Molecular Aspects of the Functioning of Pathogenic Bacteria Biofilm Based on Quorum Sensing (QS) Signal-Response System and Innovative Non-Antibiotic Strategies for Their Elimination

One of the key mechanisms enabling bacterial cells to create biofilms and regulate crucial life functions in a global and highly synchronized way is a bacterial communication system called quorum sensing (QS). QS is a bacterial cell-to-cell communication process that depends on the bacterial population density and is mediated by small signalling molecules called autoinducers (AIs). In bacteria, QS controls the biofilm formation through the global regulation of gene expression involved in the extracellular polymeric matrix (EPS) synthesis, virulence factor production, stress tolerance and metabolic adaptation. Forming biofilm is one of the crucial mechanisms of bacterial antimicrobial resistance (AMR). A common feature of human pathogens is the ability to form biofilm, which poses a serious medical issue due to their high susceptibility to traditional antibiotics. Because QS is associated with virulence and biofilm formation, there is a belief that inhibition of QS activity called quorum quenching (QQ) may provide alternative therapeutic methods for treating microbial infections. This review summarises recent progress in biofilm research, focusing on the mechanisms by which biofilms, especially those formed by pathogenic bacteria, become resistant to antibiotic treatment. Subsequently, a potential alternative approach to QS inhibition highlighting innovative non-antibiotic strategies to control AMR and biofilm formation of pathogenic bacteria has been discussed.

Newly Isolated Virulent Salmophages for Biocontrol of Multidrug-Resistant Salmonella in Ready-to-Eat Plant-Based Food

Due to irrational antibiotic stewardship, an increase in the incidence of multidrug resistance of bacteria has been observed recently. Therefore, the search for new therapeutic methods for pathogen infection treatment seems to be necessary. One of the possibilities is the utilization of bacteriophages (phages)—the natural enemies of bacteria. Thus, this study is aimed at the genomic and functional characterization of two newly isolated phages targeting MDR Salmonella enterica strains and their efficacy in salmonellosis biocontrol in raw carrot–apple juice. The Salmonella phage vB_Sen-IAFB3829 (Salmonella phage strain KKP 3829) and Salmonella phage vB_Sen-IAFB3830 (Salmonella phage strain KKP 3830) were isolated against S. I (6,8:l,-:1,7) strain KKP 1762 and S. Typhimurium strain KKP 3080 host strains, respectively. Based on the transmission electron microscopy (TEM) and whole-genome sequencing (WGS) analyses, the viruses were identified as members of tailed bacteriophages from the Caudoviricetes class. Genome sequencing revealed that these phages have linear double-stranded DNA and sizes of 58,992 bp (vB_Sen-IAFB3829) and 50,514 bp (vB_Sen-IAFB3830). Phages retained their activity in a wide range of temperatures (from −20 °C to 60 °C) and active acidity values (pH from 3 to 11). The exposure of phages to UV radiation significantly decreased their activity in proportion to the exposure time. The application of phages to the food matrices significantly reduced the level of Salmonella contamination compared to the control. Genome analysis showed that both phages do not encode virulence or toxin genes and can be classified as virulent bacteriophages. Virulent characteristics and no possible pathogen factors make examined phages feasible to be potential candidates for food biocontrol.

Effectiveness of a Phage Cocktail as a Potential Biocontrol Agent against Saprophytic Bacteria in Ready-To-Eat Plant-Based Food

This study aimed to evaluate the effectiveness of the phage cocktail to improve the microbiological quality of five different mixed-leaf salads: rucola, mixed-leaf salad with carrot, mixed-leaf salad with beetroot, washed and unwashed spinach, during storage in refrigerated conditions. Enterobacterales rods constituted a significant group of bacteria in the tested products. Selected bacteria were tested for antibiotic resistance profiles and then used to search for specific bacteriophages. Forty-three phages targeting bacteria dominant in mixed-leaf salads were isolated from sewage. Their titer was determined, and lytic activity was assessed using the Bioscreen C Pro automated growth analyzer. Two methods of phage cocktail application including spraying, and an absorption pad were effective for rucola, mixed leaf salad with carrot, and mixed leaf salad with beetroot. The maximum reduction level after 48 h of incubation reached 99.9% compared to the control sample. In washed and unwashed spinach, attempts to reduce the number of microorganisms did not bring the desired effect. The decrease in bacteria count in the lettuce mixes depended on the composition of the autochthonous saprophytic bacteria species. Both phage cocktail application methods effectively improved the microbiological quality of minimally processed products. Whole-spectral phage cocktail application may constitute an alternative food microbiological quality improvement method without affecting food properties.

Application of In Vitro Models for Studying the Mechanisms Underlying the Obesogenic Action of Endocrine-Disrupting Chemicals (EDCs) as Food Contaminants-A Review

Obesogenic endocrine-disrupting chemicals (EDCs) belong to the group of environmental contaminants, which can adversely affect human health. A growing body of evidence supports that chronic exposure to EDCs can contribute to a rapid increase in obesity among adults and children, especially in wealthy industrialized countries with a high production of widely used industrial chemicals such as plasticizers (bisphenols and phthalates), parabens, flame retardants, and pesticides. The main source of human exposure to obesogenic EDCs is through diet, particularly with the consumption of contaminated food such as meat, fish, fruit, vegetables, milk, and dairy products. EDCs can promote obesity by stimulating adipo- and lipogenesis of target cells such as adipocytes and hepatocytes, disrupting glucose metabolism and insulin secretion, and impacting hormonal appetite/satiety regulation. In vitro models still play an essential role in investigating potential environmental obesogens. The review aimed to provide information on currently available two-dimensional (2D) in vitro animal and human cell models applied for studying the mechanisms of obesogenic action of various industrial chemicals such as food contaminants. The advantages and limitations of in vitro models representing the crucial endocrine tissue (adipose tissue) and organs (liver and pancreas) involved in the etiology of obesity and metabolic diseases, which are applied to evaluate the effects of obesogenic EDCs and their disruption activity, were thoroughly and critically discussed.

