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Aarthi N, Dubey VK, Shylesha AN, Kukreti A, Patil J, Chandrashekara KM, Aravindaram K, Seegenahalli R, Shivakumar N, Channappa M. Insights into the whole genome sequence of Bacillus thuringiensis NBAIR BtPl, a strain toxic to the melon fruit fly, Zeugodacus cucurbitae. Curr Genet 2024; 70:13. [PMID: 39101952 DOI: 10.1007/s00294-024-01298-2] [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: 05/10/2024] [Revised: 07/16/2024] [Accepted: 07/27/2024] [Indexed: 08/06/2024]
Abstract
Bacillus thuringiensis is the most widely used biopesticide, targets a diversity of insect pests belonging to several orders. However, information regarding the B. thuringiensis strains and toxins targeting Zeugodacus cucurbitae is very limited. Therefore, in the present study, we isolated and identified five indigenous B. thuringiensisstrains toxic to larvae of Z. cucurbitae. However, of five strains NBAIR BtPl displayed the highest mortality (LC50 = 37.3 μg/mL) than reference strain B. thuringiensis var. israelensis (4Q1) (LC50 = 45.41 μg/mL). Therefore, the NBAIR BtPl was considered for whole genome sequencing to identify the cry genes present in it. Whole genome sequencing of our strain revealed genome size of 6.87 Mb with 34.95% GC content. Homology search through the BLAST algorithm revealed that NBAIR BtPl is 99.8% similar to B. thuringiensis serovar tolworthi, and gene prediction through Prokka revealed 7406 genes, 7168 proteins, 5 rRNAs, and 66 tRNAs. BtToxin_Digger analysis of NBAIR BtPl genome revealed four cry gene families: cry1, cry2, cry8Aa1, and cry70Aa1. When tested for the presence of these four cry genes in other indigenous strains, results showed that cry70Aa1 was absent. Thus, the study provided a basis for predicting cry70Aa1 be the possible reason for toxicity. In this study apart from novel genes, we also identified other virulent genes encoding zwittermicin, chitinase, fengycin, and bacillibactin. Thus, the current study aids in predicting potential toxin-encoding genes responsible for toxicity to Z. cucurbitae and thus paves the way for the development of B. thuringiensis-based formulations and transgenic crops for management of dipteran pests.
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Affiliation(s)
- Nekkanti Aarthi
- Department of Entomology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, 492 012, India
| | - Vinod K Dubey
- Department of Entomology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, 492 012, India
| | - Arakalagud N Shylesha
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India
| | - Aditya Kukreti
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India
| | - Jagadeesh Patil
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India
| | - Keerthi M Chandrashekara
- Division of Crop Protection, ICAR-Indian Institute of Horticultural Research, Bengaluru, 560 089, India
| | - Kandan Aravindaram
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India
| | - Ruqiya Seegenahalli
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India
| | - Nanditha Shivakumar
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India
| | - Manjunatha Channappa
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India.
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152
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Ahmed S, Naqvi SMZA, Hussain F, Awais M, Ren Y, Wu J, Zhang H, Zang Y, Hu J. Quantifying Plant Signaling Pathways by Integrating Luminescence-Based Biosensors and Mathematical Modeling. BIOSENSORS 2024; 14:378. [PMID: 39194607 DOI: 10.3390/bios14080378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/29/2024]
Abstract
Plants have evolved intricate signaling pathways, which operate as networks governed by feedback to deal with stressors. Nevertheless, the sophisticated molecular mechanisms underlying these routes still need to be comprehended, and experimental validation poses significant challenges and expenses. Consequently, computational hypothesis evaluation gains prominence in understanding plant signaling dynamics. Biosensors are genetically modified to emit light when exposed to a particular hormone, such as abscisic acid (ABA), enabling quantification. We developed computational models to simulate the relationship between ABA concentrations and bioluminescent sensors utilizing the Hill equation and ordinary differential equations (ODEs), aiding better hypothesis development regarding plant signaling. Based on simulation results, the luminescence intensity was recorded for a concentration of 47.646 RLUs for 1.5 μmol, given the specified parameters and model assumptions. This method enhances our understanding of plant signaling pathways at the cellular level, offering significant benefits to the scientific community in a cost-effective manner. The alignment of these computational predictions with experimental results emphasizes the robustness of our approach, providing a cost-effective means to validate mathematical models empirically. The research intended to correlate the bioluminescence of biosensors with plant signaling and its mathematical models for quantified detection of specific plant hormone ABA.
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Affiliation(s)
- Shakeel Ahmed
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Syed Muhammad Zaigham Abbas Naqvi
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Fida Hussain
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Muhammad Awais
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Yongzhe Ren
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Junfeng Wu
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Hao Zhang
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Yiheng Zang
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
| | - Jiandong Hu
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
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153
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Rajan D, Lee B, Albright A, Tang E, Maravillas A, Vargas C, Marshall WF, Cortes D. Phylogeny, morphology, and behavior of the new ciliate species Stentor stipatus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.03.606273. [PMID: 39131352 PMCID: PMC11312564 DOI: 10.1101/2024.08.03.606273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The study of evolution at the cellular level traditionally has focused on the evolution of metabolic pathways, endomembrane systems, and genomes, but there has been increasing interest in evolution of more complex cellular structures and behaviors, particularly in the eukaryotes. Ciliates have major advantages for such studies due to their easily visible surface patterning and their dramatic and complex behaviors that can be easily analyzed. Among the ciliates, the genus Stentor epitomizes the features that are useful for studying evolution: they are widespread in freshwater environments, easy to visualize because of their large size, and capable of complex behaviors such as learning, decision-making, and phototaxis. Here, we introduce the discovery of a new species within this genus: Stentor stipatus, so named for their distinctive dark brown aggregates. We present morphological, phylogenetic, ecological, and behavioral characterizations of these cells. The S. stipatus clade has a bootstrap value of 93 and is phylogenetically distinct from S. amethystinus, the closest related species which shares a sequence similarity of 98.9%. S. stipatus is capable of phototaxis and can also habituate more quickly than S. coeruleus, the Stentor species in which most habituation studies have previously been conducted. These findings expand our understanding of Stentor species diversity, natural history, and demonstrate common principles of complex behavior that are present in single-celled organisms.
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154
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Chatterjee Y, Pareek A, Singla-Pareek SL. OsLdh7, a rice lactate dehydrogenase, confers stress resilience in rice under cadmium stress through NAD +/NADH regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109009. [PMID: 39154420 DOI: 10.1016/j.plaphy.2024.109009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/20/2024]
Abstract
Lactate dehydrogenase (Ldh, EC 1.1.1.27), an oxidoreductase enzyme catalyses the interconversion of pyruvate to L-lactate and vice-versa with concomitant oxidation and reduction of NADH and NAD+. The enzyme functions as a ROS sensor and mitigates stress response by maintaining NAD+/NADH homeostasis. In this study, we delineated the role of the Ldh enzyme in imparting cadmium stress tolerance in rice. Previously, we identified a putatively active Ldh in rice (OsLdh7) through insilico modelling. Biochemical characterization of the OsLdh7 enzyme revealed it to be optimally active at pH 6.6 in the forward direction and pH 9 in the reverse direction. Overexpression of OsLdh7 in rice cv. IR64, increased tolerance of the transgenic lines to cadmium stress compared to the wild type (WT) at both seedling and reproductive stages. The transgenic lines showed increased enzyme activity in the reverse direction under cadmium stress, attributed to elevated cytosolic pH resulting from increased calcium concentration. This increased NADH content is highly essential for functioning of the ROS scavenging enzymes, RbohD and MPK6. qPCR analysis revealed that the overexpression lines had increased transcript abundance of these genes indicating an effective ROS scavenging mechanism. Additionally, the overexpression lines showed an efficient cadmium sequestration mechanism compared to the WT by increasing the transcript levels of the vacuolar transporters of cadmium as well as total phytochelatin content. Thus, our findings indicated OsLdh7 imparts cadmium stress tolerance in rice through a two-pronged approach by mitigating ROS and sequestering cadmium ions, highlighting its potential for crop improvement programs.
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Affiliation(s)
- Yajnaseni Chatterjee
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
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155
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Zhuo S, Jiang Y, Qi L, Hu Y, Jiang Z, Dong Y, Shi L. The robustness of porin-cytochrome gene clusters from Geobacter metallireducens in extracellular electron transfer. mBio 2024:e0058024. [PMID: 39092920 DOI: 10.1128/mbio.00580-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/03/2024] [Indexed: 08/04/2024] Open
Abstract
To investigate their roles in extracellular electron transfer (EET), the porin-cytochrome (pcc) gene clusters Gmet0825-0828, Gmet0908-0910, and Gmet0911-0913 of the Gram-negative bacterium Geobacter metallireducens were deleted. Failure to delete all pcc gene clusters at the same time suggested their essential roles in extracellular reduction of Fe(III)-citrate by G. metallireducens. Deletion of Gmet0825-0828 had no impact on bacterial reduction of Fe(III)-citrate but diminished bacterial reduction of ferrihydrite and abolished anode reduction and direct interspecies electron transfer (DIET) to Methanosarcina barkeri and Geobacter sulfurreducens. Although it had no impact on the bacterial reduction of Fe(III)-citrate, deletion of Gmet0908-0910 delayed ferrihydrite reduction, abolished anode reduction, and diminished DIET. Deletion of Gmet0911-0913 had little impact on DIET but diminished bacterial reductions of Fe(III)-citrate, ferrihydrite, and anodes. Most importantly, deletions of both Gmet0825-0828 and Gmet0908-0910 restored bacterial reduction of ferrihydrite and anodes and DIET. Enhanced expression of Gmet0911-0913 in this double mutant when grown in coculture with G. sulfurreducens ΔhybLΔfdnG suggested that this cluster might compensate for impaired EET functions of deleting Gmet0825-0828 and Gmet0908-0910. Thus, these pcc gene clusters played essential, distinct, overlapping, and compensatory roles in EET of G. metallireducens that are difficult to characterize as deletion of some clusters affected expression of others. The robustness of these pcc gene clusters enabled G. metallireducens to mediate EET to different acceptors for anaerobic growth even when two of its three pcc gene clusters were inactivated by mutation. The results from this investigation provide new insights into the roles of pcc gene clusters in bacterial EET. IMPORTANCE The Gram-negative bacterium Geobacter metallireducens is of environmental and biotechnological significance. Crucial to the unique physiology of G. metallireducens is its extracellular electron transfer (EET) capability. This investigation sheds new light on the robust roles of the three porin-cytochrome (pcc) gene clusters, which are directly involved in EET across the bacterial outer membrane, in the EET of G. metallireducens. In addition to their essential roles, these gene clusters also play distinct, overlapping, and compensatory roles in the EET of G. metallireducens. The distinct roles of the pcc gene clusters enable G. metallireducens to mediate EET to a diverse group of electron acceptors for anaerobic respirations. The overlapping and compensatory roles of the pcc gene clusters enable G. metallireducens to maintain and restore its EET capability for anaerobic growth when one or two of its three pcc gene clusters are deleted from the genome.
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Affiliation(s)
- Shiyan Zhuo
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yongguang Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yidan Hu
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Zhou Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yiran Dong
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
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156
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Acs-Szabo L, Papp LA, Miklos I. Understanding the molecular mechanisms of human diseases: the benefits of fission yeasts. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:288-311. [PMID: 39104724 PMCID: PMC11299203 DOI: 10.15698/mic2024.08.833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 08/07/2024]
Abstract
The role of model organisms such as yeasts in life science research is crucial. Although the baker's yeast (Saccharomyces cerevisiae) is the most popular model among yeasts, the contribution of the fission yeasts (Schizosaccharomyces) to life science is also indisputable. Since both types of yeasts share several thousands of common orthologous genes with humans, they provide a simple research platform to investigate many fundamental molecular mechanisms and functions, thereby contributing to the understanding of the background of human diseases. In this review, we would like to highlight the many advantages of fission yeasts over budding yeasts. The usefulness of fission yeasts in virus research is shown as an example, presenting the most important research results related to the Human Immunodeficiency Virus Type 1 (HIV-1) Vpr protein. Besides, the potential role of fission yeasts in the study of prion biology is also discussed. Furthermore, we are keen to promote the uprising model yeast Schizosaccharomyces japonicus, which is a dimorphic species in the fission yeast genus. We propose the hyphal growth of S. japonicus as an unusual opportunity as a model to study the invadopodia of human cancer cells since the two seemingly different cell types can be compared along fundamental features. Here we also collect the latest laboratory protocols and bioinformatics tools for the fission yeasts to highlight the many possibilities available to the research community. In addition, we present several limiting factors that everyone should be aware of when working with yeast models.
