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Search Results (244)

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17 pages, 6520 KB  
Article
Browsing Pressure Modelling: Spatial Prediction of Browsing Probabilities
by Thomas Bürscher, Dominik Dachs, Kirsten Weingarth-Dachs and Eduard Hochbichler
Forests 2025, 16(10), 1520; https://doi.org/10.3390/f16101520 - 27 Sep 2025
Viewed by 230
Abstract
The global forestry discourse frequently highlights the issue of ungulate browsing, which can significantly impact tree regeneration and tree species composition by inhibition of growth and elimination of certain, particularly ecologically valuable, tree species. The forestry field often utilizes the percentage of browsed [...] Read more.
The global forestry discourse frequently highlights the issue of ungulate browsing, which can significantly impact tree regeneration and tree species composition by inhibition of growth and elimination of certain, particularly ecologically valuable, tree species. The forestry field often utilizes the percentage of browsed trees within a specific area, ranging from single hunting grounds to broader provincial scales, as a metric of browsing intensity. This measure correlates with ungulate density, which is known to vary across landscapes, rendering spatially averaged browsing percentages less useful for silvicultural decisions even with accurate results. Addressing this gap, we utilized a GLMM with random effects to assess tree specific browsing pressure more appropriately. We incorporated data from two adjacent areas in the northeastern limestone Alps, focussing on the four important tree species in the region (Abies alba, Acer pseudoplatanus, Fagus sylvatica, and Picea abies). We analyzed data collected with distinct methodologies for the two regions, respectively, Austrian Federal Game Impact Monitoring and Austrian Regeneration and Browsing Monitoring of Federal Forests. Overall, the data documented browsing occurrence on 8933 trees over 632 sampling plots totalling 55,000 hectares. By comparing various models, including those with spatial considerations, we found that treating sampling plot location as a latent state variable improved the model fit and allowed prediction of browsing probability on a landscape scale. This study underlines the value of incorporating spatial elements into models for assessing browsing pressure and its spatial variations, thereby facilitating more informed silvicultural decisions. Full article
(This article belongs to the Section Forest Ecology and Management)
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15 pages, 1561 KB  
Article
RNA Polymerase III Regulates HIV Replication and Latency
by Landon Thompson, Imran Jamal, Juthika Das, Casey Dang, Zhenzi Hong, Doran Katz, Alberto Bosque and Vir B. Singh
Viruses 2025, 17(9), 1278; https://doi.org/10.3390/v17091278 - 20 Sep 2025
Viewed by 491
Abstract
The elimination of HIV latent reservoirs is an extremely challenging task due to the interplay of multiple mechanisms regulating latency. Thus, we need to identify novel strategies to target heterogeneous reservoirs uniformly. Recent reports have provided intriguing evidence for the novel antiviral function [...] Read more.
The elimination of HIV latent reservoirs is an extremely challenging task due to the interplay of multiple mechanisms regulating latency. Thus, we need to identify novel strategies to target heterogeneous reservoirs uniformly. Recent reports have provided intriguing evidence for the novel antiviral function of RNA Polymerase III (RNAP III), which remains to be further explored. In this study, we evaluated the role of RNA Pol III in regulating HIV latency and replication. We first demonstrated that the pharmacological inhibition of RNAP III can lead to a strong reactivation of latency in cell lines representing both T and monocytic cellular reservoirs. Next, we investigated the involvement of RNA Pol III in regulating HIV-1 replication using HIV-1 pseudotyped (DuoFluo) virus and HIV-1-Bal in THP-1 and Sup-T1 cells. We show that the pharmacological inhibition of RNAP III significantly induced HIV transcription. These findings were further confirmed in physiologically relevant primary CD4 T cells, and a consistent increase in HIV transcription was observed up to 72 h. Collectively, our study suggests that inhibition of RNAP III can increase the rate of HIV transcription, while the total HIV DNA remains unchanged. Overall, our study identifies a previously unknown role of RNA Pol III in restricting HIV transcription and advocates that targeting RNAP III-driven mechanisms could be a novel strategy to reactivate HIV latent reservoirs. Full article
(This article belongs to the Special Issue Cellular Mechanisms Regulating HIV Replication, 2nd Edition)
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11 pages, 10408 KB  
Communication
Leaving Glauber’s Salt Island: The Road to Stabilisation
by Poppy O’Neill, Anastasia Stamatiou and Ludger Fischer
Colloids Interfaces 2025, 9(5), 60; https://doi.org/10.3390/colloids9050060 - 9 Sep 2025
Viewed by 430
Abstract
Glauber’s salt is a promising phase change material for thermal energy storage due to its high latent heat capacity of 234 J/g and melting point of 34 °C, making it well-suited for low-temperature heating applications. However, its practical use has been limited by [...] Read more.
