antibiotic premix containing oxytetracycline (positive control, PC). In order to simulate low ambient temperature, room temperature was maintained at 32°C during the first 3 d of the trial and afterwards, the temperature was gradually reduced by approximately 1.5°C each day to 14°C on d 21. PFE and PC treatments exerted a significant effect on body weight gain at d 28. Diet PFE was effective in reducing mortality when compared with diet NC (p < 0.05). Furthermore, diet PFE caused increases in ileal  digestibility of gross energy, dry matter and organic matter when compared with diet NC (p < 0.05). Diets PFE and PC decreased coliforms, total aerobic bacteria and total anaerobic bacteria loads in the caeca when compared with diet NC (p < 0.05). Moreover, the addition of PFE to the diet improved villous height in all small intestinal segments as well as villous height:crypt depth ratio in the duodenum when compared with diet NC (p < 0.05). The results indicated that PFE is not only a valid alternative to oxytetracycline under cold stress conditions, with no antibiotic resistance, but also has the potential to increase the resistance of broiler chickens against ascites syndrome. Moreover, the addition of RCE at the concentration of 200 mg/kg to the diet was not sufficient to improve the performance of broiler chickens (similar to diet PC) but maybe more effective at higher concentrations.

WITHDRAWN:Investigating population structure and genetic diversity of some Iranian native cattle breeds using SNP markers

Ahead of Print article withdrawn by publisher.

Sensitivity of chaotic behavior to low optical frequencies of a double-beam torsional actuator

We investigate here how the optical properties at low frequencies affect the actuation dynamics and emerging chaotic behavior in a double-beam torsion actuator at nanoscale separations (<200nm), where the Casimir forces and torques play a major role. In fact, we take into account differences of the Casimir force due to alternative modeling of optical properties at low frequencies, where measurements are not feasible, via the Drude and plasma models, and repercussions by different material preparation conditions. For conservative autonomous actuation, bifurcation and phase portrait analysis indicate that both factors affect the stability of an actuating device in such a way that stronger Casimir forces and torques will favor increased unstable behavior. The latter will be enhanced by unbalanced application of electrostatic voltages in double-beam actuating systems. For the case of a time-periodic driving force, we use a Melnikov function and a phase plane analysis to study the emerging chaotic behavior with respect to the Drude and plasma modeling and material preparation conditions. We find indications that any factor that leads to stronger Casimir interactions will aid chaotic behavior and prevent long term prediction of the actuating dynamics. Moreover, in a double-beam actuator chaoticity will be amplified by the application of unbalanced electrostatic voltages. Therefore, the details of modeling of optical properties and the material preparations conditions must be carefully considered in the design of actuating devices at nanoscale because here Casimir forces are omnipresent and broadband type interactions.

Dependence of non-equilibrium Casimir forces on material optical properties toward chaotic motion during device actuation

The sensitivity of nonequilibrium Casimir forces on material optical properties can have strong impact on the actuation of devices. For this purpose, we considered nonequilibrium Casimir interactions between good and poor conductors, for example, gold (Au) and highly doped silicon carbide (SiC), respectively. Indeed, for autonomous conservative systems, the bifurcation and phase portrait analysis have shown that the nonequilibrium Casimir forces can have significant impact on the stable and unstable operating regimes depending on the material optical properties. At a few micrometer separations, for systems with high conductivity materials, an increasing temperature difference between the actuating components can enhance the stable operation range due to the reduction of the Casimir force, while for the poor conductive materials, the opposite takes place. For periodically driven dissipative systems, the Melnikov function and Poincare portrait analysis have shown that for poor conductive systems, the nonequilibrium Casimir forces lead to an increased possibility for chaotic behavior and stiction with an increasing temperature difference between the actuating components. However, for good conducting systems, the thermal contribution to Casimir forces reduces the possibility for chaotic behavior with increasing temperature, as comparison with systems without thermal fluctuations shows. Nevertheless, the positive benefit of good conductors toward increased actuation stability and reduced the chaotic behavior under nonequilibrium conditions can be easily compromised by any voltage application. Therefore, thermal, nonequilibrium Casimir forces can influence the actuation of devices toward unstable and chaotic behavior in strong correlation with their optical properties, and associated conduction state, as well as applied electrostatic potentials.

