Search Results (134)

The giant freshwater prawn Macrobrachium rosenbergii is a globally farmed decapod species of high economic and nutritional value, but its genetic improvement has been constrained by the lack of an efficient genome editing workflow. Here, we optimized a CRISPR/Cas9 microinjection system for targeted mutagenesis in M. rosenbergii embryos. A controlled mating-based approach enabled routine collection of one-cell embryos, and developmental staging identified 0.5–2 h post-fertilization as the optimal injection window. Optimization of the needle tip (~1 μm) minimized mechanical damage, lowering early embryo mortality to ~10%. Using this system, the eye-development gene MrPAX6 and the sex-related gene MrIAG were successfully edited. MrPAX6 editing produced a 46.9% mutation rate and an average 50% reduction in eye pigment area. MrIAG editing achieved an 84% mutation rate, while post-injection survival to hatching was approximately 35%. These results establish an efficient and reproducible CRISPR/Cas9 editing system in M. rosenbergii, providing a foundation for functional genomics and genetic improvement in this commercially important prawn species. Full article

Three main hypotheses have been proposed to explain the origin of viruses: the exogenisation (escape) hypothesis, suggesting that mobile genetic elements gained infectivity and autonomy; the degeneration hypothesis, proposing that viruses arose through gene loss from more complex, possibly cellular ancestors; and the virus-first hypothesis, which argues that viruses are ancient, pre-cellular entities. This review evaluates these models in light of molecular, structural, and ecological evidence. Key considerations include the lack of homologues for many viral proteins, the presence of giant DNA viruses with extensive gene repertoires, the conservation of capsid structures across diverse viruses, and the universal dependence of viruses on living hosts. Also discussed is the vast diversity of the global virosphere revealed by recent metaviromic studies, particularly in marine ecosystems, where viruses play key roles in structuring microbial communities and driving biogeochemical cycles. Such findings highlight that viruses are integral components of biological systems rather than merely parasitic outliers. Although no single hypothesis fully explains the origin of all viruses, their extraordinary genetic and functional complexity suggests a unified evolutionary theory may forever remain elusive. Rather, understanding the origins of viruses requires integrating genomic traits with ecological roles across their wide diversity. Full article

Although giant viruses have introduced new perspectives on the definition and evolution of viruses and are increasingly recognized for their significant biological roles within marine ecosystems, systematic evaluations of development trends and scientific contributions in this research field remain limited. This study conducted a bibliometric analysis of the global academic literature on marine giant viruses (MGVs), focusing on nucleocytoplasmic large DNA viruses (NCLDVs), from 1996 to 2024. Using the Web of Science Core Collection, 1544 publications related to giant viruses were identified. After filtering using marine-related keywords and manual review, 300 studies specifically addressing marine giant viruses were selected for the final analysis. This study comprehensively examined the structural characteristics and evolutionary trends in this field by analyzing annual publication productivity, citation patterns, contributions by countries and institutions, author collaboration networks, and keyword co-occurrence patterns. The results show that research on MGVs has steadily increased since the mid-2000s, with a notable surge after 2018 driven by advancements in metagenomics, next-generation sequencing technologies, and global ocean exploration initiatives. The United States and France have taken leading positions in terms of research productivity and impact, with key institutions such as the CNRS (Centre National de la Recherche Scientifique) and Aix-Marseille Université playing central roles. A multipolar network of international collaborations between countries and institutions has been formed. Research topics have evolved from an early focus on virus classification and genome analysis to more diverse themes, including interactions with marine microbiota, viral ecological functions, infection dynamics, virophage research, and metagenome-based ecosystem-level studies. This study provides an overview of the chronological and structural evolution of the marine giant virus research field by systematically presenting key research themes and collaborative networks. The results provide a valuable foundation for determining future academic directions and planning strategic research initiatives. Furthermore, it is expected to facilitate interdisciplinary research in marine biology, environmental science, systems biology, and artificial intelligence-based functional predictions. Full article

