Comparative Sequence Analysis Research Articles

Transcriptome analysis of the effect of HERV-K env gene knockout in ovarian cancer cell lines.

Human endogenous retroviruses (HERVs) have been implicated in the pathogenesis of various diseases, particularly cancers. Previous investigations from our group demonstrated that targeted knockout (KO) of the HERV-K env gene led to a significant reduction in tumorigenic attributes, including proliferation, migration, and invasion of ovarian cancer cells. In this study, we aimed to elucidate the impact of HERV-K env KO on gene expression in ovarian cancer cell lines through comparative RNA sequencing (RNA-Seq) analysis with two distinct HERV-K env KO ovarian cancer cell lines, SKOV3 and OVCAR3. HERV-K env gene KO was achieved in SKOV3 and OVCAR3 ovarian cancer cell lines using the CRISPR-Cas9 system. Next-generation mRNA sequencing was employed to assess the gene expression profiles of both mock and HERV-K env KO ovarian cancer cells. Furthermore, comprehensive analyses involving gene ontology and pathway assessments were conducted. Transcriptome analysis revealed that 23 differentially expressed genes (DEGs) were upregulated and 17 DEGs were downregulated in SKOV3 cells. In OVCAR3 cells, 198 DEGs were upregulated, and 17 DEGs were downregulated. Notably, 53 DEGs exhibited statistically significant differences among the 1,612 DEGs identified. Our findings indicate that HERV-K env gene KO exerts a profound influence on gene expression patterns in OVCAR3 cells, while genetic alterations in expression were relatively modest in SKOV3 cells. Nevertheless, genes ND1, ND2, and CYTB displayed a common increase in expression, while ERRFI1 and NDRG1 exhibited a decrease in expression in both cell lines. Our study demonstrates that KO of the HERV-K env gene in ovarian cancer cell lines has a substantial impact on gene expression patterns and can be used to identify potential therapeutic targets for ovarian cancer and related diseases.

Nocardiopsis codii sp. nov., and Rhodococcus chondri sp. nov., two novel actinomycetal species isolated from macroalgae collected in the northern Portuguese coast.

Two novel actinomycetal strains, designated CC-R113T and CC-R104T, were isolated from the tissues of two macroalgae collected on the northern Portuguese coast. Phylogenetic analyses based on the 16S rRNA gene showed that strain CT-R113T belongs to the genus Nocardiopsis, being closely related to Nocardiopsis umidischolae 66/93T and Nocardiopsis tropica VKM Ac-1457T, with 98.65 and 98.39 % sequence similarity, respectively. The clade formed between the three type strains was confirmed by phylogenomic analysis. The genome of strain CT-R113T was 7.27 Mb in size with a G+C content of 71.3 mol %, with average nucleotide identity (ANI) values of 89.59 and 90.14 % with strains 66/93T and VKM Ac-1457T, respectively. The major cellular fatty acids were identified as C18 : 1 ω9c, iso-C16 : 0 and anteiso-C17 : 0. Menaquinone 10 (MK-10) was the major respiratory quinone. Comparative analysis of 16S rRNA gene sequences showed that strain CC-R104T belongs to the genus Rhodococcus and is most closely related to Rhodococcus pyridinivorans DSM 44555T, with 98.24 % sequence similarity. However, phylogenomic analysis revealed that strain CC-R104T establishes a clade with Rhodococcus artemisae DSM 45380T, being more distant from Rhodococcus pyridinivorans DSM 44555T. The genome of strain CC-R104T was 5.34 Mb in size with a G+C content of 67.01 mol%. The ANI value between strains CC-R104T and DSM 45380T was 81.2 % and between strains CC-R104T and DSM 44555T was 81.5 %. The major cellular fatty acids were identified as C18 : 1 ω9c, C16 : 0 and summed feature 3. Menaquinone 8 (MK-8) was the only respiratory quinone. For both CC-R113T and CC-R104T, optimum growth was observed at pH 7.0, 28 °C and 0-5 % NaCl and whole-cell hydrolysates contained meso-diaminopimelic acid as the cell-wall diamino acid. On the basis of phenotypic, molecular and chemotaxonomic characteristics, strains CT-R113T and CC-R104T are considered to represent novel species, for which the names Nocardiopsis codii sp. nov. (type strain CT-R113T=LMG33234T=UCCCB172T) and Rhodococcus chondri sp. nov. (type strain CC-R104T=LMG33233T=UCCCB171T) are proposed.

