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Naffaa MM. Neurogenesis dynamics in the olfactory bulb: deciphering circuitry organization, function, and adaptive plasticity. Neural Regen Res 2025; 20:1565-1581. [PMID: 38934393 DOI: 10.4103/nrr.nrr-d-24-00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Adult neurogenesis persists after birth in the subventricular zone, with new neurons migrating to the granule cell layer and glomerular layers of the olfactory bulb, where they integrate into existing circuitry as inhibitory interneurons. The generation of these new neurons in the olfactory bulb supports both structural and functional plasticity, aiding in circuit remodeling triggered by memory and learning processes. However, the presence of these neurons, coupled with the cellular diversity within the olfactory bulb, presents an ongoing challenge in understanding its network organization and function. Moreover, the continuous integration of new neurons in the olfactory bulb plays a pivotal role in regulating olfactory information processing. This adaptive process responds to changes in epithelial composition and contributes to the formation of olfactory memories by modulating cellular connectivity within the olfactory bulb and interacting intricately with higher-order brain regions. The role of adult neurogenesis in olfactory bulb functions remains a topic of debate. Nevertheless, the functionality of the olfactory bulb is intricately linked to the organization of granule cells around mitral and tufted cells. This organizational pattern significantly impacts output, network behavior, and synaptic plasticity, which are crucial for olfactory perception and memory. Additionally, this organization is further shaped by axon terminals originating from cortical and subcortical regions. Despite the crucial role of olfactory bulb in brain functions and behaviors related to olfaction, these complex and highly interconnected processes have not been comprehensively studied as a whole. Therefore, this manuscript aims to discuss our current understanding and explore how neural plasticity and olfactory neurogenesis contribute to enhancing the adaptability of the olfactory system. These mechanisms are thought to support olfactory learning and memory, potentially through increased complexity and restructuring of neural network structures, as well as the addition of new granule granule cells that aid in olfactory adaptation. Additionally, the manuscript underscores the importance of employing precise methodologies to elucidate the specific roles of adult neurogenesis amidst conflicting data and varying experimental paradigms. Understanding these processes is essential for gaining insights into the complexities of olfactory function and behavior.
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Affiliation(s)
- Moawiah M Naffaa
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
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2
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Sovi S, Adomako K, Kyei B, Kena AW, Olympio OS, Aggrey SE. A comparative study of population structure and genetic diversity of commercial and indigenous chickens from different agro-ecological zones in Ghana using SilicoDArT and SNP markers. Gene 2024; 929:148823. [PMID: 39122230 DOI: 10.1016/j.gene.2024.148823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 07/19/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024]
Abstract
Chicken production, both in the local and commercial sectors, contributes significantly to human livelihood and food security. Precise use of diverse genetic resources is primary in breeding programs. The study analyzed the genetic diversity and population structure of commercial chickens and indigenous chicken ecotypes from three different agro-ecological zones (Semi-Deciduous Rainforest Zone, Guinea Savannah, and Coastal Savannah) using SilicoDArT and SNP markers, utilizing whole-genome sequencing and phenotypic data. Phenotypic data were collected from 72 indigenous chicken ecotypes across the three AEZs, and 32 commercial birds kept at the Kwame Nkrumah University of Science and Technology (KNUST). DNA samples used for sequencing were obtained from 88 chickens (62 indigenous chicken ecotypes and 26 commercial chickens). A total of 54,995 SilicoDArT and 85,396 SNPs markers were generated from DArTseq genotyping. After filtering, 44,784 SilicoDArT and 58,353 SNP were used for genetic diversity and population structure analysis. Both markers showed high reproducibility and call rate. Polymorphic information content (PIC) values ranged from 0.00 to 0.50, while ≥ 50 % showed PIC values more than the median. Furthermore, we obtained FST values, Nei's genetic distance, dendrogram analysis, and principal component analysis (PCA) of commercial and indigenous chickens. The FST and Nei's genetic distance showed that there is high genetic diversity between the commercial chickens and the indigenous chicken ecotypes. However, there was low genetic diversity among the indigenous chicken ecotypes. The PCA analysis indicated a clear separation between the commercial and indigenous chicken ecotypes, while no clear separation was observed between the indigenous chicken ecotypes. The phenotypic data and the dendrogram indicated that naked and frizzle genes do not markedly alter the genetics of indigenous and commercial birds, and their influence on economic traits may be solely determined by the prevailing environmental conditions. The results indicate that there is high genetic differentiation between commercial and indigenous chickens based on SilicoDArT and SNP markers. The indigenous chickens from the agro-ecological zones have low genetic diversity and might have a common origin. Naked neck and frizzle genes do not markedly alter the genetic performance of birds in terms of economic traits. Therefore, the superiority of birds carrying these genes in economic traits may be solely due to environmental variation.
