Pedigree analysis of Korean native chickens: unraveling inbreeding and genetic diversity.

This study assessed the trends in inbreeding, effective population size, and genetic diversity across six Korean native chicken lines using pedigree records from 54,383 chickens. Understanding these genetic parameters is significantly important for maintaining healthy and viable chicken populations. The primary objective was to analyze the pedigree data to assess the levels of inbreeding and genetic diversity and to evaluate the effective population size across the different lines. Pedigree analysis revealed that pedigree completeness peaked in the first generation and declined in subsequent generations for all lines. Line A exhibited a mean inbreeding coefficient of 0.0201, whereas the other lines displayed lower mean values ranging from 0.0009 to 0.0098, indicating that inbreeding levels were within an acceptable range and considered safe from extinction. Average relatedness consistently increased with time. Individual increases in inbreeding were the highest in Line A (0.62%), with smaller increases in the other lines ranging from 0.02 to 0.23%. Effective population sizes varied from 81 to 2500, with average coancestry within parental populations ranging from 0.0032 to 0.0290. The fe/fa ratio between 1.00 and 1.69 in the 6 lines suggested a moderate impact during bottleneck events, with subsequent populations recovering well. The genetic diversity loss due to genetic drift and unequal founder contributions ranged from 0.66-3.15%, indicating that considerable genetic variability remains within the populations. The results of this study have practical applications in the management and conservation of genetic resources in poultry breeding programs. By highlighting the importance of monitoring inbreeding and maintaining genetic diversity, the findings can help develop strategies to ensure the long-term sustainability of these chicken lines. This study provides valuable insights into the genetic management of Korean native chicken lines, emphasizing the need for strategic breeding practices to preserve genetic health and diversity.

Does Religion Mitigate the Effect of Neighborhood Disorder on Cognitive Decline?: Evidence from A National Longitudinal Study of US Older Adults.

OBJECTIVES: This paper examines whether perceived neighborhood disorder is associated with trajectories of cognitive functioning and whether religion mitigates this association among US older adults. METHODS: Data are drawn from the 2006-2016 Health and Retirement Study (N=12,669). Religious belief and religious attendance are assessed as potential moderators. Growth curve models are used to estimate trajectories of cognitive functioning over time. RESULTS: We find that perceived neighborhood disorder is associated with lower cognitive functioning at baseline; however, religious belief mitigates the impact of perceived neighborhood disorder on the level of cognitive functioning. For instance, individuals with high religious belief, despite experiencing high perceived neighborhood disorder, show better cognitive functioning at baseline compared to those with high disorder but low belief. While frequent religious attendance is associated with higher cognitive functioning at baseline, it does not moderate the impact of perceived neighborhood disorder on cognitive functioning. DISCUSSION: This study underscores the protective role of religious belief against cognitive aging in the face of neighborhood disorder, suggesting that personal faith may provide a cognitive reserve or coping mechanism. Our findings also imply that the absence of religious belief, combined with high perceived neighborhood disorder, may produce a compounded negative impact on cognitive aging.

Comparative genomics of Deinococcus radiodurans: unveiling genetic discrepancies between ATCC 13939K and BAA-816 strains.

The Deinococcus genus is renowned for its remarkable resilience against environmental stresses, including ionizing radiation, desiccation, and oxidative damage. This resilience is attributed to its sophisticated DNA repair mechanisms and robust defense systems, enabling it to recover from extensive damage and thrive under extreme conditions. Central to Deinococcus research, the D. radiodurans strains ATCC BAA-816 and ATCC 13939 facilitate extensive studies into this remarkably resilient genus. This study focused on delineating genetic discrepancies between these strains by sequencing our laboratory's ATCC 13939 specimen (ATCC 13939K) and juxtaposing it with ATCC BAA-816. We uncovered 436 DNA sequence differences within ATCC 13939K, including 100 single nucleotide variations, 278 insertions, and 58 deletions, which could induce frameshifts altering protein-coding genes. Gene annotation revisions accounting for gene fusions and the reconciliation of gene lengths uncovered novel protein-coding genes and refined the functional categorizations of established ones. Additionally, the analysis pointed out genome structural variations due to insertion sequence (IS) elements, underscoring the D. radiodurans genome's plasticity. Notably, ATCC 13939K exhibited a loss of six ISDra2 elements relative to BAA-816, restoring genes fragmented by ISDra2, such as those encoding for α/ß hydrolase and serine protease, and revealing new open reading frames, including genes imperative for acetoin decomposition. This comparative genomic study offers vital insights into the metabolic capabilities and resilience strategies of D. radiodurans.

