Transcriptome analysis of boar spermatozoa with different freezability using RNA-Seq.

Semen freezability is associated with genetic markers, and there is a diverse set of sperm transcripts that have been attributed to various cellular functions. RNA-Seq was performed to compare the transcript profiles of spermatozoa from boars with different semen freezability. We examined ejaculates from the Polish large white (PLW) boars that were classified as having good and poor semen freezability (GSF and PSF, respectively; n = 3 boars per group) by assessing post-thaw motility characteristics, mitochondrial membrane potential, plasma membrane and acrosome integrity. Total RNA was isolated from fresh spermatozoa from boars of the GSF and PSF groups and subjected to RNA-Seq (Illumina NextSeq 500 platform). Transcript abundance was assessed with the DESeq2, DESeq, and EdgeR Bioconductor R packages, and varying numbers of differentially expressed gene (DEG) transcripts were detected in the spermatozoa of each boar. Using RNA-Seq, we identified several genes associated with inflammation and apoptosis (FOS, NFATC3, ITGAL, EAF2 and ZDHHC14), spermatogenesis (FGF-14 and BAMBI), autophagy (RAB33B), protein phosphorylation (PTPRU and PTPN2) and energy metabolism (ND6 and ACADM) that were predominantly up-regulated in poor freezability ejaculates. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) validated the transcript expression levels detected by RNA-Seq and thus confirmed the reliability of this technique. Subsequent validation with western blotting showed that the expression of three proteins was in accordance with the transcript abundance. Overall, we demonstrated that the up-regulation of the DEG transcripts in spermatozoa was associated with poor semen freezability. We suggest that spermatozoa transcriptome profiling provides a foundation to further elucidate the relevance of sperm-related transcripts on cryo-survival. The sperm-related transcripts, namely FOS, NFATC3, EAF2, BAMBI, PTPRU, PTPN2, ND6 and ACADM, are potential markers for predicting the freezability of boar semen.

Ultrasound-guided intermediate cervical plexus and additional peripheral facial nerve block for carotid endarterectomy : A prospective pilot study.

BACKGROUND AND OBJECTIVES: Ultrasound-guided intermediate cervical plexus block with perivascular local anesthetic infiltration is an established anesthetic procedure for carotid endarterectomy. In this prospective pilot study an additional subplatysmal block of the superficial ansa cervicalis is presented for the first time. The target structures are the anastomoses between the facial nerve (cervical and marginal mandibular branches) and cervical plexus. METHODS: An ultrasound-guided intermediate cervical plexus block (20 ml of ropivacaine 0.75%) was performed (n = 28). Then, depending on the individual sonoanatomy, 5 ml of prilocaine 1% was injected into the carotid sheath (group 1: no perivascular infiltration, n = 14, group 2: perivascular infiltration, n = 14). The third step was subplatysmal injection of 5 ml of prilocaine 1% between the medial edge of the sternocleidomastoid muscle and the submandibular gland (n = 28). The investigated parameters included the need for supplementation and block-related side effects. RESULTS: The requirement for supplemental local anesthetic infiltration in the skin incision area was minimal at mean (M) 1.1 ml (standard deviation (SD) ±2.4 ml). Perivascular infiltration in group 2 significantly decreased the total amount of local anesthetic supplemented: group 1 M = 4.2 ml (SD = ±3.1 ml), group 2 M = 1.7 ml (SD = ±2.0 ml) (p = 0.018). The incidence of block-related side effects was not significantly different between the two groups. CONCLUSION: This study presents an ultrasound-guided subplatysmal block of the superficial ansa cervicalis for the first time, with the aim of optimizing anesthesia quality during surgical interventions in the carotid triangle.

Transcriptomic hallmarks of bone remodelling revealed by RNA-Seq profiling in blood of Arabian horses during racing training regime.

The impact of exercises on young developing organisms is still of interest to researchers. Similarly like Thoroughbreds, Arabian horses competing at the race track. The high percent of lameness and loss of days in training are often the result of weakness in the condition of the musculoskeletal system. The objective of the presented study was to identify by RNA-Seq method, the possible skeletal system originating transcriptomic profile in peripheral blood of Arabian horses undergoing race training. Obtained results showed that one of the most significantly deregulated pathway involved in bone homeostasis was those involved in osteoclast differentiation. Among the significantly expressed molecules, we recognized twelve genes potentially involved in the metabolism of the skeletal system: BGLAP, CTSK, TYROBP, PDLIM7, SLC9B2, TWSG1, NOTCH2, IL6ST, VAV3, NFATc1, CLEC5A, TXLNG. The panel of identified genes should be evaluated as candidate biomarkers for bone homeostasis indicators of Arabians performing on race tracks to assess bone remodelling states during training for race track competitions.