Specialized herbivores like giant pandas (Ailuropoda melanoleuca), red pandas (Ailurus fulgens), and bamboo rats, which primarily consume bamboo, are at risk of nutrient deficiencies, particularly vitamin B12 (VB12), potentially leading to cardiovascular diseases. This study explored the effects of VB12 supplementation on cardiovascular health in silver star bamboo rats (Rhizomys pruinosus). We first conducted a comprehensive genome annotation of R. pruinosus, laying the foundation for in-depth evolutionary studies. Comparative transcriptomic analysis revealed that genes related to cardiovascular disease (e.g., Sgcb, Adcy2, Itga1, Itgb8, Ifng, and Gpc1) were upregulated in the livers of R. pruinosus compared to carnivorous and omnivorous rodents, indicating a higher cardiovascular disease risk. After 60 days of VB12 supplementation, liver transcriptome analysis revealed significant improvements in cardiovascular health markers, including reduced cholesterol synthesis and enhanced fatty acid metabolism. Serum biochemical assays indicated that VB12 supplementation led to reduced homocysteine levels, decreased low-density lipoprotein (LDL)-to-high-density lipoprotein (HDL) ratios, and increased the apolipoprotein A-to-apolipoprotein B ratio. These findings suggest that VB12 may mitigate cardiovascular disease risk and could be considered in the dietary management of specialized bamboo-eating species. Our study provides valuable insights into disease prevention strategies for these species with similar dietary habits. Full article

Tropical forage crops vary widely in biochemical composition, resulting in inconsistent silage quality. Understanding how plant traits shape microbial and metabolic networks during ensiling is crucial for optimizing fermentation outcomes. Eight tropical forages—Sorghum bicolor (sweet sorghum), Sorghum × drummondii (sorghum–Sudangrass hybrid), Sorghum sudanense (Sudangrass), Pennisetum giganteum (giant Napier grass), Pennisetum purpureum cv. Purple (purple elephant grass), Pennisetum sinese (king grass), Leymus chinensis (sheep grass), and Zea mexicana (Mexican teosinte)—were ensiled under uniform conditions. Fermentation quality, bacterial and fungal communities (16S rRNA and ITS sequencing), and metabolite profiles (untargeted liquid chromatography–mass spectrometry, LC-MS) were analyzed after 60 days. Sweet sorghum and giant Napier grass showed optimal fermentation, with high lactic acid levels (111.2 g/kg and 99.4 g/kg, respectively), low NH₄⁺-N (2.4 g/kg and 3.1 g/kg), and dominant Lactiplantibacillus plantarum. In contrast, sheep grass and Mexican teosinte exhibited poor fermentation, with high NH₄⁺-N (6.7 and 6.1 g/kg) and Clostridium dominance. Fungal communities were dominated by Kazachstania humilis (>95%), while spoilage-associated genera such as Cladosporium, Fusarium, and Termitomyces proliferated in poorly fermented silages. Metabolomic analysis identified 15,827 features, with >3000 significantly differential metabolites between silages. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed divergence in flavonoid biosynthesis, lipid metabolism, and amino acid pathways. In the sweet sorghum vs. sheep grass comparison, oxidative stress markers ((±) 9-HODE, Agrimonolide) were elevated in sheep grass, while sweet sorghum accumulated antioxidants like Vitamin D3. Giant Napier grass exhibited higher levels of antimicrobial flavonoids (e.g., Apigenin) than king grass, despite both being dominated by lactic acid bacteria. Sorghum–Sudangrass hybrid silage showed enrichment of lignan and flavonoid derivatives, while Mexican teosinte accumulated hormone-like compounds (Gibberellin A53, Pterostilbene), suggesting microbial dysbiosis. These findings indicate that silage fermentation outcomes are primarily driven by forage-intrinsic traits. A “forage–microbiota–metabolite” framework was proposed to explain how plant-specific properties regulate microbial assembly and metabolic output. These insights can guide forage selection and development of precision inoculant for high-quality tropical silage. Full article

