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A new species of the genus Panagrolaimus, P. hamomucronatus sp. n., is described from oak bark with lichens in the southern Iberian Peninsula. This species is characterised by having body 1.15-1.18 mm long in females and 0.91-1.16 mm long in males, habitus slightly sigmoid after fixation in females and ‘J’-shaped in males, cuticle with transverse striations, lateral fields with three longitudinal incisures, a lip region with six conoid lips ending in a setiform process, amphids rounded to oval, stoma with cheilostom bearing scarcely refringent rhabdia, a gymnostom as long as wide with very refringent rhabdia and stegostom short with well-sclerotised rhabdia, pharynx with pharyngeal corpus subcylindrical (1.6-1.9 times isthmus length) with metacorpus not swollen, nerve ring surrounding the anterior part of the isthmus, excretory pore at isthmus level, deirids at level of the isthmus, female reproductive system monodelphic-prodelphic with ovary without flexures and post-vulval uterine sac 0.6-0.7 times the corresponding body diam. long, rectum 1.3-1.5 times anal body width long, female tail conoid with fishhook-like mucron and phasmids at 73-76% of its length, male reproductive system monorchid with testis ventrally flexioned anteriorly, eight pairs of genital papillae (three precloacal and five postcloacal) with phasmids located posterior to the papilla GP6, spicules with manubrium ventrally bent and lamina with reduced dorsal hump and well-developed ventral velum, and gubernaculum slightly deltoid. Its phylogenetic position is studied based on 18S rDNA. An updated list of species is provided together with a new illustrated key to species identification. [ABSTRACT FROM AUTHOR]

The superfamily Pseudocerotoidea Lang encompasses Euryleptidae Stimpson, Pseudocerotidae Lang, and Stylostomidae Dittman. These families include conspicuous, flamboyant marine flatworms with a worldwide distribution. Here, we describe a new euryleptid species belonging to Prostheceraeus Schmarda, 1859, based on specimens collected by dredging at depths of 100–180 m off Misaki, Japan. The new species, Prostheceraeus fragumsp. n., is distinguished by its unique dorsal colouration in that oval red maculae are radially distributed along the translucent cream body periphery. Additionally, based on newly collected topotypic specimens, we transfer the poorly known pseudocerotid species Pseudoceros sagamianus Kato, 1937, to the genus Phrikoceros Newman and Cannon, 1996. These specimens possess (1) a pharynx with shallow, simple folds, (2) a deeply ruffled body margin, and (3) ear-like pseudotentacles with folds. Our molecular phylogeny, based on partial 18S and 28S rDNA sequences, yielded two key findings: (1) Pr. fragumsp. n. nested within the clade containing all other Prostheceraeus species, and (2) Phrikoceros sagamianuscomb. n. formed a clade with all other Phrikoceros and Monobiceros species, distinct from the Pseudoceros clade. These results support the generic affiliations established through our morphological examinations. Furthermore, based on the resulting phylogenetic trees, we discuss the systematics of Euryleptidae in relation to Stylostomidae. [ABSTRACT FROM AUTHOR]

To battle seasonal outbreaks of influenza B virus infection, which continue to pose a major threat to world health, new and improved vaccines are urgently needed. In this article, we discuss the current state of next-generation influenza B vaccine development, including both advancements and challenges. This review covers the shortcomings of existing influenza vaccines and stresses the need for more-effective and broadly protective vaccines and more-easily scalable manufacturing processes. New possibilities for vaccine development have emerged due to recent technical developments such as virus-like particle (VLP) platforms, recombinant DNA technologies, and reverse genetics. By using these methods, vaccines can be developed that elicit stronger and longer-lasting immune responses against various strains of influenza B virus. Vaccines may be more effective and immunogenic when adjuvants and new delivery mechanisms are used. Progress has been made in the development of influenza B vaccine mRNA vaccines, nanoparticle-based vaccines, and vector-based vaccines. However, there are still several obstacles to overcome before next-generation influenza B vaccines can be widely used, including the challenge of antigenic drift, the extinction of the B/Yamagata lineage, and difficulties in strain selection. There are also other challenges related to public acceptance, vaccine distribution, manufacturing complexity, and regulations. To overcome these challenges, scientists, politicians, and pharmaceutical firms must work together to expedite the development and licensing of vaccines and the establishment of immunization programs. The need for constant monitoring and quick adaptation of vaccines to match the currently circulating strains is further highlighted by the appearance of novel influenza B virus variants. To be ready for future pandemics and influenza B outbreaks, we need better vaccines and better monitoring systems. [ABSTRACT FROM AUTHOR]

The article discusses the Asilomar conference of 1975, where molecular biologists gathered to evaluate risks of recombinant DNA technology and establish guidelines for research. The legacy of Asilomar emphasizes scientific self-regulation and governance, aiming to secure public trust and future benefits of technology. However, the article raises concerns about the exclusionary nature of expert-driven governance, which may limit democratic oversight and public engagement in shaping technological futures. The text calls for a reevaluation of the role of science in American democracy, advocating for a more inclusive and deliberative approach to governance that aligns with societal values and aspirations. [Extracted from the article]

\nHighlightsTrebouxia microalgae have previously been mostly reported as lichen photobionts. However, in recent years, reports of their occurrence outside the lichen symbiosis has been more common. This study provides evidence of free-living Trebouxia species, as well as the re-evaluation of six strains from the Coimbra Collection of Algae (ACOI 1141, ACOI 1821, ACOI 2621, ACOI 2622, ACOI 2623 and ACOI 3426) obtained via micropipette single-cell isolation. The nuclear Internal Transcribed Spacer rDNA was sequenced to infer its phylogenetic position within Trebouxia genus. Strains ACOI 1141, ACOI 1821, ACOI 2621 and ACOI 3426 clustered in a large clade with a species-level lineage previously named as Trebouxia sp. A13. This lineage comprises sequences belonging to three previously described Trebouxia species: Trebouxia crenulata, Trebouxia arboricola and Trebouxia aggregata. Strain ACOI 2623 clustered with a species-level lineage not yet formally described, but previously detected and coded as Trebouxia sp. A19. ACOI 2622 separated into an independent clade distinct from all other sequences included in the dataset. This strain has not been previously identified as a species-level lineage in other studies, thus we code it as A60 and describe it as Trebouxia valentina sp. nov. based on morphological, ultrastructural, molecular and phylogenetic analyses. Our findings highlight the ability of these microalgae, typically associated with lichens, to thrive independently and expand our understanding of their biology and ecology. Free-living Trebouxia species were isolated and added to the ACOI.ACOI 2623 clustered with a species-level lineage not yet described.ACOI 2622 is here described as Trebouxia valentina sp. nov.Free-living Trebouxia species were isolated and added to the ACOI.ACOI 2623 clustered with a species-level lineage not yet described.ACOI 2622 is here described as Trebouxia valentina sp. nov. [ABSTRACT FROM AUTHOR]