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Affiliation(s)
- Lajos Acs-Szabo
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of DebrecenDebrecen, 4032Hungary
| | - Laszlo Attila Papp
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of DebrecenDebrecen, 4032Hungary
| | - Ida Miklos
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of DebrecenDebrecen, 4032Hungary
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157
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Shiraliyev R, Orman MA. Metabolic disruption impairs ribosomal protein levels, resulting in enhanced aminoglycoside tolerance. eLife 2024; 13:RP94903. [PMID: 39093940 PMCID: PMC11296704 DOI: 10.7554/elife.94903] [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] [Indexed: 08/04/2024] Open
Abstract
Aminoglycoside antibiotics target ribosomes and are effective against a wide range of bacteria. Here, we demonstrated that knockout strains related to energy metabolism in Escherichia coli showed increased tolerance to aminoglycosides during the mid-exponential growth phase. Contrary to expectations, these mutations did not reduce the proton motive force or aminoglycoside uptake, as there were no significant changes in metabolic indicators or intracellular gentamicin levels between wild-type and mutant strains. Our comprehensive proteomics analysis unveiled a noteworthy upregulation of proteins linked to the tricarboxylic acid (TCA) cycle in the mutant strains during the mid-exponential growth phase, suggesting that these strains compensate for the perturbation in their energy metabolism by increasing TCA cycle activity to maintain their membrane potential and ATP levels. Furthermore, our pathway enrichment analysis shed light on local network clusters displaying downregulation across all mutant strains, which were associated with both large and small ribosomal binding proteins, ribosome biogenesis, translation factor activity, and the biosynthesis of ribonucleoside monophosphates. These findings offer a plausible explanation for the observed tolerance of aminoglycosides in the mutant strains. Altogether, this research provides valuable insights into the mechanisms of aminoglycoside tolerance, paving the way for novel strategies to combat such cells.
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Affiliation(s)
- Rauf Shiraliyev
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of HoustonHoustonUnited States
| | - Mehmet A Orman
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of HoustonHoustonUnited States
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158
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Zhang P, Li S, Wang W, Sun J, Chen Z, Wang J, Ma Q. Enhanced photodynamic inactivation against Escherichia coli O157:H7 provided by chitosan/curcumin coating and its application in food contact surfaces. Carbohydr Polym 2024; 337:122160. [PMID: 38710575 DOI: 10.1016/j.carbpol.2024.122160] [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: 12/14/2023] [Revised: 03/10/2024] [Accepted: 04/11/2024] [Indexed: 05/08/2024]
Abstract
Sterilisation technologies are essential to eliminate foodborne pathogens from food contact surfaces. However, most of the current sterilisation methods involve high energy and chemical consumption. In this study, a photodynamic inactivation coating featuring excellent antibacterial activity was prepared by dispersing curcumin as a plant-based photosensitiser in a chitosan solution. The coating generated abundant reactive oxygen species (ROS) after light irradiation at 420 nm, which eradicated ≥99.999 % of Escherichia coli O157:H7. It was also found that ROS damaged the cell membrane, leading to the leakage of cell contents and cell shrinkage on the basis of chitosan. In addition, the production of ROS first excited the bacterial antioxidant defence system resulting in the increase of peroxidase (POD) and superoxide dismutase (SOD). ROS levels exceed its capacity, causing damage to the defence system and further oxidative decomposition of large molecules, such as DNA and proteins, eventually leading to the death of E. coli O157:H7. We also found the curcumin/chitosan coating could effectively remove E. coli O157:H7 biofilms by oxidative of extracellular polysaccharides and proteins. All the contributors made the chitosan/curcumin coating an efficient detergent comparable with HClO.
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Affiliation(s)
- Pengmin Zhang
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, PR China
| | - Shuang Li
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, PR China
| | - Wenxiu Wang
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, PR China
| | - Jianfeng Sun
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, PR China
| | - Zhizhou Chen
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, PR China
| | - Jie Wang
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, PR China
| | - Qianyun Ma
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, PR China.
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159
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Zhang R, Qu Z, Yang W, Li J, Wang L, Liu Q, Zhang D, Qiao T, Zhao Y. Evaluating annual soil carbon emissions under biochar-added farmland subjecting from freeze-thaw cycle. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121506. [PMID: 38901319 DOI: 10.1016/j.jenvman.2024.121506] [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: 04/03/2024] [Revised: 05/29/2024] [Accepted: 06/15/2024] [Indexed: 06/22/2024]
Abstract
Straw biochar is a commonly recognized agricultural amendment that can improve soil quality and reduce carbon emissions while sequestering soil carbon. However, the mechanisms underlying biochar's effects on annual soil carbon emissions in seasonally frozen soil areas and intrinsic drivers have not been clarified. Here, a 2-y field experiment was conducted to investigate the effects of different biochar dosages (0, 15, and 30, t ha-1; B0 (CK), B15, and B30, respectively) on carbon emissions (CO2 and CH4) microbial colony count, and soil-environment factors. The study period was the full annual cycle, including the freeze-thaw period (FTP) and the crop growth period (CP). Structural equation modeling (SEM) was developed to reveal the key drivers and potential mechanisms of biochar on carbon emissions. Biochar application reduced soil carbon emissions, with the reduction rate positively related to the biochar application rate (B30 best). During FTP, the reduction rate was 11.5% for CO2 and 48.2% for CH4. During CP, the reduction rate was 17.9% for CO2 and 34.5% for CH4. Overall, compared with CK, B30 treatment had a significant effect on reducing total soil carbon emissions (P < 0.05), with an average decrease of 16.7% during the two-year test period. The study also showed that for soils with continuous annual cycles (FTP and CP), carbon emissions were best observed from 10:00-13:00. After two years of freeze-thaw cycling, biochar continued to improve soil physical and chemical properties, thereby increasing soil microbial colony count. Compared with B0, the B30 treatment significantly increased the total colony count by 74.3% and 263.8% during FTP and CP (P < 0.05). Structural equation modeling (SEM) indicated that, with or without biochar application, the soil physicochemical properties directly or indirectly affected soil CO2 and CH4 emission fluxes through microbial colony count. The total effects of biochar application on CO2 emission fluxes were 0.50 (P < 0.05) and 0.64 (P < 0.01), respectively, but there was no significant effect on CH4 emission fluxes (P > 0.05). Among them, soil water content (SWC), soil temperature (ST) and soil organic carbon (SOC) were the main environmental determinants of CO2 emission fluxes during the FTP and CP. The total effects were 0.57, 0.65, and 0.53, respectively. For CH4, SWC, soil salinity (SS) and actinomycete colony count were the main environmental factors affecting its emission. The total effects were 0.50, 0.45, 0.44, respectively. For freeze-thaw alternating soils, the application of biochar is a feasible option for addressing climate change through soil carbon sequestration and greenhouse gas emissions mitigation. Soil water-heat-salt-fertilization and microbial communities are important for soil carbon emissions as the reaction matrix and main participants of soil carbon and nitrogen biochemical transformation.
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Affiliation(s)
- Ruxin Zhang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Zhongyi Qu
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China; Autonomous Region Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in the Inner Mongolia Reaches of the Yellow River, Hohhot, 010018, China.
| | - Wei Yang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, 010018, China; Autonomous Region Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in the Inner Mongolia Reaches of the Yellow River, Hohhot, 010018, China.
| | - Junjie Li
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Liping Wang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China; Autonomous Region Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in the Inner Mongolia Reaches of the Yellow River, Hohhot, 010018, China
| | - Qi Liu
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Dongliang Zhang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Tian Qiao
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yibo Zhao
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
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160
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Verma P, Sikka K, Verma H, Kumar R, Thakar A, Soneja M, Singh V. Factors Impacting Outcome and Prognosis of Invasive Fungal Sinusitis: How Vital is Iron Metabolism? Indian J Otolaryngol Head Neck Surg 2024; 76:3189-3195. [PMID: 39130265 PMCID: PMC11306875 DOI: 10.1007/s12070-024-04643-6] [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: 02/06/2024] [Accepted: 03/11/2024] [Indexed: 08/13/2024] Open
Abstract
Iron is an important micronutrient involved in cell biology through vital reactions. We examined the correlations between iron metabolism parameters and the course of invasive fungal sinusitis. Patients with invasive fungal sinusitis were enrolled. Serum iron and ferritin levels, total iron-binding capacity, and transferrin saturation were measured at the initiation of treatment. Patients were followed for 6 months, and the clinical course was categorised as improvement or worsening/death. A total of 35 patients were enrolled. The average ferritin levels in mucormycosis patients was 944.9 ng/ml, versus 110.7 ng/ml for aspergillosis patients. Iron levels were significantly lower in mucormycosis than in aspergillosis (29.14 µg/dl vs. 68.55 µg/dl). Total iron-binding capacity was significantly different between the two groups (16.76 µg/dl vs. 330.36 µg/dl). After 6 months, improvement, worsening, and death were noted for 18, 8, and 9 patients, respectively. Higher iron levels and lower ferritin levels were linked with improvement. Total iron-binding capacity was significantly higher in improved patients (2314 vs. 151). Iron metabolism parameters play significant roles in the preemptive judgment of the course of fungal sinusitis. Based on these findings, studies on drugs affecting iron metabolism should be conducted.
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Affiliation(s)
- Prankur Verma
- Department of ENT, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Kapil Sikka
- Department of ENT, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Hitesh Verma
- Department of ENT, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Rakesh Kumar
- Department of ENT, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Alok Thakar
- Department of ENT, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Manish Soneja
- Department of Internal Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Vishwajeet Singh
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
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Tao Y, Yang C, Dong K, Luo W, Ye L, Pu J, Yang J, Zheng H, Xu J. Two new members of the genus Sphingobacterium: Sphingobacterium zhuxiongii sp. nov. and Sphingobacterium luzhongxinii sp. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 39140715 DOI: 10.1099/ijsem.0.006488] [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: 08/15/2024] Open
Abstract
Four strains, designated dk4302T, dk4209, xlx-73T, and xlx-183, were isolated from Tibetan gazelle and red swamp crawfish collected from the Qinghai-Tibet Plateau and Jiangxi Province, PR China. The strains were Gram-stain-negative, aerobic, rod-shaped, non-motile, mucoid, and yellow-pigmented. Strains dk4302T and dk4209 grew at 10-40 °C and pH 6.0-9.0, while strains xlx-73T/xlx-183 grew at 15-40 °C and pH 6.0-10.0. Both strains exhibited growth in the presence of up to 3.5 % (w/v) NaCl. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene sequences and 652 core genes, respectively, revealed that the four strains formed two distinct clusters in the genus Sphingobacterium. Strains dk4302T and dk4209 formed a distinct clade with Sphingobacterium hotanense XH4T and Sphingobacterium humi D1T. The most closely related strains to xlx-73T and xlx-183 were Sphingobacterium nematocida M-SX103T. The DNA G+C contents were 38.9 and 39.8 mol%. The digital DNA-DNA hybridization (dDDH) values between dk4302T and S. humi D1T and S. hotanense XH4T were 19.2 and 21.8 % (19.0 and 21.6 % for strain dk4209), respectively. The corresponding average nucleotide identity (ANI) values were 74.3 and 78.1 % (74.4 and 78.3 % for strain dk4209), respectively. The dDDH values between xlx-73T (xlx-183) and S. nematocida M-SX103T was 24.6 % (25.7 %). The corresponding ANI value was 85.7 % (85.5 % for strain xlx-183). The major fatty acid and respiratory quinone of dk4302T and xlx-73T were iso-C15:0 and MK7. The polar lipids identified in all of the novel strains were phosphatidylethanolamine, phosphoglycolipids, aminophospholipids, and phospholipids. A total of 61/190 (32.1 %) and 82/190 (43.2 %) carbon substrates were metabolized by strains dk4302T and xlx-73T in the Biolog MicroPlates, respectively. Based on the results from this polyphasic taxonomic study, two novel species in the genus Sphingobacteruim are proposed, namely Sphingobacteruim zhuxiongii sp. nov. (type strain dk4302T=CGMCC 1.16795T=JCM 33600T) and Sphingobacteruimluzhongxinii sp. nov. (type strain xlx-73T=GDMCC 1.1712T=JCM 33886T).
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Affiliation(s)
- Yuanmeihui Tao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Caixin Yang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
| | - Kui Dong
- Shanxi Eye Hospital, Shanxi Province Key Laboratory of Ophthalmology, Taiyuan 030002, PR China
| | - Wenbo Luo
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Lin Ye
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
| | - Ji Pu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Han Zheng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
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Rajan AAN, Hutchins EJ. Post-transcriptional regulation as a conserved driver of neural crest and cancer-cell migration. Curr Opin Cell Biol 2024; 89:102400. [PMID: 39032482 PMCID: PMC11346372 DOI: 10.1016/j.ceb.2024.102400] [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: 05/02/2024] [Revised: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024]
Abstract
Cells have evolved mechanisms to migrate for diverse biological functions. A process frequently deployed during metazoan cell migration is the epithelial-mesenchymal transition (EMT). During EMT, adherent epithelial cells undergo coordinated cellular transitions to mesenchymalize and reduce their intercellular attachments. This is achieved via tightly regulated changes in gene expression, which modulates cell-cell and cell-matrix adhesion to allow movement. The acquisition of motility and invasive properties following EMT allows some mesenchymal cells to migrate through complex environments to form tissues during embryogenesis; however, these processes may also be leveraged by cancer cells, which often co-opt these endogenous programs to metastasize. Post-transcriptional regulation is now emerging as a major conserved mechanism by which cells modulate EMT and migration, which we discuss here in the context of vertebrate development and cancer.