Bacterial Pathogens in the Food Industry: Antibiotic Resistance and Virulence Factors of Salmonella enterica Strains Isolated from Food Chain Links

Salmonella is one of the most important foodborne pathogens. Fifty-three strains of Salmonella deposited in the Culture Collection of Industrial Microorganisms-Microbiological Resources Center (IAFB) were identified using molecular and proteomic analyses. Moreover, the genetic similarity of the tested strains was determined using the PFGE method. Main virulence genes were identified, and phenotypical antibiotic susceptibility profiles and prevalence of resistance genes were analyzed. Subsequently, the occurrence of the main mechanisms of β-lactam resistance was determined. Virulence genes, invA, fimA, and stn were identified in all tested strains. Phenotypic tests, including 28 antibiotics, showed that 50.9% of the strains were MDR. The tet genes associated with tetracyclines resistance were the most frequently identified genes. Concerning the genes associated with ESBL-producing Salmonella, no resistance to the TEM and CTX-M type was identified, and only two strains (KKP 1597 and KKP 1610) showed resistance to SHV. No strains exhibited AmpC-type resistance but for six Salmonella strains, the efflux-related resistance of PSE-1 was presented. The high number of resistant strains in combination with multiple ARGs in Salmonella indicates the possible overuse of antibiotics. Our results showed that it is necessary to monitor antimicrobial resistance profiles in all food chain links constantly and to implement a policy of proper antibiotic stewardship to contain or at least significantly limit the further acquisition of antibiotic resistance among Salmonella strains.

The NF-κB signaling pathway in mare's endometrium infiltrated with the inflammatory cells

Endometritis is an important issue decreasing mares' fertility. In the case of endometritis both, inflammatory cells infiltration and proinflammatory molecules production are regulated by various cellular and gene-regulatory mechanisms, including the nuclear factor-κB (NF-κB) dependent pathway. NF-κB signaling pathway has been recently studied in the equine endometrium in the context of endometrosis. Thus, this study aimed to determine gene transcription of NF-κB subunits (RelA; NF-κB1; NF-κB2), proinflammatory molecules (MCP-1; IL-6), and hyaluronan synthases (HAS 1; HAS 2; HAS 3) in endometritis and compare them with the intensity and type of inflammatory cell infiltration. Endometrial samples, collected post-mortem from cyclic mares in estrus or diestrus, were classified histologically and examined using quantitative PCR. Transcription NF-κB subunits genes did not differ with either inflammatory intensity or type of inflammatory cell infiltration. Transcription of MCP-1 and IL-6 genes increased with the severity of inflammation, with the involvement of HAS 3 and HAS 2 genes, as opposed to HAS 1 genes. These proinflammatory molecules and hyaluronan synthases in the equine inflamed endometrium do not seem to be regulated by the NF-κB pathway. Hence, separate signaling pathways for the development and progression of equine endometritis and endometrosis may be suggested.

Characterization and Genome Study of Novel Lytic Bacteriophages against Prevailing Saprophytic Bacterial Microflora of Minimally Processed Plant-Based Food Products

The food industry is still searching for novel solutions to effectively ensure the microbiological safety of food, especially fresh and minimally processed food products. Nowadays, the use of bacteriophages as potential biological control agents in microbiological food safety and preservation is a promising strategy. The aim of the study was the isolation and comprehensive characterization of novel bacteriophages with lytic activity against saprophytic bacterial microflora of minimally processed plant-based food products, such as mixed leaf salads. From 43 phages isolated from municipal sewage, four phages, namely Enterobacter phage KKP 3263, Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 have lytic activity against Enterobacter ludwigii KKP 3083, Citrobacter freundii KKP 3655, Enterobacter cloacae KKP 3082, and Serratia fonticola KKP 3084 bacterial strains, respectively. Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) identified Enterobacter phage KKP 3263 as an Autographiviridae, and Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 as members of the Myoviridae family. Genome sequencing revealed that these phages have linear double-stranded DNA (dsDNA) with sizes of 39,418 bp (KKP 3263), 61,608 bp (KKP 3664), 84,075 bp (KKP 3262), and 148,182 bp (KKP 3264). No antibiotic resistance genes, virulence factors, integrase, recombinase, or repressors, which are the main markers of lysogenic viruses, were annotated in phage genomes. Serratia phage KKP 3264 showed the greatest growth inhibition of Serratia fonticola KKP 3084 strain. The use of MOI 1.0 caused an almost 5-fold decrease in the value of the specific growth rate coefficient. The phages retained their lytic activity in a wide range of temperatures (from -20 °C to 50 °C) and active acidity values (pH from 4 to 11). All phages retained at least 70% of lytic activity at 60 °C. At 80 °C, no lytic activity against tested bacterial strains was observed. Serratia phage KKP 3264 was the most resistant to chemical factors, by maintaining high lytic activity across a broader range of pH from 3 to 11. The results indicated that these phages could be a potential biological control agent against saprophytic bacterial microflora of minimally processed plant-based food products.

