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Carpenter KA, Altman RB. Databases of ligand-binding pockets and protein-ligand interactions. Comput Struct Biotechnol J 2024; 23:1320-1338. [PMID: 38585646 PMCID: PMC10997877 DOI: 10.1016/j.csbj.2024.03.015] [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: 02/06/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 04/09/2024] Open
Abstract
Many research groups and institutions have created a variety of databases curating experimental and predicted data related to protein-ligand binding. The landscape of available databases is dynamic, with new databases emerging and established databases becoming defunct. Here, we review the current state of databases that contain binding pockets and protein-ligand binding interactions. We have compiled a list of such databases, fifty-three of which are currently available for use. We discuss variation in how binding pockets are defined and summarize pocket-finding methods. We organize the fifty-three databases into subgroups based on goals and contents, and describe standard use cases. We also illustrate that pockets within the same protein are characterized differently across different databases. Finally, we assess critical issues of sustainability, accessibility and redundancy.
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Affiliation(s)
- Kristy A. Carpenter
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Russ B. Altman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
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Vijh RK, Sharma U, Arora R, Kapoor P, Raheja M, Sharma R, Ahlawat S, Dureja V. Development and validation of the Axiom-MaruPri SNP chip for genetic analyses of domesticated old world camelids. Gene 2024; 921:148541. [PMID: 38723784 DOI: 10.1016/j.gene.2024.148541] [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: 12/18/2023] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Camels play a crucial socio-economic role in sustaining the livelihoods of millions in arid and semi-arid regions. They possess remarkable physiological attributes which enable them to thrive in extreme environments, and provide a source of meat, milk and transportation. With their unique traits, camels embody an irreplaceable source of untapped genomic knowledge. This study introduces Axiom-MaruPri, a medium-density SNP chip meticulously designed and validated for both Camelus bactrianus and Camelus dromedarius. Comprising of 182,122 SNP markers, derived from the re-sequenced data of nine Indian dromedary breeds and the double-humped Bactrian camel, this SNP chip offers 34,894 markers that display polymorphism in both species. It achieves an estimated inter-marker distance of 14 Kb, significantly enhancing the coverage of the camel genome. The medium-density chip has been successfully genotyped using 480 camel samples, achieving an impressive 99 % call rate, with 96 % of the 182,122 SNPs being highly reliable for genotyping. Phylogenetic analysis and Discriminant Analysis of Principal Components yield clear distinctions between Bactrian camels and dromedaries. Moreover, the discriminant functions substantially enhance the classification of dromedary camels into different breeds. The clustering of various camel breeds reveals an apparent correlation between geographical and genetic distances. The results affirm the efficacy of this SNP array, demonstrating high genotyping precision and clear differentiation between Bactrian and dromedary camels. With an enhanced genome coverage, accuracy and economic efficiency the Axiom_MaruPri SNP chip is poised to advance genomic breeding research in camels. It holds the potential to serve as an invaluable genetic resource for investigating population structure, genome-wide association studies and implementing genomic selection in domesticated camelid species.
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Affiliation(s)
- Ramesh Kumar Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Prerna Kapoor
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Meenal Raheja
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Vandana Dureja
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
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Parvin S, Dey AR, Shohana NN, Anisuzzaman, Talukder MH, Alam MZ. Haemonchus contortus, an obligatory haematophagus worm infection in small ruminants: Population genetics and genetic diversity. Saudi J Biol Sci 2024; 31:104030. [PMID: 38854893 PMCID: PMC11157266 DOI: 10.1016/j.sjbs.2024.104030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/19/2024] [Accepted: 05/25/2024] [Indexed: 06/11/2024] Open
Abstract
Haemonchus contortus, a stomach worm, is prevalent in ruminants worldwide. They particularly hamper profitable small ruminant production. Here, we estimate the genetic variation of H. contortus collected from slaughtered goats and sheep from various geographic zones of Bangladesh using multiple genes. To perform this, adult parasites were isolated from the abomasum of slaughtered animals (sheep and goats). Among them, 79 male H. contortus were identified by microscopy. Following the extraction of DNA, ITS-2 and cox1 genes were amplified and subsequently considered for sequencing. After alignment and editing, sequences were analyzed to find out sequence variation, diversity pattern of genes, and population genetics of isolates. Among the sequence data, the analyses identified 19 genotypes of ITS-2 and 77 haplotypes of cox1 genes. The diversity of nucleotides was 0.0103 for ITS-2 and 0.029 for cox1 gene. The dendogram constructed by the genotype and haplotype sequences of H. contortus revealed that two populations were circulating in Bangladesh without any demarcation of host and geographic regions. Analysis of population genetics demonstrated a high flow of genes (89.2 %) within the population of the worm in Bangladesh. The Fst value showed very little amount of genetic difference among the worm populations of Bangladesh but marked genetic variation between different continents. The findings are expected to help explain the risks of anthelmintic resistance and the transmission pattern of the parasite, and also provide a control strategy against H. contortus.
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Affiliation(s)
- Shanaz Parvin
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
- Department of Para-Clinical Courses, Faculty of Veterinary and Animal Sciences, Gono Bishwabidyalay, Dhaka, Bangladesh
| | - Anita Rani Dey
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Nusrat Nowrin Shohana
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Anisuzzaman
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md. Hasanuzzaman Talukder
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Mohammad Zahangir Alam
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
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Taki Y, Ueno Y, Oda M, Kitaguchi Y, Ibrahim OMA, Aketa N, Yamaguchi T. Analysis of the performance of the CorneAI for iOS in the classification of corneal diseases and cataracts based on journal photographs. Sci Rep 2024; 14:15517. [PMID: 38969757 PMCID: PMC11226423 DOI: 10.1038/s41598-024-66296-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024] Open
Abstract
CorneAI for iOS is an artificial intelligence (AI) application to classify the condition of the cornea and cataract into nine categories: normal, infectious keratitis, non-infection keratitis, scar, tumor, deposit, acute primary angle closure, lens opacity, and bullous keratopathy. We evaluated its performance to classify multiple conditions of the cornea and cataract of various races in images published in the Cornea journal. The positive predictive value (PPV) of the top classification with the highest predictive score was 0.75, and the PPV for the top three classifications exceeded 0.80. For individual diseases, the highest PPVs were 0.91, 0.73, 0.42, 0.72, 0.77, and 0.55 for infectious keratitis, normal, non-infection keratitis, scar, tumor, and deposit, respectively. CorneAI for iOS achieved an area under the receiver operating characteristic curve of 0.78 (95% confidence interval [CI] 0.5-1.0) for normal, 0.76 (95% CI 0.67-0.85) for infectious keratitis, 0.81 (95% CI 0.64-0.97) for non-infection keratitis, 0.55 (95% CI 0.41-0.69) for scar, 0.62 (95% CI 0.27-0.97) for tumor, and 0.71 (95% CI 0.53-0.89) for deposit. CorneAI performed well in classifying various conditions of the cornea and cataract when used to diagnose journal images, including those with variable imaging conditions, ethnicities, and rare cases.
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Affiliation(s)
- Yosuke Taki
- Department of Ophthalmology, Tokyo Dental College Ichikawa General Hospital, 5-11-13, Sugano, Ichikawa, Chiba, 272-8513, Japan
| | - Yuta Ueno
- Department of Ophthalmology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masahiro Oda
- Scholarly Information Division, Information Technology Center, Nagoya University, Nagoya, Aichi, Japan
- Graduate School of Informatics, Nagoya University, Nagoya, Aichi, Japan
| | - Yoshiyuki Kitaguchi
- Department of Ophthalmology, Osaka University Gradual School of Medicine, Suita, Osaka, Japan
| | - Osama M A Ibrahim
- Department of Ophthalmology, Tokyo Dental College Ichikawa General Hospital, 5-11-13, Sugano, Ichikawa, Chiba, 272-8513, Japan
| | - Naohiko Aketa
- Department of Ophthalmology, Tokyo Dental College Ichikawa General Hospital, 5-11-13, Sugano, Ichikawa, Chiba, 272-8513, Japan
- Clinical and Translational Research Center, Keio University Hospital, Shinjuku, Tokyo, Japan
| | - Takefumi Yamaguchi
- Department of Ophthalmology, Tokyo Dental College Ichikawa General Hospital, 5-11-13, Sugano, Ichikawa, Chiba, 272-8513, Japan.
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Meier SSM, Multamäki E, Ranzani AT, Takala H, Möglich A. Leveraging the histidine kinase-phosphatase duality to sculpt two-component signaling. Nat Commun 2024; 15:4876. [PMID: 38858359 PMCID: PMC11164954 DOI: 10.1038/s41467-024-49251-8] [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: 02/07/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
Bacteria must constantly probe their environment for rapid adaptation, a crucial need most frequently served by two-component systems (TCS). As one component, sensor histidine kinases (SHK) control the phosphorylation of the second component, the response regulator (RR). Downstream responses hinge on RR phosphorylation and can be highly stringent, acute, and sensitive because SHKs commonly exert both kinase and phosphatase activity. With a bacteriophytochrome TCS as a paradigm, we here interrogate how this catalytic duality underlies signal responses. Derivative systems exhibit tenfold higher red-light sensitivity, owing to an altered kinase-phosphatase balance. Modifications of the linker intervening the SHK sensor and catalytic entities likewise tilt this balance and provide TCSs with inverted output that increases under red light. These TCSs expand synthetic biology and showcase how deliberate perturbations of the kinase-phosphatase duality unlock altered signal-response regimes. Arguably, these aspects equally pertain to the engineering and the natural evolution of TCSs.
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Affiliation(s)
| | - Elina Multamäki
- Department of Anatomy, University of Helsinki, Helsinki, Finland
| | - Américo T Ranzani
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Heikki Takala
- Department of Anatomy, University of Helsinki, Helsinki, Finland.
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.
- Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, Bayreuth, Germany.
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany.
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García de Fuentes A, Möglich A. Reduction midpoint potential of a paradigm light-oxygen-voltage receptor and its modulation by methionine residues. RSC Chem Biol 2024; 5:530-543. [PMID: 38846079 PMCID: PMC11151830 DOI: 10.1039/d4cb00056k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/08/2024] [Indexed: 06/09/2024] Open
Abstract
Light-dependent adaptations of organismal physiology, development, and behavior abound in nature and depend on sensory photoreceptors. As one class, light-oxygen-voltage (LOV) photoreceptors harness flavin-nucleotide chromophores to sense blue light. Photon absorption drives the LOV receptor to its signaling state, characterized by a metastable thioadduct between the flavin and a conserved cysteine residue. With this cysteine absent, LOV receptors instead undergo photoreduction to the flavin semiquinone which however can still elicit downstream physiological responses. Irrespective of the cysteine presence, the LOV photochemical response thus entails a formal reduction of the flavin. Against this backdrop, we here investigate the reduction midpoint potential E 0 in the paradigmatic LOV2 domain from Avena sativa phototropin 1 (AsLOV2), and how it can be deliberately varied. Replacements of residues at different sites near the flavin by methionine consistently increase E 0 from its value of around -280 mV by up to 40 mV. Moreover, methionine introduction invariably impairs photoactivation efficiency and thus renders the resultant AsLOV2 variants less light-sensitive. Although individual methionine substitutions also affect the stability of the signaling state and downstream allosteric responses, no clear-cut correlation with the redox properties emerges. With a reduction midpoint potential near -280 mV, AsLOV2 and, by inference, other LOV receptors may be partially reduced inside cells which directly affects their light responsiveness. The targeted modification of the chromophore environment, as presently demonstrated, may mitigate this effect and enables the design of LOV receptors with stratified redox sensitivities.
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Affiliation(s)
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth 95447 Bayreuth Germany
- Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth 95447 Bayreuth Germany
- North-Bavarian NMR Center, Universität Bayreuth 95447 Bayreuth Germany
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Yuan J, Hu J, Liu W, Chen S, Zhang F, Wang S, Zhang Z, Wang L, Xiao B, Li F, Hofreiter M, Lai X, Westbury MV, Sheng G. Camelus knoblochi genome reveals the complex evolutionary history of Old World camels. Curr Biol 2024; 34:2502-2508.e5. [PMID: 38754423 DOI: 10.1016/j.cub.2024.04.050] [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: 10/17/2023] [Revised: 12/22/2023] [Accepted: 04/22/2024] [Indexed: 05/18/2024]
Abstract
Extant Old World camels (genus Camelus) contributed to the economic and cultural exchanges between the East and West for thousands of years.1,2 Although many remains have been unearthed,3,4,5 we know neither whether the prevalent hybridization observed between extant Camelus species2,6,7 also occurred between extinct lineages and the ancestors of extant Camelus species nor why some populations became extinct while others survived. To investigate these questions, we generated paleogenomic and stable isotope data from an extinct two-humped camel species, Camelus knoblochi. We find that in the mitochondrial phylogeny, all C. knoblochi form a paraphyletic group that nests within the diversity of modern, wild two-humped camels (Camelus ferus). In contrast, they are clearly distinguished from both wild and domesticated (Camelus bactrianus) two-humped camels on the nuclear level. Moreover, the divergence pattern of the three camel species approximates a trifurcation, because the most common topology is only slightly more frequent than the two other possible topologies. This mito-nuclear phylogenetic discordance likely arose due to interspecific gene flow between all three species, suggesting that interspecific hybridization is not exclusive to modern camels but a recurrent phenomenon throughout the evolutionary history of the genus Camelus. These results suggest that the genomic complexity of Old World camels' evolutionary history is underestimated when considering data from only modern species. Finally, we find that C. knoblochi populations began declining prior to the last glacial maximum and, by integrating palaeoecological evidence and stable isotope data, suggest that this was likely due to failure to adapt to a changing environment.
