Synergistic Antioxidant and Anti-Inflammatory Effects of Phenolic Acid-Conjugated Glutamine-Histidine-Glycine-Valine (QHGV) Peptides Derived from Oysters (Crassostrea talienwhanensis).

The glutamine-histidine-glycine-valine (QHGV), a peptide derived from oysters, exhibits antioxidant activity and is being actively researched as a potential pharmaceutical and functional cosmetic ingredient. In this study, we synthesized the QHGV peptide and explored the hitherto unknown anti-inflammatory effects of QHGV. The antioxidant property was also characterized by conjugating with various naturally derived phenolic acids, such as caffeic, gallic, ferulic, sinapinic, and vanillic acids. Conjugation with phenolic acids not only enhanced the antioxidant activity of QHGV but also diminished the lipopolysaccharide-induced generation of reactive oxygen species (ROS) in the murine macrophage cell line, RAW 264.7. The reduction in the levels of reactive oxygen species led to the reduced mRNA expression of inducible nitric oxide synthase (iNos) and cyclooxygenase 2 (Cox-2), resulting in an anti-inflammatory effect through the inhibition of the phosphorylation of mitogen-activated protein kinase, including extracellular signal-activated protein kinase, c-Jun NH2-terminal kinase, and p38. Furthermore, the phenolic acid-conjugated peptides increased the mRNA and protein levels of collagen type I, indicative of a wrinkle-improvement effect. The phenolic acid conjugates of the peptide were not cytotoxic to human keratinocytes such as HaCaT cells. These results suggest that phenolic acid conjugation can enhance the potential of peptides as drug and cosmetic resources.

Expansion of the HSP70 gene family in Tegillarca granosa and expression profiles in response to zinc toxicity.

Zinc (Zn) is an essential micronutrient in organisms and an abundant element in the Earth's crust. Trace amounts of Zn released from natural sources can enter aquatic ecosystems through weathering and erosion. Zn accumulates in organisms, and when its intracellular concentration exceeds a certain level, it can induce oxidative stress and trigger oxidative stress-mediated heat shock protein (HSP) modulation. HSP70 is the most evolutionarily conserved among the HSP families. Despite extensive research on HSP70 genes in bivalves, the HSP70 gene family of Tegillarca granosa is still poorly characterized. We identified 65 HSP70 genes belonging to 6 families in the T. granosa genome, with 50 HSPa12 and 11 HSPa B2 genes highly expanded. On chromosome 11, 39 HSP70 (60%) genes were identified, and the HSPa12A genes were highly duplicated. A total of 527 and 538 differentially expressed genes were identified in the gills and mantle based on Zn exposure, respectively. The Gene Ontology of cellular anatomical entities was significantly enriched with upregulated differentially expressed genes in the gills and mantle. Eight of the 11 HSPa B2 genes were upregulated in both tissues. Most of the genes identified in both tissues were involved in "protein homeostasis" and "inhibition of apoptosis," which are associated with the HSP70 family's resistance to extrinsic and intrinsic stress. Hence, this study identified that the HSP70 gene family plays a vital role in the adaptation of aquatic organisms to heavy metal (e.g., Zn) stress in contaminated environments by compiling the different physiological responses to preserve homeostasis.

An Antarctic lichen isolate (Cladonia borealis) genome reveals potential adaptation to extreme environments.

Cladonia borealis is a lichen that inhabits Antarctica's harsh environment. We sequenced the whole genome of a C. borealis culture isolated from a specimen collected in Antarctica using long-read sequencing technology to identify specific genetic elements related to its potential environmental adaptation. The final genome assembly produced 48 scaffolds, the longest being 2.2 Mbp, a 1.6 Mbp N50 contig length, and a 36 Mbp total length. A total of 10,749 protein-coding genes were annotated, containing 33 biosynthetic gene clusters and 102 carbohydrate-active enzymes. A comparative genomics analysis was conducted on six Cladonia species, and the genome of C. borealis exhibited 45 expanded and 50 contracted gene families. We identified that C. borealis has more Copia transposable elements and expanded transporters (ABC transporters and magnesium transporters) compared to other Cladonia species. Our results suggest that these differences contribute to C. borealis' remarkable adaptability in the Antarctic environment. This study also provides a useful resource for the genomic analysis of lichens and genetic insights into the survival of species isolated from Antarctica.

Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna.

The Antarctic whitefin plunderfish Pogonophryne albipinna belongs to the family Artedidraconidae, a key component of Antarctic benthic ecosystems within the order Perciformes and the suborder Notothenioidei. While genome research on P. albipinna using short-read sequencing is available, high-quality genome assembly and annotation employing long-read sequencing have yet to be performed. This study presents a chromosome-scale genome assembly and annotation for P. albipinna, utilizing a combination of Illumina short-read, PacBio long-read, and Hi-C sequencing technologies. The resulting genome assembly spans approximately 1.07 Gb, with a longest scaffold measuring 59.39 Mb and an N50 length of 41.76 Mb. Of the 1,111 Hi-C scaffolds, 23 exceeded 10 Mb and were thus classified as chromosome-level. BUSCO completeness was assessed at 95.6%. The assembled genome comprises 50.68% repeat sequences, and a total of 31,128 protein-coding genes were predicted. This study will enhance our understanding of the genomic characteristics of cryonotothenioids and facilitate comparative analyses of their adaptation and evolution in extreme environments.

Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti.