A scallop IκB protein involved in innate immunity acts as a key regulator of NF-κB

Chlamys farreri, a commercially important bivalve mollusk, is extensively cultivated in China. In recent years, the frequent occurrence of diseases has led to significant mortality in scallop farms. Despite this, our understanding of scallop's innate immune mechanisms remains limited. The NF-κB signaling pathway plays a crucial role in various biological processes, including cellular, developmental, and immune defense mechanisms. Inhibitors of NF-κB (IκB) proteins block the nuclear localization and DNA binding of NF-κB, thereby inhibiting its activity. However, the role of these proteins in invertebrates is not well understood. In this study, we identified a new homolog of the IκB gene in C. farreri, named CfIκB1. The open reading frame of CfIκB1 spans 1,089 bp, encoding 362 amino acids. Through sequence comparison and phylogenetic analysis, CfIκB1 was classified as a member of the invertebrate IκB family. Quantitative real-time PCR revealed that CfIκB1 transcripts are present in all examined tissues, with the highest expression observed in hemocytes. Expression levels were significantly upregulated following exposure to lipopolysaccharide, peptidoglycan, and polyinosinic:polycytidylic acid. Co-immunoprecipitation studies confirmed that CfIκB1 interacts with NF-κB family proteins CfRel-1 and CfRel. Dual-luciferase reporter assays demonstrated that CfIκB1 inhibits CfRel-dependent activation of NF-κB, ISRE, IFNβ, and AP-1. These findings suggest that CfIκB1 plays a crucial role in regulating NF-κB activity, which is integral to the innate immunity of C. farreri. This research enhances our understanding of the innate immune system in invertebrates and provides a theoretical basis for developing disease-resistant scallops at the molecular level.

Characterization of mesothelin gene expression in dogs and overexpression in canine mesotheliomas

IntroductionCanine mesotheliomas are uncommon malignant tumors typically detected late. Minimally invasive diagnostic biomarkers would facilitate diagnosis at earlier stages, thereby improving clinical outcomes. We hypothesized that mesothelin could be used as a reliable diagnostic biomarker for canine mesotheliomas since it has been used as a cancer biomarker for human mesothelioma. We aimed to explore and characterize mesothelin gene expression in dogs and assess its use as a diagnostic biomarker for canine mesotheliomas.Materials and methodsWe quantified expressed canine mesothelin transcripts via reverse transcription polymerase chain reaction (RT-PCR) and sequenced them using ribonucleic acid (RNA) extracted from a canine mesothelioma cell line. After confirming mesothelin expression, we assessed its levels in major organ tissues and compared them with those in the mesothelioma tissues using quantitative PCR (qPCR). Mesothelin overexpression in mesotheliomas was detected, and we further compared its levels using qPCR between mesotheliomas and non-mesotheliomas using tumor tissues and clinical sample effusions, confirming its significance as a diagnostic biomarker for canine mesothelioma.ResultsMesothelin complementary deoxyribonucleic acid (cDNA) was amplified via RT-PCR, yielding a single band of expected upon DNA electrophoresis. Sequence analyses confirmed it as a predicted canine mesothelin transcript from the genome sequence database. Comparative sequence analysis of the deduced amino acid sequence of the expressed canine mesothelin demonstrated molecular signature similarities with the human mesothelin. However, the pre-sequence of canine mesothelin lacks the mature megakaryocyte potentiating factor (MPF) portion, which is typically cleaved post-translationally with furin. Mesothelin expression was quantified via qPCR revealing low levels in the mesothelial and lung tissues, with negligible expression in the other major organs. Canine mesothelin exhibited significantly higher expression in the canine mesotheliomas than in the noncancerous tissues. Moreover, analysis of clinical samples using qPCR demonstrated markedly elevated mesothelin expression in canine mesotheliomas compared to non-mesothelioma cases.Discussion and conclusionCanine mesothelin exhibits molecular and biological characteristics akin to human mesothelin. It could serve as a vital biomarker for diagnosing canine mesotheliomas, applicable to both tissue- and effusion-based samples.

