The mechanisms of UV mutagenesis

Interplay of replication timing, DNA repair, and translesion synthesis in UV mutagenesis in yeast

Replication timing during S-phase impacts mutation rates in yeast and human cancers; however, the exact mechanism involved remains unclear. Here, we analyze the impact of replication timing on UV mutagenesis in Saccharomyces cerevisiae. Our analysis indicates that UV mutations are enriched in early-replicating regions of the genome in wild-type cells, but in cells deficient in global genomic-nucleotide excision repair (GG-NER), mutations are enriched in late-replicating regions. Analysis of UV damage maps revealed that cyclobutane pyrimidine dimers are enriched in late-replicating regions, but this enrichment is almost entirely due to repetitive ribosomal DNA. Complex mutations typically associated with TLS activity are also elevated in late-replicating regions in GG-NER deficient cells. We propose that UV mutagenesis is higher in early-replicating regions in repair-competent cells because there is less time to repair the lesion prior to undergoing replication. However, in the absence of GG-NER, increased TLS activity promotes UV mutagenesis in late-replicating regions.

Unveiling the Anti-Aging Potential of Marine Natural Bioproducts

Aging is a natural process resulting in the progressive impairment of multiple functions in the human body, leading to a decline in cellular functionality and the development of aging-related diseases. External stress factors, such as ultraviolet (UV) radiation, pollution, and toxin exposure, increase oxidative stress, damage cellular repair mechanisms, and speed up aging processes. With the rise in the world's aging population, there are enlarged demands for the use of sustainable natural products in food, nutrient supplements and cosmetics that can slow down aging and prolong healthy life and longevity. Algae, including both macroalgae and microalgae, have been recognised as a source of valuable proteins, amino acids, fatty acids, vitamins, and minerals useful for human consumption and medical applications. With increasing demands for nutraceutical and pharmaceutical bioproducts from environmentally friendly resources, the biotechnological industry, over recent decades, has had to provide new, advanced solutions using modern high-throughput omics technologies. The application of proteomics in the area of discoveries of natural products with anti-aging properties has become more popular for wide industry applications. New proteomics profiling provides a better understanding of changes occurring in protein and peptide content, their structure, function and interactions, as well as the regulatory processes and molecular pathways. Mass spectrometry-based proteomics has been used for a wide range of applications including protein identification, characterisation, as well as quantification of proteins within the proteome and sub-proteome. The application of chemical proteomics facilitated the identification of natural products approach and included the synthesis of probes and target fishing, allowing the advanced identification of proteins of interest. This review focuses on marine macro- and microalgal anti-aging compounds and novel proteomics approaches, providing recent experimental evidence of their involvement in anti-aging processes that should facilitate their use in innovative approaches and sustainable biotechnological applications.

Basal Cell Nevus Syndrome and Sporadic Basal Cell Carcinoma: A Comparative Study of Clinicopathological Features

Basal cell nevus syndrome is caused by mutations in the Sonic hedgehog pathway and characterized by early-onset basal cell carcinoma. The features of basal cell carcinoma in basal cell nevus syndrome compared with sporadic basal cell carcinoma have not been explored. This study is a retrospective study of patients with basal cell nevus syndrome in two medical centres in Taiwan from 1991 to 2021 and patients with sporadic basal cell carcinoma excised from 2015 to 2020. An analysis of 18 patients with basal cell nevus syndrome showed an older mean age at the first diagnosis of basal cell carcinoma (37.5 years) than reported in Western countries. The majority of basal cell carcinomas were located in the head and neck region (80.7%), with nodular BCC being the most common tumour type (47.0%). Compared with sporadic basal cell carcinomas, basal cell carcinomas in basal cell nevus syndrome patients occurred more frequently on the scalp (34.7% vs 6.1%, p < 0.001). In addition, the superficial type of basal cell carcinoma was more likely to be seen in basal cell nevus syndrome (24.7% vs 10.4%, p < 0.001). The limitations were that some features of the basal cell nevus syndrome patients might not have been present yet at the time of examination or they did not receive thorough screening. In conclusion, the distinct features of basal cell carcinomas in basal cell nevus syndrome patients have important implications for the prevention, diagnosis, and management of basal cell carcinoma in basal cell nevus syndrome patients.

UVA-light-induced mutagenesis in the exome of human nucleotide excision repair-deficient cells

Skin cancer is associated with genetic mutations caused by sunlight exposure, primarily through ultraviolet (UV) radiation that damages DNA. While UVA is less energetic, it is the predominant solar UV component reaching the Earth's surface. However, the mechanisms of UVA-induced mutagenesis and its role in skin cancer development remain poorly understood. This study employed whole exome sequencing of clones from human XP-C cells, which lack nucleotide excision repair (NER), to characterize somatic mutations induced by UVA exposure. DNA sequence analysis of UVA-irradiated XP-C cells revealed a marked increase in mutation frequency across nearly all types of base substitutions, with particular enrichment in C > T transitions within the CCN and TCN trinucleotide context-potential sites for pyrimidine dimer formation. The C > T mutation primarily occurred at the 3' base of the 5'TC dimer, and an enrichment of CC > TT tandem mutations. We also identified the SBS7b COSMIC mutational signature within irradiated cells, which has been associated with tumors in sun-exposed skin. C > A transversions, often linked to oxidized guanine, were the second most frequently induced mutation, although a specific context for this base substitution was not identified. Moreover, C > T mutations were significantly increased in unirradiated XP-C compared to NER-proficient cells, which may be caused by unrepaired spontaneous DNA damage. Thus, this study indicates that pyrimidine dimers are the primary lesions contributing to UVA-induced mutagenesis in NER-deficient human cells and demonstrates that UVA generates mutational signatures similar to those of UVB irradiation.

ZymoSoups: A High-Throughput Forward Genetics Method for Rapid Identification of Virulence Genes in Zymoseptoria tritici

Septoria tritici blotch is caused by the fungus Zymoseptoria tritici and poses a major threat to wheat productivity. There are over 20 mapped loci in wheat that confer strong (gene-for-gene) resistance against this pathogen, but the corresponding genes in Z. tritici that confer virulence against distinct R genes remain largely unknown. In this study, we developed a rapid forward genetics methodology to identify genes that enable Z. tritici to gain virulence on previously resistant wheat varieties. We used the known gene-for-gene interaction between Stb6 and AvrStb6 as a proof of concept that this method could quickly recover single candidate virulence genes. We subjected the avirulent Z. tritici strain IPO323, which carries the recognized AvrStb6 allele, to ultraviolet (UV) mutagenesis and generated a library of over 66,000 surviving spores. We screened these survivors on leaves of the resistant wheat variety Cadenza in mixtures (soups) ranging from 100 to 500 survivors per soup. We identified five soups with a gain-of-virulence (GoV) phenotype relative to the IPO323 parental strain and re-sequenced 18 individual isolates, including four control isolates and two isolates lacking virulence, when screened individually. Of the 12 confirmed GoV isolates, one had a single nucleotide polymorphism (SNP) in the AvrStb6 coding region. The other 11 GoV isolates exhibited large (approximately 70 kb) deletions at the end of chromosome 5, including the AvrStb6 locus. Our findings demonstrate the efficiency of this forward genetic approach in elucidating the genetic basis of qualitative resistance to Z. tritici and the potential to rapidly identify other, currently unknown, Avr genes in this pathogen. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Effect of UV exposure on DNA deposited on drug capsules

Illicit drugs are often made in less-than-sterile environments and can be stored in ways which can be detrimental to any DNA present, such as whether they are exposed to UV radiation. Previously, analysis of how exposure to UV impacted DNA for forensic applications has been in controlled laboratory conditions isolating a single component of UV radiation and often on DNA-rich samples such as bloodstains or saliva. To evaluate DNA persistence in more realistic conditions, capsules, such as those used to distribute controlled substances, were manually made and then packed into ziplock bags. The persistence of DNA deposited on capsules was examined when left indoors in either, complete darkness, direct sunlight in high UV conditions (summer) or in low UV conditions (winter) for three weeks in ambient room temperature. The DNA yield, STR DNA profile quality and degradation index were all analysed to determine the impact of varied UV exposure on DNA in a semi-temperature-controlled environment. Capsule samples exposed to high UV conditions had significantly reduced DNA yields, a lower number of alleles from the capsule handler and, thus, reduced likelihood ratios compared to capsules exposed to darkness and low UV conditions. Samples exposed to either darkness or low UV had little-to-no differences in all DNA quality measures tested. Despite a decreased DNA yield and poorer quality DNA profiles, capsules left in high UV conditions for three weeks have sufficient DNA for DNA profiles with over half the genetic information present. The storage conditions of drug capsules, either before or after seizure by law enforcement, can impact the DNA persistence in as little as three weeks, which is problematic for often already low concentrations of DNA in trace samples.

