Search Results (324)

Horizontal Gene Transfer (HGT) is a hallmark of the evolution of parasitic plants, facilitated by the haustorial connection. While mitochondrial HGT is widespread, the extent of nuclear HGT and the long-term retention of foreign genetic material in holoparasitic lineages remain poorly understood. This study explores the genomic architecture of Prosopanche americana (Hydnoraceae), a non-photosynthetic holoparasite currently specialized on Fabaceae. Through a comparative phylogenomic approach integrating draft mitochondrial genomes (mtDNA) and nuclear transcriptomes of P. americana, we identified a multi-layered landscape of foreign DNA. The mtDNA of P. americana contains 18 foreign regions (>500 bp) primarily derived from Solanales, Malvales, and Fabales. Notably, 13 of these regions are shared with P. panguanensis, indicating they were acquired in their common ancestor before speciation and ecological shift. In the nuclear genome, we identified 303 horizontally acquired transcripts (99 orthogroups) with high confidence. Functional analysis revealed an enrichment of foreign genes involved in metabolic pathways and plastid functions (e.g., photosystems and thylakoids) exclusively derived from the ancestral host order Solanales. Our results demonstrate that the genome of P. americana acts as a “molecular fossil,” preserving evidence of past ecological interactions with diverse host lineages. The disparity in HGT footprints between the current host (Fabaceae) and ancestral hosts suggests a period of high genomic plasticity followed by host specialization, providing new insights into the timing and dynamics of horizontal gene flow in holoparasitic Piperales. Full article

Encapsulation is a major cellular defense reaction in lepidopterans. However, in the oriental armyworm (Mythimna separata), the molecular regulators that coordinate hemocyte adhesion and multilayer capsule assembly remain poorly defined. In this study, we identified Mythimna separata encapsulation related gene 1 (MysERG1) as a novel cellular immune regulatory gene. MysERG1 transcripts were most abundant in hemocytes and were notably upregulated in adherent hemocytes as well as in samples of capsules, indicating an association with adhesion-dependent hemocyte activation. Following separation of granulocytes and plasmatocytes, MysERG1 expression was observed to be higher in adherent plasmatocytes than in adherent granulocytes. However, recombinant MysERG1 selectively increased granulocyte adhesion but did not significantly affect plasmatocyte adhesion and was specifically localized on granulocytes. Additionally, recombinant MysERG1 enhanced hemocyte aggregation on foreign surfaces, highlighting its functional role in facilitating encapsulation. Functional knockdown using double-stranded RNA significantly reduced the size of the capsules, indicating that MysERG1 is required for robust capsule formation. This study identifies MysERG1 as a novel factor involved in hemocyte cooperation during encapsulation in M. separata and presents a conceptual framework for inter-hemocyte communication mechanisms in lepidopteran cellular immunity. Full article

Background/Objectives: Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is the sentinel implant-associated malignancy, illustrating how long-lived biomaterials can reshape local tissue–immune ecology. Although textured (high-surface-area) implants show the strongest epidemiologic association, the rarity of disease despite widespread exposure suggests additional host modifiers. We synthesize evidence supporting a gene–environment (G × E) framework and critically appraise emerging host-susceptibility signals (including BRCA1/BRCA2 and HLA associations). Methods: We conducted a narrative, evidence-based synthesis of peer-reviewed epidemiologic and registry studies, peri-implant niche biology (biofilm/foreign-body response and cytokine milieu), tumor genomic profiling, and current guidelines/regulatory communications, prioritizing primary studies for key claims. Results: Textured exposure dominates risk attribution, whereas absolute-risk estimates vary with denominators, exposure ascertainment, and follow-up duration. Mechanistic studies support a chronically inflamed capsule niche. Genomic analyses repeatedly converge on JAK/STAT pathway activation with frequent co-alterations in epigenetic regulators and recurrent copy-number changes, consistent with stepwise evolution under sustained selection. Immune-evasion features—including frequent PD-L1 expression and CD274 (9p24.1) copy-number alterations—provide a plausible checkpoint route, while host-susceptibility signals remain preliminary and require multi-center, multi-ancestry replication. Conclusions: BIA-ALCL is a multistep, context-dependent lymphoma in which implant-mediated inflammation intersects with host susceptibility to enable somatic evolution and immune escape. Clinically, prevention currently relies on exposure mitigation, standardized risk communication, and symptom-driven evaluation; precision prevention will require integrative cohorts linking verified device exposure, immunogenetics, microenvironment profiling, and tumor multi-omics. Full article