Catalytic selectivity and evolution of cytochrome P450 enzymes involved in monoterpene indole alkaloids biosynthesis.

Cytochrome P450 enzyme (CYP)-catalyzed functional group transformations are pivotal in the biosynthesis of metabolic intermediates and products, as exemplified by the CYP-catalyzed C7-hydroxylation and the subsequent C7-C8 bond cleavage reaction responsible for the biosynthesis of the well-known antitumor monoterpene indole alkaloid (MIA) camptothecin. To determine the key amino acid residues responsible for the catalytic selectivity of the CYPs involved in MIA biosynthesis, we characterized the enzymes CYP72A728 and CYP72A729 as stereoselective 7-deoxyloganic acid 7-hydroxylases (7DLHs). We then conducted a comparative analysis of the amino acid sequences and the predicted structures of the CYP72A homologs involved in camptothecin biosynthesis, as well as those of the CYP72A homologs implicated in the pharmaceutically significant MIAs biosynthesis in Catharanthus roseus. The crucial amino acid residues for the catalytic selectivity of the CYP72A-catalyzed reactions were identified through fragmental and individual residue replacement, catalytic activity assays, molecular docking, and molecular dynamic simulations analysis. The fragments 1 and 3 of CYP72A565 were crucial for its C7-hydroxylation and C7-C8 bond cleavage activities. Mutating fragments 1 and 2 of CYP72A565 transformed the bifunctional CYP72A565 into a monofunctional 7DLH. Evolutionary analysis of the CYP72A homologs suggested that the bifunctional CYP72A in MIA-producing plants may have evolved into a monofunctional CYP72A. The gene pairs CYP72A728-CYP72A610 and CYP72A729-CYP72A565 may have originated from a whole genome duplication event. This study provides a molecular basis for the CYP72A-catalyzed hydroxylation and C-C bond cleavage activities of CYP72A565, as well as evolutionary insights of CYP72A homologs involved in MIAs biosynthesis.

Identification of a Novel Parvovirus in the Arctic Wolf (Canis lupus arctos).

A novel virus, temporarily named "Arctic wolf parvovirus" (AWPV), was discovered in a pharyngeal metagenomic library derived from an Arctic wolf (Canis lupus arctos) in China. The genome sequence was assigned GenBase accession number C_AA071902.1. AWPV has a genome comprised of 4,920 base pairs with a nucleotide composition of 36.4% A, 23.4% T, 18.2% G, and 22.0% C, with a GC content of 40.2%. Its structure resembles parvoviruses, containing two open reading frames: the nonstructural (NS) region encoding replication enzymes and the structural (VP) region encoding capsid protein. Pairwise sequence comparison and phylogenetic analysis suggest AWPV may represent a novel species within the genus Protoparvovirus. This discovery enhances our understanding of mammalian virus ecology and potential future infectious diseases.

Prospects for a sequence-based taxonomy of influenza A virus subtypes.