Patterns of spontaneous and induced genomic alterations in Yarrowia lipolytica

This study explored the genomic alterations in Yarrowia lipolytica, a key yeast in industrial biotechnology, under both spontaneous and mutagen-induced conditions. Our findings reveal that spontaneous mutations occur at a rate of approximately 4 × 10-10 events per base pair per cell division, primarily manifesting as single-nucleotide variations (SNVs) and small insertions and deletions (InDels). Notably, C-to-T/G-to-A transitions and C-to-A/G-to-T transversions dominate the spontaneous SNVs, while 1 bp deletions, likely resulting from template slippage, are the most frequent InDels. Furthermore, chromosomal aneuploidy and rearrangements occur, albeit at a lower frequency. Exposure to ultraviolet (UV) light, methylmethane sulfonate (MMS), and Zeocin significantly enhances the rates of SNVs and alters their mutational spectra in distinct patterns. Notably, Zeocin-induced SNVs are predominantly T-to-A and T-to-G substitutions, often occurring within the 5'-TGT*-3' motif (* denotes the mutated base). Additionally, Zeocin exhibits a higher potency in stimulating InDels compared to UV and MMS. Translesion DNA synthesis is implicated as the primary mechanism behind most Zeocin-induced SNVs and some InDels, whereas non-homologous end joining serves as the main pathway for Zeocin-mediated InDels. Intriguingly, the study identifies the gene YALI1_E21053g, encoding a protein kinase, as negatively associated with Zeocin resistance. Overall, our results not only deepened our knowledge about the genome evolution in Y. lipolytica but also provided reference to develop innovative strategies to harness its genetic potential.IMPORTANCEYarrowia lipolytica exhibits high environmental stress tolerance and lipid metabolism capabilities, making it a microorganism with significant industrial application potential. In this study, we investigated the genomic variation and evolutionary patterns of this yeast under both spontaneous and induced mutation conditions. Our results reveal distinctive mutation spectra induced by different mutagenic conditions and elucidate the underlying genetic mechanisms. We further highlight the roles of non-homologous end joining and translesion synthesis pathways in Zeocin-induced mutations, demonstrating that such treatments can rapidly confer drug resistance to the cells. Overall, our research enhances the understanding of how yeast genomes evolve under various conditions and provides guidance for developing more effective mutagenesis and breeding techniques.

Ultraviolet C Decontamination Devices in a Hospital Pharmacy: An Evaluation of Their Contribution

PURPOSE

The COVID-19 pandemic led to a major interest in ultraviolet C (UVC) disinfection devices and accelerated the implementation of UVC devices in healthcare facilities due to their proven efficacy in the inactivation of various pathogens. While UVC technology offers several advantages, some drawbacks remain. This report, drawing on studies, guidelines, and practical experiences related to the use of UVC technology in healthcare settings, examines the efficacy, advantages, and drawbacks of UVC devices, and their applications in aseptic drug-compounding pharmaceutical units.

SUMMARY

Studies, guidelines, and practical experiences were selected. UVC technology offers advantages such as rapid disinfection, reduced reliance on chemical agents, minimal waste, and freedom from manual disinfection variability, making it particularly valuable for maintaining aseptic conditions in compounding environments. However, some drawbacks persist, as it is a germ-dependent method and there is currently no standardized method for ensuring effectiveness.

CONCLUSIONS

This opinion paper highlights the effectiveness of UCV technology in pharmaceutical compounding units, proving that it is a viable alternative to the traditionally used manual and operator-dependent methods. However, there is a need for standardized methods to evaluate UVC devices.

[Ophthalmic oncology in a warmer world: climate-related increase in the prevalence of eyelid cancer]

BACKGROUND

Damage induced by ultraviolet (UV) radiation plays a decisive role in the carcinogenesis of malignant tumors of the eyelids.

METHODS

A selective literature search was performed in PubMed and Google Scholar.

RESULTS

Large epidemiological studies show an increase in the prevalence of eyelid tumors in recent decades. The incidence of malignant eyelid tumors has increased especially in the white population over the last 70 years. A UV-induced damage to tumor suppressor genes and oncogenes which play a key role in the carcinogenesis of malignant eyelid tumors has been demonstrated. Strong intermittent UV exposure and sunburn have been identified as risk factors for basal cell carcinoma and malignant melanoma. For squamous cell carcinoma, cumulative UV exposure over a longer period of time is considered a risk factor.

CONCLUSION

In order to counteract the UV-related increase in malignant eyelid tumors, preventive protective measures, early detection and increased public awareness are essential. On the one hand, changes in behavior, appropriate clothing, wearing hats and sunglasses or contact lenses with UV filters are effective measures for UV protection. On the other hand, the underlying mechanisms of carcinogenesis should be investigated further in order to be able to carry out effective prevention and further develop treatment.

Full-spectrum cannabidiol reduces UVB damage through the inhibition of TGF-β1 and the NLRP3 inflammasome

The thermodynamic characteristics, antioxidant potential, and photoprotective benefits of full-spectrum cannabidiol (FS-CBD) against UVB-induced cellular death were examined in this study. In silico analysis of CBD showed antioxidant capacity via proton donation and UV absorption at 209.09, 254.73, and 276.95 nm, according to the HAT and SPLET methodologies. FS-CBD protected against UVB-induced bacterial death for 30 min. FS-CBD protected against UVB-induced cell death by 42% (1.5 μg/mL) and 35% (3.5 μg/mL) in an in vitro keratinocyte cell model. An in vivo acute irradiated CD-1et/et mouse model (UVB-irradiated for 5 min) presented very low photoprotection when FS-CBD was applied cutaneously, as determined by histological analyses. In vivo skin samples showed that FS-CBD regulated inflammatory responses by inhibiting the inflammatory markers TGF-β1 and NLRP3. The docking analysis showed that the CBD molecule had a high affinity for TGF-β1 and NLRP3, indicating that protection against inflammation might be mediated by blocking these proinflammatory molecules. This result was corroborated by the docking interactions between CBD and TGF-β1 and NLRP3, which resulted in a high affinity and inhibition of both proteins The present work suggested a FS-CBD moderate photoprotective agent against UVB light-induced skin damage and that this effect is partially mediated by its anti-inflammatory activity.

Analysis of Variants Induced by Combined Ex Vivo Irradiation and In Vivo Tumorigenesis Suggests a Role for the ZNF831 p.R1393Q Variant in Cutaneous Melanoma Development

UVR is known to be the most important environmental carcinogen for cutaneous melanoma. Whereas genomic analyses of melanoma tumors implicate a high rate of UV damage, the experimental induction and recovery of bona fide UV-signature changes have not been directly observed. To replicate recurrent UV variants from The Cancer Genome Atlas_SKCM specimens, we UV irradiated cultured immortalized human melanocytes and subjected them to in vivo tumorigenesis assays. Exome sequencing of the xenografted tumors revealed an increase in UV-signature mutations within the tumors and identified 48 induced variants that overlap with The Cancer Genome Atlas skin cutaneous melanoma UV-hotspot mutations. A UV-induced mutation, ZNF831 p.R1393Q, was correlated with a decreased survival (hazard ratio = 5.44, 95% confidence interval = 1.92-15.47, P = .0015) and was preferentially observed in melanomas compared with that in all The Cancer Genome Atlas tumors (P = 4.42 × 10-7). In addition, ZNF831 mRNA expression loss was strongly associated with decreased patient survival (hazard ratio = 2.14, 95% confidence interval = 1.62-2.83, P = 7.91 × 10-8), although the transcripts may arise from multiple cell types, including T cells. In multiple melanoma lines, overexpression of wild-type ZNF831 reduced spheroid growth, heightened apoptosis, and increased cell motility, with the ZNF831 p.R1393Q variant partially or wholly abolishing these functional phenotypes. We thus experimentally recovered a "functional UV-hotspot mutation" in ZNF831 that is altered in human melanoma specimens.