Equine Endometrosis Pathological Features: Are They Dependent on NF-κB Signaling Pathway?

Simple Summary

Endometrosis is a serious problem mainly affecting older mares’ fertility. Despite the importance of this disease, its etiology and pathogenesis are not fully known. Thus, no effective treatment exists to cease or restore degenerative processes and fibrogenesis in the mares’ endometria. The nuclear factor kappaB (NF-κB) is an important factor regulating cell metabolism. Nevertheless, it is also known to promote inflammation and fibrosis in various tissues and species, as well as in the mares’ endometria. The main goal was to bring new knowledge regarding endometrosis pathogenesis, which could allow for therapy development. Endometrial samples, collected postmortem from cyclic mares in estrus or diestrus, were classified histologically and used for gene expression assessment. Gene transcription of NF-κB subunits (subunit RelA—RelA; subunit 1—NF-κB1; subunit 2—NF-κB2), pro-inflammatory molecules (monocyte chemoattractant protein-1—MCP-1; interleukin-6—IL-6), and hyaluronan synthases (hyaluronan synthase 1—HAS 1; hyaluronan synthase 2—HAS 2; hyaluronan synthase 3—HAS 3) were compared among endometrosis types (active, non-active, destructive, non-destructive), according to the classification of Hoffmann and co-authors. These results suggest that activation of the NF-κB canonical pathway is involved especially in destructive endometrosis, the type when endometrial glands are damaged. These data give substantial information for further evaluations and treatment development.

Abstract

Endometrosis is an important mares’ disease which considerably decreases their fertility. As classic endometrial classification methods might be insufficient for tissue pathological evaluation, further categorization into active/inactive and destructive/non-destructive types was developed by Hoffmann and others. This study aimed to compare NF-κB pathway genes transcription among histopathological types of endometrosis, following Hoffmann and co-authors’ classification. Endometrial samples, collected postmortem from cyclic mares (n = 100) in estrus or diestrus, were classified histologically and used for gene transcription assessment. Gene transcription of NF-κB subunits (RelA, NF-κB1, NF-κB2), pro-inflammatory molecules (MCP-1, IL-6), and hyaluronan synthases (HAS 1, HAS 2, HAS 3) was compared among endometrosis types (active, non-active, destructive, non-destructive). Most individual mRNA samples showed high expression of RelA, NF-κB1, and MCP-1 gene transcripts and the destructive type of endometrosis, simultaneously. The expression of RelA and NF-κB1 genes was higher in active destructive group than in the other groups only in the follicular phase, as well as being higher in the inactive destructive group than in the others, only in the mid-luteal phase. The increase in gene transcription of the NF-κB canonical activation pathway in destructive endometrosis may suggest the highest changes in extracellular matrix deposition. Moreover, the estrous cycle phase might influence fibrosis pathogenesis.

Effect of High Hydrostatic Pressure on Stress-Related dnaK, hrcA, and ctsR Expression Patterns in Selected Lactobacilli Strains

Lactic acid bacteria (LAB) in the natural environment meet multiple stressors such as pH and temperature variations, increased nutrition and metabolite concentrations, harmful chemicals, acidic/oxidative conditions, osmotic pressure, and starvation. However, LAB strains are not subjected to high hydrostatic pressure (HHP) which currently is the most common non-thermal decontamination technology in the food industry. In this context, the LAB response to HHP is more difficult to identify compared to other stress-induced responses, and dnaK, ctsR, and hrcA can serve as essential regulators in this reaction. In the present study, the expression level of dnaK, ctsR, and hrcA mRNAs in 15 LAB strains after the HHP (300 MPa/5′) exposure was evaluated. As a result, the HHP-treatment affected the up-regulation of dnaK, ctsR, and hrcA in L. backii KKP 3565, L. backii KKP 3566, L. rhamnosus KKP 3570, L. brevis KKP 3575 strains, whereas, in L. plantarum KKP 3569, L. rhamnosus KKP 3571, L. brevis KKP 3573 all genes were lower expressed. The relative expression level of the dnaK, ctsR, and hrcA either before or after the pressure treatment for L. brevis DSM 6235, L. rhamnosus KKP 3572, L. brevis KKP 3574, L. brevis KKP 3576, L. rossiae KKP 3577, L. curvatus KKP 3578 strains were undetectable. Significant differences in the expression levels were observed, between the control and the HHP treatment strains for dnaK in L. backii KKP 3565, L. backii KKP 3566, L. plantarum KKP 3569, L. rhamnosus KKP 3570, L. rhamnosus KKP 3571, ctsR in, L. backii KKP 3565, L. rhamnosus KKP 3570, L. rhamnosus KKP 3571, and hrcA in L. plantarum KKP 3569, L. rhamnosus KKP 3571. Overall, the studied genes, dnaK, ctsR, and hrcA can be useful markers to indicate the LAB cellular response to HHP. These molecular parameters can help to optimize the desirable LAB growing conditions in industrial processes and to understand the complexity of the stress-related mechanism.

