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.

Genome-wide association study of copy number variations with shank traits in a F2 crossbred chicken population.

Copy number variations (CNVs) are large-scale changes in the DNA sequence that can affect the genetic structure and phenotype of an organism. The purpose of this study was to investigate the existing CNVs and their associations with the shank diameter (ShD) and shank length (ShL) traits using data from an F2 crossbred chicken population. To carry out the study, 312 chickens were genotyped using the Illumina 60k SNP Beadchip. The shank traits of the birds were measured from day 1 to 12 weeks of age. penncnv and cnvruler tools were used to find copy numbers and regions with copy number changes (CNVR), respectively. The CNVRanger package was used to perform a genome-wide association study between shank traits and CNVs. Gene ontology research in CNVRs was carried out using the david database. In this investigation, 966 CNVs and 606 regions with copy number changes were discovered. The copy number states and variations were randomly distributed along the length of the autosomal chromosomes. Weeks 1-4, 9 and 12 of growth revealed a significant association of copy number variations with shank traits, false discovery rate (FDR-corrected p-value < 0.01), and the majority of CNVs that were statistically significant were found on chromosomes 1-3. These CNV segments are nearby genes such as KCNJ12, FGF6 and MYF5, which are fundamental to growth and development. In addition, gene set analyses revealed terms related to muscle physiology, regulation of cellular processes and potassium channels.

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.

A single phenylalanine residue in ß-arrestin2 critically regulates its binding to G protein-coupled receptors.

Arrestins and their yeast homologs, arrestin-related trafficking adaptors (ARTs), share a stretch of 29 amino acids called the ART motif. However, the functionality of that motif is unknown. We now report that deleting this motif prevents agonist-induced ubiquitination of ß-arrestin2 (ß-arr2) and blocks its association with activated G protein-coupled receptors (GPCRs). Within the ART motif, we have identified a conserved phenylalanine residue, Phe116, that is critical for the formation of ß-arr2-GPCR complexes. ß-arr2 Phe116Ala mutant has negligible effect on blunting ß2-adrenergic receptor-induced cAMP generation unlike ß-arr2, which promotes rapid desensitization. Furthermore, available structures for inactive and inositol hexakisphosphate 6-activated forms of bovine ß-arr2 revealed that Phe116 is ensconced in a hydrophobic pocket, whereas the adjacent Phe117 and Phe118 residues are not. Mutagenesis of Phe117 and Phe118, but not Phe116, preserves GPCR interaction of ß-arr2. Surprisingly, Phe116 is dispensable for the association of ß-arr2 with its non-GPCR partners. ß-arr2 Phe116Ala mutant presents a significantly reduced protein half-life compared with ß-arr2 and undergoes constitutive Lys-48-linked polyubiquitination, which tags proteins for proteasomal degradation. We also found that Phe116 is critical for agonist-dependent ß-arr2 ubiquitination with Lys-63-polyubiquitin linkages that are known mediators of protein scaffolding and signal transduction. Finally, we have shown that ß-arr2 Phe116Ala interaction with activated ß2-adrenergic receptor can be rescued with an in-frame fusion of ubiquitin. Taken together, we conclude that Phe116 preserves structural stability of ß-arr2, regulates the formation of ß-arr2-GPCR complexes that inhibit G protein signaling, and promotes subsequent ubiquitin-dependent ß-arr2 localization and trafficking.

Mechanism of intracellular allosteric ß2AR antagonist revealed by X-ray crystal structure.

