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Cell Mar 2024The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level...
The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case reporting throughout the epidemic, and a large degree of transmission heterogeneity. We find that viral introductions played a limited role in prolonging spread after initial dissemination, suggesting that travel bans would have had only a minor impact. We find that mpox transmission in North America began declining before more than 10% of high-risk individuals in the USA had vaccine-induced immunity. Our findings highlight the importance of broader routine specimen screening surveillance for emerging infectious diseases and of joint integration of genomic and epidemiological information for early outbreak control.
Topics: Humans; Communicable Diseases, Emerging; Disease Outbreaks; Epidemics; Mpox (monkeypox); Public Health; Monkeypox virus
PubMed: 38428425
DOI: 10.1016/j.cell.2024.02.003 -
Medical Education Online Dec 2024Medical school educators face challenges determining which new and emerging topics to incorporate into medical school curricula, and how to do so. A study was conducted...
PURPOSE
Medical school educators face challenges determining which new and emerging topics to incorporate into medical school curricula, and how to do so. A study was conducted to gain a better understanding of the integration of emerging topics related to microbiology and immunology in the undergraduate medical curriculum (UME).
METHODS
An anonymous survey with 17 questions was emailed to medical school faculty who teach immunology and/or microbiology through the DR-Ed listserv, the American Society for Microbiology (ASM) Connect listserv, and attendees of the Association of Medical School Microbiology and Immunology Chairs (AMSMIC) Educational Strategies Workshop. Participants were asked about experiences, perceptions, and the decision-making process regarding integrating emerging topics into UME.
RESULTS
The top emerging topics that were added to the curriculum or considered for addition in the last 10 years included COVID-19, Zika virus, mRNA vaccines, and Mpox (formerly known as monkeypox). Most respondents reported lectures and active learning as the major methods for topic delivery, with most faculty indicating that formative assessment was the best way to assess emerging topics. Content experts and course directors were the most cited individuals making these decisions. Top reasons for incorporating emerging topics into curricula included preparing students for clinical treatment of cases, followed by demonstrating the importance of basic science, and opportunities to integrate basic science into other disciplines. Challenges for incorporating these topics included making room in an already crowded curriculum, followed by content overload for students.
CONCLUSIONS
This study describes the rationale for integrating emerging topics related to microbiology and immunology into UME, and identifies the current new and emerging topics, as well as the main methods of integration and assessment. These results may be used by medical educators to inform curricular decisions at their institutions. Future studies will include developing innovative learning modules that overcome barriers to integration.
Topics: Humans; United States; Education, Medical, Undergraduate; Curriculum; Problem-Based Learning; Zika Virus; Zika Virus Infection
PubMed: 38577972
DOI: 10.1080/10872981.2024.2336331 -
Nature Communications Nov 2023Retrovirus integration into a host genome is essential for productive infections. The integration strand transfer reaction is catalyzed by a nucleoprotein complex...
Retrovirus integration into a host genome is essential for productive infections. The integration strand transfer reaction is catalyzed by a nucleoprotein complex (Intasome) containing the viral integrase (IN) and the reverse transcribed (RT) copy DNA (cDNA). Previous studies suggested that DNA target-site recognition limits intasome integration. Using single molecule Förster resonance energy transfer (smFRET), we show prototype foamy virus (PFV) intasomes specifically bind to DNA strand breaks and gaps. These break and gap DNA discontinuities mimic oxidative base excision repair (BER) lesion-processing intermediates that have been shown to affect retrovirus integration in vivo. The increased DNA binding events targeted strand transfer to the break/gap site without inducing substantial intasome conformational changes. The major oxidative BER substrate 8-oxo-guanine as well as a G/T mismatch or +T nucleotide insertion that typically introduce a bend or localized flexibility into the DNA, did not increase intasome binding or targeted integration. These results identify DNA breaks or gaps as modulators of dynamic intasome-target DNA interactions that encourage site-directed integration.
