Analysis of cattle olfactory subgenome: the first detail study on the characteristics of the complete olfactory receptor repertoire of a ruminant

BACKGROUND: Mammalian olfactory receptors (ORs) are encoded by the largest mammalian multigene family. Understanding the OR gene repertoire in the cattle genome could lead to link the effects of genetic differences in these genes to variations in olfaction in cattle. RESULTS: We report here a whole genome analysis of the olfactory receptor genes of Bos taurus using conserved OR gene-specific motifs and known OR protein sequences from diverse species. Our analysis, using the current cattle genome assembly UMD 3.1 covering 99.9% of the cattle genome, shows that the cattle genome contains 1,071 OR-related sequences including 881 functional, 190 pseudo, and 352 partial OR sequences. The OR genes are located in 49 clusters on 26 cattle chromosomes. We classified them into 18 families consisting of 4 Class I and 14 Class II families and these were further grouped into 272 subfamilies. Comparative analyses of the OR genes of cattle, pigs, humans, mice, and dogs showed that 6.0% (n = 53) of functional OR cattle genes were species-specific. We also showed that significant copy number variations are present in the OR repertoire of the cattle from the analysis of 10 selected OR genes. CONCLUSION: Our analysis revealed the almost complete OR gene repertoire from an individual cattle genome. Though the number of OR genes were lower than in pigs, the analysis of the genetic system of cattle ORs showed close similarities to that of the pig

Characterization of Cronobacter sakazakii Strains Originating from Plant-Origin Foods Using Comparative Genomic Analyses and Zebrafish Infectivity Studies

Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours, dairy powders, cereals, nuts, and spices, in addition to the conventional sources of powdered infant formulae (PIF) and PIF production environments. To understand the sequence diversity, phylogenetic relationship, and virulence of C. sakazakii originating from plant-origin foods, comparative molecular and genomic analyses, and zebrafish infection (ZI) studies were applied to 88 strains. Whole genome sequences of the strains were generated for detailed bioinformatic analysis. PCR analysis showed that all strains possessed a pESA3-like virulence plasmid similar to reference C. sakazakii clinical strain BAA-894. Core genome analysis confirmed a shared genomic backbone with other C. sakazakii strains from food, clinical and environmental strains. Emerging nucleotide diversity in these plant-origin strains was highlighted using single nucleotide polymorphic alleles in 2000 core genes. DNA hybridization analyses using a pan-genomic microarray showed that these strains clustered according to sequence types (STs) identified by multi-locus sequence typing (MLST). PHASTER analysis identified 185 intact prophage gene clusters encompassing 22 different prophages, including three intact Cronobacter prophages: ENT47670, ENT39118, and phiES15. AMRFinderPlus analysis identified the CSA family class C β-lactamase gene in all strains and a plasmid-borne mcr-9.1 gene was identified in three strains. ZI studies showed that some plant-origin C. sakazakii display virulence comparable to clinical strains. Finding virulent plant-origin C. sakazakii possessing significant genomic features of clinically relevant STs suggests that these foods can serve as potential transmission vehicles and supports widening the scope of continued surveillance for this important foodborne pathogen

Age-Related Changes in the Characteristics of the Elderly Females Using the Signal Features of an Earlobe Photoplethysmogram

Non-invasive measurement of physiological parameters and indicators, specifically among the elderly, is of utmost importance for personal health monitoring. In this study, we focused on photoplethysmography (PPG), and developed a regression model that calculates variables from the second (SDPPG) and third (TDPPG) derivatives of the PPG pulse that can observe the inflection point of the pulse wave measured by a wearable PPG device. The PPG pulse at the earlobe was measured for 3 min in 84 elderly Korean women (age: 71.19 ± 6.97 years old). Based on the PPG-based cardiovascular function, we derived additional variables from TDPPG, in addition to the aging variable to predict the age. The Aging Index (AI) from SDPPG and Sum of TDPPG variables were calculated in the second and third differential forms of PPG. The variables that significantly correlated with age were c/a, Tac, AI of SDPPG, sum of TDPPG, and correlation coefficient ‘r’ of the model. In multiple linear regression analysis, the r value of the model was 0.308, and that using deep learning on the model was 0.839. Moreover, the possibility of improving the accuracy of the model using supervised deep learning techniques, rather than the addition of datasets, was confirmed

Antibiotic Susceptibility, Genetic Diversity, and the Presence of Toxin Producing Genes in Campylobacter Isolates from Poultry