[Objective] In order to isolate and identify the pathogen of root rot of Knoxia roxburghii and master the biological characteristics of the pathogen. [Method] According to the morphological characteristics of the pathogen, combined with ITS-5.8S rDNA, tub2 and ACT sequence analysis, the pathogenicity test was carried out according to Koch's Rule. [Result] The morphologically consistent pathogen was reisolated from the inoculated plants and finally identified as Boeremia exigua. The studies of biological characteristics showed that the optimum growth medium of pathogen was PDA, the optimum growth temperature was 20 °C or 25 °C, and the optimum pH was 5. The optimum carbon source was lactose, and the optimum nitrogen source was potassium nitrate. [Conclusion] This is the first report of B.exigua causing root rot of K. roxburghii in China. Mastering its biological characteristics will lay a theoretical foundation for the prevention of root rot of K. roxburghii. [ABSTRACT FROM AUTHOR]

AbstractDuring an investigation of Korean Ascomycetes in 2023, we found two undescribed species from South Korea. We analyzed them using a combined approach, including morphological and phylogenetic analyses of the rDNA regions (internal transcribed spacer and large subunit). The two species were identified to belong to the genus Geoglossum; the species G. simile and a new species named G. subdifforme sp. nov. The phylogenetic tree constructed using the ITS region showed that G. subdifforme is closely related to G. difforme. These species are distinguishable by certain morphological characteristics, particularly the size and septae of ascospores. Morphologically, G. simile is related to G. glabrum, but it is distinguishable by the morphological characteristics of paraphyses as well as ITS sequences. In this study, the descriptions, photographs, and phylogenetic relationships of these Geoglossum species are presented. [ABSTRACT FROM AUTHOR]

The Chikungunya virus (CHIKV) is a mosquito-borne virus with a long history of recurring epidemics transmitted through Aedes mosquitoes. The rapid spread of CHIKV has intensified the need for potent vaccines. Escherichia coli (E.coli), a vital part of human gut microbiota, is utilized in recombinant DNA technology for cloning. However, its high adaptability can lead to severe infections in humans. This study aimed to develop the candidate dual vaccine against CHIKV and E. coli. For this, we expressed the CHIKV E2 protein in the E. coli Rosetta Bl21 cells and the protein expression was confirmed by western blotting. The IgG immune response of the candidate vaccine was determined against CHIKV and E. coli by ELISA. Further, the potential of antibodies to neutralize CHIKV was evaluated via Tissue Culture Infectious Dose 50 (TCID50). We observed that cells expressing E2 protein with alum immunized mice serum showed a five-fold higher IgG immune response against CHIKV, compared to control cells. The CHIKV neutralization assay results showed a two-fold decrease in CHIKV TCID50 value after 12 hours and a three-fold reduction after 120 hours. Similarly, the vaccine formulation also elicited a significantly higher IgG immune response against E. coli. The results suggested that expressing CHIKV E2 protein in E. coli is a potential approach for generating an IgG immune response against CHIKV and E. coli both. This study proposes a faster, safer, and cost-effective recombinant protein-based vaccine development. [ABSTRACT FROM AUTHOR]

Copyright of Food & Fermentation Industries is the property of Food & Fermentation Industries and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Posidonia oceanica retains a large amount of carbon within its belowground recalcitrant structure, the 'matte,' which is characterized by low oxygen availability and biodegradation. Fungi may play a pivotal role in carbon sequestration within the matte, even if little/no information is available. To fill this gap, we profiled fungal communities from the upper and lower layers of alive and dead matte, by using an ITS2-5.8S rDNA metabarcoding approach. The study was conducted in a shallow coastal stretch of the Aegean Sea (Crete). Then, 184 operational taxonomic units were identified, predominantly belonging to Ascomycota, in alive and dead matte. Nevertheless, their composition significantly differed: the host-specific Posidoniomyces atricolor was dominant in alive but not in dead matte, while fast-growing saprotrophs, potentially accelerating the decomposition rate, increased in dead matte. These findings lay the groundwork for future investigations on the possible increase of biodegradation under the changing environmental conditions. [ABSTRACT FROM AUTHOR]

There is limited information on the occurrence of Hyalomma turanicum and Hyalomma asiaticum ticks, as well as associated Rickettsia, Anaplasma, and Ehrlichia species in Pakistan. Addressing this knowledge gap, the current study aimed at morphomolecular confirmation of these ticks and molecular assessment of associated Rickettsiales bacteria (Rickettsia, Anaplasma , and Ehrlichia spp.) in Balochistan, Pakistan. A total of 314 ticks were collected from 74 of 117 (63.2%) hosts, including 41 of 74 (55.4%) goats and 33 of 74 (44.5%) sheep. Subsequently, a subset of microscopically identified ticks was subjected to DNA extraction and PCR to amplify 16S rDNA and cox1 fragments. Additionally, gltA , ompA, and ompB fragments were targeted for Rickettsia spp. and 16S rDNA fragments for both Anaplasma and Ehrlichia spp. The 16S rDNA and cox1 sequences of Hy. turanicum demonstrated 100% identity with those of the same species previously reported from Pakistan. The 16S rDNA and cox1 sequences of Hy. asiaticum exhibited 99.52 and 100% identities, respectively, with corresponding species reported from China, Kazakhstan, and Turkey. The gltA, ompA, and ompB fragments associated with Hy. turanicum showed 100% identities with Rickettsia aeschlimannii reported from Egypt, Italy, Kazakhstan, Kenya, Pakistan, and Senegal. The 16S rDNA sequences of Anaplasma sp. and Ehrlichia sp. associated with both Hy. asiaticum and Hy. turanicum exhibited 99.67 and 100% identities with unknown Anaplasma sp. and Ehrlichia sp. reported from Morocco and Pakistan, respectively. In the 16S rDNA and cox1 phylogenetic trees of ticks, Hy. turanicum and Hy. asiaticum from the current study clustered with their respective species. Similarly, in gltA, ompA, and ompB phylogenetic trees of Rickettsia , R. aeschlimannii of the present study clustered with the same species, whereas Anaplasma sp. and Ehrlichia sp. of this study clustered with undetermined Anaplasma spp. and Ehrlichia spp. in the 16S rDNA phylogenetic tree of Anaplasmataceae. Among the DNA samples from the screened ticks, a coinfection rate of R. aeschlimannii , Anaplasma sp., and Ehrlichia sp. (2 of 80, 2.5%) was observed in Hy. turanicum , whereas individual infection rates were noted as follows: R. aeschlimannii (8 of 80, 10%), Anaplasma sp. (5 of 80, 6.3%), and Ehrlichia sp. (5 of 80, 6.3%). This study marks the first record of molecular characterization of Hy. turanicum and Hy. asiaticum as well as the detection of associated R. aeschlimannii , Anaplasma sp., and Ehrlichia sp. in Balochistan, Pakistan. [ABSTRACT FROM AUTHOR]