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Affiliation(s)
- Junxia Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; Faculty of Materials Science and Chemistry, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China.
| | - Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; School of Earth Sciences, China University of Geosciences, Lumo Road 388, Wuhan 430074, People's Republic of China
| | - Wenhui Liu
- Institute of Environmental Archaeology, National Museum of China, East Chang'an Street 16, Beijing 100006, People's Republic of China
| | - Shungang Chen
- Faculty of Materials Science and Chemistry, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China
| | - Fengli Zhang
- Daqing Museum, Wenyuan Street 2, Daqing, Heilongjiang 163711, People's Republic of China
| | - Siren Wang
- Daqing Museum, Wenyuan Street 2, Daqing, Heilongjiang 163711, People's Republic of China
| | - Zhen Zhang
- Zhaoyuan Museum, Zhongyang Street 192, Daqing, Heilongjiang 166599, People's Republic of China
| | - Linying Wang
- Faculty of Materials Science and Chemistry, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; School of Earth Sciences, China University of Geosciences, Lumo Road 388, Wuhan 430074, People's Republic of China
| | - Fuqiang Li
- Yifu Museum, China University of Geosciences, Lumo Road 388, Wuhan 430074, People's Republic of China
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; School of Earth Sciences, China University of Geosciences, Lumo Road 388, Wuhan 430074, People's Republic of China
| | - Michael V Westbury
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1353 Copenhagen, Denmark.
| | - Guilian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; School of Environmental Studies, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China.
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Hanycz SA, Noorani A, Hung PSP, Walker MR, Zhang AB, Latypov TH, Hodaie M. Hippocampus diffusivity abnormalities in classical trigeminal neuralgia. Pain Rep 2024; 9:e1159. [PMID: 38655236 PMCID: PMC11037743 DOI: 10.1097/pr9.0000000000001159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 02/16/2024] [Accepted: 02/24/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Patients with chronic pain frequently report cognitive symptoms that affect memory and attention, which are functions attributed to the hippocampus. Trigeminal neuralgia (TN) is a chronic neuropathic pain disorder characterized by paroxysmal attacks of unilateral orofacial pain. Given the stereotypical nature of TN pain and lack of negative symptoms including sensory loss, TN provides a unique model to investigate the hippocampal implications of chronic pain. Recent evidence demonstrated that TN is associated with macrostructural hippocampal abnormalities indicated by reduced subfield volumes; however, there is a paucity in our understanding of hippocampal microstructural abnormalities associated with TN. Objectives To explore diffusivity metrics within the hippocampus, along with its functional and structural subfields, in patients with TN. Methods To examine hippocampal microstructure, we utilized diffusion tensor imaging in 31 patients with TN and 21 controls. T1-weighted magnetic resonance images were segmented into hippocampal subfields and registered into diffusion-weighted imaging space. Fractional anisotropy (FA) and mean diffusivity were extracted for hippocampal subfields and longitudinal axis segmentations. Results Patients with TN demonstrated reduced FA in bilateral whole hippocampi and hippocampal body and contralateral subregions CA2/3 and CA4, indicating microstructural hippocampal abnormalities. Notably, patients with TN showed significant correlation between age and hippocampal FA, while controls did not exhibit this correlation. These effects were driven chiefly by female patients with TN. Conclusion This study demonstrates that TN is associated with microstructural hippocampal abnormalities, which may precede and potentially be temporally linked to volumetric hippocampal alterations demonstrated previously. These findings provide further evidence for the role of the hippocampus in chronic pain and suggest the potential for targeted interventions to mitigate cognitive symptoms in patients with chronic pain.
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Affiliation(s)
- Shaun Andrew Hanycz
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Division of Brain, Imaging, and Behaviour—Systems Neuroscience, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Alborz Noorani
- Division of Brain, Imaging, and Behaviour—Systems Neuroscience, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Peter Shih-Ping Hung
- Division of Brain, Imaging, and Behaviour—Systems Neuroscience, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Matthew R. Walker
- Division of Brain, Imaging, and Behaviour—Systems Neuroscience, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Ashley B. Zhang
- MD Program, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Timur H. Latypov
- Division of Brain, Imaging, and Behaviour—Systems Neuroscience, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mojgan Hodaie
- Division of Brain, Imaging, and Behaviour—Systems Neuroscience, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Krembil Brain Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
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Du K, Dong L, Zhang K, Guan M, Chen C, Xie L, Kong W, Li H, Zhang R, Zhou W, Wu H, Dong H, Wei W. Deep learning system for screening AIDS-related cytomegalovirus retinitis with ultra-wide-field fundus images. Heliyon 2024; 10:e30881. [PMID: 38803983 PMCID: PMC11128864 DOI: 10.1016/j.heliyon.2024.e30881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Background Ophthalmological screening for cytomegalovirus retinitis (CMVR) for HIV/AIDS patients is important to prevent lifelong blindness. Previous studies have shown good properties of automated CMVR screening using digital fundus images. However, the application of a deep learning (DL) system to CMVR with ultra-wide-field (UWF) fundus images has not been studied, and the feasibility and efficiency of this method are uncertain. Methods In this study, we developed, internally validated, externally validated, and prospectively validated a DL system to detect AIDS-related from UWF fundus images from different clinical datasets. We independently used the InceptionResnetV2 network to develop and internally validate a DL system for identifying active CMVR, inactive CMVR, and non-CMVR in 6960 UWF fundus images from 862 AIDS patients and validated the system in a prospective and an external validation data set using the area under the curve (AUC), accuracy, sensitivity, and specificity. A heat map identified the most important area (lesions) used by the DL system for differentiating CMVR. Results The DL system showed AUCs of 0.945 (95 % confidence interval [CI]: 0.929, 0.962), 0.964 (95 % CI: 0.870, 0.999) and 0.968 (95 % CI: 0.860, 1.000) for detecting active CMVR from non-CMVR and 0.923 (95 % CI: 0.908, 0.938), 0.902 (0.857, 0.948) and 0.884 (0.851, 0.917) for detecting active CMVR from non-CMVR in the internal cross-validation, external validation, and prospective validation, respectively. Deep learning performed promisingly in screening CMVR. It also showed the ability to differentiate active CMVR from non-CMVR and inactive CMVR as well as to identify active CMVR and inactive CMVR from non-CMVR (all AUCs in the three independent data sets >0.900). The heat maps successfully highlighted lesion locations. Conclusions Our UWF fundus image-based DL system showed reliable performance for screening AIDS-related CMVR showing its potential for screening CMVR in HIV/AIDS patients, especially in the absence of ophthalmic resources.
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Affiliation(s)
- Kuifang Du
- Department of Ophthalmology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Li Dong
- Beijing Tongren Eye Centre, Beijing Key Laboratory of Intraocular Tumour Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Kai Zhang
- Chongqing Chang'an Industrial Group Co. Ltd, Chongqing, China
| | - Meilin Guan
- Department of Ophthalmology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Chao Chen
- Department of Ophthalmology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Lianyong Xie
- Department of Ophthalmology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Wenjun Kong
- Department of Ophthalmology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Heyan Li
- Beijing Tongren Eye Centre, Beijing Key Laboratory of Intraocular Tumour Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ruiheng Zhang
- Beijing Tongren Eye Centre, Beijing Key Laboratory of Intraocular Tumour Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wenda Zhou
- Beijing Tongren Eye Centre, Beijing Key Laboratory of Intraocular Tumour Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Haotian Wu
- Beijing Tongren Eye Centre, Beijing Key Laboratory of Intraocular Tumour Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Hongwei Dong
- Department of Ophthalmology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Wenbin Wei
- Beijing Tongren Eye Centre, Beijing Key Laboratory of Intraocular Tumour Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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Wilenzik IV, Barger BB, Pyron RA. Fossil-informed biogeographic analysis suggests Eurasian regionalization in crown Squamata during the early Jurassic. PeerJ 2024; 12:e17277. [PMID: 38708352 PMCID: PMC11067913 DOI: 10.7717/peerj.17277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/01/2024] [Indexed: 05/07/2024] Open
Abstract
Background Squamata (lizards, snakes, and amphisbaenians) is a Triassic lineage with an extensive and complex biogeographic history, yet no large-scale study has reconstructed the ancestral range of early squamate lineages. The fossil record indicates a broadly Pangaean distribution by the end- Cretaceous, though many lineages (e.g., Paramacellodidae, Mosasauria, Polyglyphanodontia) subsequently went extinct. Thus, the origin and occupancy of extant radiations is unclear and may have been localized within Pangaea to specific plates, with potential regionalization to distinct Laurasian and Gondwanan landmasses during the Mesozoic in some groups. Methods We used recent tectonic models to code extant and fossil squamate distributions occurring on nine discrete plates for 9,755 species, with Jurassic and Cretaceous fossil constraints from three extinct lineages. We modeled ancestral ranges for crown Squamata from an extant-only molecular phylogeny using a suite of biogeographic models accommodating different evolutionary processes and fossil-based node constraints from known Jurassic and Cretaceous localities. We hypothesized that the best-fit models would not support a full Pangaean distribution (i.e., including all areas) for the origin of crown Squamata, but would instead show regionalization to specific areas within the fragmenting supercontinent, likely in the Northern Hemisphere where most early squamate fossils have been found. Results Incorporating fossil data reconstructs a localized origin within Pangaea, with early regionalization of extant lineages to Eurasia and Laurasia, while Gondwanan regionalization did not occur until the middle Cretaceous for Alethinophidia, Scolecophidia, and some crown Gekkotan lineages. While the Mesozoic history of extant squamate biogeography can be summarized as a Eurasian origin with dispersal out of Laurasia into Gondwana, their Cenozoic history is complex with multiple events (including secondary and tertiary recolonizations) in several directions. As noted by previous authors, squamates have likely utilized over-land range expansion, land-bridge colonization, and trans-oceanic dispersal. Tropical Gondwana and Eurasia hold more ancient lineages than the Holarctic (Rhineuridae being a major exception), and some asymmetries in colonization (e.g., to North America from Eurasia during the Cenozoic through Beringia) deserve additional study. Future studies that incorporate fossil branches, rather than as node constraints, into the reconstruction can be used to explore this history further.
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Affiliation(s)
- Ian V. Wilenzik
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - Benjamin B. Barger
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - R. Alexander Pyron
- Department of Biology, George Washington University, Washington D.C., United States of America
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11
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Zhu S, Zhou R, Tang X, Fu W, Jia W. Hypoxia/inflammation-induced upregulation of HIF-1α and C/EBPβ promotes nephroblastoma cell EMT by improving HOXA11-AS transcription. Heliyon 2024; 10:e27654. [PMID: 38524550 PMCID: PMC10958367 DOI: 10.1016/j.heliyon.2024.e27654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 03/26/2024] Open
Abstract
Background Homeobox (HOX) A11 antisense RNA (HOXA11-AS) has been identified as a cancer promoting lncRNA and is overexpressed in nephroblastoma. However, how HOXA11-AS is regulated in a hypoxic inflammatory environment has not been studied. Methods In this study, gene expression and epithelial-mesenchymal transition (EMT) ability were detected in the nephroblastoma cell line WiT49 under conditions of hypoxia and inflammation. Next, HOXA11-AS transcription factors were predicted by datasets and subsequently confirmed by CHIP-QPCR, EMSA, and dual-luciferase reporter assays. Moreover, the regulatory relationships of HOXA11-AS and its transcription factors were further confirmed by rescue experiments. Results Our results showed that a hypoxic microenvironment promoted HOXA11-AS expression and nephroblastoma progression, induced EMT, and activated the Wnt signaling pathway. Combined hypoxia and inflammation had a more substantial effect on nephroblastoma than either hypoxia or inflammation alone. HIF-1α and C/EBPβ were confirmed to be the transcription factors for HOXA11-AS. Silencing of HIF-1α or C/EBPβ downregulated HOXA11-AS expression and suppressed EMT and the Wnt signaling pathway in nephroblastoma cells exposed to a hypoxic or inflammatory microenvironment. HOXA11-AS overexpression partly reversed the effect of HIF-1α or C/EBPβ knockdown. Conclusion We demonstrated that hypoxia/inflammation-induced upregulation of HIF-1α and C/EBPβ promoted nephroblastoma EMT by improving HOXA11-AS transcription. HOXA11-AS might be a therapy target for nephroblastoma.
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Affiliation(s)
- Shibo Zhu
- Department of Pediatric Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Rui Zhou
- Department of Pediatric Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiangliang Tang
- Department of Pediatric Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wen Fu
- Department of Pediatric Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wei Jia
- Department of Pediatric Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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12
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Lanh PT, Duong BT, Thu HT, Hoa NT, Quyen DV. Comprehensive analysis of the microbiome in Apis cerana honey highlights honey as a potential source for the isolation of beneficial bacterial strains. PeerJ 2024; 12:e17157. [PMID: 38560453 PMCID: PMC10981410 DOI: 10.7717/peerj.17157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Background Honey is a nutritious food made by bees from nectar and sweet deposits of flowering plants and has been used for centuries as a natural remedy for wound healing and other bacterial infections due to its antibacterial properties. Honey contains a diverse community of bacteria, especially probiotic bacteria, that greatly affect the health of bees and their consumers. Therefore, understanding the microorganisms in honey can help to ensure the quality of honey and lead to the identification of potential probiotic bacteria. Methods Herein, the bacteria community in honey produced by Apis cerana was investigated by applying the next-generation sequencing (NGS) method for the V3-V4 hypervariable regions of the bacterial 16S rRNA gene. In addition, lactic acid bacteria (LAB) in the honey sample were also isolated and screened for in vitro antimicrobial activity. Results The results showed that the microbiota of A. cerana honey consisted of two major bacterial phyla, Firmicutes (50%; Clostridia, 48.2%) and Proteobacteria (49%; Gammaproteobacteria, 47.7%). Among the 67 identified bacterial genera, the three most predominant genera were beneficial obligate anaerobic bacteria, Lachnospiraceae (48.14%), followed by Gilliamella (26.80%), and Enterobacter (10.16%). Remarkably, among the identified LAB, Lactobacillus kunkeei was found to be the most abundant species. Interestingly, the isolated L. kunkeei strains exhibited antimicrobial activity against some pathogenic bacteria in honeybees, including Klebsiella spp., Escherichia coli, Enterococcus faecalis, Pseudomonas aeruginosa and Staphylococcus aureus. This underscores the potential candidacy of L. kunkeei for developing probiotics for medical use. Taken together, our results provided new insights into the microbiota community in the A. cerana honey in Hanoi, Vietnam, highlighting evidence that honey can be an unexplored source for isolating bacterial strains with potential probiotic applications in honeybees and humans.