Glauber’s salt is a promising phase change material for thermal energy storage due to its high latent heat capacity of 234 J/g and melting point of 34 °C, making it well-suited for low-temperature heating applications. However, its practical use has been limited by phase separation and associated loss of performance during repeated thermal cycling. This study aimed to address this limitation through a novel stabilisation approach. The material was encapsulated within an emulsion matrix designed to physically constrain the salt and inhibit separation during melting and to form a phase change dispersion. The phase change dispersion was subjected to 100 controlled heating–cooling cycles whilst monitoring the latent heat capacity and phase transition plateaus. The phase change dispersion retained its thermal properties throughout testing, showing no measurable degradation in storage capacity nor shift in phase transition temperature. These results demonstrate that this encapsulation mechanism can effectively maintain the functional performance of Glauber’s salt under repeated thermal cycling. This approach may form the basis for more durable salt hydrate-based storage media and has potential relevance for applications in building heating, waste heat recovery and renewable energy integration. By improving stability, this method helps unlock the long-term operational viability of phase change materials. Full article
(This article belongs to the Special Issue Recent Advances on Emulsions and Applications: 3rd Edition)
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25 pages, 690 KB  
Review
Chemical Treatments Tested Against Xylella fastidiosa: Strategies, Successes and Limitations
by Letizia Portaccio, Marzia Vergine, Alessandro Bene, Mariarosaria De Pascali, Erika Sabella, Luigi De Bellis and Andrea Luvisi
Pathogens 2025, 14(9), 840; https://doi.org/10.3390/pathogens14090840 - 23 Aug 2025
Viewed by 1025
Abstract
Xylella fastidiosa (Xf) is a Gram-negative bacterium responsible for severe diseases in several commercially significant crops, including olive, grapevine, citrus and almond. Its management is particularly challenging due to its transmission via widespread vector insects, its ability to form biofilms, its [...] Read more.
Xylella fastidiosa (Xf) is a Gram-negative bacterium responsible for severe diseases in several commercially significant crops, including olive, grapevine, citrus and almond. Its management is particularly challenging due to its transmission via widespread vector insects, its ability to form biofilms, its high genetic diversity and, sometimes, latent symptoms. Current control strategies focus on integrated and preventive approaches, including the use of resistant varieties, agronomic practices, and vector control through chemical and biological methods. Direct control of the bacterium has always been a complex challenge that includes strategies to limit vector presence and activity in the field; however, several compounds have recently been evaluated that are able to inhibit biofilm formation and Xf growth. This review provides an up-to-date summary of studies investigating the efficacy of various treatments based on organic compounds, synthetic molecules and salt- or metal-based formulations. By evaluating the results of in vitro and in vivo experiments, the most promising solutions were identified that address the main challenges and limitations of chemical control strategies. These include N-acetylcysteine and zinc- and copper-based formulations, which are effective and potentially transferable to the field for crops such as citrus and olive trees. Antimicrobial peptides and nanoparticles, on the other hand, have demonstrated high efficacy in vitro, although further studies directly in the field are required. The evidence emerging from the analyzed studies offer insights to guide future research towards more effective and sustainable management approaches to mitigate the spread and impact of Xf. Full article
(This article belongs to the Section Bacterial Pathogens)
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28 pages, 2489 KB  
Review
Role of the Virome in Vaccine-Induced Immunization
by Rossella Cianci, Mario Caldarelli, Paola Brani, Annalisa Bosi, Alessandra Ponti, Cristina Giaroni and Andreina Baj
Vaccines 2025, 13(9), 895; https://doi.org/10.3390/vaccines13090895 - 23 Aug 2025
Cited by 1 | Viewed by 963
Abstract
The human virome—comprising viruses that can persist in a host, those that benefit the host, and those that remain latent—has gained increasing acceptance as a modulator of immune response toward vaccination. The factors known to influence vaccine efficacy include host genetics, age, and [...] Read more.