RNA-protein interaction prediction without high-throughput data: An overview and benchmark of in silico tools

RNA-protein interactions (RPIs) are crucial for accurately operating various processes in and between organisms across kingdoms of life. Mutual detection of RPI partner molecules depends on distinct sequential, structural, or thermodynamic features, which can be determined via experimental and bioinformatic methods. Still, the underlying molecular mechanisms of many RPIs are poorly understood. It is further hypothesized that many RPIs are not even described yet. Computational RPI prediction is continuously challenged by the lack of data and detailed research of very specific examples. With the discovery of novel RPI complexes in all kingdoms of life, adaptations of existing RPI prediction methods are necessary. Continuously improving computational RPI prediction is key in advancing the understanding of RPIs in detail and supplementing experimental RPI determination. The growing amount of data covering more species and detailed mechanisms support the accuracy of prediction tools, which in turn support specific experimental research on RPIs. Here, we give an overview of RPI prediction tools that do not use high-throughput data as the user's input. We review the tools according to their input, usability, and output. We then apply the tools to known RPI examples across different kingdoms of life. Our comparison shows that the investigated prediction tools do not favor a certain species and equip the user with results varying in degree of information, from an overall RPI score to detailed interacting residues. Furthermore, we provide a guide tree to assist users which RPI prediction tool is appropriate for their available input data and desired output.

Engineering industrial yeast for improved tolerance and robustness

As an important cell factory, industrial yeast has been widely used for the production of compounds ranging from bulk chemicals to complex natural products. However, various adverse conditions including toxic products, extreme pH, and hyperosmosis etc., severely restrict microbial growth and metabolic performance, limiting the fermentation efficiency and diminishing its competitiveness. Therefore, enhancing the tolerance and robustness of yeasts is critical to ensure reliable and sustainable production of metabolites in complex industrial production processes. In this review, we provide a comprehensive review of various strategies for improving the tolerance of yeast cells, including random mutagenesis, system metabolic engineering, and material-mediated immobilization cell technology. It is expected that this review will provide a new perspective to realize the response and intelligent regulation of yeast cells to environmental stresses.

Inherited Basaloid Neoplasms Associated With SUFU Pathogenic Variants

Importance

Germline SUFU pathogenic variants (PVs) have previously been associated with basal cell nevus syndrome (BCNS) and multiple infundibulocystic basal cell carcinoma syndrome; however, a broader spectrum of cutaneous findings in patients with SUFU PVs has not been well delineated.

Objective

To define the clinical and histopathologic spectrum of cutaneous findings in patients with germline SUFU PVs.

Design, Setting, and Participants

This case series was conducted in multiple US academic dermatology, medical genetics, and medical oncology clinics between July 2014 and July 2022. The study included patients with confirmed germline SUFU PVs who were evaluated by a dermatologist. The analysis took place from March to September 2023.

Main Outcomes and Measures

Histopathologic evaluation of skin biopsies with or without immunohistochemical staining, and targeted next-generation sequencing (NGS) on tumor specimens.

Results

All 5 patients were women. The mean (range) age at presentation was 50.2 (31-68) years, with skin manifestations initially appearing in the fourth to sixth decades of life. None had keratocystic odontogenic tumors. A total of 29 skin pathology specimens from the 5 patients were reviewed; of these, 3 (10.3%) were diagnosed as basaloid follicular hamartomas (BFHs), 10 (34.5%) classified as infundibulocystic basal cell carcinomas (iBCCs), 6 (20.7%) classified as nodular basal cell carcinomas (nBCCs), and 1 (3.4%) as infiltrative basal cell carcinoma (BCC). Targeted NGS studies on tumor specimens suggest that an increased number of UV-signature variants is associated with basal cell carcinomas compared with more indolent basaloid follicular hamartomas.

Conclusions and Relevance

Patients with germline SUFU PVs may present with multiple indolent basaloid neoplasms in addition to conventional basal cell carcinomas, typically appearing in the fourth to sixth decades of life. Although there are overlapping clinical manifestations, these findings help to differentiate the clinical syndrome associated with SUFU PVs from PTCH1 BCNS. Awareness of the clinicopathologic spectrum of SUFU-associated basaloid neoplasms is important for dermatologists and dermatopathologists because many (although not all) of these lesions are indolent and do not require aggressive surgical treatment. Importantly, because SUFU lies downstream of the protein smoothened, vismodegib and other smoothened inhibitors are unlikely to be effective therapies in this subset of patients.

Dose-dependent inactivation of Plasmodium falciparum in red blood cell concentrates by treatment with short-wavelength ultraviolet light

BACKGROUND AND OBJECTIVES

Plasmodium species are naturally transmitted by Anopheles mosquitos. The parasite infects red blood cells (RBCs) and can be transfused with blood products. In non-endemic areas, the main risk of infection arises from travellers coming back and people immigrating from malaria-endemic regions. Endemic countries face a permanent risk of infection from transfusion-transmitted malaria (TTM). TTM may cause life-threatening complications in patients dependent on blood donations. This study aimed to investigate the efficacy of Plasmodium falciparum inactivation in RBC units by treatment with short-wavelength ultraviolet C (UVC) light in the absence of photochemical additives.

MATERIALS AND METHODS

RBC units were spiked with P. falciparum to a parasite density of 0.1%-1% and irradiated with up to 4.5 J/cm2 UVC. The parasite density of UVC-treated dilution series and untreated controls were compared over 3 weeks after irradiation.

RESULTS

The lowest dose of 1.5 J/cm2 UVC led to a 3.1 log reduction in parasite load compared with the untreated control. The inactivation capacity was dose-dependent. Strikingly, 4.5 J/cm2 led to ≥5.3 log unit reduction, which was equivalent to a complete inactivation in two out of three experiments.

CONCLUSION

Pathogen reduction with UVC light was previously shown to be effective for different bacteria and viruses, but the inactivation of parasites in RBC concentrates was not addressed until now. The present study provides evidence for significant inactivation of P. falciparum-infected RBCs by UVC light.

Evaluating the polymerization effectiveness and biocompatibility of bio-sourced, visible light-based photoinitiator systems

The use of photopolymerization is expanding across a multitude of biomedical applications, from drug delivery to bioprinting. Many of these current and emerging photopolymerization systems employ visible light, as motivated by safety and energy efficiency considerations. However, the "library" of visible light initiators is limited compared with the wealth of options available for UV polymerization. Furthermore, the synthesis of traditional photoinitiators relies on diminishing raw materials, and several traditional photoinitiators are considered emerging environmental contaminants. As such, there has been recent focus on identifying and characterizing biologically sourced, visible light-based photoinitiator systems that can be effectively used in photopolymerization applications. In this regard, several bio-sourced molecules have been shown to act as photoinitiators, primarily through Type II photoinitiation mechanisms. However, whether bio-sourced molecules can also act as effective synergists in these reactions remains unknown. In this study, we evaluated the effectiveness of bio-sourced synergist candidates, with a focus on amino acids, due to their amine functional groups, in combination with two bio-sourced photoinitiator molecules: riboflavin and curcumin. We tested the effectiveness of these photoinitiator systems under both violet (405 nm) and blue (460-475 nm) light using photo-rheology. We found that several synergist candidates, namely lysine, arginine, and histidine, increased the polymerization effectiveness of riboflavin when used with both violet and blue light. With curcumin, we found that almost all tested synergist candidates slightly decreased the polymerization effectiveness compared with curcumin alone under both light sources. These results show that bio-sourced molecules have the potential to be used as synergists with bio-sourced photoinitiators in visible light photopolymerization. However, more work must be done to fully characterize these reactions and to investigate more synergist candidates. Ultimately, this information is expected to expand the range of available visible light-based photoinitiator systems and increase their sustainability.

Mechanisms of radiation-induced tissue damage and response

Radiation-induced tissue injury (RITI) is the most common complication in clinical tumor radiotherapy. Due to the heterogeneity in the response of different tissues to radiation (IR), radiotherapy will cause different types and degrees of RITI, which greatly limits the clinical application of radiotherapy. Efforts are continuously ongoing to elucidate the molecular mechanism of RITI and develop corresponding prevention and treatment drugs for RITI. Single-cell sequencing (Sc-seq) has emerged as a powerful tool in uncovering the molecular mechanisms of RITI and for identifying potential prevention targets by enhancing our understanding of the complex intercellular relationships, facilitating the identification of novel cell phenotypes, and allowing for the assessment of cell heterogeneity and spatiotemporal developmental trajectories. Based on a comprehensive review of the molecular mechanisms of RITI, we analyzed the molecular mechanisms and regulatory networks of different types of RITI in combination with Sc-seq and summarized the targeted intervention pathways and therapeutic drugs for RITI. Deciphering the diverse mechanisms underlying RITI can shed light on its pathogenesis and unveil new therapeutic avenues to potentially facilitate the repair or regeneration of currently irreversible RITI. Furthermore, we discuss how personalized therapeutic strategies based on Sc-seq offer clinical promise in mitigating RITI.

