Search Results (86)

Bacteriophages (phages), the most abundant biological entities on Earth, have long served as both model systems and therapeutic tools. Recent advances in synthetic biology and genetic engineering have revolutionized the capacity to tailor phages with enhanced functionality beyond their natural capabilities. This review outlines the current landscape of synthetic and functional engineering of phages, encompassing both in-vivo and in-vitro strategies. We describe in-vivo approaches such as phage recombineering systems, CRISPR-Cas-assisted editing, and bacterial retron-based methods, as well as synthetic assembly platforms including yeast-based artificial chromosomes, Gibson, Golden Gate, and iPac assemblies. In addition, we explore in-vitro rebooting using TXTL (transcription–translation) systems, which offer a flexible alternative to cell-based rebooting but are less effective for large genomes or structurally complex phages. Special focus is given to the design of customized phages for targeted applications, including host range expansion via receptor-binding protein modifications, delivery of antimicrobial proteins or CRISPR payloads, and the construction of biocontained, non-replicative capsid systems for safe clinical use. Through illustrative examples, we highlight how these technologies enable the transformation of phages into programmable bactericidal agents, precision diagnostic tools, and drug delivery vehicles. Together, these advances establish a powerful foundation for next-generation antimicrobial platforms and synthetic microbiology. Full article

Tripterygium wilfordii has extremely important pharmaceutical value in both traditional and modern medicine. The mitogenome of T. wilfordii was subjected to assembly and annotation with Nanopore long reads and Illumina short reads in this study. The mitogenome is 720,306 bp in length and is responsible for encoding 55 specific genes, including 35 protein-coding genes (PCGs), 17 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Upon repetitive sequence analysis, 223 simple sequence repeats (SSRs), 24 long tandem repeats (LTRs), and 47 dispersed repetitive sequences (DRSs) were identified. The 24 common PCGs were used for phylogenetic analysis, which revealed that T. wilfordii is more closely related to Euonymus alatus. Moreover, mitochondrial plastid DNA (MTPT) analysis revealed eight MTPTs in the mitochondrial genome. Furthermore, 600 RNA-editing sites were detected in the protein-coding genes according to RNA-seq results. Among these genes, the ccmB gene contained the greatest number of sites, followed by the nad4 gene. This is the first study to report the T. wilfordii mitogenome and illustrate its linear structure. The findings of this study will help elucidate the evolution of the T. wilfordii mitogenome and facilitate its potential application in genetic breeding. Full article

Walter Henry Medhurst’s translation of The Shoo King (尚書/書經) represents the first complete English rendering of this classic Chinese text. However, limited attention has been given to how Medhurst navigated the tension between Confucian thought in The Shoo King and his own religious beliefs, as well as his treatment of this tension in comparison to James Legge, Joseph de Prémare, Walter Gorn Old, and his interpretation in contrast to Cai Shen’s annotated edition of The Shoo King. This study adopts a “history of the book” approach to examine how Medhurst, as a Protestant missionary, translated key Confucian anthropocentric concepts, including “Ren” (仁), the Doctrine of Mind-Nature, people-centered governance, and religious ideas related to the divine. Through extensive textual analysis and comparison with other scholars’ translations, this study finds that Medhurst adhered to the principle of textual fidelity, striving to minimize the interference of his religious stance with the original meaning of Confucian philosophy. His translation of terms varied according to the context, especially reflecting the shift in The Shoo King from the idea of “Heaven’s mandate is inviolable” to “Heaven is not trustworthy.” Additionally, he enhanced the communication of the original text’s meanings through paratextual elements such as illustrations and footnotes, while retaining Cai Shen’s historical background interpretations and significantly reducing the philological commentary, presenting a “concise and focused” annotation approach. These findings highlight Medhurst’s unique contribution to the cross-cultural transmission of the Confucian canonical text. Full article

CRISPR/Cas9 genome editing holds promise for precise genetic modifications, yet off-target effects remain a concern—particularly in gene families with high sequence similarity. In this study, we present a computational framework for analyzing editing specificity and cross-reactivity in gene families using long-read sequencing data. The pipeline integrates multiplex PCR, NGS, and CRISPECTOR-based analysis to detect and quantify on- and off-target events with high sensitivity. As a use case, we applied this framework to Solanum lycopersicum, evaluating on-target editing in thirteen gene families and analyzing off-target cross-reactivity in five representative families. While the biological results are illustrative, the primary contribution lies in the generalizable analysis approach, which can support genome editing studies in complex plant genomes and beyond. Full article

