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This study examined the association, promoter methylation of Interferon alpha-inducible protein 6 (IFI6) gene, and their effects on mRNA expression and meat quality traits in pig. Muscle samples (n=300) were randomly collected from the Longissimus thoracis et lumborum (LTL) to determine meat quality traits including drip loss, thawing loss, cooking loss, meat pH [at 45 minutes (pH45min) and at 24 hours (pH24h) post-mortem], shear force (for tenderness), and lightness (L*) in pigs. Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Muscle samples (5 per group) with divergent meat pH (low vs high) were selected for promoter methylation study using bisulfate and pyrosequencing. Muscle samples from animals (5 per group) with divergent phenotypes (low vs high meat pH and low vs high drip loss) were used for mRNA expression study by quantitative real-time polymerase chain reaction (qRT-PCR). Results showed that a polymorphism in IFI6 gene (g.370A>G) was significantly (P < 0.01) associated with meat pH24h. Furthermore, four CpG regions were identified in IFI6 promoter, of which DNA methylation in a CG site was higher in low meat pH24h group compared to high meat pH24h group (P < 0.05). The mRNA expression of IFI6 gene was significantly (P < 0.01) downregulated in low meat pH24h group than high meat pH24h group. This result postulated that high DNA methylation at CG site in the promoter region might downregulate the IFI6 gene expression, hence lower the muscle pH that might lead to higher drip loss and lower tenderness. Therefore, porcine IFI6 gene might be a potential candidate gene for meat quality trait in pig. Nevertheless, further research is needed to confirm the role of IFI6 gene in controlling meat quality traits in other commercial populations. This study analysed association of a SNP in IFI6 gene with meat quality traits, and promotor methylation and transcriptome expression of IFI6 gene in relation to meat pH. The result suggested that polymorphism affects meat pH. The high DNA methylation at a specific CG site in the IFI6 promoter is involved in IFI6 gene downregulation in low meat pH. [ABSTRACT FROM AUTHOR]

Microplastic pollution is an emerging issue of increasing concern in the environment. The abundance and distribution of microplastics in surface water and sediment in the Jamuna River and Turag River in Bangladesh have been determined in this study. Surface water and sediment samples were collected in triplicate for each station from 6 sampling stations of two rivers in July 2019. Of all the microplastics were identified by a digital binocular microscope. A total of 145 and 261 microplastic particles were identified in the surface water samples, while the sediment samples, it accounted for 93 and 774 particles in Jamuna River and Turag River, respectively. The mean abundance of microplastics was 16.11±2.22 particles/100L in the surface water of Jamuna River and for Turag River it was 29.00±10.68 particles/100L. The mean abundance of microplastics in sediment was observed 10.33±1.45 particles/kg for the Jamuna River and 86.00±12.17 particles/kg for the Turag River. Recorded microplastics were categorized into shape, size, and color. Among which foam and film were the most abundant shape of microplastics in both surface water (foam= 52%; film= 31%) and sediment (foam= 31%; film= 45%) of Jamuna River and Turag River, respectively. Small sizes of microplastics were common in both the rivers except surface water of Turag River while white color of microplastics was the most dominant in both rivers. Turag River was found more abundant with microplastics than that of the Jamuna River. The industrial establishments along the pathway of Turag River could be the source of abundant microplastics. This is the first time study on microplastics in surface water and sediment in Jamuna River and Turag River. The outcome of the study could be a baseline for microplastic pollution in such a large freshwater ecosystem of Bangladesh. Findings can also provide a better understanding of sources of microplastic pollution towards planning for remedy. [ABSTRACT FROM AUTHOR]