MutaT7GDE: A Single Chimera for the Targeted, Balanced, Efficient, and Processive Installation of All Possible Transition Mutations In Vivo

Deaminase-T7 RNA polymerase fusion (MutaT7) proteins are a growing class of synthetic biology tools used to diversify target genes during in vivo laboratory evolution. To date, MutaT7 chimeras comprise either a deoxyadenosine or deoxycytidine deaminase fused to a T7 RNA polymerase. Their expression drives targeted deoxyadenosine-to-deoxyguanosine or deoxycytidine-to-deoxythymidine mutagenesis, respectively. Here, we repurpose recently engineered substrate-promiscuous general deaminases (GDEs) to establish a substantially simplified system based on a single chimeric enzyme capable of targeting both deoxyadenosine and deoxycytidine. We assess on- and off-target mutagenesis, strand and context preference, and parity of deamination for four different MutaT7GDE constructs. We identify a single chimera that installs all possible transition mutations more efficiently than preexisting, more cumbersome MutaT7 tools. The optimized MutaT7GDE chimera reported herein is a next-generation hypermutator capable of mediating efficient and uniform target-gene diversification during in vivo directed evolution.

Pervasive Induction of Regulatory Mutation Microclones in Sun-exposed Skin

Carcinogen-induced mutations are thought near-random, with rare cancer-driver mutations underlying clonal expansion. Using high-fidelity Duplex Sequencing to reach a mutation frequency sensitivity of 4×10 -9 per nt, we report that sun exposure creates pervasive mutations at sites with ∼100-fold UV-sensitivity in RNA-processing gene promoters - cyclobutane pyrimidine dimer (CPD) hyperhotspots - and these mutations have a mini-driver clonal expansion phenotype. Numerically, human skin harbored 10-fold more genuine mutations than previously reported, with neonatal skin containing 90,000 per cell; UV signature mutations increased 8,000-fold in sun-exposed skin, averaging 3×10 -5 per nt. Clonal expansion by neutral drift or passenger formation was nil. Tumor suppressor gene hotspots reached variant allele frequency 0.1-10% via 30-3,000 fold clonal expansion, in occasional biopsies. CPD hyperhotspots reached those frequencies in every biopsy, with modest clonal expansion. In vitro, tumor hotspot mutations arose occasionally over weeks of chronic low-dose exposure, whereas CPD hyperhotspot mutations arose in days at 1000-fold higher frequencies, growing exponentially. UV targeted mini-drivers in every skin cell.

Souza AB, Levita DP, Mello CC, da Silva AFM, dos Santos TC, Ronconi CM. Innovating Leishmaniasis Treatment: A Critical Chemist's Review of Inorganic Nanomaterials

Leishmaniasis, a critical Neglected Tropical Disease caused by Leishmania protozoa, represents a significant global health risk, particularly in resource-limited regions. Conventional treatments are effective but suffer from serious limitations, such as toxicity, prolonged treatment courses, and rising drug resistance. Herein, we highlight the potential of inorganic nanomaterials as an innovative approach to enhance Leishmaniasis therapy, aligning with the One Health concept by considering these treatments' environmental, veterinary, and public health impacts. By leveraging the adjustable properties of these nanomaterials─including size, shape, and surface charge, tailored treatments for various diseases can be developed that are less harmful to the environment and nontarget species. We review recent advances in metal-, oxide-, and carbon-based nanomaterials for combating Leishmaniasis, examining their mechanisms of action and their dual use as standalone treatments or drug delivery systems. Our analysis highlights a promising yet underexplored frontier in employing these materials for more holistic and effective disease management.

The use of droplet-based microfluidic technologies for accelerated selection of Yarrowia lipolytica and Phaffia rhodozyma yeast mutants

Microorganisms are widely used for the industrial production of various valuable products, such as pharmaceuticals, food and beverages, biofuels, enzymes, amino acids, vaccines, etc. Research is constantly carried out to improve their properties, mainly to increase their productivity and efficiency and reduce the cost of the processes. The selection of microorganisms with improved qualities takes a lot of time and resources (both human and material); therefore, this process itself needs optimization. In the last two decades, microfluidics technology appeared in bioengineering, which allows for manipulating small particles (from tens of microns to nanometre scale) in the flow of liquid in microchannels. The technology is based on small-volume objects (microdroplets from nano to femtolitres), which are manipulated using a microchip. The chip is made of an optically transparent inert to liquid medium material and contains a series of channels of small size (<1 mm) of certain geometry. Based on the physical and chemical properties of microparticles (like size, weight, optical density, dielectric constant, etc.), they are separated using microsensors. The idea of accelerated selection of microorganisms is the application of microfluidic technologies to separate mutants with improved qualities after mutagenesis. This article discusses the possible application and practical implementation of microfluidic separation of mutants, including yeasts like Yarrowia lipolytica and Phaffia rhodozyma after chemical mutagenesis will be discussed.

PTGES2 and RNASET2 identified as novel potential biomarkers and therapeutic targets for basal cell carcinoma: insights from proteome-wide mendelian randomization, colocalization, and MR-PheWAS analyses

Introduction

Basal cell carcinoma (BCC) is the most common skin cancer, lacking reliable biomarkers or therapeutic targets for effective treatment. Genome-wide association studies (GWAS) can aid in identifying drug targets, repurposing existing drugs, predicting clinical trial side effects, and reclassifying patients in clinical utility. Hence, the present study investigates the association between plasma proteins and skin cancer to identify effective biomarkers and therapeutic targets for BCC.

Methods

Proteome-wide mendelian randomization was performed using inverse-variance-weight and Wald Ratio methods, leveraging 1 Mb cis protein quantitative trait loci (cis-pQTLs) in the UK Biobank Pharma Proteomics Project (UKB-PPP) and the deCODE Health Study, to determine the causal relationship between plasma proteins and skin cancer and its subtypes in the FinnGen R10 study and the SAIGE database of Lee lab. Significant association with skin cancer and its subtypes was defined as a false discovery rate (FDR) < 0.05. pQTL to GWAS colocalization analysis was executed using a Bayesian model to evaluate five exclusive hypotheses. Strong colocalization evidence was defined as a posterior probability for shared causal variants (PP.H4) of ≥0.85. Mendelian randomization-Phenome-wide association studies (MR-PheWAS) were used to evaluate potential biomarkers and therapeutic targets for skin cancer and its subtypes within a phenome-wide human disease category.

Results

PTGES2, RNASET2, SF3B4, STX8, ENO2, and HS3ST3B1 (besides RNASET2, five other plasma proteins were previously unknown in expression quantitative trait loci (eQTL) and methylation quantitative trait loci (mQTL)) were significantly associated with BCC after FDR correction in the UKB-PPP and deCODE studies. Reverse MR showed no association between BCC and these proteins. PTGES2 and RNASET2 exhibited strong evidence of colocalization with BCC based on a posterior probability PP.H4 >0.92. Furthermore, MR-PheWAS analysis showed that BCC was the most significant phenotype associated with PTGES2 and RNASET2 among 2,408 phenotypes in the FinnGen R10 study. Therefore, PTGES2 and RNASET2 are highlighted as effective biomarkers and therapeutic targets for BCC within the phenome-wide human disease category.

Conclusion

The study identifies PTGES2 and RNASET2 plasma proteins as novel, reliable biomarkers and therapeutic targets for BCC, suggesting more effective clinical application strategies for patients.

Evolutionary patterns of DNA base composition at polymorphic sites highlight the role of the environment in shaping barley and rice genomes

Insights into changes in genome base composition underlying crop domestication can be gained by using comparative genomics. With this approach, previous studies have reported that crop genomes during domestication accumulate more nucleotides adenine (A) and thymine (T) (termed as [AT]-increase) across polymorphic sites. However, the potential influence of the environment or its factors, for example, solar ultraviolet (UV) radiation and temperature, on the [AT]-increase has not been well elucidated. Here, we investigated the [AT]-increase in barley (Hordeum vulgare L.) and rice (Oryza sativa L.) and the association with natural environments, where accessions are distributed. With 12,798,376 and 2,861,535 single-nucleotide polymorphisms from 368 barley and 1375 rice accessions, respectively, we discovered that [AT] increases from wild accessions to improved cultivars, and genomic regions with larger [AT]-increase tend to have higher UV-related motif frequencies, suggesting solar UV radiation as a potential factor in driving genome variation. To link [AT] change with the geographic distribution, we gathered georeferenced accessions and examined their local environments. Interestingly, negative correlations between [AT] and environmental factors were observed (r = -0.39 ∼ -0.75) and modern accessions with higher [AT] values, as compared with wild relatives, are from the environments with lower solar UV radiation or lower temperature. With [AT] and environmental factors as phenotypes, genome-wide association mapping identified three candidate genes that have the potential to contribute to [AT] variation under the effect of environmental conditions. Our findings provide genomic and environmental insights into evolutionary pattern of DNA base composition and underlying mechanisms.