The Latin (De Homine, 1662, 1664) and French (L’Homme, 1664) editions of René Descartes’ Treatise on Man present different iconographic traditions, but the iconography of the Latin editions is little known. Dutch physician and botanist Florentius Schuyl edited De Homine and illustrated it himself with a mix of woodcut and copperplate illustrations. This paper examines Schuyl’s innovative depictions of purported dynamic aspects of the pineal gland as claimed by Descartes: (1) repeatedly illustrating the pineal gland as the corporeal–spiritual linkage of the brain and soul; and (2) using a movable flap anatomy to illustrate the pineal gland as a motile structure that both responds to and directs animal spirits. None of the canonical illustrations in the later French edition attempted to depict the corporeal–spiritual linkage of the brain and soul, and the modest attempts in the French edition to depict the motility of the pineal gland relied simply on superimposition of two purported positions of the gland, a technique also employed by Schuyl. This paper also reviews how Schuyl’s illustration of a corporeal–spiritual linkage of the brain and soul in a goat sharply contrasts with his written defense of Descartes’ bête-machine doctrine in the extended preface to De Homine. Full article

Over the last 40 years, several studies have provided evidence demonstrating that viral vectors can result in effective gene targeting/insertions in a host’s genome. The traditional approaches of gene knock-down, -out, or -in involve an intensive transgenesis process that is plagued by extensive timescales. Plant viruses have the potential to target specific genes and integrate exogenous DNA molecules at the target locus. Their ability to manipulate a host’s genetic material and become a part of it makes them remarkable agents and helpful for molecular and synthetic biology. In this review, we describe how geminivirus-based vectors can be utilized to overcome traditional transgenesis. We highlight the progress that has been made so far and also discuss the hurdles that hinder the employment of geminivirus-based vectors. Furthermore, we conclude with a comparison of geminivirus-based vectors with other plant-derived vectors. Geminivirus-based vectors stand poised to revolutionize plant genome editing by making nucleic acid manipulation cheaper and easier to deploy, thus lessening the major technical constraints, including homology-directed repair (HDR)-mediated genome editing and time-inefficient tissue culture procedures. The insights given in this review illustrate a broader picture of geminiviral vectors, with an emphasis on engineering plant viruses to ease genome editing practices for crop improvements as well as boost experimental timescales from years to months. Full article

This paper examines the Nanatsu-dera manuscript of the Dafangguang Rulai Xingqi Weimizang Jing (RXWJ) through the lens of scribal practices, with a focus on variant characters (yitizi, 異體字) and textual transmission. As a “separately produced scripture” (bie sheng jing, 別生經), the RXWJ was not included in the woodblock-printed editions of the Chinese Buddhist canon, which limited its circulation and made manuscript copies—such as the Nanatsu-dera manuscript—critical for reconstructing its textual evolution, transmission, and scribal modifications. A detailed paleographic investigation reveals scribal variants, orthographic fluidity, and phonetic substitutions, illustrating both intentional adaptations and unintentional errors in textual transmission. Comparative analysis with Dunhuang fragments and the Taishō Canon further contextualizes these variations, shedding light on the interpretive challenges scribes and readers face. The findings suggest that the Nanatsu-dera manuscript underwent three stages of transmission: (1) it originated from the Fifty-Fascicle edition circulating in China, (2) it was used as a base text (diben, 底本) for manuscript copying in Japan, and (3) it was subsequently re-copied and preliminarily collated by Japanese scribes. By tracing scribal variants and textual transmission through a paleographic approach, this research underscores the critical role of manuscript culture in preserving texts outside the canonical tradition, offering new insights into the mechanisms of Buddhist textual transmission and adaptation in medieval East Asia. Full article