Bile salt hydrolase (BSH; EC 3.5.1.24) is the microbial enzyme that catalyzes the conversion of primary bile acids (BAs) into secondary ones, promoting microbial adaptation and modulating several host's biological functions. Probiotics with BSH activity are supposed to survive harsh intestinal conditions and exert a cholesterol-lowering effect. Here, Lacticaseibacillus rhamnosus strains (VB4 and VB1), isolated from the vaginal ecosystem, were submitted to a genomic survey, in vitro BSH activity, and BAs tolerance assay to unravel their probiotic potential as BAs modulators. The draft genomes of Lcb. rhamnosus VB4 and VB1 strains comprised 2769 and 2704 CDSs, respectively. Gene annotation revealed numerous strain-specific genes involved in metabolism and transport, as well as in DNA recombination. Each strain harbors a single bsh gene, encoding a C-N amide hydrolase, which conserved the essential residues required in the BSH core site. According to the results, compared to VB1, the VB4 strain tolerated better BAs stress and was more active in deconjugating BAs. However, BAs stress increased the bsh gene transcription in the VB1 strain but not in the VB4 strain, suggesting a partially nonlinear relationship between BSH activity and gene expression. In conclusion, despite the complexity of the BSH transcriptional system, the results support the VB4 strain as a promising BAs-deconjugating probiotic candidate. [ABSTRACT FROM AUTHOR]

Simple Summary: This study highlights the genetic diversity of Bulinus globosus in Kenya, demonstrating that the AkInt3 intron is a valuable marker for detecting detailed intra-specific genetic variation, surpassing COI sequences. The presence of DNA recombination between AkInt3 haplogroups suggests that cross-fertilization is a common reproductive strategy, which may reduce inbreeding effects. Additionally, evidence of potential polyploidy points to further genetic complexity, warranting more studies. The findings indicate that AkInt3 primers could aid genetic studies in other Bulinus species, with distinct haplogroups suggesting significant genetic diversity. Future research across Africa will be essential for understanding B. globosus evolution and its role in disease transmission. Urinary schistosomiasis is caused by the blood fluke Schistosoma haematobium, which is predominantly found in Africa. The freshwater snail Bulinus globosus is its main intermediate host. The species that make up the B. globosus group are genetically complex, and their taxonomic status remains controversial. Genetic variation, heterozygosity, and DNA recombination in B. globosus were examined using the mitochondrial cytochrome c oxidase subunit 1 (COI) and the intron 3 region of the arginine kinase gene (AkInt3). A total of 81 B. globosus snails were collected from three different localities in Kwale County, Kenya. Genomic diversity, heterozygosity, DNA recombination, and haplotype network were calculated using AkInt3 sequences. Low polymorphism in the COI sequence divided B. globosus into six haplotypes (C1–C6). However, AkInt3 sequencing studies showed high polymorphisms, classifying 81 B. globosus snails into 44 haplotypes (H1–H44). These haplotypes were separated into three haplogroups (I–III). AkInt3 sequence heterozygosity was also found. DNA recombination haplotypes between haplogroups were commonly found in heterozygous samples. AkInt3 sequence studies showed high levels of genetic polymorphism and heterozygosity, supporting its use as a genetic marker for elucidating the population genetics of B. globosus. Furthermore, our study showed that B. globosus populations in Kenya form a "species complex". [ABSTRACT FROM AUTHOR]

Gregarines from the families Dactylophoridae and Trichorhynchidae parasitize exclusively centipedes and have a distinct morphology among other terrestrial eugregarines, but their evolutionary relationships have not yet been studied with molecular methods. Here we obtain rDNA operon sequences for the dactylophorids and trichorhynchids. We describe a new species Trichorhynchus efeykini sp. n. from a scutigeromorph Thereuopoda longicornis from Vietnam. Phylogenetic analyses with combined SSU, 5.8S and LSU rDNA dataset support the previously proposed separation of Trichorhynchus to the Trichorhynchidae based on morphology and recover the dactylophorids and trichorhynchids as sister groups in a monophyletic clade. This clade appears sister to the clade of the Actinocephaloidea and Stylocephaloidea, and represents a new major lineage of terrestrial gregarines that we designate as a new superfamily Dactylophoroidea. [ABSTRACT FROM AUTHOR]

Gene-silencing by small interfering RNA (siRNA) is an attractive therapy to regulate cancer death, tumor recurrence or metastasis. Because siRNAs are easily degraded, it is necessary to develop transport and delivery systems to achieve efficient tumor targeting. Self-nanoemulsifying systems (SNEDDS) have been successfully used for pDNA transport and delivery, so they may be useful for siRNA. The aim of this work is to introduce siRNA-RAD51 into a SNEDDS prepared with Phospholipon-90G, Labrafil-M1944-CS and Cremophor-RH40 and evaluate its efficacy in preventing homologous recombination of DNA double-strand breaks caused by photodynamic therapy (PDT) and ionizing radiation (IR). The siRNA-RAD51 was loaded into SNEDDS using chitosan. Transfection capacity was estimated by comparison with Lipofectamine-2000. SNEDDS(siRNA-RAD51) induced gene silencing effect on the therapies evaluated by cell viability and clonogenic assays using T47D breast cancer cells. SNEDDS(siRNA-RAD51) shown to be an effective siRNA-delivery system to decrease cellular resistance in PDT or IR. [ABSTRACT FROM AUTHOR]

DNA double-strand breaks (DSBs) are nucleolytically processed to generate single-stranded DNA for homologous recombination. In Saccharomyces cerevisiae meiosis, this resection involves nicking by the Mre11–Rad50–Xrs2 complex (MRX), then exonucleolytic digestion by Exo1. Chromatin remodeling at meiotic DSBs is thought necessary for resection, but the remodeling enzyme was unknown. Here we show that the SWI/SNF-like ATPase Fun30 plays a major, nonredundant role in meiotic resection. A fun30 mutation shortened resection tracts almost as severely as an exo1-nd (nuclease-dead) mutation, and resection was further shortened in a fun30 exo1-nd double mutant. Fun30 associates with chromatin in response to DSBs, and the constitutive positioning of nucleosomes governs resection endpoint locations in the absence of Fun30. We infer that Fun30 promotes both the MRX- and Exo1-dependent steps in resection, possibly by removing nucleosomes from broken chromatids. Moreover, the extremely short resection in fun30 exo1-nd double mutants is accompanied by compromised interhomolog recombination bias, leading to defects in recombination and chromosome segregation. Thus, this study also provides insight about the minimal resection lengths needed for robust recombination. Synopsis: Chromatin remodeling is likely to be required for resection of DNA double-strand breaks (DSB) created during meiosis. Here, the SWI/SNF family chromatin remodeler Fun30 is found to play a uniquely important and nonredundant role in promoting DNA break resection during yeast meiosis, thereby enhancing recombination efficiency. Fun30 promotes both resection initiation by Mre11 and resection extension by Exo1. Fun30 is recruited directly to chromatin in response to DSB formation, and facilitates the ability of Mre11 and Exo1 nucleases to overcome the inhibitory effects of nucleosomes. Critically short resection tracts in fun30 exo1 double-mutant cells are associated with frequent recombination failure caused by a loss of interhomolog recombination bias. The yeast SWI/SNF family chromatin remodeler Fun30 plays a uniquely important and nonredundant role in promoting DNA break resection during meiosis, thereby enhancing recombination efficiency. [ABSTRACT FROM AUTHOR]