Random deposition with a power-law noise model: Multiaffine analysis

We study the random deposition model with power-law distributed noise and rare-event dominated fluctuation. In this model instead of particles with unit sizes, rods with variable lengths are deposited onto the substrate. The length of each rod is chosen from a power-law distribution P(l)∼l^{-(μ+1)}, and the site at which each rod is deposited is chosen randomly. The results show that for μ<μ_{c}=3 the log-log diagram of roughness, W(t), versus deposition time, t, increases as a step function, where the roughness in each interval acts as W_{loc}(t)≈t^{β_{loc}}. The local growth exponent, β_{loc}, is zero for μ=1. By increasing the μ exponent, the value of β_{loc} is increased. It tends to the growth exponent of the random distribution model with Gaussian noise, β=1/2, at μ_{c}=3. The fractal analysis of the height fluctuations for this model was performed by multifractal detrended fluctuation analysis algorithm. The results show multiaffinity behavior for the height fluctuations at μ<μ_{c} and the multiaffinity strength is greater for smaller values of the μ exponent.

Dependence of chaotic behavior on optical properties and electrostatic effects in double-beam torsional Casimir actuation

We investigate the influence of Casimir and electrostatic torques on double-beam torsional microelectromechanical systems with materials covering a broad range of conductivities of more than three orders of magnitude. For the frictionless autonomous systems, bifurcation and phase space analysis shows a significant difference between stable and unstable operating regimes for equal and unequal applied voltages on both sides of the double torsional system giving rise to heteroclinic and homoclinic orbits, respectively. For equal applied voltages, only the position of a symmetric unstable saddle equilibrium point is dependent on the material optical properties and electrostatic effects, while in any other case stable and unstable equilibrium points are dependent on both factors. For the periodically driven system, a Melnikov function approach is used to show the presence of chaotic motion rendering predictions of whether stiction or stable actuation will take place over long times impossible. Chaotic behavior introduces significant risk for stiction, and it is more likely to occur for the more conductive systems that experience stronger Casimir forces and torques. Indeed, when unequal voltages are applied, the sensitive dependence of chaotic motion on electrostatics is more pronounced for the highest conductivity systems.

Genome-wide association study of cell-mediated immune response in chicken

Cell-mediated immunity (CMI) causes the intracellular destruction of the antigen or elimination of the host cell to make animals resistant against exogenous antigens and cancers. In this study, a genome-wide association study (GWAS) was carried out to identify genomic regions associated with CMI in chicken using chicken 60k high-density single nucleotide polymorphism (SNP) array. Genomic relationships were taken into account to adjust for population structure. In order to account for multiple testing, chromosome-wise false discovery rate was controlled at 5% and 10% levels. Moreover, a comparison of the power of fixed and mixed linear models based on genomic inflation factor was carried out. Mixed linear model (MLM) had better inflation rate, and therefore the results from MLM were used for subsequent analysis. Three significantly associated SNPs (FDR < 0.05) on chromosome 24 and linkage group E22C19W28_E50C23, and three suggestively associated SNPs (FDR < 0.1) on chromosome 1, 5 and 16 were identified. Pathway analysis showed that two biological pathways, which are related to immune response, were strongly associated with the candidate genes surrounding identified SNPs, and their influences were mostly on antigen processing and presentation, and cellular structure.

Differential Expression of the Alpha S1 Casein and Beta-Lactoglobulin Genes in Different Physiological Stages of the Adani Goats Mammary Glands

Background

Milk proteins genes have been the focus of the researches as the candidate target genes that play a decisive role when animal breeding is desired.

Objectives

In the present study, the transcriptional levels of Beta-lactoglobulin (BLG) and Alpha S1 casein (CSN1S1) genes were investigated during prenatal, milking and drying times in mammary glands of the Adani goats which showed high and low breeding values.