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Affiliation(s)
- Arvind Arul Nambi Rajan
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Erica J Hutchins
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
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163
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Lv J, Zhao Q, Wang K, Jiang J, Ding J, Wei L. A critical review of approaches to enhance the performance of bio-electro-Fenton and photo-bio-electro-Fenton systems. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121633. [PMID: 38955044 DOI: 10.1016/j.jenvman.2024.121633] [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: 03/14/2024] [Revised: 06/12/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024]
Abstract
The development of sustainable advanced energy conversion technologies and efficient pollutant treatment processes is a viable solution to the two global crises of the lack of non-renewable energy resources and environmental harm. In recent years, the interaction of biological and chemical oxidation units to utilize biomass has been extensively studied. Among these systems, bio-electro-Fenton (BEF) and photo-bio-electro-Fenton (PBEF) systems have shown prospects for application due to making rational and practical conversion and use of energy. This review compared and analyzed the electron transfer mechanisms in BEF and PBEF systems, and systematically summarized the techniques for enhancing system performance based on the generation, transfer, and utilization of electrons, including increasing the anode electron recovery efficiency, enhancing the generation of reactive oxygen species, and optimizing operational modes. This review compared the effects of different methods on the electron flow process and fully evaluated the benefits and drawbacks. This review may provide straightforward suggestions and methods to enhance the performance of BEF and PBEF systems and inspire the reader to explore the generation and utilization of sustainable energy more deeply.
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Affiliation(s)
- Jiaqi Lv
- State Key Laboratory of Urban Water Resources and Environments (SKLURE), School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Qingliang Zhao
- State Key Laboratory of Urban Water Resources and Environments (SKLURE), School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Kun Wang
- State Key Laboratory of Urban Water Resources and Environments (SKLURE), School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Junqiu Jiang
- State Key Laboratory of Urban Water Resources and Environments (SKLURE), School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Jing Ding
- State Key Laboratory of Urban Water Resources and Environments (SKLURE), School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Liangliang Wei
- State Key Laboratory of Urban Water Resources and Environments (SKLURE), School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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164
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Sadowska-Bartosz I, Bartosz G. Antioxidant Defense in the Toughest Animals on the Earth: Its Contribution to the Extreme Resistance of Tardigrades. Int J Mol Sci 2024; 25:8393. [PMID: 39125965 PMCID: PMC11313143 DOI: 10.3390/ijms25158393] [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: 06/22/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Tardigrades are unique among animals in their resistance to dehydration, mainly due to anhydrobiosis and tun formation. They are also very resistant to high-energy radiation, low and high temperatures, low and high pressure, and various chemical agents, Interestingly, they are resistant to ionizing radiation both in the hydrated and dehydrated states to a similar extent. They are able to survive in the cosmic space. Apparently, many mechanisms contribute to the resistance of tardigrades to harmful factors, including the presence of trehalose (though not common to all tardigrades), heat shock proteins, late embryogenesis-abundant proteins, tardigrade-unique proteins, DNA repair proteins, proteins directly protecting DNA (Dsup and TDR1), and efficient antioxidant system. Antioxidant enzymes and small-molecular-weight antioxidants are an important element in the tardigrade resistance. The levels and activities of many antioxidant proteins is elevated by anhydrobiosis and UV radiation; one explanation for their induction during dehydration is provided by the theory of "preparation for oxidative stress", which occurs during rehydration. Genes coding for some antioxidant proteins are expanded in tardigrades; some genes (especially those coding for catalases) were hypothesized to be of bacterial origin, acquired by horizontal gene transfer. An interesting antioxidant protein found in tardigrades is the new Mn-dependent peroxidase.
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Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszów, 4 Zelwerowicza Street, 35-601 Rzeszow, Poland;
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Lima NF, Maciel GM, Lima NP, Fernandes IDAA, Haminiuk CWI. Bacterial cellulose in cosmetic innovation: A review. Int J Biol Macromol 2024; 275:133396. [PMID: 38945719 DOI: 10.1016/j.ijbiomac.2024.133396] [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: 03/28/2024] [Revised: 06/10/2024] [Accepted: 06/22/2024] [Indexed: 07/02/2024]
Abstract
Bacterial cellulose (BC) emerges as a versatile biomaterial with a myriad of industrial applications, particularly within the cosmetics sector. The absence of hemicellulose, lignin, and pectin in its pure cellulose structure enables favorable interactions with both hydrophilic and hydrophobic biopolymers. This enhances compatibility with active ingredients commonly employed in cosmetics, such as antioxidants, vitamins, and botanical extracts. Recent progress in BC-based materials, which encompasses membranes, films, gels, nanocrystals, and nanofibers, highlights its significant potential in cosmetics. In this context, BC not only serves as a carrier for active ingredients but also plays a crucial role as a structural agent in formulations. The sustainability of BC production and processing is a central focus, highlighting the need for innovative approaches to strengthen scalability and cost-effectiveness. Future research endeavors, including the exploration of novel cultivation strategies and functionalization techniques, aim to maximize BC's therapeutic potential while broadening its scope in personalized skincare regimes. Therefore, this review emphasizes the crucial contribution of BC to the cosmetics sector, underlining its role in fostering innovation, sustainability, and ethical skincare practices. By integrating recent research findings and industry trends, this review proposes a fresh approach to advancing both skincare science and environmental responsibility in the cosmetics industry.
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Affiliation(s)
- Nicole Folmann Lima
- Programa de Pós-Graduação em Engenharia de Alimentos (PPGEAL), Universidade Federal do Paraná (UFPR), CEP (81531-980) Curitiba, Paraná, Brazil
| | - Giselle Maria Maciel
- Laboratório de Biotecnologia, Universidade Tecnológica Federal do Paraná (UTFPR), CEP (81280-340) Curitiba, Paraná, Brazil
| | - Nayara Pereira Lima
- Programa de Pós-Graduação em Engenharia de Alimentos (PPGEAL), Universidade Federal do Paraná (UFPR), CEP (81531-980) Curitiba, Paraná, Brazil
| | - Isabela de Andrade Arruda Fernandes
- Programa de Pós-Graduação em Ciência e Tecnologia Ambiental (PPGCTA), Universidade Tecnológica Federal do Paraná (UTFPR), CEP (81280-340) Curitiba, Paraná, Brazil
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Pham DN, Mai DHA, Lee EY. Biosynthesis of polyhydroxybutyrate from methane and carbon dioxide using type II methanotrophs. BIORESOURCE TECHNOLOGY 2024; 405:130931. [PMID: 38838829 DOI: 10.1016/j.biortech.2024.130931] [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: 03/13/2024] [Revised: 05/31/2024] [Accepted: 06/02/2024] [Indexed: 06/07/2024]
Abstract
Methane (CH4) and carbon dioxide (CO2) are the dominant greenhouse gases (GHGs) that are increasing at an alarming rate. Methanotrophs have emerged as potential CH4 and CO2 biorefineries. This study demonstrated the synchronous incorporation of CH4 and CO2 into polyhydroxybutyrate (PHB) for the first time using 13C-labeling experiments in methanotrophs. By supplying substantial amounts of CO2, PHB content was enhanced in all investigated type II methanotrophic strains by 140 %, 146 %, and 162 %. The highest content of PHB from CH4 and CO2 in flask-scale cultivation reached 38 % dry cell weight in Methylocystis sp. MJC1, in which carbon percentage in PHB from CO2 was 45 %. Flux balance analysis predicted the critical roles of crotonyl-CoA carboxylase/reductase and phosphoenolpyruvate carboxylase in CO2 recycling. This study provided proof of the conversion of GHGs into a valuable and practical product using methanotrophic bacteria, contributing to addressing GHG emissions.
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Affiliation(s)
- Diep Ngoc Pham
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Dung Hoang Anh Mai
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea.
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167
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Ichikawa Y, Kaneko N, Thwin KM, Senpuku H, Nohno K, Ogawa H. Low Salivary IgA Levels Against PAc (361-386) as a Risk Factor for Root Caries in Older Adults. Clin Exp Dent Res 2024; 10:e945. [PMID: 39104139 DOI: 10.1002/cre2.945] [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: 02/21/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 08/07/2024] Open
Abstract
OBJECTIVES This study aimed to assess the intricate relationship between salivary IgA antibody levels to PAc (361-386) (PPA), mutans streptococci colonization, and root caries development in older adults. MATERIALS AND METHODS This study included 307 participants aged 76 years residing in Niigata city, Japan. Clinical oral examinations were performed at baseline in 2004 and 1 year later, during which the total number of untreated and treated root caries was assessed using the root decayed, filled tooth (DFT) index. The stimulated saliva samples were collected using the spitting method during the baseline survey. Salivary IgA antibody levels to amino acid residues 361-386 of Streptococcus mutans PAc were quantified using an enzyme-linked immunosorbent assay. Statistical analyses, including the χ2 test, Mann-Whitney U test, and logistic regressions, were performed to examine the association of increased root DFT with the independent variables. RESULTS Among the 307 participants (53.1% men), the mean root DFT at baseline was 3.77 ± 3.66, and 36.5% of the study sample exhibited increased root DFT after 1 year with a mean increment of 0.36 ± 0.48. Participants with increase in root DFT after 1 year had significantly higher rates of low PPA levels (≤ 25th percentile) than those without increased root DFT (p = 0.020). Low PPA levels (≤ 25th percentile) were significantly more likely to have an increased risk of root caries development compared with PPA levels > 25th percentile (adjusted OR: 1.88, 95% CI: 1.09-3.25). CONCLUSION Low PPA levels and root caries incidence correlated significantly, suggesting that low levels of salivary IgA antibody to PAc (361-386) may serve as a risk factor for increased root caries in older adults.
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Affiliation(s)
- Yu Ichikawa
- Division of Preventive Dentistry, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Noboru Kaneko
- Division of Preventive Dentistry, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Kaung Myat Thwin
- Division of Preventive Dentistry, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Hidenobu Senpuku
- Department of Microbiology and Immunology, Nihon University School of Dentistry at Matsudo, Chiba, Japan
| | - Kaname Nohno
- Division of Oral Science for Health Promotion, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Hiroshi Ogawa
- Division of Preventive Dentistry, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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Grettenberger CL, Abou‐Shanab R, Hamilton TL. Limiting factors in the operation of photosystems I and II in cyanobacteria. Microb Biotechnol 2024; 17:e14519. [PMID: 39101352 PMCID: PMC11298993 DOI: 10.1111/1751-7915.14519] [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: 04/03/2024] [Accepted: 06/16/2024] [Indexed: 08/06/2024] Open
Abstract
Cyanobacteria are important targets for biotechnological applications due to their ability to grow in a wide variety of environments, rapid growth rates, and tractable genetic systems. They and their bioproducts can be used as bioplastics, biofertilizers, and in carbon capture and produce important secondary metabolites that can be used as pharmaceuticals. However, the photosynthetic process in cyanobacteria can be limited by a wide variety of environmental factors such as light intensity and wavelength, exposure to UV light, nutrient limitation, temperature, and salinity. Carefully considering these limitations, modifying the environment, and/or selecting cyanobacterial species will allow cyanobacteria to be used in biotechnological applications.
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Affiliation(s)
- Christen L. Grettenberger
- Department of Earth and Planetary SciencesUniversity of California DavisDavisCaliforniaUSA
- Department of Environmental ToxicologyUniversity of California DavisDavisCaliforniaUSA
| | - Reda Abou‐Shanab
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - Trinity L. Hamilton
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
- The Biotechnology Institute, University of MinnesotaSt. PaulMinnesotaUSA
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Merouani EFO, Ferdowsi M, Buelna G, Jones JP, Benyoussef EH, Malhautier L, Heitz M. Exploring the potential of biofiltration for mitigating harmful gaseous emissions from small or old landfills: a review. Biodegradation 2024; 35:469-491. [PMID: 38748305 DOI: 10.1007/s10532-024-10082-5] [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: 08/07/2023] [Accepted: 04/13/2024] [Indexed: 07/14/2024]
Abstract
Landfills are widely employed as the primary means of solid waste disposal. However, this practice generates landfill gas (LFG) which contains methane (CH4), a potent greenhouse gas, as well as various volatile organic compounds and volatile inorganic compounds. These emissions from landfills contribute to approximately 25% of the total atmospheric CH4, indicating the imperative need to valorize or treat LFG prior to its release into the atmosphere. This review first aims to outline landfills, waste disposal and valorization, conventional gas treatment techniques commonly employed for LFG treatment, such as flares and thermal oxidation. Furthermore, it explores biotechnological approaches as more technically and economically feasible alternatives for mitigating LFG emissions, especially in the case of small and aged landfills where CH4 concentrations are often below 3% v/v. Finally, this review highlights biofilters as the most suitable biotechnological solution for LFG treatment and discusses several advantages and challenges associated with their implementation in the landfill environment.
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Affiliation(s)
- El Farouk Omar Merouani
- Department of Chemical Engineering and Biotechnological Engineering, Faculty of Engineering, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Milad Ferdowsi
- Department of Chemical Engineering and Biotechnological Engineering, Faculty of Engineering, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Gerardo Buelna
- Department of Chemical Engineering and Biotechnological Engineering, Faculty of Engineering, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - J Peter Jones
- Department of Chemical Engineering and Biotechnological Engineering, Faculty of Engineering, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - El-Hadi Benyoussef
- Laboratoire de Valorisation des Énergies Fossiles, École Nationale Polytechnique, 10 Avenue Hassan Badi El Harrach, BP182, 16200, Algiers, Algeria
| | - Luc Malhautier
- Laboratoire des Sciences des Risques, IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Michèle Heitz
- Department of Chemical Engineering and Biotechnological Engineering, Faculty of Engineering, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, Québec, J1K 2R1, Canada.