Hemagglutinin (HA) and neuraminidase (NA) proteins are the primary antigenic targets of influenza A virus (IAV) infections. IAV infections are generally classified into subtypes of HA and NA proteins, e.g. H3N2. Most of the known subtypes were originally defined by a lack of antibody cross-reactivity. However, genetic sequencing has played an increasingly important role in characterizing the evolving diversity of IAV. Novel subtypes have recently been described solely by their genetic sequences, and IAV infections are routinely subtyped by molecular assays, or the comparison of sequences to references. In this study, I carry out a comparative analysis of all available IAV protein sequences in the Genbank database (over 1.1 million, reduced to 272,292 unique sequences prior to phylogenetic reconstruction) to determine whether the serologically defined subtypes can be reproduced with sequence-based criteria. I show that a robust genetic taxonomy of HA and NA subtypes can be obtained using a simple clustering method, namely, by progressively partitioning the phylogeny on its longest internal branches. However, this taxonomy also requires some amendments to the current nomenclature. For example, two IAV isolates from bats previously characterized as a divergent lineage of H9N2 should be separated into their own subtype. With the exception of these small and highly divergent lineages, the phylogenies relating each of the other six genomic segments do not support partitions into major subtypes.

Wild raccoons demonstrate flexibility and individuality in innovative problem-solving.

Cognitive skills, such as innovative problem-solving, are hypothesized to aid animals in urban environments. However, the significance of innovation in wild populations, and its expression across individuals and socio-ecological conditions, is poorly understood. To identify how and when innovation arises in urban-dwelling species, we used advanced technologies and new testing and analytical methods to evaluate innovative problem-solving abilities of wild raccoons (Procyon lotor). We deployed multi-compartment puzzle boxes with either one or multiple solution types and identified raccoons using radio frequency identification. Raccoons solved these novel extractive foraging tasks, and their success was influenced by age and exploratory diversity. Successful raccoons always discovered multiple different solution types, highlighting flexible problem-solving. Using a unique, comparative sequence analysis approach, we found that variation in raccoon solving techniques was greater between individuals than within individuals, and this self-similarity intensified during times of competition. Finally, the inclusion of an easier solution in the multi-solution trials enabled previously unsuccessful raccoons to bootstrap their learning and successfully open multiple difficult solutions. Our study suggests that innovative problem-solving is probably influenced by many factors and has provided novel field and analytical methods, as well as new insights on the socio-ecological dynamics of urban populations.

A new strain of Rhodococcus indonesiensis T22.7.1T and its functional potential for deacetylation of chitin and chitooligsaccharides.

Chitin, abundant in marine environments, presents significant challenges in terms of transformation and utilization. A strain, T22.7.1T, with notable chitin deacetylation capabilities, was isolated from the rhizosphere of Acanthus ebracteatus in the North Sea of China. Comparative 16S rDNA sequence analysis showed that the new isolate had the highest sequence similarity (99.79%) with Rhodococcus indonesiensis CSLK01-03T, followed by R. ruber DSM 43338T, R. electrodiphilus JC435T, and R. aetherivorans 10bc312T (98.97%, 98.81%, and 98.83%, respectively). Subsequent genome sequencing and phylogenetic analysis confirmed that strain T22.7.1T belongs to the R. indonesiensis species. However, additional taxonomic characterization identified strain T22.7.1T as a novel type strain of R. indonesiensis distinct from CSLK01-03T. This study refines the taxonomic description of R. indonesiensis and investigates its application in converting chitin into chitosan. The chitin deacetylase (RiCDA) activity of strain T22.7.1T was optimized, and the enzyme was isolated and purified from the fermentation products. Through optimization, the RiCDA activity of strain T22.7.1T reached 287.02 U/mL, which is 34.88 times greater than the original enzyme's activity (8.0 U/mL). The natural CDA enzyme was purified with a purification factor of 31.83, and the specific activity of the enzyme solution reached 1200.33 U/mg. RiCDA exhibited good pH and temperature adaptability and stability, along with a wide range of substrate adaptabilities, effectively deacetylating chitin, chitooligosaccharides, N-acetylglucosamine, and other substrates. Product analysis revealed that RiCDA treatment increased the deacetylation degree (DD) of natural chitin to 83%, surpassing that of commercial chitosan. Therefore, RiCDA demonstrates significant potential as an efficient deacetylation tool for natural chitin and chitooligosaccharides, highlighting its applicability in the biorefining of natural polysaccharides.

