Chromosome-level genome assembly of Korean holoparasitic plants, Orobanche coerulescens.

Orobanche coerulescens is a parasitic plant that cannot complete its life cycle without a host and is incapable of photosynthesis. The habitats of O. coerulescens span the coasts of Korea and its volcanic islands, Ulleungdo and Dokdo. Those on the volcanic islands exhibit morphological differences and have distinct hosts compared to those on the peninsula. The family of Orobanchaceae, encompassing both autotrophic and parasitic species, serves as a model for evolutionary studies of parasitic states. However, there are limited genome assemblies for the Orobanche genus. In our study, we produced approximately 100x ONT long reads to construct a chromosome-level genome of O. coerulescens. The resulting assembly has a total size of 3,648 Mb with an N50 value of 195 Mb, and 82.0% of BUSCO genes were identified as complete. Results of the repeat annotation revealed that 86.3% of the genome consisted of repeat elements, and 29,395 protein-coding genes were annotated. This chromosome-level genome will be an important biological resource for conserving biodiversity and further understanding parasitic plants.

Identifying genes within pathways in unannotated genomes with PaGeSearch.

In biological research, the identification and comparison of genes within specific pathways across the genomes of various species are invaluable. However, annotating the entire genome is resource intensive, and sequence similarity searches often yield results that are not actually genes. To address these limitations, we introduce Pathway Gene Search (PaGeSearch), a tool designed to identify genes from predefined lists, especially those in specific pathways, within genomes. The tool uses an initial sequence similarity search to identify relevant genomic regions, followed by targeted gene prediction and neural network-based result filtering. PaGeSearch suggests the regions that are most likely the orthologs of the genes in the query and is designed to be applicable for species within five classes: mammals, fish, birds, eudicotyledons, and Liliopsida. Compared with GeMoMa and miniprot, PaGeSearch generally outperforms in terms of sensitivity and positive predictive value, as well as negative predictive value. Also, the exon coverage of gene models from PaGeSearch is higher compared with those in GeMoMa and miniprot. Although its performance shows increased variability when applied to actual biological pathways, it nonetheless maintains an acceptable level of accuracy. Evaluating PaGeSearch across different assembly levels, chromosome, scaffold, and contig shows minimal variation in outcomes, indicating that PaGeSearch is resilient to variations in assembly quality.

Integrating immunoinformatics and computational epitope prediction for a vaccine candidate against respiratory syncytial virus.

Respiratory syncytial virus (RSV) poses a significant global health threat, especially affecting infants and the elderly. Addressing this, the present study proposes an innovative approach to vaccine design, utilizing immunoinformatics and computational strategies. We analyzed RSV's structural proteins across both subtypes A and B, identifying potential helper T lymphocyte, cytotoxic T lymphocyte, and linear B lymphocyte epitopes. Criteria such as antigenicity, allergenicity, toxicity, and cytokine-inducing potential were rigorously examined. Additionally, we evaluated the conservancy of these epitopes and their population coverage across various RSV strains. The comprehensive analysis identified six major histocompatibility complex class I (MHC-I) binding, five MHC-II binding, and three B-cell epitopes. These were integrated with suitable linkers and adjuvants to form the vaccine. Further, molecular docking and molecular dynamics simulations demonstrated stable interactions between the vaccine candidate and human Toll-like receptors (TLR4 and TLR5), with a notable preference for TLR4. Immune simulation analysis underscored the vaccine's potential to elicit a strong immune response. This study presents a promising RSV vaccine candidate and offers theoretical support, marking a significant advancement in vaccine development efforts. However, the promising in silico findings need to be further validated through additional in vivo studies.

Discovering peptides and computational investigations of a multiepitope vaccine target Mycobacterium tuberculosis.

Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), a prevalent airborne infectious disease. Despite the availability of the Bacille Calmette-Guerin vaccine, its global efficacy remains modest, and tuberculosis persists as a significant global public health threat. Addressing this challenge and advancing towards the End MTB Strategy, we developed a multiepitope vaccine (MEV) based on immunoinformatics and computational approaches. Immunoinformatics screening of MBT protein identified immune-dominant epitopes based on Major Histocompatibility Complex (MHC) allele binding, immunogenicity, antigenicity, allergenicity, toxicity, and cytokine inducibility. Selected epitopes were integrated into an MEV construct with adjuvant and linkers, forming a fully immunogenic vaccine candidate. Comprehensive analyses encompassed the evaluation of immunological and physicochemical properties, determination of tertiary structure, molecular docking with Toll-Like Receptors (TLR), molecular dynamics (MD) simulations for all atoms, and immune simulations. Our MEV comprises 534 amino acids, featuring 6 cytotoxic T lymphocyte, 8 helper T lymphocyte, and 7 linear B lymphocyte epitopes, demonstrating high antigenicity and stability. Notably, molecular docking studies and triplicate MD simulations revealed enhanced interactions and stability of MEV with the TLR4 complex compared to TLR2. In addition, the immune simulation indicated the capacity to effectively induce elevated levels of antibodies and cytokines, emphasizing the vaccine's robust immunogenic response. This study presents a promising MEV against TB, exhibiting favorable immunological and physicochemical attributes. The findings provide theoretical support for TB vaccine development. Our study aligns with the global initiative of the End MTB Strategy, emphasizing its potential impact on addressing persistent challenges in TB control.

Immunoinformatics and computational approaches driven designing a novel vaccine candidate against Powassan virus.

Powassan virus (POWV) is an arthropod-borne virus (arbovirus) capable of causing severe illness in humans for severe neurological complications, and its incidence has been on the rise in recent years due to climate change, posing a growing public health concern. Currently, no vaccines to prevent or medicines to treat POWV disease, emphasizing the urgent need for effective countermeasures. In this study, we utilize bioinformatics approaches to target proteins of POWV, including the capsid, envelope, and membrane proteins, to predict diverse B-cell and T-cell epitopes. These epitopes underwent screening for critical properties such as antigenicity, allergenicity, toxicity, and cytokine induction potential. Eight selected epitopes were then conjugated with adjuvants using various linkers, resulting in designing of a potentially stable and immunogenic vaccine candidate against POWV. Moreover, molecular docking, molecular dynamics simulations, and immune simulations revealed a stable interaction pattern with the immune receptor, suggesting the vaccine's potential to induce robust immune responses. In conclusion, our study provided a set of derived epitopes from POWV's proteins, demonstrating the potential for a novel vaccine candidate against POWV. Further in vitro and in vivo studies are warranted to advance our efforts and move closer to the goal of combatting POWV and related arbovirus infections.

B. longum CKD1 enhances the efficacy of anti-diabetic medicines through upregulation of IL- 22 response in type 2 diabetic mice.

The gut microbiota plays a pivotal role in metabolic disorders, notably type 2 diabetes mellitus (T2DM). In this study, we investigated the synergistic potential of combining the effects of Bifidobacterium longum NBM7-1 (CKD1) with anti-diabetic medicines, LobeglitazoneⓇ (LO), SitagliptinⓇ (SI), and MetforminⓇ (Met), to alleviate hyperglycemia in a diabetic mouse model. CKD1 effectively mitigated insulin resistance, hepatic steatosis, and enhanced pancreatic ß-cell function, as well as fortifying gut-tight junction integrity. In the same way, SI-CKD1 and Met- CKD1 synergistically improved insulin sensitivity and prevented hepatic steatosis, as evidenced by the modulation of key genes associated with insulin signaling, ß-oxidation, gluconeogenesis, adipogenesis, and inflammation by qRT-PCR. The comprehensive impact on modulating gut microbiota composition was observed, particularly when combined with MetforminⓇ. This combination induced an increase in the abundance of Rikenellaceae and Alistipes related negatively to the T2DM incidence while reducing the causative species of Cryptosporangium, Staphylococcaceae, and Muribaculaceae. These alterations intervene in gut microbiota metabolites to modulate the level of butyrate, indole-3-acetic acid, propionate, and inflammatory cytokines and to activate the IL-22 pathway. However, it is meaningful that the combination of B. longum NBM7-1(CKD1) reduced the medicines' dose to the level of the maximal inhibitory concentrations (IC50). This study advances our understanding of the intricate relationship between gut microbiota and metabolic disorders. We expect this study to contribute to developing a prospective therapeutic strategy modulating the gut microbiota.