Topics: DNA, Viral; Integrases; Retroviridae; Spumavirus; DNA, Complementary; Virus Integration
PubMed: 37923737
DOI: 10.1038/s41467-023-42641-4 -
Frontiers in Oral Health 2023Maintaining a microbe-free environment in healthcare facilities has become increasingly crucial for minimizing virus transmission, especially in the wake of recent... (Review)
Review
Maintaining a microbe-free environment in healthcare facilities has become increasingly crucial for minimizing virus transmission, especially in the wake of recent epidemics like COVID-19. To meet the urgent need for ongoing sterilization, autonomous ultraviolet disinfection (UV-D) robots have emerged as vital tools. These robots are gaining popularity due to their automated nature, cost advantages, and ability to instantly disinfect rooms and workspaces without relying on human labor. Integrating disinfection robots into medical facilities reduces infection risk, lowers conventional cleaning costs, and instills greater confidence in patient safety. However, UV-D robots should complement rather than replace routine manual cleaning. To optimize the functionality of UV-D robots in medical settings, additional hospital and device design modifications are necessary to address visibility challenges. Achieving seamless integration requires more technical advancements and clinical investigations across various institutions. This mini-review presents an overview of advanced applications that demand disinfection, highlighting their limitations and challenges. Despite their potential, little comprehensive research has been conducted on the sterilizing impact of disinfection robots in the dental industry. By serving as a starting point for future research, this review aims to bridge the gaps in knowledge and identify unresolved issues. Our objective is to provide an extensive guide to UV-D robots, encompassing design requirements, technological breakthroughs, and in-depth use in healthcare and dentistry facilities. Understanding the capabilities and limitations of UV-D robots will aid in harnessing their potential to revolutionize infection control practices in the medical and dental fields.
PubMed: 38024151
DOI: 10.3389/froh.2023.1270959 -
International Journal of Molecular... Sep 2023Persistent high-risk human papillomavirus (HPV) infection is a pivotal factor in the progression of cervical cancer. In recent years, an increasing interest has emerged...
Persistent high-risk human papillomavirus (HPV) infection is a pivotal factor in the progression of cervical cancer. In recent years, an increasing interest has emerged in comprehending the influence of HPV on head and neck squamous cell carcinoma (HNSCC). Notably, it is well established that HPV-associated HNSCC show cases with distinct molecular and clinical attributes compared to HPV-negative cases. The present study delves into the epigenetic landscape of HPV16, specifically its gene and untranslated region (UTR), through pyrosequencing, while the HPV16 DNA physical status was evaluated using E2/E6 ratio analysis in HPV16-positive HNSCC FFPE biopsies. Our findings reveal substantial methylation across six sites within the HPV16 gene and seven sites in the UTR. Specifically, methylation percentages of two L1 CpG sites (7136, 7145) exhibit significant associations with tumor histological grade ( < 0.01), while proving concurrent methylation across multiple sites. The HPV16 DNA physical status was not correlated with the methylation of viral genome or tumor characteristics. This is the first study that examines epigenetic modifications and the HPV16 DNA physical status in Greek HNSCC patients. Our findings suggest an orchestrated epigenetic modulation among specific sites, impacting viral gene expression and intricate virus-host interactions.
Topics: Female; Humans; Squamous Cell Carcinoma of Head and Neck; Human Papillomavirus Viruses; Carcinoma, Squamous Cell; DNA Methylation; Papillomavirus Infections; Head and Neck Neoplasms; DNA; Oncogene Proteins, Viral; DNA, Viral
PubMed: 37834041
DOI: 10.3390/ijms241914593 -
Environmental Science and Pollution... Jan 2024Fluoroquinolones (FQs) are a class of broad-spectrum antimicrobial agents that are used to treat variety of infectious diseases. This class of antibiotics was being used... (Review)
Review
Fluoroquinolones (FQs) are a class of broad-spectrum antimicrobial agents that are used to treat variety of infectious diseases. This class of antibiotics was being used for patients exhibiting early symptoms of a human respiratory disease known as the COVID-19 virus. As a result, this outbreak causes an increase in drug-resistant strains and environmental pollution, both of which pose serious threats to biota and human health. Thus, to ensure public health and prevent antimicrobial resistance, it is crucial to develop effective detection methods for FQs determination in water bodies even at trace levels. Due to their characteristics like specificity, selectivity, sensitivity, and low detection limits, electrochemical biosensors are promising future platforms for quick and on-site monitoring of FQs residues in a variety of samples when compared to conventional detection techniques. Despite their excellent properties, biosensor stability continues to be a problem even today. However, the integration of nanomaterials (NMs) could improve biocompatibility, stability, sensitivity, and speed of response in biosensors. This review concentrated on recent developments and contemporary methods in FQs biosensors. Furthermore, a variety of modification materials on the electrode surface are discussed. We also pay more attention to the practical applications of electrochemical biosensors for FQs detection. In addition, the existing challenges, outlook, and promising future perspectives in this field have been proposed. We hope that this review can serve as a bedrock for future researchers and provide new ideas for the development of electrochemical biosensors for antibiotics detection in the future.
