Analysis of runs of homozygosity in Yeonsan Ogye chickens using 600K single nucleotide polymorphism arrays.

Runs of homozygosity (ROHs) are caused by identical haplotypes inherited from ancestors. ROHs provide useful information regarding the inbreeding rate, demographics, and selection history. The Yeonsan Ogye (YO) breed is an indigenous chicken in Korea that is characterized by a completely black body.

Systems serology-based comparison of humoral immune responses induced by liposome or aluminum hydroxide adjuvanted SARS-CoV-2 spike protein.

Adjuvants play a crucial role in enhancing vaccine-induced immune responses by shaping the magnitude and quality of humoral and cellular immunity. However, the mechanism through which different adjuvants modulate effector functions is not fully understood. Here, we developed an International Vaccine Institute liposome-based adjuvant (ILA) and comprehensively compared humoral immune profiles in mice following the administration of SARS-CoV-2 spike (S) protein formulated with either ILA or aluminum hydroxide (alum) using a systems serology approach.

Genome-wide association studies of the fatty acid composition of Korean native chicken breast meat.

The fatty acid composition of meat, which affects both its quality and the consumer's health, is a complex trait influenced by genetic and environmental factors. Identification of the genes influencing the fatty acid composition of meat is very important for the selection and breeding of chickens with desirable and healthier fatty acid profiles. The objective of this study was to identify functional candidate genes for fatty acid profiles of the breast meat of the Korean native chicken-red-brown line (KNC-R) through genome-wide association studies.

Selection signature analysis using whole genome resequencing data reveals candidate genes for white plumage color in Korean native ducks.

Objective: Domestication alters the phenotypes of wild animals to meet human demands and leaves characteristic patterns in their genomes. Various selection signature analysis methods have been developed to identify these characteristic patterns left in the genome. The Korean native duck (KND) is one of the domesticated species in Korea.

RSV Vaccine with Nanoparticle-Based Poly-Sorbitol Transporter (PST) Adjuvant Improves Respiratory Protection Against RSV Through Inducing Both Systemic and Mucosal Humoral Immunity.

Respiratory syncytial virus (RSV) causes symptoms similar to a mild cold for adults, but in case of infants, it causes bronchitis and/or pneumonia, and in some cases, mortality. Mucosal immunity within the respiratory tract includes tissue-resident memory T (T) cells and tissue-resident memory B (B) cells, which provides rapid and efficient protection against RSV re-infection. Therefore, vaccine strategies should aim to generate mucosal immune responses.

Characterisation of runs of homozygosity and inbreeding coefficients in the red-brown Korean native chickens.

Objective: The analysis of runs of homozygosity (ROH) has been applied to assess the level of inbreeding and identify selection signatures in various livestock species. The objectives of this study were to characterize the ROH pattern, estimate the rate of inbreeding, and identify signatures of selection in the red-brown Korean native chickens.

Methods: The Illumina 60K single nucleotide polymorphism chip data of 651 chickens was used in the analysis.

Association of histamine-N-methyl transferase gene polymorphisms with carnosine content in red-brown Korean native chickens.

Objective: Carnosine and anserine affect the meat flavor. The contents of carnosine and anserine in meat are affected by genetic and environmental factors. This study aimed to discover the single-nucleotide polymorphisms (SNPs) in the histamine-N-methyl transferase (HNMT) and histamine-N-methyl transferase-like (HNMT-like) genes and to associate them with the content of carnosine and anserine in Korean native chickenred brown line (KNC-R).

Genome-wide association studies of anserine and carnosine contents in the breast meat of Korean native chickens.

Histidine-containing dipeptides (HCDs), such as anserine and carnosine, are enormously beneficial to human health and contribute to the meat flavor in chickens. Meat quality traits, including flavor, are polygenic traits with medium to high heritability. Polygenic traits can be improved through a better understanding of their genetic mechanisms.

Identification of new major histocompatibility complex-B Haplotypes in Bangladesh native chickens.