Time Evolution of Microbial Composition and Metabolic Profile for Biogenic Amines and Free Amino Acids in a Model Cucumber Fermentation System Brined with 0.5% to 5.0% Sodium Chloride

Salt concentrations in brine and temperature are the major environmental factors that affect activity of microorganisms and, thus may affect formation of biogenic amines (BAs) during the fermentation process. A model system to ferment cucumbers with low salt (0.5%, 1.5% or 5.0% NaCl) at two temperatures (11 or 23 °C) was used to study the ability of indigenous microbiota to produce biogenic amines and metabolize amino acid precursors. Colony counts for presumptive Enterococcus and Enterobacteriaceae increased by 4 and up to 2 log of CFU∙mL⁻¹, respectively, and remained viable for more than 10 days. 16S rRNA sequencing showed that Lactobacillus and Enterobacter were dominant in fermented cucumbers with 0.5% and 1.5% salt concentrations after storage. The initial content of BAs in raw material of 25.44 ± 4.03 mg∙kg⁻¹ fluctuated throughout experiment, but after 6 months there were no significant differences between tested variants. The most abundant BA was putrescine, that reached a maximum concentration of 158.02 ± 25.11 mg∙kg⁻¹. The Biogenic Amines Index (BAI) calculated for all samples was significantly below that needed to induce undesirable effects upon consumption. The highest value was calculated for the 23 °C/5.0% NaCl brine variant after 192 h of fermentation (223.93 ± 54.40). Results presented in this work indicate that possibilities to control spontaneous fermentation by changing salt concentration and temperature to inhibit the formation of BAs are very limited.

Transcriptional Regulation of the Multiple Resistance Mechanisms in Salmonella-A Review

The widespread use of antibiotics, especially those with a broad spectrum of activity, has resulted in the development of multidrug resistance in many strains of bacteria, including Salmonella. Salmonella is among the most prevalent causes of intoxication due to the consumption of contaminated food and water. Salmonellosis caused by this pathogen is pharmacologically treated using antibiotics such as fluoroquinolones, ceftriaxone, and azithromycin. This foodborne pathogen developed several molecular mechanisms of resistance both on the level of global and local transcription modulators. The increasing rate of antibiotic resistance in Salmonella poses a significant global concern, and an improved understanding of the multidrug resistance mechanisms in Salmonella is essential for choosing the suitable antibiotic for the treatment of infections. In this review, we summarized the current knowledge of molecular mechanisms that control gene expression related to antibiotic resistance of Salmonella strains. We characterized regulators acting as transcription activators and repressors, as well as two-component signal transduction systems. We also discuss the background of the molecular mechanisms of the resistance to metals, regulators of multidrug resistance to antibiotics, global regulators of the LysR family, as well as regulators of histone-like proteins.

Probiotics as a biological detoxification tool of food chemical contamination: A review

Nowadays, people are exposed to diverse environmental and chemical pollutants produced by industry and agriculture. Food contaminations such as persistent organic pollutants (POPs), heavy metals, and mycotoxins are a serious concern for global food safety with economic and public health implications especially in the newly industrialized countries (NIC). Mounting evidence indicates that chronic exposure to food contaminants referred to as xenobiotics exert a negative effect on human health such as inflammation, oxidative stress, and intestinal disorders linked with perturbation of the composition and metabolic profile of the gut microflora. Although the physicochemical technologies for food decontamination are utilized in many cases but require adequate conditions which are often not feasible to be met in many industrial sectors. At present, one promising approach to reduce the risk related to the presence of xenobiotics in foodstuffs is a biological detoxification done by probiotic strains and their enzymes. Many studies confirmed that probiotics are an effective, feasible, and inexpensive tool for preventing xenobiotic-induced dysbiosis and alleviating their toxicity. This review aims to summarize the current knowledge of the direct mechanisms by which probiotics can influence the detoxification of xenobiotics. Moreover, probiotic-xenobiotic interactions with the gut microbiota and the host response were also discussed.

Acute-phase proteins, cortisol and haematological parameters in ewes during the periparturient period

Numerous subclinical diseases in sheep occur in the periparturient period and involve inflammatory processes; therefore, determining markers, such as acute-phase proteins (APPs), can allow an early diagnosis. Therefore, the objective of the present study was to assess changes in the plasma concentration of APPs and cortisol in clinically healthy ewes in the periparturient period for use in future studies. At the same time, haematological parameters were monitored. We showed that plasma APPs and cortisol concentrations were significantly higher in pregnant ewes than before insemination. A gradual increase in the SAA concentration was observed from the 14th day before to the day of parturition, while Hp was reduced from 2 weeks before up to 2 weeks after delivery. A significant increase in the Fb concentration was detected from the 14th day before to the 1st week after delivery. The cortisol concentration did not undergo significant changes in the periparturient period. We found an increase in the SAA and Fb concentrations and decrease in Hp in the periparturient period. The direction of the change in APPs of healthy ewes in the current study may be related to their distinct regulatory mechanisms during pregnancy. The APPs are usually altered during infection, inflammation, neoplasia, stress and trauma; therefore, knowing their reference values could help lead to an early diagnosis of subclinical forms of some diseases and pregnancy complications in ewes. The haematological analysis showed that ewes in late pregnancy and postpartum compared to dry period were under metabolic stress related to pregnancy and lactation.

Association of CAST gene polymorphism with carcass value and meat quality in two synthetic lines of sheep

The aim of study was to estimate genotype frequencies of the polymorphism in the intron 12 of CAST gene of growing lambs, and to evaluate associations between the CAST genotype and carcass and meat traits. A total number of 317 rams representing the synthetic BCP (163) and SCP (154) meaty lines were genotyped by the RFLP/MspI/NcoI/Hin6I. Three genotypes including "aa", "ae" and "ac" with most frequencies of 0.48, 0.27 and 0.19, were observed in whole population. Lambs with the "aa" CAST genotype showed the highest muscle percentage and the lowest fat percentage in the hind legs. On the other hand, the loins of rams with "ac" genotype had the highest intramuscular fat content, indicative of beneficial health-related properties and technological usefulness. However, differences between CAST genotype stated for the sensory properties, texture and thawing and cooking losses of the meat were insignificant. Breeding efforts aimed at the improvement of lamb meat quality should prioritize the selection of the "ac" genotype.

Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq

Global gene expression in liver transcriptome varies among cattle breeds. The present investigation was aimed to identify the differentially expressed genes (DEGs), metabolic gene networks and metabolic pathways in bovine liver transcriptome of young bulls. In this study, we comparatively analyzed the bovine liver transcriptome of dairy (Polish Holstein Friesian (HF); n = 6), beef (Hereford; n = 6), and dual purpose (Polish-Red; n = 6) cattle breeds. This study identified 895, 338, and 571 significant (p < 0.01) differentially expressed (DE) gene-transcripts represented as 745, 265, and 498 hepatic DE genes through the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-HF versus Polish-Red breeds comparisons, respectively. By combining all breeds comparisons, 75 hepatic DE genes (p < 0.01) were identified as commonly shared among all the three breed comparisons; 70, 160, and 38 hepatic DE genes were commonly shared between the following comparisons: (i) Polish-Red versus Hereford and Polish-HF versus Hereford; (ii) Polish-Red versus Hereford and Polish-HF versus Polish-Red; and (iii) Polish-HF versus Hereford and Polish-HF versus Polish-Red, respectively. A total of 440, 82, and 225 hepatic DE genes were uniquely observed for the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-Red versus Polish-HF comparisons, respectively. Gene ontology (GO) analysis identified top-ranked enriched GO terms (p < 0.01) including 17, 16, and 31 functional groups and 151, 61, and 140 gene functions that were DE in all three breed liver transcriptome comparisons. Gene network analysis identified several potential metabolic pathways involved in glutamine family amino-acid, triglyceride synthesis, gluconeogenesis, p38MAPK cascade regulation, cholesterol biosynthesis (Polish-Red versus Hereford); IGF-receptor signaling, catecholamine transport, lipoprotein lipase, tyrosine kinase binding receptor (Polish-HF versus Hereford), and PGF-receptor binding, (Polish-HF versus Polish-Red). Validation results showed that the relative expression values were consistent to those obtained by RNA-seq, and significantly correlated between the quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson’s r  > 0.90). Our results provide new insights on bovine liver gene expressions among dairy versus dual versus beef breeds by identifying the large numbers of DEGs markers submitted to NCBI gene expression omnibus (GEO) accession number GSE114233, which can serve as useful genetic tools to develop the gene assays for trait-associated studies as well as, to effectively implement in genomics selection (GS) cattle breeding programs in Poland.

A porcine gluteus medius muscle genome-wide transcriptome analysis: dietary effects of omega-6 and omega-3 fatty acids on biological mechanisms

Background

The level of omega-6 and omega-3 polyunsaturated fatty acids can affect many cellular systems and function via nuclear receptors or the bioactive lipid regulation of gene expression. The objective of this study was to investigate changes in the muscle transcriptome and the biological functions regulated by increased consumption of omega-3 and omega-6 fatty acids in the pig gluteus medius muscle.

Results

The transcriptome of the gluteus medius muscle was studied for pigs subjected to either a control diet or a diet supplemented with linseed and rapeseed oil to increase polyunsaturated fatty acid content. Next-generation sequencing (NGS) was used to generate the muscle tissue transcriptome database pointing differentially expressed genes (DEG). Comparative expression analyses identified 749 genes significantly differing at least in the twofold of change between two groups of animals fed with divergent level of omega-3 and omega-6 fatty acids. The expression of 219 genes was upregulated, and the expression of 530 genes was downregulated in the group of pigs supplemented with omega-3 and omega-6 fatty acids in relation to control group pigs. Results of RNA-seq indicated a role of fatty acid in the regulation of the expression of genes which are essential for muscle tissue development and functioning. Functional analysis revealed that the identified genes were important for a number of biological processes including inflammatory response, signaling, lipid metabolism, and homeostasis.

Conclusions

Summarizing, obtained results provide strong evidence that omega-6 and omega-3 fatty acids regulate fundamental metabolic processes in muscle tissue development and functioning.

Electronic supplementary material

The online version of this article (doi:10.1186/s12263-017-0552-8) contains supplementary material, which is available to authorized users.

Study of bovine gene: the temporal-spatial expression patterns, polymorphism and association analysis with meat production traits