Copyright of Food & Fermentation Industries is the property of Food & Fermentation Industries and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Botryobasidium bambusinum sp. nov. was collected in Yunnan Province, China, is described here as a new species based on its morphology and phylogeny. In this study, the taxon Botryobasidium bambusinum is characterised by its resupinate, coriaceous conidiomata with a smooth, hypochnoid, rubiginous to slightly reddish-brown hymenial surface, a slightly thick-walled basal hyphae with simple septa, subcylindrical, septate subglobose to globose, slightly thick-walled conidia measuring as 7.2–9.5 × 7–9 µm. Phylogenetic analyses of the new species were based on the internal transcribed spacer (ITS) and large subunit (nrLSU) of ribosomal DNA (rDNA) sequences. The phylogenetic tree indicated that the new species belonged to the genus Botryobasidium, and was closely related to B. gossypirubiginosum, B. rubiginosum and B. simile. Botryobasidium gossypirubiginosum differs from B. bambusinum by having a floccose to cotton conidiomata. Botryobasidium rubiginosum differentiates from B. bambusinum by having a cottony conidiomata, and ovoid to ellipsoid, larger conidia (14.5–16 × 10.5–12.5 µm vs 7.2–9.5 × 7–9 µm). Botryobasidium simile can be distinguished from B. bambusinum by having an ochraceous to fulvous conidiomata, and larger conidia (21.5–27 × 16–18 µm vs 7.2–9.5 × 7–9 µm). A detailed description, illustrations and phylogenetic analysis of the new species are provided. [ABSTRACT FROM AUTHOR]

The current work presents comparative assessment of affinity of the designed DNA aptamers for extracellular domain of the human epidermal growth factor receptor (EGFR*). The affinity data of the 20 previously published aptamers are summarized. Diversity of the aptamer selection methods and techniques requires unification of the comparison algorithms, which is also necessary for designing aptamers used in the post-selection fitting to the target EGFR* protein. In this study affinities of the DNA aptamers from two families, U31 and U2, previously obtained by Wu et al. from the same selection [Wu et al. (2014) PLoS One, 9, e90752] and their derivatives – GR20, U2s, and Gol1 obtained by us through rational design, were compared. Affinity of the aptamers to EGFR* was measured by two different methods: a solution-phase technique – fluorescence polarization of FAM-labeled aptamers, and by a kinetic method using biolayer interferometry technique with aptamers immobilized on the surface. Unlike the values of equilibrium dissociation constants obtained through titration and expressed in units of protein concentration, analysis of the titration curve profiles themselves and kinetics of interaction proved to be more informative. This allowed us to identify how even subtle changes in the aptamers and their structures affect affinity. Hypotheses regarding the "structure–function" relationships and recognition mechanisms were formulated. The data obtained for the set of aptamer constructs are critical for moving forward to examination of aptamer interactions with EGFR on the cell surface. [ABSTRACT FROM AUTHOR]

Molecular data is provided firstly for the newly erected genus Qinia, and the phylogenetic position of the genus Qinia within the Cymbellales is discussed. Despite the presence of apical pore fields bisected by the distal raphe fissure being a very distinctive feature for Qinia, molecular analysis demonstrates this character as homoplasious, having evolved independently in Qinia and Cymbella. Two new species, Qinia hubeii sp. nov. and Cymbella wuhanensis sp. nov., are described based on multigene molecular investigation (genetic markers 18S rDNA, 28S rDNA and rbcL) and morphological comparisons with the diatoms from the family Cymbellaceae. Molecular data suggest a close relationship between Qinia hubeii sp. nov. and Karthickia and Encyonopsis, while Cymbella wuhanensis sp. nov. forms a clade with Cymbella aspera and Cymbella bengalensis. Morphological features of the new species were observed with light and scanning electron microscopy. Comparison of Qinia hubeii sp. nov. with other species in Qinia and Cymbella wuhanensis sp. nov. with similar Cymbella species were discussed. [ABSTRACT FROM AUTHOR]

Ribosomal DNA (rDNA) genes encode the structural RNAs of the ribosome and are present in hundreds of copies in mammalian genomes. Age-linked DNA hypermethylation throughout the rDNA constitutes a robust "methylation clock" that accurately reports age, yet the consequences of hypermethylation on rDNA function are unknown. We confirmed that pervasive hypermethylation of rDNA occurs during mammalian aging and senescence while rDNA copy number remains stable. We found that DNA methylation is exclusively found on the promoters and gene bodies of inactive rDNA. To model the effects of age-linked methylation on rDNA function, we directed de novo DNA methylation to the rDNA promoter or gene body with a nuclease-dead Cas9 (dCas9)–DNA methyltransferase fusion enzyme in human cells. Hypermethylation at each target site had no detectable effect on rRNA transcription, nucleolar morphology, or cellular growth rate. Instead, human UBF and Pol I remain bound to rDNA promoters in the presence of increased DNA methylation. These data suggest that promoter methylation is not sufficient to impair transcription of the human rDNA and imply that the human rDNA transcription machinery may be resilient to age-linked rDNA hypermethylation. [ABSTRACT FROM AUTHOR]

In this study, we introduce RecombiCraft, an innovative, rapid, and cost-efficient method for constructing DNA libraries in E. coli. This method uses seamless ligation cloning extract (SLiCE) coupled with liquid culture amplification to effectively minimize sequence biases. The technique capitalizes on the natural homologous recombination capabilities of E. coli cell lysates, eliminating the need for multiple purified enzymes and reducing costs. We first synthesized the library backbone and inserts via PCR, employing high-fidelity polymerase to minimize sequence bias. The SLiCE technique was then used to assemble the DNA fragments introduced into E. coli through electroporation. To ensure the integrity of the library, we optimized culture times based on next-generation sequencing analysis which confirmed the minimal sequence bias. The RecombiCraft method demonstrates that this approach is economical and maintains the library's uniformity. By using liquid culture, this method can complete DNA library generation in about 12 hours and final extraction is simple, making it a promising tool for genetic research and biotechnology applications. [ABSTRACT FROM AUTHOR]

Over 50 hereditary degenerative disorders are caused by expansions of short tandem DNA repeats (STRs). (GAA)n repeat expansions are responsible for Friedreich's ataxia as well as late-onset cerebellar ataxias (LOCAs). Thus, the mechanisms of (GAA)n repeat expansions attract broad scientific attention. To investigate the role of DNA nicks in this process, we utilized a CRISPR-Cas9 nickase system to introduce targeted nicks adjacent to the (GAA)n repeat tract. We found that DNA nicks 5' of the (GAA)100 run led to a dramatic increase in both the rate and scale of its expansion in dividing cells. Strikingly, they also promoted large-scale expansions of carrier-and large normal-size (GAA)n repeats, recreating, in a model system, the expansion events that occur in human pedigrees. DNA nicks 3' of the (GAA)100 repeat led to a smaller but significant increase in the expansion rate as well. Our genetic analysis implies that in dividing cells, conversion of nicks into double-strand breaks (DSBs) during DNA replication followed by DSB or fork repair leads to repeat expansions. Finally, we showed that 5' GAA-strand nicks increase expansion frequency in nondividing yeast cells, albeit to a lesser extent than in dividing cells. [ABSTRACT FROM AUTHOR]