Objective: The major histocompatibility complex in chicken demonstrates a great range of variations within varities, breeds, populations and that can eventually influence their immuneresponses. The preset study was conducted to understand the major histocompatibility complex-B (MHC-B) variability in five major populations of Bangladesh native chicken: Aseel, Hilly, Junglefowl, Non-descript Deshi, and Naked Neck.

Methods: These five major populations of Bangladesh native chicken were analyzed with a subset of 89 single nucleotide polymorphisms (SNPs) in the high-density MHC-B SNP panel and Kompetitive Allele-Specific polymerase chain reaction genotyping was applied.

A genome-wide association study for the fatty acid composition of breast meat in an F2 crossbred chicken population.

The composition of fatty acids determines the flavor and quality of meat. Flavor compounds are generated during the cooking process by the decomposition of volatile fatty acids via lipid oxidation. A number of research on candidate genes related to fatty acid content in livestock species have been published.

Application of genomic big data to analyze the genetic diversity and population structure of Korean domestic chickens.

Genetic diversity analysis is crucial for maintaining and managing genetic resources. Several studies have examined the genetic diversity of Korean domestic chicken (KDC) populations using microsatellite markers, but it is difficult to capture the characteristics of the whole genome in this manner. Hence, this study analyzed the genetic diversity of several KDC populations using high-density single nucleotide polymorphism (SNP) genotype data.

Phytochemical and Agronomic Characterization of High-Flavonoid Lettuce Lines Grown under Field Conditions.

Flavonoids are antioxidant phytochemicals that confer a beneficial effect on human health. We have previously developed and characterized eight lettuce ( L.) lines that accumulated high levels of diverse flavonoids and their precursors in controlled environment conditions.

Genome-Wide Association Study on the Content of Nucleotide-Related Compounds in Korean Native Chicken Breast Meat.

Meat flavor is an important factor that influences the palatability of chicken meat. Inosine 5'-monophosphate (IMP), inosine, and hypoxanthine are nucleic acids that serve as taste-active compounds, mainly enhancing flavor in muscle tissue. For this study, we performed a genome-wide association study (GWAS) using a mixed linear model to identify single-nucleotide polymorphisms (SNPs) that are significantly associated with changes in the contents of the nucleotide-related compounds of breast meat in the Korean native chicken (KNC) population.

Association of single-nucleotide polymorphisms in dual specificity phosphatase 8 and insulin-like growth factor 2 genes with inosine-5'-monophosphate, inosine, and hypoxanthine contents in chickens.

Objective: This study aimed to identify the single-nucleotide polymorphisms (SNPs) in the dual-specificity phosphatase 8 (DUSP8) and insulin-like growth factor 2 (IGF2) genes and to explore their effects on inosine-5'-monophosphate (IMP), inosine, and hypoxanthine contents in Korean native chicken -red-brown line (KNC-R Line).

Methods: A total sample of 284 (males, n = 127; females n = 157) and 230 (males, n = 106; females, n = 124) aged of 10 weeks old KNC-R line was used for genotyping of DUSP8 and IGF2 genes, respectively. One SNP (rs313443014 C>T) in DUSP8 gene and two SNPs (rs315806609A/G and rs313810945T/C) in IGF2 gene were used for genotyping by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and KASP methods, respectively.

Value-Added Products from Coffee Waste: A Review.

Coffee waste is often viewed as a problem, but it can be converted into value-added products if managed with clean technologies and long-term waste management strategies. Several compounds, including lipids, lignin, cellulose and hemicelluloses, tannins, antioxidants, caffeine, polyphenols, carotenoids, flavonoids, and biofuel can be extracted or produced through recycling, recovery, or energy valorization. In this review, we will discuss the potential uses of by-products generated from the waste derived from coffee production, including coffee leaves and flowers from cultivation; coffee pulps, husks, and silverskin from coffee processing; and spent coffee grounds (SCGs) from post-consumption.

Genome-wide association study for the free amino acid and nucleotide components of breast meat in an F crossbred chicken population.

Flavor is an important sensory trait of chicken meat. The free amino acid (FAA) and nucleotide (NT) components of meat are major factors affecting meat flavor during the cooking process. As a genetic approach to improve meat flavor, we performed a genome-wide association study (GWAS) to identify the potential candidate genes related to the FAA and NT components of chicken breast meat.