The gene () encodes a transcription factor belonging to the MEF2 family that plays an important role in myogenesis by transcriptional regulation of genes involved in skeletal muscle growth and development. Despite the established importance of the factors in the muscular growth and development, the temporal-spatial expression and biological function of have not been reported in cattle. The aim of this study was to analyze the level of expression in the developing longissimus dorsi muscle (LM) of 4 cattle breeds (Polish Holstein-Friesian [HF], Limousine [LIM], Hereford [HER], Polish Red [PR]), differing in terms of meat production and utility type, at 6, 9, and 12 mo of age. The genetic polymorphism and expression patterns in 6 tissues (heart, spleen, liver, semitendinosus muscle [ST], gluteus medius muscle [GM], and LM) were also investigated. The results showed that mRNA was expressed at a high level in adult skeletal and cardiac muscles. Moreover, expression was markedly greater in the GM than in the LM ( 0.05) and ST ( 0.01). An age-dependent and breed-specific comparison of mRNA level in skeletal muscle of HF, LIM, HER, and PR bulls showed that age was significant differentiating factor of transcript/protein abundance in the LM of HER and LIM ( 0.001) compared to HF and PR, for which the differences in mRNA level were not significant ( > 0.05). Regarding the breed effect on the expression, significantly greater mRNA/protein level was noticed in the LM of 9 and 12 mo-old HER than of LIM ( 0.01), HF ( 0.001), and PR ( 0.001). Four novel SNP, namely, (promoter), (exon 7), (exon 8), and (3'UTR), were identified. We found that 3'UTR variant, situated within the seed region of the miR-5187-3p and miR-6931-5p binding sites, was associated with the level of mRNA/protein in LM of 12-mo-old HF bulls. In addition, we observed a significant association between some carcass quality traits, including meat and carcass fatness quality traits, and various 3'UTR genotypes in the investigated population of HF cattle. Our finding provides new evidence of the significant role in the postnatal muscle growth and development in cattle, and indicates that can be a promising molecular marker for carcass quality-related traits in adult cattle.

Effect of Inorganic Dietary Selenium Supplementation on Selenoprotein and Lipid Metabolism Gene Expression Patterns in Liver and Loin Muscle of Growing Lambs

Effect of selenium (Se) supplementation on the selenoprotein and lipid metabolism gene expression patterns in ruminants, especially in lambs is not yet fully understood. The aim of study was to evaluate the effect of Se supplementation on the messenger RNA (mRNA) expression patterns of selected selenoproteins and genes related to lipid metabolism in growing lambs. The experiment was conducted on 48 Polish Merino lambs divided into two groups (n = 24): control (C)-lambs fed with a basal diet (BD) with no Se supplementation, and supplemented (S)-lambs fed with a BD, supplemented with 0.5 mg Se/kg as sodium selenate for 8 weeks. Expression of 12 selenoproteins and six genes related to lipid metabolism was analyzed in the liver and longissimus dorsi (LD) muscle of growing lambs by qPCR. Significant differences were found in the expression of GPX1, GPX2, SEPM, SEPW1, SEP15, SEPGS2, and TXNRD1 in the liver, and GPX1, SEPP1, SEPN1, SEPW1, SEP15, and MSRB1 in the LD muscle between S and C lambs. Se supplementation mainly upregulated SEPW1, SEP15 (P < 0.001; P < 0.01) mRNA expression in the liver, and GPX1, SEPP1, SEPN1, SEPW1 (P < 0.001; P < 0.01) in the muscle of S group. On the other hand, significant decrease in GPX2 (P < 0.01), SEPM (P < 0.001), and SEPHS2 (P < 0.01) mRNA expression levels were observed in the liver of S group of lambs. Se supplementation did not affect PON1, LXRα, and PPARα mRNA expression levels, but a significant increase in mRNA levels of APOE and LPL in the LD muscle (P < 0.05) as well as LPL (P < 0.05) in the liver were noticed in the group of Se supplemented lambs. Our study confirmed that, in lambs, similarly to other species, mRNA expression patterns of several selenoproteins highly depend on dietary Se levels, and their expression is ruled by hierarchical principles and tissue-specific mechanisms. Moreover, the study showed that changes Se intake leads to different levels of genes expression related with lipid metabolism.

Effect of a diet enriched with omega-6 and omega-3 fatty acids on the pig liver transcriptome

The optimal ratio of omega-6 to omega-3 polyunsaturated fatty acids (PUFAs) is important for keeping the homeostasis of biological processes and metabolism, yet the underlying biological mechanism is poorly understood. The objective of this study was to identify changes in the pig liver transcriptome induced by a diet enriched with omega-6 and omega-3 fatty acids and to characterize the biological mechanisms related to PUFA metabolism.

Polish Landrace pigs (n = 12) were fed diet enriched with linoleic acid (LA, omega-6) and α-linolenic acid (ALA, omega-3) or standard diet as a control. The fatty acid profiling was assayed in order to verify how feeding influenced the fatty acid content in the liver, and subsequently next-generation sequencing (NGS) was used to identify differentially expressed genes (DEG) between transcriptomes between dietary groups. The biological mechanisms and pathway interaction networks were identified using DAVID and Cytoscape tools. Fatty acid profile analysis indicated a higher contribution of PUFAs in the liver for LA- and ALA-enriched diet group, particularly for the omega-3 fatty acid family, but not omega-6. Next-generation sequencing identified 3565 DEG, 1484 of which were induced and 2081 were suppressed by PUFA supplementation. A low ratio of omega-6/omega-3 fatty acids resulted in the modulation of fatty acid metabolism pathways and over-representation of genes involved in energy metabolism, signal transduction, and immune response pathways.

In conclusion, a diet enriched with omega-6 and omega-3 fatty acids altered the transcriptomic profile of the pig liver and would influence animal health status.

Postnatal expression patterns and polymorphism analysis of the bovine myocyte enhancer factor 2C (Mef2C) gene

The aim of this study was to analyze the level of expression of the Mef2C gene in the developing bovine longissimus dorsi (LD) muscle (at 6, 9 and 12months of age) and to evaluate differences in expression among Polish Holstein-Friesian (HO) and Limousine (LM) bulls. Moreover, the expression patterns of Mef2C in different tissues were determined. The results showed that Mef2C mRNA was expressed at a high level in adult skeletal and cardiac muscles. Moreover, Mef2C expression was markedly lower in the semitendinosus (ST) than in the gluteus medius (GM) and LD muscles. A relatively higher Mef2C mRNA and MEF2C protein level was estimated in the muscles of HO bulls at the age of 12months in comparison with its lower expression in LM bulls. Furthermore, we found that the Mef2C promoter variant (GU211004:g.-1606C>T) does not affect the level of mRNA in the LD and ST muscles of 12-month-old HO bulls.

