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Sakai T, Oishi T, Takashina Y, Hirao M. Serum 25(OH)D and vitamin K 1 levels in patients with severe motor and intellectual disability: A Japanese single-center experience. Brain Dev 2024; 46:268-273. [PMID: 38876823 DOI: 10.1016/j.braindev.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 05/29/2024] [Accepted: 06/09/2024] [Indexed: 06/16/2024]
Abstract
PURPOSE To investigate whether patients with severe motor and intellectual disability (SMID) have nutritional vitamin D and K insufficiencies and clarify the required vitamin supplementation. METHODS This prospective observational study enrolled Japanese adults with SMID receiving institutionalized care who underwent blood sampling between February 2020 and February 2022 during annual medical checkups. Serum vitamin K1 and 25-hydroxy vitamin D (25(OH)D) levels were measured to determine their relationship with serum uncarboxylated osteocalcin (ucOC) levels. Vitamin D and K intake was compared among tube-fed and oral-intake patients with SMID and control participants using corresponding serum levels. RESULTS The study included 124 patients with SMID (56 men and 68 women; mean age: 53.0 years) and 20 control participants. Serum 25(OH)D levels were significantly higher in the SMID group than in the control group and the oral intake SMID group than in the tube-fed SMID group. In the tube-fed SMID group, vitamin D intake was lower than the daily recommended intake and correlated with serum 25(OH)D levels. Daily vitamin K intake in the tube-fed group was lower than recommended but not correlated with serum vitamin K levels. Serum ucOC levels were significantly higher in the SMID group than in the control group. Tube feeding was significantly and positively correlated with serum 25(OH)D levels. Serum 25(OH)D levels were not correlated with serum vitamin K1 levels. CONCLUSIONS The SMID group had higher ucOC levels than the control group, possibly owing to daily vitamin K and D deficiencies. Vitamin D supplementation is recommended to decrease ucOC levels.
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Affiliation(s)
- Tomoko Sakai
- Department of Rehabilitation Medicine, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Tsutomu Oishi
- Department of Pediatrics, Akitsu Ryoiku-en, Tokyo, Japan
| | - Yusuke Takashina
- Department of Rehabilitation Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masanobu Hirao
- Department of Rehabilitation Medicine, Tokyo Medical and Dental University, Tokyo, Japan
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252
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Liu K, Wang X, Qi Y, Li Y, Shi Y, Ren Y, Wang A, Cheng P, Wang B. Effector Protein Serine Carboxypeptidase FgSCP Is Essential for Full Virulence in Fusarium graminearum and Is Involved in Modulating Plant Immune Responses. PHYTOPATHOLOGY 2024; 114:2131-2142. [PMID: 38831556 DOI: 10.1094/phyto-02-24-0068-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Fusarium head blight caused by Fusarium graminearum is a significant pathogen affecting wheat crops. During the infection process, effector proteins are secreted to modulate plant immunity and promote infection. The toxin deoxynivalenol is produced in infected wheat grains, posing a threat to human and animal health. Serine carboxypeptidases (SCPs) belong to the α/β hydrolase family of proteases and are widely distributed in plant and fungal vacuoles, as well as animal lysosomes. Research on SCPs mainly focuses on the isolation, purification, and production of a small number of fungi. The role of SCPs in plant secretion, growth and development, and stress resistance has also been extensively studied. However, their functions in F. graminearum, a fungal pathogen, remain relatively unknown. In this study, the biological functions of the FgSCP gene in F. graminearum were investigated. The study revealed that mutations in FgSCP affected the nutritional growth, sexual reproduction, and stress tolerance of F. graminearum. Furthermore, the deletion of FgSCP resulted in reduced pathogenicity and hindered the biosynthesis of deoxynivalenol. The upregulation of FgSCP expression 3 days after infection indicated its involvement in host invasion, possibly acting as a "smokescreen" to deceive the host and suppress the expression of host defensive genes. Subsequently, we confirmed the secretion ability of FgSCP and its ability to inhibit the cell death induced by INF1 in Nicotiana benthamiana cells, indicating its potential role as an effector protein in suppressing plant immune responses and promoting infection. In summary, we have identified FgSCP as an essential effector protein in F. graminearum, playing critical roles in growth, virulence, secondary metabolism, and host invasion.
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Affiliation(s)
- Kouhan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xintong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuzhe Qi
- Jilin Academy of Agricultural Sciences (Northeast Agricultural Research of China), Changchun, Jilin 136100, China
| | - Ying Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yifeng Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanyan Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Aolin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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253
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Bakker AT, Kotsogianni I, Avalos M, Punt JM, Liu B, Piermarini D, Gagestein B, Slingerland CJ, Zhang L, Willemse JJ, Ghimire LB, van den Berg RJHBN, Janssen APA, Ottenhoff THM, van Boeckel CAA, van Wezel GP, Ghilarov D, Martin NI, van der Stelt M. Discovery of isoquinoline sulfonamides as allosteric gyrase inhibitors with activity against fluoroquinolone-resistant bacteria. Nat Chem 2024; 16:1462-1472. [PMID: 38898213 PMCID: PMC11374673 DOI: 10.1038/s41557-024-01516-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/22/2024] [Indexed: 06/21/2024]
Abstract
Bacteria have evolved resistance to nearly all known antibacterials, emphasizing the need to identify antibiotics that operate via novel mechanisms. Here we report a class of allosteric inhibitors of DNA gyrase with antibacterial activity against fluoroquinolone-resistant clinical isolates of Escherichia coli. Screening of a small-molecule library revealed an initial isoquinoline sulfonamide hit, which was optimized via medicinal chemistry efforts to afford the more potent antibacterial LEI-800. Target identification studies, including whole-genome sequencing of in vitro selected mutants with resistance to isoquinoline sulfonamides, unanimously pointed to the DNA gyrase complex, an essential bacterial topoisomerase and an established antibacterial target. Using single-particle cryogenic electron microscopy, we determined the structure of the gyrase-LEI-800-DNA complex. The compound occupies an allosteric, hydrophobic pocket in the GyrA subunit and has a mode of action that is distinct from the clinically used fluoroquinolones or any other gyrase inhibitor reported to date. LEI-800 provides a chemotype suitable for development to counter the increasingly widespread bacterial resistance to fluoroquinolones.
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Affiliation(s)
- Alexander T Bakker
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Ioli Kotsogianni
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Mariana Avalos
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Jeroen M Punt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Bing Liu
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Diana Piermarini
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Berend Gagestein
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Cornelis J Slingerland
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Le Zhang
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Joost J Willemse
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Leela B Ghimire
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | | | - Antonius P A Janssen
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Constant A A van Boeckel
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Dmitry Ghilarov
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK.
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands.
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
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254
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Hamidi F, Taghipour N. miRNA, New Perspective to World of Intestinal Protozoa and Toxoplasma. Acta Parasitol 2024; 69:1690-1703. [PMID: 39158784 DOI: 10.1007/s11686-024-00888-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024]
Abstract
BACKGROUND miRNAs are known as non-coding RNAs that can regulate gene expression. They are reported in many microorganisms and their host cells. Parasite infection can change or shift host miRNAs expression, which can aim at both parasite eradication and infection. PURPOSE This study dealt with examination of miRNA expressed in intestinal protozoan, coccidia , as well as profile changes in host cell miRNA after parasitic infection and their role in protozoan clearance/ survival. METHODS The authors searched ISI Web of Sciences, Pubmed, Scholar, Scopus, another databases and articles published up to 2024 were included. The keywords of miRNA, intestinal protozoa, toxoplasma and some words associated with topics were used in this search. RESULTS Transfection of miRNA mimics or inhibitors can control parasitic diseases, and be introduced as a new therapeutic option in parasitology. CONCLUSION This review can be used to provide up-to date knowledge for future research on these issues.
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Affiliation(s)
- Faezeh Hamidi
- Department of Laboratory Sciences and Microbiology, Faculty of Medical Sciences, Tabriz Medical Sciences, Islamic Azad University, Tabriz, Iran
| | - Niloofar Taghipour
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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255
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Iram D, Sansi MS, Puniya AK, Gandhi K, Meena S, Vij S. Phenotypic and molecular characterization of clinically isolated antibiotics-resistant S. aureus (MRSA), E. coli (ESBL) and Acinetobacter 1379 bacterial strains. Braz J Microbiol 2024; 55:2293-2312. [PMID: 38773046 PMCID: PMC11405748 DOI: 10.1007/s42770-024-01347-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 04/15/2024] [Indexed: 05/23/2024] Open
Abstract
Antibiotic-resistant bacteria causing nosocomial infections pose a significant global health concern. This study focused on examining the lipid profiles of both non-resistant and clinically resistant strains of Staphylococcus aureus (MRSA 1418), E. coli (ESBL 1384), and Acinetobacter 1379. The main aim was to investigate the relationship between lipid profiles, hydrophobicity, and antibiotic resistance so as to identify the pathogenic potential and resistance factors of strains isolated from patients with sepsis and urinary tract infections (UTIs). The research included various tests, such as antimicrobial susceptibility assays following CLSI guidelines, biochemical tests, biofilm assays, and hydrophobicity assays. Additionally, gas chromatography mass spectrometry (GC-MS) and GC-Flame Ionization Detector (GC-FID) analysis were used for lipid profiling and composition. The clinically isolated resistant strains (MRSA-1418, ESBL-1384, and Acinetobacter 1379) demonstrated resistance phenotypes of 81.80%, 27.6%, and 63.6%, respectively, with a multiple antibiotic resistance index of 0.81, 0.27, and 0.63. Notably, the MRSA-1418 strain, which exhibited resistance, showed significantly higher levels of hemolysin, cell surface hydrophobicity, biofilm index, and a self-aggregative phenotype compared to the non-resistant strains. Gene expression analysis using quantitative real-time PCR (qPCR). Indicated elevated expression levels of intercellular adhesion biofilm-related genes (icaA, icaC, and icaD) in MRSA-1418 (pgaA, pgaC, and pgaB) and Acinetobacter 1379 after 24 h compared to non-resistant strains. Scanning electron microscopy (SEM) was employed for structural investigation. These findings provide valuable insights into the role of biofilms in antibiotic resistance and suggest potential target pathways for combating antibiotic-resistant bacteria.
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Affiliation(s)
- Daraksha Iram
- Antimicrobial Peptides, Biofunctional Probiotics and Peptidomics Laboratory, Dairy Microbiology Division, National Dairy Research Institute, Karnal, India
| | - Manish Singh Sansi
- Biofunctional Peptidomics and Metabolic Syndrome Laboratory, Animal Biochemistry Division, National Dairy Research Institute, Karnal, India
| | - Anil Kumar Puniya
- Anaerobic Microbial Fermentation Laboratory, Dairy Microbiology Division, National Dairy Research Institute, Karnal, India
| | - Kamal Gandhi
- Dairy Chemistry Division, National Dairy Research Institute, Karnal, India
| | - Sunita Meena
- Biofunctional Peptidomics and Metabolic Syndrome Laboratory, Animal Biochemistry Division, National Dairy Research Institute, Karnal, India
| | - Shilpa Vij
- Antimicrobial Peptides, Biofunctional Probiotics and Peptidomics Laboratory, Dairy Microbiology Division, National Dairy Research Institute, Karnal, India.
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256
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Ishaq N, Zhang M, Gao L, Ilan M, Li Z. Microbulbifer spongiae sp. nov., isolated from marine sponge Diacarnus erythraeanus. Int J Syst Evol Microbiol 2024; 74. [PMID: 39325661 DOI: 10.1099/ijsem.0.006521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024] Open
Abstract
A novel bacterium, designated as MI-GT, was isolated from marine sponge Diacarnus erythraeanus. Cells of strain MI-GT are Gram-stain-negative, aerobic, and rod or coccoid-ovoid in shape. MI-GT is able to grow at 10-40 °C (optimum, 28 °C), with 1.0-8.0% (w/v) NaCl (optimum, 4.0%), and at pH 5.5-9.0 (optimum, pH 8.0). The 16S rRNA gene sequence of strain MI-GT shows 98.35, 97.32 and 97.25% similarity to those of Microbulbifer variabilis Ni-2088T, Microbulbifer maritimus TF-17T and Microbulbifer echini AM134T, respectively. Phylogenetic analysis also exhibits that strain MI-GT falls within a clade comprising members of the genus Microbulbifer (class Gammaproteobacteria). The genome size of strain MI-GT is 4478124 bp with a G+C content of 54.51 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MI-GT and other type strains are 71.61-76.44% (ANIb), 83.27-84.36% (ANIm) and 13.4-18.7% (dDDH), respectively. These values are significantly lower than the recommended threshold values for bacterial species delineation. Percentage of conserved proteins and average amino acid identity values among the genomes of strain MI-GT and other closely related species are 52.04-59.13% and 67.47-77.21%, respectively. The major cellular fatty acids of MI-GT are composed of summed feature 8 (C18 : 1 ω7c or C18 : 1 ω6c), iso-C11 : 0 3-OH, iso-C15 : 0, C16 : 0, and summed feature 9 (C17 : 1 iso ω9c or C16 : 0 10-methyl). The polar lipids of MI-GT mainly consist of phosphatidylethanolamine, phosphatidylglycerol, aminolipid, and two glycolipids. The major respiratory quinone is Q-8. Based on differential phenotypic and phylogenetic data, strain MI-GT is considered to represent a novel species of genus Microbulbifer, for which the name Microbulbifer spongiae sp. nov. is proposed. The type strain is MI-GT (=MCCC 1K07826T=KCTC 8081T).