The human virome—comprising viruses that can persist in a host, those that benefit the host, and those that remain latent—has gained increasing acceptance as a modulator of immune response toward vaccination. The factors known to influence vaccine efficacy include host genetics, age, and bacterial microbiota, while the virome is a much less considered fourth dimension. This article reviews how components of the virome such as Torque Teno Virus (TTV), cytomegalovirus (CMV), Epstein–Barr virus (EBV), and bacteriophages impact both innate and adaptive immune responses, including mechanisms of immune pre-activation, trained immunity, and molecular mimicry from both beneficial and detrimental perspectives for vaccine-induced immunization. Emphasis is given to immunocompromised populations such as transplant recipients and those with HIV, where virome composition has been shown to correlate with vaccine responsiveness. Experimental models support clinical observations on how chronic viral exposures can either enhance or inhibit vaccine efficacy. Finally, we discuss virome-aware precision vaccinology and call for the integration of the virome in the development of immunization strategies, thus improving outcomes through customization. Full article
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16 pages, 4167 KB  
Article
A Novel Lytic Salmonella Phage Harboring an Unprecedented Tail-Protein Domain Combination Capable of Lysing Cross-Host-Transmitted Salmonella Strains
by Ling Zhang, Mingqiang Guo, Xiaoyu Ma, Wei Wang, Wanpeng Ma, Yifan Liu, Junxiang Wei and Zhanqiang Su
Foods 2025, 14(16), 2850; https://doi.org/10.3390/foods14162850 - 17 Aug 2025
Viewed by 656
Abstract
The emergence of multidrug-resistant Salmonella poses a significant threat to global public health and food safety, necessitating the urgent search for new strategies to replace conventional antibiotics. Phages are viruses that can directly target bacteria and have garnered attention in recent years for [...] Read more.
The emergence of multidrug-resistant Salmonella poses a significant threat to global public health and food safety, necessitating the urgent search for new strategies to replace conventional antibiotics. Phages are viruses that can directly target bacteria and have garnered attention in recent years for their development as antibiotic alternatives. In this study, 4458 samples were collected from farms, supermarkets, and human feces, yielding 65 strains of Salmonella, which were serotyped using multiplex PCR. Subsequently, a lytic phage was isolated and identified using the dominant serotype of Salmonella as the host bacterium. We further explored the biological characteristics of this phage through host range, growth properties, and genomic analysis. Finally, we analyzed the potential of the phage to block the cross-host transmission of Salmonella, combining PFGE Salmonella classification, strain sources, and phage lytic phenotypes. The results showed that phage gmqsjt-1 could lyse 69.23% (45/65) of Salmonella, of which 75.56% (34/45) were resistant strains. The optimal multiplicity of infection (MOI) for gmqsjt-1 was 0.01, with a latent period of about 10 min, maintaining high activity within the temperature range of 30 to 60 °C and pH range of 2 to 13. No virulence or resistance genes were detected in the gmqsjt-1 genome, which carries two tail spike proteins (contain FAD binding_2 superfamily, the Tail spike TSP1/Gp66 N-terminal domain, and the Pectin lyase fold) and a holin–lysozyme–spanin lytic system. Phylogenetic classification indicates that phage gmqsjt-1 belongs to a new genus and species of an unnamed family within the class Caudoviricetes. PFGE classification results show a high genetic relationship among human, farm animal, and food source Salmonella, and the comprehensive lytic phenotype reveals that phage gmqsjt-1 can lyse Salmonella with high genetic correlation. These results suggest that this novel lytic Salmonella phage has the potential to inhibit cross-host transmission of Salmonella, making it a promising candidate for developing alternative agents to control Salmonella contamination sources (farms), thereby reducing the risk of human infection with Salmonella through ensuring food system safety. Full article
(This article belongs to the Section Food Microbiology)
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20 pages, 1605 KB  
Article
Latent Human Cytomegalovirus Infection Activates the STING Pathway but p-IRF3 Translocation Is Limited
by Wang Ka Lee, Zuodong Ye and Allen Ka Loon Cheung
Viruses 2025, 17(8), 1109; https://doi.org/10.3390/v17081109 - 12 Aug 2025
Viewed by 805
Abstract
Human cytomegalovirus (HCMV) is a ubiquitous betaherpesvirus that establishes lifelong latent infection in CD34+ haematopoietic stem and progenitor cells. A unique subset of viral genes is expressed during latency, which functions to modulate cellular mechanisms without supporting viral replication. One potential function [...] Read more.