Detection of genetic variants between different Polish Landrace and Pulawska pigs by means of RNA-seq analysis.

Variant calling analysis based on RNA sequencing data provides information about gene variants. RNA-seq is cheaper and faster than is DNA sequencing. However, it requires individual hard filters during data processing due to post-transcriptional modifications such as splicing and RNA editing. In the present study, RNA-seq transcriptome data on two Polish pig breeds (Pulawska, PUL, n = 8, and Polish Landrace, PL, n = 8) were included. The pig breeds are significantly different with regard to meat qualities such as texture, water exudation, growth traits and fat content in carcasses. A total of 2451 significant mutations were identified by a chi square tests, and functional analysis was carried out using Panther, KEGG and Kobas. Interesting missense gene variants and mutations located in regulatory regions were found in a few genes related to fatty acid metabolism and lipid storage such as ACSL5, ALDH3A2, FADS1, SCD, PLA2G12A and ATGL. A validation of mutational influences on pig traits was performed for ALDH3A2, ATGL, PLA2G12A and MYOM1 variants using association analysis including 215 pigs of the PL and PUL breeds. The ALDH3A2ENSSSCT00000019636.2:c.470T>C polymorphism was found to affect the weight of the ham and loin eye area. In turn, an ENSSSCT00000004091.2:c.2836G>A MYOM1 mutation, which could be implicated in myofibrillar network organisation, had an effect on meatiness and loin texture parameters. The study aimed to estimate the usefulness of RNA-seq results for a purpose other than differentially expressed gene analysis. The analysis performed indicated interesting gene variants that could be used in the future as markers during selection.

Common variants in DLG1 locus are associated with non-syndromic cleft lip with or without cleft palate.

Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a common craniofacial anomaly with a complex and heterogeneous aetiology. Knowledge regarding specific genetic factors underlying this birth defect is still not well understood. Therefore, we conducted an independent replication analysis for the top-associated variants located within the DLG1 locus at chromosome 3q29, which was identified as a novel cleft-susceptibility locus in our genome-wide association study (GWAS). Mega-analysis of the pooled individual data from the GWAS and replication study confirmed that common DLG1 variants are associated with the risk of nsCL/P. Two single nucleotide polymorphisms (SNPs), rs338217 and rs7649443, were statistically significant even at the genome-wide level (Ptrend = 9.70E-10 and Ptrend = 8.96E-09, respectively). Three other SNPs, rs9826379, rs6805920 and rs6583202, reached a suggestive genome-wide significance threshold (Ptrend < 1.00E-05). The location of the strongest individual SNP in the intronic sequence of the gene encoding DLG1 antisense RNA suggests that the true causal variant implicated in the risk of nsCL/P may affect the DLG1 gene expression level rather than structure of the encoded protein. In conclusion, we identified a novel cleft-susceptibility locus at chromosome 3q29 with a DLG1 as a novel candidate gene for this common craniofacial anomaly.

A549 and MRC-5 cell aggregation in a microfluidic Lab-on-a-chip system.

In this paper, we present a culture of A549 and MRC-5 spheroids in a microfluidic system. The aim of our work was to develop a good lung cancer model for the evaluation of drug cytotoxicity. Our research was focused on determining the progress of cell aggregation depending on such factors as the depth of culture microwells in the microdevices, a different flow rate of the introduced cell suspensions, and the addition of collagen to cell suspensions. We showed that these factors had a significant influence on spheroid formation. It was found that both MRC-5 and A549 cells exhibited higher aggregation in 500 µm microwells. We also noticed that collagen needs to be added to A549 cells to form the spheroids. Optimizing the mentioned parameters allowed us to form 3D lung tissue models in the microfluidic system during the 10-day culture. This study indicates how important an appropriate selection of the specified parameters is (e.g., geometry of the microwells in the microsystem) to obtain the spheroids characterized by high viability in the microfluidic system.

Ultrasound-guided intermediate cervical plexus block and perivascular local anesthetic infiltration for carotid endarterectomy : A randomized controlled trial.