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Affiliation(s)
- Nabila Ishaq
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Mimi Zhang
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Luyao Gao
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Micha Ilan
- School of Zoology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
- Yazhou Bay Institute of Deepsea Science and Technology, Shanghai Jiao Tong University, Shanghai, PR China
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257
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Kim YM, Son JY, Ahn DK. Botulinum toxin type A is a potential therapeutic drug for chronic orofacial pain. J Oral Biosci 2024; 66:496-503. [PMID: 38908515 DOI: 10.1016/j.job.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
BACKGROUND Botulinum toxin type A (BTX-A), produced by the gram-positive anaerobic bacterium Clostridium botulinum, acts by cleaving synaptosome-associated protein-25 (SNAP-25), an essential component of the presynaptic neuronal membrane that is necessary for fusion with the membrane proteins of neurotransmitter-containing vesicles. Recent studies have highlighted the efficacy of BTX-A in treating chronic pain conditions, including lower back pain, chronic neck pain, neuropathic pain, and trigeminal neuralgia, particularly when patients are unresponsive to traditional painkillers. This review focuses on the analgesic effects of BTX-A in various chronic pain conditions, with a particular emphasis on the orofacial region. HIGHLIGHT This review focuses on the mechanisms by which BTX-A induces analgesia in patients with inflammatory and temporomandibular joint pain. This review also highlights the fact that BTX-A can effectively manage neuropathic pain and trigeminal neuralgia, which are difficult-to-treat chronic pain conditions. Herein, we present a comprehensive assessment of the central analgesic effects of BTX-A and a discussion of its various applications in clinical dental practice. CONCLUSION BTX-A is an approved treatment option for various chronic pain conditions. Although there is evidence of axonal transport of BTX-A from peripheral to central endings in motor neurons, the precise mechanism underlying its pain-modulating effects remains unclear. This review discusses the evidence supporting the effectiveness of BTX-A in controlling chronic pain conditions in the orofacial region. BTX-A is a promising therapeutic agent for treating pain conditions that do not respond to conventional analgesics.
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Affiliation(s)
- Yu-Mi Kim
- Department of Oral Physiology, School of Dentistry, Kyungpook National University, Daegu, South Korea
| | - Jo-Young Son
- Department of Oral Physiology, School of Dentistry, Kyungpook National University, Daegu, South Korea
| | - Dong-Kuk Ahn
- Department of Oral Physiology, School of Dentistry, Kyungpook National University, Daegu, South Korea.
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258
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Liu J, Wang J, Zhang Z, Bai Q, Pan X, Chen R, Yao H, Yu Y, Ma J. Streptococcus suis Deploys Multiple ATP-Dependent Proteases for Heat Stress Adaptation. J Basic Microbiol 2024; 64:e2400030. [PMID: 39031597 DOI: 10.1002/jobm.202400030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 04/24/2024] [Accepted: 05/19/2024] [Indexed: 07/22/2024]
Abstract
Streptococcus suis is an important zoonotic pathogen, causing cytokine storms of Streptococcal toxic shock-like syndrome amongst humans after a wound infection into the bloodstream. To overcome the challenges of fever and leukocyte recruitment, invasive S. suis must deploy multiple stress responses forming a network and utilize proteases to degrade short-lived regulatory and misfolded proteins induced by adverse stresses, thereby adapting and evading host immune responses. In this study, we found that S. suis encodes multiple ATP-dependent proteases, including single-chain FtsH and double-subunit Clp protease complexes ClpAP, ClpBP, ClpCP, and ClpXP, which were activated as the fever of infected mice in vivo. The expression of genes ftsH, clpA/B/C, and clpP, but not clpX, were significantly upregulated in S. suis in response to heat stress, while were not changed notably under the treatments with several other stresses, including oxidative, acidic, and cold stimulation. FtsH and ClpP were required for S. suis survival within host blood under heat stress in vitro and in vivo. Deletion of ftsH or clpP attenuated the tolerance of S. suis to heat, oxidative and acidic stresses, and significantly impaired the bacterial survival within macrophages. Further analysis identified that repressor CtsR directly binds and controls the clpA/B/C and clpP operons and is relieved by heat stress. In summary, the deployments of multiple ATP-dependent proteases form a flexible heat stress response network that appears to allow S. suis to fine-tune the degradation or refolding of the misfolded proteins to maintain cellular homeostasis and optimal survival during infection.
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Affiliation(s)
- Jianan Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Jianzhong Wang
- Suzhou Xiangcheng Fisheries Technology Promotion Center, Suzhou Animal Disease Prevention and Control Center, Suzhou, China
| | - Zhen Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Qiankun Bai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Xinming Pan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Rong Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Huochun Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Yong Yu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
| | - Jiale Ma
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
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259
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Deng J, Zhang W, Zhang L, Qin C, Wang H, Ling W. Micro-interfacial behavior of antibiotic-resistant bacteria and antibiotic resistance genes in the soil environment: A review. ENVIRONMENT INTERNATIONAL 2024; 191:108972. [PMID: 39180776 DOI: 10.1016/j.envint.2024.108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/11/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024]
Abstract
Overutilization and misuse of antibiotics in recent decades markedly intensified the rapid proliferation and diffusion of antibiotic resistance genes (ARGs) within the environment, thereby elevating ARGs to the status of a global public health crisis. Recognizing that soil acts as a critical reservoir for ARGs, environmental researchers have made great progress in exploring the sources, distribution, and spread of ARGs in soil. However, the microscopic state and micro-interfacial behavior of ARGs in soil remains inadequately understood. In this study, we reviewed the micro-interfacial behaviors of antibiotic-resistant bacteria (ARB) in soil and porous media, predominantly including migration-deposition, adsorption, and biofilm formation. Meanwhile, adsorption, proliferation, and degradation were identified as the primary micro-interfacial behaviors of ARGs in the soil, with component of soil serving as significant determinant. Our work contributes to the further comprehension of the microstates and processes of ARB and ARGs in the soil environments and offers a theoretical foundation for managing and mitigating the risks associated with ARG contamination.
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Affiliation(s)
- Jibao Deng
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenkang Zhang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lingyu Zhang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hefei Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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260
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Wu YJ, Weng TY, Yeh TY, Chou PJ, Whang LM. Nitrogen removal strategy for real swine wastewater by combining partial nitrification-denitrification process with anammox. CHEMOSPHERE 2024; 364:143116. [PMID: 39159763 DOI: 10.1016/j.chemosphere.2024.143116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 08/06/2024] [Accepted: 08/14/2024] [Indexed: 08/21/2024]
Abstract
Anammox process offers reduced operational cost and energy requirement compared to nitrification-denitrification methods due to lower biomass generation and no need for external carbon sources and aeration. High ammonia concetration and low biodegradable anaerobic digester of swaine wastewater provided an advantage for the growth of anammox microorangism. An anoxic/oxic (A/O) SBR and an anammox SBR were implemented parallelly to treat the same swine wastewater with partial nitrification/denitrification and partial nitrification/anammox process, respectively, and to compare their nitrogen removal efficiency. The nitrogen removal rates (NRRs) of the A/O SBR and anammox SBR were 0.054 and 0.26 kg-N/m3/day, respectively. The lower NRR of the A/O SBR could be attributed to insufficient biodegradable organic carbon sources in the denitrification process. The kinetic parameters obtained from the two SBRs were applied to estimate the time required for using the A/O process and partial nitrification/anammox process to treat the same amount of ammonia with the same reaction volume. Results showed that the A/O process required 3.3 times the reaction time of the partial nitrification/anammox process, suggesting that the partial nitrification/anammox process is a more efficient and economic nitrogen removal process for swine wastewater treatment. The next generation sequencing results revealed that Candidatus Brocadia, ranging from 10 to 23%, was the predominant anammox bacteria in the anammox SBR. More than 78.2 % of nitrite in the anammox SBR was removed through the anammox reaction.
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Affiliation(s)
- Yi-Ju Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan, 70101, Taiwan.
| | - Tzu-Ya Weng
- Department of Environmental Engineering, National Cheng Kung University, Tainan, 70101, Taiwan.
| | - Ting-Yu Yeh
- Department of Environmental Engineering, National Cheng Kung University, Tainan, 70101, Taiwan.
| | - Pei-Jane Chou
- Taiwan Sugar Research Institute (TSRI), Tainan, 701036, Taiwan
| | - Liang-Ming Whang
- Department of Environmental Engineering, National Cheng Kung University, Tainan, 70101, Taiwan; Sustainable Environment Research Laboratory (SERL), National Cheng Kung University, Tainan, 70101, Taiwan.
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261
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Mundada R, Tanpure SB, Mapare S, Karra A, Yannawar V, Gilani R. The Effect of Nanoparticles Against Streptococcus mutans in the Orthodontic Primer Used for Aligner Attachment: An In Vitro Study. Cureus 2024; 16:e68359. [PMID: 39355471 PMCID: PMC11443300 DOI: 10.7759/cureus.68359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2024] [Accepted: 08/28/2024] [Indexed: 10/03/2024] Open
Abstract
Objective This study investigates the antimicrobial properties of silver (1%) and chitosan (1%) nanoparticles against Streptococcus mutans (S. mutans) when added to an orthodontic primer used for aligner attachments. While aligner treatments are becoming increasingly popular for their aesthetics and convenience, their attachments can create retention sites for bacteria, potentially leading to white spot lesions (WSLs). This in vitro study aims to address this issue by enhancing the antimicrobial efficacy of aligner primers. Methodology Thirty freshly extracted teeth were classified into the following three groups: Group A with the standard primer, Group B with chitosan nanoparticles mixed in the primer, and Group C with silver nanoparticles mixed in the primer. The samples were incubated with S. mutans and bacterial colonies were counted at 12, 24, 48, and 72 hours. Results The results showed a significant reduction in colony-forming units (CFUs) in the groups with nanoparticles compared to the control group, with silver nanoparticles exhibiting a higher antimicrobial effect than chitosan. Conclusions This study suggests that incorporating silver nanoparticles into orthodontic primers can effectively reduce bacterial growth, potentially improving oral hygiene and reducing the risk of WSLs in patients undergoing aligner treatment.
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Affiliation(s)
- Ram Mundada
- Department of Orthodontics and Dentofacial Orthopedics, Dr. Hedgewar Smruti Rugna Seva Mandal's Dental College and Hospital, Hingoli, IND
| | - Saurabh B Tanpure
- Department of Orthodontics and Dentofacial Orthopedics, Dr. Hedgewar Smruti Rugna Seva Mandal's Dental College and Hospital, Hingoli, IND
| | - Sagar Mapare
- Department of Orthodontics and Dentofacial Orthopedics, Dr. Hedgewar Smruti Rugna Seva Mandal's Dental College and Hospital, Hingoli, IND
| | - Arjun Karra
- Department of Orthodontics and Dentofacial Orthopedics, Dr. Hedgewar Smruti Rugna Seva Mandal's Dental College and Hospital, Hingoli, IND
| | - Vijay Yannawar
- Department of Orthodontics and Dentofacial Orthopedics, Dr. Hedgewar Smruti Rugna Seva Mandal's Dental College and Hospital, Hingoli, IND
| | - Rizwan Gilani
- Department of Orthodontics and Dentofacial Orthopedics, Sharad Pawar Dental College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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Basak P, Dastidar DG, Ghosh D, Chakraborty T, Sau S, Chakrabarti G. Staphylococcus aureus major cell division protein FtsZ assembly is inhibited by silibinin, a natural flavonolignan that also blocked bacterial growth and biofilm formation. Int J Biol Macromol 2024; 279:135252. [PMID: 39222779 DOI: 10.1016/j.ijbiomac.2024.135252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/04/2024]
Abstract
The bacterial cell division protein FtsZ has been considered a potential therapeutic target due to its rapid treadmilling that induces cellular wall construction in bacteria. The current study discovered a novel antimicrobial compound, silibinin, a natural flavonolignan and its impact on the recombinant S. aureus FtsZ (SaFtsZ). Silibinin inhibited S. aureus Newman growth in a dose-dependent manner. The IC50 and MIC values for silibinin were 75 μM and 200 μM, respectively. It had no cytotoxicity against HEK293 cells in vitro. Silibinin also enlarged the bacterial cell morphology by ∼40 folds and showed antibiofilm property. It perturbed the S. aureus membrane potential both at IC50 conc. and at MIC conc. Further, it inhibited both the polymerization and GTPase activity of SaFtsZ. It did not inhibit tubulin assembly, a eukaryotic FtsZ homolog. A fluorescence quenching study yielded the Kd value for SaFtsZ-Silibinin interaction and binding stoichiometry 0.857 ± 0.188 μM and 1:1, respectively. Both in silico study and competition assay indicated that silibinin binds at the GTP binding site on SaFtsZ. The Ki value for the silibinin-mediated inhibition of SaFtsZ was 8.8 μM. Therefore, these findings have comprehensively shown the antimicrobial behavior of silibinin on S. aureus Newman cells targeting SaFtsZ.