G-protein-coupled receptors (GPCRs) pose challenges for drug discovery efforts because of the high degree of structural homology in the orthosteric pocket, particularly for GPCRs within a single subfamily, such as the nine adrenergic receptors. Allosteric ligands may bind to less-conserved regions of these receptors and therefore are more likely to be selective. Unlike orthosteric ligands, which tonically activate or inhibit signalling, allosteric ligands modulate physiologic responses to hormones and neurotransmitters, and may therefore have fewer adverse effects. The majority of GPCR crystal structures published to date were obtained with receptors bound to orthosteric antagonists, and only a few structures bound to allosteric ligands have been reported. Compound 15 (Cmpd-15) is an allosteric modulator of the ß2 adrenergic receptor (ß2AR) that was recently isolated from a DNA-encoded small-molecule library. Orthosteric ß-adrenergic receptor antagonists, known as beta-blockers, are amongst the most prescribed drugs in the world and Cmpd-15 is the first allosteric beta-blocker. Cmpd-15 exhibits negative cooperativity with agonists and positive cooperativity with inverse agonists. Here we present the structure of the ß2AR bound to a polyethylene glycol-carboxylic acid derivative (Cmpd-15PA) of this modulator. Cmpd-15PA binds to a pocket formed primarily by the cytoplasmic ends of transmembrane segments 1, 2, 6 and 7 as well as intracellular loop 1 and helix 8. A comparison of this structure with inactive- and active-state structures of the ß2AR reveals the mechanism by which Cmpd-15 modulates agonist binding affinity and signalling.

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.

Polarization fading mitigation in distributed acoustic sensors based on a high-speed polarization rotator.

A distributed optical fiber acoustic sensor based on interferometric demodulation technique with no polarization fading is demonstrated. A polarization diversity scheme based on a high-speed polarization rotator is used to eliminate signal fading due to polarization mismatch in the Rayleigh backscattered signal between adjacent points on the sensing fiber. This technique yields a spatially uniform response to the applied strain. The sensor exhibited spatial and strain resolutions of <4 m and <7 nɛ, respectively.

Allosteric nanobodies reveal the dynamic range and diverse mechanisms of G-protein-coupled receptor activation.

G-protein-coupled receptors (GPCRs) modulate many physiological processes by transducing a variety of extracellular cues into intracellular responses. Ligand binding to an extracellular orthosteric pocket propagates conformational change to the receptor cytosolic region to promote binding and activation of downstream signalling effectors such as G proteins and ß-arrestins. It is well known that different agonists can share the same binding pocket but evoke unique receptor conformations leading to a wide range of downstream responses ('efficacy'). Furthermore, increasing biophysical evidence, primarily using the ß2-adrenergic receptor (ß2AR) as a model system, supports the existence of multiple active and inactive conformational states. However, how agonists with varying efficacy modulate these receptor states to initiate cellular responses is not well understood. Here we report stabilization of two distinct ß2AR conformations using single domain camelid antibodies (nanobodies)­a previously described positive allosteric nanobody (Nb80) and a newly identified negative allosteric nanobody (Nb60). We show that Nb60 stabilizes a previously unappreciated low-affinity receptor state which corresponds to one of two inactive receptor conformations as delineated by X-ray crystallography and NMR spectroscopy. We find that the agonist isoprenaline has a 15,000-fold higher affinity for ß2AR in the presence of Nb80 compared to the affinity of isoprenaline for ß2AR in the presence of Nb60, highlighting the full allosteric range of a GPCR. Assessing the binding of 17 ligands of varying efficacy to the ß2AR in the absence and presence of Nb60 or Nb80 reveals large ligand-specific effects that can only be explained using an allosteric model which assumes equilibrium amongst at least three receptor states. Agonists generally exert efficacy by stabilizing the active Nb80-stabilized receptor state (R80). In contrast, for a number of partial agonists, both stabilization of R80 and destabilization of the inactive, Nb60-bound state (R60) contribute to their ability to modulate receptor activation. These data demonstrate that ligands can initiate a wide range of cellular responses by differentially stabilizing multiple receptor states.

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.

Long Range Raman-Amplified Distributed Acoustic Sensor Based on Spontaneous Brillouin Scattering for Large Strain Sensing.

A Brillouin distributed acoustic sensor (DAS) based on optical time-domain refractometry exhibiting a maximum detectible strain of 8.7 mε and a low signal fading is developed. Strain waves with frequencies of up to 120 Hz are measured with an accuracy of 12 µÎµ at a sampling rate of 1.2 kHz and a spatial resolution of 4 m over a sensing range of 8.5 km. The sensing range is further extended by using a modified inline Raman amplifier configuration. Using 80 ns Raman pump pulses, the signal-to-noise ratio is improved by 3.5 dB, while the accuracy of the measurement is enhanced by a factor of 2.5 to 62 µÎµ at the far-end of a 20 km fiber.