Effects of new polymorphisms in the bovine myocyte enhancer factor 2D (MEF2D) gene on the expression rates of the longissimus dorsi muscle

Myocyte enhancer factor 2D (MEF2D), a product of the MEF2D gene, belongs to the myocyte enhancer factor 2 (MEF2) protein family which is involved in vertebrate skeletal muscle development and differentiation during myogenesis. The aim of the present study was to search for polymorphisms in the bovine MEF2D gene and to analyze their effect on MEF2D mRNA and on protein expression levels in the longissimus dorsi muscle of Polish Holstein–Friesian cattle. Overall, three novel variations, namely, insertion/deletion g.−818_−814AGCCG and g.−211C<A transversion in the promoter region as well as g.7C<T transition in the 5′untranslated region (5′UTR), were identified by DNA sequencing. A total, 375 unrelated bulls belonging to six different cattle breeds were genotyped, and three combined genotypes (Ins-C-C/Ins-C-C, Del-A-T/Del-A-T and Ins-C-C/Del-A-T) were determined. The frequency of the combined genotype Ins-C-C/Ins-C-C and Del-A-T/Del-A-T was varied between the breeds and the average frequency was 0.521 and 0.037, respectively. Expression analysis showed that the MEF2D variants were highly correlated with MEF2D mRNA and protein levels in the longissimus dorsi muscle of Polish Holstein–Friesian bulls carrying the three different combined genotypes. The highest MEF2D mRNA and protein levels were estimated in the muscle of bulls with the Ins-C-C/Ins-C-C homozygous genotype as compared to the Del-A-T/Del-A-T homozygotes (P < 0.01) and Ins-C-C/Del-A-T heterozygotes (P < 0.05). A preliminary association study showed no significant differences in the carcass quality traits between bulls with various MEF2D combined genotypes in the investigated population of Polish Holstein–Friesian cattle.

Promoter variant-dependent mRNA expression of the MEF2A in longissimus dorsi muscle in cattle

The myocyte enhancer factor 2A (MEF2A) gene encodes a member of the myocyte enhancer factor 2 (MEF2) protein family that is involved in vertebrate skeletal, cardiac, and smooth muscle development and differentiation during myogenesis. According to recent studies, MEF2 genes might be major regulators of postnatal skeletal muscle growth; thus, they are considered to be important, novel candidates for muscle development and body growth in farm animals. The aim of the present study was to search for polymorphisms in the bovine MEF2A gene and analyze their effect on the MEF2A mRNA expression level in the longissimus dorsi muscle of Polish Holstein-Fresian cattle. In total, 4094 bp of the whole coding sequence and the promoter region of MEF2A were re-sequenced in 30 animals, resulting in the detection of 6 novel variants as well as one previously reported SNP. Three linked mutations in the promoter region (-780T/G, g.-768T/G, and g.-222A/G) and only two genotypes were identified in two Polish breeds (TTA/TTA and TTA/GGG). Three SNPs in the coding region [g.1599G/A (421aa), g.1626G/A (429aa), and g.1641G/A (434aa)] appeared to be silent substitutions and segregated as two intragene haplotypes: GGG and AAA. Expression analysis showed that the mutations in the promoter region are highly associated with the MEF2A mRNA level in the longissimus dorsi muscle of bulls carrying two different genotypes. The higher MEF2A mRNA level was estimated in the muscle of bulls carrying the TTA/TTA (p<0.01) genotype as compared with those with TTA/GGG. The results obtained suggest that the nucleotide sequence mutation in MEF2A might be useful marker for body growth traits in cattle.

Nucleotide sequence and variations of the bovine myocyte enhancer factor 2C (MEF2C) gene promoter in Bos taurus cattle

Myocyte Enhancer Factor 2 (MEF2) proteins are a small family of transcription factors that play pivotal role in morphogenesis and myogenesis of skeletal, cardiac, and smooth muscle cells. In vertebrates, there are four MEF2 genes, referred to as MEF2A, -B, -C, and -D, that are located on different chromosomes. After birth MEF2A, MEF2B, MEF2D transcriptions are expressed ubiquitously, whereas MEF2C transcripts are restricted to skeletal muscle, brain, and spleen. In this study, on the basis of the sequences of the bovine chromosome 7 genomic contig, available in the GenBank database, sets of PCR primers were designed and to amplify the bovine MEF2C gene promoter region, exon 1 (5′UTR) and part sequence of the intron 1. Seven overlapping fragments of the bovine MEF2C gene were amplified and then sequenced. Altogether, these fragments were composed in the 3,120-bp sequence which was deposited in the GenBank database under accession no. GU211007. The sequence fragment included the putative site of the promoter region and transcription start of the exon 1. The sequence analysis of these fragments in individual animals representing different Bos taurus breeds revealed four variations in promoter region: g.-1606C>T, g.-1336_-1335DelG, g.-818C>T, g.-613_-612DelA and four SNPs within intron 1: g.2711A>G, g. 2913A>G, g.2962G>T and g.3014A>G. No polymorphism was found within sequence of the exon 1 (5′UTR). These polymorphisms were identified for first time using these sequences and were confirmed by RFLP or MSSCP methods.