Evaluation of mitochondrial stress following ultraviolet radiation and 5G radiofrequency field exposure in human skin cells

Whether human cells are impacted by environmental electromagnetic fields (EMF) is still a matter of debate. With the deployment of the fifth generation (5G) of mobile communication technologies, the carrier frequency is increasing and the human skin becomes the main biological target. Here, we evaluated the impact of 5G-modulated 3.5 GHz radiofrequency (RF) EMF on mitochondrial stress in human fibroblasts and keratinocytes that were exposed for 24 h at specific absorption rate of 0.25, 1, and 4 W/kg. We assessed cell viability, mitochondrial reactive oxygen species (ROS) production, and membrane polarization. Knowing that human skin is the main target of environmental ultraviolet (UV), using the same read-out, we investigated whether subsequent exposure to 5G signal could alter the capacity of UV-B to damage skin cells. We found a statistically significant reduction in mitochondrial ROS concentration in fibroblasts exposed to 5G signal at 1 W/kg. On the contrary, the RF exposure slightly but statistically significantly enhanced the effects of UV-B radiation specifically in keratinocytes at 0.25 and 1 W/kg. No effect was found on mitochondrial membrane potential or apoptosis in any cell types or exposure conditions suggesting that the type and amplitude of the observed effects are very punctual.

Current insights and future perspectives of ultraviolet radiation (UV) exposure: Friends and foes to the skin and beyond the skin

Ultraviolet (UV) radiation is ubiquitous in the environment, which has been classified as an established human carcinogen. As the largest and outermost organ of the body, direct exposure of skin to sunlight or UV radiation can result in sunburn, inflammation, photo-immunosuppression, photoaging and even skin cancers. To date, there are tactics to protect the skin by preventing UV radiation and reducing the amount of UV radiation to the skin. Nevertheless, deciphering the essential regulatory mechanisms may pave the way for therapeutic interventions against UV-induced skin disorders. Additionally, UV light is considered beneficial for specific skin-related conditions in medical UV therapy. Recent evidence indicates that the biological effects of UV exposure extend beyond the skin and include the treatment of inflammatory diseases, solid tumors and certain abnormal behaviors. This review mainly focuses on the effects of UV on the skin. Moreover, novel findings of the biological effects of UV in other organs and systems are also summarized. Nevertheless, the mechanisms through which UV affects the human organism remain to be fully elucidated to achieve a more comprehensive understanding of its biological effects.

Thallium(I) induces a prolonged inhibition of (6-4)photoproduct binding and UV damage excision repair activities in zebrafish (Danio rerio) embryos via protein inactivation

Cyclobutane pyrimidine dimer (CPD) and (6-4)photoproduct (6-4 PP) are two major types of UV-induced DNA lesion and 6-4 PP is more mutagenic than CPD. Activated by lesion detection, nucleotide excision repair (NER) eliminates CPDs and 6-4 PPs. Thallium (Tl) is a toxic metal existing primarily as Tl+ in the aquatic environment. Ingestion of Tl+-contaminated foods and water is a major route of human poisoning. As Tl+ may inhibit enzyme activities via binding to sulfhydryl groups, this study explored if Tl+ could intensify UV mutagenicity by inactivating NER-linked damage recognition factors using zebrafish (Danio rerio) embryo as a model system. Incubation of Tl+ (as thallium nitrate) at 0.1-0.4 μg/mL with zebrafish extracts for 20 min caused a concentration-dependent inhibition of 6-4 PP binding activities as shown by a photolesion-specific band shift assay, while CPD binding activities were insensitive to Tl+. The ability of Tl+ to suppress 6-4 PP detection was stronger than that of Hg2+. Exposure of zebrafish embryos at 1 h post fertilization (hpf) to Tl+ at 0.4-1 μg/mL for 9 or 71 h also specifically inhibited 6-4 PP detection, indicating that Tl+ induced a prolonged inhibition of 6-4 PP sensing ability primarily via its direct interaction with damage recognition molecules. Tl+-mediated inhibition of 6-4 PP binding in embryos at distinct stages resulted in a suppression of NER capacity monitored by a transcription-based DNA repair assay. Our results revealed the potential of Tl+ to enhance UV mutagenicity by disturbing the removal of 6-4 PP through repressing the lesion detection step of NER.

High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma

Noncoding mutation hotspots have been identified in melanoma and many of them occur at the binding sites of E26 transformation-specific (ETS) proteins; however, their formation mechanism and functional impacts are not fully understood. Here, we used UV (Ultraviolet) damage sequencing data and analyzed cyclobutane pyrimidine dimer (CPD) formation, DNA repair, and CPD deamination in human cells at single-nucleotide resolution. Our data show prominent CPD hotspots immediately after UV irradiation at ETS binding sites, particularly at sites with a conserved TTCCGG motif, which correlate with mutation hotspots identified in cutaneous melanoma. Additionally, CPDs are repaired slower at ETS binding sites than in flanking DNA. Cytosine deamination in CPDs to uracil is suggested as an important step for UV mutagenesis. However, we found that CPD deamination is significantly suppressed at ETS binding sites, particularly for the CPD hotspot on the 5' side of the ETS motif, arguing against a role for CPD deamination in promoting ETS-associated UV mutations. Finally, we analyzed a subset of frequently mutated promoters, including the ribosomal protein genes RPL13A and RPS20, and found that mutations in the ETS motif can significantly reduce the promoter activity. Thus, our data identify high UV damage and low repair, but not CPD deamination, as the main mechanism for ETS-associated mutations in melanoma and uncover important roles of often-overlooked mutation hotspots in perturbing gene transcription.

Biosynthesis of 10-Hydroxy-2-decenoic Acid through a One-Step Whole-Cell Catalysis

10-Hydroxy-2-decenoic acid (10-HDA) is an important component of royal jelly, known for its antimicrobial, anti-inflammatory, blood pressure-lowering, and antiradiation effects. Currently, 10-HDA biosynthesis is limited by the substrate selectivity of acyl-coenzyme A dehydrogenase, which restricts the technique to a two-step process. This study aimed to develop an efficient and simplified method for synthesizing 10-HDA. In this study, ACOX from Candida tropicalis 1798, which catalyzes 10-hydroxydecanoyl coenzyme A desaturation for 10-HDA synthesis, was isolated and heterologously coexpressed with FadE, Macs, YdiI, and CYP in Escherichia coli/SK after knocking out FadB, FadJ, and FadR genes. The engineered E. coli/AKS strain achieved a 49.8% conversion of decanoic acid to 10-HDA. CYP expression was improved through ultraviolet mutagenesis and high-throughput screening, increased substrate conversion to 75.6%, and the synthesis of 10-HDA was increased to 0.628 g/L in 10 h. This is the highest conversion rate and product concentration achieved in the shortest time to date. This study provides a simple and efficient method for 10-HDA biosynthesis and offers an effective method for developing strains with high product yields.

Development of porcine embryos cultured in media irradiated with ultraviolet-C

Sterilization of the culture medium using ultraviolet (UV)-C reduces the potential adverse effects of microorganisms and allows for long-term use. In the present study, we investigated the effects of a medium directly irradiated with UV-C prior to in vitro culture on the development and quality of porcine in vitro-fertilized embryos and the free amino acid composition of the culture media. The culture media (porcine zygote medium [PZM-5] and porcine blastocyst medium [PBM]) were irradiated with UV-C at 228 and 260 nm for 1 and 3 days, respectively. Next, the culture media were irradiated with UV-C at 228 nm for 3, 7, or 14 days. After in vitro fertilization, the embryos were cultured in the UV-C-irradiated media for 7 days. Free amino acid levels in culture media irradiated with 228 and 260 nm UV-C for 3 days were analysed. The blastocyst formation rate of embryos cultured in media irradiated with 260 nm UV-C for 3 days was significantly lower than that of embryos cultured in non-irradiated control media. However, 228 nm UV-C irradiation for up to 14 days did not affect blastocyst formation rates and quality in the resulting blastocysts. Moreover, 260 nm UV-C irradiation significantly increased the taurine concentration in both culture media and decreased methionine concentration in the PBM. In conclusion, UV-C irradiation at 228 nm before in vitro culture had no detrimental effects on embryonic development. However, 260 nm UV-C irradiation decreased embryo development and altered the composition of free amino acids in the medium.

Knowledge and the behavioral patterns of photoprotection among Koreans with skin disease

BACKGROUND

Photoprotection is crucial in preventing the development and progression of various skin diseases. However, patients with skin disease have limited awareness of photoprotection. We evaluated the knowledge and behavioral patterns of photoprotection among Koreans with skin diseases.