Allosteric activation of proto-oncogene kinase Src by GPCR-beta-arrestin complexes.

G protein-coupled receptors (GPCRs) initiate signaling cascades via G-proteins and beta-arrestins (ßarr). ßarr-dependent actions begin with recruitment of ßarr to the phosphorylated receptor tail and are followed by engagement with the receptor core. ßarrs are known to act as adaptor proteins binding receptors and various effectors, but it is unclear whether in addition to the scaffolding role ßarrs can allosterically activate their downstream targets. Here we demonstrate the direct allosteric activation of proto-oncogene kinase Src by GPCR-ßarr complexes in vitro and establish the conformational basis of the activation. Whereas free ßarr1 had no effect on Src activity, ßarr1 in complex with M2 muscarinic or ß2-adrenergic receptors reconstituted in lipid nanodiscs activate Src by reducing the lag phase in Src autophosphorylation. Interestingly, receptor-ßarr1 complexes formed with a ßarr1 mutant, in which the finger-loop, required to interact with the receptor core, has been deleted, fully retain the ability to activate Src. Similarly, ßarr1 in complex with only a phosphorylated C-terminal tail of the vasopressin 2 receptor activates Src as efficiently as GPCR-ßarr complexes. In contrast, ßarr1 and chimeric M2 receptor with nonphosphorylated C-terminal tail failed to activate Src. Taken together, these data demonstrate that the phosphorylated GPCR tail interaction with ßarr1 is necessary and sufficient to empower it to allosterically activate Src. Our findings may have implications for understanding more broadly the mechanisms of allosteric activation of downstream targets by ßarrs.

152 km-range single-ended distributed acoustic sensor based on inline optical amplification and a micromachined enhanced-backscattering fiber.

In this Letter, a distributed acoustic sensor (DAS) with a sensing range in excess of 150 km is reported. This extended sensing range is achieved by adding a low-loss enhanced-backscattering fiber at the far end of a standard single-mode fiber. A conventional DAS system along with inline optical amplifiers are used to interrogate the sensing fiber. The combined system exhibits a minimum detectable strain of 40 nε at 1 Hz over a spatial resolution of 5 m.

Numerical Modelling of a Distributed Acoustic Sensor Based on Ultra-Low Loss-Enhanced Backscattering Fibers.

In this study, a distributed acoustic sensor (DAS) was numerically modeled based on the non-ideal optical components with their noises and imperfections. This model is used to compare the response of DAS systems to standard single-mode fibers and ultra-low loss-enhanced backscattering (ULEB) fibers, a fiber with an array of high reflective points equally spaced along its length. It is shown that using ULEB fibers with highly reflective points improves the signal-to-noise ratio and linearity of the measurement, compared with the measurement based on standard single-mode fibers.

Curvature sensing with a D-shaped multicore fibre and Brillouin optical time-domain reflectometry.

A distributed curvature sensor based on Brillouin optical time-domain reflectometry interrogation technique in a D-shaped 7-core fibre is presented. By comparing the relative Brillouin frequency shift between the central core and three of the outer cores of the 7-core fibre, the curvature of various spools with different diameters is measured with a deviation from the actual value ranging between 9% and 15%. The analysis and results presented in this study show the first demonstration of distributed bend sensing using a specially designed multicore D-shaped fibre, paving the way for fully distributed 3D shape sensing.

Low-noise distributed acoustic sensing using enhanced backscattering fiber with ultra-low-loss point reflectors.

