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One of the most promising ways to diagnose cancer especially colorectal cancer (CRC) is to trace its epigenetic events. In this article, a discovery step for detection of methylated DNA markers (MDMs) was performed using SureSelectXT Methyl-Seq in CRC case and control groups in addition to several methylation profiling datasets (GSE48684, GSE53051, GSE77718, GSE101764, and GSE42752). In silico validation of MDMs in colorectal and other cancers was conducted by Lnc2met. MethyLight assay was run on 40 and 47 case and control formalin-fixed paraffin-embedded tissues, respectively and the performance of selected genes were classified by support vector machine (SVM). As a result, 180 regions were identified among all common genes. In addition to SEPT9 and SFRP2, the best three MDM regions were selected from SLC30A10, AKR1B1 and GALNT14. Based on all assays, the best performance was accomplished by SEPT9/AKR1B1 with 98% sensitivity, 99% specificity, 125 positive likelihood ratio, 0.02 negative likelihood ratio and 5074 diagnostic odds ratio. Our results indicate that the AKR1B1/SEPT9 methylation panel detects CRC with a higher performance than SEPT9 methylation, which is a commercial diagnostic test for CRC. However, the creation of a clinically valuable test derived from this study requires performance evaluation in liquid biopsies.

One of the most effective methods for increasing the antimicrobial activity of a substance is to combine it with one or more other antimicrobial agents. The aim of the present study was to evaluate the antimicrobial effect of buforin I and nisin alone and investigate the synergistic action of these compounds against the most important food spoilage microorganisms in clouding B. subtilis, S. epidermidis, L. innocua, E. coli, S. Enteritidis, A. oryzae, R. glutinis and G. candidum. The results of MIC and MBC/MFC examinations showed that buforin I had higher antimicrobial activity than nisin on all the microbial strains used in this study (p≤0.5). E.coli was the most resistant to both antimicrobial agents, while Listeria innocua and Staphylococcus epidermidis were the most sensitive to nisin and buforin I, respectively. The results of synergistic interaction between buforin I and nisin indicated that the combination of buforin I and nisin on B. subtilis, S. epidermidis and A. oryzae showed synergistic effect, while it had no effect on S. Enteritidis and Geotrichum candidum. The combination of buforin I and nisin showed partial synergistic effect on Listeria innocua, Escherichia coli, Rhodotorula glutinis. Assessment of viability of the microorganisms under the antimicrobial agents alone and in combination with each other at MICs and FICs indicated that use of these antimicrobial agents in combination enhances antimicrobial activity at lower concentrations of both agents. The present study investigated the antimicrobial properties of buforin I against food spoilage microorganisms for the first time and suggests that its use alone or in combination with nisin may provide a clear horizon for the application of antimicrobial peptides as natural preservatives. Thus, the combination of antimicrobial peptides and traditional antimicrobial food preservative could be a promising option for the prevention of contamination, spoilage, and infestation of food and beverage products.

The production of polysaccharides derived from lactic acid bacteria (LAB) can be a valuable alternative to current polysaccharides. In this study, eight samples of Kishk (traditional dairy product) were collected in sterile conditions and directly cultured on MRS agar medium. Following purification and examination of microscopic, macroscopic characteristics and doing biochemical tests, 143 isolates were selected, and the production of exopolysaccharide (EPS) was investigated by the ruthenium red and disc methods. The EPS production of 79 isolates was confirmed. Total carbohydrate of EPS was determined by the phenol sulfuric acid method. Finally, Enterococcus durans K48, Enterococcus faecium R114, and Enterococcus faecium T52 strains were selected as the best EPS producers. The optimization of EPS production was then performed using Central Composite Design (CCD) and Response Surface Methodology (RSM) approaches. Optimization plots showed the highest EPS yield for E. durans K48, E. faecium R114, and E. faecium T52 occurred at 38.4, 37.4 and 36.7 °C and pH of 5.9, 5.6 and 5.8, respectively, cultured in a Sucrose-MRS medium. Under optimal conditions, the maximum predicted and actual production of EPSs for the examined isolates were 3.18, 3.21, 2.99 and 3.02, 3.15, 3.15, g L, respectively. As determined by Gel Permeation Chromatography, the EPSs molecular weights were in the range of 2.93 × 10 to 3.52 × 10 Da. Analysis of the component monosaccharides by HPLC showed that all three tested EPSs were heteropolysaccharides. After appropriate evaluation, the EPSs produced by native species of LAB isolated from Iranian Kishk could be of interest for industrial applications or as functional food ingredients., This work was financially supported by a grant (No. 3/47333) from the Ferdowsi University of Mashhad (Research Affairs), Iran.