Designing a Multiepitope Vaccine against Eastern Equine Encephalitis Virus: Immunoinformatics and Computational Approaches.

Eastern equine encephalitis virus (EEEV) is a significant threat to human and animal populations, causing severe encephalitis, often leading to long-term neurological complications and even mortality. Despite this, no approved antiviral treatments or EEEV human vaccines currently exist. In response, we utilized immunoinformatics and computational approaches to design a multiepitope vaccine candidate for EEEV. By screening the structural polyprotein of EEEV, we predicted both T-cell and linear B-cell epitopes. These epitopes underwent comprehensive evaluations for their antigenicity, toxicity, and allergenicity. From these evaluations, we selected ten epitopes highly suitable for vaccine design, which were connected with adjuvants using a stable linker. The resulting vaccine construct demonstrated exceptional antigenic, nontoxic, nonallergenic, and physicochemical properties. Subsequently, we employed molecular docking and molecular dynamics simulations to reveal a stable interaction pattern between the vaccine candidate and Toll-like receptor 5. Besides, computational immune simulations predicted the vaccine's capability to induce robust immune responses. Our study addresses the urgent need for effective EEEV preventive strategies and offers valuable insights for EEEV vaccine development. As EEEV poses a severe threat with potential spread due to climate change, our research provides a crucial step in enhancing public health defenses against this menacing zoonotic disease.

Exploring the genetic factors behind the discrepancy in resistance to bovine tuberculosis between African zebu cattle and European taurine cattle.

Caused by the pathogenic agent Mycobacterium bovis, bovine tuberculosis (bTB) is a major concern in cattle breeding due to both its zoonotic potential and economic impact. Greater resistance to this disease has been reported in certain African zebu breeds compared to European taurine breeds. However the genetic basis for the lower susceptibility to bTB infection observed in zebu cattle remains poorly explored. This study was conducted on whole genome sequencing data of three bTB infection-resistant African zebu breeds and two bTB infection-susceptible taurine breeds to decipher the genetic background. A set of four selection signature statistics based on linkage disequilibrium, site frequency spectrum, and population differentiation were used on SNPs whereas between population variance based VST and t-test were used on CNVs. As a complement, genes from previous literature reported as candidate genes for bTB resistance were also inspected to identify genetic variations. Interestingly, the resulting nine candidate genes had deleterious missense variants (SHC3, IFNGR1, TLR2, TLR6, IL1A, LRRK2, EP300 and IRAK4) or a CNV difference (CD48) segregating between the groups. The genes found in the study play a role in immune pathways activated during Mycobacterium infection, contributing to the proliferation of immune cells and the granuloma formation, ultimately modulating the outcome of the infectious event. In particular, a deleterious variant in the LRRK2 gene, whose deficiency has been linked to improved prognosis upon tuberculosis infection, was found in the bTB infection-resistant zebu breeds. Therefore, these genes constitute credible candidates in explaining the discrepancy in Mycobacterium bovis infection susceptibility among different breed.

Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean.