Topics: Humans; Fluoroquinolones; Anti-Bacterial Agents; Nanostructures; SARS-CoV-2; Biosensing Techniques; Electrochemical Techniques
PubMed: 38110684
DOI: 10.1007/s11356-023-30223-2 -
Journal of Virology Nov 2023The HIV-1 genome encodes a small number of proteins with structural, enzymatic, regulatory, and accessory functions. These viral proteins interact with a number of host... (Review)
Review
The HIV-1 genome encodes a small number of proteins with structural, enzymatic, regulatory, and accessory functions. These viral proteins interact with a number of host factors to promote the early and late stages of HIV-1 infection. During the early stages of infection, interactions between the viral proteins and host factors enable HIV-1 to enter the target cell, traverse the cytosol, dock at the nuclear pore, gain access to the nucleus, and integrate into the host genome. Similarly, the viral proteins recruit another set of host factors during the late stages of infection to orchestrate HIV-1 transcription, translation, assembly, and release of progeny virions. Among the host factors implicated in HIV-1 infection, Cyclophilin A (CypA) was identified as the first host factor to be packaged within HIV-1 particles. It is now well established that CypA promotes HIV-1 infection by directly binding to the viral capsid. Mechanistic models to pinpoint CypA's role have spanned from an effect in the producer cell to the early steps of infection in the target cell. In this review, we will describe our understanding of the role(s) of CypA in HIV-1 infection, highlight the current knowledge gaps, and discuss the potential role of this host factor in the post-nuclear entry steps of HIV-1 infection.
Topics: Humans; Capsid Proteins; Cell Nucleus; Cyclophilin A; HIV Infections; HIV-1; Viral Proteins; Host-Pathogen Interactions
PubMed: 37843371
DOI: 10.1128/jvi.00732-23 -
Pflugers Archiv : European Journal of... Dec 2023Optogenetic actuators are rapidly advancing tools used to control physiology in excitable cells, such as neurons and cardiomyocytes. In neuroscience, these tools have...
Optogenetic actuators are rapidly advancing tools used to control physiology in excitable cells, such as neurons and cardiomyocytes. In neuroscience, these tools have been used to either excite or inhibit neuronal activity. Cell type-targeted actuators have allowed to study the function of distinct cell populations. Whereas the first described cation channelrhodopsins allowed to excite specific neuronal cell populations, anion channelrhodopsins were used to inhibit neuronal activity. To allow for simultaneous excitation and inhibition, opsin combinations with low spectral overlap were introduced. BiPOLES (Bidirectional Pair of Opsins for Light-induced Excitation and Silencing) is a bidirectional optogenetic tool consisting of the anion channel Guillardia theta anion-conducting channelrhodopsin 2 (GtACR2 with a blue excitation spectrum and the red-shifted cation channel Chrimson. Here, we studied the effects of BiPOLES activation in cardiomyocytes. For this, we knocked in BiPOLES into the adeno-associated virus integration site 1 (AAVS1) locus of human-induced pluripotent stem cells (hiPSC), subjected these to cardiac differentiation, and generated BiPOLES expressing engineered heart tissue (EHT) for physiological characterization. Continuous light application activating either GtACR2 or Chrimson resulted in cardiomyocyte depolarization and thus stopped EHT contractility. In contrast, short light pulses, with red as well as with blue light, triggered action potentials (AP) up to a rate of 240 bpm. In summary, we demonstrate that cation, as well as anion channelrhodopsins, can be used to activate stem cell-derived cardiomyocytes with pulsed photostimulation but also to silence cardiac contractility with prolonged photostimulation.