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Affiliation(s)
- Pham T. Lanh
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Bui T.T. Duong
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha T. Thu
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nguyen T. Hoa
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Dong Van Quyen
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
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13
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Fertan E, Böken D, Murray A, Danial JSH, Lam JYL, Wu Y, Goh PA, Alić I, Cheetham MR, Lobanova E, Zhang YP, Nižetić D, Klenerman D. Cerebral organoids with chromosome 21 trisomy secrete Alzheimer's disease-related soluble aggregates detectable by single-molecule-fluorescence and super-resolution microscopy. Mol Psychiatry 2024; 29:369-386. [PMID: 38102482 PMCID: PMC11116105 DOI: 10.1038/s41380-023-02333-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
Understanding the role of small, soluble aggregates of beta-amyloid (Aβ) and tau in Alzheimer's disease (AD) is of great importance for the rational design of preventative therapies. Here we report a set of methods for the detection, quantification, and characterisation of soluble aggregates in conditioned media of cerebral organoids derived from human iPSCs with trisomy 21, thus containing an extra copy of the amyloid precursor protein (APP) gene. We detected soluble beta-amyloid (Aβ) and tau aggregates secreted by cerebral organoids from both control and the isogenic trisomy 21 (T21) genotype. We developed a novel method to normalise measurements to the number of live neurons within organoid-conditioned media based on glucose consumption. Thus normalised, T21 organoids produced 2.5-fold more Aβ aggregates with a higher proportion of larger (300-2000 nm2) and more fibrillary-shaped aggregates than controls, along with 1.3-fold more soluble phosphorylated tau (pTau) aggregates, increased inflammasome ASC-specks, and a higher level of oxidative stress inducing thioredoxin-interacting protein (TXNIP). Importantly, all this was detectable prior to the appearance of histological amyloid plaques or intraneuronal tau-pathology in organoid slices, demonstrating the feasibility to model the initial pathogenic mechanisms for AD in-vitro using cells from live genetically pre-disposed donors before the onset of clinical disease. Then, using different iPSC clones generated from the same donor at different times in two independent experiments, we tested the reproducibility of findings in organoids. While there were differences in rates of disease progression between the experiments, the disease mechanisms were conserved. Overall, our results show that it is possible to non-invasively follow the development of pathology in organoid models of AD over time, by monitoring changes in the aggregates and proteins in the conditioned media, and open possibilities to study the time-course of the key pathogenic processes taking place.
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Affiliation(s)
- Emre Fertan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- UK Dementia Research Institute at University of Cambridge, Cambridge, CB2 0AH, UK
| | - Dorothea Böken
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- UK Dementia Research Institute at University of Cambridge, Cambridge, CB2 0AH, UK
| | - Aoife Murray
- The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, E1 2AT, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - John S H Danial
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- UK Dementia Research Institute at University of Cambridge, Cambridge, CB2 0AH, UK
| | - Jeff Y L Lam
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- UK Dementia Research Institute at University of Cambridge, Cambridge, CB2 0AH, UK
| | - Yunzhao Wu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- UK Dementia Research Institute at University of Cambridge, Cambridge, CB2 0AH, UK
| | - Pollyanna A Goh
- The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, E1 2AT, UK
| | - Ivan Alić
- The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, E1 2AT, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Matthew R Cheetham
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- UK Dementia Research Institute at University of Cambridge, Cambridge, CB2 0AH, UK
| | - Evgeniia Lobanova
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- UK Dementia Research Institute at University of Cambridge, Cambridge, CB2 0AH, UK
| | - Yu P Zhang
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- UK Dementia Research Institute at University of Cambridge, Cambridge, CB2 0AH, UK
| | - Dean Nižetić
- The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, E1 2AT, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
- UK Dementia Research Institute at University of Cambridge, Cambridge, CB2 0AH, UK.
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14
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Xiang S, Lu X. Selective type II TRK inhibitors overcome xDFG mutation mediated acquired resistance to the second-generation inhibitors selitrectinib and repotrectinib. Acta Pharm Sin B 2024; 14:517-532. [PMID: 38322338 PMCID: PMC10840435 DOI: 10.1016/j.apsb.2023.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/15/2023] [Accepted: 10/24/2023] [Indexed: 02/08/2024] Open
Abstract
Neurotrophic receptor kinase (NTRK) fusions are actionable oncogenic drivers of multiple pediatric and adult solid tumors, and tropomyosin receptor kinase (TRK) has been considered as an attractive therapeutic target for "pan-cancer" harboring these fusions. Currently, two generations TRK inhibitors have been developed. The representative second-generation inhibitors selitrectinib and repotrectinib were designed to overcome clinic acquired resistance of the first-generation inhibitors larotrectinib or entrectinib resulted from solvent-front and gatekeeper on-target mutations. However, xDFG (TRKAG667C/A/S, homologous TRKCG696C/A/S) and some double mutations still confer resistance to selitrectinib and repotrectinib, and overcoming these resistances represents a major unmet clinical need. In this review, we summarize the acquired resistance mechanism of the first- and second-generation TRK inhibitors, and firstly put forward the emerging selective type II TRK inhibitors to overcome xDFG mutations mediated resistance. Additionally, we concluded our perspectives on new challenges and future directions in this field.
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Affiliation(s)
- Shuang Xiang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China
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15
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Anyubaga SB, Shallangwa GA, Uzairu A, Abechi SE. Chemo-informatics applications in the design of novel 7-keto-sempervirol derivatives as SmCB1 inhibitors with potential for treatment of Schistosomiasis. Heliyon 2024; 10:e23115. [PMID: 38173516 PMCID: PMC10761359 DOI: 10.1016/j.heliyon.2023.e23115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
The quest for a sound treatment on the vulnerable population suffering and dying as a result of the blood flukes, S. mansoni is on the increase because both Praziquantel and Oxamniquine widely used for the treatment of Schistosomiasis for over 51 years suffer resistance and recurrence. Here-in, chemo-informatics techniques such as QSAR modeling, pharmacokinetic, docking alongside MD simulation were harnessed in designing novel 7-keto- sempevirolsempevirol derivatives that are more competent against S. mansoni. Upon QSAR screening, compound 15, which appears to be in the model's acceptability space, emerges the best with a high predicted activity. 5 new analogues with improved activity against Schistosomiasis better than the standard drug PZQ were designed from compound 15 (template 15*) on an account of the descriptors significance from the model with robust and validated parameters. Also their pharmacokinetic profiles indicates that the designed compounds have the characteristics of a good drug. Furthermore, docking evaluation fulfilled ranges from -113.121 to -100.79 kcal/mol (moldock score), with compound U1 being the best (least moldock score of -113.121 compared to PZQ and 15* (template) having a moldock score value of (-87.21 and -83.37 kcal/mol). 100-ns MD Simulation on the U1-docked complex was run using Desmond 2019-4 package. The nature and steadiness of U1 compound within the enzyme active site was further confirmed by RMSD, RMSF, RoG and H-bond assessment. Hence, we recommend compound U1 targeting the SmCB1 enzyme (6YI7) for Schistosomiasis treatment and for further medicinal evaluation and utilization.
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Affiliation(s)
| | | | - Adamu Uzairu
- Department of Chemistry Ahmadu Bello University, P.M.B. 1044, Zaria, Nigeria
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16
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Rahman KMT, Butzin NC. Counter-on-chip for bacterial cell quantification, growth, and live-dead estimations. Sci Rep 2024; 14:782. [PMID: 38191788 PMCID: PMC10774380 DOI: 10.1038/s41598-023-51014-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/29/2023] [Indexed: 01/10/2024] Open
Abstract
Quantifying bacterial cell numbers is crucial for experimental assessment and reproducibility, but the current technologies have limitations. The commonly used colony forming units (CFU) method causes a time delay in determining the actual numbers. Manual microscope counts are often error-prone for submicron bacteria. Automated systems are costly, require specialized knowledge, and are erroneous when counting smaller bacteria. In this study, we took a different approach by constructing three sequential generations (G1, G2, and G3) of counter-on-chip that accurately and timely count small particles and/or bacterial cells. We employed 2-photon polymerization (2PP) fabrication technology; and optimized the printing and molding process to produce high-quality, reproducible, accurate, and efficient counters. Our straightforward and refined methodology has shown itself to be highly effective in fabricating structures, allowing for the rapid construction of polydimethylsiloxane (PDMS)-based microfluidic devices. The G1 comprises three counting chambers with a depth of 20 µm, which showed accurate counting of 1 µm and 5 µm microbeads. G2 and G3 have eight counting chambers with depths of 20 µm and 5 µm, respectively, and can quickly and precisely count Escherichia coli cells. These systems are reusable, accurate, and easy to use (compared to CFU/ml). The G3 device can give (1) accurate bacterial counts, (2) serve as a growth chamber for bacteria, and (3) allow for live/dead bacterial cell estimates using staining kits or growth assay activities (live imaging, cell tracking, and counting). We made these devices out of necessity; we know no device on the market that encompasses all these features.
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Affiliation(s)
- K M Taufiqur Rahman
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57006, USA
| | - Nicholas C Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57006, USA.
- Department of Chemistry, Biochemistry and Physics, South Dakota State University, Brookings, SD, 57006, USA.
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17
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Sun W. Fungal mycelia: From innovative materials to promising products: Insights and challenges. Biointerphases 2024; 19:018502. [PMID: 38415769 DOI: 10.1116/6.0003441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 01/25/2024] [Indexed: 02/29/2024] Open
Abstract
In transitioning toward a sustainable economy, mycelial materials are recognized for their adaptability, biocompatibility, and eco-friendliness. This paper updates the exploration of mycelial materials, defining their scope and emphasizing the need for precise terminology. It discusses the importance of mycelial type and characteristics, reviews existing and future research directions, and highlights the need for improved understanding, clarity, and standardization in this emerging field, aiming to foster and guide future research and development in sustainable material science.
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Affiliation(s)
- Wenjing Sun
- Institute of Materials (IMX), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
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18
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Litunenko DN, Moskalensky AE. Wireless monitoring of cell cultures based on light scattering: A novel optical scheme and portable prototype. JOURNAL OF BIOPHOTONICS 2024; 17:e202300234. [PMID: 37795552 DOI: 10.1002/jbio.202300234] [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: 06/15/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/06/2023]
Abstract
Cell cultures are widely used in scientific research, biomedicine, and industry. When culturing, it is important to maintain certain conditions, including the concentration of cells. Monitoring of the culture growth and cell counting is an urgent task for the optimization of technological processes. Most existing methods require sampling from a culture flask. This procedure is time-consuming and associated with the risks of contamination. We present a device able to monitor the growth of cells number in a suspension noninvasively. The device uses a laser beam that pass through the culture flask and measures the intensity of scattered light as a function of coordinate along the beam. This optical scheme allows one to obtain accurate results for both high- and low-scattering samples. We constructed the wireless portable prototype for monitoring of cell culture growth directly in the incubator and demonstrated the applicability of the device for Jurkat cells and Escherichia coli bacteria.
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19
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Jefferson TB, Wang T, Jefferson WN, Li Y, Hamilton KJ, Wade PA, Williams CJ, Korach KS. Multiple tissue-specific epigenetic alterations regulate persistent gene expression changes following developmental DES exposure in mouse reproductive tissues. Epigenetics 2023; 18:2139986. [PMID: 36328762 PMCID: PMC9980695 DOI: 10.1080/15592294.2022.2139986] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Clinically, developmental exposure to the endocrine disrupting chemical, diethylstilboestrol (DES), results in long-term male and female infertility. Experimentally, developmental exposure to DES results in abnormal reproductive tract phenotypes in male and female mice. Previously, we reported that neonatal DES exposure causes ERα-mediated aberrations in the transcriptome and in DNA methylation in seminal vesicles (SVs) of adult mice. However, only a subset of DES-altered genes could be explained by changes in DNA methylation. We hypothesized that alterations in histone modification may also contribute to the altered transcriptome during SV development. To test this idea, we performed a series of genome-wide analyses of mouse SVs at pubertal and adult developmental stages in control and DES-exposed wild-type and ERα knockout mice. Neonatal DES exposure altered ERα-mediated mRNA and lncRNA expression in adult SV, including genes encoding chromatin-modifying proteins that can impact histone H3K27ac modification. H3K27ac patterns, particularly at enhancers, and DNA methylation were reprogrammed over time during normal SV development and after DES exposure. Some of these reprogramming changes were ERα-dependent, but others were ERα-independent. A substantial number of DES-altered genes had differential H3K27ac peaks at nearby enhancers. Comparison of gene expression changes, H3K27ac marks and DNA methylation marks between adult SV and adult uterine tissue from ovariectomized mice neonatally exposed to DES revealed that most of the epigenetic changes and altered genes were distinct in the two tissues. These findings indicate that the effects of developmental DES exposure cause reprogramming of reproductive tract tissue differentiation through multiple epigenetic mechanisms.