Chub mackerels (Scomber japonicus) are a migratory marine fish widely distributed in the Indo-Pacific Ocean. They are globally consumed for their high Omega-3 content, but their population is declining due to global warming. Here, we generated the first chromosome-level genome assembly of chub mackerel (fScoJap1) using the Vertebrate Genomes Project assembly pipeline with PacBio HiFi genomic sequencing and Arima Hi-C chromosome contact data. The final assembly is 828.68 Mb with 24 chromosomes, nearly all containing telomeric repeats at their ends. We annotated 31,656 genes and discovered that approximately 2.19% of the genome contained DNA transposon elements repressed within duplicated genes. Analyzing 5-methylcytosine (5mC) modifications using HiFi reads, we observed open/close chromatin patterns at gene promoters, including the FADS2 gene involved in Omega-3 production. This chromosome-level reference genome provides unprecedented opportunities for advancing our knowledge of chub mackerels in biology, industry, and conservation.

Inference of Admixture Origins in Indigenous African Cattle.

Present-day African cattle retain a unique genetic profile composed of a mixture of the Bos taurus and Bos indicus populations introduced into the continent at different time periods. However, details of the admixture history and the exact origins of the source populations remain obscure. Here, we infer the source of admixture in the earliest domestic cattle in Africa, African taurine. We detect a significant contribution (up to ∼20%) from a basal taurine lineage, which might represent the now-extinct African aurochs. In addition, we show that the indicine ancestry of African cattle, although most closely related to so-far sampled North Indian indicine breeds, has a small amount of additional genetic affinity to Southeast Asian indicine breeds. Our findings support the hypothesis of aurochs introgression into African taurine and generate a novel hypothesis that the origin of indicine ancestry in Africa might be different indicine populations than the ones found in North India today.

Supplementation with the Probiotic Strains Bifidobacterium longum and Lactiplantibacillus rhamnosus Alleviates Glucose Intolerance by Restoring the IL-22 Response and Pancreatic Beta Cell Dysfunction in Type 2 Diabetic Mice.

Type 2 diabetes (T2D) is known as adult-onset diabetes, but recently, T2D has increased in the number of younger people, becoming a major clinical burden in human society. The objective of this study was to determine the effects of Bifidobacterium and Lactiplantibacillus strains derived from the feces of 20 healthy humans on T2D development and to understand the mechanism underlying any positive effects of probiotics. We found that Bifidobacterium longum NBM7-1 (Chong Kun Dang strain 1; CKD1) and Lactiplantibacillus rhamnosus NBM17-4 (Chong Kun Dang strain 2; CKD2) isolated from the feces of healthy Korean adults (n = 20) have anti-diabetic effects based on the insulin sensitivity. During the oral gavage for 8 weeks, T2D mice were supplemented with anti-diabetic drugs (1.0-10 mg/kg body weight) to four positive and negative control groups or four probiotics (200 uL; 1 × 109 CFU/mL) to groups separately or combined to the four treatment groups (n = 6 per group). While acknowledging the relatively small sample size, this study provides valuable insights into the potential benefits of B. longum NBM7-1 and L. rhamnosus NBM17-4 in mitigating T2D development. The animal gene expression was assessed using a qRT-PCR, and metabolic parameters were assessed using an ELISA assay. We demonstrated that B. longum NBM7-1 in the CKD1 group and L. rhamnosus NBM17-4 in the CKD2 group alleviate T2D development through the upregulation of IL-22, which enhances insulin sensitivity and pancreatic functions while reducing liver steatosis. These findings suggest that B. longum NBM7-1 and L. rhamnosus NBM17-4 could be the candidate probiotics for the therapeutic treatments of T2D patients as well as the prevention of type 2 diabetes.

Selenobaculum gbiensis gen. nov. sp. nov., a new bacterium isolated from the gut microbiota of a patient with Crohn's disease.