Background and Clinical Significance: Men who engage in anal fisting may experience full rectal and colon thickness injury resulting in an endoscopic emergency. The endoscopist does not routinely question patients about their sexual habits, nor are patients compliant with counseling during the endoscopy procedure as indicated by the infectious disease clinician. Case Presentation: A 47-years-old HIV- and monkeypox virus (MPXV)-negative Caucasian gay man underwent colonoscopy because of changes in bowel habits with anal discomfort and rectal bleeding. The first colonoscopy showed a vegetative annular neoformation of the anal canal. There was a concentric stenosis of the lumen. The endoscopist suspected the diagnosis of anal squamous cell carcinoma and a histopathology investigation was requested. Biopsy histology excluded a frank neoplasm or anal intraepithelial neoplasia (AIN). Then, the patient was referred to a multidisciplinary team. With adequate counseling, the patient disclosed his habitual anal fisting. Laboratory identification of L1–L3 Chlamydia trachomatis (CT) genovars was positive for CT L1, L2, real-time PCR for Neisseria gonorrhoeae (NG), and Mycoplasma hominis. Human Papillomavirus (HPV)-DNA detection identified HPV type 70, 68, and 61. We illustrate this case with plenty of histology and immunohistochemistry. We also review the differential diagnosis of AIN according to the 5th edition (2019) WHO Classification of Digestive System Tumours. Conclusions: Our patient emphasizes two important aspects of endoscopy and pathology: first, the significance of understanding patients’ sexual behaviors in diagnosing rectal and colon injuries, as well as the need for sexually transmitted infections (STI) screening especially for CT; and second, the effectiveness of a multidisciplinary communication model that encourages private discussions to alleviate patients’ fears and improve prevention efforts. Full article

Climate change profoundly impacts the health, productivity, and resilience of forest ecosystems and threatens the sustainability of forest products and wood-based industries. Innovations to enhance tree growth, development, and adaptation offer unprecedented opportunities to strengthen ecosystem resilience and mitigate the effects of climate change. Here, we established a method for protoplast isolation, purification, and CRISPR-Cas ribonucleoprotein (RNP) delivery in Pinus taeda and Abies fraseri as a step towards accelerating the genetic improvement of these coniferous tree species. In this system, purified protoplasts could be isolated from somatic embryos with up to 2 × 10⁶ protoplasts/g of tissue and transfected with proteins and nucleotides, achieving delivery efficiencies up to 13.5%. The delivery of functional RNPs targeting phenylalanine ammonia lyase in P. taeda and phytoene desaturase in A. fraseri yielded gene editing efficiencies that reached 2.1% and 0.3%, respectively. This demonstration of RNP delivery for DNA-free genome editing in the protoplasts of P. taeda and A. fraseri illustrates the potential of CRISPR-Cas to enhance the traits of value in ecologically and economically important tree species. The editing system provides a foundation for future efforts to regenerate genome-edited forest trees to improve ecosystem health and natural resource sustainability. Full article

Using plants as bioreactors, molecular farming has emerged as a versatile and sustainable platform for producing recombinant vaccines, therapeutic proteins, industrial enzymes, and nutraceuticals. This innovative approach leverages the unique advantages of plants, including scalability, cost-effectiveness, and reduced risk of contamination with human pathogens. Recent advancements in gene editing, transient expression systems, and nanoparticle-based delivery technologies have significantly enhanced the efficiency and versatility of plant-based systems. Particularly in vaccine development, molecular farming has demonstrated its potential with notable successes such as Medicago’s Covifenz for COVID-19, illustrating the capacity of plant-based platforms to address global health emergencies rapidly. Furthermore, edible vaccines have opened new avenues in the delivery of vaccines, mainly in settings with low resources where the cold chain used for conventional logistics is a challenge. However, optimization of protein yield and stability, the complexity of purification processes, and regulatory hurdles are some of the challenges that still remain. This review discusses the current status of vaccine development using plant-based expression systems, operational mechanisms for plant expression platforms, major applications in the prevention of infectious diseases, and new developments, such as nanoparticle-mediated delivery and cancer vaccines. The discussion will also touch on ethical considerations, the regulatory framework, and future trends with respect to the transformative capacity of plant-derived vaccines in ensuring greater global accessibility and cost-effectiveness of the vaccination. This field holds great promise for the infectious disease area and, indeed, for applications in personalized medicine and biopharmaceuticals in the near future. Full article