Biodegradation of oxidized low density polyethylene by Pelosinus fermentans lipase.

Polyethylene (PE) exhibits high resistance to degradation, contributing to plastic pollution. PE discarded into the environment is photo-oxidized by sunlight and oxygen. In this study, a key enzyme capable of degrading oxidized PE is reported for the first time. Twenty different enzymes from various lipase families were evaluated for hydrolytic activity using substrates mimicking oxidized PE. Among them, Pelosinus fermentans lipase 1 (PFL1) specifically cleaved the ester bonds within the oxidized carbon-carbon backbone. Moreover, PFL1 (6 µM) degraded oxidized PE film, reducing the weight average and number average molecular weights by 44.6 and 11.3 %, respectively, within five days. Finally, structural analysis and molecular docking simulations were performed to elucidate the degradation mechanism of PFL1. The oxidized PE-degrading enzyme reported here will provide the groundwork for advancing PE waste treatment technology and for engineering microbes to repurpose PE waste into valuable chemicals.

Characteristics of Purified Horse Oil by Supercritical Fluid Extraction with Different Deodorants Agents.

This study investigated the impact of activated carbon, palm activated carbon, and zeolite on horse oil (HO) extracted from horse neck fat using supercritical fluid extraction with deodorant-untreated HO (CON) as a comparison. The yield and lipid oxidation of deodorant untreated HO (CON) were not significantly affected by the three deodorants. However, deodorant-treated HOs exhibited significantly elevated levels of α-linolenic acid (C18:3n3) and eicosenoic acid (C20:1n9) compared to CON (p<0.05), while other fatty acids remained consistent. Zeolite-purified HO demonstrated significantly lower levels of volatile organic compounds (VOCs) than other treatments (p<0.05). Remarkably, zeolite decreased the concentration of pentane, 2,3-dimethyl (gasoline odor), by over 90%, from 177.17 A.U. ×106 in CON to 15.91 A.U. ×106. Zeolite also effectively eliminates sec-butylamine (ammonia and fishy odor) as compared to other deodorant-treated HOs (p<0.05). Additionally, zeolite reduced VOCs associated with the fruity citrus flavor, such as nonanal, octanal, and D-limonene in HO (p<0.05). This study suggests that integrating zeolite in supercritical fluid extraction enhances HO purification by effectively eliminating undesirable VOCs, presenting a valuable approach for producing high-quality HO production in the cosmetic and functional food industries.

Characterization of a unique pH-dependent amylosucrase from Deinococcus cellulosilyticus.

The amylosucrase (ASase, EC 2.4.1.4) utilizes sucrose as the sole substrate to catalyze multifunctional reactions. It can naturally synthesize α-1,4-linked glucans such as amylose as well as sucrose isomers with more favorable properties than sucrose with a lower intestinal digestibility and non-cariogenic properties. The amino acid sequence of the asase gene from Deinococcus cellulosilyticus (DceAS) exhibits low homology with those of other ASases from other Deinococcus species. In this study, we cloned and expressed DceAS and demonstrated its high activity at pH 6 and pH 8 and maintained stability. It showed higher polymerization activity at pH 6 than at pH 8, but similar isomerization activity and produced more turanose and trehalulose at pH 6 than at pH 8 and produced more isomaltulose at pH 8. Furthermore, the molecular weight of DceAS was 226.6 kDa at pH 6 and 145.5 kDa at pH 8, indicating that it existed as a trimer and dimer, respectively under those conditions. Additionally, circular dichroism spectra showed that the DceAS secondary structure was different at pH 6 and pH 8. These differences in reaction products at different pHs can be harnessed to naturally produce sucrose alternatives that are more beneficial to human health.

A genome-wide association study on growth traits of Korean commercial pig breeds using Bayesian methods.