METHODS

A cross-sectional study was conducted in 11 general hospitals across South Korea. The study population consisted of patients aged 19 years or older who visited dermatologic clinics for their skin diseases. A self-administered questionnaire was used to collect patient demographics, knowledge of photoprotection, and photoprotective habits.

RESULTS

In this study, 1173 patients with skin cancer, hyperpigmentary disorders, hypopigmentary disorders, or other skin diseases participated. Females scored significantly higher in knowledge of photoprotection compared to males (mean score 8.4 vs. 7.8; p < .001), and younger patients (<50 years) scored higher than older patients (mean score 8.7 vs. 7.5; p < .001). Males also reported longer sun exposure times and lower usage of photoprotective measures (both p < .001). Patients with skin cancer had the lowest mean knowledge score (7.1 ± 2.6) and were less likely to use photoprotective measures compared to other groups (p < .001). In contrast, patients with hyperpigmentation actively avoided sun exposure compared with other groups (p < 0.001).

CONCLUSIONS

Knowledge of photoprotection among Korean patients with skin diseases varied depending on the gender, age, and type of skin disease. Their photoprotective behaviors were inadequate, especially among males and those with skin cancer. These findings emphasize the importance of educating and tailoring photoprotection strategies for patients with skin diseases.

UV-C LED-induced cyclobutane pyrimidine dimer formation, lesion repair and mutagenesis in the biofilm-forming diatom, Navicula incerta

The use of ultraviolet-C (UV-C) irradiation in marine biofouling control is a relatively new and potentially disruptive technology. This study examined effects of UV-C exposure on the biofilm-forming diatom, Navicula incerta. UV-C-induced mutations were identified via Illumina HiSeq. A de novo genome was assembled from control sequences and reads from UV-C-exposed treatments were mapped to this genome, with a quantitative estimate of mutagenesis then derived from the frequency of single nucleotide polymorphisms. UV-C exposure increased cyclobutane pyrimidine dimer (CPD) abundance with a direct correlation between lesion formation and fluency. Cellular repair mechanisms gradually reduced CPDs over time, with the highest UV-C fluence treatments having the fastest repair rates. Mutation abundances were, however, negatively correlated with CPD abundance suggesting that UV-C exposure may influence lesion repair. The threshold fluence for CPD formation exceeding CPD repair was >1.27 J cm-2. Fluences >2.54 J cm-2 were predicted to inhibit repair mechanisms. While UV-C holds considerable promise for marine antifouling, diatoms are just one, albeit an important, component of marine biofouling communities. Determining fluence thresholds for other representative taxa, highlighting the most resistant, would allow UV-C treatments to be specifically tuned to target biofouling organisms, whilst limiting environmental effects and the power requirement.

Protocol for the generation of Symbiodiniaceae mutants using UV mutagenesis

Genetic approaches are limited in the dinoflagellate family, Symbiodiniaceae, causing a bottleneck in the discovery of useful mutants toward the goal of preventing future coral bleaching events. In this protocol, we demonstrate the application of UV exposure, coupled with downstream phenotypic screening and mutant isolation, to form a UV mutagenesis pipeline. This pipeline provides an avenue to generate Symbiodiniaceae mutants to help link genotype to phenotype, as well as address previously unanswered questions surrounding relationships with host organisms, like coral. For complete details on the use and execution of this protocol, please refer to Jinkerson et al. (2022).1.

Random mutagenesis as a tool for industrial strain improvement for enhanced production of antibiotics: a review

Secondary metabolites are produced by microbes in minimal quantities in the natural environment out of necessity. However, in the pharmaceutical industry, their overproduction becomes essential. To achieve higher yields, genetic modifications are employed to create strains that surpass the productivity of the initially isolated strains. While rational screening and genetic engineering have emerged as valuable practices in recent years, the cost-effective technique of mutagenesis and selection, known as "random screening," remains a preferred method for efficient short-term strain development. This review aims to comprehensively explore all aspects of strain improvement, focusing on why random mutagenesis continues to be widely adopted.

Differing structures and dynamics of two photolesions portray verification differences by the human XPD helicase

Ultraviolet light generates cyclobutane pyrimidine dimer (CPD) and pyrimidine 6-4 pyrimidone (6-4PP) photoproducts that cause skin malignancies if not repaired by nucleotide excision repair (NER). While the faster repair of the more distorting 6-4PPs is attributed mainly to more efficient recognition by XPC, the XPD lesion verification helicase may play a role, as it directly scans the damaged DNA strand. With extensive molecular dynamics simulations of XPD-bound single-strand DNA containing each lesion outside the entry pore of XPD, we elucidate strikingly different verification processes for these two lesions that have very different topologies. The open book-like CPD thymines are sterically blocked from pore entry and preferably entrapped by sensors that are outside the pore; however, the near-perpendicular 6-4PP thymines can enter, accompanied by a displacement of the Arch domain toward the lesion, which is thereby tightly accommodated within the pore. This trapped 6-4PP may inhibit XPD helicase activity to foster lesion verification by locking the Arch to other domains. Furthermore, the movement of the Arch domain, only in the case of 6-4PP, may trigger signaling to the XPG nuclease for subsequent lesion incision by fostering direct contact between the Arch domain and XPG, and thereby facilitating repair of 6-4PP.

Ultra-high static magnetic field induces a change in the spectrum but not frequency of DNA spontaneous mutations in Arabidopsis thaliana

Biological effects of magnetic fields have been extensively studied in plants, microorganisms and animals, and applications of magnetic fields in regulation of plant growth and phytoprotection is a promising field in sustainable agriculture. However, the effect of magnetic fields especially ultra-high static magnetic field (UHSMF) on genomic stability is largely unclear. Here, we investigated the mutagenicity of 24.5, 30.5 and 33.0 T UHSMFs with the gradient of 150, 95 and 0 T/m, respectively, via whole genome sequencing. Our results showed that 1 h exposure of Arabidopsis dried seeds to UHSMFs has no significant effect on the average rate of DNA mutations including single nucleotide variations and InDels (insertions and deletions) in comparison with the control, but 33.0 T and 24.5 T treatments lead to a significant change in the rate of nucleotide transitions and InDels longer than 3 bp, respectively, suggesting that both strength and gradient of UHSMF impact molecular spectrum of DNA mutations. We also found that the decreased transition rate in UHSMF groups is correlated with the upstream flanking sequences of G and C mutation sites. Furthermore, the germination rate of seeds exposed to 24.5 T SMF with -150 T/m gradient showed a significant decrease at 24 hours after sowing. Overall, our data lay a basis for precisely assessing the potential risk of UHSMF on DNA stability, and for elucidating molecular mechanism underlying gradient SMF-regulated biological processes in the future.

Efficacy and mechanism of retinyl palmitate against UVB-induced skin photoaging

Retinyl palmitate (RP) is a vitamin A derivative that has been widely used in anti-aging and skin treatment. The aim of this study is to investigate the effect of RP on UVB (Ultraviolet radiation B) induced photoaging and its potential mechanism. Immunofluorescence assay demonstrates that RP can reduce collagen degradation in skin cells by UVB radiation and reduce apoptosis of skin cells. Cell migration assay reveals that RP can increase cell migration rate, helping to repair skin damage and restore cell viability. Immunohistochemical assays indicate that RP can significantly reduce the expression of IL-6, IL-1β, TNF-α induced by UVB radiation. Moreover, metabolomics and transcriptomics results suggest that RP regulates several metabolic pathways and gene expression, particularly in inflammatory signaling pathways, collagen synthesis and apoptosis, exhibiting significant regulatory effects. Furthermore, network pharmacological analysis predicts that RP may affect UVB-induced photoaging by regulating multiple key proteins and signaling pathways. Overall, this study demonstrates that RP has significant anti-photoaging ability, acting through several pathways including inhibition of inflammatory response, promotion of collagen synthesis and inhibition of apoptosis. These results provide a scientific basis for the application of RP in skin anti-photoaging and therapy, enabling the potential usage of RP to skin care products.

APE1-dependent base excision repair of DNA photodimers in human cells

UV irradiation induces "bulky" DNA photodimers such as (6-4)-photoproducts and cyclobutane pyrimidine dimers that are removed by nucleotide excision repair, a complex process defective in the sunlight-sensitive and cancer-prone disease xeroderma pigmentosum. Some bacteria and lower eukaryotes can also repair photodimers by enzymatically simpler mechanisms, but such pathways have not been reported in normal human cells. Here, we have identified such a mechanism. We show that normal human cells can employ a DNA base excision repair process involving NTH1, APE1, PARP1, XRCC1, and FEN1 to rapidly remove a subset of photodimers at early times following UVC irradiation. Loss of these proteins slows the early rate of repair of photodimers in normal cells, ablates their residual repair in xeroderma pigmentosum cells, and increases UVC sensitivity ∼2-fold. These data reveal that human cells can excise photodimers using a long-patch base excision repair process that functions additively but independently of nucleotide excision repair.