The majority of giant algal viruses belong to the family Phycodnaviridae, class Algavirales, phylum Nucleocytoviricota. Among them, the genus Chlorovirus is the most studied, with three recognized groups based on genomics and host range, although many fundamental questions remain to be elucidated, particularly regarding their diversity. In this study, we focus on betachloroviruses, a poorly explored subgroup that infects the alga Micractinium conductrix Pbi. Here, we describe the isolation and genomic analysis of 11 new betachloroviruses from water samples collected in Nebraska, USA. With 25 fully sequenced genomes now available, we assessed the genomic diversity of these viruses. They have double-stranded DNA genomes ranging from 295 to 374 kbp, encoding hundreds of ORFs, of which a large number (~40%) lack known function. Comparative genomics and phylogenetic analyses revealed three species of betachlorovirus, each with high intra-species genomic identity. Notably, some isolates with over 99.5% genomic identity display markedly different plaque phenotypes, which led us to propose the use of the term genomovar among giant algal viruses, a concept potentially applicable to other giant viral groups yet to be explored. Altogether, this work advances our understanding of betachloroviruses and highlights the importance of linking viral genotype to phenotype, opening new avenues for exploring the diversity of giant algal viruses. Full article

Proteus mirabilis is a zoonotic pathogen that poses a growing threat to both animal and human health due to rising antimicrobial resistance (AMR). It is widely found in animals, including China’s nationally protected captive giant and red pandas. This study isolated Proteus mirabilis from panda feces to assess AMR and virulence traits, and used whole-genome sequencing (WGS) to evaluate the spread of resistance genes (ARGs) and virulence genes (VAGs). In this study, 37 isolates were obtained, 20 from red pandas and 17 from giant pandas. Multidrug-resistant (MDR) strains were present in both hosts. Giant panda isolates showed the highest resistance to ampicillin and cefazolin (58.8%), while red panda isolates were most resistant to trimethoprim/sulfamethoxazole (65%) and imipenem (55%). Giant panda-derived strains also exhibited stronger biofilm formation and swarming motility. WGS identified 31 ARGs and 73 VAGs, many linked to mobile genetic elements (MGEs) such as plasmids, integrons, and ICEs. In addition, we found frequent co-localization of drug resistance genes/VAGs with MGEs, indicating a high possibility of horizontal gene transfer (HGT). This study provides crucial insights into AMR and virulence risks in P. mirabilis from captive pandas, supporting targeted surveillance and control strategies. Full article

Three novel Aeromonas phages vB_AerVS_332-Yuliya, vB_AerVM_332-Vera, and vB_AerVM_332-Igor and their host Aeromonas veronii CEMTC7594 were found in the same water + sediments sample collected in a freshwater pond. Complete genome sequencing indicated that vB_AerVS_332-Yuliya (43,584 bp) is a siphophage, whereas vB_AerVM_332-Vera (294,685 bp) and vB_AerVM_332-Igor (237,907 bp) are giant phages. The host strain can grow at temperatures from 5 °C to 37 °C with an optimum of 25–37 °C; siphophage vB_AerVS_332-Yuliya effectively reproduced at temperature ≤ 25 °C, the optimal temperature for giant phage vB_AerVM_332-Igor was 25 °C, and giant phage vB_AerVM_332-Vera infected host cells at 5–10 °C. The genomes of these phages differed significantly from known phages; their level of nucleotide identity and values of intergenomic similarity with the corresponding neighboring phages indicated that each of these phages is a member of a new genus/subfamily. Giant phage vB_AerVM_332-Vera is a member of the proposed Chimallinviridae family, which forms Cluster D of giant phages that possibly evolved from phages with shorter genomes. Giant phage vB_AerVM_332-Igor is part of Cluster E, the known members of which preserve the size of genomes. Phages from Cluster F, containing Aeromonas phages among others, show a gradual decrease and/or increase in genomes during evolution, which indicates different strategies for giant phages. Full article