OBJECTIVE: This study aims to identify the significant regions and candidate genes of growth-related traits (adjusted backfat thickness [ABF], average daily gain [ADG], and days to 90 kg [DAYS90]) in Korean commercial GGP pig (Duroc, Landrace, and Yorkshire) populations. METHODS: A genome-wide association study (GWAS) was performed using single-nucleotide polymorphism (SNP) markers for imputation to Illumina PorcineSNP60. The BayesB method was applied to calculate thresholds for the significance of SNP markers. The identified windows were considered significant if they explained ≥1% genetic variance. RESULTS: A total of 28 window regions were related to genetic growth effects. Bayesian GWAS revealed 28 significant genetic regions including 52 informative SNPs associated with growth traits (ABF, ADG, DAYS90) in Duroc, Landrace, and Yorkshire pigs, with genetic variance ranging from 1.00% to 5.46%. Additionally, 14 candidate genes with previous functional validation were identified for these traits. CONCLUSION: The identified SNPs within these regions hold potential value for future markerassisted or genomic selection in pig breeding programs. Consequently, they contribute to an improved understanding of genetic architecture and our ability to genetically enhance pigs. SNPs within the identified regions could prove valuable for future marker-assisted or genomic selection in pig breeding programs.

The impact of overnight lairage on meat quality and storage stability of pork loin.

Lairage, a part of the animal welfare practices, has been known to mitigate pre-slaughter stress in animals. However, research investigating the relationship between lairage and pork meat quality remains scarce. In this study, we conducted a comparative analysis of the physicochemical quality and storage stability of pork from pigs subjected to immediate slaughter (CON) and those provided with a 24 h lairage before slaughter (LRG) over a 7-day storage period. The loins from 20 castrated pigs in each group, respectively, were collected at 1, 3, 5, and 7 days and used for analysis of meat quality and storage stability, including pH, meat color, moisture, water holding capacity, drip loss, cooking loss, shear force, fatty acid composition, lipid oxidation, antioxidant activity, and electrical resistance. Overall, there were no significant differences in physicochemical meat quality parameters between CON and LRG groups. Similarly, no differences were observed in the storage stability of pork including 2-thiobarbituric acid reactive substances, 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity and electrical resistance. However, the proportion of unsaturated fatty acids was significantly higher in LRG compared to CON. In conclusion, 24 h lairage for castrated pigs had limited impact on meat quality and storage stability but led to an increase in the unsaturated fatty acid proportion.

The results of meat quality traits and sensory characteristics according to the concentration of androstenone in uncastrated pigs.

Pork quality is determined by several attributes, among which odor and taste are the utmost significant. Therefore, this study was aimed to assess the effects of boar odor hormone concentration on the quality traits and sensory acceptability of pork. A total twenty-six (26) non-castrated 3-way crossbred (Landrace × Yorkshire × Duroc) pigs were selected with an average body weight (ABW) 115.6 kg before to slaughter. The three treatment groups (low, medium and high) were divided according to the androstenone concentration. In experiment 1, for meat quality traits carcass was selected based on androstenone concentration: low (LC, 0.64-0.69 µg/g, n = 9), medium (MC, 0.70-0.99 µg/g, n = 7) and high (HC, 1.00-1.69 µg/g, n = 10). In experiment 2, for sensory evaluation carcasses were also selected based on the abovementioned conditions. Results revealed that androstenone concentration not effect on proximate components, meat quality traits and fatty acids except palmitoleic acid. Sensory evaluation data showed that boar taint and meat boar taint were significantly increased in a concentration-dependent manner from low to high, whereas, gravy and meat flavor preference were significantly increased in LC group than HC group. In addition, correlation analysis showed that boar taint and meat boar taint were positively, and gravy and meat flavor preference were negatively correlated with boar taint hormones. In essence, our findings indicate that androstenone concentration had no effect on meat qualities, but a high concentration of androstenone had a negative effect on the sensory characteristics in uncastrated pigs.

From microbes to molecules: a review of microbial-driven antioxidant peptide generation.