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Affiliation(s)
- Prithvi Basak
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, WB 700 019, India
| | - Debabrata Ghosh Dastidar
- Guru Nanak Institute of Pharmaceutical Science & Technology, 157/F Nilgunj Road, Panihati, Kolkata 700114, West Bengal, India
| | - Dipanjan Ghosh
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, WB 700 019, India
| | - Tushar Chakraborty
- Department of Biological Sciences, Bose Institute, Kolkata 700091, West Bengal, India
| | - Subrata Sau
- Department of Biological Sciences, Bose Institute, Kolkata 700091, West Bengal, India
| | - Gopal Chakrabarti
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, WB 700 019, India.
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Strotmann U, Durand MJ, Thouand G, Eberlein C, Heipieper HJ, Gartiser S, Pagga U. Microbiological toxicity tests using standardized ISO/OECD methods-current state and outlook. Appl Microbiol Biotechnol 2024; 108:454. [PMID: 39215841 PMCID: PMC11365844 DOI: 10.1007/s00253-024-13286-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/19/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Microbial toxicity tests play an important role in various scientific and technical fields including the risk assessment of chemical compounds in the environment. There is a large battery of normalized tests available that have been standardized by ISO (International Organization for Standardization) and OECD (Organization for Economic Co-operation and Development) and which are worldwide accepted and applied. The focus of this review is to provide information on microbial toxicity tests, which are used to elucidate effects in other laboratory tests such as biodegradation tests, and for the prediction of effects in natural and technical aqueous compartments in the environment. The various standardized tests as well as not normalized methods are described and their advantages and disadvantages are discussed. In addition, the sensitivity and usefulness of such tests including a short comparison with other ecotoxicological tests is presented. Moreover, the far-reaching influence of microbial toxicity tests on biodegradation tests is also demonstrated. A new concept of the physiological potential of an inoculum (PPI) consisting of microbial toxicity tests whose results are expressed as a chemical resistance potential (CRP) and the biodegradation adaptation potential (BAP) of an inoculum is described that may be helpful to characterize inocula used for biodegradation tests. KEY POINTS: • Microbial toxicity tests standardized by ISO and OECD have large differences in sensitivity and applicability. • Standardized microbial toxicity tests in combination with biodegradability tests open a new way to characterize inocula for biodegradation tests. • Standardized microbial toxicity tests together with ecotoxicity tests can form a very effective toolbox for the characterization of toxic effects of chemicals.
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Affiliation(s)
- Uwe Strotmann
- Dept. of Chemistry, Westfälische Hochschule, Recklinghausen, Germany
| | - Marie-José Durand
- UMR 6144, Nantes Université, ONIRIS, CNRS, GEPEA, 85000, La Roche Sur Yon, France
| | - Gerald Thouand
- UMR 6144, Nantes Université, ONIRIS, CNRS, GEPEA, 85000, La Roche Sur Yon, France
| | - Christian Eberlein
- Department of Molecular Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hermann J Heipieper
- Department of Molecular Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
| | | | - Udo Pagga
- , Rüdigerstr. 49, 67069, Ludwigshafen, Germany
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Duran AD, Danhart EM, Ma X, Nagy ABK, Musier-Forsyth K, Foster MP. NMR-based solution structure of the Caulobacter crescentus ProXp-ala trans-editing enzyme. BIOMOLECULAR NMR ASSIGNMENTS 2024:10.1007/s12104-024-10193-3. [PMID: 39214936 DOI: 10.1007/s12104-024-10193-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
ProXp-ala is a key component of the translational machinery in all three Domains of life. This enzyme helps to maintain the fidelity of proline codon translation through aminoacyl-tRNAPro proofreading. In the first step of tRNA aminoacylation, the cognate aminoacyl-tRNA synthetase (aaRS) binds and activates an amino acid in the enzyme's synthetic active site. If a non-cognate amino acid passes this first selection step and is charged onto the tRNA, a distinct aaRS editing active site may recognize the mischarged tRNA and deacylate it. Alternatively, this editing reaction may be carried out by a separate enzyme that deacylates the mischarged tRNA in trans. ProXp-ala is responsible for editing Ala mischarged onto tRNAPro. Since trans-editing domains such as ProXp-ala bind their substrates after release from the synthetase, they must recognize not only the mischarged amino acid, but also the specific tRNA. Previous studies showed that Caulobacter crescentus (Cc) ProXp-ala distinguishes tRNAPro from tRNAAla, in part, based on the unique tRNAPro acceptor stem base pair C1:G72. Previous crystallographic and NMR data also revealed a role for conformational selection by the ProXp-ala α2 helix in Ala- versus Pro-tRNAPro substrate discrimination. The α2 helix makes lattice contacts in the crystal, which left some uncertainty as to its position in solution. We report resonance assignments for the substrate-free Cc ProXp-ala and the NMR-derived three-dimensional structure of the protein. These data reveal the position of the α2 helix in solution, with implications for substrate binding and recognition.
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Affiliation(s)
- Antonia D Duran
- Center for RNA Biology, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
- , 484 W 12th Ave, Columbus, OH, 43017, USA
| | - Eric M Danhart
- Center for RNA Biology, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
- , 484 W 12th Ave, Columbus, OH, 43017, USA
| | - Xiao Ma
- Center for RNA Biology, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
- , 484 W 12th Ave, Columbus, OH, 43017, USA
| | - Alexandra B Kuzmishin Nagy
- Center for RNA Biology, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
- , 484 W 12th Ave, Columbus, OH, 43017, USA
| | - Karin Musier-Forsyth
- Center for RNA Biology, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
- , 484 W 12th Ave, Columbus, OH, 43017, USA
| | - Mark P Foster
- Center for RNA Biology, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA.
- , 484 W 12th Ave, Columbus, OH, 43017, USA.
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265
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Duller S, Vrbancic S, Szydłowski Ł, Mahnert A, Blohs M, Predl M, Kumpitsch C, Zrim V, Högenauer C, Kosciolek T, Schmitz RA, Eberhard A, Dragovan M, Schmidberger L, Zurabischvili T, Weinberger V, Moser AM, Kolb D, Pernitsch D, Mohammadzadeh R, Kühnast T, Rattei T, Moissl-Eichinger C. Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome. Nat Commun 2024; 15:7593. [PMID: 39217206 PMCID: PMC11366006 DOI: 10.1038/s41467-024-52037-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
Archaea are vital components of the human microbiome, yet their study within the gastrointestinal tract (GIT) is limited by the scarcity of cultured representatives. Our study presents a method for the targeted enrichment and isolation of methanogenic archaea from human fecal samples. The procedure combines methane breath testing, in silico metabolic modeling, media optimization, FACS, dilution series, and genomic sequencing through Nanopore technology. Additional analyzes include the co-cultured bacteriome, comparative genomics of archaeal genomes, functional comparisons, and structure-based protein function prediction of unknown differential traits. Successful establishment of stable archaeal cultures from 14 out of 16 fecal samples yielded nine previously uncultivated strains, eight of which are absent from a recent archaeome genome catalog. Comparative genomic and functional assessments of Methanobrevibacter smithii and Candidatus Methanobrevibacter intestini strains from individual donors revealed features potentially associated with gastrointestinal diseases. Our work broadens available archaeal representatives for GIT studies, and offers insights into Candidatus Methanobrevibacter intestini genomes' adaptability in critical microbiome contexts.
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Affiliation(s)
- Stefanie Duller
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Simone Vrbancic
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Łukasz Szydłowski
- Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
- Sano Centre for Computational Medicine, Krakow, Poland
| | - Alexander Mahnert
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Marcus Blohs
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Michael Predl
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Christina Kumpitsch
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Verena Zrim
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Christoph Högenauer
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Tomasz Kosciolek
- Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
- Sano Centre for Computational Medicine, Krakow, Poland
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Anna Eberhard
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Melanie Dragovan
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Laura Schmidberger
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Tamara Zurabischvili
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Viktoria Weinberger
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Adrian Mathias Moser
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Dagmar Kolb
- Core Facility Ultrastructure Analysis, Medical University of Graz, Graz, Austria
- Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Dominique Pernitsch
- Core Facility Ultrastructure Analysis, Medical University of Graz, Graz, Austria
| | - Rokhsareh Mohammadzadeh
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Torben Kühnast
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Christine Moissl-Eichinger
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.
- BioTechMed Graz, Graz, Austria.
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266
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Liu Y, Miao B, Li W, Hu X, Bai F, Abuduresule Y, Liu Y, Zheng Z, Wang W, Chen Z, Zhu S, Feng X, Cao P, Ping W, Yang R, Dai Q, Liu F, Tian C, Yang Y, Fu Q. Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history. Cell 2024:S0092-8674(24)00899-7. [PMID: 39326418 DOI: 10.1016/j.cell.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/01/2024] [Accepted: 08/07/2024] [Indexed: 09/28/2024]
Abstract
Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.
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Affiliation(s)
- Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Miao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China
| | - Wenying Li
- Xinjiang Cultural Relics and Archaeology Institute, Ürümchi 830000, China
| | - Xingjun Hu
- Research Center for Governance of China's Northwest Frontier in the Historical Periods, School of History, Xinjiang University, Ürümqi 830046, China
| | - Fan Bai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | | | - Yalin Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zequan Zheng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjun Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; Science and Technology Archaeology, National Centre for Archaeology, Beijing 100013, China
| | - Zehui Chen
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shilun Zhu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China
| | - Chan Tian
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Yimin Yang
- Department of Archaeology and Anthropology, University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100035, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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Sinetova MA, Kupriyanova EV, Los DA. Spirulina/Arthrospira/Limnospira-Three Names of the Single Organism. Foods 2024; 13:2762. [PMID: 39272527 PMCID: PMC11395459 DOI: 10.3390/foods13172762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/15/2024] Open
Abstract
Recent advances in research techniques have enabled rapid progress in the study of spirulina, an ancient edible cyanobacteria. Nowadays, spirulina species are classified into three genera: Spirulina, Arthrospira, and Limnospira. The latter now refers to industrially manufactured spirulina strains. Whole-genome sequencing revealed gene clusters involved in metabolite production, and the physiology of spirulina. Omics technologies demonstrated the absence of hazardous compounds in spirulina cells, confirming the safety of this biomass as a food product. Spirulina is a good source of different chemicals used in food manufacturing, food supplements, and pharmaceuticals. Spirulina's enrichment with inherent biologically active substances makes it a potential supplier of natural products for dietary and pharmaceutical applications. Spirulina is also a prospective component of both terrestrial and space-based life support systems. Here, we review current breakthroughs in spirulina research and clarify fallacies that can be found in both professional literature and public media.
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Affiliation(s)
- Maria A Sinetova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia
| | - Elena V Kupriyanova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia
| | - Dmitry A Los
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia
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268
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Detain J, Besaury L. Degradation of lignocellulose by different bacterial and fungal co-cultures. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 7:100271. [PMID: 39291138 PMCID: PMC11406349 DOI: 10.1016/j.crmicr.2024.100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
Long seen as non-valorisable waste, agricultural co-products are increasingly used in biorefinery processes. Co-culture appears as new trend for to improve the degradation of lignocellulose and improve the production of bioproducts. The goal of the study was to setup inter-domain co-cultures with high capabilities of lignocellulose degradation using a pluridisciplinary approach combining bioinformatics, enzymology, transcriptomics. Different individual lignocellulolytic strains: Trichoderma reesei QM6a and three bacteria (Streptomyces coelicolor A3(2), Rhizobium sp.XylPr11 and Sphingobacterium prati AraPr2 affiliated from different phyla) were used in that study . Synergic activities have been observed and quantified in co-culture conditions, particularly for xylanases and peroxidases activities. The enzymatic activities for the co-cultures in the most interesting co-culture (T. reesei QM6a/S. coelicolor A3(2)) reached more up to 2 IU/mL and 430 IU/mL respectively for the xylanase and peroxidase. Furthermore, ATR-FTIR analysis showed a real impact of co-culture condition on the substrate compared to the monoculture specially for hemicellulose degradation. Transcriptomics of S. coelicolor A3(2) either in mono or co-culture showed a relative similar pattern profile whatever the condition analysed with a specific overexpression of certain CAZyme genes involved in glycolysis due to the hydrolytic role played by the fungal partner. This work provided the proof of concept for technological feasibility, pertinence and usefulness of interdomain co-culture.
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Affiliation(s)
- Julian Detain
- Université de Reims Champagne Ardennes, INRAE, FARE, UMR A 614, Chaire AFERE, 51097 Reims, France
| | - Ludovic Besaury
- Université de Reims Champagne Ardennes, INRAE, FARE, UMR A 614, Chaire AFERE, 51097 Reims, France
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269
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He L, Miguel-Romero L, Patkowski JB, Alqurainy N, Rocha EPC, Costa TRD, Fillol-Salom A, Penadés JR. Tail assembly interference is a common strategy in bacterial antiviral defenses. Nat Commun 2024; 15:7539. [PMID: 39215040 PMCID: PMC11364771 DOI: 10.1038/s41467-024-51915-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Many bacterial immune systems recognize phage structural components to activate antiviral responses, without inhibiting the function of the phage component. These systems can be encoded in specific chromosomal loci, known as defense islands, and in mobile genetic elements such as prophages and phage-inducible chromosomal islands (PICIs). Here, we identify a family of bacterial immune systems, named Tai (for 'tail assembly inhibition'), that is prevalent in PICIs, prophages and P4-like phage satellites. Tai systems protect their bacterial host population from other phages by blocking the tail assembly step, leading to the release of tailless phages incapable of infecting new hosts. To prevent autoimmunity, some Tai-positive phages have an associated counter-defense mechanism that is expressed during the phage lytic cycle and allows for tail formation. Interestingly, the Tai defense and counter-defense genes are organized in a non-contiguous operon, enabling their coordinated expression.