Human cytomegalovirus (HCMV) is a ubiquitous betaherpesvirus that establishes lifelong latent infection in CD34+ haematopoietic stem and progenitor cells. A unique subset of viral genes is expressed during latency, which functions to modulate cellular mechanisms without supporting viral replication. One potential function of these genes is to regulate the differentiation state of latently infected CD34+ cells, thereby preventing their progression into antigen-presenting cells, e.g., dendritic cells. In this study, we first compared CD34+ cells that supported productive and latent infections using the RV-TB40-BACKL7-SE-EGFP virus. Over a seven-day time course, the proportion of latently infected CD34+ cell subsets within the myeloid progenitor population remained similar to that in the mock-infected control. However, starting from day 3 post-infection, there was an increase in the proportion of the early progenitor subsets, including haematopoietic stem cells (HSCs) and multipotent progenitors (MPPs). In contrast, productively infected cells, which constituted less than 1% of the population, only accounted for a small portion of the myeloid progenitors. Importantly, our data revealed that the innate immune STING/p-TBK1/p-IRF3 pathway was activated in latently infected CD34+ cells, yet type I interferon (IFN) expression was decreased. This decrease was attributed to impaired p-IRF3 nuclear translocation, limiting the induction of an autocrine type I IFN response. However, treatment with IFN-β could induce myelopoiesis in latently infected cells. In summary, HCMV modulates a key component of the STING pathway to inhibit antiviral immune responses by decreasing the type I IFN-mediated cell differentiation of CD34+ progenitor cells. This study uncovered a new mechanism of latent HCMV-mediated regulation of the host cell differentiation response. Full article
(This article belongs to the Special Issue Viral Infections and Immune Dysregulation 2024–2025)
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10 pages, 219 KB  
Article
Alopecia Areata Associated with Dupilumab: National Database Study
by Tarun Sontam, Humaira Nfn, Jodi Yanking Li, Sehar Nadeem, Katie Beier, Neil K. Jairath and Vignesh Ramachandran
Diagnostics 2025, 15(14), 1828; https://doi.org/10.3390/diagnostics15141828 - 21 Jul 2025
Viewed by 1376
Abstract
Background: Alopecia areata (AA), an autoimmune condition causing non-scarring hair loss, often coexists with atopic dermatitis (AD) due to shared T-helper cell type 2 (Th2)-mediated pathways. Dupilumab, a monoclonal antibody inhibiting IL-4 and IL-13 signaling, is a cornerstone treatment for AD but has [...] Read more.