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Affiliation(s)
- Tanner B. Jefferson
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Tianyuan Wang
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Wendy N. Jefferson
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Yin Li
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Katherine J. Hamilton
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Paul A. Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Carmen J. Williams
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Kenneth S. Korach
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
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20
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Auria E, Deschamps J, Briandet R, Dupuy B. Extracellular succinate induces spatially organized biofilm formation in Clostridioides difficile. Biofilm 2023; 5:100125. [PMID: 37214349 PMCID: PMC10192414 DOI: 10.1016/j.bioflm.2023.100125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
Clostridioides difficile infection associated to gut microbiome dysbiosis is the leading cause for nosocomial diarrhea. The ability of C. difficile to form biofilms has been progressively linked to its pathogenesis as well as its persistence in the gut. Although C. difficile has been reported to form biofilms in an increasing number of conditions, little is known about how these biofilms are formed in the gut and what factors may trigger their formation. Here we report that succinate, a metabolite abundantly produced by the dysbiotic gut microbiota, induces in vitro biofilm formation of C. difficile strains. We characterized the morphology and spatial composition of succinate-induced biofilms, and compared to non-induced or deoxycholate (DCA) induced biofilms. Biofilms induced by succinate are significantly thicker, structurally more complex, and poorer in proteins and exopolysaccharides (EPS). We then applied transcriptomics and genetics to characterize the early stages of succinate-induced biofilm formation and we showed that succinate-induced biofilm results from major metabolic shifts and cell-wall composition changes. Similar to DCA-induced biofilms, biofilms induced by succinate depend on the presence of a rapidly metabolized sugar. Finally, although succinate can be consumed by the bacteria, we found that the extracellular succinate is in fact responsible for the induction of biofilm formation through complex regulation involving global metabolic regulators and the osmotic stress response. Thus, our work suggests that as a gut signal, succinate may drive biofilm formation and help persistence of C. difficile in the gut, increasing the risk of relapse.
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Affiliation(s)
- Emile Auria
- Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Paris, France
| | - Julien Deschamps
- Institut Micalis, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Romain Briandet
- Institut Micalis, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Bruno Dupuy
- Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Paris, France
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Ashokan M, Jayanthi KV, Elango K, Sneha K, Ramesha KP, Reshma RS, Saravanan KA, Naveen KGS. Biological methylation: redefining the link between genotype and phenotype. Anim Biotechnol 2023; 34:3174-3186. [PMID: 35468300 DOI: 10.1080/10495398.2022.2065999] [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: 11/01/2022]
Abstract
The central dogma of molecular biology is responsible for the crucial flow of genetic information from DNA to protein through the transcription and translation process. Although the sequence of DNA is constant in all organs, the difference in protein and variation in the phenotype is mainly due to the quality and quantity of tissue-specific gene expression and methylation pattern. The term methylation has been defined and redefined by various scientists in the last fifty years. There is always huge excitement around this field because the inheritance of something is beyond its DNA sequence. Advanced gene methylation studies have redefined molecular genetics and these tools are considered de novo in alleviating challenges of animal disease and production. Recent emerging evidence has shown that the impact of DNA, RNA, and protein methylation is crucial for embryonic development, cell proliferation, cell differentiation, and phenotype production. Currently, many researchers are focusing their work on methylation to understand its significant role in expression, disease-resistant traits, productivity, and longevity. The main aim of the present review is to provide an overview of DNA, RNA, and protein methylation, current research output from different sources, methodologies, factors responsible for methylation of genes, and future prospects in animal genetics.
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Affiliation(s)
- M Ashokan
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K V Jayanthi
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K Elango
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Kadimetla Sneha
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K P Ramesha
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Raj S Reshma
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - K A Saravanan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kumar G S Naveen
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
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22
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Al Abri M, Alfoudari A, Mohammad Z, Almathen F, Al-Marzooqi W, Al-Hajri S, Al-Amri M, Bahbahani H. Assessing genetic diversity and defining signatures of positive selection on the genome of dromedary camels from the southeast of the Arabian Peninsula. Front Vet Sci 2023; 10:1296610. [PMID: 38098998 PMCID: PMC10720651 DOI: 10.3389/fvets.2023.1296610] [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: 09/18/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Dromedary camels (Camelus dromedarius) are members of the Camelini tribe within the Camelidae family. They are distributed throughout North Africa, the Arabian Peninsula and Southeast Asia. This domestic species is characterized by its superior adaptability to the harsh desert environment. In this study, whole autosomal data of 29 dromedary samples from the Southeast Arabian Peninsula in Oman; 10 from Muscat, 14 from Al-Batinah, and 5 from Al-Sharqiya, were investigated to assess their genetic relationship and to define candidate signatures of positive selection. A minimal genetic distinction that separates Muscat dromedaries from the other two populations was observed, with a degree of genetic admixture between them. Using the de-correlated composite of multiple signals (DCMS) approach, a total of 47 candidate regions within the autosomes of these dromedary populations were defined with signatures of positive selection. These candidate regions harbor a total of 154 genes that are mainly associated with functional categories related to immune response, lipid metabolism and energy expenditure, optical and auditory functions, and long-term memory. Different functional genomic variants were called on the candidate regions and respective genes that warrant further investigation to find possible association with the different favorable phenotypes in dromedaries. The output of this study paves the way for further research efforts aimed at defining markers for use in genomic breeding programs, with the goal of conserving the genetic diversity of the species and enhancing its productivity.
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Affiliation(s)
- Mohammad Al Abri
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ahmad Alfoudari
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zainab Mohammad
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
- Camel Research Center, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Waleed Al-Marzooqi
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - Salim Al-Hajri
- Laboratories and Research Administration, Directorate General of Veterinary Services, Royal Court Affairs, Muscat, Oman
| | - Mahmood Al-Amri
- Laboratories and Research Administration, Directorate General of Veterinary Services, Royal Court Affairs, Muscat, Oman
| | - Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
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23
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Morgenroth E, Vilaclara L, Muszynski M, Gaviria J, Vuilleumier P, Van De Ville D. Probing neurodynamics of experienced emotions-a Hitchhiker's guide to film fMRI. Soc Cogn Affect Neurosci 2023; 18:nsad063. [PMID: 37930850 PMCID: PMC10656947 DOI: 10.1093/scan/nsad063] [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: 03/16/2023] [Revised: 08/04/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023] Open
Abstract
Film functional magnetic resonance imaging (fMRI) has gained tremendous popularity in many areas of neuroscience. However, affective neuroscience remains somewhat behind in embracing this approach, even though films lend themselves to study how brain function gives rise to complex, dynamic and multivariate emotions. Here, we discuss the unique capabilities of film fMRI for emotion research, while providing a general guide of conducting such research. We first give a brief overview of emotion theories as these inform important design choices. Next, we discuss films as experimental paradigms for emotion elicitation and address the process of annotating them. We then situate film fMRI in the context of other fMRI approaches, and present an overview of results from extant studies so far with regard to advantages of film fMRI. We also give an overview of state-of-the-art analysis techniques including methods that probe neurodynamics. Finally, we convey limitations of using film fMRI to study emotion. In sum, this review offers a practitioners' guide to the emerging field of film fMRI and underscores how it can advance affective neuroscience.
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Affiliation(s)
- Elenor Morgenroth
- Neuro-X Institute, École Polytechnique Fédérale de Lausanne, Geneva 1202, Switzerland
- Department of Radiology and Medical Informatics, University of Geneva, Geneva 1202, Switzerland
- Swiss Center for Affective Sciences, University of Geneva, Geneva 1202, Switzerland
| | - Laura Vilaclara
- Neuro-X Institute, École Polytechnique Fédérale de Lausanne, Geneva 1202, Switzerland
- Department of Radiology and Medical Informatics, University of Geneva, Geneva 1202, Switzerland
| | - Michal Muszynski
- Department of Basic Neurosciences, University of Geneva, Geneva 1202, Switzerland
| | - Julian Gaviria
- Swiss Center for Affective Sciences, University of Geneva, Geneva 1202, Switzerland
- Department of Basic Neurosciences, University of Geneva, Geneva 1202, Switzerland
- Department of Psychiatry, University of Geneva, Geneva 1202, Switzerland
| | - Patrik Vuilleumier
- Swiss Center for Affective Sciences, University of Geneva, Geneva 1202, Switzerland
- Department of Basic Neurosciences, University of Geneva, Geneva 1202, Switzerland
- CIBM Center for Biomedical Imaging, Geneva 1202, Switzerland
| | - Dimitri Van De Ville
- Neuro-X Institute, École Polytechnique Fédérale de Lausanne, Geneva 1202, Switzerland
- Department of Radiology and Medical Informatics, University of Geneva, Geneva 1202, Switzerland
- CIBM Center for Biomedical Imaging, Geneva 1202, Switzerland
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24
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Soukar I, Mitra A, Pile LA. Analysis of the chromatin landscape and RNA polymerase II binding at SIN3-regulated genes. Biol Open 2023; 12:bio060026. [PMID: 37850739 PMCID: PMC10651107 DOI: 10.1242/bio.060026] [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: 06/02/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023] Open
Abstract
The chromatin environment has a significant impact on gene expression. Chromatin structure is highly regulated by histone modifications and RNA polymerase II binding dynamics. The SIN3 histone modifying complex regulates the chromatin environment leading to changes in gene expression. In Drosophila melanogaster, the Sin3A gene is alternatively spliced to produce different protein isoforms, two of which include SIN3 220 and SIN3 187. Both SIN3 isoforms are scaffolding proteins that interact with several other factors to regulate the chromatin landscape. The mechanism through which the SIN3 isoforms regulate chromatin is not well understood. Here, we analyze publicly available data sets to allow us to ask specific questions on how SIN3 isoforms regulate chromatin and gene activity. We determined that genes repressed by the SIN3 isoforms exhibited enrichment in histone H3K4me2, H3K4me3, H3K14ac and H3K27ac near the transcription start site. We observed an increase in the amount of paused RNA polymerase II on the promoter of genes repressed by the isoforms as compared to genes that require SIN3 for maximum activation. Furthermore, we analyzed a subset of genes regulated by SIN3 187 that suggest a mechanism in which SIN3 187 might exhibit hard regulation as well as soft regulation. Data presented here expand our knowledge of how the SIN3 isoforms regulate the chromatin environment and RNA polymerase II binding dynamics.
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Affiliation(s)
- Imad Soukar
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Anindita Mitra
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Lori A. Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
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25
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Woo HM, Qian X, Tan L, Jha S, Alexander FJ, Dougherty ER, Yoon BJ. Optimal decision-making in high-throughput virtual screening pipelines. PATTERNS (NEW YORK, N.Y.) 2023; 4:100875. [PMID: 38035191 PMCID: PMC10682755 DOI: 10.1016/j.patter.2023.100875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/28/2022] [Accepted: 10/13/2023] [Indexed: 12/02/2023]
Abstract
The need for efficient computational screening of molecular candidates that possess desired properties frequently arises in various scientific and engineering problems, including drug discovery and materials design. However, the enormous search space containing the candidates and the substantial computational cost of high-fidelity property prediction models make screening practically challenging. In this work, we propose a general framework for constructing and optimizing a high-throughput virtual screening (HTVS) pipeline that consists of multi-fidelity models. The central idea is to optimally allocate the computational resources to models with varying costs and accuracy to optimize the return on computational investment. Based on both simulated and real-world data, we demonstrate that the proposed optimal HTVS framework can significantly accelerate virtual screening without any degradation in terms of accuracy. Furthermore, it enables an adaptive operational strategy for HTVS, where one can trade accuracy for efficiency.
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Affiliation(s)
- Hyun-Myung Woo
- Department of Biomedical & Robotics Engineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Xiaoning Qian
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Li Tan
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Shantenu Jha
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
- Department of Electrical and Computer Engineering, Rutgers University, Piscataway, NJ 08854, USA
| | - Francis J. Alexander
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Edward R. Dougherty
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Byung-Jun Yoon
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
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26
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Fazel M, Grussmayer KS, Ferdman B, Radenovic A, Shechtman Y, Enderlein J, Pressé S. Fluorescence Microscopy: a statistics-optics perspective. ARXIV 2023:arXiv:2304.01456v3. [PMID: 37064525 PMCID: PMC10104198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fundamental properties of light unavoidably impose features on images collected using fluorescence microscopes. Modeling these features is ever more important in quantitatively interpreting microscopy images collected at scales on par or smaller than light's wavelength. Here we review the optics responsible for generating fluorescent images, fluorophore properties, microscopy modalities leveraging properties of both light and fluorophores, in addition to the necessarily probabilistic modeling tools imposed by the stochastic nature of light and measurement.
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Affiliation(s)
- Mohamadreza Fazel
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
| | - Kristin S Grussmayer
- Department of Bionanoscience, Faculty of Applied Science and Kavli Institute for Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Boris Ferdman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
| | - Yoav Shechtman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, Göttingen, Germany
| | - Steve Pressé
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
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27
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Castillo HB, Shuster SO, Tarekegn LH, Davis CM. Oleic acid differentially affects de novo lipogenesis in adipocytes and hepatocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.04.560581. [PMID: 37873279 PMCID: PMC10592964 DOI: 10.1101/2023.10.04.560581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Lipogenesis is a vital but often dysregulated metabolic pathway. We report super-resolution multiplexed vibrational imaging of lipogenesis rates and pathways using isotopically labelled oleic acid and glucose as probes in live adipocytes and hepatocytes. These findings suggest oleic acid inhibits de novo lipogenesis (DNL), but not total lipogenesis, in hepatocytes. No significant effect is seen in adipocytes. These differential effects may be due to alternate regulation of DNL between cell types and could help explain the complicated role oleic acid plays in metabolism.