Oxidative stress, arising from excess reactive oxygen species (ROS) or insufficient antioxidant defenses, can damage cellular components, such as lipids, proteins, and nucleic acids, resulting in cellular dysfunction. The relationship between oxidative stress and various health disorders has prompted investigations into potent antioxidants that counteract ROS's detrimental impacts. In this context, antioxidant peptides, composed of two to twenty amino acids, have emerged as a unique group of antioxidants and have found applications in food, nutraceuticals, and pharmaceuticals. Antioxidant peptides are sourced from natural ingredients, mainly proteins derived from foods like milk, eggs, meat, fish, and plants. These peptides can be freed from their precursor proteins through enzymatic hydrolysis, fermentation, or gastrointestinal digestion. Previously published studies focused on the origin and production methods of antioxidant peptides, describing their structure-activity relationship and the mechanisms of food-derived antioxidant peptides. Yet, the role of microorganisms hasn't been sufficiently explored, even though the production of antioxidant peptides frequently employs a variety of microorganisms, such as bacteria, fungi, and yeasts, which are recognized for producing specific proteases. This review aims to provide a comprehensive overview of microorganisms and their proteases participating in enzymatic hydrolysis and microbial fermentation to produce antioxidant peptides. This review also covers endogenous peptides originating from microorganisms. The information obtained from this review might guide the discovery of novel organisms adept at generating antioxidant peptides.

Functional Characterization of DNA N-Glycosylase Ogg1 and Ntg1 in DNA Damage Stress of Cryptococcus neoformans.

Reactive oxygen species induce DNA strand breaks and DNA oxidation. DNA oxidation leads to DNA mismatches, resulting in mutations in the genome if not properly repaired. Homologous recombination (HR) and non-homologous end-joining (NHEJ) are required for DNA strand breaks, whereas the base excision repair system mainly repairs oxidized DNAs, such as 8-oxoguanine and thymine glycol, by cleaving the glycosidic bond, inserting correct nucleotides, and sealing the gap. Our previous studies revealed that the Rad53-Bdr1 pathway mainly controls DNA strand breaks through the regulation of HR- and NHEJ-related genes. However, the functional roles of genes involved in the base excision repair system remain elusive in Cryptococcus neoformans. In the present study, we identified OGG1 and NTG1 genes in the base excision repair system of C. neoformans, which are involved in DNA oxidation repair. The expression of OGG1 was induced in a Hog1-dependent manner under oxidative stress. On the other hand, the expression of NTG1 was strongly induced by DNA damage stress in a Rad53-independent manner. We demonstrated that the deletion of NTG1, but not OGG1, resulted in elevated susceptibility to DNA damage agents and oxidative stress inducers. Notably, the ntg1Δ mutant showed growth defects upon antifungal drug treatment. Although deletion of OGG1 or NTG1 did not increase mutation rates, the mutation profile of each ogg1Δ and ntg1Δ mutant was different from that of the wild-type strain. Taken together, we found that DNA N-glycosylase Ntg1 is required for oxidative DNA damage stress and antifungal drug resistance in C. neoformans.

Childhood Adversity and Passive Suicidal Ideation in Later Life in the United States: Does Religious Attendance Matter?

This study examines whether adverse childhood experiences are associated with passive suicidal ideation in later life and whether religious attendance moderates this association among U.S. older adults. To this end, logistic regression analyses were conducted using data from the 2016 Health and Retirement Study. The results show that poor childhood health, lack of parental affection, and childhood trauma are all positively associated with passive suicidal ideation in later life. However, religious attendance modifies the association between childhood health and passive suicidal ideation. For instance, poor childhood health is associated with greater odds of passive suicidal ideation only for older adults who never attend religious services, while this is not the case for those who attend religious services. Yet, the associations of parental affection and childhood trauma with passive suicidal ideation do not appear to differ by religious attendance. We discuss the theoretical implications of these findings for views about childhood adversity, religion, and suicide risk in later life.

Deionococcus proteotlycius Genomic Library Exploration Enhances Oxidative Stress Resistance and Poly-3-hydroxybutyrate Production in Recombinant Escherichia coli.