Filamin C (FLNC) is a structural protein of muscle fibers. Mutations in the FLNC gene are known to cause myopathies and cardiomyopathies in humans. Here we report the generation by a CRISPR/Cas9 editing system injected into zygote pronuclei of two mouse strains carrying filamin C mutations—one of them (AGA) has a deletion of three nucleotides at position c.7418_7420, causing E>>D substitution and N deletion at positions 2472 and 2473, respectively. The other strain carries a deletion of GA nucleotides at position c.7419_7420, leading to a frameshift and a premature stop codon. Homozygous animals (Flnc^AGA/AGA and Flnc^GA/GA) were embryonically lethal. We determined that Flnc^GA/GA embryos died prior to the E12.5 stage and illustrated delayed development after the E9.5 stage. We performed histological analysis of heart tissue and skeletal muscles of heterozygous strains carrying mutations in different combinations (Flnc^GA/wt, Flnc^AGA/wt, and Flnc^GA/AGA). By performing physiological tests (grip strength and endurance tests), we have shown that heterozygous animals of both strains (Flnc^GA/wt, Flnc^AGA/wt) are functionally indistinguishable from wild-type animals. Interestingly, compound heterozygous mice (Flnc^GA/AGA) are viable, develop normally, reach puberty and it was verified by ECG and Eco-CG that their cardiac muscle is functionally normal. Intriguingly, Flnc^GA/AGA mice demonstrated better results in the grip strength physiological test in comparison to WT animals. We also propose a structural model that explains the complementary interaction of two mutant variants of filamin C. Full article

This study investigates how religious rhetoric and popular mobilisation contributed to the preservation and propagation of Daoist traditions at the mountain Maoshan 茅山 from late Qing to Republican China (1864–1937), focusing particularly on the corpus of religious texts related to Maoshan and its tutelary gods, the Three Mao Lords 三茅真君. Through a detailed analysis of primary sources, including editions of the Maoshan Gazetteer, liturgical manuals such as the scripture (jing 經), litany (chan 懺), and performative texts such as the precious scroll (baojuan 寶卷) of the Three Mao Lords, this study identifies six key rhetoric strategies employed by Maoshan Daoists, using the acronym IMPACT: (1) Incorporation: Appending miracle tales (lingyan ji 靈驗記) and divine medicine (xianfang 仙方) to address immediate and practical needs of contemporary society; (2) Memory: Preserving doctrinal continuity while invoking cultural nostalgia to reinforce connections to traditional values and heritage; (3) Performance: Collaborating with professional storytellers to disseminate vernacularized texts through oral performances, thereby reaching broader audiences including the illiterate. (4) Abridgment: Condensing lengthy texts into concise and accessible formats; (5) Canonization: Elevating the divine status of deities through spirit-writing, thereby enhancing their religious authority; (6) Translation: Rendering classical texts into vernacular language for broader accessibility. Building upon J.L. Austin’s speech act theory, this study reconceptualizes these textual innovations as a form of “text acts”, arguing that Maoshan texts did not merely transmit religious doctrine but actively shaped pilgrimages and devotional practices through their illocutionary and perlocutionary force. Additionally, this study also highlights the crucial role of social networks, particularly the efforts of key individuals such as Zhang Hefeng 張鶴峰 (fl. 1860–1864), Long Zehou 龍澤厚 (1860–1945), Jiang Daomin 江導岷 (1867–1939), Wang Yiting 王一亭 (1867–1938) and Teng Ruizhi 滕瑞芝 (fl. 1920–1947) who facilitated the reconstruction, reprinting and dissemination of these texts. Furthermore, this study considers pilgrimages to Maoshan as a form of popular mobilisation and resistance to anti-clerical and anti-superstition campaigns, illustrating how, against all odds, Maoshan emerged as a site where religious devotion and economic activity coalesced to sustain the local communities. Ultimately, despite the challenges identified in applying speech act theory to textual practices, the findings conclude that the survival and revival of Daoist traditions at Maoshan was not only a result of textual retention and innovation but also a testament to how religious rhetoric, when coupled with strategic social engagement, can fuel popular mobilisation, reignite collective devotion, and reshape cultural landscapes in transformative ways. Full article

With recent technological advances and significant progress in understanding the pathogenesis of acute myeloid leukemia (AML), the updated fifth edition WHO Classification (WHO-HAEM5) and the newly introduced International Consensus Classification (ICC), as well as the European LeukemiaNet (ELN) recommendations in 2022, require the integration of immunophenotypic, cytogenetic, and molecular data, alongside clinical and morphologic findings, for accurate diagnosis, prognostication, and guiding therapeutic strategies in AML. Flow cytometry offers rapid and sensitive immunophenotyping through a multiparametric approach and is a pivotal laboratory tool for the classification of AML, identification of therapeutic targets, and monitoring of measurable residual disease (MRD) post therapy. The association of immunophenotypic features and recurrent genetic abnormalities has been recognized and applied in informing further diagnostic evaluation and immediate therapeutic decision-making. Recently, the evolving role of machine learning models in assisting flow cytometric data analysis for the automated diagnosis and prediction of underlying genetic alterations has been illustrated. Full article