We present a low-noise distributed acoustic sensor using enhanced backscattering fiber with a series of localized reflectors. The point reflectors were inscribed in a standard telecom fiber in a fully automated system by focusing an ultra-fast laser through the fiber cladding. The inscribed reflectors provided a reflectance of -53 dB, significantly higher than the Rayleigh backscattering level of -70 dB/m, despite adding only 0.01 dB of loss per 100 reflection points. We constructed a coherent φ-OTDR system using a double-pulse architecture to probe the enhanced backscattering fiber. Using this system, we found that the point reflectors enabled an average phase noise of -91 dB (re rad2/Hz), 20 dB lower than sensors formed using Rayleigh backscattering in the same fiber. The sensors are immune to interference fading, exhibit a high degree of linearity, and demonstrate excellent non-local signal suppression (>50 dB). This work illustrates the potential for low-cost enhanced backscattering fiber to enable low-noise, long-range distributed acoustic sensing.

Chasing acyl carrier protein through a catalytic cycle of lipid A production.

Acyl carrier protein represents one of the most highly conserved proteins across all domains of life and is nature's way of transporting hydrocarbon chains in vivo. Notably, type II acyl carrier proteins serve as a crucial interaction hub in primary cellular metabolism by communicating transiently between partner enzymes of the numerous biosynthetic pathways. However, the highly transient nature of such interactions and the inherent conformational mobility of acyl carrier protein have stymied previous attempts to visualize structurally acyl carrier protein tied to an overall catalytic cycle. This is essential to understanding a fundamental aspect of cellular metabolism leading to compounds that are not only useful to the cell, but also of therapeutic value. For example, acyl carrier protein is central to the biosynthesis of the lipid A (endotoxin) component of lipopolysaccharides in Gram-negative microorganisms, which is required for their growth and survival, and is an activator of the mammalian host's immune system, thus emerging as an important therapeutic target. During lipid A synthesis (Raetz pathway), acyl carrier protein shuttles acyl intermediates linked to its prosthetic 4'-phosphopantetheine group among four acyltransferases, including LpxD. Here we report the crystal structures of three forms of Escherichia coli acyl carrier protein engaging LpxD, which represent stalled substrate and liberated products along the reaction coordinate. The structures show the intricate interactions at the interface that optimally position acyl carrier protein for acyl delivery and that directly involve the pantetheinyl group. Conformational differences among the stalled acyl carrier proteins provide the molecular basis for the association-dissociation process. An unanticipated conformational shift of 4'-phosphopantetheine groups within the LpxD catalytic chamber shows an unprecedented role of acyl carrier protein in product release.

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.

Performance analysis of distributed optical fiber acoustic sensors based on φ-OTDR.

The performance of distributed optical fiber acoustic sensor as a function of parameters such as the linewidth of the laser, the probe pulse width, and the amplitude and frequency of perturbation is experimentally studied. The aim of this study is to experimentally confirm the outcome of the simulation results obtained previously. It is shown that the experimental and simulation results are in good agreement, and the precision of the sensing system depends on the pulse width and linewidth of the probe pulse, as well as the frequency and amplitude of the perturbation. It is shown that the sensing precision of the system can be enhanced by reducing the width of the probe pulse while increasing the linewidth of the laser.

Flexible Mid-IR fiber bundle for thermal imaging of inaccessible areas.

We present a flexible coherent Mid-Infrared (Mid-IR) fiber bundle for thermal imaging made of 1200 Ge30As13Se32Te25 glass cores embedded in a Fluorinated Ethylene Propylene (FEP) polymer cladding. The high index contrast between the chalcogenide glass and the polymer cladding helps minimizing inter-pixel cross-talk, while the low Young's modulus of the polymer cladding gives the bundle good flexibility despite its millimeter scale outer diameter. The delivery of high contrast and high spatial resolution thermal images of a human hand through a 62.5 cm long bundle indicates its excellent imaging potential.

100-km-sensing-range single-ended distributed vibration sensor based on remotely pumped Erbium-doped fiber amplifier.

In this Letter, we report a single-ended distributed vibration sensor with the 100 km sensing range. This sensing range is achieved by remotely pumping two pieces of Er-doped fibers incorporated along the sensing fiber with a 1480 nm Raman fiber laser at the front end. A strain resolution of 100 nϵ combined with a spatial resolution of 2.6 m is achieved at the far end of the fiber.