This study examined antibiotic susceptibility, genetic diversity, and characteristics of virulence genes in Campylobacter isolates from poultry. Chicken (n = 152) and duck (n = 154) samples were collected from 18 wet markets in Korea. Campylobacter spp. isolated from the carcasses were identified by PCR. The isolated colonies were analyzed for antibiotic susceptibility to chloramphenicol, amikacin, erythromycin, tetracycline, ciprofloxacin, nalidixic acid, and enrofloxacin. The isolates were also used to analyze genetic diversity using the DiversiLabTM system and were tested for the presence of cytolethal distending toxin (cdt) genes. Campylobacter spp. were isolated from 45 poultry samples out of 306 poultry samples (14.7%) and the average levels of Campylobacter contamination were 22.0 CFU/g and 366.1 CFU/g in chicken and duck samples, respectively. Moreover, more than 90% of the isolates showed resistance to nalidixic acid and ciprofloxacin. Genetic correlation analysis showed greater than 95% similarity between 84.4% of the isolates, and three cdt genes (cdtA, cdtB, and cdtC) were present in 71.1% of Campylobacter isolates. These results indicate that Campylobacter contamination should be decreased to prevent and treat Campylobacter foodborne illness

Effects of plant-based heat killed lactic acid bacteria and its lithium chloride-extracted cellular protein on high-fat-induced obesity

The anti-obesity action of postbiotics derived from plant-based probiotics remains unclear. The effects of heat killed lactic acid bacteria (Lactobacillus plantarum, LPHK and Lactobacillus curvatus, LCHK) along with bioactive their cell envelop components known as surface layer proteins (SLPs, LPSLP, and LCSLP) on obesity were investigated. LPHK, LCHK, LPSLP, and LCSLP significantly reduced lipid accumulation in 3T3-L1 adipocytes, concurrently regulating the expression of adipogenic genes. Notably, LPHK demonstrated significant improvements in high-fat (HF)-induced body weight gain, adipose tissue weight gain, liver weight gain, and reduced plasma concentrations of triglyceride, total-cholesterol, and LDL-cholesterol in C57BL/6J mice. Additionally, LPHK significantly regulated the expression of genes related to adipogenesis and anti-apoptosis. Moreover, while LPSLP significantly reduced liver weight, plasma triglyceride and LDL-cholesterol concentrations, and upregulated genes associated with hepatic fatty acid oxidation, it did not affect the body weight and adipose tissue weight gain. These results suggest that additional components other than SLP are necessary for the anti-obesity action of LPHK. In conclusion, non-viable plant-based LPHK can be used as a naturally occurring product for preventing obesity, especially in individuals with immunocompromised conditions

Characterization of Cronobacter sakazakii Strains Originating from Plant-Origin Foods Using Comparative Genomic Analyses and Zebrafish Infectivity Studies

Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours, dairy powders, cereals, nuts, and spices, in addition to the conventional sources of powdered infant formulae (PIF) and PIF production environments. To understand the sequence diversity, phylogenetic relationship, and virulence of C. sakazakii originating from plant-origin foods, comparative molecular and genomic analyses, and zebrafish infection (ZI) studies were applied to 88 strains. Whole genome sequences of the strains were generated for detailed bioinformatic analysis. PCR analysis showed that all strains possessed a pESA3-like virulence plasmid similar to reference C. sakazakii clinical strain BAA-894. Core genome analysis confirmed a shared genomic backbone with other C. sakazakii strains from food, clinical and environmental strains. Emerging nucleotide diversity in these plant-origin strains was highlighted using single nucleotide polymorphic alleles in 2000 core genes. DNA hybridization analyses using a pan-genomic microarray showed that these strains clustered according to sequence types (STs) identified by multi-locus sequence typing (MLST). PHASTER analysis identified 185 intact prophage gene clusters encompassing 22 different prophages, including three intact Cronobacter prophages: ENT47670, ENT39118, and phiES15. AMRFinderPlus analysis identified the CSA family class C β-lactamase gene in all strains and a plasmid-borne mcr-9.1 gene was identified in three strains. ZI studies showed that some plant-origin C. sakazakii display virulence comparable to clinical strains. Finding virulent plant-origin C. sakazakii possessing significant genomic features of clinically relevant STs suggests that these foods can serve as potential transmission vehicles and supports widening the scope of continued surveillance for this important foodborne pathogen

Analysis of expressions of deglutamylases (<i>CCP1</i>, <i>Ccp4</i>, <i>CCP5</i>, <i>and CCP6</i>) in testes and ovaries of <i>pcd</i>^<i>3J+/+</i> and <i>pcd^3J-/-</i> mice using semi-quantitative RT-PCR.

<p>The double bands for <i>Ccp4</i> indicate two alternatively spliced forms of <i>Ccp4</i>. <i>Gapdh</i> was used as a quantitative control.</p