Comparative Genomic Analysis of Prophages in Human Vaginal Isolates of Streptococcus agalactiae.

Prophages, viral genomes integrated into bacterial genomes, are known to enhance bacterial colonization, adaptation, and ecological fitness, providing a better chance for pathogenic bacteria to disseminate and cause infection. Streptococcus agalactiae (Group B Streptococcus or GBS) is a common bacterium found colonizing the genitourinary tract of humans. However, GBS-colonized pregnant women are at risk of passing the organism to the neonate, where it can cause severe infections. GBS typically encode one or more prophages in their genomes, yet their role in pathogen fitness and virulence has not yet been described. Sequencing and bioinformatic analysis of the genomic content of GBS human isolates identified 42 complete prophages present in their genomes. Comparative genomic analyses of the prophage sequences revealed that the prophages could be classified into five distinct clusters based on their genomic content, indicating significant diversity in their genetic makeup. Prophage diversity was also identified across GBS capsule serotypes, sequence types (STs), and clonal clusters (CCs). Comprehensive genomic annotation revealed that all GBS strains encode paratox, a protein that prevents the uptake of DNA in Streptococcus, either on the chromosome, on the prophage, or both, and each prophage genome has at least one toxin-antitoxin system.

Analyzing the Impact of the Highest Expressed Epstein-Barr Virus-Encoded microRNAs on the Host Cell Transcriptome.

The Epstein-Barr virus (EBV) has a very high prevalence (>90% in adults), establishes a lifelong latency after primary infection, and exerts an oncogenic potential. This dsDNA virus encodes for various molecules, including microRNAs (miRs), which can be detected in the latent and lytic phases with different expression levels and affect, among others, immune evasion and malignant transformation. In this study, the different EBV miRs are quantified in EBV-positive lymphomas, and the impact on the host cell transcriptome of the most abundant EBV miRs will be analyzed using comparative RNA sequencing analyses. The EBV miRs ebv-miR-BART1, -BART4, -BART17, and -BHRF1-1 were most highly expressed, and their selective overexpression in EBV-negative human cells resulted in a large number of statistically significantly down- and up-regulated host cell genes. Functional analyses showed that these dysregulated target genes are involved in important cellular processes, including growth factor pathways such as WNT, EGF, FGF, and PDGF, as well as cellular processes such as apoptosis regulation and inflammation. Individual differences were observed between these four analyzed EBV miRs. In particular, ebv-miR-BHRF1-1 appears to be more important for malignant transformation and immune evasion than the other EBV miRs.

Heat treatment effects and variant selection in multi-material laser powder bed fusion of FeNi- and CoCr-based alloys

ABSTRACT This study demonstrates the successful fabrication of a multi-material 18Ni(300) maraging steel – CoCrMo alloy using laser powder bed fusion (L-PBF), which in its as-built state, displays suboptimal mechanical performance. Addressing this, we propose different heat treatments that mutually enhance the properties of both alloys. Comparative analysis of texture development, precipitation sequence and mechanical properties of the dual structures at different scales has been conducted. The results indicate the cooperative strengthening of intragranular γ–ϵ transformation in CoCrMo, and Ni3Ti precipitation in maraging steel. Adding the solution treatment also balanced the formation of acicular Ni3Ti clusters with (Fe, Ni, Co)2(Ti, Mo) precipitates, and revealed that chemical segregation influences austenite reversion. Initial evidence of local grain variant selection has been revealed in as-built samples due to thermal cycling and austenite reversion, which generates residual stresses, recoil forces and convective flow. Surprisingly, the missing variants can also be inherited after heat treatment with insufficient solution temperatures.

