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.

Major histocompatibility complex genes exhibit a potential immunological role in mixed Eimeria-infected broiler cecum analyzed using RNA sequencing.

Objective: This study was conducted to investigate the differential expression of the major histocompatibility complex (MHC) gene region in Eimeria-infected broiler.

Methods: We profiled gene expression of Eimeria-infected and uninfected ceca of broilers sampled at 4, 7, and 21 days post-infection (dpi) using RNA sequencing. Differentially expressed genes (DEGs) between two sample groups were identified at each time point.

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.

A Rapid Assessing Method of Drug Susceptibility Using Flow Cytometry for Mycobacterium tuberculosis Isolates Resistant to Isoniazid, Rifampin, and Ethambutol.

Background: The current conventional drug susceptibility test (DST) for Mycobacterium tuberculosis (Mtb) takes several weeks of incubation to obtain results. As a rapid method, molecular DST requires only a few days to get the results but does not fully cover the phenotypic resistance. A new rapid method based on the ability of viable Mtb bacilli to hydrolyze fluorescein diacetate to free fluorescein with detection of fluorescent mycobacteria by flow cytometric analysis, was recently developed.

A retroviral insertion in the tyrosinase () gene is associated with the recessive white plumage color in the Yeonsan Ogye chicken.

The recessive white (locus ) phenotype observed in chickens is associated with three alleles (recessive white , albino , and red-eyed white ) and causative mutations in the tyrosinase () gene. The recessive white mutation () inhibits the transcription of exon 5 due to a retroviral sequence insertion in intron 4. In this study, we genotyped and sequenced the insertion in intron 4 to identify the mutation causing the unusual white plumage of Yeonsan Ogye chickens, which normally have black plumage.

Comparison of Selection Signatures between Korean Native and Commercial Chickens Using 600K SNP Array Data.

Korean native chickens (KNCs) comprise an indigenous chicken breed of South Korea that was restored through a government project in the 1990s. The KNC population has not been developed well and has mostly been used to maintain purebred populations in the government research institution. We investigated the genetic features of the KNC population in a selection signal study for the efficient improvement of this breed.

Embryonic Expression of Nras Leads to Embryonic Lethality and Cardiac Defects.

Ras proteins control a complex intracellular signaling network. Gain-of-function mutations in genes lead to RASopathy disorders in humans, including Noonan syndrome (NS). NS is the second most common syndromic cause of congenital heart disease.

2-NPPA Mitigates Osteoclastogenesis via Reducing TRAF6-Mediated c-fos Expression.

Excessive bone resorption leads to bone destruction in pathological bone diseases. Osteoporosis, which occurs when osteoclast-mediated bone resorption exceeds osteoblast-mediated bone synthesis, is regarded a global health challenge. Therefore, it is of great importance to identify agents that can regulate the activity of osteoclasts and prevent bone diseases mediated mainly by bone loss.