Bovine respiratory syncytial virus (BRSV) is a major viral pathogen associated with bovine respiratory disease (BRD), a leading cause of illness and economic loss in cattle worldwide. In June 2022, an acute respiratory outbreak occurred in a dairy herd in Photharam District, Ratchaburi Province, Thailand, affecting 25 of 103 cows (24.3%) and resulting in three deaths (2.9%). This study aimed to confirm BRSV as the etiological agent of the outbreak and to genetically and phylogenetically characterize Thai BRSV strains using partial G gene sequencing. Clinical signs included fever, nasal discharge, coughing, and subcutaneous emphysema. Nested reverse transcription-polymerase chain reaction (nested RT-PCR), a sensitive method for detecting viral RNA and targeting the F and G genes, confirmed BRSV in all samples. At the same time, bovine parainfluenza virus type 3 (BPIV-3), bovine viral diarrhea virus (BVDV), and bovine herpesvirus 1 (BoHV-1) were not detected. Phylogenetic analysis of partial G gene sequences showed that all Thai isolates clustered closely within subgroup III, with 100% nucleotide identity among themselves and 85.9–97.7% similarity to subgroup III strains from other countries. Amino acid alignment indicated conservation of key antigenic motifs, including the cysteine noose, with only minor substitutions compared to some foreign strains. This study provides the first genetic and phylogenetic characterization of BRSV in Thailand, highlighting the genetic stability of subgroup III and providing baseline molecular data to support regional surveillance, diagnostics, and vaccine strategies. Full article

Exogenous genes are generally expressed by integration into the chromosomes of Pichia pastoris. However, systematic studies on the chromosomal position effect are lacking, and locations that are conducive to the high expression of foreign genes are rarely reported. In this study, a genomic random insertion mutagenesis library for P. pastoris was successfully constructed using the piggyBac (PB) transposon system. Through sequencing, the sequence TTAA was identified as the major recognition site of the PB transposon, which exhibited relatively high coverage on P. pastoris chromosomes, making it a valuable tool for studying position effect variegation in P. pastoris. Using the enhanced green fluorescent protein gene (eGFP) as a reporter, two libraries including low-expression positions and high-expression positions were obtained by flow cytometry. The low-expression sites were mainly located upstream of ORFs around the promoter region and downstream near the terminator region, while the high-expression sites were predominantly located at the gene interior. KEGG and GO analyses showed that genes in high-expression positions were significantly enriched in the ATP-dependent chromatin remodeling and histone binding pathways, and genes in low-expression positions were significantly enriched in the MAPK signaling pathway, autophagy, mitochondrial autophagy, ABC transporters, and the arginine synthesis pathway. This study has clarified the genome-wide landscape of position effect variegation in P. pastoris. Additionally, it has provided novel insights into high-throughput screening strategies for strains with high exogenous gene expression. Full article

Cyanobacteria harbor sophisticated molecular defense systems that have evolved over billions of years to protect against viral invasion and foreign genetic elements. These ancient photosynthetic organisms possess a diverse array of restriction-modification (R-M) systems and CRISPR-Cas arrays that present challenges for genetic engineering, but also offer unique opportunities for cancer-targeted biotechnological applications. These systems exist in prokaryotes mainly as defense mechanisms but they are currently used in molecular applications as gene editing tools. Moreover, latest developments in nucleases such as zinc finger nucleases (ZFNs), TALENs (transcription-activator-like effector nucleases) are discussed. A comprehensive genomic analysis of 126 cyanobacterial species found 89% encode multiple R-M systems, averaging 3.2 systems per genome, creating formidable barriers to transformation but also providing molecular machinery that could be harnessed for precise recognition and targeting of cancer cells. This review critically examines the dual nature of these defense systems, their ecological functions, and the emerging strategies to translate their molecular precision into advanced anticancer therapeutics. Hence, the review main objectives are to explore the recent understanding of these mechanisms and to exploit the knowledge gained in opening new avenues for cancer-focused targeted interventions, while acknowledging the significant challenges to translate these systems from laboratory curiosities to practical applications. Full article