Low-dose daylight exposure induces nitric oxide release and maintains cell viability in vitro

Any potential positive effects conferred via sunlight exposure have to be carefully balanced against carcinogenic effects. Here we provide evidence UK sunlight exposure upregulates the cardio protectant nitric oxide (NO) within in vitro skin cell lines with negligible increases in DNA damage and cell death at 1 SED, when compared against unexposed samples. The whole of the ultraviolet A (UV-A) spectrum appears to be responsible for NO release, with efficiency higher at exposures closer to shorter UV-A wavelengths and decreasing with wavelength increases. These results support further in vivo work, which could be of benefit for demographics such as the elderly (that exhibit a natural decline in NO bioavailability).

An efficient mutagenesis system to improve the propamocarb tolerance in Lecanicillium lecanii (Zimmermann) Zare & Gams

Lecanicillium lecanii (Zimmermann) Zare & Gams is used as an effective biopesticide for the control of sap-sucking insect pests on agricultural crops. However, low fungicide tolerance limits its large-scale field application. To improve the propamocarb tolerance in L. lecanii, a composite mutagenesis system was established by using UV-light (U), N-Methyl-N'-nitro-N-nitrosoguanidine (NTG) (N) and N+ ion-beam (I). The permutation type of three agents was a consecutive mutagenesis treatment (I/N/U) after an intermittent treatment (U + N + I). The "U" mutagenesis was performed at 254 nm for 60 s and at a distance of 45 cm under a 20 W germicidal lamp, the "N" mutagenesis was performed at a concentration of 1.0 mg/mL NTG for 60 min, and the "I" mutagenesis was performed by low energy N+ ion-beam using a dose of 10 × 1013 ions/cm2 at 30 keV. This composite mutagenesis system was recorded as the "U + N + I + I/N/U," and then the mutagenesis efficiency in improving propamocarb tolerance was assessed by analyzing changes of mutants in the propamocarb sensitivity, mitotic stability, mycelial growth speed on plates or in liquid, sporulation on plates or aphids, conidial germination, 50% lethal concentration (LC50) and 50% lethal time (LT50) to aphids, lipid constituent and cell membrane permeability and control against aphids in the presence or absence of propamocarb. Compared to the wild-type isolate with a 50% effective concentration (EC50) value of 503.6 μg/mL propamocarb, the Ll-IC-UNI produced by the "U + N + I + I/N/U" had the highest EC50 value of 3576.4 μg/mL and a tolerance ratio of 7.1. The mutant was mitotically stable in 20-passage cultivation and did not show any unfavorable changes in growth and virulence indicators. The mutant showed the highest ability to resist or avoid the damaging effects of propamocarb as reflected by the alternations of lipid constituents and membrane permeability. The interval time for applying fungal agent was significantly shortened in this mutant after spraying a field recommended dose of 550 μg/mL propamocarb. In conclude, the "U + N + I + I/N/U" composite mutagenesis mode was efficient and useful to improve the propamocarb-tolerance of L. lecanii and the obtained Ll-IC-UNI could have commercial potential for field application.

Flow-cytometric cell sorting coupled with UV mutagenesis for improving pectin lyase expression

Introduction: Alkaline pectin lyase is an important enzyme with a wide range of applications in industrial production, It has been widely used in many important fields such as fruit juice processing and extraction, the dyeing and processing of cotton and linen textiles, degumming plant fibers, environmental industrial wastewater treatment, and pulp and paper production. PGLA-rep4 was previously generated as a modified alkaline pectin lyase with high specific activity at pH 11.0°C and 70°C. However, the pre-constructed high-activity pectin lyase expression strains are still difficult to apply in industrial production due to their limited enzymatic activity. We hope to solve these problems by combining modern breeding techniques with high-throughput equipment to rapidly screen alkaline pectin lyase with higher enzymatic activity and lower cost. Methods: We fused the genes encoding PGLA-rep4 and fluorescent protein egfp using a flexible linker peptide and ligated them into a temperature-sensitive plasmid, pKD46. The constructed screening plasmid pKD46-PGLA-rep4-egfp was then transformed into an expression host and screened via flow-cytometric cell sorting coupled with UV mutagenesis. Results: Following mutagenesis, primary screening, and secondary screening, the high-expression strain, named Escherichia coli BL21/1G3, was obtained. The screening plasmid pKD46-PGLA-rep4-egfp was eliminated, and the original expression plasmid pET28a-PGLA-rep4 was then retransformed into the mutant strains. After induction and fermentation, pectin lyase activity in E. coli BL21/1G3 was significantly increased (1.37-fold relative to that in the parental E. coli BL21/PGLA-rep4 strain, p < 0.001), and the highest activity was 230, 240 U/mL at 144 h. Genome sequencing revealed that genes encoding ribonuclease E (RNase E) and diadenosine tetraphosphatase (ApaH) of E. coli BL21/1G3 were mutated compared to the sequence in the original E. coli BL21 (DE3) strain, which could be associated with increased enzyme expression. Discussion: Our work provides an effective method for the construction of strains expressing pectin lyase at high levels.

Sequence dependencies and mutation rates of localized mutational processes in cancer

BACKGROUND

Cancer mutations accumulate through replication errors and DNA damage coupled with incomplete repair. Individual mutational processes often show nucleotide sequence and functional region preferences. As a result, some sequence contexts mutate at much higher rates than others, with additional variation found between functional regions. Mutational hotspots, with recurrent mutations across cancer samples, represent genomic positions with elevated mutation rates, often caused by highly localized mutational processes.

METHODS

We count the 11-mer genomic sequences across the genome, and using the PCAWG set of 2583 pan-cancer whole genomes, we associate 11-mers with mutational signatures, hotspots of single nucleotide variants, and specific genomic regions. We evaluate the mutation rates of individual and combined sets of 11-mers and derive mutational sequence motifs.

RESULTS

We show that hotspots generally identify highly mutable sequence contexts. Using these, we show that some mutational signatures are enriched in hotspot sequence contexts, corresponding to well-defined sequence preferences for the underlying localized mutational processes. This includes signature 17b (of unknown etiology) and signatures 62 (POLE deficiency), 7a (UV), and 72 (linked to lymphomas). In some cases, the mutation rate and sequence preference increase further when focusing on certain genomic regions, such as signature 62 in transcribed regions, where the mutation rate is increased up to 9-folds over cancer type and mutational signature average.

CONCLUSIONS

We summarize our findings in a catalog of localized mutational processes, their sequence preferences, and their estimated mutation rates.

Role of Substrate Binding Interactions on DNA Repair by Photolyase

The repair of the cyclobutane pyrimidine dimer (CPD) lesion in DNA by photolyase is determined by its initial recognition, and the catalytic efficiency depends on a series of intermolecular electron-transfer (ET) processes. Here, we investigated the repair of a CPD structural isomer, replacing the deoxyribose with a pyranose sugar on the 5' site, and found a loss in binding efficiency and repair quantum yield. Using femtosecond spectroscopy, we characterized all elementary repair steps and observed a systemic slowdown of the four intermolecular ET reactions and the second bond splitting. Our observations and molecular dynamics simulations suggest that the sugar replacement disrupts the lesion binding configuration, weakening the electronic coupling between the cofactor and lesion and altering the stability of lesion intermediates. These findings highlight how the CPD photolyases have utilized the structural features of the CPD lesion and optimized its interactions with the cofactor and key active-site residues to maximize repair yields.

Genome-wide maps of UVA and UVB mutagenesis in yeast reveal distinct causative lesions and mutational strand asymmetries

Ultraviolet (UV) light primarily causes C > T substitutions in lesion-forming dipyrimidine sequences. However, many of the key driver mutations in melanoma do not fit this canonical UV signature, but are instead caused by T > A, T > C, or C > A substitutions. To what extent exposure to the UVB or UVA spectrum of sunlight can induce these noncanonical mutation classes, and the molecular mechanism involved is unclear. Here, we repeatedly exposed wild-type or repair-deficient yeast (Saccharomyces cerevisiae) to UVB or UVA light and characterized the resulting mutations by whole genome sequencing. Our data indicate that UVB induces C > T and T > C substitutions in dipyrimidines, and T > A substitutions that are often associated with thymine-adenine (TA) sequences. All of these mutation classes are induced in nucleotide excision repair-deficient cells and show transcriptional strand asymmetry, suggesting they are caused by helix-distorting UV photoproducts. In contrast, UVA exposure induces orders of magnitude fewer mutations with a distinct mutation spectrum. UVA-induced mutations are elevated in Ogg1-deficient cells, and the resulting spectrum consists almost entirely of C > A/G > T mutations, indicating they are likely derived from oxidative guanine lesions. These mutations show replication asymmetry, with elevated G > T mutations on the leading strand, suggesting there is a strand bias in the removal or bypass of guanine lesions during replication. Finally, we develop a mutation reporter to show that UVA induces a G > T reversion mutation in yeast that mimics the oncogenic NRAS Q61K mutation in melanoma. Taken together, these findings indicate that UVA and UVB exposure can induce many of the noncanonical mutation classes that cause driver mutations in melanoma.