Background: Alopecia areata (AA), an autoimmune condition causing non-scarring hair loss, often coexists with atopic dermatitis (AD) due to shared T-helper cell type 2 (Th2)-mediated pathways. Dupilumab, a monoclonal antibody inhibiting IL-4 and IL-13 signaling, is a cornerstone treatment for AD but has conflicting reports regarding its impact on AA, with some suggesting therapeutic benefits and others indicating AA induction. Methods: This retrospective study, utilizing the TriNetX Research Network’s de-identified data from over 300 million patient records, investigates the association between dupilumab use and AA risk in AD patients. Results: After propensity score matching, 23,782 dupilumab users were compared with an equal number of controls. Results revealed a statistically significant increased AA risk in dupilumab users (odds ratio: 1.436, 95% CI: 1.066–1.935, p = 0.0167) after 16 weeks. Cases occurring within 16 weeks were excluded. Conclusions: Potential mechanisms include immune rebalancing, with Th2 suppression possibly upregulating Th1/Th17 pathways or unmasking latent AA in predisposed individuals. These findings challenge dupilumab’s potential as an AA treatment and highlight the need for vigilant monitoring, including routine scalp examinations and patient education. Future research should focus on mechanistic pathways, risk stratification, and comparative studies with other biologics to optimize personalized treatment strategies for AD and AA. Full article
(This article belongs to the Special Issue Diagnosis, Treatment, and Management of Hair Disorders)
34 pages, 981 KB  
Review
Applying CRISPR Technologies for the Treatment of Human Herpesvirus Infections: A Scoping Review
by Chloë Hanssens and Jolien Van Cleemput
Pathogens 2025, 14(7), 654; https://doi.org/10.3390/pathogens14070654 - 1 Jul 2025
Viewed by 2937
Abstract
Background: Human herpesviruses are double-stranded DNA viruses of which eight types have been identified at present. Herpesvirus infection comprises an active lytic phase and a lifelong latency phase with the possibility of reactivation. These infections are highly prevalent worldwide and can lead to [...] Read more.
Background: Human herpesviruses are double-stranded DNA viruses of which eight types have been identified at present. Herpesvirus infection comprises an active lytic phase and a lifelong latency phase with the possibility of reactivation. These infections are highly prevalent worldwide and can lead to a broad spectrum of clinical manifestations, ranging from mild symptoms to severe disease, particularly in immunocompromised individuals. Clustered regularly interspaced palindromic repeats (CRISPR)-based therapy is an interesting alternative to current antiviral drugs, which fail to cure latent infections and are increasingly challenged by viral resistance. Objective: This scoping review aimed to summarize the current state of CRISPR-based antiviral strategies against herpesvirus infections, highlighting the underlying mechanisms, study design and outcomes, and challenges for clinical implementation. Design: A literature search was conducted in the databases PubMed and Web of Science, using both a general and an individual approach for each herpesvirus. Results: This scoping review identified five main mechanisms of CRISPR-based antiviral therapy against herpesvirus infections in vitro and/or in vivo. First, CRISPR systems can inhibit the active lytic replication cycle upon targeting viral lytic genes or host genes. Second, CRISPR technologies can remove latent viral genomes from infected cells by targeting viral genes essential for latency maintenance or destabilizing the viral genome. Third, reactivation of multiple latent herpesvirus infections can be inhibited by CRISPR-Cas-mediated editing of lytic viral genes, preventing a flare-up of clinical symptoms and reducing the risk of viral transmission. Fourth, CRISPR systems can purposefully induce viral reactivation to enhance recognition by the host immune system or improve the efficacy of existing antiviral therapies. Fifth, CRISPR technology can be applied to develop or enhance the efficiency of cellular immunotherapy. Conclusions: Multiple studies demonstrate the potential of CRISPR-based antiviral strategies to target herpesvirus infections through various mechanisms in vitro and in vivo. However, aspects regarding the delivery and biosafety of CRISPR systems, along with the time window for treatment, require further investigation before broad clinical implementation can be realized. Full article
(This article belongs to the Special Issue Herpesvirus Latency and Reactivation)
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14 pages, 807 KB  
Review
Applications of CRISPR-Cas-Based Genome Editing Approaches Against Human Cytomegalovirus Infection
by Andra Zhang, Isadora Zhang and Fenyong Liu
Biomedicines 2025, 13(7), 1590; https://doi.org/10.3390/biomedicines13071590 - 30 Jun 2025
Viewed by 918
Abstract
Human cytomegalovirus (HCMV), a globally ubiquitous herpesvirus with the ability to carry out both lytic productive and lifelong latent infections, is a major cause of congenital infections, often leading to intellectual disabilities and neurological disorders. Moreover, HCMV is an opportunistic pathogen commonly found [...] Read more.