Ganoderma sichuanense is a widely used medicinal and edible fungus. Genomic studies have revealed substantial genetic variation among its different strains, indicating that a genetic transformation system optimized for one genotype may not be effective in others. However, no study has systematically evaluated the efficiency of a genetic transformation system across diverse genotypes, which has potentially limited functional genetic studies in this species. In this study, we first evaluated eight wild and cultivated monokaryotic strains with different genotypes based on their hygromycin B resistance and green fluorescent protein (GFP) expression efficiency. Three strains (CCMJ1500101, CCMJ1509001, and CCMJ1507802) were identified as capable of stable foreign gene expression, achieving transformation efficiencies of 20.0–66.7% via PEG-mediated protoplast transformation. Subsequently, a CRISPR/Cas9 system incorporating seven key elements to enhance editing efficiency was constructed and applied to these three strains using the ura3 gene as a test target. Gene editing efficiencies varied significantly among genotypes, ranging from 14.3% to 75.0%, confirming the system’s high efficacy and genotype dependence. Importantly, to rigorously assess the robustness and versatility of the established transformation platform, we further validated its broad applicability in the best-performing strain, CCMJ1500101, by successfully editing five functional genes involved in growth, development, and metabolism. Notably, gene inversion events were detected for the first time in edited transformants of Ganoderma, providing new clues for understanding non-homologous end joining (NHEJ) repair in this species. This study establishes a robust dual-sgRNA CRISPR/Cas9 platform for G. sichuanense and provides valuable strain resources to facilitate future gene functional studies and genetic improvement. Full article

The RNA interference machinery is crucial for regulating the activity of both native and foreign genes across all eukaryotes. The core protein families involved in this process are Dicer-like, Argonaute, and RNA-dependent RNA polymerase. However, plants exhibit remarkable diversity within each family and extensively use RNA interference mechanisms in their intricate immune responses. This review examines the role of RNA interference in plant interactions with various pathogens, including viruses, viroids, fungi, oomycetes, and bacteria. Plant diseases cause an estimated $220 billion in annual damage, with microorganisms accounting for approximately $150 billion. Hence, the focus is on the most severe plant diseases, specifically those caused by fungi and viruses. Additionally, recent biotechnological advancements are discussed, with an emphasis on the application of RNA interference for the development of novel plant defence strategies. Full article

There remains an urgent need for knowledge regarding the molecular and genetic mechanisms in Aedes aegypti to support the fight against mosquito-borne illness, one of these areas being xenobiotic transport. If xenobiotic transport is disrupted, the accumulation of foreign molecules can reach toxic levels, leading to mortality. Therefore, transport by transmembrane proteins is an important consideration in the processes that govern mosquito metabolism and survival. We have identified six genes we speculate to be novel organic cation transporters (OCTNs) or organic cation transporters (OCTs) in Ae. aegypti. To measure the potential function of these transporters, female Ae. aegypti were injected with a blood meal size bolus of saline containing the xenobiotics Alizarin Yellow GG, Alizarin Yellow R, and Olsalazine and then clearance was quantified. mRNA expressions were analyzed 2 h and 24 h post injections in relation to xenobiotic exposure. Our findings demonstrate that xenobiotics had limited effect on the putative transporter expression profiles, but the molecular structure of the xenobiotics dramatically modified the volume and composition of the excreted materials, as well as changing the mortality. Overall, the mechanisms and key players underlying Ae. aegypti xenobiotic transport remain largely uncharacterized, but the results of this study are an important step in expanding knowledge of OCT(N)s in mosquitoes and understanding mosquito physiology. Targeting these proteins may offer new avenues for mosquito control. Full article