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Affiliation(s)
- Lingchen He
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Laura Miguel-Romero
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - Jonasz B Patkowski
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nasser Alqurainy
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences & King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Tiago R D Costa
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Alfred Fillol-Salom
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
| | - José R Penadés
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
- School of Health Sciences, Universidad CEU Cardenal Herrera, CEU Universities, Alfara del Patriarca, Spain.
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270
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Nyman IB, Wessel Ø, Bjørgen H, Alarcon M, Tengs T, Rimstad E. Evaluating Atlantic Salmon ( Salmo salar) as a Natural or Alternative Host for Piscine Myocarditis Virus (PMCV) Infection. Pathogens 2024; 13:744. [PMID: 39338935 PMCID: PMC11434702 DOI: 10.3390/pathogens13090744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/09/2024] [Accepted: 08/26/2024] [Indexed: 09/30/2024] Open
Abstract
Cardiomyopathy syndrome (CMS) caused by piscine myocarditis virus (PMCV) has emerged with the rise of the aquaculture of Atlantic salmon (Salmo salar). The lack of cell culture cultivation has hampered the study of this infection. In this study, samples from naturally PMCV-infected Atlantic salmon from different commercial farms were collected and used. In situ hybridization (ISH) revealed intense staining of PMCV RNA in myocardial cells in the spongiform layer of the heart ventricle but almost no staining in the compact layer. In the kidneys, only sporadic staining was seen. Viral RNA was present in all organs, with the highest loads in the heart, kidney, and spleen. The high viral PMCV RNA loads in the heart were due to extensive viral mRNA transcription. The high ratio of viral mRNA to viral genomic dsRNA indicated active transcription but limited production of new viral particles. This suggests that the histopathological changes in the heart are caused by viral mRNA and corresponding viral proteins and not by virus particle formation. The production of full-length transcripts is regulated, with a reduction in the relative number of ORF3-containing transcripts at high transcription rates. Efforts to identify alternative hosts, such as fungi, were inconclusive, as fungal sequences were found inconsistently in the salmon tissue samples. The results of this study reinforce the need for further research to fully understand PMCV's life cycle and potential alternative hosts and its whereabouts when it is not infecting the hearts of the Atlantic salmon.
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Affiliation(s)
- Ingvild B Nyman
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Øystein Wessel
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Håvard Bjørgen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Marta Alarcon
- Pharmaq Analytic, Harbitzaléen 2A, 0275 Oslo, Norway
| | | | - Espen Rimstad
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1433 Ås, Norway
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271
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Tamamura M, Gibu N, Toda T, Takenaka K, Hang DT, Huong NL, Andler R, Kasai D. Characterization of the conversion system of natural rubber to poly(3-Hydroxyalkanoate) in Piscinibacter gummiphilus strain NS21 T. N Biotechnol 2024; 84:1-8. [PMID: 39216800 DOI: 10.1016/j.nbt.2024.08.507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 08/29/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
Poly(3-hydroxyalkanoate) (PHA), a bacteria-synthesized biodegradable polyester, is a useful alternative to fossil resources, and current systems for its production rely predominantly on edible resources, raising concerns about microbial competition for nutrients. Therefore, we investigated mechanisms underlying PHA production from non-edible resources by Piscinibacter gummiphilus strain NS21T. Strain NS21T can utilize natural rubber as a carbon source on solid media and potentially produces PHA. Gas chromatography and nuclear magnetic resonance analyses of NS21T cell extracts revealed the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and poly(3-hydroxybutyrate) from natural rubber and glucose, respectively. Transcriptional analysis suggested that phaC is involved in PHA production. An increased PHBV accumulation rate under nitrogen-limiting conditions indicates the potential of this strain to be used as a PHBV production enhancement strategy. Furthermore, the disruption of PHA depolymerase genes resulted in enhanced PHA production, indicating the involvement of these genes in PHA degradation. These findings highlight the potential of NS21T for PHBV production from natural rubber, a non-edible resource.
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Affiliation(s)
- Masaki Tamamura
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Namiko Gibu
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Tomoyuki Toda
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Katsuhiko Takenaka
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Dam Thuy Hang
- School of Chemistry and Life Sciences, Hanoi University of Science and Technology, No 1 Dai Co Viet, Hai Ba Trung, Hanoi, Viet Nam
| | - Nguyen Lan Huong
- School of Chemistry and Life Sciences, Hanoi University of Science and Technology, No 1 Dai Co Viet, Hai Ba Trung, Hanoi, Viet Nam
| | - Rodrigo Andler
- Escuela de Ingeniería en Biotecnología, Centro de Biotecnología de los Recursos Naturales (Cenbio), Universidad Católica del Maule, Talca, Maule, Chile
| | - Daisuke Kasai
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.
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272
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Dias RA. Towards a Comprehensive Definition of Pandemics and Strategies for Prevention: A Historical Review and Future Perspectives. Microorganisms 2024; 12:1802. [PMID: 39338476 PMCID: PMC11433773 DOI: 10.3390/microorganisms12091802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 08/22/2024] [Accepted: 08/28/2024] [Indexed: 09/30/2024] Open
Abstract
The lack of a universally accepted definition of a pandemic hinders a comprehensive understanding of and effective response to these global health crises. Current definitions often lack quantitative criteria, rendering them vague and limiting their utility. Here, we propose a refined definition that considers the likelihood of susceptible individuals contracting an infectious disease that culminates in widespread global transmission, increased morbidity and mortality, and profound societal, economic, and political consequences. Applying this definition retrospectively, we identify 22 pandemics that occurred between 165 and 2024 AD and were caused by a variety of diseases, including smallpox (Antonine and American), plague (Justinian, Black Death, and Third Plague), cholera (seven pandemics), influenza (two Russian, Spanish, Asian, Hong Kong, and swine), AIDS, and coronaviruses (SARS, MERS, and COVID-19). This work presents a comprehensive analysis of past pandemics caused by both emerging and re-emerging pathogens, along with their epidemiological characteristics, societal impact, and evolution of public health responses. We also highlight the need for proactive measures to reduce the risk of future pandemics. These strategies include prioritizing surveillance of emerging zoonotic pathogens, conserving biodiversity to counter wildlife trafficking, and minimizing the potential for zoonotic spillover events. In addition, interventions such as promoting alternative protein sources, enforcing the closure of live animal markets in biodiversity-rich regions, and fostering global collaboration among diverse stakeholders are critical to preventing future pandemics. Crucially, improving wildlife surveillance systems will require the concerted efforts of local, national and international entities, including laboratories, field researchers, wildlife conservationists, government agencies and other stakeholders. By fostering collaborative networks and establishing robust biorepositories, we can strengthen our collective capacity to detect, monitor, and mitigate the emergence and transmission of zoonotic pathogens.
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Affiliation(s)
- Ricardo Augusto Dias
- School of Veterinary Medicine, University of Sao Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, São Paulo 05508-270, Brazil
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273
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Rissanen AJ, Mangayil R, Khanongnuch R. Genome of Methylomonas sp. AM2-LC, representing a methanotrophic bacterial species isolated from water column of a boreal, oxygen-stratified lake. Front Genet 2024; 15:1440435. [PMID: 39280097 PMCID: PMC11392852 DOI: 10.3389/fgene.2024.1440435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/19/2024] [Indexed: 09/18/2024] Open
Affiliation(s)
- Antti J Rissanen
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
- Natural Resources Institute Finland, Helsinki, Finland
| | - Rahul Mangayil
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, Finland
| | - Ramita Khanongnuch
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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274
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Chakraborty P, Mukherjee C. The interplay of metabolic and epigenetic players in disease development. Biochem Biophys Res Commun 2024; 734:150621. [PMID: 39217811 DOI: 10.1016/j.bbrc.2024.150621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 08/14/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
Epigenetic modifications and their alterations can cause variation in gene expression patterns which can ultimately affect a healthy individual. Until a few years ago, it was thought that the epigenome affects the transcriptome which can regulate the proteome and the metabolome. Recent studies have shown that the metabolome independently also plays a major role in regulating the epigenome bypassing the need for transcriptomic control. Alternatively, an imbalanced metabolome, stemming from transcriptome abnormalities, can further impact the transcriptome, creating a self-perpetuating cycle of interconnected occurrences. As a result, external factors such as nutrient intake and diet can have a direct impact on the metabolic pools and its reprogramming can change the levels and activity of epigenetic modifiers. Thus, the epigenetic landscape steers toward a diseased condition. In this review, we have discussed how different metabolites and dietary patterns can bring about changes in different arms of the epigenetic machinery such as methylation, acetylation as well as RNA mediated epigenetic mechanisms. We checked for limiting metabolites such as αKG, acetyl-CoA, ATP, NAD+, and FAD, whose abundance levels can lead to common diseases such as cancer, neurodegeneration etc. This gives a clearer picture of how an integrated approach including both epigenetics and metabolomics can be used for therapeutic purposes.
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Affiliation(s)
- Pallavi Chakraborty
- RNABio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal, India; Shiv Nadar Institute of Eminence, Greater Noida, Uttar Pradesh, India
| | - Chandrama Mukherjee
- RNABio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal, India.
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275
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Igarashi Y, Nohda M, Katoh H, Zhang Z, Triningsih DW, Karim MRU, Akasaka K, Harunari E, Oku N. Sporangimicins A-D, acylated maltose derivatives from a rare actinomycete of the genus Pseudosporangium. J Antibiot (Tokyo) 2024:10.1038/s41429-024-00768-6. [PMID: 39210002 DOI: 10.1038/s41429-024-00768-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/22/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
Sporangimicins A-D (1-4), four anomeric pairs of diacyl disaccharides that represent a new metabolite class, were discovered from the culture extract of an actinomycete Pseudosporangium sp. RD061809. Compounds 1-4 caused peak separation in the HPLC chromatogram and partial duplication of the NMR resonances by anomeric interconversion of a maltose core modified at the two sugar 6-positions with an isobutanoyl and a methyl-branched long-chain dienoyl groups. A highlight of the structure elucidation was application of Ohrui-Akasaka's method to a chromatographically inseparable mixture of 3 and 4, which proved the composition ratio of 3 and 4 to be 82:18 and the R/S ratio at the anteiso-methyl bearing chiral center in 3 to be 66:34. Compounds 1-4 showed antimicrobial activity against Gram-positive bacteria and modest cytotoxicity toward P388 murine leukemia cells.
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Affiliation(s)
- Yasuhiro Igarashi
- Biotechnology Research Center, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.
| | - Miku Nohda
- Biotechnology Research Center, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Hiroki Katoh
- Biotechnology Research Center, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Zhiwei Zhang
- Biotechnology Research Center, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | | | - Md Rokon Ul Karim
- Biotechnology Research Center, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Kazuaki Akasaka
- Shokei Gakuin University, 4-10-1 Yurigaoka, Natori, Miyagi, 981-1295, Japan
| | - Enjuro Harunari
- Biotechnology Research Center, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Naoya Oku
- Biotechnology Research Center, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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276
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Ni Y, Liao Q, Gou S, Shi T, Li W, Feng R, Zhao Z, Zhao X. Study on Enzyme Activity and Metabolomics during Culture of Liquid Spawn of Floccularia luteovirens. J Fungi (Basel) 2024; 10:618. [PMID: 39330377 PMCID: PMC11433261 DOI: 10.3390/jof10090618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 08/20/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024] Open
Abstract
To comprehensively investigate the physiological characteristics and metabolic processes of the mycelium of Floccularia luteovirens (F. luteovirens), a wild edible fungus unique to the plateau region, we conducted an in-depth analysis of the mycelium enzyme activity and metabolites during different culture periods. The activity of seven enzymes all followed a trend of initially increasing and then decreasing. The intra- and extracellular activity peaks of three hydrolases-amylase, protease, and cellulase-all occurred on the 20th day, except for the extracellular amylase, which peaked on the 15th day. In contrast, the peak activity of laccase occurred on the 10th day. Moreover, three types of oxidoreductases in the mycelium (catalase (CAT), superoxide dismutase (SOD), and 2,3,5-triphenyltetrazolium chloride (TTC)-dehydrogenase (TTC-DH)) also exhibited significant changes in activity. CAT and SOD activity reached their maximum on the 20th day, whereas TTC-DH showed high activity on both the 10th and 20th days. Through a comprehensive assessment of the evolving trends of these physiological parameters, we determined that the optimal cultivation cycle for F. luteovirens liquid spawn is 20 days. An untargeted metabolomic analysis revealed that 3569 metabolites were detected in the F. luteovirens mycelium, including a variety of secondary metabolites and functional components, with terpenoids being particularly abundant, accounting for 148 types. By comparing three different culture stages (10 days, 20 days, and 30 days), 299, 291, and 381 metabolites, respectively, showed different accumulation patterns in the comparison groups of 10d vs. 20d, 20d vs. 30d, and 10d vs. 30d. These differential metabolites were primarily concentrated in carboxylic acids and their derivatives, fatty acyl groups, organic oxygen compounds, and lipid compounds. In addition, there were several amino acids whose abundance continued to grow during culturing. The metabolism of amino acids greatly affects mycelium growth and development. This research delineates the interplay between mycelium growth and metabolism, offering empirical support for a cultivation strategy for liquid F. luteovirens, and an exploration of its metabolites for potential applications.