Spatio-temporal analysis of genetic diversity of merozoite surface protein-3 alpha in Myanmar Plasmodium vivax isolates

Myanmar aims to eliminate malaria by 2030. However, recent increase of malaria incidence is a great challenge to archive that goal. Increasing prevalence of Plasmodium vivax also hinders this endeavor. Monitoring genetic structure of the parasite is necessary to understand genetic nature and evolutionary aspect of P. vivax population in Myanmar. Partial fragment flanking blocks I and II of merozoite surface protein-3 alpha of P. vivax (pvmsp-3α) was amplified from P. vivax isolates collected in Pyin Oo Lwin, Mandalay Region, Myanmar in 2013–2015. Sequence analysis of pvmsp-3α was performed to determine genetic diversity and natural selection of this gene. Spatio-temporal genetic changes of pvmsp-3α in Myanmar P. vivax population were also investigated via comparative analysis of gene sequences obtained in this study and previously reported Myanmar pvmsp-3α sequences. Genetic diversity of Myanmar pvmsp-3α was detected in P. vivax isolates analyzed. Size polymorphisms in block I and amino acid changes and recombination events in block II were main factors contributing to the genetic diversity of pvmsp-3α. Comparative spatio-temporal analysis with previously reported Myanmar pvmsp-3α populations revealed the presence of genetic differences by population with moderate genetic differentiation between populations. Similar pattern of natural selection was also detected in Myanmar pvmsp-3α populations. These suggested that enough size of the P. vivax population sufficient to generate or maintain the genetic diversity remains in the population. Thus, continuous molecular surveillance of genetic structure of Myanmar P. vivax is necessary.

Comparative High-Throughput Sequencing Analysis of the Bacterial Community Associated with the Rhizosphere of Date Palm (Phoenix dactyllifera L.) Irrigated with Treated Wastewater and Groundwater

Water scarcity is a major agricultural issue in most arid and semi-arid regions of the world. Alternative water supplies, such as the reuse of wastewater for agricultural irrigation, have been introduced. However, little is known about their impact on the soil and rhizosphere microbiomes that receive irrigation. Therefore, this work evaluates the impact of treated wastewater (TWW) irrigation on the soil and rhizosphere bacterial communities of date palms in Al Madinah, Saudi Arabia. In this study, metagenomic DNA from the rhizosphere of the date palm was sequenced using Illumina high-throughput sequencing. According to the observed OTUs, Chao1 richness estimations, and Shannon diversity values, soils from groundwater-irrigated date palms showed higher microbial diversity than did soils from TWW-irrigated date palms. A total of 569 OTUs were generated; most of them (97.3%) were assigned into 15 different phyla, whereas 2.7% were marked as unclassified. DNA sequence analysis of the WWT-irrigated rhizosphere showed that the most abundant phyla were Firmicutes (43.6%), Bacteroidetes (17.3%), Proteobacteria (15.2%), and Actinobacteria (14.6%), representing more than 90.7% of the total community, while the soil of the rhizosphere irrigated with GW was dominated by Actinobacteria (44.1%), Proteobacteria (23.4%), Firmicutes (15.5%), and Gemmatimonadetes (4.9%). The most frequently observed species in the two soils were also different. The dominant species in TWW-irrigated soil was Planococcus plakortidis, which is prevalent in saline and moderately saline habitats and can play an important ecological role. The GW-irrigated rhizosphere exhibited higher levels of biocontrol bacteria, particularly Nocardioides mesophilus. These results provide a comprehensive understanding and insights into the population dynamics and microbiome of date palm rhizosphere. The findings show that the irrigation water quality has a significant impact on the microbiome composition. Identifying the microbial diversity is the first step toward determining the best way to use TWW in irrigation.

First detection of multiple cases related to CV-A16 strain of B1c clade in Beijing in 2022.