The human gut microbiota is a complex ecology comprising approximately 10 to 100 trillion microbial cells. Most of the bacteria detected by 16s rRNA sequencing have yet to be cultured, but intensive attempts to isolate the novel bacteria have improved our knowledge of the gut microbiome composition and its roles within human host. In our culturomics study, a novel gram-negative, motile, obligately anaerobic, rod-shaped bacteria, designated as strain ICN-92133T, was isolated from a fecal sample of a 26-year-old patient with Crohn's disease. Based on the 16s rRNA sequence of strain ICN-92133T, the phylogeny analysis placed the strain into the family Selenomonadaceae, showing 93.91% similarity with the closely related Massilibacillus massiliensis strain DSM 102838T. Strain ICN-92133T exhibited a genome size of 2,679,003 bp with a GC content of 35.5% which was predicted to contain 26 potential virulence factors and five antimicrobial resistance genes. In comparative genomic analysis, strain ICN-92133T showed digital DNA-DNA Hybridization and OrthoANI values lower than 21.9% and 71.9% with the closest type strains, respectively. In addition, comparing phenotypic, biochemical, and cellular fatty acids with those of closely related strains revealed the distinctiveness of strain ICN-92133T. Based on the taxonogenomic results, strain ICN-92133T is proposed as a novel species belonging to a new genus. Therefore, we suggest the name of the new genus Selenobaculum gen. nov. within the family Selenomonadaceae and strain ICN-92133T (= KCTC 25622T = JCM 36070T) as a type strain of new species Selenobaculum gbiensis sp. nov.

Repurposing existing drugs for monkeypox: applications of virtual screening methods.

BACKGROUND: Monkeypox is endemic to African region and has become of Global concern recently due to its outbreaks in non-endemic countries. Although, the disease was first recorded in 1970, no monkeypox specific drug or vaccine exists as of now. METHODS: We applied drug repositioning method, testing effectiveness of currently approved drugs against emerging disease, as one of the most affordable approaches for discovering novel treatment measures. Techniques such as virtual ligand-based and structure-based screening were applied to identify potential drug candidates against monkeypox. RESULTS: We narrowed down our results to 6 antiviral and 20 anti-tumor drugs that exhibit theoretically higher potency than tecovirimat, the currently approved drug for monkeypox disease. CONCLUSIONS: Our results indicated that selected drug compounds displayed strong binding affinity for p37 receptor of monkeypox virus and therefore can potentially be used in future studies to confirm their effectiveness against the disease.

The first high-quality genome assembly and annotation of Patiria pectinifera.

The blue bat star, a highly adaptive species in the East Sea of Korea, has displayed remarkable success in adapting to recent climate change. The genetic mechanisms behind this success were not well-understood, prompting our report on the first chromosome-level assembly of the Patiria genus. We assembled the genome using Nanopore and Illumina sequences, yielding a total length of 615 Mb and a scaffold N50 of 24,204,423 bp. Hi-C analysis allowed us to anchor the scaffold sequences onto 22 pseudochromosomes. K-mer based analysis revealed 5.16% heterozygosity rate of the genome, higher than any previously reported echinoderm species. Our transposable element analysis exposed a substantial number of genome-wide retrotransposons and DNA transposons. These results offer valuable resources for understanding the evolutionary mechanisms behind P. pectinifera's successful adaptation in fluctuating environments.

Chromosome-level genome assembly of Korean native cattle and pangenome graph of 14 Bos taurus assemblies.

This study presents the first chromosome-level genome assembly of Hanwoo, an indigenous Korean breed of Bos taurus taurus. This is the first genome assembly of Asian taurus breed. Also, we constructed a pangenome graph of 14 B. taurus genome assemblies. The contig N50 was over 55 Mb, the scaffold N50 was over 89 Mb and a genome completeness of 95.8%, as estimated by BUSCO using the mammalian set, indicated a high-quality assembly. 48.7% of the genome comprised various repetitive elements, including DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. A total of 27,314 protein-coding genes were identified, including 25,302 proteins with inferred gene names and 2,012 unknown proteins. The pangenome graph of 14 B. taurus autosomes revealed 528.47 Mb non-reference regions in total and 61.87 Mb Hanwoo-specific regions. Our Hanwoo assembly and pangenome graph provide valuable resources for studying B. taurus populations.

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.

Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last ~500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).

Molecular dynamics simulation of pyruvate kinase to investigate improved thermostability of artificially selected strain in Enterococcus faecium.