Impact of polymorphism of the regulatory subunit of the μ-calpain (CAPN1S) on the proteolysis process and meat tenderness of young cattle

The objective of this study was to estimate the impact of the polymorphism of μ-calpain (CAPN1S) gene on protein changes of the cattle muscle tissue and its tenderness during 10-day cold storage. The analysis was performed on the longest dorsal and lumbar muscles collected from 76 bulls 6 to 12 months of age. Polymorphism identification of the above-mentioned gene was conducted using the PCR-RFLP technique. Its effect on the course of the proteolysis process was assessed by monitoring changes in proportions of tissue proteins during 10-day process of meat ageing. Special attention was focused on changes in native titin (T1) share and products of its degradation (proteins of molecular weight (m.w.) of 2400 and 200 kDa), α-actinin and protein of 37 kDa as well as myosin heavy chains (MHC). In the case of the last proteins, their polymorphism was evaluated as well. Meat tenderness was estimated measuring the value of shear force and sensorially. The highest tenderness was ascertained for the heterozygote. Its improvement was associated with a significant decrease in proportions of proteins of molecular weight of approximately 37 kDa accompanied by an increase of those with 200 kDa molecular weight. Muscles derived from cattle of CT genotype were characterised by the highest proportions of type 2a MHC isoform. Value differences between proportions determined for the heterozygote and CC and TT homozygotes of the CAPN1S gene were statistically significant. Therefore, it can be presumed that the process of meat tenderisation was especially connected with MHC polymorphism.

A novel polymorphisms in intron 12 of the bovine calpastatin gene

Calpastatin (CAST) is a specific inhibitor of the ubiquitous calcium-dependent proteases-mu-calpain and m-calpain, found in mammalian tissues. This proteolytic system plays a key role in the tenderization process that occurs during post-mortem storage of meat under refrigerated conditioning. Fragments of the bovine CAST gene including intron 12 were amplified and subjected to SSCP analysis. Four new SNPs were found within intron 12 of the CAST gene: a transition T/C at position 3893+155* A/G at position 3893+163, a transversion T/A at position 3893+223 and a substitution A/G at position 3893+428 (consensus sequence--GenBank AY834771). The genetic variants in the bovine CAST gene can be analyzed with RFLP method and was studied in 375 bulls of six breeds, including Hereford, Aberdeen-angus, Simmental, Charolaise, Limousine and Polish Black-and-White (BW; Fresian) breeds.

Skeletal muscle and liver protein degradation in mice divergently selected for low and high body weight over 108 generations

Abstract. Experiment was carried out on 111 and 13-14 weeks old mice divergently selected for low (L) and high (C) body weight over 108 generations. In leg muscle and liver cathepsin D (CatD) was determined as pepstatin sensitive activity (PSCatD), and as pepstatin-insensitive (PIA) and leupeptin-insensitive (LIA) acid autolytic activities (AAA) were measured. In leg muscle and liver all measured activities were higher in L as compared to C and control (K) mice. The percent of inhibition of LIA was lower in L then C mice in both examined tissues. In the leg muscles, in L mice protein catabolism was mostly influenced by CatD, but in the liver CatD was mostly active in K mice. CatD, PSCatD, AAA and LIA in leg muscle of L mice as compare to K were higher in female (F) by 68 %, 68.5 %, 91.3 % and 94.5 %, respectively, and in male (M) mice by 43.4 %, 54 %, 47.1 % and 64 %, respectively. The percent of inhibition by leupeptin in AAA was higher in C mice by 61.9 % in F and by 40 % in M mice. In the liver, PIA was higher by about 45 % in L and by 28.5 % in C mice as compare to K ones. There were about 36% of 30.00-39.99 μm muscle fibrils in M mice and in males of L group 40.00-49.99 μm fibrils appeared at 25% (absent in 3 weeks mice). In female, all measured fibril diameters were in higher percent in L than in C group. RNA variables were higher by about 25% (in average) in C as compare to K and L groups. Functional cell size (FCS) was lowered in L and C group as compared to K by about 10 % (in average). These results indicate on faster proteins turnover in L than in C group of mice.

Bovine mu-calpain (CAPN1) gene: new SNP within intron 14

The calpain system originally comprised molecules: two Ca2+-dependent proteases, mu-calpain and m-calpain, and a third polypeptide, calpastatin, whose only known function is to inhibit the two calpains. This proteolytic system plays a key role in the tenderisation process that occurs during post-mortem storage of meat under refrigerated conditioning. Their polymorphism is examined from the point of view of their effect on corresponding production traits. The calpain genes are investigated as potential candidate genes for a quantitative trait locus (QTL) affecting meat tenderness. In this study a new single nucleotide polymorphism (SNP) was found within intron 14 of the bovine CAPN1 gene, being transition C --> T at position 4685 nt (consensus sequence - GenBank No. AF 248054), as this mutation creates a new FokI restriction site detected with PCR-RFLP analysis. This sequence fragment of the SNP position has already been deposited in the GenBank database under accession No. AY639597. The RFLP-FokI polymorphism was studied in 141 bulls of seven breeds, including the native Polish Red (PR, preserved), and Polish Black-and White (BW) breed. The frequency of alleles T and C varied between the breeds considered, the mean reaching 0.38 and 0.62, respectively. Associations between CAPN1/FokI gene polymorphism and meat production traits were studied in BW (n = 84) young bulls. In the animals of the TT genotype the lean share in valuable cuts (%) was found more favourable than in CC animals.