Human cytomegalovirus (HCMV), a globally ubiquitous herpesvirus with the ability to carry out both lytic productive and lifelong latent infections, is a major cause of congenital infections, often leading to intellectual disabilities and neurological disorders. Moreover, HCMV is an opportunistic pathogen commonly found in immunocompromised individuals such as organ transplant recipients, HIV-positive individuals, and cancer patients, causing severe and life-threatening complications. While effective in inhibiting viral lytic infection, current FDA-approved compounds cannot eliminate the latent viral genome and have little effect on viral latent infection. Developing novel antiviral therapeutic approaches to eliminate HCMV lytic and latent infections is a major public health priority for controlling HCMV infection and preventing viral-associated diseases. The genome-editing technology based on the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) RNA-guided nuclease system represents a novel and promising antiviral approach through modifying or destroying the genetic material of human viruses. This review summarizes the recently published progress in using the CRISPR-Cas approach to study and inhibit HCMV infections and discusses prospects for developing the CRISPR-based genome-editing technology for therapeutic applications against HCMV infection and associated diseases. Full article
(This article belongs to the Section Molecular Genetics and Genetic Diseases)
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18 pages, 1935 KB  
Review
Progress in CRISPR Technology for Antiviral Treatments: Genome Editing as a Potential Cure for Chronic Viral Infections
by Fatemeh Nouri, Farnaz Alibabaei, Behina Forouzanmehr, Hamed Tahmasebi, Valentyn Oksenych and Majid Eslami
Microbiol. Res. 2025, 16(5), 104; https://doi.org/10.3390/microbiolres16050104 - 20 May 2025
Cited by 1 | Viewed by 2626
Abstract
The CRISPR–Cas system has transformed molecular biology by providing precise tools for genome editing and pathogen detection. Originating from bacterial adaptive immunity, CRISPR technology identifies and cleaves genetic material from pathogens, thereby preventing infections. CRISPR–Cas9, the most widely utilized variant, creates double-stranded breaks [...] Read more.
The CRISPR–Cas system has transformed molecular biology by providing precise tools for genome editing and pathogen detection. Originating from bacterial adaptive immunity, CRISPR technology identifies and cleaves genetic material from pathogens, thereby preventing infections. CRISPR–Cas9, the most widely utilized variant, creates double-stranded breaks in the target DNA, enabling genetic disruptions or edits. This approach has shown significant potential in antiviral therapies, addressing chronic infections, such as HIV, SARS-CoV-2, and hepatitis viruses. In HIV, CRISPR–Cas9 edits the essential viral genes and disrupts latent reservoirs, while CCR5 gene modifications render the T cells resistant to viral entry. Similarly, SARS-CoV-2 is targeted using CRISPR–Cas13d to inhibit the conserved viral genes, significantly reducing viral loads. Hepatitis B and C treatments leverage CRISPR technologies to target conserved genomic regions, limiting replication and expression. Emerging innovations, such as the PAC-MAN approach for influenza and base-editing systems to reduce off-target effects, further highlight the therapeutic versatility of CRISPR. Additionally, advances in Cas12a and Cas13 have driven the development of diagnostic platforms like DETECTR and SHERLOCK, which provide rapid and cost-effective viral detection. Innovative tools like AIOD-CRISPR enable accessible point-of-care diagnostics for early viral detection. Experimental approaches, such as targeting latent HSV-1 reservoirs, highlight the transformative potential of CRISPR in combating persistent infections. Full article
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13 pages, 1232 KB  
Article
Investigation of β-Carboline Alkaloid Harmaline Against Cyvirus cyprinidallo3 Infection In Vitro and In Vivo
by Clement Manes, Kristen Larson, Shelby Matsuoka, Xisheng Wang, Ruth Milston-Clements and Ling Jin
Viruses 2025, 17(5), 687; https://doi.org/10.3390/v17050687 - 9 May 2025
Viewed by 687
Abstract
Cyvirus cyprinidallo3, also known as Cyprinid herpesvirus 3 (CyHV-3), is a common pathogen of koi and common carp (Cyprinus carpio). Infection of CyHV-3 can lead to high mortality in fry under 4 months of age. CyHV-3 can become latent in [...] Read more.