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Affiliation(s)
- Yanqing Ni
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, China; (Y.N.); (Q.L.)
- College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Qiuhong Liao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, China; (Y.N.); (Q.L.)
- Chengdu National Agricultural Science and Technology Center, Chengdu 610299, China
| | - Siyuan Gou
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, China; (Y.N.); (Q.L.)
- College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Tongjia Shi
- College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
- Chengdu National Agricultural Science and Technology Center, Chengdu 610299, China
| | - Wensheng Li
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, China; (Y.N.); (Q.L.)
- College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Rencai Feng
- College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
- Chengdu National Agricultural Science and Technology Center, Chengdu 610299, China
| | - Zhiqiang Zhao
- Zhuoni County Agricultural Technology Extension Station, Gannan 747600, China
| | - Xu Zhao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, China; (Y.N.); (Q.L.)
- Chengdu National Agricultural Science and Technology Center, Chengdu 610299, China
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277
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Russell MW, Kilian M, Mestecky J. Role of IgA1 protease-producing bacteria in SARS-CoV-2 infection and transmission: a hypothesis. mBio 2024:e0083324. [PMID: 39207101 DOI: 10.1128/mbio.00833-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
Secretory (S) IgA antibodies against severe acute respiratory syndrome (SARS)-CoV-2 are induced in saliva and upper respiratory tract (URT) secretions by natural infection and may be critical in determining the outcome of initial infection. Secretory IgA1 (SIgA1) is the predominant isotype of antibodies in these secretions. Neutralization of SARS-CoV-2 is most effectively accomplished by polymeric antibodies such as SIgA. We hypothesize that cleavage of SIgA1 antibodies against SARS-CoV-2 by unique bacterial IgA1 proteases to univalent Fabα antibody fragments with diminished virus neutralizing activity would facilitate the descent of the virus into the lungs to cause serious disease and also enhance its airborne transmission to others. Recent studies of the nasopharyngeal microbiota of patients with SARS-CoV-2 infection have revealed significant increases in the proportions of IgA1 protease-producing bacteria in comparison with healthy subjects. Similar considerations might apply also to other respiratory viral infections including influenza, possibly explaining the original attribution of influenza to Haemophilus influenzae, which produces IgA1 protease.
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Affiliation(s)
- Michael W Russell
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Mogens Kilian
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jiri Mestecky
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- 4Institute of Microbiology, laboratory of Cellular and Molecular Immunology, Czech Academy of Sciences, Prague, Czechia
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278
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Taboada-Castro H, Hernández-Álvarez AJ, Escorcia-Rodríguez JM, Freyre-González JA, Galán-Vásquez E, Encarnación-Guevara S. Rhizobium etli CFN42 and Sinorhizobium meliloti 1021 bioinformatic transcriptional regulatory networks from culture and symbiosis. FRONTIERS IN BIOINFORMATICS 2024; 4:1419274. [PMID: 39263245 PMCID: PMC11387232 DOI: 10.3389/fbinf.2024.1419274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/24/2024] [Indexed: 09/13/2024] Open
Abstract
Rhizobium etli CFN42 proteome-transcriptome mixed data of exponential growth and nitrogen-fixing bacteroids, as well as Sinorhizobium meliloti 1021 transcriptome data of growth and nitrogen-fixing bacteroids, were integrated into transcriptional regulatory networks (TRNs). The one-step construction network consisted of a matrix-clustering analysis of matrices of the gene profile and all matrices of the transcription factors (TFs) of their genome. The networks were constructed with the prediction of regulatory network application of the RhizoBindingSites database (http://rhizobindingsites.ccg.unam.mx/). The deduced free-living Rhizobium etli network contained 1,146 genes, including 380 TFs and 12 sigma factors. In addition, the bacteroid R. etli CFN42 network contained 884 genes, where 364 were TFs, and 12 were sigma factors, whereas the deduced free-living Sinorhizobium meliloti 1021 network contained 643 genes, where 259 were TFs and seven were sigma factors, and the bacteroid Sinorhizobium meliloti 1021 network contained 357 genes, where 210 were TFs and six were sigma factors. The similarity of these deduced condition-dependent networks and the biological E. coli and B. subtilis independent condition networks segregates from the random Erdös-Rényi networks. Deduced networks showed a low average clustering coefficient. They were not scale-free, showing a gradually diminishing hierarchy of TFs in contrast to the hierarchy role of the sigma factor rpoD in the E. coli K12 network. For rhizobia networks, partitioning the genome in the chromosome, chromids, and plasmids, where essential genes are distributed, and the symbiotic ability that is mostly coded in plasmids, may alter the structure of these deduced condition-dependent networks. It provides potential TF gen-target relationship data for constructing regulons, which are the basic units of a TRN.
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Affiliation(s)
| | | | | | | | - Edgardo Galán-Vásquez
- Institute of Applied Mathematics and in Systems (IIMAS), National Autonomous University of México, Mexico City, Mexico
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279
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Azua-Bustos A, González-Silva C, Freedman K, Carrizo D, Sánchez-García L, Fernández-Martínez MÁ, Balsera-Manzanero M, Muñoz-Iglesias V, Fernández-Sampedro M, Dang TQ, Vargas-Carrera C, Wierzchos J. Sea spray allows for the growth of subaerial microbialites at the driest desert on Earth. Sci Rep 2024; 14:19915. [PMID: 39198637 PMCID: PMC11358262 DOI: 10.1038/s41598-024-70447-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/16/2024] [Indexed: 09/01/2024] Open
Abstract
Due to its extreme conditions, microbial life in the Atacama Desert is known to survive in well-protected micro-habitats (hypolithic, endolithic, etc.), but rarely directly exposed to the environment, that is, epilithic habitats. Here we report a unique site, La Portada, a cliff confronting the Pacific Ocean in the Coastal Range of this desert, in which the constant input of water provided by the sea spray allows for the growth of a black-colored epilithic subaerial microbial ecosystem. Formed by a complex community of halophilic microorganisms belonging to the three domains of life, this ecosystem displays the typical three-dimensional structure of benthic microbialites, coherent with the presence of a diversity of cyanobacteria (including species from the genera that are known to form them), a constant high water activity and an ample availability of carbonate ions. From these microbialites we isolated Hortae werneckii, a fungal species which by producing melanin, not only explains the dark color of these microbialites, but may also play the role of protecting the whole community from extreme UV radiation. A number of biosignatures not only confirmed sea spray as the main source of water, but also suggests that one place to consider for the search of evidences of life on Mars would be on the paleo-coastlines that surrounded vanished oceans such as that on Aeolis Dorsa.
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Affiliation(s)
| | | | | | - Daniel Carrizo
- Centro de Astrobiología (CAB), CSIC-INTA, 28850, Madrid, Spain
| | | | - Miguel Ángel Fernández-Martínez
- Departamento de Ecología, Facultad de Ciencias, Universidad Autónoma de Madrid y Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Madrid, Spain
| | | | - Victoria Muñoz-Iglesias
- Centro de Astrobiología (CAB), CSIC-INTA, 28850, Madrid, Spain
- Laboratoire de Planétologie et Géosciences, CNRS, LPG UMR 6112, Nantes Université, Univ Angers, Le Mans Université, 44000, Nantes, France
| | | | | | | | - Jacek Wierzchos
- Museo Nacional de Ciencias Naturales (CSIC), 28006, Madrid, Spain
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280
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Reifenberg P, Zimmer A. Branched-chain amino acids: physico-chemical properties, industrial synthesis and role in signaling, metabolism and energy production. Amino Acids 2024; 56:51. [PMID: 39198298 PMCID: PMC11358235 DOI: 10.1007/s00726-024-03417-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024]
Abstract
Branched-chain amino acids (BCAAs)-leucine (Leu), isoleucine (Ile), and valine (Val)-are essential nutrients with significant roles in protein synthesis, metabolic regulation, and energy production. This review paper offers a detailed examination of the physico-chemical properties of BCAAs, their industrial synthesis, and their critical functions in various biological processes. The unique isomerism of BCAAs is presented, focusing on analytical challenges in their separation and quantification as well as their solubility characteristics, which are crucial for formulation and purification applications. The industrial synthesis of BCAAs, particularly using bacterial strains like Corynebacterium glutamicum, is explored, alongside methods such as genetic engineering aimed at enhancing production, detailing the enzymatic processes and specific precursors. The dietary uptake, distribution, and catabolism of BCAAs are reviewed as fundamental components of their physiological functions. Ultimately, their multifaceted impact on signaling pathways, immune function, and disease progression is discussed, providing insights into their profound influence on muscle protein synthesis and metabolic health. This comprehensive analysis serves as a resource for understanding both the basic and complex roles of BCAAs in biological systems and their industrial application.
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Affiliation(s)
- Philipp Reifenberg
- Merck Life Science KGaA, Upstream R&D, Frankfurter Strasse 250, 64293, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich‑Weiss‑Strasse 4, 64287, Darmstadt, Germany
| | - Aline Zimmer
- Merck Life Science KGaA, Upstream R&D, Frankfurter Strasse 250, 64293, Darmstadt, Germany.
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281
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Tenore A, Russo F, Jacob J, Grattepanche JD, Buttaro B, Klapper I. A Mathematical Model of Diel Activity and Long Time Survival in Phototrophic Mixed-Species Subaerial Biofilms. Bull Math Biol 2024; 86:123. [PMID: 39196435 PMCID: PMC11358337 DOI: 10.1007/s11538-024-01348-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 08/01/2024] [Indexed: 08/29/2024]
Abstract
Subaerial biofilms (SAB) are intricate microbial communities living on terrestrial surfaces, of interest in a variety of contexts including cultural heritage preservation, microbial ecology, biogeochemical cycling, and biotechnology. Here we propose a mathematical model aimed at better understanding the interplay between cyanobacteria and heterotrophic bacteria, common microbial SAB constituents, and their mutual dependence on local environmental conditions. SABs are modeled as thin mixed biofilm-liquid water layers sitting on stone. A system of ordinary differential equations regulates the dynamics of key SAB components: cyanobacteria, heterotrophs, polysaccharides and decayed biomass, as well as cellular levels of organic carbon, nitrogen and energy. These components are interconnected through a network of energetically dominant metabolic pathways, modeled with limitation terms reflecting the impact of biotic and abiotic factors. Daily cylces of temperature, humidity, and light intensity are considered as input model variables that regulate microbial activity by influencing water availability and metabolic kinetics. Relevant physico-chemical processes, including pH regulation, further contribute to a description of the SAB ecology. Numerical simulations explore the dynamics of SABs in a real-world context, revealing distinct daily activity periods shaped by water activity and light availability, as well as longer time scale survivability conditions. Results also suggest that heterotrophs could play a substantial role in decomposing non-volatile carbon compounds and regulating pH, thus influencing the overall composition and stability of the biofilm.
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Affiliation(s)
- A Tenore
- Department of Mathematics and Applications, University of Naples Federico II, Naples, Italy.
| | - F Russo
- Department of Mathematics and Applications, University of Naples Federico II, Naples, Italy
| | - J Jacob
- U.S. National Park Service, North Atlantic-Appalachian Region, Historic Architecture, Conservation, and Engineering Program, New York, USA
| | | | - B Buttaro
- Sol Sherry Thrombosis Research Center, Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - I Klapper
- Department of Mathematics, Temple University, Philadelphia, PA, USA
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282
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Lee H, Chaudhary DK, Kim DU. Paenibacillus gyeongsangnamensis sp. nov., Isolated from Soil. J Microbiol Biotechnol 2024; 34:1636-1641. [PMID: 39086223 PMCID: PMC11380503 DOI: 10.4014/jmb.2404.04038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/16/2024] [Accepted: 05/31/2024] [Indexed: 08/02/2024]
Abstract
A Gram-stain-positive, aerobic, white-coloured, rod-shaped bacteria, designated as a strain dW9T, was isolated from soil. Strain dW9T was catalase-positive and oxidase-negative. Strain dW9T grew at temperature of 20-37°C and at pH of 5.0-7.0. Phylogenetic and 16S rRNA gene analysis indicated that strain dW9T belonged to the genus Paenibacillus with its closest relative being Paenibacillus filicis S4T (97.4% sequence similarity). The genome size of dW9T was 7,787,916 bp with DNA G+C content of 51.3%. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of dW9T with its closest relatives were found to be <22.0% and <74.0%, respectively. The only respiratory quinone was MK-7, and the major fatty acids were antiso-C15:0 and iso-C16:0. Overall, the comprehensive taxonomic analysis revealed that strain dW9T met all the fundamental criteria to be classified as a novel species within the genus Paenibacillus. Accordingly, we propose the name Paenibacillus gyeongsangnamensis sp. nov., with the type strain dW9T (=KCTC 43431T =NBRC 116022T).