Basel humanists shaped religious discourse beyond the Reformed sphere through their collections of exempla, short narratives designed to illustrate a moral or doctrinal message. Because scholars of early modern exempla typically focus on either Lutheran or Catholic exempla collections, the role of Reformed compilers as mediators between confessions has been obscured. This article uses methods from the field of digital humanities and corpus linguistics to examine the lasting influence of Theodor Zwinger (1533–1588), Conrad Lycosthenes (1518–1561), and Johannes Herold (1514–1567) on Lutheran and Catholic exempla collections in a newly quantitative way. Using the concordance software AntConc, this study identifies numerous citations that demonstrate that Zwinger and Lycosthenes facilitated confessional cross-pollination of exemplary narratives from the mid-sixteenth through the early eighteenth century. Although citations of Zwinger, Lycosthenes, and Herold are more frequent in Lutheran exempla collections, the existence of several Catholic editions of Zwinger’s Theatrum vitae humanae indicates that Catholic readers also valued Zwinger’s work. This examination showcases the vital role of Swiss humanists in cross-confessional networks of information exchange and religious discourse in early modern Europe. Full article

Heat stress severely affects the yield and quality of maize. Melatonin (N-acetyl-5-methoxy-tryptamin, MT) plays an important role in various types of stress resistance in plants, including heat tolerance. Enolase (ENO, 2-phospho-D-glycerate hydrolyase) contributes to plant growth, development, and stress response. As of now, the molecular mechanisms by which MT and ENO1 affect heat tolerance are unknown. In our research, we have revealed that heat stress (H) and heat stress + MT (MH) treatment upregulate ZmENO1 expression levels by 15 and 20 times, respectively. ZmENO1 overexpression and mutant maize lines were created by transgenic and genome editing. These results illustrate that heat stress has a significant impact on the growth of maize at the seedling stage. However, ZmENO1-OE lines showed a lower degree of susceptibility to heat stress, whereas the mutant exhibited the most severe effects. Under heat stress, exogenous application of MT improves heat resistance in maize. The ZmENO1-OE lines exhibited the best growth and highest survival rate, while the zmeno1 mutants showed the least desirable results. Following treatment with H and MH, the level of MT in ZmENO1-OE lines exhibited the greatest increase and reached the maximum value, whereas the level of MT in the zmeno1 mutant was the lowest. Heat stress decreased the maize’s relative water content and fresh weight, although ZmENO1-OE lines had the highest and zmeno1 mutants had the lowest. Heat stress led to an increase in the levels of MDA, hydrogen peroxide, and superoxide in all plants. Additionally, the ionic permeability and osmotic potential of the plants were significantly increased. However, the levels of MT were decreased in all plants, with the greatest decrease observed in the ZmENO1-OE lines. Interestingly, the zmeno1 mutant plants had the highest expression levels of MT. Heat stress-induced upregulation of ZmSOD, ZmPOD, ZmAPX, ZmCAT, ZmP5CS, and ZmProDH in all plants. However, the ZmENO1-OE lines exhibited the greatest increase in expression levels, while the zmeno1 mutants showed the lowest increase following MT spraying. The patterns of SOD, POD, APX, and CAT enzyme activity, as well as proline and soluble protein content, aligned with the variations in the expression levels of these genes. Our findings indicate that MT can upregulate the expression of the ZmENO1 gene. Upregulating the ZmENO1 gene resulted in elevated expression levels of ZmSOD, ZmPOD, ZmAPX, ZmCAT, ZmP5CS, and ZmProDH. This led to increased activity of antioxidant enzymes and higher levels of osmoregulatory substances. Consequently, it mitigated the cell membrane damage caused by heat stress and ultimately improved the heat resistance of maize. The results of this study provide genetic resources for molecular design breeding and lay a solid foundation for further exploring the molecular mechanism of MT regulation of heat stress tolerance in maize. Full article