Materials and Methods

The breeding values of the animals were estimated first by applying multi-trait random regression model. Using the biopsy gun, the mammary gland samples were taken and real-time PCR was applied to search the expression of the genes. Fixed factors of the model were the breeding value groups, sampling times and their interactions.

Results

The interactions were significant for both genes. At milking time, the high breeding value group exhibited more transcriptional levels for BLG and less transcriptional levels for CSN1S1 gene compared with the low breeding value group. The expression patterns of these genes were also different between the two breeding value groups. The maximum level of BLG and CSN1S1 transcriptions were found to occur at drying time.

Conclusions

A difference in the gene expression was observed between the two groups which indicate the change in the nucleotide sequence for transcription factor binding sites, or miRNA binding sites, otherwise in the coding regions. Therefore, the variations in the coding and promoter regions of this gene should be investigated in the further studies.

Association of mitochondrial function and sperm progressivity in slow- and fast-growing roosters

The objectives of the current study were to investigate the activity of the electron transport chain (ETC) complexes, adenosine triphosphate (ATP), and reactive oxygen species (ROS) in the sperm mitochondria of 2 Iranian slow- and fast-growing chickens, namely native and Aryan strains. In this study, semen of 133 roosters was analyzed by computer-assisted sperm analysis (CASA). The roosters were categorized by sperm progressivity, as a low or high sperm motility phenotype. Mitochondrial complex I (NADH ubiquinone oxidoreductase), II (succinate dehydrogenase), III (ubiquinol cytochrome C reductase), IV (cytochrome C oxidase) activity, ATP, and ROS production in sperm were assayed. As a result, Aryan roosters with high progressive motility levels (HPL) had the greatest progressivity. Progressive motility was significant in in both strains (Aryan and native; P = 0.020) and motility levels (high and low; P = 0.007). The highest activity of complexes I was observed in Aryan with HPL roosters (P = 0.004). Native roosters with HPLs demonstrated higher complex activities I compared with Aryan and native roosters with low progressive motility levels (LPL) (P = 0.004). Significant differences were observed not only in the mitochondrial amounts of ATP of the strains (P = 0.000) but also between HPL and LPL (P = 0.003). The highest mitochondrial amounts of ATP was found in Aryan roosters with HPL (P = 0.021). Native roosters with LPL had the highest concentration of mitochondrial ROS (P = 0.033). The Aryan roosters with HPL, on the other hand, indicated less concentration of the mitochondrial ROS compared with Aryan having LPL and native roosters with HPL and LPL (P = 0.033). A significant difference was observed in the mitochondrial ROS between the strains (P = 0.004) and between HPL and LPL (P = 0.000). There was positive relationship between progressivity and each of mitochondrial complexes and ATP (r = 0.71, 0.62, 0.90 and 0.65 respectively). Based on our results, the sperm progressivity largely depends on the whole energy production originating in the mitochondrial compartment. Therefore, the deficiency in the function of mitochondria in the sperm and energy production could be responsible for low progressive motility.

Changes in the Expression of the Prolactin Receptor (PRLR) Gene in Different Physiological Stages in the Mammary Gland of the Iranian Adani Goat

The actions of prolactin hormone are mediated by prolactin receptor (PRLR), and proliferation and differentiation of secretory mammary epithelium are dependent on the presence of its receptors. To understand the PRLR expression pattern in mammary gland of dairy goat during different lactation stages, in this study, we first estimated the milk yield breeding value by multitrait random regression model and then compared the expression of the gene in different physiological stage of mammary gland between high- and low-breeding value groups. We assayed the transcription level of the gene by quantitative real-time PCR method, and its outcomes were analysed by a statistical model containing breeding value groups, sampling times and their interactions as fixed effects. The results indicated that the expression levels of PRLR gene were significantly upregulated in the drying stage (p < 0.01). The transcription pattern of the gene was significantly different between the two breeding value groups (p < 0.01), so that the amount of PRLR mRNA was significantly higher in the low-breeding value groups of animals in the lactation stage (p < 0.01). Based on the results of this study, it could be suggested that the abundance of PRLR transcripts in mammary gland of goat might be changed by some physiological, environmental and genetic factors. Nucleotide variations in the promoter region might be resulted in various transcription activities of the gene which should be studied in a complementary research.