BACKGROUND AND OBJECTIVE: Ultrasound-guided blocks of the cervical plexus are established anesthetic procedures for carotid endarterectomy. This randomized, double-blind, placebo-controlled study tested the hypothesis that an additional ultrasound-guided periarterial injection of local anesthetic leads to a lower frequency of periarterial supplementation by the surgeon. METHODS: A total of 40 patients were randomly assigned to 1 of 2 groups. In both groups an ultrasound-guided intermediate cervical plexus block (20 ml of 0.75 % ropivacaine) at the level of the fourth cervical vertebra was performed. In a second step, the needle was inserted from posterolateral to anteromedial (in-plane technique) relative to the internal carotid artery and then, depending on the randomized group assignment, 5 ml of 0.75 % ropivacaine (group 2) or 5 ml of 0.9 % saline (group 1) was injected. The parameters investigated included the need for supplementation, patient comfort, the incidence of side effects and circulatory changes. RESULTS: The two groups did not significantly differ (p = 0.459) in terms of the need for intraoperative supplementation with 1 % prilocaine with a mean (range) in group 2 of 4.9 ml (0-20 ml), in group 1 of 3.7 ml (0-16 ml) and patient comfort (p = 0.144). In addition, a trend towards a higher complication rate was observed in group 2. CONCLUSION: For ultrasound-guided intermediate blocks of the cervical plexus, an additional periarterial infiltration showed no advantage. Abandoning this technique leads to a relevant simplification of the blocking technique and tends to reduce block-related side effects.

Single nucleotide polymorphisms in the CXCR1 gene and its association with clinical mastitis incidence in Polish Holstein-Friesian cows.

The aim of this study was to identify the association between single nucleotide polymorphisms (SNPs) in the bovine chemokine receptor (CXCR1) gene and the resistance or susceptibility of cows to mastitis. The analysis of the CXCR1 polymorphism was carried out using polymerase chain reaction restriction fragment length polymorphism analysis for six SNP mutations (c.+291C>T, c.+365T>C, c.+816C>A, c.+819G>A, +1093C>T, and +1373C>A), of which four were located within the coding region and two in the 3'UTR region of the CXCR1 gene. Genetic material from 146 Polish Holstein-Friesian cows was analyzed after dividing into two groups depending on the incidence of clinical mastitis. Identified polymorphisms were in linkage disequilibrium and formed two linkage groups. Three haplotypes (CCCATA, TTAGCC, CTCGCC), forming six haplotype combinations, were detected. The logistic regression showed a significant association between the CC genotype at c.+365T>C and susceptibility of cows to clinical mastitis (P = 0.047). The frequency of haplotype combination 1/1 (CCCATA/CCCATA) was not significantly higher in cows susceptible to mastitis (P = 0.062). Of the identified SNP mutations, only c.+365T>C is a nonsynonymous mutation that induces a change in the coded protein [GCC (Ala) to GTC (Val) at the 122nd amino acid]. This amino acid change can result in changes in receptor function, which may be a reason for the increased mastitis incidence observed in cows with polymorphism at this site.

The use of runs of homozygosity for estimation of recent inbreeding in Holstein cattle.

Controlling inbreeding in livestock populations is of great importance because excess relatedness among animals leads to a rapid loss of genetic variation and to adverse phenotypical effects associated with an inbreeding depression. Recent advances in genotyping technology have made it possible to study inbreeding at a molecular level by the analysis of genome-wide single nucleotide polymorphism panels. In this study, we used BovineSNP50 assay (Illumina) to estimate genomic inbreeding coefficient in 298 Holstein cattle by the analysis of the genome portion in runs of homozygosity (FROH) or using genomic relationship matrix (FGRM), and compared this data with conventional pedigree-based inbreeding coefficients (FPED). Weak or moderate Spearman's rank correlations were observed between FROH and FPED which depended on the ROH length categories used for calculations and inclusion of animals with different number of complete generations registered in pedigrees. The highest correlations were observed when using ROH with lengths over 8 Mb (0.334). The correlations tended to increase as pedigree depth increased, and were the highest for animals with seven complete generations of pedigree data. FGRM correlated poorly with pedigree-based estimates, which suggests that ROH-based inbreeding coefficients better reflect recent relatedness among animals.

Genome-wide RNA-Seq analysis of breast muscles of two broiler chicken groups differing in shear force.

In this study, a whole transcriptome analysis of breast muscles was conducted in broiler chicken groups differing in shear force. Shear force is a determinant of tenderness, which in turn is one of the most important parameters of meat quality in chickens. In our analysis, a total of 11,560 transcripts and 9824 genes per sample were identified. In chickens with more tender meat, up-regulation of 19 genes and down-regulation of 49 genes was observed. The up-regulated gene group included the ASB2 gene, which is probably involved in the meat conversion process, as its product results in the degradation of filamins, proteins which form muscle fibres. In the down-regulated gene group, genes which play a role in lipogenesis (THRSP, PLIN1) and in collagen synthesis (P4HA3, LEPREL4, PCOLCE2, COL16A1, COL20A1, VWA1) were detected. Their presence suggests the involvement of the extracellular matrix in the determination of meat tenderness. Thus, our study identified a pool of genes that may participate in the tenderisation process in broiler chickens.