The commercial importance of cephalopods has increased considerably, being an important fishing resource. However, during the preparation for commercialization of those species, they suffer the process known as "finning" which includes removing and separating the head, arm, skin or even having the body structure cut into rings, which ends up making it difficult or often prevents the identification of the species, which can lead to replacements. In this sense, the present study aimed to use the large ribosomal region, rrnL (16S rDNA) to genetically identify cephalopod species sold in markets and fairs in Latin America. Whole and processed samples were collected from supermarkets and directly from local fishers the approximate collection location. Each generated sequence was submitted to the blastn portal for molecular comparison and included in the database for subsequent genetic identification. Our results indicate labeling errors in samples from the State of Pará that contained the species Dosidicus gigas found only in the Pacific Ocean and were generically labeled as "National Lula". No type of substitution was found among the samples that were being sold at fairs and markets, only labeling errors. Thus, our results demonstrate the effectiveness of the rrnL for identifying species and evaluating labeling errors. [ABSTRACT FROM AUTHOR]

Some DNA helicases play central and specific roles in genome maintenance and plasticity through their branch migration activity in different pathways of homologous recombination. RadA is a highly conserved bacterial helicase involved in DNA repair throughout all bacterial species. In Gram-positive Firmicutes, it also has a role in natural transformation, while in Gram-negative bacteria, ComM is the canonical transformation-specific helicase. Both RadA and ComM helicases form hexameric rings and use ATP hydrolysis as an energy source to propel themselves along DNA. In this study, we present the cryoEM structures of RadA and ComM interacting with DNA and ATP analogs. These structures reveal important molecular interactions that couple ATP hydrolysis and DNA binding in RadA, as well as the role of the Lon protease-like domain, shared by RadA and ComM, in this process. Taken together, these results provide new molecular insights into the mechanisms of DNA branch migration in different pathways of homologous recombination. Synopsis: The bacterial hexameric ATPases RadA and ComM mediate DNA branch migration in the homologous recombination pathway of genetic transformation in distinct bacterial species. This study offers structural insights into the structural commonalities and differences of RadA and ComM interactions with ATP and DNA. Cryo-EM reveals structures of RadA and ComM interacting with DNA and ATP analogs. The structures reveal molecular details of ATP and DNA binding in RadA and ComM. The Lon protease-like domain shared by RadA and ComM is required for their oligomerization and DNA translocation. Cryo-EM structures of bacterial hexameric ATPases RadA and ComM reveal the structural commonalities and differences of their interactions with ATP and DNA. [ABSTRACT FROM AUTHOR]

Background: With the rise in green chemistry, the synthesis of antibiotic compounds through enzymatic processes is a preferred option. Penicillin-G acylase (PGA) is an important enzyme for producing important antibiotics, such as penicillin and its derivatives. Therefore, studies on PGA have been conducted worldwide. In the penicillin biosynthetic pathway, PGA catalyzes the conversion of penicillin G into 6-amino penicillanic acid (6-APA), a precursor for the enzymatic synthesis of penicillin derivatives. Unfortunately, bacteria naturally produce PGA in small quantities. Objective: One strategy for producing this enzyme in large quantities is DNA recombination, which is expressed in Escherichia coli. The formation of inclusion bodies (IBs) is a common obstacle to protein overexpression in Escherichia coli. In this study, we discuss IBs solubilization methods for recombinant PGA derived from E. coli (rPGAEc) expressed in E. coli BL21 (DE3). Recombinant E. coli BL21 (DE3) cells harboring rPGAEc were induced with IPTG for enzyme expression. Induction was performed at 16 °C for 4 h and 24 h. The PGA enzyme expressed in the IBs form was then incubated in two solutions containing 8 M urea and 0.2% sarcosine to obtain a soluble enzyme. Results: Based on protein analysis by SDS-PAGE, a solution containing 8 M urea solubilized PGA more abundantly than 0,2% sarcosine. Conclusion: The solubilization technique of PGA expressed by E. coli proposed in this study is an alternative solution that can be considered for this purpose. [ABSTRACT FROM AUTHOR]

The genus Fractonotus was erected on the basis of the peculiar appearance of the apophyses for the insertion of the stylet muscles on the buccal tube, and it has been attributed, together with the genus Microhypsibius, to the family Microhypsibiidae on the basis of the structure of the claws. A subsequent molecular investigation on Microhypsibius (18S and 28S rRNA) assigned the family Microhypsibiidae to the superfamily Hypsibioidea. Recently two other species, Isohypsibius gilvus and Calohypsibius verrucosus were transferred to Fractonotus and the latter was sequenced (18S and 28S rDNA, ITS-2), with the conclusion that the genus Fractonotus should be assigned to the family Isohypsibiidae, superfamily Isohypsibioidea. However, the transfer of I. gilvus and C. verrucosus to Fractonotus was incorrect. In fact, these two species definitely have claws of the Isohypsibius type, while Fractonotus caelatus, the type species of the genus, clearly has claws of the Microhypsibius type, in addition to other characters of the Hypsibioidea. Therefore, Fractonotus remains a monospecific genus in the Microhypsibiidae family, superfamily Hypsibioidea. The other two species belong to Isohypsibius or, if later confirmed by further morphological and new molecular data, to a new genus of Isohypsibiidae. [ABSTRACT FROM AUTHOR]

The food enzyme endo‐1,4‐β‐xylanase (4‐β‐d‐xylan xylanohydrolase, EC 3.2.1.8) is produced with the genetically modified Bacillus subtilis strain LMG S‐24584 by Puratos NV. In a previous opinion, the Panel noted the presence of recombinant DNA in all food enzyme batches tested. As a follow‐up, the applicant changed the manufacturing process of the food enzyme and provided new data. The genetic modifications do not give rise to safety concerns and the production strain fulfils the requirements for the QPS approach to safety assessment. The food enzyme is free from viable cells of the production organism and its DNA. It is intended to be used in the processing of cereals and other grains for the production of baked products. Dietary exposure is estimated to be up to 0.010 mg TOS/kg body weight per day in European populations. As no concerns arising from the microbial source and its genetic modifications or from the manufacturing process have been identified, the Panel considered that toxicological tests were not needed for the assessment of this food enzyme. A search for the homology of the amino acid sequence of the food enzyme to known allergens was made and no match was found. The Panel considered that the risk of allergic reactions upon dietary exposure cannot be excluded, but the likelihood is low. Based on the data provided, the Panel concluded that this food enzyme does not give rise to safety concerns, under the intended conditions of use. [ABSTRACT FROM AUTHOR]

The food enzyme glucose oxidase (β‐d‐glucose: oxygen 1‐oxidoreductase; EC 1.1.3.4) is produced with the genetically modified Trichoderma reesei strain AR‐352 by AB Enzymes GmbH. In a previous opinion, the Panel on Food Contact Materials, Enzymes and Processing Aids of the European Food Safety Authority could not conclude on the absence of recombinant DNA from the production strain in the food enzyme due to uncertainties about the limit of detection of the applied methodology. New data provided by the applicant showed that no DNA from the production strain was found in the food enzyme with a limit of detection meeting the requirements of the applicable guidance. Based on the new data provided, the Panel concludes that this food enzyme is free from recombinant DNA from the production strain. [ABSTRACT FROM AUTHOR]