Identification of learning and memory genes in canine; promoter investigation and determining the selective pressure

One of the important behaviors of dogs is trainability which is affected by learning and memory genes. These kinds of the genes have not yet been identified in dogs. In the current research, these genes were found in animal models by mining the biological data and scientific literatures. The proteins of these genes were obtained from the UniProt database in dogs and humans. Not all homologous proteins perform similar functions, thus comparison of these proteins was studied in terms of protein families, domains, biological processes, molecular functions, and cellular location of metabolic pathways in Interpro, KEGG, Quick Go and Psort databases. The results showed that some of these proteins have the same performance in the rat or mouse, dog, and human. It is anticipated that the protein of these genes may be effective in learning and memory in dogs. Then, the expression pattern of the recognized genes was investigated in the dog hippocampus using the existing information in the GEO profile. The results showed that BDNF, TAC1 and CCK genes are expressed in the dog hippocampus, therefore, these genes could be strong candidates associated with learning and memory in dogs. Subsequently, due to the importance of the promoter regions in gene function, this region was investigated in the above genes. Analysis of the promoter indicated that the HNF-4 site of BDNF gene and the transcription start site of CCK gene is exposed to methylation. Phylogenetic analysis of protein sequences of these genes showed high similarity in each of these three genes among the studied species. The dN/dS ratio for BDNF, TAC1 and CCK genes indicates a purifying selection during the evolution of the genes.

Association of single nucleotide polymorphism of GHSR and TGFB2 genes with growth and body composition traits in sire and dam lines of a broiler chicken

Growth hormone secretagogue receptor (GHSR) modulates many physiological processes by binding to its ligand, as well as transforming growth factor-beta 2 (TGFB2) regulates cell growth and development in animals and, therefore, are candidate genes for performance in chickens. In the current study, single nucleotide polymorphisms of GHSR C3286 > T and TGFB2 T(-640) > C were genotyped in sire and dam lines of a broiler chicken to evaluate the association with the growth and body composition traits. Least squares means analysis showed that the GHSR C3286 > T SNP was significantly (P < 0.01) associated with growth (DFI and ADG) and body composition traits (AFW and %AFW). In addition, the TGFB2 T(-640) > C SNP was associated with ADG (P < 0.05) and DFI and body composition traits (DW, LBW, BAKWT, %BMW, %HNDWT and %CW) (P < 0.01). Significant associations of the single nucleotide polymorphisms (SNPs) on the traits reported in the present study might be the distinct usage of codons in avian, or relating to an enhancer element and modulating the expression of the gene in chicken. The data indicated that these SNPs could be valuable genetic elements for selection of chickens for better performance in the population.

Exclusion of NEU1 and PPGB from candidate genes for a lysosomal storage disease in Japanese Black cattle

A case of lysosomal storage disease has been reported in a calf of Japanese Black cattle. Lysosomal storage diseases are hereditary diseases caused by deficiency of lysosomal hydrolases. The clinical and pathological features and accumulated substrates of the affected animal indicated a possibility of sialidosis or galactosialidosis caused by deficiency of neuraminidase (NEU1) or protective protein for beta-galactosidase (PPGB). In the present study, we investigated nucleotide sequences of the genes encoding these two proteins to evaluate whether mutation of these genes is involved in this disease. We determined cattle genomic sequences of these two genes by using bovine EST sequences and the nucleotide sequences of all exons of these genes were compared between affected and normal animals. The results showed several nucleotide substitutions, but none of them was a functional mutation or specific to the affected animal. Furthermore, genotyping of the microsatellite markers in the vicinity of these two genes revealed no homozygosity of the chromosomal regions including these genes in the affected animal. These findings indicated that neither NEU1 nor PPGB gene is responsible for the lysosomal storage disease of Japanese Black cattle and therefore the disease is neither sialidosis nor galactosialidosis.