Coxsackievirus A16 (CV-A16) is a significant etiologic agent of hand, foot, and mouth disease (HFMD) and herpangina (HA), with the capacity to progress to severe complications, including encephalitis, aseptic meningitis, acute flaccid paralysis, myocarditis, and other critical conditions. Beijing's epidemiological surveillance system, established in 2008, encompasses 29 hospitals and 16 district disease control centers. From 2019 to 2021, the circulation of CV-A16 was characterized by the co-circulation of B1a and B1b clades. Multiple cases of HFMD linked to clade B1c has not been reported in Beijing until 2022. This study enrolled 400 HFMD and 493 HA cases. Employing real-time RT-PCR, 368 enterovirus-positive cases were identified, with 180 selected for sequencing. CV-A16 was detected in 18.89% (34/180) of the cases, second only to CV-A6, identified in 63.33% (114/180). Full-length VP1 gene sequences were successfully amplified and sequenced in 22 cases, revealing the presence of clades B1a, B1b, and B1c in 14, 3, and 5 cases, respectively. A cluster of five B1c clade cases occurred between June 29 and July 17, 2022, within a 7-km diameter region in Shunyi District. Phylogenetic analysis of five complete VP1 gene sequences and two full-genome sequences revealed close clustering with the 2018 Indian strain (GenBank accession: MH780757.1) within the B1c India branch, with NCBI BLAST results showing over 98% similarity. Comparative sequence analysis identified three unique amino acid variations (P3S, V25A, and I235V). The 2022 Shunyi District HFMD cases represent the first instances of spatiotemporally correlated CV-A16 B1c clade infections in Beijing, underscoring the necessity for heightened surveillance of B1c clade CV-A16 in HFMD and HA in this region.

Identification of linear B cell epitopes on the leukotoxin protein of Fusobacterium necrophorum

Fusobacterium necrophorum can casuse Lemierre's syndrome in humans and a range of illnesses, including foot rot and liver abscesses, in animals. The main virulence factor released by F. necrophorum is leukotoxin, which has been shown to have a strong correlation with the severity of the disease. Leukotoxin is commonly employed as the key antigen in the formulation of subunit vaccines. Therefore, identification of the B-cell epitope of F. necrophorum leukotoxin is necessary. In this research, we utilized lymphocyte hybridoma technology to develop a monoclonal antibody (mAb), 3D7, targeting the F. necrophorum leukotoxin protein. Identification of B-cell epitopes recognized by 3D7 mAb through Western blot, ELISA and dot blot using leukotoxin-truncated recombinant proteins and peptides, and through SWISS-MODEL homology modeling and PyMOL visualization. The 3D7 mAb was identified as belonging to the IgG1 subclass with a κ-chain light chain. It demonstrated reactivity with the natural leukotoxin. The results showed that the 3D7 mAb recognizes a B-cell epitope of the F. necrophorum leukotoxin protein, I2168SSFGVGV2175 (EP-3D7). Sequence comparison analysis showed that EP-3D7 was highly conserved in F. necrophorum strains, but less conserved in other bacteria, indicating the specificity of EP-3D7. EP-3D7 is present on the surface of leukotoxin proteins in a β-folded manner. In summary, these results establish EP-3D7 as a conserved antigenic epitope of F. necrophorum leukotoxin. It could be valuable in the development of vaccines and diagnostic reagents for F. necrophorum epitopes.

In silico comparative analysis of the complete chloroplast genome sequences in the mulberry family (Moraceae)

The mulberry family (Moraceae) encompasses a wide range of angiosperms and includes several important fruit plants, such as jackfruit, breadfruit, and figs, among others. While there have been multiple published complete chloroplast (cp) genomes within this family, there has been no comprehensive study that summarizes the characteristics of these sequences. In the current study, a comprehensive analysis was conducted using a dataset consisting of 32 cp genomes obtained from NCBI GenBank. These genomes belong to 32 species, encompassing 12 genera within the mulberry family. The collected data were used to conduct genomic comparisons and phylogenetic analyses, employing a range of bioinformatics tools. The findings revealed length variations among the cp genomes of different species, ranging from 158,459 bp in Morus mongolica to 162,594 bp in Broussonetia luzonica. Additionally, the study detected structural variations in simple sequence repeat motifs including gene losses. Overall, the phylogenetic results in this study generally supported the existing taxonomy of species within this family, with the exception that Malaisia scandens and Trophis scandens are clustered in the clade of the Broussonetia genus. This investigation provides further evidence of the effectiveness of characterizing the entire cp genome when classifying species and genera within the mulberry family.