In recent years, viral and bacterial diseases have posed serious challenges to the sustainable development of Macrobrachium rosenbergii (giant freshwater prawn) aquaculture, resulting in considerable economic losses across China. Among the bacterial pathogens, Aeromonas caviae has emerged as a notable opportunistic agent capable of causing large-scale mortality in various aquatic species. In this study, a highly virulent strain of A. caviae (designated GMRS4) was isolated from diseased M. rosenbergii exhibiting mass mortality in Yangzhou, Jiangsu Province. The isolate, a Gram-negative bacillus, was identified as the causative agent based on morphological, molecular, and histopathological analyses. Pathogenicity was confirmed through experimental infection, with the strain displaying marked virulence, evidenced by an LD₅₀ of 1.91 × 10⁶ CFU/mL at 96 h. Whole-genome sequencing of GMRS4 revealed 4078 coding sequences, including a suite of virulence-associated genes encoding extracellular enzymes (DNase, hemolysin, caseinase, and lecithinase) and toxins (serine protease, elastase, and flagellin). Antimicrobial susceptibility testing indicated resistance to several antibiotics, particularly those in the penicillin and sulfonamide classes, while maintaining sensitivity to quinolones. Genomic analysis further revealed multiple antibiotic resistance genes and virulence genes, offering insights into the pathogenic mechanisms and resistance profile of the strain. This study underscores the threat posed by A. caviae to freshwater prawn aquaculture and provides a genetic basis for developing targeted disease management strategies. Full article

A histological evaluation remains the cornerstone of diagnosing highly malignant osteosarcoma, having demonstrated its efficacy and reliability over several decades. However, despite these advancements, misdiagnoses with severe consequences, including inadequate surgical procedures, continue to occur. Consequently, there is a pressing need to further enhance diagnostic security. Adjunct immunohistochemical approaches have demonstrated significant effectiveness in regard to cancer diagnostics, generally. However, their utility for identifying highly malignant osteosarcoma is limited. Molecular genetic findings have significantly improved the diagnosis of Ewing’s sarcoma by identifying specific translocations and have been used to detect specific IDH gene mutations in chondrosarcoma. Nevertheless, molecular genetic alterations in highly malignant osteosarcoma exhibit a high degree of complexity, thereby limiting their diagnostic utility. Given that only 1–2% of the human genome comprises protein-coding sequences, the growing number of non-coding regulatory RNAs, which are increasingly being elucidated, has garnered substantial attention in the field of clinical cancer diagnostics. Over the past several years, patterns of altered non-coding RNA expression have been identified that facilitate the distinction between benign and malignant tumors in various organs. In the field of bone tumors, the experience of this approach has been limited thus far. The divergent expression of microRNAs has demonstrated utility for differentiating osteosarcoma from osteoblastoma and discriminating between osteosarcoma and giant-cell tumors of bone and fibrous dysplasia. However, the application of non-coding RNA expression patterns for the differential diagnosis of osteosarcoma is still in its preliminary stages. This review provides an overview of the current status of non-coding RNAs in osteosarcoma diagnostics, in conjunction with a histological evaluation. The potential of this approach is discussed comprehensively. Full article

Interactions between bacteria and bacteriophages are important for the maintenance of soil communities. In this study, we characterized the giant bacteriophages found within diverse soil bacteria and 14 additional phages isolated directly from soil samples. Based on their genome sizes and genetic composition, we concluded that these phages belong to the Dolichocephalovirinae subfamily. In addition, we used pulsed-field gel electrophoresis to show that the genomes of these phages were present as episomal pseudolysogens in the cytoplasm of their host cells. These findings suggest that episomal phages are important components of soil microbial ecosystems. Understanding the interactions between bacteriophages and bacteria is essential for microbial ecology, as they influence nutrient cycling, community composition, and host evolution. Furthermore, these phage-bacteria dynamics offer potential applications in plant disease control, as bacteriophages could serve as biocontrol agents against soilborne pathogens, promoting sustainable agricultural practices. Full article