()-2-(Cyclobutylamino)--(3-(3,4-dihydroisoquinolin-2(1)-yl)-2-hydroxypropyl)isonicotinamide Attenuates RANKL-Induced Osteoclast Differentiation by Inhibiting NF-κB Nuclear Translocation.

Osteoporosis is a common skeletal disease; however, effective pharmacological treatments still need to be discovered. This study aimed to identify new drug candidates for the treatment of osteoporosis. Here, we investigated the effect of EPZ compounds, protein arginine methyltransferase 5 (PRMT5) inhibitors, on RANKL-induced osteoclast differentiation via molecular mechanisms by in vitro experiments.

Crucial Role of Lysine-Specific Histone Demethylase 1 in RANKL-Mediated Osteoclast Differentiation.

Epigenetic regulators are involved in osteoclast differentiation. This study proposes that the inhibitors of epigenetic regulators could be effective in the treatment of osteoporosis. This study identified GSK2879552, a lysine-specific histone demethylase 1 (LSD1) inhibitor, as a candidate for the treatment of osteoporosis from epigenetic modulator inhibitors.

Peroxiredoxin 5 regulates osteogenic differentiation through interaction with hnRNPK during bone regeneration.

Peroxiredoxin 5 (Prdx5) is involved in pathophysiological regulation via the stress-induced cellular response. However, its function in the bone remains largely unknown. Here, we show that Prdx5 is involved in osteoclast and osteoblast differentiation, resulting in osteoporotic phenotypes in knockout () male mice.

Application of next-generation sequencing for the high-resolution typing of MHC- in Korean native chicken.

The major histocompatibility complex- (MHC-) region of chicken is crucially important in their immunogenesis and highly diverse among different breeds, lines, and even populations. Because it determines the resistance/susceptibility to numerous infectious diseases, it is important to analyze this genomic region, particularly classical class I and II genes, to determine the variation and diversity that ultimately affect antigen presentation. This study investigated five lines of indigenous Korean native chicken (KNC) and the Ogye breed using next-generation sequencing (NGS) data with Geneious Prime-based assembly and variant calling with the Genome Analysis Toolkit (GATK) best practices pipeline.

Single nucleotide polymorphism marker combinations for classifying Yeonsan Ogye chicken using a machine learning approach.

Genetic analysis has great potential as a tool to differentiate between different species and breeds of livestock. In this study, the optimal combinations of single nucleotide polymorphism (SNP) markers for discriminating the Yeonsan Ogye chicken () breed were identified using high-density 600K SNP array data. In 3,904 individuals from 198 chicken breeds, SNP markers specific to the target population were discovered through a case-control genome-wide association study (GWAS) and filtered out based on the linkage disequilibrium blocks.

Time-series transcriptome analysis identified differentially expressed genes in broiler chicken infected with mixed species.

Coccidiosis caused by the species is a highly problematic disease in the chicken industry. Here, we used RNA sequencing to observe the time-dependent host responses of -infected chickens to examine the genes and biological functions associated with immunity to the parasite. Transcriptome analysis was performed at three time points: 4, 7, and 21 days post-infection (dpi).

Identification of Novel Genes for Cell Fusion during Osteoclast Formation.

Osteoclasts are derived from hematopoietic stem cells. Monocyte preosteoclasts obtain resorbing activity via cell-cell fusion to generate multinucleated cells. However, the mechanisms and molecules involved in the fusion process are poorly understood.

Evaluation of TBMDR® and XDRA® for the detection of multidrug resistant and pre-extensively drug resistant tuberculosis.

This study evaluated the diagnostic performance of the AccuPower® TB&MDR Real-Time PCR (TBMDR®) and AccuPower® XDR-TB Real-Time PCR Kit-A (XDRA®) to detect multidrug-resistant (MDR-TB) and pre-extensively drug-resistant tuberculosis (pre-XDR-TB) in comparison with phenotypic drug susceptibility testing (DST) using MGIT 960 on 234 clinical isolates. Discrepant results were confirmed by direct-sequencing. Sensitivity and specificity of TBMDR and XDRA for cultured isolates were 81.