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170
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Kang M, Wang LF, Sun BW, Wan WB, Ji X, Baele G, Bi YH, Suchard MA, Lai A, Zhang M, Wang L, Zhu YH, Ma L, Li HP, Haerheng A, Qi YR, Wang RL, He N, Su S. Zoonotic infections by avian influenza virus: changing global epidemiology, investigation, and control. THE LANCET. INFECTIOUS DISEASES 2024; 24:e522-e531. [PMID: 38878787 DOI: 10.1016/s1473-3099(24)00234-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/21/2024] [Accepted: 04/07/2024] [Indexed: 07/28/2024]
Abstract
Avian influenza virus continues to pose zoonotic, epizootic, and pandemic threats worldwide, as exemplified by the 2020-23 epizootics of re-emerging H5 genotype avian influenza viruses among birds and mammals and the fatal jump to humans of emerging A(H3N8) in early 2023. Future influenza pandemic threats are driven by extensive mutations and reassortments of avian influenza viruses rooted in frequent interspecies transmission and genetic mixing and underscore the urgent need for more effective actions. We examine the changing global epidemiology of human infections caused by avian influenza viruses over the past decade, including dramatic increases in both the number of reported infections in humans and the spectrum of avian influenza virus subtypes that have jumped to humans. We also discuss the use of advanced surveillance, diagnostic technologies, and state-of-the-art analysis methods for tracking emerging avian influenza viruses. We outline an avian influenza virus-specific application of the One Health approach, integrating enhanced surveillance, tightened biosecurity, targeted vaccination, timely precautions, and timely clinical management, and fostering global collaboration to control the threats of avian influenza viruses.
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Affiliation(s)
- Mei Kang
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China; Clinical Research Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-Fang Wang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Bo-Wen Sun
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Wen-Bo Wan
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Yu-Hai Bi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA; Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alexander Lai
- School of Science, Technology, Engineering, and Mathematics, Kentucky State University, Frankfort, KY, USA
| | - Min Zhang
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Wang
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan-Hong Zhu
- Department of Scientific Research Management, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Ma
- Department of Scientific Research Management, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hai-Peng Li
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Ayidana Haerheng
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Yang-Rui Qi
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Rui-Lan Wang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Na He
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Shuo Su
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China.
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Graziosi G, Lupini C, Favera FD, Martini G, Dosa G, Trevisani G, Garavini G, Mannelli A, Catelli E. Characterizing the domestic-wild bird interface through camera traps in an area at risk for avian influenza introduction in Northern Italy. Poult Sci 2024; 103:103892. [PMID: 38865769 PMCID: PMC11223120 DOI: 10.1016/j.psj.2024.103892] [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: 01/10/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024] Open
Abstract
Direct or indirect interactions between sympatric wildlife and poultry can lead to interspecies disease transmission. Particularly, avian influenza (AI) is a viral epidemic disease for which the poultry-wild bird interface shapes the risks of new viral introductions into poultry holdings. Given this background, the study hereby presented aimed to identify wild bird species in poultry house surroundings and characterize the spatiotemporal patterns of these visits. Eight camera traps were deployed for a year (January to December 2021) in 3 commercial chicken layer farms, including free-range and barn-type setups, located in a densely populated poultry area in Northern Italy at high risk for AI introduction via wild birds. Camera traps' positions were chosen based on wildlife signs identified during preliminary visits to the establishments studied. Various methods, including time series analysis, correspondence analysis, and generalized linear models, were employed to analyze the daily wild bird visits. A total of 1,958 camera trap days yielded 5,978 videos of wild birds from 27 different species and 16 taxonomic families. The animals were predominantly engaged in foraging activities nearby poultry houses. Eurasian magpies (Pica pica), ring-necked pheasants (Phasianus colchicus), and Eurasian collared doves (Streptopelia decaocto) were the most frequent visitors. Mallards (Anas platyrhynchos), an AI reservoir species, were observed only in a farm located next to a fishing sport lake. Time series analysis indicated that wild bird visits increased during spring and winter. Farm and camera trap location also influenced visit frequencies. Overall, the results highlighted specific species that could be prioritized for future AI epidemiological surveys. However, further research is required to assess their susceptibility and infectivity to currently circulating AI viruses, essential for identifying novel bridge hosts.
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Affiliation(s)
- Giulia Graziosi
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna 40064, Italy.
| | - Caterina Lupini
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna 40064, Italy
| | - Francesco Dalla Favera
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna 40064, Italy
| | - Gabriella Martini
- Veterinary Services, Local Health Unit of Imola (A.U.S.L. di Imola), Imola, Bologna 40026, Italy
| | - Geremia Dosa
- Veterinary Services, Local Health Unit of Imola (A.U.S.L. di Imola), Imola, Bologna 40026, Italy
| | | | - Gloria Garavini
- Veterinary Services of Eurovo Group, Imola, Bologna 40026, Italy
| | - Alessandro Mannelli
- Department of Veterinary Sciences, University of Torino, Grugliasco, Turin 10095, Italy
| | - Elena Catelli
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna 40064, Italy
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172
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Kumar S, Lezia A, Hasty J. Engineering plasmid copy number heterogeneity for dynamic microbial adaptation. Nat Microbiol 2024; 9:2173-2184. [PMID: 38890490 DOI: 10.1038/s41564-024-01706-w] [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: 04/27/2023] [Accepted: 04/19/2024] [Indexed: 06/20/2024]
Abstract
Natural microbial populations exploit phenotypic heterogeneity for survival and adaptation. However, in engineering biology, limiting the sources of variability is a major focus. Here we show that intentionally coupling distinct plasmids via shared replication mechanisms enables bacterial populations to adapt to their environment. We demonstrate that plasmid coupling of carbon-metabolizing operons facilitates copy number tuning of an essential but burdensome construct through the action of a stably maintained, non-essential plasmid. For specific cost-benefit situations, incompatible two-plasmid systems can stably persist longer than compatible ones. We also show using microfluidics that plasmid coupling of synthetic constructs generates population-state memory of previous environmental adaptation without additional regulatory control. This work should help to improve the design of synthetic populations by enabling adaptive engineered strains to function under changing growth conditions without strict fine-tuning of the genetic circuitry.
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Affiliation(s)
- Shalni Kumar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
| | - Andrew Lezia
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Jeff Hasty
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
- Synthetic Biology Institute, University of California, San Diego, San Diego, CA, USA
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173
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Durant AC, Donini A. Ammonia transport in the excretory system of mosquito larvae (Aedes aegypti): Rh protein expression and the transcriptome of the rectum. Comp Biochem Physiol A Mol Integr Physiol 2024; 294:111649. [PMID: 38670480 DOI: 10.1016/j.cbpa.2024.111649] [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: 12/23/2023] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
The role of the mosquito excretory organs (Malpighian tubules, MT and hindgut, HG) in ammonia transport as well as expression and function of the Rhesus (Rh protein) ammonia transporters within these organs was examined in Aedes aegypti larvae and adult females. Immunohistological examination revealed that the Rh proteins are co-localized with V-type H+-ATPase (VA) to the apical membranes of MT and HG epithelia of both larvae and adult females. Of the two Rh transporter genes present in A. aegypti, AeRh50-1 and AeRh50-2, we show using quantitative real-time PCR (qPCR) and an RNA in-situ hybridization (ISH) assay that AeRh50-1 is the predominant Rh protein expressed in the excretory organs of larvae and adult females. Further assessment of AeRh50-1 function in larvae and adults using RNAi (i.e. dsRNA-mediated knockdown) revealed significantly decreased [NH4+] (mmol l-1) levels in the secreted fluid of larval MT which does not affect overall NH4+ transport rates, as well as significantly decreased NH4+ flux rates across the HG (haemolymph to lumen) of adult females. We also used RNA sequencing to identify the expression of ion transporters and enzymes within the rectum of larvae, of which limited information currently exists for this important osmoregulatory organ. Of the ammonia transporters in A. aegypti, AeRh50-1 transcript is most abundant in the rectum thus validating our immunohistochemical and RNA ISH findings. In addition to enriched VA transcript (subunits A and d1) in the rectum, we also identified high Na+-K+-ATPase transcript (α subunit) expression which becomes significantly elevated in response to HEA, and we also found enriched carbonic anhydrase 9, inwardly rectifying K+ channel Kir2a, and Na+-coupled cation-chloride (Cl-) co-transporter CCC2 transcripts. Finally, the modulation in excretory organ function and/or Rh protein expression was examined in relation to high ammonia challenge, specifically high environmental ammonia (HEA) rearing of larvae. NH4+ flux measurements using the scanning-ion selective electrode (SIET) technique revealed no significant differences in NH4+ transport across organs comprising the alimentary canal of larvae reared in HEA vs freshwater. Further, significantly increased VA activity, but not NKA, was observed in the MT of HEA-reared larvae. Relatively high Rh protein immunostaining persists within the hindgut epithelium, as well as the ovary, of females at 24-48 h post blood meal corresponding with previously demonstrated peak levels of ammonia formation. These data provide new insight into the role of the excretory organs in ammonia transport physiology and the contribution of Rh proteins in mediating ammonia movement across the epithelia of the MT and HG, and the first comprehensive examination of ion transporter and channel expression in the mosquito rectum.
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Affiliation(s)
- Andrea C Durant
- Department of Biology, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - Andrew Donini
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.
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174
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Roberts NJ, Sarria JC. Recognizing the roles of fever in host survival and in medical intervention in infectious diseases. Am J Med Sci 2024; 368:85-89. [PMID: 38795968 DOI: 10.1016/j.amjms.2024.05.013] [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: 12/13/2023] [Revised: 03/10/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
Fever has roles both in host defense against infectious challenges and in guidance of medical intervention. These roles remain insufficiently acknowledged and considered by both health care providers and patients and their families. This review cites reports in support of both roles and provides recommendations regarding the clinician's approach to fever, as well as points relevant for education of patients and their families.
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Affiliation(s)
- Norbert J Roberts
- Division of Infectious Diseases and Immunology, Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA; Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA.
| | - Juan C Sarria
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
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175
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Wang J, Zou Z, Hu M, Shan X, Zhang Y, Miao Y, Zhang X, Islam N, Hu Q. Riemerella anatipestifer UvrC is required for iron utilization, biofilm formation and virulence. Avian Pathol 2024; 53:247-256. [PMID: 38420684 DOI: 10.1080/03079457.2024.2317431] [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: 10/10/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024]
Abstract
UvrC is a subunit of excinuclease ABC, which mediates nucleotide excision repair (NER) in bacteria. Our previous studies showed that transposon Tn4531 insertion in the UvrC encoding gene Riean_1413 results in reduced biofilm formation by Riemerella anatipestifer strain CH3 and attenuates virulence of strain YZb1. In this study, whether R. anatipestifer UvrC has some biological functions other than NER was investigated. Firstly, the uvrC of R. anatipestifer strain Yb2 was in-frame deleted by homologous recombination, generating deletion mutant ΔuvrC, and its complemented strain cΔuvrC was constructed based on Escherichia coli - R. anatipestifer shuttle plasmid pRES. Compared to the wild-type (WT) R. anatipestifer strain Yb2, uvrC deleted mutant ΔuvrC significantly reduced biofilm formation, tolerance to H2O2- and HOCl-induced oxidative stress, iron utilization, and adhesion to and invasion of duck embryonic hepatocytes, but not its growth curve and proteolytic activity. In addition, animal experiments showed that the LD50 value of ΔuvrC in ducklings was about 13-fold higher than that of the WT, and the bacterial loads in ΔuvrC infected ducklings were significantly lower than those in Yb2-infected ducklings, indicating uvrC deletion in R. anatipestifer attenuated virulence. Taken together, the results of this study indicate that R. anatipestifer UvrC is required for iron utilization, biofilm formation, oxidative stress tolerance and virulence of strain Yb2, demonstrating multiple functions of UvrC.RESEARCH HIGHLIGHTSDeletion of uvrC in R. anatipestfer Yb2 significantly reduced its biofilm formation.uvrC deletion led to reduced tolerance to H2O2- and HOCl-induced oxidative stress.The iron utilization of uvrC deleted mutant was significantly reduced.The uvrC deletion in R. anatipestifer Yb2 attenuated its virulence.
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Affiliation(s)
- Jialing Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Zuocheng Zou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Mengmeng Hu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Xinggen Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Ying Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Yiqin Miao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - XiaoYing Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Nazrul Islam
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Qinghai Hu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
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176
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Li HZ, Peng J, Yang K, Zhang Y, Chen QL, Zhu YG, Cui L. Single-cell exploration of active phosphate-solubilizing bacteria across diverse soil matrices for sustainable phosphorus management. NATURE FOOD 2024; 5:673-683. [PMID: 39103543 DOI: 10.1038/s43016-024-01024-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 07/10/2024] [Indexed: 08/07/2024]
Abstract
Phosphate-solubilizing bacteria (PSB) are crucial for enhancing phosphorus bioavailability and regulating phosphorus transformation processes. However, the in situ phosphorus-solubilizing activity and the link between phenotypes and genotypes for PSB remain unidentified. Here we employed single-cell Raman spectroscopy combined with heavy water to discern and quantify soil active PSB. Our results reveal that PSB abundance and in situ activity differed significantly between soil types and fertilization treatments. Inorganic fertilizer input was the key driver for active PSB distribution. Targeted single-cell sorting and metagenomic sequencing of active PSB uncovered several low-abundance genera that are easily overlooked within bulk soil microbiota. We elucidate the underlying functional genes and metabolic pathway, and the interplay between phosphorus and carbon cycling involved in high phosphorus solubilization activity. Our study provides a single-cell approach to exploring PSB from native environments, enabling the development of a microbial solution for the efficient agronomic use of phosphorus and mitigating the phosphorus crisis.
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Affiliation(s)
- Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | | | - Kai Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yiyue Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yong-Guan Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.