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Affiliation(s)
- Hyosun Lee
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju 26339, Republic of Korea
| | | | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju 26339, Republic of Korea
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283
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Akbarzadeh S, Coşkun Ö, Günçer B. Studying protein-protein interactions: Latest and most popular approaches. J Struct Biol 2024; 216:108118. [PMID: 39214321 DOI: 10.1016/j.jsb.2024.108118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
PPIs, or protein-protein interactions, are essential for many biological processes. According to the findings, abnormal PPIs have been linked to several diseases, such as cancer and infectious and neurological disorders. Consequently, focusing on PPIs is a path toward disease treatment and a crucial tool for producing novel medications. Many methods exist to investigate PPIs, including low- and high-throughput studies. Since many PPIs have been discovered using in vitro and in vivo experimental approaches, the use of computational methods to predict PPIs has grown due to the expanding scale of PPI data and the intrinsic complexity of interacting mechanisms. Recognizing PPI networks offers a systematic means of predicting protein functions, and pathways that are included. These investigations can help uncover the underlying molecular mechanisms of complex phenotypes and clarify the biological processes related to health and diseases. Therefore, our goal in this study is to provide an overview of the latest and most popular approaches for investigating PPIs. We also overview some important clinical approaches based on the PPIs and how these interactions can be targeted.
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Affiliation(s)
- Sama Akbarzadeh
- Department of Biophysics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye; Institute of Graduate Studies in Health Sciences, Istanbul University, Istanbul, Türkiye
| | - Özlem Coşkun
- Department of Biophysics, Faculty of Medicine, Çanakkale Onsekiz Mart University, Çanakkale, Türkiye
| | - Başak Günçer
- Department of Biophysics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye.
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284
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Reed KB, Kim W, Lu H, Larue CT, Guo S, Brooks SM, Montez MR, Wagner JW, Zhang YJ, Alper HS. Evolving dual-trait EPSP synthase variants using a synthetic yeast selection system. Proc Natl Acad Sci U S A 2024; 121:e2317027121. [PMID: 39159366 PMCID: PMC11363307 DOI: 10.1073/pnas.2317027121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 07/13/2024] [Indexed: 08/21/2024] Open
Abstract
The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) functions in the shikimate pathway which is responsible for the production of aromatic amino acids and precursors of other essential secondary metabolites in all plant species. EPSPS is also the molecular target of the herbicide glyphosate. While some plant EPSPS variants have been characterized with reduced glyphosate sensitivity and have been used in biotechnology, the glyphosate insensitivity typically comes with a cost to catalytic efficiency. Thus, there exists a need to generate additional EPSPS variants that maintain both high catalytic efficiency and high glyphosate tolerance. Here, we create a synthetic yeast system to rapidly study and evolve heterologous EPSP synthases for these dual traits. Using known EPSPS variants, we first validate that our synthetic yeast system is capable of recapitulating growth characteristics observed in plants grown in varying levels of glyphosate. Next, we demonstrate that variants from mutagenesis libraries with distinct phenotypic traits can be isolated depending on the selection criteria applied. By applying strong dual-trait selection pressure, we identify a notable EPSPS mutant after just a single round of evolution that displays robust glyphosate tolerance (Ki of nearly 1 mM) and improved enzymatic efficiency over the starting point (~2.5 fold). Finally, we show the crystal structure of corn EPSPS and the top resulting mutants and demonstrate that certain mutants have the potential to outperform previously reported glyphosate-resistant EPSPS mutants, such as T102I and P106S (denoted as TIPS), in whole-plant testing. Altogether, this platform helps explore the trade-off between glyphosate resistance and enzymatic efficiency.
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Affiliation(s)
- Kevin B. Reed
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - Wantae Kim
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - Hongyuan Lu
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | | | - Shirley Guo
- Crop Science Division, Bayer, Chesterfield, MO63017
| | - Sierra M. Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - Michael R. Montez
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - James W. Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - Y. Jessie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX78712
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX78712
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285
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Pyle JD, Lund SR, O'Toole KH, Saleh L. Virus-encoded glycosyltransferases hypermodify DNA with diverse glycans. Cell Rep 2024; 43:114631. [PMID: 39154342 DOI: 10.1016/j.celrep.2024.114631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 07/08/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024] Open
Abstract
Enzymatic modification of DNA nucleobases can coordinate gene expression, nuclease protection, or mutagenesis. We recently discovered a clade of phage-specific cytosine methyltransferase (MT) and 5-methylpyrimidine dioxygenase (5mYOX) enzymes that produce 5-hydroxymethylcytosine (5hmC) as a precursor for enzymatic hypermodifications on viral genomes. Here, we identify phage MT- and 5mYOX-associated glycosyltransferases (GTs) that catalyze linkage of diverse sugars to 5hmC nucleobase substrates. Metavirome mining revealed thousands of biosynthetic gene clusters containing enzymes with predicted roles in cytosine sugar hypermodification. We developed a platform for high-throughput screening of GT-containing pathways, relying on the Escherichia coli metabolome as a substrate pool. We successfully reconstituted several pathways and isolated diverse sugar modifications appended to cytosine, including mono-, di-, or tri-saccharides comprised of hexoses, N-acetylhexosamines, or heptose. These findings expand our knowledge of hypermodifications on nucleic acids and the origins of corresponding sugar-installing enzymes.
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Affiliation(s)
- Jesse D Pyle
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Sean R Lund
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Katherine H O'Toole
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Lana Saleh
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA.
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286
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Nogawa S, Morishita S, Saito K, Kato H. Genome-wide association meta-analysis identifies two novel loci associated with dental caries. BMC Oral Health 2024; 24:1003. [PMID: 39192244 PMCID: PMC11348739 DOI: 10.1186/s12903-024-04799-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 08/23/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND Tooth loss significantly impacts oral function and overall health deterioration. Dental caries and periodontal disease are major contributors to tooth loss, emphasizing the critical need to prevent these conditions. Genetic studies have played a crucial role in deepening our understanding of the underlying mechanisms of these diseases. While large-scale genome-wide association studies (GWAS) on dental caries and periodontal disease have been conducted extensively, research focusing on Asian populations remains limited. Given substantial genetic and lifestyle variations across ethnicities, conducting studies across diverse populations is imperative. This study aimed to uncover new insights into the genetic mechanisms of these diseases, contributing to broader knowledge and potential targeted interventions. METHODS We conducted a GWAS using genome data from 45,525 Japanese individuals, assessing their self-reported history of dental caries and periodontal disease. Additionally, we performed a meta-analysis by integrating our results with those from a previous large-scale GWAS predominantly involving European populations. RESULTS While no new loci associated with periodontal disease were identified, we discovered two novel loci associated with dental caries. The lead variants of these loci were intron variant rs10974056 in GLIS3 and intron variant rs4801882 in SIGLEC5. CONCLUSION Our study findings are anticipated to advance understanding of the underlying mechanisms of dental caries and periodontal disease. Thes insights may inform better management strategies for patients affected by these conditions.
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Affiliation(s)
- Shun Nogawa
- Genequest Inc, Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Satoru Morishita
- Research and Development Headquarters, Lion Corporation, Odawara, Kanagawa, Japan
| | - Kenji Saito
- Genequest Inc, Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Hisanori Kato
- Laboratory of Health Nutrition, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Department of Applied Nutrition, School of Nutrition, Kagawa Nutrition University, 3-9-21 Chiyoda, Sakado, 350-0299, Saitama, Japan.
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287
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Ingmer H, Leisner JJ, Fulaz S. Forssman and the staphylococcal hemolysins. APMIS 2024. [PMID: 39188243 DOI: 10.1111/apm.13459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/05/2024] [Indexed: 08/28/2024]
Abstract
Forssman was a Swedish pathologist and microbiologist who, in the 1920s and 1930s conducted a long series of experiments that led to unique insights into surface antigens of blood cells, as well as added to the discrimination of toxins produced by staphylococci that lyse red blood cells. This review takes offset in the studies published by Forssman in APMIS addressing the hemolytic properties of staphylococcal toxins displayed against erythrocytes of animal and human origin. In light of current knowledge, we will discuss the insights we now have and how they may pave the way for curing infections with pathogenic staphylococci, including Staphylococcus aureus.
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Affiliation(s)
- Hanne Ingmer
- Department of Veterinary and Animal Science, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen J Leisner
- Department of Veterinary and Animal Science, University of Copenhagen, Copenhagen, Denmark
| | - Stephanie Fulaz
- Department of Veterinary and Animal Science, University of Copenhagen, Copenhagen, Denmark
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288
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Salasar Moghaddam F, Tabibian M, Absalan M, Tavoosidana G, Ghahremani MH, Tabatabaei N, Abdolhosseini M, Shafiee Sabet M, Motevaseli E. Comparative analysis of Escherichia coli Nissle 1917 ghosts quality: a study of two chemical methods. Arch Microbiol 2024; 206:386. [PMID: 39190149 DOI: 10.1007/s00203-024-04095-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 07/25/2024] [Accepted: 07/28/2024] [Indexed: 08/28/2024]
Abstract
The gram-negative bacterium Escherichia coli Nissle 1917 (EcN) has long been recognized for its therapeutic potential in treating various intestinal diseases. Bacterial ghosts (BGs) are empty shells of non-living bacterial cells that demonstrate enormous potential for medicinal applications. Genetic and chemical techniques can create these BGs. In the current study, we produced Escherichia coli Nissle 1917 ghosts (EcNGs) for the first time using benzoic acid (BA) and sodium hydroxide (SH). BA is a feeble acidic chemical that enhances gram-negative bacteria's external membrane permeability, reduces energy production, and decreases internal pH. SH has shown success in producing BGs from some gram-negative and gram-positive organisms. This research aims to produce EcNGs using the minimum inhibitory concentration (MIC) of SH and BA, specifically 3.125 mg/mL. We assessed the bacterial quality of the BGs produced using quantitative PCR (qPCR) and Bradford protein assays. Field emission scanning electron microscopy (FE-SEM) showed the three-dimensional structure of EcNGs. The study confirmed the presence of tunnel-like pores on the outer surface, indicating the preservation of cell membrane integrity. Importantly, this investigation introduces BA as a novel chemical inducer of EcNGs, suggesting its potential alongside SH for efficient EcNG formation.
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Affiliation(s)
- Fahimeh Salasar Moghaddam
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mobina Tabibian
- Department of Cellular and Molecular Biology, Faculty of Life Sciences and Biotechnologies, Shahid Beheshti University, Tehran, Iran
| | - Moloud Absalan
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholamreza Tavoosidana
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hossein Ghahremani
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Pharmacology-Toxicology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Nasrollah Tabatabaei
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mansoreh Abdolhosseini
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Shafiee Sabet
- Department of Neurology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Elahe Motevaseli
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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289
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Ruan J, Yang Y, Carrière Y, Wu Y. Development of resistance monitoring for Helicoverpa armigera (Lepidoptera: Noctuidae) resistance to pyramided Bt cotton in China. JOURNAL OF ECONOMIC ENTOMOLOGY 2024:toae194. [PMID: 39186571 DOI: 10.1093/jee/toae194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/26/2024] [Accepted: 08/09/2024] [Indexed: 08/28/2024]
Abstract
The cotton bollworm, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae), is a significant cotton pest worldwide. Bacillus thuringiensis (Bt) cotton producing Cry1Ac has been used since 1997 for the control of this pest in China and a significant increase in H. armigera resistance to Cry1Ac has occurred in northern China. To mitigate resistance evolution, it is necessary to develop and plant pyramided 2- and 3-toxin Bt cotton to replace Cry1Ac cotton. For sustainable use of pyramided Bt cotton, we used diet overlay bioassays to measure the baseline susceptibility of H. armigera to Cry2Ab in 33 populations collected in 2017, 2018, and 2021 in 12 locations from major cotton-producing areas of China. The lethal concentration killing 50% (LC50) or 99% (LC99) of individuals from the populations ranged from 0.030 to 0.138 µg/cm2 and 0.365 to 2.964 µg/cm2, respectively. The ratio of the LC50 for the most resistant and susceptible population was 4.6, indicating moderate among-population variability in resistance. The susceptibility of H. armigera to Cry2Ab did not vary significantly over years. A diagnostic concentration of 2 µg/cm2 was calculated as twice the LC99 from an analysis of pooled data for the field-collected populations. This concentration discriminated well between susceptible and resistant individuals, as it killed all larvae from a susceptible laboratory strain and 0%, 0%, and 23% of larvae from 3 laboratory strains with > 100-fold resistance to Cry2Ab. These baseline susceptibility data and diagnostic concentration for Cry2Ab will be useful for monitoring the evolution of H. armigera resistance to pyramided Bt cotton in China.