The absence of canonical respiratory complex I subunits in male-type mitogenomes of three Donax species

Bivalves are an extraordinary class of animals in which species with a doubly uniparental inheritance (DUI) of mitochondrial DNA have been described. DUI is characterized as a mitochondrial homoplasmy of females and heteroplasmy of male individuals where F-type mitogenomes are passed to the progeny with mother egg cells and divergent M-type mitogenomes are inherited with fathers sperm cells. However, in most cases only male individuals retain divergent mitogenome inherited with spermatozoa. Additionally, in many of bivalves, unique mitochondrial features, like additional genes, gene duplication, gene extensions, mitochondrial introns, and recombination, were observed. In this study, we sequenced and assembled male-type mitogenomes of three Donax species. Comparative analysis of mitochondrial sequences revealed a lack of all seven NADH dehydrogenase subunits as well as the presence of three long additional open reading frames lacking identifiable homology to any of the existing genes.

Điều tra bệnh hại sau thu hoạch trên giống chuối Tiêu hồng (Musa acuminata) và chuối Nam Mỹ (Musa paradisiaca) ở Việt Nam

The survey implemented in the 2021 winter season on the Tieu hong banana cultivar (Musa acuminata) grown in Phu Tho and Hung Yen provinces showed that the most severe diseases were fruit rot and fruit spot with infection rates of 79.1% and 75.5%, respectively. Peel cracking and end rot (cigar rot) were also recorded at less than 5.0%. Fruit spot was the main disease that affected the South-American banana cultivar (Musa paradisiaca) during the 2022 spring-summer season in Gia Lai province. Of the 24 fungal and 37 bacterial strains isolated from the disease samples collected during the investigation and tested for their pathogenicity via artificial infection on healthy bananas, only 17 fungal strains showed the ability of lesion formation of which 4 strains caused typical symptoms of the fruit rot disease. There was not a single bacterial strain ascertained as phytopathogen indicating that fungi were the primary agents of post-harvest diseases on bananas. These four fungal strains were taxonomically characterized based on their morphology (colony and spore), comparative analysis of the ITS sequences of the 18S rDNA gene, and were then identified as Corynespora torulosa B2B, Microdochium colombiense B6, Fusarium circinatum B13F, and Aspergillus niger GL2.1. The ITS sequences of these strains were deposited to GenBank under the accession numbers OP855524, OP855525, OP855526, and OP855527, respectively.

Comparative analysis and classification of highly divergent mouse rDNA units based on their intergenic spacer (IGS) variability.

Ribosomal DNA (rDNA) repeat units are organized into tandem clusters in eukaryotic cells. In mice, these clusters are located on at least eight chromosomes and show extensive variation in the number of repeats between mouse genomes. To analyze intra- and inter-genomic variation of mouse rDNA repeats, we selectively isolated 25 individual rDNA units using Transformation-Associated Recombination (TAR) cloning. Long-read sequencing and subsequent comparative sequence analysis revealed that each full-length unit comprises an intergenic spacer (IGS) and a ∼13.4 kb long transcribed region encoding the three rRNAs, but with substantial variability in rDNA unit size, ranging from ∼35to ∼46 kb. Within the transcribed regions of rDNA units, we found 209 variants, 70 of which are in external transcribed spacers (ETSs); but the rDNA size differences are driven primarily by IGS size heterogeneity, due to indels containing repetitive elements and some functional signals such as enhancers. Further evolutionary analysis categorized rDNA units into distinct clusters with characteristic IGS lengths; numbers of enhancers; and presence/absence of two common SNPs in promoter regions, one of which is located within promoter (p)RNA and may influence pRNA folding stability. These characteristic features of IGSs also correlated significantly with 5'ETS variant patterns described previously and associated with differential expression of rDNA units. Our results suggest that variant rDNA units are differentially regulated and open a route to investigate the role of rDNA variation on nucleolar formation and possible associations with pathology.