The crocodile icefish, Chionobathyscus dewitti, belonging to the family Channichthyidae, is an endemic species of the Southern Ocean. The study of its biological features and genetics is challenging as the fish inhabits the deep sea around Antarctic waters. The icefish, the sole cryopelagic species, shows unique physiological and genetic features, unlike other teleosts. It lacks hemoglobin and has evolved antifreeze proteins. Here, we report the genome sequencing data of crocodile icefish produced using the Illumina Novaseq 6000 platform. The estimated genome size was 0.88 Gb with a K-value of 19, and the unique sequence, heterozygosity, error, and duplication rates were 57.4%, 0.421%, 0.317%, and 0.738%, respectively. A genome assembly of 880.69 Mb, with an N50 scaffold length of 2401 bp, was conducted. We identified 2,252,265 microsatellite motifs from the genome assembly data, and dinucleotide repeats (1,920,127; 85.25%) had the highest rate. We selected 84 primer pairs from the genome survey assembly and randomly selected 30 primer pairs for validation. As a result, 15 primer pairs were validated as microsatellite markers.

The HLA-B*13:01 and the dapsone hypersensitivity syndrome in Korean and Asian populations: genotype- and meta-analyses.

BACKGROUND: The human leukocyte antigen (HLA)-B*13:01 was reported as an important risk factor for dapsone hypersensitivity syndrome (DHS) in Chinese and Thai populations. RESEARCH DESIGN AND METHODS: From the Korean nationwide registry, seven subjects with previous DHS were included. Their HLA allele/phenotype frequencies were compared with 8 dapsone-tolerant subjects recruited from a single institution, and general population (n = 485) in Korea. The authors also performed a meta-analysis with these data using previous Chinese and Thai studies. RESULTS: Among the seven DHS subjects, 85.7% presented with the HLA-B*13:01 allele. The HLA-C*03:04, HLA-DRB1*12:02 (both in linkage disequilibrium with HLA-B*13:01), and HLA-A*02:01 alleles were also presented in 85.7%, 71.4%, and 71.4%, respectively. Subjects with HLA-B*13:01 were susceptible to developing DHS compared to dapsone-tolerant controls (odds ratio [OR]: 73.667) and the Korean general population (OR: 139.500). HLA-C*03:04 (OR: 40.935), HLA-DRB*12:02 (OR: 36.613), and HLA-A*02:01 (OR: 5.862) showed similar results. In meta-analysis, HLA-B*13:01 was associated with dapsone-induced hypersensitivity (overall OR: 42.692), and subgroup analyses according to the control types demonstrated similar results (OR:43.694 and 41.866, respectively). CONCLUSIONS: Similar to previous Asian population studies, HLA-B*13:01 is significantly associated with the risk of DHS in Korea. These associations may be useful for preventing DHS and improving drug safety.

Transcription through the HIV-1 nucleosomes: effects of the PBAF complex in Tat activated transcription.

The SWI/SNF complex remodels nucleosomes, allowing RNA Polymerase II access to the HIV-1 proviral DNA. It has not been determined which SWI/SNF complex (BAF or PBAF) remodels nucleosomes at the transcription start site. These complexes differ in only three subunits and determining which subunit(s) is required could explain the regulation of Tat activated transcription. We show that PBAF is required for chromatin remodeling at the nuc-1 start site and transcriptional elongation. We find that Baf200 is required to ensure activation at the LTR level and for viral production. Interestingly, the BAF complex was observed on the LTR whereas PBAF was present on both LTR and Env regions. We found that Tat activated transcription facilitates removal of histones H2A and H2B at the LTR, and that the FACT complex may be responsible for their removal. Finally, the BAF complex may play an important role in regulating splicing of the HIV-1 genome.

Human T-lymphotropic virus type 1 transcription and chromatin-remodeling complexes.

Human T-lymphotropic virus type 1 (HTLV-1) encodes the viral protein Tax, which is believed to act as a viral transactivator through its interactions with a variety of transcription factors, including CREB and NF-kappaB. As is the case for all retroviruses, the provirus is inserted into the host DNA, where nucleosomes are deposited to ensure efficient packaging. Nucleosomes act as roadblocks in transcription, making it difficult for RNA polymerase II (Pol II) to proceed toward the 3' end of the genome. Because of this, a variety of chromatin remodelers can act to modify nucleosomes, allowing for efficient transcription. While a number of covalent modifications are known to occur on histone tails in HTLV-1 infection (i.e., histone acetyltransferases [HATs], histone deacetylases [HDACs], and histone methyltransferases [HMTs]), evidence points to the use of chromatin remodelers that use energy from ATP hydrolysis to remodel nucleosomes. Here we confirm that BRG1, which is the core subunit of eight chromatin-remodeling complexes, is essential not only for Tax transactivation but also for viral replication. This is especially evident when wild-type infectious clones of HTLV-1 are used. BRG1 associates with Tax at the HTLV-1 long terminal repeat (LTR), and coexpression of BRG1 and Tax results in increased rates of transcription. The interaction of BRG1 with Tax additionally recruits the basal transcriptional machinery and removes some of the core histones from the nucleosome at the start site (Nuc 1). When using the BRG1-deficient cell lines SW13, C33A, and TSUPR1, we observed little viral transcription and no viral replication. Importantly, while these three cell lines do not express detectable levels of BRG1, much of the SWI/SNF complex remains assembled in the cells. Knockdown of BRG1 and associated SWI/SNF subunits suggests that the BRG1-utilizing SWI/SNF complex PBAF is responsible for HTLV-1 nucleosome remodeling. Finally, HTLV-1 infection of cell lines with a knockdown in BRG1 or the PBAF complex results in a significant reduction in viral production. Overall, we concluded that BRG1 is required for Tax transactivation and HTLV-1 viral production and that the PBAF complex appears to be responsible for nucleosome remodeling.