Cell growth is inhibited by abiotic stresses during industrial processes, which is a limitation of microbial cell factories. Microbes with robust phenotypes are critical for its maximizing the yield of the target products in industrial biotechnology. Currently, there are several reports on the enhanced production of industrial metabolite through the introduction of Deinococcal genes into host cells, which confers cellular robustness. Deinococcus is known for its unique genetic function thriving in extreme environments such as radiation, UV, and oxidants. In this study, we established that Deinococcus proteolyticus showed greater resistance to oxidation and UV-C than commonly used D. radiodurans. By screening the genomic library of D. proteolyticus, we isolated a gene (deipr_0871) encoding a response regulator, which not only enhanced oxidative stress, but also promoted the growth of the recombinant E. coli strain. The transcription analysis indicated that the heterologous expression of deipr_0871 upregulated oxidative-stress-related genes such as ahpC and sodA, and acetyl-CoA-accumulation-associated genes via soxS regulon. Deipr_0871 was applied to improve the production of the valuable metabolite, poly-3-hydroxybutyrate (PHB), in the synthetic E. coli strain, which lead to the remarkably higher PHB than the control strain. Therefore, the stress tolerance gene from D. proteolyticus should be used in the modification of E. coli for the production of PHB and other biomaterials.

Endophyte Bacillus tequilensis improves the growth of microalgae Haematococcus lacustris by regulating host cell metabolism.

This study identified an endosymbiotic bacterium, Bacillus tequilensis, residing within the cells of the microalga Haematococcus lacustris through 16S rRNA analysis. To confirm the optimal interactive conditions between H. lacustris and B. tequilensis, the effects of different ratios of cells using H. lacustris of different growth stages were examined. Under optimized conditions, the cell density, dry weight, chlorophyll content, and astaxanthin content of H. lacustris increased significantly, and the fatty acid content improved 1.99-fold. Microscopy demonstrated the presence of bacteria within the H. lacustris cells. The interaction upregulated amino acid and nucleotide metabolism in H. lacustris. Interestingly, muramic and phenylacetic acids were found exclusively in H. lacustris cells in the presence of B. tequilensis. Furthermore, B. tequilensis delayed pigment degradation in H. lacustris. This study reveals the impact of the endosymbiont B. tequilensis on the metabolism of H. lacustris and offers new perspectives on the symbiotic relationship between them.

Deinococcus radiodurans-derived membrane vesicles protect HaCaT cells against H2O2-induced oxidative stress via modulation of MAPK and Nrf2/ARE pathways.

BACKGROUND: Deinococcus radiodurans is a robust bacterium that can withstand harsh environments that cause oxidative stress to macromolecules due to its cellular structure and physiological functions. Cells release extracellular vesicles for intercellular communication and the transfer of biological information; their payload reflects the status of the source cells. Yet, the biological role and mechanism of Deinococcus radiodurans-derived extracellular vesicles remain unclear. AIM: This study investigated the protective effects of membrane vesicles derived from D. radiodurans (R1-MVs) against H2O2-induced oxidative stress in HaCaT cells. RESULTS: R1-MVs were identified as 322 nm spherical molecules. Pretreatment with R1-MVs inhibited H2O2-mediated apoptosis in HaCaT cells by suppressing the loss of mitochondrial membrane potential and reactive oxygen species (ROS) production. R1-MVs increased the superoxide dismutase (SOD) and catalase (CAT) activities, restored glutathione (GSH) homeostasis, and reduced malondialdehyde (MDA) production in H2O2-exposed HaCaT cells. Moreover, the protective effect of R1-MVs against H2O2-induced oxidative stress in HaCaT cells was dependent on the downregulation of mitogen-activated protein kinase (MAPK) phosphorylation and the upregulation of the nuclear factor E2-related factor 2 (Nrf2)/antioxidant response element (ARE) pathway. Furthermore, the weaker protective capabilities of R1-MVs derived from ΔDR2577 mutant than that of the wild-type R1-MVs confirmed our inferences and indicated that SlpA protein plays a crucial role in R1-MVs against H2O2-induced oxidative stress. CONCLUSION: Taken together, R1-MVs exert significant protective effects against H2O2-induced oxidative stress in keratinocytes and have the potential to be applied in radiation-induced oxidative stress models.

Whole-cell bioconversion using non-Leloir transglycosylation reactions: a review.