BACKGROUND: Enterococcus faecium (E. faecium) is a member of symbiotic lactic acid bacteria in gastrointestinal tract and it was successfully used to treat diarrhea cases in humans. For a lactobacteria to survive during the pasteurization process, resistance of proteins to denaturation at high temperatures is crucial. Pyruvate kinase (PYK) is one of the proteins possessing such property. It plays a major role during glycolysis by producing pyruvate and adenosine triphosphate (ATP). OBJECTIVE: To assess the acquired thermostability of PYK of ALE strain using in silico methods. METHODS: First, we predicted and assessed tertiary structures of our proteins using SWISS-MODEL homology modelling server. Second, we then applied molecular dynamics (MD) simulation to simulate and assess multiple properties of molecules. Therefore, we implemented comparative MD to evaluate thermostability of PYK of recently developed high temperature resistant strain of E. faecium using Adaptive Laboratory Evolution (ALE) method. After 20ns of simulation at different temperatures, we observed that ALE enhanced strain demonstrated slightly better stability at 300, 340 and 350 K compared to that of the wild type (WT) strain. RESULTS: We collected the results of MD simulation at four temperature points: 300, 340, 350 and 400 K. Our results showed that the protein demonstrated increased stability at 340 and 350 K. CONCLUSION: Results of these study suggest that PYK of ALE enhanced strain of E. faecium demonstrates overall better stability at elevated temperatures compared to that of WT strain.

Oral Administration of Mixed Probiotics Improves Photoaging by Modulating the Cecal Microbiome and MAPK Pathway in UVB-Irradiated Hairless Mice.

SCOPE: Continuous ultraviolet (UV) exposure causes skin photoaging, wrinkle formation, and skin barrier damage. In this study, the protective effect of mixed probiotics (MP) against photoaging in UVB-irradiated Hs68 fibroblasts and SKH-1 hairless mice is investigated. METHODS AND RESULTS: The mice are irradiated with UVB for 8 weeks to induce photoaging, and MP (15 and 50 mg day-1 ) is orally administered once a day. Skin parameters are measured in the dorsal skin and wrinkle formation factors are analyzed in skin replicas. To evaluate the mitogen-activated protein kinase (MAPK) signaling pathway, western blotting and qRT-PCR are performed. MP (50 mg day-1 ) significantly improves skin moisture, transepidermal water loss, erythema, and skin thickness. MP also effectively suppresses wrinkle formation by regulating the transcriptional expression of matrix metalloproteinases (MMPs) and tissue inhibitors of MMPs. MP also reduces inflammatory cytokine levels and phosphorylation of extracellular signaling regulatory kinase, Jun N-terminal kinase, and p38 protein. Furthermore, the intestinal microbiome of the MP groups is significantly different compared with that of the UVB group, and the relative abundance of Lactobacillus and Akkermansia is significantly increased. CONCLUSION: Collectively, these findings suggest that MP modulates the gut microbiome and ameliorates UVB-induced photoaging by downregulating the MAPK pathway.

The idiosyncratic genome of Korean long-tailed chicken as a valuable genetic resource.

Today, breeds with ornamental traits such as exceptionally long tail feathers are economically valuable. However, the genetic basis of long-tail feathers is yet to be understood. To provide better understanding of long tail feathers, we sequenced Korean long-tailed chicken (KLC) genomes and compared them with genomes of other chicken breeds. We first analyzed the genome structure of KLC and its genomic relationship with other chickens and observed unique characteristics. Subsequently, we searched for genomic regions under selection. Feather keratin 1-like enriched region and several genes were found to have novel putative functions and effects on the long tail trait in KLC. Our findings support the value of KLC as a unique genetic resource and cast light on the genetic basis of long tail traits in avian species. We expect this novel knowledge to provide new genomic evidence and options for designing and implementing genetic improvements of ornamental chicken productivity through precision crossbreeding aids.