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Affiliation(s)
- Hannah B. Castillo
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, United States
| | - Sydney O. Shuster
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, United States
| | - Lydia H. Tarekegn
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, United States
| | - Caitlin M. Davis
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, United States
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28
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Liu Y, Hu C, Serna JA, Biedermann F, Levkin PA. Binding affinity-based intracellular drug detection enabled by a unimolecular cucurbit[7]uril-dye conjugate. RSC Chem Biol 2023; 4:760-764. [PMID: 37799577 PMCID: PMC10549235 DOI: 10.1039/d3cb00131h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023] Open
Abstract
Label-free fluorescence-based chemosensing has been increasingly brought into focus due to its simplicity and high sensitivity for intracellular monitoring of molecules. Currently used methods, such as conventional indicator displacement assays (IDAs), pose limitations related to dissociation upon dilution, random diffusion of the released indicators, and high sensitivity to interference by agents from the ambient cellular environment (e.g., salts, enzymes, and proteins). Herein we report a potentially widely applicable strategy to overcome the limitations of conventional IDAs by employing a macrocyclic cucurbit[7]uril (CB7) host covalently coupled to a nitrobenzoxadiazole (NBD) fluorescent dye (CB7-NBD conjugate). As a proof of concept, we demonstrated that the CB7-NBD unimolecular conjugate responded to various target analytes even in the complex live cell system. Moreover, the sensing system was compatible with fluorescence imaging, fluorescence-assisted cell sorting (FACS), and fluorescence spectrometry with a microplate reader. These experiments demonstrated an application of covalently bound unimolecular CB7-NBD conjugate as a sensor for detecting diverse analytes in the intracellular compartment of live cells.
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Affiliation(s)
- Yanxi Liu
- Karlsruhe Institute of Technology (KIT), Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Hermann-von-Helmholtz-Platz 1 Eggenstein-Leopoldshafen 76344 Germany
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China Chongqing 400038 China
| | - Changming Hu
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology (INT), Hermann-von-Helmholtz Platz 1 Eggenstein-Leopoldshafen 76344 Germany
| | - Julian A Serna
- Karlsruhe Institute of Technology (KIT), Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Hermann-von-Helmholtz-Platz 1 Eggenstein-Leopoldshafen 76344 Germany
| | - Frank Biedermann
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology (INT), Hermann-von-Helmholtz Platz 1 Eggenstein-Leopoldshafen 76344 Germany
| | - Pavel A Levkin
- Karlsruhe Institute of Technology (KIT), Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Hermann-von-Helmholtz-Platz 1 Eggenstein-Leopoldshafen 76344 Germany
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry (IOC) Kaiserstraße 12 Karlsruhe 76131 Germany
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29
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Gupta SV, Campos L, Schmidt KH. Mitochondrial superoxide dismutase Sod2 suppresses nuclear genome instability during oxidative stress. Genetics 2023; 225:iyad147. [PMID: 37638880 PMCID: PMC10550321 DOI: 10.1093/genetics/iyad147] [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: 02/24/2023] [Accepted: 07/14/2023] [Indexed: 08/29/2023] Open
Abstract
Oxidative stress can damage DNA and thereby contribute to genome instability. To avoid an imbalance or overaccumulation of reactive oxygen species (ROS), cells are equipped with antioxidant enzymes that scavenge excess ROS. Cells lacking the RecQ-family DNA helicase Sgs1, which contributes to homology-dependent DNA break repair and chromosome stability, are known to accumulate ROS, but the origin and consequences of this oxidative stress phenotype are not fully understood. Here, we show that the sgs1 mutant exhibits elevated mitochondrial superoxide, increased mitochondrial mass, and accumulation of recombinogenic DNA lesions that can be suppressed by antioxidants. Increased mitochondrial mass in the sgs1Δ mutant is accompanied by increased mitochondrial branching, which was also inducible in wildtype cells by replication stress. Superoxide dismutase Sod2 genetically interacts with Sgs1 in the suppression of nuclear chromosomal rearrangements under paraquat (PQ)-induced oxidative stress. PQ-induced chromosome rearrangements in the absence of Sod2 are promoted by Rad51 recombinase and the polymerase subunit Pol32. Finally, the dependence of chromosomal rearrangements on the Rev1/Pol ζ mutasome suggests that under oxidative stress successful DNA synthesis during DNA break repair depends on translesion DNA synthesis.
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Affiliation(s)
- Sonia Vidushi Gupta
- Department of Molecular Biosciences, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Lillian Campos
- Department of Molecular Biosciences, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Kristina Hildegard Schmidt
- Department of Molecular Biosciences, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
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30
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Esteban-Sánchez L, Panayotova-Pencheva M, Qablan M, Modrý D, Hofmannová L, Ponce-Gordo F. Question of agent of camel balantidiosis solved: Molecular identity, taxonomic solution and epidemiological considerations. Vet Parasitol 2023; 321:109984. [PMID: 37494847 DOI: 10.1016/j.vetpar.2023.109984] [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: 06/14/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023]
Abstract
Domestic camels (Camelus bactrianus, the Bactrian camel; and Camelus dromedarius, the dromedary) are pseudo-ruminant herbivores kept as livestock in rural, inhospitable regions (cold deserts and dry steppes of Asia, arid to semi-arid regions of Africa, western and central Asia). Their close contact with humans makes them a potential reservoir for zoonotic parasite infections, as has been suggested for human balantidiasis. However, there is confusion about the ciliate species that infects camels: Infundibulorium cameli was originally described in dromedaries, but this name has almost never been used and most authors identified their findings as Balantioides coli and, to a lesser extent, Buxtonella sulcata, a cattle ciliate. To clarify the taxonomic status of the parasite and the corresponding zoonotic significance for camels, we performed morphological characterization of cysts and genetic analysis (SSU-rDNA and ITS markers) of B. coli-like isolates from Bactrian camels from Bulgaria and from dromedaries from Spain and the United Arab Emirates. Our results indicate that the camel ciliate is not B. coli, nor is it B. sulcata, but is a different species that should be placed in the same genus as the latter. Thus, camels are not a reservoir for human balantidiasis. Although the correct genus name would be Infundibulorium according to the principle of priority, this would lead to confusion since this name has almost fallen into disuse since its initial description, but Buxtonella is almost universally used by researchers and veterinarians for the cattle ciliate. We therefore propose to apply the reversal of precedence and use Buxtonella as the valid genus name. Consequently, we propose Buxtonella cameli n.comb. as the name for the camel ciliate.
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Affiliation(s)
- Lorena Esteban-Sánchez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Mariana Panayotova-Pencheva
- Department of Experimental Parasitology, Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., BI. 25, 1113 Sofia, Bulgaria
| | - Moneeb Qablan
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - David Modrý
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources/CINeZ, Czech University of Life Sciences Prague, 16500 Praha-Suchdol, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 61137 Brno, Czech Republic
| | - Lada Hofmannová
- State Veterinary Institute Prague, Sídlištní 136/24, Praha 6 165 03, Lysolaje, Czech Republic
| | - F Ponce-Gordo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain.
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31
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Pich-Bavastro C, Yerly L, Di Domizio J, Tissot-Renaud S, Gilliet M, Kuonen F. Activin A-Mediated Polarization of Cancer-Associated Fibroblasts and Macrophages Confers Resistance to Checkpoint Immunotherapy in Skin Cancer. Clin Cancer Res 2023; 29:3498-3513. [PMID: 37327314 PMCID: PMC10472111 DOI: 10.1158/1078-0432.ccr-23-0219] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 05/05/2023] [Accepted: 06/14/2023] [Indexed: 06/18/2023]
Abstract
PURPOSE Cemiplimab is approved for the treatment of locally advanced basal cell carcinomas (BCC), although with mitigated results. We sought to interrogate the cellular and molecular transcriptional reprogramming underlying BCC resistance to immunotherapy. EXPERIMENTAL DESIGN Here, we combined spatial and single-cell transcriptomics to deconvolute the spatial heterogeneity of the tumor microenvironment in regard with response to immunotherapy, in a cohort of both naïve and resistant BCCs. RESULTS We identified subsets of intermingled cancer-associated fibroblasts (CAF) and macrophages contributing the most to CD8 T-cell exclusion and immunosuppression. Within this spatially resolved peritumoral immunosuppressive niche, CAFs and adjacent macrophages were found to display Activin A-mediated transcriptional reprogramming towards extracellular matrix remodeling, suggesting active participation to CD8 T-cell exclusion. In independent datasets of human skin cancers, Activin A-conditioned CAFs and macrophages were associated with resistance to immune checkpoint inhibitors (ICI). CONCLUSIONS Altogether, our data identify the cellular and molecular plasticity of tumor microenvironment (TME) and the pivotal role of Activin A in polarizing the TME towards immune suppression and ICI resistance.
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Affiliation(s)
- Christine Pich-Bavastro
- Department of Dermatology and Venereology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Laura Yerly
- Department of Dermatology and Venereology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jeremy Di Domizio
- Department of Dermatology and Venereology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stéphanie Tissot-Renaud
- Department of Oncology, Immune Landscape Laboratory, Center of Experimental Therapeutics, Lausanne University Hospital, Lausanne, Switzerland
- Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Michel Gilliet
- Department of Dermatology and Venereology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - François Kuonen
- Department of Dermatology and Venereology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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32
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Zhao J, Zhao F, Li X, Yuan J, Zhang K, Liu H, Wang Y. Multi-omics reveals the mechanisms underlying Lactiplantibacillus plantarum P8-mediated attenuation of oxidative stress in broilers challenged with dexamethasone. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2023; 14:281-302. [PMID: 37600839 PMCID: PMC10432922 DOI: 10.1016/j.aninu.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 05/31/2023] [Accepted: 06/14/2023] [Indexed: 08/22/2023]
Abstract
Oxidative stress is a common phenomenon in poultry production. Several molecules, including antioxidant genes, miRNAs, and gut microbiota metabolites, have been reported to participate in redox regulation. Lactiplantibacillus plantarum P8 (P8) was shown to improve the antioxidant capacity of chickens, but the specific molecular mechanisms remain unclear. In this study, 400 broilers were allocated to 4 treatment groups: control diet (Con group), control diet + dexamethasone injection (DEX group), control diet containing 1 × 108 CFU/g P8 (P8 group), and control diet containing 1 × 108 CFU/g P8 + DEX injection (DEX_P8 group). Integrated analysis of the microbiome, metabolomics, and miRNAomics was conducted to investigate the roles of P8 in oxidative stress in broilers. Results demonstrated that P8 supplementation significantly improved growth performance, jejunal morphology, and antioxidant function in DEX-treated broilers. Analysis of the gut microbiota revealed a higher abundance of Barnesiella (P = 0.01) and Erysipelatoclostridium (P = 0.05) in the DEX_P8 group than in the DEX group. Functional prediction indicated that certain pathways, including the phenylacetate degradation pathway, were enriched in the DEX_P8 group compared to the DEX group. Metabolites in the cecal contents were distinct between the groups. P8 supplementation increased the content of metabolites with antioxidant capacity, e.g., urobilinogen (P < 0.01), and decreased that of metabolites related to oxidative stress, e.g., genistein (P < 0.01). Functional prediction indicated that metabolites that differed between the DEX_P8 and DEX groups were enriched in pathways including "tryptophan metabolism" and "primary bile acid biosynthesis". The miRNAomics analysis further showed that, compared to the DEX group, several miRNAs in the jejunum, such as gga-miR-21-3p (P = 0.03), were increased, whereas gga-miR-455-3p (P = 0.02) was decreased in the DEX_P8 group. The PI3K-Akt, Ras, and Rap1 signaling pathways were enriched in the DEX_P8 group compared to the DEX group through KEGG analysis. Correlation analysis revealed potential interactions between growth performance, oxidation/antioxidation, jejunal morphology, gut microbiota, cecal content metabolites, and jejunal miRNAs. Overall, our results indicate that P8 supplementation may improve the growth performance, jejunal morphology and antioxidant capacity of DEX-treated broilers by regulating gut microbiota, its metabolites, and intestinal miRNAs.
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Affiliation(s)
| | | | - Xuemin Li
- College of Animal Science and Technology, Qingdao Agricultural University, 266109, Qingdao, China
| | - Junmeng Yuan
- College of Animal Science and Technology, Qingdao Agricultural University, 266109, Qingdao, China
| | - Kai Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, 266109, Qingdao, China
| | - Huawei Liu
- College of Animal Science and Technology, Qingdao Agricultural University, 266109, Qingdao, China
| | - Yang Wang
- College of Animal Science and Technology, Qingdao Agricultural University, 266109, Qingdao, China
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Royer J, Larivière S, Rodriguez-Cruces R, Cabalo DG, Tavakol S, Auer H, Ngo A, Park BY, Paquola C, Smallwood J, Jefferies E, Caciagli L, Bernasconi A, Bernasconi N, Frauscher B, Bernhardt BC. Cortical microstructural gradients capture memory network reorganization in temporal lobe epilepsy. Brain 2023; 146:3923-3937. [PMID: 37082950 PMCID: PMC10473569 DOI: 10.1093/brain/awad125] [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: 11/07/2022] [Revised: 02/21/2023] [Accepted: 03/23/2023] [Indexed: 04/22/2023] Open
Abstract
Temporal lobe epilepsy (TLE), one of the most common pharmaco-resistant epilepsies, is associated with pathology of paralimbic brain regions, particularly in the mesiotemporal lobe. Cognitive dysfunction in TLE is frequent, and particularly affects episodic memory. Crucially, these difficulties challenge the quality of life of patients, sometimes more than seizures, underscoring the need to assess neural processes of cognitive dysfunction in TLE to improve patient management. Our work harnessed a novel conceptual and analytical approach to assess spatial gradients of microstructural differentiation between cortical areas based on high-resolution MRI analysis. Gradients track region-to-region variations in intracortical lamination and myeloarchitecture, serving as a system-level measure of structural and functional reorganization. Comparing cortex-wide microstructural gradients between 21 patients and 35 healthy controls, we observed a reorganization of this gradient in TLE driven by reduced microstructural differentiation between paralimbic cortices and the remaining cortex with marked abnormalities in ipsilateral temporopolar and dorsolateral prefrontal regions. Findings were replicated in an independent cohort. Using an independent post-mortem dataset, we observed that in vivo findings reflected topographical variations in cortical cytoarchitecture. We indeed found that macroscale changes in microstructural differentiation in TLE reflected increased similarity of paralimbic and primary sensory/motor regions. Disease-related transcriptomics could furthermore show specificity of our findings to TLE over other common epilepsy syndromes. Finally, microstructural dedifferentiation was associated with cognitive network reorganization seen during an episodic memory functional MRI paradigm and correlated with interindividual differences in task accuracy. Collectively, our findings showing a pattern of reduced microarchitectural differentiation between paralimbic regions and the remaining cortex provide a structurally-grounded explanation for large-scale functional network reorganization and cognitive dysfunction characteristic of TLE.