Microbial biocatalysts are evolving technological tools for glycosylation research in food, feed and pharmaceuticals. Advances in bioengineered Leloir and non-Leloir carbohydrate-active enzymes allow for whole-cell biocatalysts to curtail production costs of purified enzymes while enhancing glucan synthesis through continued enzyme expression. Unlike sugar nucleotide-dependent Leloir glycosyltransferases, non-Leloir enzymes require inexpensive sugar donors and can be designed to match the high value, yield and selectivity of the former. This review addresses the current state of bacterial cell-based production of glucans and glycoconjugates via transglycosylation, and describes how alterations made to microbial hosts to surpass purified enzymes as the preferred mode of catalysis are steadily being acquired through genetic engineering, rational design and process optimization. A comprehensive exploration of relevant literature has been summarized to describe whole-cell biocatalysis in non-Leloir glycosylation reactions with various donors and acceptors, and the characterization, application and latest developments in the optimization of their use.

Quality Enhancement of Frozen Chicken Meat Marinated with Phosphate Alternatives.

The effects of phosphate alternatives on meat quality in marinated chicken were investigated with the application of chilling and freezing. Breast muscles were injected with solution of the green weight containing 1.5% NaCl and 2% sodium tripolyphosphate (STPP) or phosphate alternatives. Treatment variables consisted of no phosphate [control (-)], 0.3% sodium tripolyphosphate [control (+)], 0.3% prune juice (PJ), 0.3% oyster shell, 0.3% nano-oyster shell, and 0.3% yeast and lemon extract (YLE) powder. One-third of the meat samples were stored at 4°C for 1 d, and the rest of the meats were kept at -18°C for 7 d. In chilled meat, a lower drip loss was noted for control (+) and YLE, whereas higher cooking yield in YLE compared to all tested groups. Compared with control (+), the other treatments except PJ showed higher pH, water holding capacity, moisture content, lower thawing and cooking loss, and shear force. Natural phosphate alternatives except for PJ, improved the CIE L* compared to control (-), and upregulated total protein solubility. However, phosphate alternatives showed similar or higher oxidative stability and impedance measurement compared to control (+), and an extensive effect on myofibrillar fragmentation index. A limited effect was observed for C*, h°, and free amino acids in treated meat. Eventually, the texture profile attributes in cooked of phosphate alternatives improved except for PJ. The results indicate the high potential use of natural additives could be promising and effective methods for replacing synthetic phosphate in chilled and frozen chicken with quality enhancement.

Do Divine Struggles Moderate the Association Between Interpersonal Conflict at Work and Worker Well-Being in Singapore?

The purpose of this study is to examine how divine struggles moderate the association between interpersonal workplace conflict and worker well-being in Singapore. Using data from the Work, Religion, and Health survey (2021), the analyses show that interpersonal workplace conflict is positively associated with psychological distress and negatively associated with job satisfaction. Although divine struggles fail to function as a moderator in the former, these moderate its association in the latter. Specifically, the negative association between interpersonal conflict at work and job satisfaction is stronger for those with higher levels of divine struggles. These findings support the idea of stress amplification, indicating that troubled relationships with God may exacerbate the deleterious psychological effects of antagonistic interpersonal relationships at work. Ramifications of this aspect of religion, job stressor, and worker well-being will be discussed.

Childhood emotional abuse and adult mental health at the intersection of social relationship and education.

BACKGROUND: Previous research has established that childhood emotional abuse has long-term, negative consequences for adult mental health. Yet, less is known about the ways that social relationship and education intersect to shape the link between childhood emotional abuse and mental health in adulthood. AIM: The current study aims to examine whether perceived quality of social relationships moderates the association between childhood emotional abuse and adult mental health. Moreover, it assesses how the moderating effect of perceived quality of social relationship differs across levels of education. METHOD: The current study analyzes data from the 2012 Korean General Social Survey, a nationally representative sampling of Korean adults. It uses OLS regression models. RESULTS: Childhood emotional abuse is positively associated with depression and psychological distress in adulthood. However, perceived quality of social relationships mitigates the positive association of childhood emotional abuse with depression and psychological distress. Further, this buffering effect of perceived quality of social relationships operates only for individuals with less than or equal to a high school education, but not for individuals with college education or more. CONCLUSION: The results lend support to the resource substitution thesis, suggesting that positive perceptions of social relationship act as a protective factor against childhood emotional abuse for individuals with lower levels of education.