Greener approach to the comprehensive utilization of algal biomass and oil using novel Clostridial fusants and bio-based solvents

A greener method has been tested to utilize algal biomass as a feedstock to produce bio-oil in addition to acetone, butanol, and ethanol (ABE) products. Various hydrolysis treatments were used prior to fermentation including combination of thermal, chemical, and enzymatic, which resulted in maximum sugar release of 27.78 g/L. Bio-based terpenes was used instead of common toxic chemicals together with Clostridial fustants to produce bio-alcoholic fuels. Protoplast fusion technique were used to produce the novel Clostridia fusants (C. beijernickii + C. thermocellum and C. acetobutylicum + C. thermocellocum). Fused strains were then subjected to UV radiation for strain enhancement. Final fusansts showed clear improvement in thermal stability and resistance to biobutanol toxicity. Fermentation experiments showed maximum biobutanol final production of 7.98 g/L using CbCt versus 7.39 g/L using CaCt. Oil extraction from virgin algae was tested using a green, bio-based approach using terpenes with ultrasonication and green Bligh and Dyer method, separately. In preliminary study on algal biomass, the combinations of ultrasonication followed by the green Bligh and Dyer have resulted in oil yield of 46.27% (d-limonene) and 39.85% (p-cymene). Oil extraction from an algae sample following fermentation using the combined extraction method resulted in significantly higher oil yield of 65.04%.

Base-resolution UV footprinting by sequencing reveals distinctive damage signatures for DNA-binding proteins

Decades ago, it was shown that proteins binding to DNA can quantitatively alter the formation of DNA damage by UV light. This established the principle of UV footprinting for non-intrusive study of protein-DNA contacts in living cells, albeit at limited scale and precision. Here, we perform deep base-resolution quantification of the principal UV damage lesion, the cyclobutane pyrimidine dimer (CPD), at select human promoter regions using targeted CPD sequencing. Several transcription factors exhibited distinctive and repeatable damage signatures indicative of site occupancy, involving strong (up to 17-fold) position-specific elevations and reductions in CPD formation frequency relative to naked DNA. Positive damage modulation at some ETS transcription factor binding sites coincided at base level with melanoma somatic mutation hotspots. Our work provides proof of concept for the study of protein-DNA interactions at individual loci using light and sequencing, and reveals widespread and potent modulation of UV damage in regulatory regions.

Pulsed ultraviolet (PUV) disinfection of artificially contaminated seawater seeded with high levels of pathogen disease indicators as an alternative for the shellfish industry depuration systems

The increase in pathogen levels in seawater threatens the safety of entire aquatic ecosystems. Foodborne pathogens can potentially accumulate in shellfish, especially in filter feeders such as bivalves, requiring an efficient depuration process before consumption. Alternative approaches to promote a cost-efficient purge at depuration plants are urgently needed. A small prototype pulsed ultraviolet (PUV) light recirculation system was designed, and its depuration potential was tested in a seawater matrix artificially contaminated with high levels of microbial pathogens Escherichia coli, Staphylococcus aureus, Salmonella typhimurium, Bacillus cereus and Candida albicans. The analysis of treatment parameters including voltage, number of pulses and duration of treatment was performed to ensure the highest reduction in contaminant levels. Optimal PUV disinfection was attained at 60 pulses/min at 1 kV for 10 min (a UV output of 12.9 J/cm²). All reductions were statistically significant, and the greatest was observed for S. aureus (5.63 log₁₀), followed by C. albicans (5.15 log₁₀), S. typhimurium (5 log₁₀), B. cereus (4.59 log₁₀) and E. coli (4.55 log₁₀). PUV treatment disrupted the pathogen DNA with the result that S. aureus, C. albicans and S. typhimurium were not detectable by PCR. Regulations were reviewed to address the applicability of PUV treatment as a promising alternative to assist in the reduction of microbial pathogens at depuration plants due to its high efficiency, short treatment period, high UV dose and recirculation system as currently employed in shellfish depuration plants.

Contributions of replicative and translesion DNA polymerases to mutagenic bypass of canonical and atypical UV photoproducts

UV exposure induces a mutation signature of C > T substitutions at dipyrimidines in skin cancers. We recently identified additional UV-induced AC > TT and A > T substitutions that could respectively cause BRAF V600K and V600E oncogenic mutations. The mutagenic bypass mechanism past these atypical lesions, however, is unknown. Here, we whole genome sequenced UV-irradiated yeast and used reversion reporters to delineate the roles of replicative and translesion DNA polymerases in mutagenic bypass of UV-lesions. Our data indicates that yeast DNA polymerase eta (pol η) has varied impact on UV-induced mutations: protecting against C > T substitutions, promoting T > C and AC > TT substitutions, and not impacting A > T substitutions. Surprisingly, deletion rad30Δ increased novel UV-induced C > A substitutions at CA dinucleotides. In contrast, DNA polymerases zeta (pol ζ) and epsilon (pol ε) participated in AC > TT and A > T mutations. These results uncover lesion-specific accurate and mutagenic bypass of UV lesions, which likely contribute to key driver mutations in melanoma.

Multiple strategies for the development of multienzyme complex for one-pot reactions

The main intention in the modern era is to make life and activities on earth more comfortable by adding necessary products through biological machinery. Millions of tons of biological raw materials and lignocellulosic biomass are wasted by burning each year without providing benefits to living organisms. Instead of being the cause of disturbing the natural environment by increasing global warming and pollutants worldwide, now, it is the need of the hour to develop an advanced strategy to utilize these biological raw materials to produce renewable energy resources to meet the energy crisis. The review presents the idea of multiple enzymes in one step to hydrolyze complex biomaterials into useful products. The paper discusses how multiple enzymes are arranged in a cascade for complete hydrolysis of raw material in one-pot to prevent multistep, time consuming, and expensive methods. Furthermore, there was the immobilization of multiple enzymes in a cascade system with in vitro and in vivo conditions for reusability of enzymes. The role of genetic engineering, metabolic engineering, and random mutation techniques is described for the development of multiple enzyme cascades. Techniques that are involved in the improvement of native strain to recombinant strain for the enhancement of hydrolytic capacity were used. The preparative steps, before enzymatic hydrolysis like acid, and base treatment methods are more effective for improving the hydrolysis of biomass by multiple enzymes in a one-pot system. Finally, the applications of one-pot multienzyme complexes in biofuel production from lignocellulosic biomass, biosensor production, medicine, food industry, and the conversion of biopolymers into useful products are described.

Exploring Mycosporine-like Amino Acid UV-Absorbing Natural Products for a New Generation of Environmentally Friendly Sunscreens

Human skin needs additional protection from damaging ultraviolet radiation (UVR: 280-400 nm). Harmful UVR exposure leads to DNA damage and the development of skin cancer. Available sunscreens offer chemical protection from detrimental sun radiation to a certain extent. However, many synthetic sunscreens do not provide sufficient UVR protection due to the lack of photostability of their UV-absorbing active ingredients and/or the lack of ability to prevent the formation of free radicals, inevitably leading to skin damage. In addition, synthetic sunscreens may negatively affect human skin, causing irritation, accelerating skin aging and even resulting in allergic reactions. Beyond the potential negative effect on human health, some synthetic sunscreens have been shown to have a harmful impact on the environment. Consequently, identifying photostable, biodegradable, non-toxic, and renewable natural UV filters is imperative to address human health needs and provide a sustainable environmental solution. In nature, marine, freshwater, and terrestrial organisms are protected from harmful UVR through several important photoprotective mechanisms, including the synthesis of UV-absorbing compounds such as mycosporine-like amino acids (MAAs). Beyond MAAs, several other promising, natural UV-absorbing products could be considered for the future development of natural sunscreens. This review investigates the damaging impact of UVR on human health and the necessity of using sunscreens for UV protection, specifically UV-absorbing natural products that are more environmentally friendly than synthetic UV filters. Critical challenges and limitations related to using MAAs in sunscreen formulations are also evaluated. Furthermore, we explain how the genetic diversity of MAA biosynthetic pathways may be linked to their bioactivities and assess MAAs' potential for applications in human health.