The resting spore stage of Cerataulina bicornis has been reported sporadically from the Indian Sundarbans, with one sediment core record that dates back to ∼2000 yrs. BP, but its vegetative stage has remained elusive during this entire period. The present report of its vegetative stage is a new record from this estuarine system. A comprehensive morphometric description along with molecular data of rbcL and 18s rDNA of the vegetative stage of C. bicornis is presented. The morphological and morphometric characters observed in the light microscope (LM) and scanning electron microscope (SEM) studies, along with a detailed description of the copulae, establish its distinction from other Cerataulina spp. described from different parts of the world. [ABSTRACT FROM AUTHOR]

Land planarians (Geoplanidae) are predatory platyhelminths that inhabit mainly forest soils. The subfamily Geoplaninae is exclusive to the Neotropics. Although some phylogenetic studies have included a range of Geoplaninae genera, some, such as Amaga and Bogga, have not yet been considered in detail. This work aims to improve the understanding of the systematics of these two genera, focusing on the morphological and molecular (28S rDNA and COX1 genes) aspects of three species. We examined 13 geoplanin specimens recently collected in Colombia. Two of the described species are new to science (Amaga vesiculosa sp. nov. and Amaga aglandulosa sp. nov.), and Bogga bogotensis is redescribed from newly collected material. Complementary description of Amaga becki is also given from photomicrographs of the type material. The molecular phylogenetic relationships showed that the two new species are monophyletic, while the genus Amaga is merophyletic because it includes Bogga. The morphological reinterpretation of Bogga bogotensis and molecular phylogenies support the view that this species is a member of Amaga. Accordingly, Amaga is rediagnosed and Bogga is considered its junior synonym. [ABSTRACT FROM AUTHOR]

Plant-parasitic nematodes (PPNs) pose a significant threat to global agriculture, leading to substantial yield losses. Managing nematode populations remains a challenging option due to financial, technical and environmental constraints. In Ontario, Canada, the presence of Xiphinema nematodes, a virus vector species, is of particular concern. This study reports the discovery of X. diversicaudatum in a peach field in Southern Ontario, Canada. The description includes morphological and molecular characterization using the 18S and 28S rDNA sequences. Morphological and molecular characterization of Ontario's population matched those from Europe. While X. diversicaudatum was presumed eradicated from Canada, the present finding showed that the nematode could have spread beyond greenhouses. The study highlights the importance of intensive soil sampling for early nematode detection, even as strict reporting requirements may deter such efforts. We report for the first time the presence of X. diversicaudatum on peaches in Canada and in North America. [ABSTRACT FROM AUTHOR]

Subtribe Calypsoinae (Epidendroideae, Orchidaceae) comprises several fully mycoheterotrophic species. Phylogenetic analysis indicates that full mycoheterotrophy has evolved independently at least four times within this group, including the Yoania clade. The taxonomic classification of Yoania species has been challenging. Therefore, to understand the plastomic degeneration during the evolution of mycoheterotrophy and to uncover the phylogenetic relationship within Yoania , we conducted a phylogenetic analysis using eight specimens representing all six recognized Yoania taxa from the complete plastome and partial ribosomal DNA (rDNA) operon sequence (ETS–18S–ITS1–5.8S–ITS2–26S). Among the Calypsoinae taxa examined, Yoania possessed the shortest plastome, ranging from 43 998 to 44 940 bp. Comparative analysis of the plastomes revealed a relatively conserved gene structure, content, and order, with species-level sequence variation (in the form of indels) primarily observed in the intergenic spacer regions. Plastomic gene-block inversions were observed between Yoania and Danxiaorchis singchiana , but not between Yoania and other related genera. Phylogenetic analyses based on the plastome and rDNA data strongly supported the monophyletic placement of Yoania within Calypsoinae, and indicated substantial molecular divergence between Yoania and other Calypsoinae taxa. Yoania can thus be considered genetically isolated from the other Calypsoinae taxa. [ABSTRACT FROM AUTHOR]

We report the presence of Pristigenys serrula Gilbert 1891 off Zapallar (−32.568253, −71.464225), central Chile, during the ENSO 2023–2024 event. Morphology and a partial fragment of the mitochondrial markers cytochrome oxidase 1 (COX1) and 16S rDNA identified one specimen fished by artisanal fishermen. This report extends the known southern range limit of P. serrula by 9° of latitude (~1000 km) to central Chile (−32°) during strong negative ENSO conditions. [ABSTRACT FROM AUTHOR]

Birds are frequent hosts of the immature stages of many tick species, among them Amblyomma longirostre (Koch, 1844), whose larvae and nymphs have been reported from several families of Passeriformes. The objective of this study was to determine the extent to which A. longirostre parasitizes birds at the Centro de Investigación y Transferencia de Tecnología Forestal 'El Tormento' (CITTFOR-El Tormento), Escárcega, Campeche, Mexico. A total of 59 birds representing 22 species were examined for ticks. Thirteen bird species, all Passeriformes, yielded 69 tick specimens: 57 larvae and 12 nymphs. Nine of the 12 nymphs were determined morphologically as A. longirostre; the three remaining nymphs were identified as Amblyomma sp. Additionally, 48 partial sequences of the 16S rDNA gene were obtained from 41 larvae and seven nymphs. Thirty sequences were similar (≤95%) to A. longirostre, one sequence to Amblyomma sabanerae, and one to Amblyomma nodosum. On the other hand, 15 sequences and one sequence showed low identity (>95%) to A. longirostre and A. nodosum, respectively. Cyanocompsa parellina, Passerina caerulea, Xiphorhynchus flavigaster and Uropsila leucogastra represent new host associations for A. longirostre in the Americas. Amblyomma sabanerae from Habia rubica and A. nodosum from P. caerulea represent new host associations. [ABSTRACT FROM AUTHOR]

Human genome projects in the 1990s identified about 20,000 protein-coding sequences. We are now in the RNA revolution, propelled by the realization that genes determine phenotype beyond the foundational central molecular biology dogma, stating that inherited linear pieces of DNA are transcribed to RNAs and translated into proteins. Crucially, over 95% of the genome, initially considered junk DNA between protein-coding genes, encodes essential, functionally diverse non-protein-coding RNAs, raising the gene count by at least one order of magnitude. Most inherited phenotype-determining changes in DNA are in regulatory areas that control RNA and regulatory sequences. RNAs can directly or indirectly determine phenotypes by regulating protein and RNA function, transferring information within and between organisms, and generating DNA. RNAs also exhibit high structural, functional, and biomolecular interaction plasticity and are modified via editing, methylation, glycosylation, and other mechanisms, which bestow them with diverse intra- and extracellular functions without altering the underlying DNA. RNA is, therefore, currently considered the primary determinant of cellular to populational functional diversity, disease-linked and biomolecular structural variations, and cell function regulation. As demonstrated by RNA-based coronavirus vaccines' success, RNA technology is transforming medicine, agriculture, and industry, as did the advent of recombinant DNA technology in the 1980s. [ABSTRACT FROM AUTHOR]