Clostridioides difficile Infection (CDI) continues to be a major cause of antibiotic-associated diarrhea and pseudomembranous colitis, fueled in large measure by virulence factors TcdA and TcdB. These giant glucosyltransferase toxins interfere with host cytoskeletal integrity and inflammatory signaling by inhibiting Rho GTPase; however, the detailed structural dynamics, receptor selectivity, and subcellular trafficking mechanisms remain in part unspecified. This review integrates recent insights from cryo-electron microscopy (cryo-EM) and X-ray crystallography to describe the quaternary architecture of TcdA/B, emphasizing conformational changes key to pore formation and endosomal escape. We also examine the genomic heterogeneity of hypervirulent C. difficile strains (e.g., ribotype 027), correlating toxin gene polymorphisms (e.g., tcdC mutations) with increased toxin production and virulence. Mechanistic explanations of toxin-driven inflammasome activation and epithelial barrier dysfunction are situated within host immune evasion mechanisms, including microbiota-derived bile acid regulation of toxin stability. Subsequent innovative therapeutic strategies, encompassing the utilization of engineered neutralizing antibodies that specifically target the autoprocessing domain alongside structure-guided small-molecule inhibitors, are subjected to a rigorous evaluation. By integrating structural biology, systems-level omics, and clinical epidemiology, this review establishes a comprehensive framework for understanding C. difficile toxin pathogenesis and guiding next-generation precision antimicrobials. Full article

Microtubule-actin cross-linking factor 1 (MACF1), also known as actin cross-linking family protein 7 (ACF7), is a giant cytolinker protein with multiple conserved domains that can orchestrate cytoskeletal networks of actin and microtubules. MACF1 is involved in various biological processes, including cell polarity, cell–cell connection, cell proliferation, migration, vesicle transport, signal transduction, and neuronal development. In this review, we updated the physiological and pathological roles of MACF1, highlighting the components and signaling pathways involved. Novel evidence showed that MACF1 is involved in diverse human diseases, including multiple neuronal diseases, congenital myasthenic syndrome, premature ovarian insufficiency, spectraplakinopathy, osteoporosis, proliferative diabetic retinopathy, and various types of cancer. We also reviewed the physiological roles of MACF1, including its involvement in adhesome formation, bone formation, neuronal aging, and tooth development. In addition, MACF1 plays other roles, functioning as a biomarker for the prediction of infections in patients with burns and as a marker for genome selection breeding. These studies reinforce the idea that MACF1 is a bona fide versatile, multifaceted giant protein. Identifying additional MACF1 functions would finally help with the treatment of diseases caused by MACF1 defects. Full article

Translation is a sine qua non process for life as we know it. Translation factors (TFs) and tRNAs are rare among viruses but are commonly found in giant viruses of the class Megaviricetes. In this study, we explored the diversity and distribution of tRNAs in giant viruses that were isolated and replicated in amoebae (phylum Amoebozoa), and investigated the evolutionary history of TFs to gain insights into their origins in these viruses. We analyzed the genomes of 77 isolated giant viruses, 52 of which contained at least 1 tRNA. In most of these viruses, tRNA sequences are dispersed throughout the genome, except in Tupanviruses and Yasmineviruses, where most tRNAs are clustered in specific genomic islands. The tRNAs in giant viruses often contain introns, with 73.1% of the genomes exhibiting at least one intronic region in these genes. Codon usage bias (CUB) analysis of various giant viruses revealed at least two distinct patterns of codon preferences among closely related viruses. We did not observe a clear correlation between the presence of tRNAs and CUB in giant viruses. Due to the limited size of these genes, we could not confidently investigate their phylogenetic relationships. However, phylogenetic analysis of TFs found in giant viruses often position these viruses as sister groups or embedded between different eukaryotic taxa with high statistical support. Overall, our findings reinforce the complexity of key components of the translation apparatus in different members of Nucleocytoviricota isolated from different regions of Earth. Full article

Members of the Dolichocephalovirinae subfamily are giant viruses with an elongated head and a flexible tail that is used to infect Caulobacter strains. In this paper, we describe the isolation and characterization of nine newly isolated phages and present evidence that seven of these phages represent a new Dolichocephalovirinae genus that has significant differences from the four previously described Dolichocephalovirinae genera. In addition, since these new phages were isolated from a single sampling site over the course of three years, a comparison of their genome sequences reveals a low level of within-population diversity resulting from both single-nucleotide polymorphisms and insertions or deletions. A comparison of the host ranges of these phages suggests that differences in host susceptibility may be an important factor in maintaining this diversity. Full article