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Affiliation(s)
- Jianqiu Ruan
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Yihua Yang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Yves Carrière
- Department of Entomology, The University of Arizona, Tucson, AZ, USA
| | - Yidong Wu
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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290
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Awal SK, Swu AK. Beyond the Bite: Detailed findings on Chikungunya and Dengue co-detection in Punjab, North India - clinical insights and diagnostic challenges. Braz J Microbiol 2024:10.1007/s42770-024-01493-w. [PMID: 39222222 DOI: 10.1007/s42770-024-01493-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
OBJECTIVES The co-circulation of Chikungunya virus (CHIKV) and Dengue virus (DENV) in India poses a challenge for the diagnosing clinician, as they share similar clinical signs and symptoms and geographical distribution. Both arthropod-borne viruses are maintained in the environment by the Aedes mosquito, commonly found in tropical countries including India. Here we aim to investigate the clinical and laboratory aspects of Chikungunya/Dengue suspected cases in Punjab, India during 2021-2022, focusing on the differential diagnosis of Dengue. METHODS All suspected cases were submitted to serological differential diagnosis approaches to arboviruses like Chikungunya and Dengue. For the detection of Chikungunya Infection, CHIK IgM Capture ELISA was employed. Whereas, for Dengue NS1 antigen ELISA and IgM Capture ELISA assays were employed. RESULTS A total of 370 cases suspected of arboviral infection were investigated and 38.3% (142/370) were confirmed as Chikungunya. Chikungunya cases were slightly more prevalent in males (54%) and the most frequently affected age group was adults between 16 and 30 years old (45.7%). Polyarthralgia affected 79.5% of patients, 63.3% exhibited headache and 50% presented with retro-orbital pain. 28.9% (107/370) had serological evidence of DENV exposure by detection of specific anti-DENV IgM or NS1 and 9.1% (34/370) cases of co-detection of Chikungunya and Dengue were reported. Urban populations had a higher infection rate of co-detection of Chikungunya and Dengue than rural populations with 83% versus 17%, respectively. CONCLUSIONS Despite an initial clinical diagnosis of Dengue, most patients with fever and arthralgia were serologically confirmed as Chikungunya cases, with a notable prevalence of CHIKV/DENV co-detection. Strengthening differential diagnosis of circulating arboviruses is crucial for improving patient care and enhancing vector control and environmental management strategies.
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Affiliation(s)
- Sampreet Kaur Awal
- Department of Microbiology, Manipal Tata Medical College, Manipal Academy of Higher Education, Manipal, India.
| | - Anato K Swu
- Consultant Microbiologist & Head of Laboratory Services Putuonuo Hospital, Kohima, Nagaland, India
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291
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Chen X, Wei Y, Meng G, Wang M, Peng X, Dai J, Dong C, Huo G. Telomere-to-Telomere Haplotype-Resolved Genomes of Agrocybe chaxingu Reveals Unique Genetic Features and Developmental Insights. J Fungi (Basel) 2024; 10:602. [PMID: 39330362 PMCID: PMC11433599 DOI: 10.3390/jof10090602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/19/2024] [Accepted: 08/23/2024] [Indexed: 09/28/2024] Open
Abstract
Agrocybe chaxingu is a widely cultivated edible fungus in China, which is rich in nutrients and medicinal compounds. However, the lack of a high-quality genome hinders further research. In this study, we assembled the telomere-to-telomere genomes of two sexually compatible monokaryons (CchA and CchB) derived from a primarily cultivated strain AS-5. The genomes of CchA and CchB were 50.60 Mb and 51.66 Mb with contig N50 values of 3.95 Mb and 3.97 Mb, respectively. Each contained 13 complete chromosomes with telomeres at both ends. The high mapping rate, uniform genome coverage, high LAI score, all BUSCOs with 98.5%, and all base accuracy exceeding 99.999% indicated the high level of integrity and quality of these two assembled genomes. Comparison of the two genomes revealed that approximately 30% of the nucleotide sequences between homologous chromosomes were non-syntenic, including 19 translocations, 36 inversions, and 15 duplications. An additional gene CchA_000467 was identified at the Mat A locus of CchA, which was observed exclusively in the Cyclocybe cylindracea species complex. A total of 613 (4.26%) and 483 (3.4%) unique genes were identified in CchA and CchB, respectively, with over 80% of these being hypothetical proteins. Transcriptomic analysis revealed that the expression levels of unique genes in CchB were significantly higher than those in CchA, and both CchA and CchB had unique genes specifically expressed at stages of mycelium and fruiting body. It was indicated that the growth and development of the A. chaxingu strain AS-5 required the coordinated action of two different nuclei, with CchB potentially playing a more significant role. These findings contributed to a more profound comprehension of the growth and developmental processes of basidiomycetes.
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Affiliation(s)
- Xutao Chen
- Jiangxi Key Laboratory for Excavation and Utilization of Agricultural Microorganisms, Jiangxi Agricultural University, Nanchang 330045, China;
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (G.M.); (M.W.)
- Jiangxi Provincial Key Laboratory of Agricultural Non-Point Source Pollution Control and Waste Comprehensive Utilization, Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China; (Y.W.); (X.P.); (J.D.)
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yunhui Wei
- Jiangxi Provincial Key Laboratory of Agricultural Non-Point Source Pollution Control and Waste Comprehensive Utilization, Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China; (Y.W.); (X.P.); (J.D.)
| | - Guoliang Meng
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (G.M.); (M.W.)
| | - Miao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (G.M.); (M.W.)
| | - Xinhong Peng
- Jiangxi Provincial Key Laboratory of Agricultural Non-Point Source Pollution Control and Waste Comprehensive Utilization, Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China; (Y.W.); (X.P.); (J.D.)
| | - Jiancheng Dai
- Jiangxi Provincial Key Laboratory of Agricultural Non-Point Source Pollution Control and Waste Comprehensive Utilization, Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China; (Y.W.); (X.P.); (J.D.)
| | - Caihong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (G.M.); (M.W.)
| | - Guanghua Huo
- Jiangxi Key Laboratory for Excavation and Utilization of Agricultural Microorganisms, Jiangxi Agricultural University, Nanchang 330045, China;
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292
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Buglione M, Rivieccio E, Aceto S, Paturzo V, Biondi C, Fulgione D. The Domestication of Wild Boar Could Result in a Relaxed Selection for Maintaining Olfactory Capacity. Life (Basel) 2024; 14:1045. [PMID: 39202786 PMCID: PMC11355481 DOI: 10.3390/life14081045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024] Open
Abstract
Domesticated animals are artificially selected to exhibit desirable traits, however not all traits of domesticated animals are the result of deliberate selection. Loss of olfactory capacity in the domesticated pig (Sus scrofa domesticus) is one example. We used whole transcriptome analysis (RNA-Seq) to compare patterns of gene expression in the olfactory mucosa of the pig and two subspecies of wild boar (Sus scrofa), and investigate candidate genes that could be responsible for the loss of olfactory capacity. We identified hundreds of genes with reductions in transcript abundance in pig relative to wild boar as well as differences between the two subspecies of wild boar. These differences were detected mainly in genes involved in the formation and motility of villi, cilia and microtubules, functions associated with olfaction. In addition, differences were found in the abundances of transcripts of genes related to immune defenses, with the highest levels in continental wild boar subspecies. Overall, the loss of olfactory capacity in pigs appears to have been accompanied by reductions in the expression of candidate genes for olfaction. These changes could have resulted from unintentional selection for reduced olfactory capacity, relaxed selection for maintaining olfactory capacity, pleiotropic effects of genes under selection, or other non-selective processes. Our findings could be a cornerstone for future researches on wild boars, pigs, feral populations, and their evolutionary trajectories, aimed to provide tools to better calibrate species management as well as guidelines for breeders.
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Affiliation(s)
- Maria Buglione
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
| | - Eleonora Rivieccio
- Department of Humanities Studies, University of Naples Federico II, 80133 Naples, Italy;
| | - Serena Aceto
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
| | - Vincenzo Paturzo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
| | - Carla Biondi
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
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293
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Coleman HJ, Yang Q, Robert A, Padgette H, Funke HH, Catalano CE, Randolph TW. Formulation of three tailed bacteriophages by spray-drying and atomic layer deposition for thermal stability and controlled release. J Pharm Sci 2024:S0022-3549(24)00305-8. [PMID: 39173744 DOI: 10.1016/j.xphs.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/08/2024] [Accepted: 08/08/2024] [Indexed: 08/24/2024]
Abstract
Deep infection is the second most common complication of arthroplasty following loosening of the implant. Antibiotic-loaded bone cements (ALBCs) and high concentrations of systemic broad-spectrum antibiotics are commonly used to prevent infections following injury and surgery. However, clinical data fails to show that ALBCs are effective against deep infection, and negative side effects can result following prolonged administration of antibiotics. Additionally, the rise of multidrug resistant (MDR) bacteria provides an urgent need for alternatives to broad-spectrum antibiotics. Phage therapy, or the use of bacteriophages (viruses that infect bacteria) to target pathogenic bacteria, might offer a safe alternative to combat MDR bacteria. Application of phage therapy in the setting of deep infections requires formulation strategies that would stabilize bacteriophage against chemical and thermal stress during bone-cement polymerization, that maintain bacteriophage activity for weeks or months at physiological temperatures, and that allow for sustained release of phage to combat slow-growing, persistent bacteria. Here, we demonstrate the formulation of three phages that target diverse bacterial pathogens, which includes spray-drying of the particles for enhanced thermal stability at 37 °C and above. Additionally, we use atomic layer deposition (ALD) to coat spray-dried powders with alumina to allow for delayed release of phage from the dry formulations, and potentially protect phage against chemical damage during bone cement polymerization. Together, these findings present a strategy to formulate phages that possess thermal stability and sustained release properties for use in deep infections.
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Affiliation(s)
- Holly J Coleman
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, CO, 80303, USA
| | - Qin Yang
- Department of Pharmaceutical Chemistry, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Amanda Robert
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, CO, 80303, USA
| | - Hannah Padgette
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, CO, 80303, USA
| | - Hans H Funke
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, CO, 80303, USA
| | - Carlos E Catalano
- Department of Pharmaceutical Chemistry, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Theodore W Randolph
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, CO, 80303, USA.
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294
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Schmitz LM, Kreitli N, Obermaier L, Weber N, Rychlik M, Angenent LT. Power-to-vitamins: producing folate (vitamin B 9) from renewable electric power and CO 2 with a microbial protein system. Trends Biotechnol 2024:S0167-7799(24)00177-X. [PMID: 39271416 DOI: 10.1016/j.tibtech.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 09/15/2024]
Abstract
We recently proposed a two-stage Power-to-Protein technology to produce microbial protein from renewable electric power and CO2. Two stages were operated in series: Clostridium ljungdahlii in Stage A to reduce CO2 with H2 into acetate, and Saccharomyces cerevisiae in Stage B to utilize O2 and produce microbial protein from acetate. Renewable energy can be used to power water electrolysis to produce H2 and O2. A drawback of Stage A was the need for continuous vitamin supplementation. In this study, by using the more robust thermophilic acetogen Thermoanaerobacter kivui instead of C. ljungdahlii, vitamin supplementation was no longer needed. Additionally, S. cerevisiae produced folate when grown with acetate as a sole carbon source, achieving a total folate concentration of 6.7 mg per 100 g biomass with an average biomass concentration of 3 g l-1. The developed Power-to-Vitamin system enables folate production from renewable power and CO2 with zero or negative net-carbon emissions.
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Affiliation(s)
- Lisa Marie Schmitz
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, 72074 Tübingen, Germany
| | - Nicolai Kreitli
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, 72074 Tübingen, Germany
| | - Lisa Obermaier
- Analytical Food Chemistry, Technical University of Munich, 85354 Freising, Germany
| | - Nadine Weber
- Analytical Food Chemistry, Technical University of Munich, 85354 Freising, Germany
| | - Michael Rychlik
- Analytical Food Chemistry, Technical University of Munich, 85354 Freising, Germany
| | - Largus T Angenent
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, 72074 Tübingen, Germany; AG Angenent, Max Planck Institute for Biology, Max Planck Ring 5, D-72076 Tübingen, Germany; Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10D, 8000Aarhus C, Denmark; The Novo Nordisk Foundation CO(2) Research Center (CORC), Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, C, Denmark; Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72074 Tübingen, Germany.
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295
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Mai LD, Wimberley SC, Champion JA. Intracellular delivery strategies using membrane-interacting peptides and proteins. NANOSCALE 2024; 16:15465-15480. [PMID: 39091235 PMCID: PMC11340348 DOI: 10.1039/d4nr02093f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
While the cellular cytosol and organelles contain attractive targets for disease treatments, it remains a challenge to deliver therapeutic biomacromolecules to these sites. This is due to the selective permeability of the plasma and endosomal membranes, especially for large and hydrophilic therapeutic cargos such as proteins and nucleic acids. In response, many different delivery systems and molecules have been devised to help therapeutics cross these barriers to reach cytosolic targets. Among them are peptide and protein-based systems, which have several advantages over other natural and synthetic materials including their ability to interact with cell membranes. In this review, we will describe recent advances and current challenges of peptide and protein strategies that leverage cell membrane association and modulation to enable cytosolic delivery of biomacromolecule cargo. The approaches covered here include peptides and proteins derived from or inspired by natural sequences as well as those designed de novo for delivery function.