Group A rotavirus (RVA) is a major cause of severe gastroenteritis in infants and young children globally, despite the availability of live‐attenuated vaccines. Challenges such as limited efficacy in low‐income regions, safety concerns for immunocompromised individuals, and cold‐chain dependency necessitate alternative vaccine strategies. Subunit vaccines, which use specific viral proteins to elicit immunity, provide a safer and more adaptable approach. This review highlights biotechnological advancements in producing subunit vaccines, focusing on recombinant expression systems like bacterial, yeast, insect, mammalian, and plant‐based platforms for scalable and cost‐effective production of viral proteins. Key innovations include molecular engineering, adjuvant development, and delivery system improvements to enhance vaccine immunogenicity and efficacy. Subunit vaccines and virus‐like particles expressed in various systems have demonstrated promising preclinical and clinical results, with some candidates nearing commercial readiness. Reverse vaccinology, combined with Artificial Intelligence and Machine Learning, is driving the development of innovative multiepitope vaccines and antivirals. Strategies such as passive immunization, single‐chain antibodies, immunobiotics, and novel antivirals are also explored as alternative management options. The review also underscores advanced genome editing and reverse genetics approaches to improve vaccine design and antiviral therapies. These biotechnological interventions offer hope for equitable and effective control of rotavirus diarrhea, particularly in resource‐limited settings, and represent significant progress toward addressing current vaccine limitations. Summary: The development of subunit vaccines against Group A rotavirus (RV‐A) is a critical step in combating rotavirus‐induced diarrhea, a leading cause of morbidity and mortality in children worldwide. This paper highlights biotechnological strategies for the efficient production of subunit vaccines, focusing on the use of recombinant DNA technology, plant‐based expression systems, and viral vector platforms. By leveraging these advanced techniques, the study aims to provide a more cost‐effective, scalable, and safe alternative to traditional vaccine production methods. The research offers insights into optimizing antigen expression, purification processes, and immune responses, potentially improving vaccine efficacy and accessibility in low‐resource settings. These biotechnological innovations could revolutionize rotavirus vaccine development, significantly contributing to global efforts to reduce the burden of rotavirus infections. [ABSTRACT FROM AUTHOR]

The HIV integrase inhibitor, dolutegravir (DTG), in the absence of eliciting integrase (int) resistance, has been reported to select mutations in the virus 3′-polypurine tract (3′-PPT) adjacent to the 3′-LTR U3. An analog of DTG, cabotegravir (CAB), has a high genetic barrier to drug resistance and is used in formulations for treatment and long-acting pre-exposure prophylaxis. We examined whether mutations observed for DTG would emerge in vitro with CAB. HIV-1IIIB was cultured in paired experiments of continuous high (300 nM) CAB initiated 2 h or 24 h after infection. After eight months of CAB treatment, no int resistance was detected. Conversely, HIV RNA 3′-PPT mutants were detected within one month and were the majority virus by day 98. The appearance of 3′-PPT variants coincided with a rapid accumulation of HIV 1-LTR and 2-LTR circles. RNA amplification from the 3′-LTR TAR identified transcripts crossing 2-LTR circle junctions, which incorporated the adjacent U5 sequence identical to the 3′-PPT mutants. 3′-PPT variants were only identified in LTR circles and transcripts. Additionally, we found evidence of linear HIV and LTR circle recombination with human DNA at motifs homologous to 3′-PPT sequences. HIV persistence under CAB was associated with transcription and recombination of LTR circle sequences. [ABSTRACT FROM AUTHOR]

During surveys in the centres of origin of the coffee leaf rust (CLR), Hemileia vastatrix in Africa, as well as in its exotic range in Brazil, 23 isolates of the genus Cladosporium were obtained from uredinial pustules. Using a phylogenetic analysis of all isolates involving a combination of partial sequences of the internal transcribed spacer region of rDNA (ITS) and two gene regions: actin (act) and translation elongation factor-1a (tef1), 12 species were delimited; including four new species - Cladosporium chlamydosporiformans, C. hemileiicola, C. mucilaginosum and C. setoides. GCPSR criteria were employed for species recognition, supported by morphological and cultural characters. The potential of these purported mycoparasites is discussed in the context of biological control of CLR in Latin America. [ABSTRACT FROM AUTHOR]

Genus Calvatia belongs to a gasteroid fungi which are commonly known as a puffball mushrooms including around 47 species worldwide. Approximately 25 species of the genus Calvatia have been reported previously in India from various forest regions; however, only 15 species of these are accepted on their current taxonomic status because several of them are synonymized with other genera or species. The present study reports the distribution of Calvatia holothurioides which was collected from Jambughoda Wildlife Sanctuary in Gujarat state, India. The identification was carried out based on the morphological characteristics as well as molecular phylogenetic analysis using nuclear rDNA Internal Transcribed Spacer (ITS) and rDNA LSU gene sequences data. Nucleotide sequences of different gene loci (ITS and LSU) were submitted into the BOLD data system for DNA barcoding. Additionally, this study also provides a literature-based checklist for the present status of Calvatia species reported in India so far. [ABSTRACT FROM AUTHOR]

Helicases are involved in almost every nucleic acid metabolism process. Within this family, RecQ helicase proteins protect genome integrity across all organisms through DNA recombination, repair, and replication. This study focused on five Arabidopsis thaliana RecQ-like (AtRecQl) genes with diverse functionalities. Analysis of ProAtRecQl: GUS expression during vegetative and reproductive development stages revealed organ- and tissue-specific patterns. Changes in AtRecQl s transcript levels in response to abiotic stressors suggest their involvement in diverse stimuli responses. Notably, germination and growth rates were lower in atrecql2 and atrecql3 mutants under various salt concentrations and cold conditions. These findings indicate that AtRecQl2 and AtRecQl3 act as positive regulators of abiotic stress tolerance during the germinative and postgerminative phases. [ABSTRACT FROM AUTHOR]

Amanita is a diverse and important genus of fungi, encompassing species that are edible, poisonous, ectomycorrhizal, or saprotrophic. Antioxidant characteristics of Amanita caesarea, A. citrina, A. franchetii, A. muscaria, A. pantherina, A. phalloides, and A. rubescens were assessed in this study. Fungal specimens were collected from different parts of Türkiye and their identity was confirmed by DNA sequence analyses based on ITS rDNA gene region. The highest concentration of total phenolics (5.45 mg gallic acid equivalent, GAE/g dry matter, dw) was determined in A. rubescens, while A. muscaria had the lowest amount (2.44 mg GAE/g dw). Interestingly, the biological activity of A. citrina was very close to A. caesarea (5.11 mg GAE/g dw). Three distinct approaches, namely DPPH, ABTS, and FRAP assays, were used to study the antioxidant capacities of the different Amanita species. Amanita citrina (21.15 μmol trolox equivalent, TE/g dw), A. caesarea (66.54 μmol TE/g dw), and A. rubescens (13.99 μmol TE/g dw) had the maximum DPPH, ABTS, and FRAP activity, respectively. Except for the top values, ABTS radical scavenging potential ranged between 20.80 and 55.98 μmol TE/g dw, however, DPPH was in the gap of 11.76–19.79 μmol TE/g dw. There were significant differences among FRAP results (p < 0.05). Polyphenolic compounds of Amanita species were strongly associated with antioxidant molecules that can be reacted with both DPPH and ABTS radicals (p < 0.05). [ABSTRACT FROM AUTHOR]