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Affiliation(s)
- Jessica Royer
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- Analytical Neurophysiology Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Sara Larivière
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Raul Rodriguez-Cruces
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Donna Gift Cabalo
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Shahin Tavakol
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Hans Auer
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alexander Ngo
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Bo-yong Park
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
- Department of Data Science, Inha University, Incheon 22212, Republic of Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon 34126, Republic of Korea
| | - Casey Paquola
- Multiscale Neuroanatomy Lab, INM-1, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Jonathan Smallwood
- Department of Psychology, Queen’s University, Kingston, ON, K7L 3N6, Canada
| | | | - Lorenzo Caciagli
- Department of Bioengineering, University of Pennsylvania, Philadelphia, MA 19104, USA
| | - Andrea Bernasconi
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Neda Bernasconi
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Birgit Frauscher
- Analytical Neurophysiology Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Boris C Bernhardt
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
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Jimenez Gonzalez A, Baranasic D, Müller F. Zebrafish regulatory genomic resources for disease modelling and regeneration. Dis Model Mech 2023; 16:dmm050280. [PMID: 37529920 PMCID: PMC10417509 DOI: 10.1242/dmm.050280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
In the past decades, the zebrafish has become a disease model with increasing popularity owing to its advantages that include fast development, easy genetic manipulation, simplicity for imaging, and sharing conserved disease-associated genes and pathways with those of human. In parallel, studies of disease mechanisms are increasingly focusing on non-coding mutations, which require genome annotation maps of regulatory elements, such as enhancers and promoters. In line with this, genomic resources for zebrafish research are expanding, producing a variety of genomic data that help in defining regulatory elements and their conservation between zebrafish and humans. Here, we discuss recent developments in generating functional annotation maps for regulatory elements of the zebrafish genome and how this can be applied to human diseases. We highlight community-driven developments, such as DANIO-CODE, in generating a centralised and standardised catalogue of zebrafish genomics data and functional annotations; consider the advantages and limitations of current annotation maps; and offer considerations for interpreting and integrating existing maps with comparative genomics tools. We also discuss the need for developing standardised genomics protocols and bioinformatic pipelines and provide suggestions for the development of analysis and visualisation tools that will integrate various multiomic bulk sequencing data together with fast-expanding data on single-cell methods, such as single-cell assay for transposase-accessible chromatin with sequencing. Such integration tools are essential to exploit the multiomic chromatin characterisation offered by bulk genomics together with the cell-type resolution offered by emerging single-cell methods. Together, these advances will build an expansive toolkit for interrogating the mechanisms of human disease in zebrafish.
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Affiliation(s)
- Ada Jimenez Gonzalez
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Damir Baranasic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London SW7 2AZ, UK
- MRC London Institute of Medical Sciences, London W12 0NN, UK
- Division of Electronics, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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35
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Tong Y, Rozeboom HJ, Loonstra MR, Wijma HJ, Fraaije MW. Characterization of two bacterial multi-flavinylated proteins harboring multiple covalent flavin cofactors. BBA ADVANCES 2023; 4:100097. [PMID: 37455753 PMCID: PMC10339131 DOI: 10.1016/j.bbadva.2023.100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
In recent years, studies have shown that a large number of bacteria secrete multi-flavinylated proteins. The exact roles and properties, of these extracellular flavoproteins that contain multiple covalently anchored FMN cofactors, are still largely unknown. Herein, we describe the biochemical and structural characterization of two multi-FMN-containing covalent flavoproteins, SaFMN3 from Streptomyces azureus and CbFMN4 from Clostridiaceae bacterium. Based on their primary structure, these proteins were predicted to contain three and four covalently tethered FMN cofactors, respectively. The genes encoding SaFMN3 and CbFMN4 were heterologously coexpressed with a flavin transferase (ApbE) in Escherichia coli, and could be purified by affinity chromatography in good yields. Both proteins were found to be soluble and to contain covalently bound FMN molecules. The SaFMN3 protein was studied in more detail and found to display a single redox potential (-184 mV) while harboring three covalently attached flavins. This is in line with the high sequence similarity when the domains of each flavoprotein are compared. The fully reduced form of SaFMN3 is able to use dioxygen as electron acceptor. Single domains from both proteins were expressed, purified and crystallized. The crystal structures were elucidated, which confirmed that the flavin cofactor is covalently attached to a threonine. Comparison of both crystal structures revealed a high similarity, even in the flavin binding pocket. Based on the crystal structure, mutants of the SaFMN3-D2 domain were designed to improve its fluorescence quantum yield by changing the microenvironment of the isoalloxazine moiety of the flavin cofactor. Residues that quench the flavin fluorescence were successfully identified. Our study reveals biochemical details of multi-FMN-containing proteins, contributing to a better understanding of their role in bacteria and providing leads to future utilization of these flavoprotein in biotechnology.
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36
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Amandykova M, Dossybayev K, Mussayeva A, Saitou N, Zhunusbayeva Z, Bekmanov B. A Study of the Genetic Structure of Hybrid Camels in Kazakhstan. Genes (Basel) 2023; 14:1373. [PMID: 37510278 PMCID: PMC10379372 DOI: 10.3390/genes14071373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Camel farming is gaining scientific interest due to its unique agricultural characteristics. Camels are versatile for milk and meat production, wool, racing, transport, and tourism. To use their full potential, it is essential to improve our understanding of the genetic structure of these animals. One-humped and two-humped camels have received detailed genetic descriptions, while there is no such information for their hybrids, which outperform their parent species in several agricultural characteristics. Thus, in this study, for the first time, the whole genome sequencing data (WGS) of five hybrid camels bred in the Almaty region of Kazakhstan are presented in comparison with the WGS data of one-humped, two-humped, and wild camels. A total of 43,552,164 single-nucleotide polymorphisms were found across the studied groups. Further comparison of these SNPs showed the following number of private SNPs among the populations: hybrid camels (3,271,083), wild camels (2,515,591), Bactrians (1,244,694), and dromedaries (531,224). The genetic structure of the studied animals was described, and a phylogenetic tree was built to assess their genetic distance. It was found that the studied hybrids are genetically closer to dromedaries since they were on the close branch of the phylogenetic tree.
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Affiliation(s)
- Makpal Amandykova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050040, Kazakhstan
- Laboratory of Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan
| | - Kairat Dossybayev
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050040, Kazakhstan
- Laboratory of Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan
| | - Aizhan Mussayeva
- Laboratory of Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan
| | - Naruya Saitou
- Saitou Naruya Laboratory, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Shizuoka, Japan
| | - Zhazira Zhunusbayeva
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050040, Kazakhstan
| | - Bakytzhan Bekmanov
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050040, Kazakhstan
- Laboratory of Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan
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37
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van Driel MS, Linssen JDG, Flanagan DJ, Vlahov N, Nijman LE, de Groot NE, Elbers CC, Koster J, Sansom OJ, Vermeulen L, van Neerven SM. Caffeine Limits Expansion of Apc-Deficient Clones in the Intestine by NOTUM Inhibition. Cell Mol Gastroenterol Hepatol 2023; 16:652-655. [PMID: 37364735 PMCID: PMC10511923 DOI: 10.1016/j.jcmgh.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023]
Affiliation(s)
- Milou S van Driel
- Amsterdam UMC, Location University of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, The Netherlands; Cancer Center Amsterdam, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Oncode Institute, Amsterdam, The Netherlands
| | - Jasmijn D G Linssen
- Amsterdam UMC, Location University of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, The Netherlands; Cancer Center Amsterdam, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Oncode Institute, Amsterdam, The Netherlands; Amsterdam UMC, Location University of Amsterdam, Department of Gastroenterology and Hepatology, Amsterdam, The Netherlands
| | - Dustin J Flanagan
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia; Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, Australia; Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Nikola Vlahov
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Lisanne E Nijman
- Amsterdam UMC, Location University of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, The Netherlands; Cancer Center Amsterdam, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Oncode Institute, Amsterdam, The Netherlands
| | - Nina E de Groot
- Amsterdam UMC, Location University of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, The Netherlands; Cancer Center Amsterdam, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Oncode Institute, Amsterdam, The Netherlands
| | - Clara C Elbers
- Amsterdam UMC, Location University of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, The Netherlands; Cancer Center Amsterdam, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Oncode Institute, Amsterdam, The Netherlands
| | - Jan Koster
- Amsterdam UMC, Location University of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, The Netherlands; Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom; Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Louis Vermeulen
- Amsterdam UMC, Location University of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, The Netherlands; Cancer Center Amsterdam, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Oncode Institute, Amsterdam, The Netherlands.
| | - Sanne M van Neerven
- Amsterdam UMC, Location University of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam, The Netherlands; Cancer Center Amsterdam, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Oncode Institute, Amsterdam, The Netherlands; Wellcome Trust-Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.
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38
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Das J, Kumar R, Yadav SK, Jha G. Nicotinic Acid Catabolism Modulates Bacterial Mycophagy in Burkholderia gladioli Strain NGJ1. Microbiol Spectr 2023; 11:e0445722. [PMID: 37014254 PMCID: PMC10269826 DOI: 10.1128/spectrum.04457-22] [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: 11/04/2022] [Accepted: 03/03/2023] [Indexed: 04/05/2023] Open
Abstract
Burkholderia gladioli strain NGJ1 exhibits mycophagous activity on a broad range of fungi, including Rhizoctonia solani, a devastating plant pathogen. Here, we demonstrate that the nicotinic acid (NA) catabolic pathway in NGJ1 is required for mycophagy. NGJ1 is auxotrophic to NA and it potentially senses R. solani as a NA source. Mutation in the nicC and nicX genes involved in NA catabolism renders defects in mycophagy and the mutant bacteria are unable to utilize R. solani extract as the sole nutrient source. As supplementation of NA, but not FA (fumaric acid, the end product of NA catabolism) restores the mycophagous ability of ΔnicC/ΔnicX mutants, we anticipate that NA is not required as a carbon source for the bacterium during mycophagy. Notably, nicR, a MarR-type of transcriptional regulator that functions as a negative regulator of the NA catabolic pathway is upregulated in ΔnicC/ΔnicX mutant and upon NA supplementation the nicR expression is reduced to the basal level in both the mutants. The ΔnicR mutant produces excessive biofilm and is completely defective in swimming motility. On the other hand, ΔnicC/ΔnicX mutants are compromised in swimming motility as well as biofilm formation, potentially due to the upregulation of nicR. Our data suggest that a defect in NA catabolism alters the NA pool in the bacterium and upregulates nicR which in turn suppresses bacterial motility as well as biofilm formation, leading to mycophagy defects. IMPORTANCE Mycophagy is an important trait through which certain bacteria forage over fungal mycelia and utilize fungal biomass as a nutrient source to thrive in hostile environments. The present study emphasizes that nicotinic acid (NA) is important for bacterial motility and biofilm formation during mycophagy by Burkholderia gladioli strain NGJ1. Defects in NA catabolism potentially alter the cellular NA pool, upregulate the expression of nicR, a negative regulator of biofilm, and therefore suppress bacterial motility as well as biofilm formation, leading to mycophagy defects.
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Affiliation(s)
- Joyati Das
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, New Delhi, India
| | - Rahul Kumar
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, New Delhi, India
| | - Sunil Kumar Yadav
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, New Delhi, India
| | - Gopaljee Jha
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, New Delhi, India
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James A, Reynaud-Bouret P, Mezzadri G, Sargolini F, Bethus I, Muzy A. Strategy inference during learning via cognitive activity-based credit assignment models. Sci Rep 2023; 13:9408. [PMID: 37296163 PMCID: PMC10256696 DOI: 10.1038/s41598-023-33604-2] [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: 11/01/2022] [Accepted: 04/15/2023] [Indexed: 06/12/2023] Open
Abstract
We develop a method for selecting meaningful learning strategies based solely on the behavioral data of a single individual in a learning experiment. We use simple Activity-Credit Assignment algorithms to model the different strategies and couple them with a novel hold-out statistical selection method. Application on rat behavioral data in a continuous T-maze task reveals a particular learning strategy that consists in chunking the paths used by the animal. Neuronal data collected in the dorsomedial striatum confirm this strategy.