Cyvirus cyprinidallo3, also known as Cyprinid herpesvirus 3 (CyHV-3), is a common pathogen of koi and common carp (Cyprinus carpio). Infection of CyHV-3 can lead to high mortality in fry under 4 months of age. CyHV-3 can become latent in recovered fish, and latent CyHV-3 can reactivate under stress conditions and spread the virus. Reactivation of CyHV-3 can also lead to mortality and diseases in latently infected fish. No effective drugs are available to prevent CyHV-3 infection or reactivation from latency. There is a need for the discovery of anti-CyHV-3 drugs. Harmine (HAR) and harmaline (HAL) are β-carboline alkaloids found in the medicinal plant Peganum harmala with antiviral activities against many viruses, including HSV. Here, HAL was evaluated against CyHV-3 infection in vitro and in vivo, respectively. Immediately after a one-hour infection exposure of ~1000 FPU/plate or ~500 PFU/plate, cells treated with 5 µM HAL for 2 h can block nearly 50% or 90% plaque formation in vitro. Only around 50% inhibition was observed in cells treated with the common anti-herpesvirus drug acyclovir (ACV) at 10 or 20 µM for 2 h following 1 h post-infection of ~500 PFU/plate. Cells treated with 10 µM HAL for 30 min, 60 min, 2 h, and 6 h can reduce 60%, 65%, 85.5%, and 85% CyHV-3 replication in vitro, respectively. HAL at 20 µM is still effective against CyHV-3 DNA replication and virion production when the treatment started at 3 and 5 days post-infection for 1 or 2 h, respectively. HAL under 50 µM has little toxicity to cells treated for 24 h. Immersion treatment with 10 µM HAL for 3–4 h daily within the first 5 days post-infection can increase the survival of fry by 60%. In addition, IM injection of HAL at 20 µM can reduce the rate of CyHV-3 reactivation induced by heat stress in latently infected koi. This study demonstrated that HAL could potentially be used to prevent CyHV-3 infection or reactivation from latency. Full article
(This article belongs to the Section Animal Viruses)
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16 pages, 10955 KB  
Article
Characterizations of Newly Isolated Erwinia amylovora Loessnervirus-like Bacteriophages from Hungary
by Elene Lomadze, György Schneider, Szilvia Papp, Dominika Bali, Roberta Princz-Tóth and Tamás Kovács
Viruses 2025, 17(5), 677; https://doi.org/10.3390/v17050677 - 6 May 2025
Viewed by 1167
Abstract
This study explores alternative methods to combat bacterial infections like fire blight caused by Erwinia amylovora (Ea) using bacteriophages as potential antimicrobial agents. Two lytic phages, Ea PF 7 and Ea PF 9, were isolated from apple samples and classified as Loessnervirus-like based [...] Read more.
This study explores alternative methods to combat bacterial infections like fire blight caused by Erwinia amylovora (Ea) using bacteriophages as potential antimicrobial agents. Two lytic phages, Ea PF 7 and Ea PF 9, were isolated from apple samples and classified as Loessnervirus-like based on their genomes. Both phages showed strong efficacy, lysing 95% of the tested 37 Ea strains. They inhibited bacterial growth for up to 10 h, even at low infection rates. The phages had a short latent period of 10 min and produced high burst sizes of 108 and 125 phage particles per infected cell. Stability tests revealed that both phages were stable at moderate temperatures (37–45 °C) and within a pH range of 4–10. However, their viability decreased at higher temperatures and extreme pH levels. Both phages exhibited notable desiccation tolerance and moderate resistance to UV-B radiation during UV testing. The phages were exposed to carefully controlled irradiation, considering factors like lamp type, radiation intensity, exposure time, and object distance. This method introduces a complex approach to research, ensuring repeatable and comparable results. These findings suggest that Ea PF 7 and Ea PF 9 hold promise as antimicrobial agents for therapeutic and biotechnological applications, potentially helping to combat antibiotic resistance in the future. Full article
(This article belongs to the Special Issue Recent Advances in Phage-Plant Interactions)
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16 pages, 4091 KB  
Article
TFProtBert: Detection of Transcription Factors Binding to Methylated DNA Using ProtBert Latent Space Representation
by Saima Gaffar, Kil To Chong and Hilal Tayara
Int. J. Mol. Sci. 2025, 26(9), 4234; https://doi.org/10.3390/ijms26094234 - 29 Apr 2025
Viewed by 683
Abstract
Transcription factors (TFs) are fundamental regulators of gene expression and perform diverse functions in cellular processes. The management of 3-dimensional (3D) genome conformation and gene expression relies primarily on TFs. TFs are crucial regulators of gene expression, performing various roles in biological processes. [...] Read more.