Human DNA ligase 1 (LIG1) performs the final step in DNA repair and recombination pathways by sealing DNA breaks, and it functions as the main replicative ligase. Hypomorphic LIG1 variants R771W and R641L cause immune deficiencies in LIG1 Syndrome patients. In vitro these LIG1 variants have decreased catalytic efficiency and increased abortive ligation and it is not known if either biochemical defect is sufficient on its own to cause immune deficiency. We investigated the enzymatic activity of several new candidate LIG1 Syndrome variants chosen based on their structural proximity to known clinical variants, low minor allele frequency (MAF), high level of conservation, and concurrence in patients with similar symptoms as LIG1 Syndrome patients. The R305Q substitution is in the DNA binding domain, R768W is in the OB-fold domain, and R641S is in the nucleotidyltransferase domain. Biochemical characterization confirmed deficiencies in ligase activity for all three variants, but also revealed marked differences in comparison to the known LIG1 Syndrome variants. Both the R305Q and R768W substitutions increase the KM for DNA and decrease the catalytic efficiency, however, neither exhibit elevated levels of abortive ligation. In contrast, the R641S variant exhibits a greater impairment of activity as well as a more pronounced level of abortive ligation compared to the known LIG1 Syndrome variant, R641L. This work expands the number of LIG1 alleles that are likely candidates for LIG1 Syndrome, and it raises the question of whether distinct enzymatic deficiencies in LIG1 cause unique clinical impacts in patients harboring these alleles. [ABSTRACT FROM AUTHOR]

During the maturation of pre-B cells, the recombination activating gene 1 and 2 (RAG1/2) endonuclease complex plays a crucial role in coordinating V(D)J recombination by introducing DNA breaks in immunoglobulin (Ig) loci. Dysregulation of RAG1/2 has been linked to the onset of B cell malignancies, yet the mechanisms controlling RAG1/2 in pre-B cells exposed to excessive DNA damage are not fully understood. In this study, we show that DNA damage–induced activation of p53 initiates a negative-feedback loop which rapidly downregulates RAG1 levels. This feedback loop involves ataxia telangiectasia mutated activation, subsequent stabilization of p53, and modulation of microRNA-34a (miR-34a) levels, which is one of the p53 targets. Notably, this loop incorporates transcription factor forkhead box P1 as a downstream effector. The absence of p53 resulted in an increased proportion of IgM+ cells prompted to upregulate RAG1/2 and to undergo Ig light chain recombination. Similar results were obtained in primary pre-B cells with depleted levels of miR-34a. We propose that in pre-B cells undergoing Ig gene recombination, the DNA breaks activate a p53/miR-34a/forkhead box P1-mediated negative-feedback loop that contributes to the rapid downregulation of RAG. This regulation limits the RAG-dependent DNA damage, thereby protecting the stability of the genome during V(D)J rearrangement in developing B cells. [ABSTRACT FROM AUTHOR]

Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV), belonging to the species Alphabaculovirus spofrugiperdae , has been recently registered as an insecticide in China. This virus has a specific effect on the global major agricultural pest Spodoptera frugiperda. To gain insights into viral infection, replication processes, and the complex formation of viral particles, in vitro studies using cell lines are essential tools. Although the IPLB-Sf9 and IPLB-Sf21 ​cell lines derived from S. frugiperda are widely used for studies on the infection and replication mechanisms of Autographa californica multiple nucleopolyhedrovirus (AcMNPV), their capacity to produce viral polyhedra after SfMNPV infection is not optimal. To address this limitation, a novel cell line named IOZCAS-Sf-1 was developed from a S. frugiperda population in Yunnan, China. The mitochondrial COX1 gene analysis confirmed the species origin of the IOZCAS-Sf-1 ​cell line. Furthermore, a comparative study was carried out to contrast the COX1 gene sequence of this novel cell line with that of IPLB-Sf9, highlighting the distinctions between the two. Importantly, the IOZCAS-Sf-1 ​cells exhibited a remarkable ability to generate polyhedra when infected with AcMNPV and SfMNPV, respectively. Consequently, this cellular lineage is considered a promising and valuable resource. It serves not only to investigate the molecular mechanisms of viral replication and its impact on host cells, but also to explore the transfection efficiency of SfMNPV DNA. This exploration further expands into its potential application in recombinant DNA experiments, laying a theoretical groundwork for the advancement of more effective biopesticides and sustainable agricultural practices. • IOZCAS-Sf-1, a newly established cell line, originated from the Spodoptera frugiperda population in China. • IOZCAS-Sf-1 can be infected by two distinct viruses, SfMNPV and AcMNPV. • IOZCAS-Sf-1 could serve as a valuable tool for exploring the mechanisms of SfMNPV infection and replication. [ABSTRACT FROM AUTHOR]

A novel strain capable of fully utilizing p-nitrophenol (PNP) as the sole carbon source under high-salinity conditions was isolated from the sediments of wastewater discharged from an aquaculture company. The identification of the strain as Bordetella sp. was confirmed by analyzing its morphological, physiological, and biochemical traits in conjunction with its 16S rDNA sequence. Furthermore, pantothenic acid, serving as a carbon source for co-metabolites, could significantly enhance the biodegradation process of the tricarboxylic acid (TCA) cycle. Under the optimal growth conditions at a temperature of 30 °C, pH of 8.0, aeration of 0.32 m3·(m3·min)−1 and salinity of 3% (NaCl, w/v), the degradation rate of 350 mg·L−1 PNP increased from 60.8% to 85.9% within 72 h after adding 30 mg·L−1 of pantothenic acid to a 12-liter bioreactor. The intermediate products from the degradation process, analyzed via GC/MS, were determined to be hydroquinone, which suggests that the degradation pathway of the bacterium for PNP involves the breakdown of hydroquinone. Benefits have been derived from the microorganism's tolerance to high salinity and high PNP concentrations, coupled with its superior PNP degradation performance, offering new insights and a research basis for the efficient biological treatment of high-salinity PNP wastewater. [ABSTRACT FROM AUTHOR]

Lemon (Citrus limon (L.) Burm. f.) is a fruit plant that is widely grown in India and other countries with subtropical climates. The agricultural significance of lemon largely determines the high scientific interest in studying its genome. Such part of a genome as ribosomal DNA (rDNA) is often studied by geneticists with theoretical and applied purposes. In this work, sixteen non-transcribed spacers of the lemon 5S rDNA (8 from Lunario and 8 from Rosso varieties) were amplified with the universal 5S1/5S2 primers, purified, cloned in AT-vector, and sequenced. These sequences were processed, aligned and characterized for length, presence of mutations and distribution of different DNA motifs. Seven NTSs of the Lunario variety were 105 bp in length, and the eighth NTS was 77 bp because a large deletion was found in its start part. Five NTSs of the Rosso variety were 218 bp, two -- 216 bp, and one -- 185 bp in length. This short NTS has a 31 bp deletion in the middle part of the sequence. The emergence of typical 105 bp lemon NTSs from longer NTSs due to deletion has been suggested. The start-motif analysis and the search for poly-T, poly-C, poly-G and TATA-like motifs were carried out in the sequenced NTSs. Based on the obtained results, conclusions were made about the role of the CTCTTTT, CGCCGG, and GCGGC motifs in the appearance of deletions. Also, the results shed more light on the question of the origin of the Rosso variety. The knowledge obtained can be useful in the selection process involving lemon varieties and an analysis of citrus hybrids. [ABSTRACT FROM AUTHOR]