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Affiliation(s)
| | | | - Giulia Mezzadri
- Columbia University, Cognition and Decision Lab, New York, USA
| | - Francesca Sargolini
- Aix Marseille Université, CNRS, Laboratoire de Neurosciences Cognitives, Marseille, France
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40
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Sarno J, Domizi P, Liu Y, Merchant M, Pedersen CB, Jedoui D, Jager A, Nolan GP, Gaipa G, Bendall SC, Bava FA, Davis KL. Dasatinib overcomes glucocorticoid resistance in B-cell acute lymphoblastic leukemia. Nat Commun 2023; 14:2935. [PMID: 37217509 DOI: 10.1038/s41467-023-38456-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Resistance to glucocorticoids (GC) is associated with an increased risk of relapse in B-cell progenitor acute lymphoblastic leukemia (BCP-ALL). Performing transcriptomic and single-cell proteomic studies in healthy B-cell progenitors, we herein identify coordination between the glucocorticoid receptor pathway with B-cell developmental pathways. Healthy pro-B cells most highly express the glucocorticoid receptor, and this developmental expression is conserved in primary BCP-ALL cells from patients at diagnosis and relapse. In-vitro and in vivo glucocorticoid treatment of primary BCP-ALL cells demonstrate that the interplay between B-cell development and the glucocorticoid pathways is crucial for GC resistance in leukemic cells. Gene set enrichment analysis in BCP-ALL cell lines surviving GC treatment show enrichment of B cell receptor signaling pathways. In addition, primary BCP-ALL cells surviving GC treatment in vitro and in vivo demonstrate a late pre-B cell phenotype with activation of PI3K/mTOR and CREB signaling. Dasatinib, a multi-kinase inhibitor, most effectively targets this active signaling in GC-resistant cells, and when combined with glucocorticoids, results in increased cell death in vitro and decreased leukemic burden and prolonged survival in an in vivo xenograft model. Targeting the active signaling through the addition of dasatinib may represent a therapeutic approach to overcome GC resistance in BCP-ALL.
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Affiliation(s)
- Jolanda Sarno
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA.
| | - Pablo Domizi
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Yuxuan Liu
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Milton Merchant
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Christina Bligaard Pedersen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dorra Jedoui
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Astraea Jager
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Giuseppe Gaipa
- M. Tettamanti Research Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, (MB), Italy
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Felice-Alessio Bava
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Institut national de la santé et de la recherche médicale (INSERM), Paris, France
| | - Kara L Davis
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA.
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41
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Maity D, Bhaumik SK, Banerjee S. Contrasting luminescence in heparin and DNA-templated co-assemblies of dimeric cyanostilbenes: efficient energy transfer in heparin-based co-assemblies. Phys Chem Chem Phys 2023; 25:12810-12819. [PMID: 37129214 DOI: 10.1039/d3cp00709j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Dimeric cationic cyanostilbenes with peripheral alkyl chains demonstrated aggregation in aqueous media depending on the length of the hydrophobic segment and produced luminescent spherical nano-assemblies in the case of long alkyl chain derivatives. In the presence of heparin, a bio-polyanion that is routinely used as an anticoagulant, the self-assembled structures obtained from the amphiphilic dimers showed the formation of higher-order structures whereas the non-assembling dimers exhibited heparin-induced supramolecular structure formation. In both cases, a significant enhancement in the emission was observed. This led to the detection of heparin in aqueous buffer, serum and plasma with a "turn-on" fluorescence response. Interestingly, these derivatives also exhibited luminescence variation in the presence of ctDNA. However, the response towards DNA was opposite to that observed in the case of heparin i.e., "turn-off'' fluorescence response. Notably, depending on the length of the alkyl segment, divergent DNA binding modes of these derivatives were observed. Due to their enhanced luminescence, the heparin-based co-assemblies were further explored as artificial light-harvesting systems exhibiting an efficient energy transfer process to embedded acceptor dyes with a high antenna effect.
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Affiliation(s)
- Dhananjoy Maity
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
| | - Shubhra Kanti Bhaumik
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
| | - Supratim Banerjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
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Yisa AG, Chia MA, Sha'aba RI, Gauje B, Gadzama IMK, Oniye SJ. Risk assessment of the antibiotic amoxicillin on non-toxin-producing strains and toxin-producing strains of Microcystis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:56398-56409. [PMID: 36917389 DOI: 10.1007/s11356-023-26403-9] [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: 09/18/2021] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Amoxicillin (AMX) is a common antibiotic used to treat a variety of infectious illnesses in humans and animals, including otitis media, tonsillitis, tonsillopharyngitis, laryngitis, and pharyngitis. The drug ends up in the aquatic ecosystems through animal and human excretion and industrial effluents. The ecological consequences of broad-spectrum antibiotics on non-target species like cyanobacteria are causing considerable concern. The danger of amoxicillin to non-toxin-producing and toxin-producing strains of cyanobacteria is poorly understood. The objective of this study was to analyze the risk (RQ) and physiological effects of AMX on Microcystis aeruginosa EAWAG 198 (non-toxin producing = NTP), Microcystis aeruginosa LE3 (toxin-producing = TP), and Microcystis flos aquae UTEX-LB 2677 (toxin-producing = TP). Our study showed differences in the RQ of the drug to the tested organisms - demonstrating < Microcystis flos aquae UTEX-LB 2677 > Microcystis aeruginosa LE3 > Microcystis aeruginosa EAWAG 198. The calculated EC50 values show that AMX was more toxic to the toxin-producing strains than the non-toxin-producing strains. Amoxicillin led to significant (p < 0.05) growth inhibition and chlorophyll-a content of the exposed cultures. The observed increase in the concentration of intracellular hydrogen peroxide (H2O2) of the exposed cultures at 96 h was significant (p < 0.05), demonstrating that the expressed oxidative stress patterns observed during the study were due to AMX. The current study shows significant variation (p < 0.05) in melondialdehyde (MDA) content and the antioxidant enzymes - glutathione-S-transferase (GST) and peroxidase (POD).
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Affiliation(s)
| | | | | | - Balli Gauje
- National Institute for Chemical Technology, Zaria, Nigeria
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43
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Solanki R, Shankar A, Modi U, Patel S. New insights from nanotechnology in SARS-CoV-2 detection, treatment strategy, and prevention. MATERIALS TODAY. CHEMISTRY 2023; 29:101478. [PMID: 36950312 PMCID: PMC9981536 DOI: 10.1016/j.mtchem.2023.101478] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/13/2023] [Accepted: 02/25/2023] [Indexed: 05/14/2023]
Abstract
The recent outbreak of SARS-CoV-2 resulted into the deadly COVID-19 pandemic, which has made a profound impact on mankind and the world health care system. SARS-CoV-2 is mainly transmitted within the population via symptomatic carriers, enters the host cell via ACE2 and TMPSSR2 receptors and damages the organs. The standard diagnostic tests and treatment methods implemented lack required efficiency to beat SARS-CoV-2 in the race of its spreading. The most prominently used diagnostic test,reverse transcription-polymerase chain reaction (a nucleic acid-based method), has limitations including a prolonged time taken to reveal results, limited sensitivity, a high rate of false negative results, and lacking specificity due to a homology with other viruses. Furthermore, as part of the treatment, antiviral drugs such as remdesivir, favipiravir, lopinavir/ritonavir, chloroquine, daclatasvir, atazanavir, and many more have been tested clinically to check their potency for the treatment of SARS-CoV-2 but none of these antiviral drugs are the definitive cure or suitable prophylaxis. Thus, it is always required to combat SARS-CoV-2 spread and infection for a better and precise prognosis. This review answers the above mentioned challenges by employing nanomedicine for the development of improved detection, treatment, and prevention strategies for SARS-CoV-2. In this review, nanotechnology-based detection methods such as colorimetric assays, photothermal biosensors, molecularly imprinted nanoparticles sensors, electrochemical nanoimmunosensors, aptamer-based biosensors have been discussed. Furthermore, nanotechnology-based treatment strategies involving polymeric nanoparticles, metallic nanoparticles, lipid nanoparticles, and nanocarrier-based antiviral siRNA delivery have been depicted. Moreover, SARS-CoV-2 prevention strategies, which include the nanotechnology for upgrading personal protective equipment, facemasks, ocular protection gears, and nanopolymer-based disinfectants, have been also reviewed. This review will provide a one-site informative platform for researchers to explore the crucial role of nanomedicine in managing the COVID-19 curse more effectively.
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Affiliation(s)
- R Solanki
- School of Life Sciences, Central University of Gujarat, Sector-30, Gandhinagar, 382030, India
| | - A Shankar
- School of Life Sciences, Central University of Gujarat, Sector-30, Gandhinagar, 382030, India
| | - U Modi
- Biomaterials & Biomimetics Laboratory, School of Life Sciences, Central University of Gujarat, Sector-30, Gandhinagar, 382030, India
| | - S Patel
- School of Life Sciences, Central University of Gujarat, Sector-30, Gandhinagar, 382030, India
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44
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White JM, Ramos N, Saliganan AD, Chung JY, Bell M, Lindquist J, Conner K, Wiesend WN, Schopperle M, Patrick SM, Kim S, Heath EI, Escorcia FE, Viola NT. Selective ablation of TRA-1-60 + pluripotent stem cells suppresses tumor growth of prostate cancer. Theranostics 2023; 13:2057-2071. [PMID: 37153742 PMCID: PMC10157726 DOI: 10.7150/thno.78915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/21/2023] [Indexed: 05/10/2023] Open
Abstract
Purpose: TRA-1-60 (TRA) is an established transcription factor of embryonic signaling and a well-known marker of pluripotency. It has been implicated in tumorigenesis and metastases, is not expressed in differentiated cells, which makes it an appealing biomarker for immunopositron emission tomography (immunoPET) imaging and radiopharmaceutical therapy (RPT). Herein, we explored the clinical implications of TRA in prostate cancer (PCa), examined the potential of TRA-targeted PET to specifically image TRA+ cancer stem cells (CSCs) and assessed response to the selective ablation of PCa CSCs using TRA-targeted RPT. Experimental Design: First, we assessed the relationship between TRA (PODXL) copy number alterations (CNA) and survival using publicly available patient databases. The anti-TRA antibody, Bstrongomab, was radiolabeled with Zr-89 or Lu-177 for immunoPET imaging and RPT in PCa xenografts. Radiosensitive tissues were collected to assess radiotoxicity while excised tumors were examined for pathologic treatment response. Results: Patients with tumors having high PODXL CNA exhibited poorer progression-free survival than those with low PODXL, suggesting that it plays an important role in tumor aggressiveness. TRA-targeted immunoPET imaging specifically imaged CSCs in DU-145 xenografts. Tumors treated with TRA RPT exhibited delayed growth and decreased proliferative activity, marked by Ki-67 immunohistochemistry. Aside from minor weight loss in select animals, no significant signs of radiotoxicity were observed in the kidneys or livers. Conclusions: We successfully demonstrated the clinical significance of TRA expression in human PCa, engineered and tested radiotheranostic agents to image and treat TRA+ prostate CSCs. Ablation of TRA+ CSCs blunted PCa growth. Future studies combining CSC ablation with standard treatment will be explored to achieve durable responses.
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Affiliation(s)
- Jordan M White
- Department of Oncology, Karmanos Cancer Institute, Detroit, MI 48201
- Cancer Biology Graduate Program, Wayne State University, School of Medicine, Detroit, MI 48201
| | - Nicholas Ramos
- Department of Oncology, Karmanos Cancer Institute, Detroit, MI 48201
| | | | - Joon-Yong Chung
- Molecular Imaging Branch, Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Meghan Bell
- Molecular Imaging Branch, Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jacob Lindquist
- Department of Oncology, Karmanos Cancer Institute, Detroit, MI 48201
- Cancer Biology Graduate Program, Wayne State University, School of Medicine, Detroit, MI 48201
| | - Kayla Conner
- Department of Oncology, Karmanos Cancer Institute, Detroit, MI 48201
- Cancer Biology Graduate Program, Wayne State University, School of Medicine, Detroit, MI 48201
| | | | - Michael Schopperle
- Department of Anatomic Pathology, Beaumont Health System, Royal Oak, MI 48073
| | - Steve M Patrick
- Department of Oncology, Karmanos Cancer Institute, Detroit, MI 48201
| | - Seongho Kim
- Department of Oncology, Karmanos Cancer Institute, Detroit, MI 48201
| | - Elisabeth I Heath
- Department of Oncology, Karmanos Cancer Institute, Detroit, MI 48201
| | - Freddy E Escorcia
- Molecular Imaging Branch, Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Nerissa T Viola
- Department of Oncology, Karmanos Cancer Institute, Detroit, MI 48201
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Yan P, He N, Yu K, Xu L, Van Meerbeek K. Integrating multiple plant functional traits to predict ecosystem productivity. Commun Biol 2023; 6:239. [PMID: 36869238 PMCID: PMC9984401 DOI: 10.1038/s42003-023-04626-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 02/23/2023] [Indexed: 03/05/2023] Open
Abstract
Quantifying and predicting variation in gross primary productivity (GPP) is important for accurate assessment of the ecosystem carbon budget under global change. Scaling traits to community scales for predicting ecosystem functions (i.e., GPP) remain challenging, while it is promising and well appreciated with the rapid development of trait-based ecology. In this study, we aim to integrate multiple plant traits with the recently developed trait-based productivity (TBP) theory, verify it via Bayesian structural equation modeling (SEM) and complementary independent effect analysis. We further distinguish the relative importance of different traits in explaining the variation in GPP. We apply the TBP theory based on plant community traits to a multi-trait dataset containing more than 13,000 measurements of approximately 2,500 species in Chinese forest and grassland systems. Remarkably, our SEM accurately predicts variation in annual and monthly GPP across China (R2 values of 0.87 and 0.73, respectively). Plant community traits play a key role. This study shows that integrating multiple plant functional traits into the TBP theory strengthens the quantification of ecosystem primary productivity variability and further advances understanding of the trait-productivity relationship. Our findings facilitate integration of the growing plant trait data into future ecological models.