In most bacteria, Glutamate decarboxylase (GAD) activity significantly reduces at pH > 6. Since l -glutamate is neutral to slightly alkaline, a large amount of hydrochloric acid must be added to the reaction mixture. Acidic reaction conditions greatly increase the corrosion of production equipment and shorten the life of manufacturing equipment. Therefore, this study aims at studying the overexpression of recombinant GAD that is active at the neutral pH and high-level production of γ-aminobutyric acid. A gene sequence encoding GAD of Enterococcus faecium DO was cloned into PET21a (+) and was overexpressed in Escherichia coli BL21 (DE3). The construct was confirmed by colony PCR and double digested with BamHI and XhoI. The result from Western blot analysis showed a signal band at the molecular mass of 54 kDa. The specific activity of the recombinant GAD was 78.17 U mg−1 at 45 °C and pH = 6.6. It was reduced rapidly when pH > 7.8. The Km, Vmax, and kcat values of recombinant GAD were 1.8 mM, 12.9 μmol L−1 min−1, and 0.43 s−1, respectively. Therefore, recombinant GAD is a potent candidate for GABA production in food and pharmaceutical industries, because it increases the efficiency of GABA synthesis, especially in foods with a neutral pH range.

A large number of genome-wide association studies (GWAS) in livestock, especially in dairy cows, provide favorable conditions to integrate multiple independent studies. Methods such as meta-analysis provide the identification of effective QTLs with higher precision and power. A meta-analysis for milk production traits between different countries was conducted using the GWAS summary statistics (i.e., P-value, sample size, allele effects, and etc.) in Holstein cows. In the present study, METAL software was used for the weighted Z-score model. Gene network analysis was used as a complementary method to improve our knowledge of the genome structure of milk production traits and was implemented through the STRING plug-in in Cytoscape software. The Cytoscape ClueGO plug-in was also used for GO enrichment in order to identify biological process, cellular component, and molecular function associated with genomic regions. The aim of this study was to improve the power of QTLs detection and identify the biological mechanisms associated with milk production traits. Data were obtained from 26 published studies from 2010 to 2019. A total of 2,072 SNPs were identified for milk production traits, of which 1,583 SNPs were significant ( P 0.05 ). Meta-analysis identified 9 QTLs for milk yield, 36 QTLs for fat percentage, and 10 QTLs for protein percentage. Some QTLs were confirmed on BTA14, e.g., BTA14:1801116 close to the DGAT1 gene (milk yield, P = 2.6 × 10 − 131 ; fat percentage, P = 4.8 × 10 − 347 ; protein percentage, P = 7.6 × 10 − 24 ) and BTA14:1651311 close to the PPP1R16A gene (milk yield, P = 2.3 × 10 − 162 ; fat percentage, P = 3.5 × 10 − 153 ). We identified pleiotropic effects of lead SNPs for milk production traits, e.g., one SNP (rs109421300) at BTA14 had pleiotropic effects on milk yield, fat percentage, and protein percentage traits. The most important SNPs for studied traits across countries implicated to network scoring and visualization were including: rs109421300 (DGAT1 gene) for milk yield, fat percentage, and protein percentage; rs109146371 (PPP1R16A gene) for milk yield and fat percentage; rs109968515 (CYHR1 gene) for milk yield and fat percentage; rs134432442 (CPSF1 gene) for fat percentage; rs111018678 (TRAPPC9 gene) for protein percentage. Significant pathways involved in milk production traits through GO term enrichment analysis for biological process, cellular component, and molecular function included: regulation of cation channel activity ( P = 1.6 × 10 − 2 ), ion channel complex ( P = 1.4 × 10 − 2 ), and phosphoric diester hydrolase activity ( P = 1.1 × 10 − 3 ) for milk yield; negative regulation of organ growth ( P = 8.2 × 10 − 3 ), transmembrane transporter complex ( P = 1.6 × 10 − 3 ), and potassium ion transmembrane transporter activity ( P = 8.8 × 10 − 3 ) for fat percentage; mRNA polyadenylation ( P = 1.2 × 10 − 2 ), mRNA cleavage factor complex ( P = 9.8 × 10 − 4 ), and phosphoric diester hydrolase activity ( P = 5.3 × 10 − 3 ) for protein percentage, respectively. Thus, the combination of GWAS summary statistics through a powerful methodology such as meta-analysis will assist us to accurately identify QTLs, potential candidate genes, and biological mechanisms. This kind of studies will help us to have better understanding of QTL regions and genome structure for milk production traits and improve genomic evaluations in Holstein cows. To the best of our knowledge, this is the first meta-analysis of GWAS and GO enrichment across countries for milk production traits in Holstein cows.

The identification of animal species used in industrial meat products is very important in respect to economic considerations because European Union, which has implemented a set of very strict procedures to correctly label food. In this paper we present conserved region from mitochondrial 12S rRNA and 16S rRNA genes are powerful region for evaluate the presence of fraudulently added meat in compound food by multiplex polymerase chain reaction assay for the identification of most species (ruminant, poultry and porcine). For each food sources (ground meat, sausages and cold cut) 10 samples were collected and DNA extracted successfully. The results demonstrated that none of the samples were contaminated with porcine residuals, but 40% of sausages samples and 30% of cold cut samples were contaminated with poultry residuals. Also the ground meat samples were not contaminated with poultry residuals.