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Affiliation(s)
- Linh D Mai
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Dr NW, Atlanta, GA, 30332-2000, USA.
| | - Sydney C Wimberley
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Dr NW, Atlanta, GA, 30332-2000, USA.
- BioEngineering Program, Georgia Institute of Technology, USA
| | - Julie A Champion
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Dr NW, Atlanta, GA, 30332-2000, USA.
- BioEngineering Program, Georgia Institute of Technology, USA
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296
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Vanthienen W, Fernández-García J, Baietti MF, Claeys E, Van Leemputte F, Nguyen L, Goossens V, Deparis Q, Broekaert D, Vlayen S, Audenaert D, Delforge M, D'Amuri A, Van Zeebroeck G, Leucci E, Fendt SM, Thevelein JM. The novel family of Warbicin ® compounds inhibits glucose uptake both in yeast and human cells and restrains cancer cell proliferation. Front Oncol 2024; 14:1411983. [PMID: 39239276 PMCID: PMC11374660 DOI: 10.3389/fonc.2024.1411983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/29/2024] [Indexed: 09/07/2024] Open
Abstract
Many cancer cells share with yeast a preference for fermentation over respiration, which is associated with overactive glucose uptake and breakdown, a phenomenon called the Warburg effect in cancer cells. The yeast tps1Δ mutant shows even more pronounced hyperactive glucose uptake and phosphorylation causing glycolysis to stall at GAPDH, initiation of apoptosis through overactivation of Ras and absence of growth on glucose. The goal of the present work was to use the yeast tps1Δ strain to screen for novel compounds that would preferentially inhibit overactive glucose influx into glycolysis, while maintaining basal glucose catabolism. This is based on the assumption that the overactive glucose catabolism of the tps1Δ strain might have a similar molecular cause as the Warburg effect in cancer cells. We have isolated Warbicin ® A as a compound restoring growth on glucose of the yeast tps1Δ mutant, showed that it inhibits the proliferation of cancer cells and isolated structural analogs by screening directly for cancer cell inhibition. The Warbicin ® compounds are the first drugs that inhibit glucose uptake by both yeast Hxt and mammalian GLUT carriers. Specific concentrations did not evoke any major toxicity in mice but increase the amount of adipose tissue likely due to reduced systemic glucose uptake. Surprisingly, Warbicin ® A inhibition of yeast sugar uptake depends on sugar phosphorylation, suggesting transport-associated phosphorylation as a target. In vivo and in vitro evidence confirms physical interaction between yeast Hxt7 and hexokinase. We suggest that reversible transport-associated phosphorylation by hexokinase controls the rate of glucose uptake through hydrolysis of the inhibitory ATP molecule in the cytosolic domain of glucose carriers and that in yeast tps1Δ cells and cancer cells reversibility is compromised, causing constitutively hyperactive glucose uptake and phosphorylation. Based on their chemical structure and properties, we suggest that Warbicin ® compounds replace the inhibitory ATP molecule in the cytosolic domain of the glucose carriers, preventing hexokinase to cause hyperactive glucose uptake and catabolism.
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Affiliation(s)
- Ward Vanthienen
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
| | - Juan Fernández-García
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Maria Francesca Baietti
- TRACE PDX Platform, Laboratory of RNA Cancer Biology, LKI Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Elisa Claeys
- TRACE PDX Platform, Laboratory of RNA Cancer Biology, LKI Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Frederik Van Leemputte
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
| | - Long Nguyen
- Screening Core, VIB, Ghent, Belgium
- Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Vera Goossens
- Screening Core, VIB, Ghent, Belgium
- Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Quinten Deparis
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
| | - Dorien Broekaert
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Sophie Vlayen
- LKI Leuven Cancer Institute Leuven, KU Leuven, Leuven, Belgium
| | - Dominique Audenaert
- Screening Core, VIB, Ghent, Belgium
- Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Michel Delforge
- LKI Leuven Cancer Institute Leuven, KU Leuven, Leuven, Belgium
| | | | - Griet Van Zeebroeck
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
| | - Eleonora Leucci
- TRACE PDX Platform, Laboratory of RNA Cancer Biology, LKI Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Sarah-Maria Fendt
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Johan M Thevelein
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- NovelYeast bv, Bio-Incubator, BIO4, Leuven-Heverlee, Belgium
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297
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Jung H, Inaba Y, Banta S. CRISPR/dCas12a knock-down of Acidithiobacillus ferrooxidans electron transport chain bc 1 complexes enables enhanced metal sulfide bioleaching. J Biol Chem 2024; 300:107703. [PMID: 39173952 PMCID: PMC11421330 DOI: 10.1016/j.jbc.2024.107703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 08/24/2024] Open
Abstract
Acidithiobacillus ferrooxidans is an acidophilic chemolithoautotroph that plays an important role in biogeochemical iron and sulfur cycling and is a member of the consortia used in industrial hydrometallurgical processing of copper. Metal sulfide bioleaching is catalyzed by the regeneration of ferric iron; however, bioleaching of chalcopyrite, the dominant unmined form of copper on Earth, is inhibited by surface passivation. Here, we report the implementation of CRISPR interference (CRISPRi) using the catalytically inactive Cas12a (dCas12a) in A. ferrooxidans to knock down the expression of genes in the petI and petII operons. These operons encode bc1 complex proteins and knockdown of these genes enabled the manipulation (enhancement or repression) of iron oxidation. The petB2 gene knockdown strain enhanced iron oxidation, leading to enhanced pyrite and chalcopyrite oxidation, which correlated with reduced biofilm formation and decreased surface passivation of the minerals. These findings highlight the utility of CRISPRi/dCas12a technology for engineering A. ferrooxidans while unveiling a new strategy to manipulate and improve bioleaching efficiency.
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Affiliation(s)
- Heejung Jung
- Department of Chemical Engineering, Columbia University, New York, New York, USA
| | - Yuta Inaba
- Department of Chemical Engineering, Columbia University, New York, New York, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York, USA.
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298
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Lam NM, Tsang TF, Qu J, Tsang MW, Tao Y, Kan CH, Zou Q, Chan KH, Chu AJ, Ma C, Yang X. Development of a luciferase-based Gram-positive bacterial reporter system for the characterization of antimicrobial agents. Appl Environ Microbiol 2024; 90:e0071724. [PMID: 39016615 PMCID: PMC11337827 DOI: 10.1128/aem.00717-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 06/24/2024] [Indexed: 07/18/2024] Open
Abstract
Mechanistic investigations are of paramount importance in elucidating the modes of action of antibiotics and facilitating the discovery of novel drugs. We reported a luciferase-based reporter system using bacterial cells to unveil mechanisms of antimicrobials targeting transcription and translation. The reporter gene Nluc encoding NanoLuciferase (NanoLuc) was integrated into the genome of the Gram-positive model organism, Bacillus subtilis, to generate a reporter strain BS2019. Cellular transcription and translation levels were assessed by quantifying the amount of Nluc mRNA as well as the luminescence catalyzed by the enzyme NanoLuc. We validated this system using three known inhibitors of transcription (rifampicin), translation (chloramphenicol), and cell wall synthesis (ampicillin). The B. subtilis reporter strain BS2019 successfully revealed a decline in Nluc expression by rifampicin and NanoLuc enzyme activity by chloramphenicol, while ampicillin produced no observable effect. The assay was employed to characterize a previously discovered bacterial transcription inhibitor, CUHK242, with known antimicrobial activity against drug-resistant Staphylococcus aureus. Production of Nluc mRNA in our reporter BS2019 was suppressed in the presence of CUHK242, demonstrating the usefulness of the construct, which provides a simple way to study the mechanism of potential antibiotic candidates at early stages of drug discovery. The reporter system can also be modified by adopting different promoters and reporter genes to extend its scope of contribution to other fields of work. IMPORTANCE Discovering new classes of antibiotics is desperately needed to combat the emergence of multidrug-resistant pathogens. To facilitate the drug discovery process, a simple cell-based assay for mechanistic studies is essential to characterize antimicrobial candidates. In this work, we developed a luciferase-based reporter system to quantify the transcriptional and translational effects of potential compounds and validated our system using two currently marketed drugs. Reporter strains generated in this study provide readily available means for identifying bacterial transcription inhibitors as prospective novel antibacterials. We also provided a series of plasmids for characterizing promoters under various conditions such as stress.
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Affiliation(s)
- Nga Man Lam
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China
| | - Tsz Fung Tsang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China
| | - Jiayi Qu
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China
| | - Man Wai Tsang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China
| | - Yuan Tao
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China
| | - Cheuk Hei Kan
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China
| | - Qingyu Zou
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China
| | - King Hong Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Adrian Jun Chu
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region, China
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299
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Novikova IV, Soldatova AV, Moser TH, Thibert SM, Romano CA, Zhou M, Tebo BM, Evans JE, Spiro TG. Cryo-EM Structure of the Mnx Protein Complex Reveals a Tunnel Framework for the Mechanism of Manganese Biomineralization. J Am Chem Soc 2024; 146:22950-22958. [PMID: 39056168 DOI: 10.1021/jacs.3c06537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
The global manganese cycle relies on microbes to oxidize soluble Mn(II) to insoluble Mn(IV) oxides. Some microbes require peroxide or superoxide as oxidants, but others can use O2 directly, via multicopper oxidase (MCO) enzymes. One of these, MnxG from Bacillus sp. strain PL-12, was isolated in tight association with small accessory proteins, MnxE and MnxF. The protein complex, called Mnx, has eluded crystallization efforts, but we now report the 3D structure of a point mutant using cryo-EM single particle analysis, cross-linking mass spectrometry, and AlphaFold Multimer prediction. The β-sheet-rich complex features MnxG enzyme, capped by a heterohexameric ring of alternating MnxE and MnxF subunits, and a tunnel that runs through MnxG and its MnxE3F3 cap. The tunnel dimensions and charges can accommodate the mechanistically inferred binuclear manganese intermediates. Comparison with the Fe(II)-oxidizing MCO, ceruloplasmin, identifies likely coordinating groups for the Mn(II) substrate, at the entrance to the tunnel. Thus, the 3D structure provides a rationale for the established manganese oxidase mechanism, and a platform for further experiments to elucidate mechanistic details of manganese biomineralization.
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Affiliation(s)
- Irina V Novikova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, Washington 99354, United States
| | - Alexandra V Soldatova
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - Trevor H Moser
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, Washington 99354, United States
| | - Stephanie M Thibert
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, Washington 99354, United States
| | - Christine A Romano
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, Washington 99354, United States
| | - Bradley M Tebo
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - James E Evans
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, Washington 99354, United States
| | - Thomas G Spiro
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
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300
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Hemmati YB, Bahrami R, Pourhajibagher M. Assessing the physico-mechanical, anti-bacterial, and anti-demineralization properties of orthodontic resin composite containing different concentrations of photoactivated zinc oxide nanoparticles on Streptococcus mutans biofilm around ceramic and metal orthodontic brackets: An ex vivo study. Int Orthod 2024; 22:100901. [PMID: 39173494 DOI: 10.1016/j.ortho.2024.100901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/24/2024]
Abstract
BACKGROUND AND PURPOSE The aim of this study was to evaluate the physico-mechanical, anti-bacterial, and anti-demineralization properties of orthodontic resin composite containing photoactivated zinc oxide nanoparticles (ZnONPs) on Streptococcus mutans biofilm around ceramic and metal brackets. MATERIAL AND METHODS Following the minimum inhibitory concentration (MIC) determination for ZnONPs, shear bond strength (SBS) was tested for composites containing different concentrations of ZnONPs. The chosen concentration was used to evaluate the microleakage, anti-bacterial, and anti-demineralization properties. RESULTS Adding 50μg/mL of ZnONPs to the orthodontic composite did not negatively affect its physico-mechanical properties. ZnONPs (50μg/mL)-mediated aPDT and 0.2% chlorhexidine significantly (P=0.000) reduced S. mutans biofilms compared to the phosphate-buffered saline (PBS) groups (metal/PBS=7.47±0.7×106, and ceramic/PBS=7.47±0.7×106), with the lowest colony count observed in these groups (metal/chlorhexidine=1.06±0.4×105, ceramic/chlorhexidine=1±0.2×105, metal/ZnONPs-mediated aPDT=1.33±0.3×105, and ceramic/ZnONPs-mediated aPDT=1.2±0.3×105). Sodium fluoride varnish and ZnONPs-mediated aPDT showed the highest efficacy in anti-demineralization and significantly improving the enamel surface microhardness compared to the artificial saliva, especially in ceramic bracket groups (524.17±42.78N and 441.00±29.48N, 394.17±46.83N, P=0.000, and P=0.003, respectively). CONCLUSION ZnONPs (50μg/mL)-mediated aPDT effectively inhibited S. mutans biofilm and promoted anti-demineralization without adverse effects on the physico-mechanical properties of the composite resin. These results suggest the potential of this method in preventing white spot lesions during orthodontic treatment.
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Affiliation(s)
- Yasamin Babaee Hemmati
- Dental Sciences Research Center, Department of Orthodontics, School of Dentistry, Guilan University of Medical Sciences, Rasht, Iran
| | - Rashin Bahrami
- Department of Orthodontics, School of Dentistry, Iran University of Medical Sciences, Tehran, Iran.
| | - Maryam Pourhajibagher
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
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