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177
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Miki T, Uemura T, Kinoshita M, Ami Y, Ito M, Okada N, Furuchi T, Kurihara S, Haneda T, Minamino T, Kim YG. Salmonella Typhimurium exploits host polyamines for assembly of the type 3 secretion machinery. PLoS Biol 2024; 22:e3002731. [PMID: 39102375 DOI: 10.1371/journal.pbio.3002731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 07/02/2024] [Indexed: 08/07/2024] Open
Abstract
Bacterial pathogens utilize the factors of their hosts to infect them, but which factors they exploit remain poorly defined. Here, we show that a pathogenic Salmonella enterica serovar Typhimurium (STm) exploits host polyamines for the functional expression of virulence factors. An STm mutant strain lacking principal genes required for polyamine synthesis and transport exhibited impaired infectivity in mice. A polyamine uptake-impaired strain of STm was unable to inject effectors of the type 3 secretion system into host cells due to a failure of needle assembly. STm infection stimulated host polyamine production by increasing arginase expression. The decline in polyamine levels caused by difluoromethylornithine, which inhibits host polyamine production, attenuated STm colonization, whereas polyamine supplementation augmented STm pathogenesis. Our work reveals that host polyamines are a key factor promoting STm infection, and therefore a promising therapeutic target for bacterial infection.
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Affiliation(s)
- Tsuyoshi Miki
- Department of Microbiology, School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Takeshi Uemura
- Laboratory of Bio-analytical Chemistry, Faculty of Pharmaceutical Sciences, Josai University, Saitama, Japan
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Yuta Ami
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Masahiro Ito
- Department of Microbiology, School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Nobuhiko Okada
- Department of Microbiology, School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Takemitsu Furuchi
- Laboratory of Bio-analytical Chemistry, Faculty of Pharmaceutical Sciences, Josai University, Saitama, Japan
| | - Shin Kurihara
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Takeshi Haneda
- Department of Microbiology, School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Yun-Gi Kim
- Department of Microbiology, School of Pharmacy, Kitasato University, Tokyo, Japan
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178
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Preziosi E, Frollini E, Ghergo S, Parrone D, Ruggiero L, Sciarra A, Ciotoli G. A comprehensive monitoring approach for a naturally anoxic aquifer beneath a controlled landfill. CHEMOSPHERE 2024; 362:142657. [PMID: 38901701 DOI: 10.1016/j.chemosphere.2024.142657] [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: 01/31/2024] [Revised: 05/25/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
The processes leading to high levels of arsenic (As), iron (Fe), and manganese (Mn) in groundwater, in a naturally reducing aquifer at a controlled municipal landfill site, are investigated. The challenge is to distinguish the natural water-rock interaction processes, that allow these substances to dissolve in groundwater, from direct pollution or enhanced dissolution of hydroxides as undesired consequences of the anthropic activities above. Ordinary groundwater monitoring of physical-chemical parameters and inorganic compounds (major and trace elements) was complemented by environmental isotopes of groundwater (tritium, deuterium, oxygen-18 and carbon-13) and dissolved gases (carbon-13 of methane and carbon dioxide and carbon-14 of methane). Pearson/Spearman correlation indices, as well as Principal Component Analysis (PCA), were used to determine the main correlations among variables. The concurrent presence of As, Fe and CH4, as reported in similar anoxic environments, suggests that anaerobic oxidation of methane could drive the reductive dissolution of As-rich Fe(III)(hydro)oxides. Manganese is more sensitive to carbon dioxide, possibly due to a decrease in pH which accelerates the dissolution of Mn-oxides. Finally, we found that tritium and deuterium, which have been used for decades as leachate tracer in groundwater, may be subject to false positives due to the reuse of water recovered from leachate treatment (which has the same isotopic signature of leachate) within the plants, to comply with the requirements of the circular economy. The integration of the environmental isotope analysis into the traditional monitoring approach can effectively support the comprehension of processes. However, this strategy needs to be complemented by a good conceptual hydrogeological model and expert evaluation to avoid misinterpretations.
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Affiliation(s)
- E Preziosi
- CNR-IRSA - National Research Council - Water Research Institute, Montelibretti, Italy.
| | - E Frollini
- CNR-IRSA - National Research Council - Water Research Institute, Montelibretti, Italy
| | - S Ghergo
- CNR-IRSA - National Research Council - Water Research Institute, Montelibretti, Italy
| | - D Parrone
- CNR-IRSA - National Research Council - Water Research Institute, Montelibretti, Italy
| | - L Ruggiero
- INGV - Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Roma1, Rome, Italy
| | - A Sciarra
- INGV - Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Roma1, Rome, Italy
| | - G Ciotoli
- INGV - Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Roma1, Rome, Italy; CNR-IGAG - National Research Council, Institute of Environmental Geology and Geoengineering, Montelibretti, Italy
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179
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Vivekanandan KE, Kasimani R, Kumar PV, Meenatchisundaram S, Sundar WA. Overview of cloning in lactic acid bacteria: Expression and its application of probiotic potential in inflammatory bowel diseases. Biotechnol Appl Biochem 2024; 71:881-895. [PMID: 38576028 DOI: 10.1002/bab.2584] [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: 10/18/2023] [Accepted: 03/22/2024] [Indexed: 04/06/2024]
Abstract
Inflammatory bowel disease (IBD) imposes a significant impact on the quality of life for affected individuals. However, there was a current lack of a systematic summary regarding the latest epidemic trends and the underlying pathogenesis of IBD. This highlights the need for a thorough examination of both the epidemiological aspects of IBD and the specific mechanisms by which lactic acid bacteria (LAB) contribute to mitigating this condition. In developed countries, higher incidences and death rates of IBD have been observed, influenced by a combination of environmental and genetic factors. LAB offer significant advantages and substantial potential for enhancing IBD treatment. LAB's capabilities include the production of bioactive metabolites, regulation of gut immunity, protection of intestinal mechanical barriers, inhibition of oxidative damage, and restoration of imbalanced gut microbiota. The review suggests that screening effective LAB using cell models and metabolites, optimizing LAB intake through dose-effect studies, enhancing utilization through nanoencapsulation and microencapsulation, investigating mechanisms to deepen the understanding of LAB, and refining clinical study designs. These efforts aim to contribute to comprehending the epidemic trend, pathogenesis, and treatment of IBD, ultimately fostering the development of targeted therapeutic products, such as LAB-based interventions.
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Affiliation(s)
- K E Vivekanandan
- Department of Microbiology, Nehru Arts and Science College, Coimbatore, Tamil Nadu, India
| | - R Kasimani
- Department of Microbiology, Nehru Arts and Science College, Coimbatore, Tamil Nadu, India
| | - P Vinoth Kumar
- Department of Microbiology, Nehru Arts and Science College, Coimbatore, Tamil Nadu, India
| | - S Meenatchisundaram
- Department of Microbiology, Shree Nehru Maha Vidyalaya College of Arts and Science, Coimbatore, Tamil Nadu, India
| | - William Arputha Sundar
- Department of Pharmaceuticals, Swamy Vivekananda College of Pharmacy, Namakkal, Tamil Nadu, India
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180
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Meng X, Zhang J, Wan Z, Li T, Xie Q, Qin A, Shao H, Zhang H, Ye J. Molecular epidemiology of infectious bronchitis virus in eastern and southern China during 2021-2023. Poult Sci 2024; 103:103939. [PMID: 38909507 PMCID: PMC11254719 DOI: 10.1016/j.psj.2024.103939] [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: 03/29/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 06/25/2024] Open
Abstract
As a highly infectious and contagious pathogen in chickens, infectious bronchitis virus (IBV) is currently grouped into nine genotypes (GI to GIX). However, the classification of serotypes of IBV is still not clear. In this study, 270 field strains of IBV were isolated from dead or diseased chicken flocks in eastern and southern China during January 2021 to April 2023. These isolated IBV strains could be classified into 2 genotypes, GI (including 5 lineages GI-1, GI-13, GI-19, GI-22, and GI-28) and GVI based on the complete S1 sequence. Further analysis showed that the GI-19, GI-13, GI-22, GI-28, and GVI were the dominant genotypes with the proportions of 61.48, 8.89, 8.89, 7.78, and 8.89% respectively, and the homology of S1 protein of these isolates ranged from 86.85 to 100% in GI-19, 92.22 to 100% in GI-13, 83.1 to 100% in GI-22, 94.81 to 100% in GI-28 and 90.0 to 99.8% in GVI, respectively. Moreover, cross-neutralization test with sera revealed that these isolates in GI-19 lineage could be classified into at least 3 serotypes according to the antigenic relationship. In addition, structure assay using PyMOL indicated that one mutation such as S120 in receptor binding site (RBD) of GI-19 might alter the antigenicity and conformation of S protein of IBV. Overall, our data demonstrate that not only multiple genotypes, but also multiple serotypes in a single genotype or lineage have been co-circulated in eastern and southern China, providing novel insights into the molecular evolution of the antigenicity of IBV and highlighting the significance of the selection of the dominant isolate for vaccine development in IBV endemic region.
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Affiliation(s)
- Xianchen Meng
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Biotechnology Research laboratory, Jiangsu Lihua Animal Husbandry Co., Ltd., Changzhou, Jiangsu, 213168, China
| | - Jianjun Zhang
- Sinopharm Yangzhou VAC Biological Engineering Co., Ltd., Yangzhou, Jiangsu, 225000, China
| | - Zhimin Wan
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Tuofan Li
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Quan Xie
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Aijian Qin
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Hongxia Shao
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Haitao Zhang
- Biotechnology Research laboratory, Jiangsu Lihua Animal Husbandry Co., Ltd., Changzhou, Jiangsu, 213168, China.
| | - Jianqiang Ye
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China.
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181
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Zhu L, Sun L, Liu W, Han W, Huang G, Li J. Long-term storage does not affect the DNA methylation profiles of vitrified-warmed human embryos. Mol Reprod Dev 2024; 91:e23713. [PMID: 37882215 DOI: 10.1002/mrd.23713] [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: 05/29/2023] [Revised: 08/31/2023] [Accepted: 09/24/2023] [Indexed: 10/27/2023]
Abstract
With the widespread application of embryo cryopreservation in assisted reproductive techniques, it is necessary to assess the safety of long-term cryopreservation of human embryos and it is unclear whether storage time has an impact on the DNA methylation profiles of human embryos. Nine women who received IVF treatment were recruited for this study. The retrieved eight-cell human embryos were classified into three groups including fresh embryos, cryopreserved embryos stored for 3 years, and cryopreserved embryos stored for 8 years. Single-cell whole-genome bisulfite sequencing (scWGBS) was conducted. The genome-wide methylation pattern of the fresh and two cryopreserved groups were similar. In addition, the methylation level in different genomic regions showed comparable patterns and no significant differences were observed in the methylation level of imprinted genes among the three groups. A total of 587 differentially methylated regions (DMRs) in the 3-year group and 540 DMRs in the 8-year group were identified comparing to fresh group. However, they were not enriched in promoters and had a similar genome-wide distributions, suggesting that these DMRs may not contribute to the changes in corresponding gene expressions. Our study illustrated that long-term cryopreservation will not affect the DNA methylation profiles of human eight-cell embryos at single-cell level.
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Affiliation(s)
- Ling Zhu
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Liwei Sun
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Weiwei Liu
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Wei Han
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Guoning Huang
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jingyu Li
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
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182
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Huber KJ, Papendorf J, Pilke C, Bunk B, Spröer C, Kirstein S, Wolf J, Neumann-Schaal M, Rohde M, Pester M. Edaphobacter paludis sp. nov., a new acidophilic representative of the Acidobacteriota isolated from fen soils. Int J Syst Evol Microbiol 2024; 74. [PMID: 39196616 DOI: 10.1099/ijsem.0.006500] [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: 08/29/2024] Open
Abstract
Two new strains JP48T and JP55 affiliated with the acidobacterial class Terriglobia have been isolated from fen soil sampled in the Fichtelgebirge Mountains near Bayreuth, Germany. Both strains were Gram-stain-negative, non-motile, non-spore-forming rods that divide by binary fission, segregate exopolysaccharide-like material and form capsules. Strains JP48T and JP55 grew at 4-36 °C (optimum at 27 °C), pH 3.6-7.3 (optimum at pH 4.6-5.5) and with NaCl concentrations of 0-3% (optimum at 1.0%; w/v). Strains JP48T and JP55 grew aerobically on a wide range of organic substrates including mono- and oligosaccharides, amino acids and short-chained fatty acids. MK-8 was identified as the major respiratory quinone. The major fatty acids for strains JP48T and JP55 were iso-C15 : 0, C16 : 1 ω7c, C16 : 0 and iso-diabolic acid. Phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, lysophophatidylethanolamine, phosphatidylcholine, unidentified glyco- and glycophospholipids, and unidentified high mass lipid species were the major polar membrane lipids. The G+C content of strains JP48T and JP55 was 57.4 and 57.2 mol%, respectively. The genomes of strains JP48T and JP55 contained nine potential secondary metabolite regions encoding for the compound classes NRPS(-like), T3PKS, terpene, or lanthipeptide class IV. Phylogenetic reconstruction and 16S rRNA gene sequence similarities of 98.3 and 96.9% identified Edaphobacter dinghuensis DHF9T and Edaphobacter lichenicola DSM 104462T as the most closely related type strains to strains JP48T and JP55. Based on their phenotype, phylogeny and chemotaxonomy, we propose the novel species Edaphobacter paludis sp. nov. (type strain JP48T=DSM 109919T=CECT 30269T; additional strain JP55=DSM 109920=CECT 30268) within the class Terriglobia of the phylum Acidobacteriota.