Background/Objectives: Influenza A virus undergoes continuous antigenic drift, necessitating annual vaccine reformulation. Saudi Arabia faces unique epidemiological challenges owing to mass gatherings during religious pilgrimages and the dynamic movement of foreign workers. This study aimed to characterize the genetic diversity of hemagglutinin (HA) and neuraminidase (NA) genes of influenza A viruses circulating in Riyadh and to assess their match with vaccine strains during the 2024–2025 period. Methods: Nasopharyngeal samples (n = 363) were collected from patients presenting with influenza-like illness. RT-PCR was used for detection and subtyping. Sequence and phylogenetic analysis of the complete HA and NA gene sequences from A/H1N1pdm09 strains (n = 7) were then performed. Results: Of the 363 samples, 110 (30.3%) were positive for influenza A; among these, 68 (61.8%) were A/H1N1pdm09, and 42 (38.2%) were H3N2. Phylogenetic analysis revealed that all A/H1N1pdm09 strains belonged to clade 5a.1, distinct from vaccine strains. In comparison with the vaccine strain A/Wisconsin/67/2022, seven amino acid substitutions in the HA gene and eight in the NA gene were recorded in Saudi circulating strains. The significant genetic divergence between circulating A/H1N1pdm09 strains and current vaccine strains indicates potential vaccine mismatch. Conclusions: The significant genetic divergence between circulating A/H1N1pdm09 strains and current vaccine strains suggests potential vaccine mismatch. Continuous surveillance programs along with vaccination plans are necessary to tackle the changing influenza A virus strains in the special epidemiological context of Saudi Arabia. Full article

The HN pig, indigenous to Henan Province, is distinguished by its reduced lean meat yield and slower growth rates relative to commercial foreign breeds. To address these limitations, three hybrid combinations were generated through the crossbreeding of Huainan sows with Yorkshire, Landrace, and Berkshire sires. In this study, extensive transcriptomic and metabolomic analyses of the LD muscle were carried out for the first time, and carcass and meat quality characteristics were compared between hybrid and HN pigs. Slaughter and muscle quality assessments revealed that the lean meat percentage of LH and YH was significantly lower than that of HN, with YH exhibiting the lowest intramuscular fat level, indicating that this breed possesses enhanced lean meat production efficiency. Transcriptomic profiling revealed markedly increased expression of SLIT2, CH25H, NR4A2, NR4A1, FOSB, CRABP2, GDF10, and MRAP2 in all three hybrid groups compared to HN. Gene Ontology enrichment analysis identified that the skeletal muscle cell differentiation (GO:0035914) and transforming growth factor beta receptor signaling pathway (GO:0007179) were exclusively enriched in the YH vs. HN comparison. Non-targeted metabolomic analysis identified 31, 36, and 12 DAMs in BH vs. HN, LH vs. HN, and YH vs. HN comparisons, with pyruvate metabolism being the sole pathway common to all groups. An integrated multi-omics analysis revealed significant correlations between phytosphingosine levels and DEGs across all three comparisons. In summary, these results indicate that crossbreeding substantially improves lean meat yield in HN pigs while providing novel molecular insights into the underlying genetic and metabolic mechanisms. Full article

Background: The fat-tailed coarse-wooled sheep breeds exhibit excellent reproductive performance, exceptional adaptability to pasture conditions, and high precocity, contributing to enhanced meat, fat, and wool productivity in sheep breeding. Despite the significant role of these sheep breeds in Kazakhstan’s livestock production, their genetics remain poorly studied. This raises concerns about the potential loss of unique, breed-specific traits that could be important for the future development and resilience of Kazakh stan’s sheep farming sector. This study aimed to analyze genome-wide genotyping SNP data of local fat-tailed coarse-wooled sheep breeds (Kazakh fat-tailed coarse-wooled, Edilbay, and Gissar) to reveal their genetic diversity, breed characteristics, and phylogenetic relationships with worldwide domestic sheep breeds and wild sheep. Methods: The OvineSNP50 Genotyping BeadChip was used to obtain genome-wide SNP genotyping data from 160 fat-tailed coarse-wooled sheep from Kazakhstan. Population structure analysis, principal component analysis, phylogenetic and the maximum likelihood tree analysis were performed in comparison with foreign domestic sheep breeds and wild sheep populations. Results: Kazakh breeds exhibited high genetic diversity, with Edilbay showing the greatest allelic richness. PCA and Admixture revealed clear differentiation among the three breeds: Edilbay and Gissar formed homogeneous clusters, while Kazakh fat-tailed coarse-wooled sheep displayed admixture and substructure. Evidence of gene flow from Edilbay into other Kazakh populations supports its role as a genetic source for regional breeds. Phylogenetic analysis placed Kazakhstani sheep close to other Central Asian breeds, while clearly distinct from East Asian and European populations. Wild sheep (Argali and Urial) formed separate clades, with Kerman wild sheep clustering closer to Urial. Conclusions: Our results highlight the value of genotyping data for studying genetic diversity and population structure. Developing genetic resources for Kazakhstan’s native sheep breeds will help preserve their unique diversity and ensure it remains available for future use in breeding and adaptation efforts. Full article