Topics: Humans; Optogenetics; Channelrhodopsins; Myocytes, Cardiac; Anions; Cations
PubMed: 37863976
DOI: 10.1007/s00424-023-02869-x -
MBio Aug 2023Infection by retroviruses as HIV-1 requires the stable integration of their genome into the host cells. This process needs the formation of integrase (IN)-viral DNA...
Infection by retroviruses as HIV-1 requires the stable integration of their genome into the host cells. This process needs the formation of integrase (IN)-viral DNA complexes, called intasomes, and their interaction with the target DNA wrapped around nucleosomes within cell chromatin. To provide new tools to analyze this association and select drugs, we applied the AlphaLISA technology to the complex formed between the prototype foamy virus (PFV) intasome and nucleosome reconstituted on 601 Widom sequence. This system allowed us to monitor the association between both partners and select small molecules that could modulate the intasome/nucleosome association. Using this approach, drugs acting either on the DNA topology within the nucleosome or on the IN/histone tail interactions have been selected. Within these compounds, doxorubicin and histone binders calixarenes were characterized using biochemical, molecular simulations and cellular approaches. These drugs were shown to inhibit both PFV and HIV-1 integration . Treatment of HIV-1-infected PBMCs with the selected molecules induces a decrease in viral infectivity and blocks the integration process. Thus, in addition to providing new information about intasome-nucleosome interaction determinants, our work also paves the way for further unedited antiviral strategies that target the final step of intasome/chromatin anchoring. IMPORTANCE In this work, we report the first monitoring of retroviral intasome/nucleosome interaction by AlphaLISA. This is the first description of the AlphaLISA application for large nucleoprotein complexes (>200 kDa) proving that this technology is suitable for molecular characterization and bimolecular inhibitor screening assays using such large complexes. Using this system, we have identified new drugs disrupting or preventing the intasome/nucleosome complex and inhibiting HIV-1 integration both and in infected cells. This first monitoring of the retroviral/intasome complex should allow the development of multiple applications including the analyses of the influence of cellular partners, the study of additional retroviral intasomes, and the determination of specific interfaces. Our work also provides the technical bases for the screening of larger libraries of drugs targeting specifically these functional nucleoprotein complexes, or additional nucleosome-partner complexes, as well as for their characterization.
Topics: Humans; Nucleosomes; Histones; Virus Integration; Chromatin; Retroviridae; Integrases; DNA, Viral; Spumavirus
PubMed: 37382440
DOI: 10.1128/mbio.01083-23 -
International Journal of Molecular... Feb 2024Since its discovery in 2012, the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) system has supposed a... (Review)
Review
Since its discovery in 2012, the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) system has supposed a promising panorama for developing novel and highly precise genome editing-based gene therapy (GT) alternatives, leading to overcoming the challenges associated with classical GT. Classical GT aims to deliver transgenes to the cells via their random integration in the genome or episomal persistence into the nucleus through lentivirus (LV) or adeno-associated virus (AAV), respectively. Although high transgene expression efficiency is achieved by using either LV or AAV, their nature can result in severe side effects in humans. For instance, an LV (NCT03852498)- and AAV9 (NCT05514249)-based GT clinical trials for treating X-linked adrenoleukodystrophy and Duchenne Muscular Dystrophy showed the development of myelodysplastic syndrome and patient's death, respectively. In contrast with classical GT, the CRISPR/Cas9-based genome editing requires the homologous direct repair (HDR) machinery of the cells for inserting the transgene in specific regions of the genome. This sophisticated and well-regulated process is limited in the cell cycle of mammalian cells, and in turn, the nonhomologous end-joining (NHEJ) predominates. Consequently, seeking approaches to increase HDR efficiency over NHEJ is crucial. This manuscript comprehensively reviews the current alternatives for improving the HDR for CRISPR/Cas9-based GTs.
Topics: Animals; Humans; CRISPR-Cas Systems; Recombinational DNA Repair; DNA End-Joining Repair; Gene Editing; Genetic Therapy; Mammals
PubMed: 38473704
DOI: 10.3390/ijms25052456