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Affiliation(s)
- Katharina J Huber
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - János Papendorf
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Carolin Pilke
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Bioinformatic Services, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Bioinformatic Services, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sarah Kirstein
- Department of Metabolomics & Services, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jacqueline Wolf
- Department of Metabolomics & Services, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Department of Metabolomics & Services, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Manfred Rohde
- Department of Medical Microbiology, Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Pester
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
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183
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Tripathi J, Gautam S. Unravelling the key steps impairing the metabolic state of Xanthomonas cells undergoing programmed cell death. Int Microbiol 2024; 27:1285-1296. [PMID: 38190087 DOI: 10.1007/s10123-023-00471-w] [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: 07/14/2023] [Revised: 11/23/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024]
Abstract
Programmed cell death (PCD) has been reported in Xanthomonas axonopodis pv. glycines (Xag) wild type earlier and was indirectly shown to be induced by metabolic stress; however, deciphering the key proteins regulating the metabolic stress remained unrevealed. In this study, transcriptomic and proteomic analyses were performed to investigate the prominent pathways, having a role in the induction of metabolic stress in Xag cells undergoing PCD. A comprehensive analysis of transcriptome and proteome data revealed the major involvement of metabolic pathways related to branched chain amino acid degradation, such as acyl-CoA dehydrogenase and energy-yielding, ubiquinol:cytochrome c oxidoreductase complex, in Xag cells undergoing PCD. Consequently, oxidative stress response genes showed major upregulation in Xag cells in PCD-inducing medium; however, no such upregulation was observed at the protein level, indicative of depleted protein levels under excessive stress conditions. Activation of stress response and DNA repair proteins was also observed in Xag cells grown in PCD-inducing medium, which is indicative of excessive cellular damage. Thus, the findings indicate that programmed cell death in Xag is an outcome of metabolic stress in nutrient condition not suitable for a plant pathogen like Xanthomonas, which is more acclimatised with altogether a different nutritional requirement predominantly having an enriched carbohydrate source.
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Affiliation(s)
- Jyoti Tripathi
- Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Satyendra Gautam
- Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, 400085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India.
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184
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Zeng Y, Lockhart AC, Jin RU. The preclinical discovery and development of zolbetuximab for the treatment of gastric cancer. Expert Opin Drug Discov 2024; 19:873-886. [PMID: 38919123 DOI: 10.1080/17460441.2024.2370332] [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: 03/31/2024] [Revised: 06/04/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
INTRODUCTION Gastric cancer remains a formidable challenge in oncology with high mortality rates and few advancements in treatment. Claudin-18.2 (CLDN18.2) is a tight junction protein primarily expressed in the stomach and is frequently overexpressed in certain subsets of gastric cancers. Targeting CLDN18.2 with monoclonal antibodies, such as zolbetuximab (IMAB362), has shown promising efficacy results in combination with chemotherapy. AREAS COVERED The molecular cell biology of CLDN18.2 is discussed along with studies demonstrating the utility of CLDN18.2 expression as a biomarker and therapeutic target. Important clinical studies are reviewed, including Phase III trials, SPOTLIGHT and GLOW, which demonstrate the efficacy of zolbetuximab in combination with chemotherapy in patients with CLDN18.2-positive advanced gastric cancer. EXPERT OPINION CLDN18.2 is involved in gastric differentiation through maintenance of epithelial barrier function and coordination of signaling pathways, and its expression in gastric cancers reflects a 'gastric differentiation' program. Targeting Claudin-18.2 represents the first gastric cancer specific 'targeted' treatment. Further studies are needed to determine its role within current gastric cancer treatment sequencing, including HER2-targeted therapies and immunotherapies. Management strategies will also be needed to better mitigate zolbetuximab-related treatment side effects, including gastrointestinal (GI) toxicities.
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Affiliation(s)
- Yongji Zeng
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, USA
| | - A Craig Lockhart
- Division of Hematology/Oncology, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Ramon U Jin
- Section of Hematology/Oncology, Department of Medicine, Baylor College of Medicine, Houston, USA
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185
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Fu M, Wang Y, Wang J, Hao Y, Zeng F, Zhang Z, Du J, Long H, Yan F. Genetic Modulation of Biosynthetic Gas Vesicles for Ultrasound Imaging. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310008. [PMID: 38533968 DOI: 10.1002/smll.202310008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/11/2024] [Indexed: 03/28/2024]
Abstract
Gas vesicles (GVs) from microorganisms are genetically air-filled protein nanostructures, and serve as a new class of nanoscale contrast agents for ultrasound imaging. Recently, the genetically encoded GV gene clusters have been heterologously expressed in Escherichia coli, allowing these genetically engineered bacteria to be visualized in vivo in a real-time manner by ultrasound. However, most of the GV genes remained functionally uncharacterized, which makes it difficult to regulate and modify GVs for broad medical applications. Here, the impact of GV proteins on GV formation is systematically investigated. The results first uncovered that the deletions of GvpR or GvpU resulted in the formation of a larger proportion of small, biconical GVs compared to the full-length construct, and the deletion of GvpT resulted in a larger portion of large GVs. Meanwhile, the combination of gene deletions has resulted in several genotypes of ultrasmall GVs that span from 50 to 20 nm. Furthermore, the results showed that E. coli carrying the ΔGvpCRTU mutant can produce strong ultrasound contrast signals in mouse liver. In conclusion, the study provides new insights into the roles of GV proteins in GV formation and produce ultrasmall GVs with a wide range of in vivo research.
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Affiliation(s)
- Meijun Fu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyuan Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jieqiong Wang
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai, 201206, China
| | - Yongsheng Hao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fengyi Zeng
- Department of Ultrasound, The Second People's Hospital of Shenzhen, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518061, China
| | | | - Jianxiong Du
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huan Long
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Fei Yan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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186
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Krewing M, Mönch E, Bolten A, Niesalla H. Resistance or tolerance? Highlighting the need for precise terminology in the field of disinfection. J Hosp Infect 2024; 150:51-60. [PMID: 38782058 DOI: 10.1016/j.jhin.2024.05.006] [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: 12/19/2023] [Revised: 04/24/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
The terms 'resistance' and 'tolerance' are well defined in the context of antibiotic research. However, in the field of disinfection, these terms are often used synonymously, which creates ambiguity and can lead to misunderstandings and misconceptions. In addition, this inconsistency in terminology makes it difficult to assess the risk of a disinfectant resistance. This general review aims to discuss existing definitions of the terms 'adaptation', 'susceptibility', 'tolerance', 'persistence' and 'resistance' in the light of disinfectants. The most ambiguity is found between tolerance and resistance. Whereas the former describes the not necessarily heritable survival of transient exposure to usually lethal concentrations, resistance is the strictly heritable ability to survive otherwise lethal concentrations of an antimicrobial agent, regardless of exposure time. A simple transfer of experience from antibiotic research is not recommended when assessing the risk of resistance to disinfectants, as there are important differences between antibiotics and disinfectants, although both are antimicrobials: (i) disinfectants are usually applied at concentrations that exceed the minimum inhibitory concentration by orders of magnitude, (ii) the exposure times of disinfectants are in the range of seconds, minutes, or a few hours, (iii) the mode of action of disinfectants is less specific, and (iv) disinfectants often contain more than one active agent with additive or synergistic effects. It is important to recognize that disinfectants, like other antimicrobial agents such as antibiotics, have a dualistic nature and should be used correctly and with caution.
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Affiliation(s)
- M Krewing
- Hartmann Science Center, BODE Chemie GmbH - a Company of the Hartmann Group, Hamburg, Germany.
| | - E Mönch
- BODE Chemie GmbH - a Company of the Hartmann Group, Hamburg, Germany
| | - A Bolten
- BODE Chemie GmbH - a Company of the Hartmann Group, Hamburg, Germany
| | - H Niesalla
- Hartmann Science Center, BODE Chemie GmbH - a Company of the Hartmann Group, Hamburg, Germany
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187
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Singh B, Jaiswal S, Kodgire P. Outer membrane proteins and vesicles as promising vaccine candidates against Vibrio spp. infections. Crit Rev Microbiol 2024; 50:417-433. [PMID: 37272649 DOI: 10.1080/1040841x.2023.2212072] [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: 10/19/2022] [Revised: 02/12/2023] [Accepted: 05/02/2023] [Indexed: 06/06/2023]
Abstract
Indiscriminate use of antibiotics to treat bacterial infections has brought unmanageable antibiotic-resistant strains into existence. Vibrio spp. represents one such gram-negative enteric pathogenic group with more than 100 species, infecting humans and fish. The Vibrio spp. is demarcated into two groups, one that causes cholera and the other producing non-cholera or vibriosis infections. People who encounter contaminated water are at risk, but young children and pregnant women are the most vulnerable. Though controllable, Vibrio infection still necessitates the development of preventative measures, such as vaccinations, that can lessen the severity of the infection and reduce reliance on antibiotic use. With emerging multi-drug resistant strains, efforts are needed to develop newer vaccines, such as subunit-based or outer membrane vesicle-based. Thus, this review strives to bring together available information about Vibrio spp. outer membrane proteins and vesicles, encompassing their structure, function, and immunoprotective role.
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Affiliation(s)
- Brijeshwar Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Surbhi Jaiswal
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Prashant Kodgire
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
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188
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Pipes SE, Lovell CR, Kathrein KL. In vivo examination of pathogenicity and virulence in environmentally isolated Vibrio vulnificus. Microbiologyopen 2024; 13:e1427. [PMID: 39041461 PMCID: PMC11264103 DOI: 10.1002/mbo3.1427] [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: 05/29/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/24/2024] Open
Abstract
Human exposure to Vibrio vulnificus, a gram-negative, halophilic environmental pathogen, is increasing. Despite this, the mechanisms of its pathogenicity and virulence remain largely unknown. Each year, hundreds of infections related to V. vulnificus occur, leading to hospitalization in 92% of cases and a mortality rate of 35%. The infection is severe, typically contracted through the consumption of contaminated food or exposure of an open wound to contaminated water. This can result in necrotizing fasciitis and the need for amputation of the infected tissue. Although several genes (rtxA1, vvpE, and vvhA) have been implicated in the pathogenicity of this organism, a defined mechanism has not been discovered. In this study, we examine environmentally isolated V. vulnificus strains using a zebrafish model (Danio rerio) to investigate their virulence capabilities. We found significant variation in virulence between individual strains. The commonly used marker gene of disease-causing strains, vcgC, did not accurately predict the more virulent strains. Notably, the least virulent strain in the study, V. vulnificus Sept WR1-BW6, which tested positive for vcgC, vvhA, and rtxA1, did not cause severe disease in the fish and was the only strain that did not result in any mortality. Our study demonstrates that virulence varies greatly among different environmental strains and cannot be accurately predicted based solely on genotype.
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Affiliation(s)
- Shannon E. Pipes
- Department of Biological SciencesUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Charles R. Lovell
- Department of Biological SciencesUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Katie L. Kathrein
- Department of Biological SciencesUniversity of South CarolinaColumbiaSouth CarolinaUSA
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189
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Lee H, Chaudhary DK, Lee KE, Cha IT, Chi WJ, Kim DU. Microbacterium humicola sp. nov., Microbacterium terrisoli sp. nov., Paenibacillus pedocola sp. nov., Paenibacillus silviterrae sp. nov., Flavobacterium terrisoli sp. nov., and Aquabacterium humicola sp. nov., isolated from soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 39120518 DOI: 10.1099/ijsem.0.006486] [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: 08/10/2024] Open
Abstract
Four Gram-stain-positive and two Gram-stain-negative bacterial strains, designated as W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T, were isolated from soil samples collected from the Republic of Korea. The 16S rRNA gene sequence analysis showed that strains W4T and FW7T belonged to the genus Microbacterium, strains TW48T and UW52T were affiliated to the genus Paenibacillus, strain PT-3T was related to the genus Flavobacterium, and strain RJY3T was associated with the genus Aquabacterium. The closest phylogenetic taxa to W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T were Microbacterium bovistercoris NEAU-LLET (97.7 %), Microbacterium protaetiae DFW100M-13T (97.9 %), Paenibacillus auburnensis JJ-7T (99.6 %), Paenibacillus allorhizosphaerae JJ-447T (95.7 %), Flavobacterium buctense T7T (97.1 %), and Aquabacterium terrae S2T (99.5 %), respectively. Average nucleotide identity and digital DNA-DNA hybridization values between the novel strains and related reference type strains were <95.0 % and <70.0 %, respectively. The major cellular fatty acid in strains W4T, FW7T TW48T, and UW52T was antiso-C15 : 0. Similarly, strain PT-3T revealed iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, and iso-C15 : 0 3-OH as its principal fatty acids. On the other hand, RJY3T exhibited summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), and C12 : 0 as its predominant fatty acids. Overall, the polyphasic taxonomic data indicated that strains W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T represent novel species within the genera Microbacterium, Paenibacillus, Flavobacterium, and Aquabacterium. Accordingly, we propose the names Microbacterium humicola sp. nov., with the type strain W4T (=KCTC 49888T=NBRC 116001T), Microbacterium terrisoli sp. nov., with the type strain FW7T (=KCTC 49859T=NBRC 116000T), Paenibacillus pedocola sp. nov., with the type strain TW48T (=KCTC 43470T=NBRC 116017T), Paenibacillus silviterrae sp. nov., with the type strain UW52T (=KCTC 43477T=NBRC 116018T), Flavobacterium terrisoli sp. nov., with the type strain PT-3T (=KCTC 92106T=NBRC 116012T), and Aquabacterium humicola sp. nov., with the type strain RJY3T (=KCTC 92105T=NBRC 115831T).