Fatty acids (FA) in ruminants, especially unsaturated FA (USFA) have important impact in meat quality, nutritional value, and flavour quality of meat, and on consumer's health. Identification of the genetic factors controlling the FA composition and metabolism is pivotal to select sheep that produce higher USFA and lower saturated (SFA) for the benefit of sheep industry and consumers. Therefore, this study was aimed to investigate the transcriptome profiling in the liver tissues collected from sheep with divergent USFA content in longissimus muscle using RNA deep-sequencing. From sheep (n = 100) population, liver tissues with higher (n = 3) and lower (n = 3) USFA content were analysed using Illumina HiSeq 2500. The total number of reads produced for each liver sample were ranged from 21.28 to 28.51 million with a median of 23.90 million. Approximately, 198 genes were differentially regulated with significance level of p-adjusted value <0.05. Among them, 100 genes were up-regulated, and 98 were down-regulated (p<0.01, FC>1.5) in the higher USFA group. A large proportion of key genes involved in FA biosynthesis, adipogenesis, fat deposition, and lipid metabolism were identified, such as APOA5, SLC25A30, GFPT1, LEPR, TGFBR2, FABP7, GSTCD, and CYP17A. Pathway analysis revealed that glycosaminoglycan biosynthesis- keratan sulfate, adipokine signaling, galactose metabolism, endocrine and other factors-regulating calcium metabolism, mineral metabolism, and PPAR signaling pathway were playing important regulatory roles in FA metabolism. Importantly, polymorphism and association analyses showed that mutation in APOA5, CFHR5, TGFBR2 and LEPR genes could be potential markers for the FA composition in sheep. These polymorphisms and transcriptome networks controlling the FA variation could be used as genetic markers for FA composition-related traits improvement. However, functional validation is required to confirm the effect of these SNPs in other sheep population in order to incorporate them in the sheep breeding program. [ABSTRACT FROM AUTHOR]

Abstract Background As an in vitro model porcine peripheral blood mononuclear cells (PBMCs) is frequently used as for immunogenetic research with the stimulation of bacterial antigens. To investigate the immunocompetence of PBMCs for recognition of Gram-positive and Gram-negative bacteria and in order to dissect the pathogenesis of diseases, gene expression assay is most commonly used. The gene expressions are required to normalize for reference genes which have tremendous effect on the results of expression study. The reference genes should be stably expressed between different cells under a variety of experimental conditions, but recent influx of data showed that expression stability of reference genes are varied under different experimental conditions. But data regarding the expression stability of reference genes in porcine PBMCs are limited. Therefore, this study was aimed to know whether the expression stability of commonly used reference genes in PBMCs is affected by various bacterial antigens under different experimental conditions in pigs. Results The mRNA expression stability of nine commonly used reference genes (B2M, BLM, GAPDH, HPRT1, PPIA, RPL4, SDHA, TBP and YWHAZ) was determined by RT-qPCR in PBMCs that were stimulated by LPS and LTA in vitro as well as cells un-stimulated control and non-cultured were also consider for this experiment. mRNA expression levels of all genes were found to be affected by the type of stimulation and duration of the stimulation (P Conclusion There was discrepancy in the ranking order of reference genes obtained by different analysing algorithms (geNorm and NormFinder). In conclusion, the geometric mean of the RPL4, B2M and PPIA seemed to be the most appropriate combination of reference genes for accurate normalization of gene expression data in porcine PBMCs without knowing the type of bacterial pathogenic status of the animals and in the case of mixed infection with Gram-negative and Gram-positive bacteria. In case of PBMCs without any stimulation, PPIA, BLM and GAPDH could be suggested as suitable reference genes.

Road dust from atmospheric deposition is considered as one of the significant environmental pollutants for containing toxic heavy metals. In this connection, to explore the present scenario of urban contamination and potential health risk of heavy metals present in road dust; this study was carried out in Tangail Municipality Area of Bangladesh. Road dust samples were collected seasonally from five different sampling sites encompassing different traffic homogeneity. Collected samples were processed and analyzed for Lead (Pb), Chromium (Cr) and Cadmium (Cd) in road dust through the atomic absorption spectrophotometer (AAS). Primarily, all metals under investigation were found in higher concentrations in the wet season, and the ordering of mean contents was Pb>Cr>Cd. Spatial analysis elucidated that the distribution of Pb and Cd was mainly associated with urban traffic activity. Mathematical models such as Contamination Factor (CF), marked Pb and Cd for contamination in road dust. At the same time, considerable disease and pollution potential on the urban environment by Cd were detected by Index of Geo-accumulation (Igeo) and Ecological Risk Factor (ER). However, collectively, no sign of pollution and the ecological risk was detected in Pollution Load Index (PLI) and Potential Ecological Risk (RI) analysis. The health risk numerical model demonstrated that ingestion was the prevalent pathway of metal exposure for both children and adults and hazard index (HI) values for the studied heavy metals were less than safety limit 1. However, hazard index values were found higher for children than adults. [ABSTRACT FROM AUTHOR]