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Affiliation(s)
- Pu Yan
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
- Division Forest, Nature and Landscape, Department of Earth and Environmental Sciences, KU Leuven, Leuven, Belgium
| | - Nianpeng He
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Ecological Research, Northeast Forestry University, Harbin, 150040, China.
| | - Kailiang Yu
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- High Meadows Environmental Institute, Princeton University, Princeton, NJ, USA
| | - Li Xu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
- Earth Critical Zone and Flux Research Station of Xing'an Mountains, Chinese Academy of Sciences, Daxing'anling, 165200, China
| | - Koenraad Van Meerbeek
- Division Forest, Nature and Landscape, Department of Earth and Environmental Sciences, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven, Leuven, Belgium
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Bahbahani H, Al-Zoubi S, Ali F, Afana A, Dashti M, Al-Ateeqi A, Wragg D, Al-Bustan S, Almathen F. Signatures of purifying selection and site-specific positive selection on the mitochondrial DNA of dromedary camels (Camelus dromedarius). Mitochondrion 2023; 69:36-42. [PMID: 36690316 DOI: 10.1016/j.mito.2023.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
The two species of the Old World Camelini tribe, dromedary and Bactrian camels, show superior adaptability to the different environmental conditions they populate, e.g. desert, mountains and coastal areas, which might be associated with adaptive variations on their mitochondrial DNA. Here, we investigate signatures of natural selection in the 13-mitochondrial protein-coding genes of different dromedary camel populations from the Arabian Peninsula, Africa and southwest Asia. The full mitogenome sequences of 42 dromedaries, 38 domestic Bactrian, 29 wild Bactrian camels and 31 samples representing the New World Lamini tribe reveal species-wise genetic distinction among Camelidae family species, with no evidence of geographic distinction among dromedary camels. We observe gene-wide signals of adaptive divergence between the Old World and New World camels, with evidence of purifying selection among Old World camel species. Upon comparing the different Camelidae tribes, 27 amino acid substitutions across ten mtDNA protein-coding genes were found to be under positive selection, in which, 24 codons were defined to be under positive adaptive divergence between Old World and New World camels. Seven codons belonging to three genes demonstrated positive selection in dromedary lineage. A total of 89 codons were found to be under positive selection in Camelidae family based on investigating the impact of amino acid replacement on the physiochemical properties of proteins, including equilibrium constant and surrounding hydrophobicity. These mtDNA variants under positive selection in the Camelidae family might be associated with their adaptation to their contrasting environments.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait.
| | - Sanaa Al-Zoubi
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - Fatima Ali
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - Arwa Afana
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - Mohammed Dashti
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Abdulaziz Al-Ateeqi
- Environment and Life Sciences research center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - David Wragg
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Suzanne Al-Bustan
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, 400 Al-Ahsa, Saudi Arabia; Camel Research Center, King Faisal University, 400 Al-Ahsa, Saudi Arabia
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47
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Martucci LL, Launay JM, Kawakami N, Sicard C, Desvignes N, Dakouane-Giudicelli M, Spix B, Têtu M, Gilmaire FO, Paulcan S, Callebert J, Vaillend C, Bracher F, Grimm C, Fossier P, de la Porte S, Sakamoto H, Morris J, Galione A, Granon S, Cancela JM. Endolysosomal TPCs regulate social behavior by controlling oxytocin secretion. Proc Natl Acad Sci U S A 2023; 120:e2213682120. [PMID: 36745816 PMCID: PMC9963339 DOI: 10.1073/pnas.2213682120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 12/14/2022] [Indexed: 02/08/2023] Open
Abstract
Oxytocin (OT) is a prominent regulator of many aspects of mammalian social behavior and stored in large dense-cored vesicles (LDCVs) in hypothalamic neurons. It is released in response to activity-dependent Ca2+ influx, but is also dependent on Ca2+ release from intracellular stores, which primes LDCVs for exocytosis. Despite its importance, critical aspects of the Ca2+-dependent mechanisms of its secretion remain to be identified. Here we show that lysosomes surround dendritic LDCVs, and that the direct activation of endolysosomal two-pore channels (TPCs) provides the critical Ca2+ signals to prime OT release by increasing the releasable LDCV pool without directly stimulating exocytosis. We observed a dramatic reduction in plasma OT levels in TPC knockout mice, and impaired secretion of OT from the hypothalamus demonstrating the importance of priming of neuropeptide vesicles for activity-dependent release. Furthermore, we show that activation of type 1 metabotropic glutamate receptors sustains somatodendritic OT release by recruiting TPCs. The priming effect could be mimicked by a direct application of nicotinic acid adenine dinucleotide phosphate, the endogenous messenger regulating TPCs, or a selective TPC2 agonist, TPC2-A1-N, or blocked by the antagonist Ned-19. Mice lacking TPCs exhibit impaired maternal and social behavior, which is restored by direct OT administration. This study demonstrates an unexpected role for lysosomes and TPCs in controlling neuropeptide secretion, and in regulating social behavior.
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Affiliation(s)
- Lora L. Martucci
- Neuroscience Paris-Saclay Institute, CNRS UMR 9197, Paris-Sud University, Paris-Saclay University, Saclay91400, France
- Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines, Inserm, Evolution of Neuromuscular Diseases: Innovative Concepts and Practices, Versailles78000, France
- Department of Pharmacology, University of Oxford, OxfordOX1 3QT, UK
| | | | - Natsuko Kawakami
- Ushimado Marine Institute, Graduate School of Natural Science and Technology, Okayama University, Ushimado, Setouchi, Okayama701-4303, Japan
| | - Cécile Sicard
- Neuroscience Paris-Saclay Institute, CNRS UMR 9197, Paris-Sud University, Paris-Saclay University, Saclay91400, France
| | - Nathalie Desvignes
- Neuroscience Paris-Saclay Institute, CNRS UMR 9197, Paris-Sud University, Paris-Saclay University, Saclay91400, France
| | - Mbarka Dakouane-Giudicelli
- Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines, Inserm, Evolution of Neuromuscular Diseases: Innovative Concepts and Practices, Versailles78000, France
| | - Barbara Spix
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine Ludwig-Maximilians-University, Munich80336, Germany
| | - Maude Têtu
- Neuroscience Paris-Saclay Institute, CNRS UMR 9197, Paris-Sud University, Paris-Saclay University, Saclay91400, France
| | - Franck-Olivier Gilmaire
- Neuroscience Paris-Saclay Institute, CNRS UMR 9197, Paris-Sud University, Paris-Saclay University, Saclay91400, France
| | - Sloane Paulcan
- Neuroscience Paris-Saclay Institute, CNRS UMR 9197, Paris-Sud University, Paris-Saclay University, Saclay91400, France
| | - Jacques Callebert
- Laboratoire de Biochimie et Biologie Moléculaire, Hôpital Lariboisière, Paris75010, France
- Inserm UMR-S 1144 Universités Paris Descartes-Paris Diderot, Optimisation Thérapeutique en Neuropsychopharmacologie - Faculté des Sciences Pharmaceutiques et Biologiques, Paris Descartes,ParisParis 75006, France
| | - Cyrille Vaillend
- Neuroscience Paris-Saclay Institute, CNRS UMR 9197, Paris-Sud University, Paris-Saclay University, Saclay91400, France
| | - Franz Bracher
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians University, Munich81377, Germany
| | - Christian Grimm
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine Ludwig-Maximilians-University, Munich80336, Germany
| | - Philippe Fossier
- Neuroscience Paris-Saclay Institute, CNRS UMR 9197, Paris-Sud University, Paris-Saclay University, Saclay91400, France
| | - Sabine de la Porte
- Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines, Inserm, Evolution of Neuromuscular Diseases: Innovative Concepts and Practices, Versailles78000, France
| | - Hirotaka Sakamoto
- Ushimado Marine Institute, Graduate School of Natural Science and Technology, Okayama University, Ushimado, Setouchi, Okayama701-4303, Japan
| | - John Morris
- Department of Physiology, Anatomy & Genetics, University of Oxford, OxfordOX1 3QX, UK
| | - Antony Galione
- Department of Pharmacology, University of Oxford, OxfordOX1 3QT, UK
| | - Sylvie Granon
- Neuroscience Paris-Saclay Institute, CNRS UMR 9197, Paris-Sud University, Paris-Saclay University, Saclay91400, France
| | - José-Manuel Cancela
- Neuroscience Paris-Saclay Institute, CNRS UMR 9197, Paris-Sud University, Paris-Saclay University, Saclay91400, France
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Louchouarn NX, Treves A. Low-stress livestock handling protects cattle in a five-predator habitat. PeerJ 2023; 11:e14788. [PMID: 36793893 PMCID: PMC9924134 DOI: 10.7717/peerj.14788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/03/2023] [Indexed: 02/12/2023] Open
Abstract
Given the ecological importance of top predators, societies are turning to non-lethal methods for coexistence. Coexistence is challenging when livestock graze within wild predator habitats. We report a randomized, controlled experiment to evaluate low-stress livestock handling (L-SLH), a form of range riding, to deter grizzly (brown) bears, gray wolves, cougars, black bears, and coyotes in Southwestern Alberta. The treatment condition was supervision by two newly hired and trained range riders and an experienced L-SLH-practicing range rider. This treatment was compared against a baseline pseudo-control condition of the experienced range rider working alone. Cattle experienced zero injuries or deaths in either condition. We infer that inexperienced range riders trained and supervised by an experienced rider did not raise or lower the risk to cattle. Also, predators did not shift to the cattle herds protected by fewer range riders. We found a correlation suggesting grizzly bears avoided herds visited more frequently by range riders practicing L-SLH. More research is required to compare different forms of range riding. However, pending experimental evaluation of other designs, we recommend use of L-SLH. We discuss the cobenefits of this husbandry method.
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Affiliation(s)
- Naomi X. Louchouarn
- Nelson Insitute for Environmental Studies, University of Wisconsin-Madison, Madison, USA
| | - Adrian Treves
- Nelson Institute for Environmental Science, University of Wisconsin-Madison, Madison, United States of America
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Rahman SU, McCoy E, Raza G, Ali Z, Mansoor S, Amin I. Improvement of Soybean; A Way Forward Transition from Genetic Engineering to New Plant Breeding Technologies. Mol Biotechnol 2023; 65:162-180. [PMID: 35119645 DOI: 10.1007/s12033-022-00456-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/21/2022] [Indexed: 01/18/2023]
Abstract
Soybean is considered one of the important crops among legumes. Due to high nutritional contents in seed (proteins, sugars, oil, fatty acids, and amino acids), soybean is used globally for food, feed, and fuel. The primary consumption of soybean is vegetable oil and feed for chickens and livestock. Apart from this, soybean benefits soil fertility by fixing atmospheric nitrogen through root nodular bacteria. While conventional breeding is practiced for soybean improvement, with the advent of new biotechnological methods scientists have also engineered soybean to improve different traits (herbicide, insect, and disease resistance) to fulfill consumer requirements and to meet the global food deficiency. Genetic engineering (GE) techniques such as transgenesis and gene silencing help to minimize the risks and increase the adaptability of soybean. Recently, new plant breeding technologies (NPBTs) emerged such as zinc-finger nucleases, transcription activator-like effector nucleases, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9), which paved the way for enhanced genetic modification of soybean. These NPBTs have the potential to improve soybean via gene functional characterization precision genome engineering for trait improvement. Importantly, these NPBTs address the ethical and public acceptance issues related to genetic modifications and transgenesis in soybean. In the present review, we summarized the improvement of soybean through GE and NPBTs. The valuable traits that have been improved through GE for different constraints have been discussed. Moreover, the traits that have been improved through NPBTs and potential targets for soybean improvements via NPBTs and solutions for ethical and public acceptance are also presented.
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Affiliation(s)
- Saleem Ur Rahman
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Evan McCoy
- Center for Applied Genetic Technologies (CAGT), University of Georgia, Athens, USA
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Zahir Ali
- Laboratory for Genome Engineering, Center for Desert Agriculture and Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan.
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50
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Jiang H, Cheng X, Liang Y, Wang Y, Li Y, Li Y. Aberrant expression of WNK lysine deficient protein kinase 1 is associated with poor prognosis of colon adenocarcinoma. Ir J Med Sci 2023; 192:57-64. [PMID: 35138567 DOI: 10.1007/s11845-021-02916-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/30/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUNDS WNK1 (WNK lysine deficient protein kinase 1) is a kind of protein kinase and participates in angiogenesis, having a potent tumor promoting role. WNK1 is ubiquitously expressed, and its upregulated expression has been reported in several tumor types. AIMS Here, we aimed to investigate the correlation between WNK1 expression and colon adenocarcinoma (COAD) progression. METHODS In the current study, WNK1 expression was evaluated by immunohistochemically in adjacent normal colonic mucosae and primary adenocarcinomas. The effect of WNK1 on overall survival (OS) and its associations with the clinicopathological parameters were analyzed in a retrospective cohort of COAD patients (n = 185). The tumor-related effects of WNK1 in COAD were further tested via cellular and mice experiments. RESULTS According to our cohort, higher WNK1 expression was significantly associated with unfavorable prognostic factors, such as high pT stage, pN stage, as well as shorter OS. Moreover, WNK1 exhibited tumor promoting role in COAD cancer cell lines as well as in nude mice. Silencing WNK1 can significantly inhibit the proliferation of COAD both in vitro and in vivo. CONCLUSIONS In all, WNK1 acts as a tumor promoter and may be used as a COAD prognostic biomarker.
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Affiliation(s)
- Huiyuan Jiang
- Department of Colorectal & Anal Surgery, Affiliated Tumor Hospital of Shanxi Medical University, Taiyuan, China
| | - Xin Cheng
- Department of Gynecology, First Affiliated Hospital of Shanxi Medical University, Taiyuan, China
| | - Yanjie Liang
- Department of Laboratory Medicine, Affiliated Tumor Hospital of Shanxi Medical University, Taiyuan, China
| | - Yan Wang
- Department of Aetiology, Affiliated Tumor Hospital of Shanxi Medical University, Taiyuan, China
| | - Yiqun Li
- Department of Colorectal & Anal Surgery, Affiliated People's Hospital of Shanxi Medical University, 29 Shuangtasi Street, Taiyuan, 030012, China
| | - Yaoping Li
- Department of Colorectal & Anal Surgery, Affiliated People's Hospital of Shanxi Medical University, 29 Shuangtasi Street, Taiyuan, 030012, China.
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