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Affiliation(s)
- Hyosun Lee
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Microbiology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - In-Tae Cha
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Won-Jae Chi
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, 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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190
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Padasas-Adalla CS, Ortega-Kindica RCM, Dalayap R, Martinez JG, Amparado O, Moneva CS, Lomelí-Ortega CO, Tabugo SR, Balcázar JL. Deciphering taxonomic and functional patterns of microbial communities associated with the tiger tail seahorse ( Hippocampus comes). Physiol Genomics 2024; 56:590-595. [PMID: 38975795 DOI: 10.1152/physiolgenomics.00039.2024] [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: 04/11/2024] [Revised: 06/04/2024] [Accepted: 07/02/2024] [Indexed: 07/09/2024] Open
Abstract
Gaining insight into the diversity, structure, and metabolic functions of microbial communities is essential for understanding their roles in host health and ecosystem dynamics. However, research on the seahorse-associated microbiome remains limited, despite these threatened fish facing increasing human pressures worldwide. Here, we explored the microbial diversity and metabolic functions of the skin and gut of the tiger tail seahorse (Hippocampus comes) and its surrounding environment using shotgun metagenomics and bioinformatics. Members of the Pseudomonadota phylum were dominant in the skin microbiome, whereas Bacteroidota was dominant in the gut. Bacillota, Actinomycetota, and Planctomycetota were also detected in the seahorse-associated microbiome. Statistical analysis revealed significant differences (P < 0.01) in species diversity between skin and gut microbiomes, with members belonging to the Moraxellaceae family being dominant on the skin and the Bacteroidaceae family in the gut. Moreover, the surrounding environment (water or sediment) did not have a direct effect on the seahorse microbiome composition. The skin microbiome exhibited a higher abundance of functional genes related to energy, lipid, and amino acid metabolism as well as terpenoids and polyketides metabolism, xenobiotics biodegradation, and metabolism compared with the gut. Despite differences among classes, the total abundance of bacteriocins was similar in both gut and skin microbiomes, which is significant in shaping microbial communities due to their antimicrobial properties. A better knowledge of seahorse microbiomes benefits conservation and sustainable aquaculture efforts, offering insights into habitat protection, disease management, and optimizing aquaculture environments, thereby promoting seahorse health and welfare while minimizing environmental impact and enhancing aquaculture sustainability.NEW & NOTEWORTHY To the best of our knowledge, this study represents the first comprehensive examination of the taxonomic and functional patterns of the skin and gut microbiome in the tiger tail seahorse. These findings have the potential to significantly enhance our understanding of the seahorse-associated microbiome, thereby contributing to the prediction and control of bacterial infections in seahorses, which are a leading cause of high mass mortality rates in seahorse aquaculture and other fish species.
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Affiliation(s)
- Chinee Surita Padasas-Adalla
- Department of Biological Sciences, College of Science and Mathematics, Mindanao State University - Iligan Institute of Technology, Iligan, Philippines
- Department of Biological Sciences, College of Arts and Sciences, Cavite State University - Main Campus, Cavite, Philippines
- Molecular Systematics and Oceanography Laboratory, Premier Research Institute of Science and Mathematics, Mindanao State University - Iligan Institute of Technology, Iligan, Philippines
| | - Rose Chinly Mae Ortega-Kindica
- Department of Biological Sciences, College of Science and Mathematics, Mindanao State University - Iligan Institute of Technology, Iligan, Philippines
- Molecular Systematics and Oceanography Laboratory, Premier Research Institute of Science and Mathematics, Mindanao State University - Iligan Institute of Technology, Iligan, Philippines
- Department of Biology and Environmental Science, University of the Philippines Cebu, Cebu City, Philippines
| | - Rodelyn Dalayap
- Department of Biology, Sultan Kudarat State University, Tacurong City, Philippines
| | - Joey Genevieve Martinez
- Department of Biological Sciences, College of Science and Mathematics, Mindanao State University - Iligan Institute of Technology, Iligan, Philippines
- Complex Systems Group, Premier Research Institute of Science and Mathematics, Mindanao State University - Iligan Institute of Technology, Iligan, Philippines
| | - Olive Amparado
- Department of Biological Sciences, College of Science and Mathematics, Mindanao State University - Iligan Institute of Technology, Iligan, Philippines
| | - Carlo Stephen Moneva
- Department of Biological Sciences, College of Science and Mathematics, Mindanao State University - Iligan Institute of Technology, Iligan, Philippines
| | | | - Sharon Rose Tabugo
- Department of Biological Sciences, College of Science and Mathematics, Mindanao State University - Iligan Institute of Technology, Iligan, Philippines
- Molecular Systematics and Oceanography Laboratory, Premier Research Institute of Science and Mathematics, Mindanao State University - Iligan Institute of Technology, Iligan, Philippines
| | - José Luis Balcázar
- Catalan Institute for Water Research, Girona, Spain
- University of Girona, Girona, Spain
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191
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Rakonjac J, Gold VAM, León-Quezada RI, Davenport CH. Structure, Biology, and Applications of Filamentous Bacteriophages. Cold Spring Harb Protoc 2024; 2024:pdb.over107754. [PMID: 37460152 DOI: 10.1101/pdb.over107754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
The closely related Escherichia coli Ff filamentous phages (f1, fd, and M13) have taken a fantastic journey over the past 60 years, from the urban sewerage from which they were first isolated, to their use in high-end technologies in multiple fields. Their relatively small genome size, high titers, and the virions that tolerate fusion proteins make the Ffs an ideal system for phage display. Folding of the fusions in the oxidizing environment of the E. coli periplasm makes the Ff phages a platform that allows display of eukaryotic surface and secreted proteins, including antibodies. Resistance of the Ffs to a broad range of pH and detergents facilitates affinity screening in phage display, whereas the stability of the virions at ambient temperature makes them suitable for applications in material science and nanotechnology. Among filamentous phages, only the Ffs have been used in phage display technology, because of the most advanced state of knowledge about their biology and the various tools developed for E. coli as a cloning host for them. Filamentous phages have been thought to be a rather small group, infecting mostly Gram-negative bacteria. A recent discovery of more than 10 thousand diverse filamentous phages in bacteria and archaea, however, opens a fascinating prospect for novel applications. The main aim of this review is to give detailed biological and structural information to researchers embarking on phage display projects. The secondary aim is to discuss the yet-unresolved puzzles, as well as recent developments in filamentous phage biology, from a viewpoint of their impact on current and future applications.
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Affiliation(s)
- Jasna Rakonjac
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- Nanophage Technologies Ltd., Palmerston North, Manawatu 4474, New Zealand
| | - Vicki A M Gold
- Living Systems Institute University of Exeter, Exeter, EX4 4QD, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, United Kingdom
| | - Rayén I León-Quezada
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- Nanophage Technologies Ltd., Palmerston North, Manawatu 4474, New Zealand
| | - Catherine H Davenport
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- Nanophage Technologies Ltd., Palmerston North, Manawatu 4474, New Zealand
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192
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Harnisch F, Deutzmann JS, Boto ST, Rosenbaum MA. Microbial electrosynthesis: opportunities for microbial pure cultures. Trends Biotechnol 2024; 42:1035-1047. [PMID: 38431514 PMCID: PMC11310912 DOI: 10.1016/j.tibtech.2024.02.004] [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: 12/08/2023] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 03/05/2024]
Abstract
Microbial electrosynthesis (MES) is an emerging technology that couples renewable electricity to microbial production processes. Although advances in MES performance have been driven largely by microbial mixed cultures, we see a great limitation in the diversity, and hence value, of products that can be achieved in undefined mixed cultures. By contrast, metabolic control of pure cultures and genetic engineering could greatly expand the scope of MES, and even of broader electrobiotechnology, to include targeted high-value products. To leverage this potential, we advocate for more efforts and activities to develop engineered electroactive microbes for synthesis, and we highlight the need for a standardized electrobioreactor infrastructure that allows the establishment and engineering of electrobioprocesses with these novel biocatalysts.
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Affiliation(s)
- Falk Harnisch
- Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research GmbH, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Jörg S Deutzmann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Santiago T Boto
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf Reichwein Strasse 23, 07745 Jena, Germany; Institute of Microbiology, Faculty for Biological Sciences, Friedrich-Schiller-University Jena, Neugasse 23, 07743 Jena, Germany
| | - Miriam A Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf Reichwein Strasse 23, 07745 Jena, Germany; Institute of Microbiology, Faculty for Biological Sciences, Friedrich-Schiller-University Jena, Neugasse 23, 07743 Jena, Germany.
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193
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Fujii Y, Masatani T, Nishiyama S, Takahashi T, Okajima M, Izumi F, Sakoda Y, Takada A, Ozawa M, Sugiyama M, Ito N. Molecular characterization of an avian rotavirus a strain detected from a large-billed crow (Corvus macrorhynchos) in Japan. Virology 2024; 596:110114. [PMID: 38781709 DOI: 10.1016/j.virol.2024.110114] [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: 02/12/2024] [Revised: 05/02/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Avian rotaviruses A (RVAs) are occasionally transmitted to animals other than the original hosts across species barriers. Information on RVAs carried by various bird species is important for identifying the origin of such interspecies transmission. In this study, to facilitate an understanding of the ecology of RVAs from wild birds, we characterized all of the genes of an RVA strain, JC-105, that was detected in a fecal sample of a large-billed crow (Corvus macrorhynchos) in Japan. All of the genes of this strain except for the VP4 and VP7 genes, which were classified as novel genotypes (P[56] and G40, respectively), were closely related to those of the avian-like RVA strain detected from a raccoon, indicating the possibility that crows had been involved in the transmission of avian RVAs to raccoons. Our findings highlight the need for further viral investigations in wild birds and mammals to understand the mechanisms of avian-to-mammal RVA transmission.
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Affiliation(s)
- Yuji Fujii
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Tatsunori Masatani
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Center for One Medicine Innovative Translational Research (COMIT), Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Shoko Nishiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Tatsuki Takahashi
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Misuzu Okajima
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Fumiki Izumi
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, Hokkaido 060-0818, Japan
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan; Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Makoto Ozawa
- Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Makoto Sugiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.
| | - Naoto Ito
- Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Center for One Medicine Innovative Translational Research (COMIT), Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.
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194
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Xu W, Yu F, Addison O, Zhang B, Guan F, Zhang R, Hou B, Sand W. Microbial corrosion of metallic biomaterials in the oral environment. Acta Biomater 2024; 184:22-36. [PMID: 38942189 DOI: 10.1016/j.actbio.2024.06.032] [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: 03/27/2024] [Revised: 05/29/2024] [Accepted: 06/21/2024] [Indexed: 06/30/2024]
Abstract
A wide variety of microorganisms have been closely linked to metal corrosion in the form of adherent surface biofilms. Biofilms allow the development and maintenance of locally corrosive environments and/or permit direct corrosion including pitting corrosion. The presence of numerous genetically distinct microorganisms in the oral environment poses a threat to the integrity and durability of the surface of metallic prostheses and implants used in routine dentistry. However, the association between oral microorganisms and specific corrosion mechanisms is not clear. It is of practical importance to understand how microbial corrosion occurs and the associated risks to metallic materials in the oral environment. This knowledge is also important for researchers and clinicians who are increasingly concerned about the biological activity of the released corrosion products. Accordingly, the main goal was to comprehensively review the current literature regarding oral microbiologically influenced corrosion (MIC) including characteristics of biofilms and of the oral environment, MIC mechanisms, corrosion behavior in the presence of oral microorganisms and potentially mitigating technologies. Findings included that oral MIC has been ascribed mostly to aggressive metabolites secreted during microbial metabolism (metabolite-mediated MIC). However, from a thermodynamic point of view, extracellular electron transfer mechanisms (EET-MIC) through pili or electron transfer compounds cannot be ruled out. Various MIC mitigating methods have been demonstrated to be effective in short term, but long term evaluations are necessary before clinical applications can be considered. Currently most in-vitro studies fail to simulate the complexity of intraoral physiological conditions which may either reduce or exacerbate corrosion risk, which must be addressed in future studies. STATEMENT OF SIGNIFICANCE: A thorough analysis on literature regarding oral MIC (microbiologically influenced corrosion) of biomedical metallic materials has been carried out, including characteristics of oral environment, MIC mechanisms, corrosion behaviors in the presence of typical oral microorganisms and potential mitigating methods (materials design and surface design). There is currently a lack of mechanistic understanding of oral MIC which is very important not only to corrosion researchers but also to dentists and clinicians. This paper discusses the significance of biofilms from a biocorrosion perspective and summarizes several aspects of MIC mechanisms which could be caused by oral microorganisms. Oral MIC has been closely associated with not only the materials research but also the dental/clinical research fields in this work.