Rational design of capripoxvirus-based vaccine vectors can be achieved by knockout of immunomodulatory genes. In this study, the effect of knockout of the immunomodulatory genes LSDV005, LSDV008 and LSDV066 on the replication of Lumpy skin disease virus in cell cultures and the immune response to an integrated foreign antigen were assessed. The knockout of genes was performed by homologous recombination under conditions of temporary dominant selection. It was found that single knockout of the LSDV005 gene and the LSDV008 gene did not affect the replicative activity of recombinant viruses in vitro (Atyrau-5 and Atyrau-B). Both single knockout of the LSDV066 gene and in combination with knockout of LSDV005 or LSDV008 led to a decrease in the replicative activity of recombinant LSDVs. The recombinant Atyrau-5J(IL18) with LSDV005 gene knockout induced production of antibodies to the integrated antigen in mice. Prime-boost vaccination with all studied recombinants increased the level of interferon-γ. In addition, during immunization with the recombinant Atyrau-5J(IL18) secretion of interleukin-2 was significantly increased. The study of the functions of immunomodulatory genes and their effect on the expression of inserted sequences of foreign antigens is promising for the creation of highly effective polyvalent vector vaccines for animals. Full article

α-Linolenic acid (ALA) is an important essential omega-3 (ω-3) polyunsaturated fatty acid for the maintenance of human health. Although ALA has traditionally been obtained from plant sources, microbial fermentation has emerged as a promising alternative for its sustainable and cost-effective production. However, most of the present approaches rely on genetically modified organisms, which present regulatory and consumer-acceptance concerns. In this study, we aimed to develop a high-ALA-producing strain of Aspergillus oryzae, a Generally Recognized As Safe (GRAS) microorganism widely used in food production in Japan, through self-cloning, a form of genetic engineering that utilizes only the host’s own DNA. To achieve this, an endogenous ω-3 desaturase gene (fad3), which catalyzes the conversion of linoleic acid to ALA, was identified via BLASTP analysis. Subsequently, a multicopy A. oryzae strain (Aofad3-MC) overexpressing fad3 was constructed. This strain increased ALA production, with ALA comprising 30.7% of the total lipids. Furthermore, k-mer analysis confirmed the absence of foreign vector sequences, verifying that Aofad3-MC was constructed through self-cloning. In addition to the identification of the A. oryzae ω-3 desaturase gene, this study provides a microbial platform for the sustainable production of ALA, with potential applications across the food, feed, and related industries. Full article

Cucumber green mottle mosaic virus (CGMMV) represents a serious threat in the production of watermelon. Small RNAs facilitate a mechanism known as RNA interference (RNAi), which regulates gene expression. RNAi technology employs foreign double-stranded RNAs (dsRNAs) to target and reduce the expression levels of specific genes in plants by interfering with their mRNAs. In this study, watermelon plants were treated with dsRNAs of CGMMV MET, IR, and HEL fragments that had been generated in E. coli HT115. We investigated variations in several factors, including viral accumulation, virus-derived small interfering RNAs (vsiRNAs), and symptom severity. MET-dsRNA, IR-dsRNA and HEL-dsRNA dramatically decreased the symptoms of CGMMV in plants in the growth chamber test. Plants treated with viral-derived dsRNA showed a considerable decrease in both virus titers and vsiRNA levels. We also explored the mobility of spray-on dsRNA-derived long dsRNA and discovered that it could be identified in both inoculated leaves and the systemic leaves. IR-dsRNA outperformed MET-dsRNA and HEL-dsRNA in dsRNA therapy. Illumina sequencing of small RNAs from watermelon plants treated with IR-dsRNA and those that were not treated showed that the decreased accumulation of vsiRNAs was consistent with interference with CGMMV infection in systemic leaves. dsRNA-treated plants showed a higher level of 24-nt viral siRNA and lower level of 22-nt viral siRNA accumulation, while 22-nt viral siRNA predominated in untreated plants, indicating that dsRNA treatment improved DCL3 activity. In conclusion, our research provides deeper insights into the mechanism of antiviral RNA interference and confirms the effectiveness of applying dsRNA locally to enhance plant antiviral activity. Full article