Transcription factors (TFs) are fundamental regulators of gene expression and perform diverse functions in cellular processes. The management of 3-dimensional (3D) genome conformation and gene expression relies primarily on TFs. TFs are crucial regulators of gene expression, performing various roles in biological processes. They attract transcriptional machinery to the enhancers or promoters of specific genes, thereby activating or inhibiting transcription. Identifying these TFs is a significant step towards understanding cellular gene expression mechanisms. Due to the time-consuming and labor-intensive nature of experimental methods, the development of computational models is essential. In this work, we introduced a two-layer prediction framework based on a support vector machine (SVM) using the latent space representation of a protein language model, ProtBert. The first layer of the method reliably predicts and identifies transcription factors (TFs), and in the second layer, the proposed method predicts and identifies transcription factors that prefer binding to methylated deoxyribonucleic acid (TFPMs). In addition, we also tested the proposed method on an imbalanced database. In detecting TFs and TFPMs, the proposed model consistently outperformed state-of-the-art approaches, as demonstrated by performance comparisons via empirical cross-validation analysis and independent tests. Full article
(This article belongs to the Special Issue Applications of Machine Learning in Bioinformatics and Biomedicine)
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16 pages, 3002 KB  
Article
PERK/Sestrin2 Signaling Pathway Mediated Autophagy Regulates Human Cardiomyocytes Apoptosis Induced by Traffic-Related PM2.5 and Diverse Constituents
by Jiayu Tian, Zeyu Niu, Huan Yang, Caihong Wang, Linlin Guan, Lifang Zhao, Dongxing Shi and Zhihong Zhang
Int. J. Mol. Sci. 2025, 26(8), 3784; https://doi.org/10.3390/ijms26083784 - 17 Apr 2025
Viewed by 765
Abstract
Although the strong causal association between PM2.5 and cardiovascular disease has been extensively studied, the latent molecular mechanisms have not been entirely explained. The objective of this research was to assess the cardiotoxicity of Traffic-related PM2.5 (TRPM2.5), water-soluble components [...] Read more.
Although the strong causal association between PM2.5 and cardiovascular disease has been extensively studied, the latent molecular mechanisms have not been entirely explained. The objective of this research was to assess the cardiotoxicity of Traffic-related PM2.5 (TRPM2.5), water-soluble components (WSC), and water-insoluble components (WIC) in human cardiomyocytes (AC16) and to investigate the underlying molecular mechanisms. Endoplasmic reticulum stress (ERS), autophagy, and apoptosis were activated 24 h after exposure to total-TRPM2.5, WSC, or WIC. WIC was predominantly related to cardiotoxicity compared to WSC. Sestrin2 is an upstream molecule in several signaling pathways, including those involved in autophagy and apoptosis. In this study, we found that the knockdown of Protein Kinase RNA-like Endoplasmic Reticulum Kinase (PERK) suppressed the expression of PERK, Sestrin2, Caspase-12, Caspase-3, LC3, and p62 in TRPM2.5-treated AC16 cells. These results indicate that ERS participates in the activation of autophagy and apoptosis through the PERK/Sestrin2 pathway. We found that inhibiting autophagy with 3-methyladenine (3-MA) decreased the expression of autophagy-related factors and aggravated apoptosis. These observations suggest that protective autophagy was initiated. Finally, our findings provide valuable insights into the molecular mechanism by which ERS might regulate autophagy through the PERK/Sestrin2 signaling pathway, and protective autophagy may be activated to relieve TRPM2.5 and component-mediated apoptosis in AC16 cells. Full article
(This article belongs to the Section Biochemistry)
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Figure 1

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