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Affiliation(s)
- Weichen Xu
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China.
| | - Fei Yu
- School of Basic Medicine, Qingdao Medical College, Qingdao University, 308 Ningxia Road, Qingdao 266021, China.
| | - Owen Addison
- Centre for Oral Clinical Translational Science, Faculty of Dentistry Oral and Craniofacial Sciences, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Binbin Zhang
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Fang Guan
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Ruiyong Zhang
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Baorong Hou
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Wolfgang Sand
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Biofilm Centre, University of Duisburg-Essen, 45141 Essen, Germany
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195
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Chrenková A, Bisiak F, Brodersen DE. Breaking bad nucleotides: understanding the regulatory mechanisms of bacterial small alarmone hydrolases. Trends Microbiol 2024; 32:769-780. [PMID: 38262803 DOI: 10.1016/j.tim.2023.12.011] [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: 11/11/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024]
Abstract
Guanosine tetra- and pentaphosphate nucleotides, (p)ppGpp, function as central secondary messengers and alarmones in bacterial cell biology, signalling a range of stress conditions, including nutrient starvation and exposure to cell-wall-targeting antibiotics, and are critical for survival. While activation of the stringent response and alarmone synthesis on starved ribosomes by members of the RSH (Rel) class of proteins is well understood, much less is known about how single-domain small alarmone synthetases (SASs) and their corresponding alarmone hydrolases, the small alarmone hydrolases (SAHs), are regulated and contribute to (p)ppGpp homeostasis. The substrate spectrum of these enzymes has recently been expanded to include hyperphosphorylated adenosine nucleotides, suggesting that they take part in a highly complex and interconnected signalling network. In this review, we provide an overview of our understanding of the SAHs and discuss their structure, function, regulation, and phylogeny.
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Affiliation(s)
- Adriana Chrenková
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Francesco Bisiak
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark.
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196
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Kwon SY, Thi-Thu Ngo H, Son J, Hong Y, Min JJ. Exploiting bacteria for cancer immunotherapy. Nat Rev Clin Oncol 2024; 21:569-589. [PMID: 38840029 DOI: 10.1038/s41571-024-00908-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2024] [Indexed: 06/07/2024]
Abstract
Immunotherapy has revolutionized the treatment of cancer but continues to be constrained by limited response rates, acquired resistance, toxicities and high costs, which necessitates the development of new, innovative strategies. The discovery of a connection between the human microbiota and cancer dates back 4,000 years, when local infection was observed to result in tumour eradication in some individuals. However, the true oncological relevance of the intratumoural microbiota was not recognized until the turn of the twentieth century. The intratumoural microbiota can have pivotal roles in both the pathogenesis and treatment of cancer. In particular, intratumoural bacteria can either promote or inhibit cancer growth via remodelling of the tumour microenvironment. Over the past two decades, remarkable progress has been made preclinically in engineering bacteria as agents for cancer immunotherapy; some of these bacterial products have successfully reached the clinical stages of development. In this Review, we discuss the characteristics of intratumoural bacteria and their intricate interactions with the tumour microenvironment. We also describe the many strategies used to engineer bacteria for use in the treatment of cancer, summarizing contemporary data from completed and ongoing clinical trials. The work described herein highlights the potential of bacteria to transform the landscape of cancer therapy, bridging ancient wisdom with modern scientific innovation.
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Affiliation(s)
- Seong-Young Kwon
- Institute for Molecular Imaging and Theranostics, Chonnam National University Medical School, Jeonnam, Republic of Korea
- Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Jeonnam, Republic of Korea
| | - Hien Thi-Thu Ngo
- Institute for Molecular Imaging and Theranostics, Chonnam National University Medical School, Jeonnam, Republic of Korea
- Department of Biomedical Sciences, Chonnam National University Medical School, Jeonnam, Republic of Korea
- Department of Biochemistry, Hanoi Medical University, Hanoi, Vietnam
| | - Jinbae Son
- CNCure Biotech, Jeonnam, Republic of Korea
| | - Yeongjin Hong
- Institute for Molecular Imaging and Theranostics, Chonnam National University Medical School, Jeonnam, Republic of Korea
- CNCure Biotech, Jeonnam, Republic of Korea
- Department of Microbiology and Immunology, Chonnam National University Medical School, Jeonnam, Republic of Korea
- National Immunotherapy Innovation Center, Chonnam National University, Jeonnam, Republic of Korea
| | - Jung-Joon Min
- Institute for Molecular Imaging and Theranostics, Chonnam National University Medical School, Jeonnam, Republic of Korea.
- Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Jeonnam, Republic of Korea.
- Department of Biomedical Sciences, Chonnam National University Medical School, Jeonnam, Republic of Korea.
- CNCure Biotech, Jeonnam, Republic of Korea.
- Department of Microbiology and Immunology, Chonnam National University Medical School, Jeonnam, Republic of Korea.
- National Immunotherapy Innovation Center, Chonnam National University, Jeonnam, Republic of Korea.
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197
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Sha Y, Huang B, Hua C, Zhu Y, Tai W, Sun J, Li Y, Xia A, Wang Q, Lu L, Tan W, Jiang S. A clinically used anti-human papilloma virus agent (3-hydroxyphthalic anhydride-modified bovine β-lactoglobulin) has a potential for topical application to prevent sexual transmission of monkeypox virus. MedComm (Beijing) 2024; 5:e677. [PMID: 39105195 PMCID: PMC11298542 DOI: 10.1002/mco2.677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 08/07/2024] Open
Abstract
A global outbreak of monkeypox (mpox) caused by the mpox virus (MPXV) has posed a serious threat to public health worldwide, thus calling for the urgent development of antivirals and vaccines to curb its further spread. In this study, we screened 41 anhydride-modified proteins and found that 3-hydroxyphthalic anhydride-modified β-lactoglobulin (3HP-β-LG), a clinically used anti-HPV agent, was highly effective in inhibiting infection of vaccinia virus Tiantan strain (VACV-VTT) and MPXV. Mechanistic studies demonstrated that 3HP-β-LG bound to the virus, not the host cell, by targeting the early stage of virus entry, possibly through the interaction between the amino acids with negatively charges in 3HP-β-LG and the key amino acids with positive charges in the target region of A29L, a key surface protein of MPXV. A synergistic effect was observed when 3HP-β-LG was combined with tecovirimat, a small-molecule antiviral drug approved by the United States Food and Drug Administration and the European Medicine Agency for the treatment of smallpox and mpox. Because of its clinically proven safety and stability, 3HP-β-LG shows promise for further development as a prophylactic agent to prevent the sexual transmission of MPXV.
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Affiliation(s)
- Yi'ou Sha
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and BiosecuritySchool of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Baoying Huang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID)NHC Key Laboratory of BiosafetyNational Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Chen Hua
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and BiosecuritySchool of Basic Medical SciencesFudan UniversityShanghaiChina
- Shanxi Key Laboratory of Functional Proteins, Fudan‐Jinbo Functional Protein Joint Research CenterShanxi Jinbo Bio‐Pharmaceutical Co.Ltd.TaiyuanShanxiChina
| | - Yun Zhu
- National Laboratory of BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Wanbo Tai
- Institute of Infectious DiseasesShenzhen Bay LaboratoryShenzhenChina
| | - Jiewei Sun
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID)NHC Key Laboratory of BiosafetyNational Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Yixin Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and BiosecuritySchool of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Anqi Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and BiosecuritySchool of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and BiosecuritySchool of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and BiosecuritySchool of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Wenjie Tan
- National Laboratory of BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and BiosecuritySchool of Basic Medical SciencesFudan UniversityShanghaiChina
- Shanxi Key Laboratory of Functional Proteins, Fudan‐Jinbo Functional Protein Joint Research CenterShanxi Jinbo Bio‐Pharmaceutical Co.Ltd.TaiyuanShanxiChina
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198
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Liu Y, Wenren M, Cheng W, Zhou X, Xu D, Chi C, Lü Z, Liu H. Identification, functional characterization and immune response profiles of interleukin-10 in Nibea albiflora. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109654. [PMID: 38810711 DOI: 10.1016/j.fsi.2024.109654] [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: 04/10/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024]
Abstract
Interleukin-10 (IL-10) is an immunosuppressive cytokine, which plays a vital role in regulating inflammation for inhibiting the generation and function of pro-inflammatory cytokines in vivo or in vitro. In the present study, the full length cDNA of IL-10 was characterized from Nibea albiflora (named as NaIL-10) of 1238 base pairs (bp), containing a 5'-UTR (untranslated region) of 350 bp, a 3'-UTR of 333 bp and an open reading frame (ORF) of 555 bp (Fig. 1A) to encode 184 amino acid residues with a signal peptide at the N-terminus. The sequence analysis showed that NaIL-10 possessed the typical IL-10 family symbolic motif and conversed cysteine residues, similar to its teleost orthologues. Real-time PCR indicated that NaIL-10 had wide distribution in different healthy tissues, with a relatively high expression in immune-related tissues (head kidney, spleen, kidney, liver and gill). Significantly, up-regulations of NaIL-10 after infection against Vibrio parahaemolyticus, Vibrio alginolyticus and Poly I:C were also observed. Subcellular localization manifested that NaIL-10 mainly distributed in the cytoplasm unevenly and aggregately, and there was also a small amount on the cell membrane, indicating that NaIL-10 was secreted to the extracellular space as the known IL-10 homologous molecules. It could co-locate with IL-10 Rα on the membrane of HEK293T cells for their potential interaction, and GST pull-down and Co-IP studies certified the specific and direct interaction between NaIL-10 and NaIL-10 Rα, confirming that an IL-10 ligand-receptor system existed in N.albiflora. The expression of pro-inflammatory cytokines, including TNF-α, IL-6, IL-1β, were dramatically inhibited in LPS-stimulated RAW264.7 macrophages pre-incubated with recombinant NaIL-10 protein, demonstrating its anti-inflammatory roles. Taken together, the results demonstrated the existence of IL-10 ligand-receptor system in N.albiflora for the first time, and indicated the suppressive function of NaIL-10 on pro-inflammatory cytokine expression in inflammatory response, which would be conducive to better comprehending the role of IL-10 in the immunomodulatory mechanisms of teleost.
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Affiliation(s)
- Yue Liu
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Mingming Wenren
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Wei Cheng
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Xu Zhou
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Dongdong Xu
- Zhejiang Marine Fisheries Research Institute, Key Lab of Mariculture and Enhancement of Zhejiang province, Zhoushan, 316100, China
| | - Changfeng Chi
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Zhenming Lü
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Huihui Liu
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
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Hernández-Herreros N, Rodríguez A, Galán B, Auxiliadora Prieto M. Boosting hydrogen production in Rhodospirillum rubrum by syngas-driven photoheterotrophic adaptive evolution. BIORESOURCE TECHNOLOGY 2024; 406:130972. [PMID: 38876276 DOI: 10.1016/j.biortech.2024.130972] [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: 03/16/2024] [Revised: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024]
Abstract
Rhodospirillum rubrum is a photosynthetic purple non-sulphur bacterium with great potential to be used for complex waste valorisation in biotechnological applications due to its metabolic versatility. This study investigates the production of hydrogen (H2) and polyhydroxyalkanoates (PHA) by R. rubrum from syngas under photoheterotrophic conditions. An adaptive laboratory evolution strategy (ALE) has been carried out to improve the yield of the process. After 200 generations, two evolved strains were selected that showed reduced lag phase and enhanced poly-3-hydroxybutyrate (PHB) and H2 synthesis compared to the parental strain. Genomic analysis of the photo-adapted (PA) variants showed four genes with single point mutations, including the photosynthesis gene expression regulator PpsR. The proteome of the variants suggested that the adapted variants overproduced H2 due to a more efficient CO oxidation through the CO-dehydrogenase enzyme complex and confirmed that energy acquisition was enhanced through overexpression of the photosynthetic system and metal cofactors essential for pigment biosynthesis.
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Affiliation(s)
- Natalia Hernández-Herreros
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Alberto Rodríguez
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Beatriz Galán
- Microbial & Plant Biotechnology Department, Environmental Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
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200
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Guo D, Wang Y, Zhang Y, Duan J, Guan F, Hou B. Effects of marine eutrophication environment on microbial corrosion: A review. MARINE POLLUTION BULLETIN 2024; 205:116637. [PMID: 38955090 DOI: 10.1016/j.marpolbul.2024.116637] [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: 05/13/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 07/04/2024]
Abstract
Metal materials undergo severe corrosion in eutrophic environments. The effect of DO decay stimulated by high concentrations of nitrogen and phosphorus pollutants on microorganisms leads to the coupling of electrochemical and microbial corrosion processes. However, there are few studies on microbial corrosion mechanisms in eutrophic environments. This article discusses the corrosive factors of marine eutrophication, summarizes the impact of marine eutrophication on microbial corrosion and the potential mechanisms, including aerobic biofilm corrosion, aerobic & anaerobic mixed biofilm corrosion, and anaerobic microbial electron transfer corrosion, and expounds on the research methods for microbial corrosion of materials serving in estuarine areas prone to pollution. Microbial prevention and control, such as nutrient restriction and microbial interspecies competition, are of research value in the field of green protection. Microbial corrosion mechanisms studies in marine eutrophication environments are significant for environment monitor development, water intake and algae control technologies, and corrosion protection in polluted environments.
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Affiliation(s)
- Ding Guo
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 88 Haijun Road, Qingdao 266071, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, China
| | - Yanan Wang
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 88 Haijun Road, Qingdao 266071, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, China
| | - Yimeng Zhang
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 88 Haijun Road, Qingdao 266071, China
| | - Jizhou Duan
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 88 Haijun Road, Qingdao 266071, China.
| | - Fang Guan
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 88 Haijun Road, Qingdao 266071, China.
| | - Baorong Hou
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 88 Haijun Road, Qingdao 266071, China
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