Taylor's frozen-flow hypothesis in Burgers turbulence

By detailed analytical treatment of the shock dynamics in the Burgers turbulence with large scale forcing we calculate the velocity structure functions between pairs of points displaced both in time and space. Our analytical treatment verifies the so-called Taylor's frozen-flow hypothesis without relying on any closure and under very general assumptions. We discuss the limitation of the hypothesis and show that it is valid up to time scales smaller than the correlation time scale of temporal velocity correlation function. We support the analytical calculation by performing numerical simulation of the periodically kicked Burgers equation.

Linkage mapping of the locus responsible for forelimb-girdle muscular anomaly of Japanese black cattle on bovine chromosome 26

Forelimb-girdle muscular anomaly is an autosomal recessive disorder of Japanese black cattle characterized by tremor, astasia and abnormal shape of the shoulders. Pathological examination of affected animals reveals hypoplasia of forelimb-girdle muscles with reduced diameter of muscle fibres. To identify the gene responsible for this disorder, we performed linkage mapping of the disorder locus using an inbred pedigree including a great-grand sire, a grand sire, a sire and 26 affected calves obtained from a herd of Japanese black cattle. Two hundred and fifty-eight microsatellite markers distributed across the genome were genotyped across the pedigree. Four markers on the middle region of bovine chromosome 26 showed significant linkage with the disorder locus. Haplotype analysis using additional markers in this region refined the critical region of the disorder locus to a 3.5-Mb interval on BTA26 between BM4505 and MOK2602. Comparative mapping data revealed several potential candidate genes for the disorder, including NRAP, PDZD8 and HSPA12A, which are associated with muscular function.

Intermittency of height fluctuations in stationary state of the Kardar-Parisi-Zhang equation with infinitesimal surface tension in 1+1 dimensions

The Kardar-Parisi-Zhang (KPZ) equation with infinitesimal surface tension, dynamically develops sharply connected valley structures within which the height derivative is not continuous. We discuss the intermittency issue in the problem of stationary state forced KPZ equation in 1+1 dimensions. It is proved that the moments of height increments C(a) = <|h(x(1)) - h(x(2))|(a)> behave as |x(1) - x(2)|(xi(a)) with xi(a) = a for length scales |x(1) - x(2)|<<sigma . The length scale sigma is the characteristic length of the forcing term. We have checked the analytical results by direct numerical simulation.

Statistical theory for the Kardar-Parisi-Zhang equation in (1+1) dimensions

The Kardar-Parisi-Zhang (KPZ) equation in (1+1) dimensions dynamically develops sharply connected valley structures within which the height derivative is not continuous. We develop a statistical theory for the KPZ equation in (1+1) dimensions driven with a random forcing that is white in time and Gaussian-correlated in space. A master equation is derived for the joint probability density function of height difference and height gradient P(h-h*, partial differential(x)h,t) when the forcing correlation length is much smaller than the system size and much larger than the typical sharp valley width. In the time scales before the creation of the sharp valleys, we find the exact generating function of h-h* and partial differential(x)h. The time scale of the sharp valley formation is expressed in terms of the force characteristics. In the stationary state, when the sharp valleys are fully developed, finite-size corrections to the scaling laws of the structure functions left angle bracket(h-h*)(n)(partial differential(x)h)(m)right angle bracket are also obtained.

Three-dimensional forced Burgers turbulence supplemented with a continuity equation

We investigate turbulent limit of the forced Burgers equation supplemented with a continuity equation in three dimensions. The scaling exponent of the conditional two-point correlation function of density, i.e., <rho(x1)rho(x2)/delta u> approximately /x1-x2/(-alpha3), is calculated self-consistently in the nonuniversal region from which we obtain alpha3=3. Also we derive an equation governing the evolution of the probability density function (PDF) of longitudinal velocity increments in length scale, from which a possible mechanism for the dependence of the inertial PDF to one-point u(rms) is developed.