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Affiliation(s)
- Selorm Sovi
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana; Nutrigenomics Laboratory, Department of Poultry Science, University of Georgia, USA
| | - Kwaku Adomako
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
| | - Bismark Kyei
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Alexander Wireko Kena
- Department of Crop and Soil Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Oscar Simon Olympio
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samuel E Aggrey
- Nutrigenomics Laboratory, Department of Poultry Science, University of Georgia, USA
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3
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Habeshian TS, Cannavale KL, Slezak JM, Shu YH, Chien GW, Chen X, Shi F, Siegmund KD, Van Den Eeden SK, Huang J, Chao CR. DNA methylation markers for risk of metastasis in a cohort of men with localized prostate cancer. Epigenetics 2024; 19:2308920. [PMID: 38525786 DOI: 10.1080/15592294.2024.2308920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/14/2024] [Indexed: 03/26/2024] Open
Abstract
Accurately identifying life-threatening prostate cancer (PCa) at time of diagnosis remains an unsolved problem. We evaluated whether DNA methylation status of selected candidate genes can predict the risk of metastasis beyond clinical risk factors in men with untreated PCa. A nested case-control study was conducted among men diagnosed with localized PCa at Kaiser Permanente California between 01/01/1997-12/31/2006 who did not receive curative treatments. Cases were those who developed metastasis within 10 years from diagnosis. Controls were selected using density sampling. Ninety-eight candidate genes were selected from functional categories of cell cycle control, metastasis/tumour suppressors, cell signalling, cell adhesion/motility/invasion, angiogenesis, and immune function, and 41 from pluripotency genes. Cancer DNA from diagnostic biopsy blocks were extracted and analysed. Associations of methylation status were assessed using CpG site level and principal components-based analysis in conditional logistic regressions. In 215 cases and 404 controls, 27 candidate genes were found to be statistically significant in at least one of the two analytical approaches. The agreement between the methods was 25.9% (7 candidate genes, including 2 pluripotency markers). The DNA methylation status of several candidate genes was significantly associated with risk of metastasis in untreated localized PCa patients. These findings may inform future risk prediction models for PCa metastasis beyond clinical characteristics.
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Affiliation(s)
- Talar S Habeshian
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kimberly L Cannavale
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Jeff M Slezak
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Yu-Hsiang Shu
- Biostatistics and Innovations, Biostatistics and Programming, Clinical Affairs, Inari Medical, CA, USA
| | - Gary W Chien
- Department of Urology, Los Angeles Medical Center, Kaiser Permanente Southern California, Los Angeles, CA, USA
| | - XuFeng Chen
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Feng Shi
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Kimberly D Siegmund
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Chun R Chao
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J Tyson School of Medicine, Pasadena, CA, USA
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4
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Howes JM, Harper MT. Application of the Cellular Thermal Shift Assay (CETSA) to validate drug target engagement in platelets. Platelets 2024; 35:2354833. [PMID: 38767506 DOI: 10.1080/09537104.2024.2354833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024]
Abstract
Small molecule drugs play a major role in the study of human platelets. Effective action of a drug requires it to bind to one or more targets within the platelet (target engagement). However, although in vitro assays with isolated proteins can be used to determine drug affinity to these targets, additional factors affect target engagement and its consequences in an intact platelet, including plasma membrane permeability, intracellular metabolism or compartmentalization, and level of target expression. Mechanistic interpretation of the effect of drugs on platelet activity requires comprehensive investigation of drug binding in the proper cellular context, i.e. in intact platelets. The Cellular Thermal Shift Assay (CETSA) is a valuable method to investigate target engagement within complex cellular environments. The assay is based on the principle that drug binding to a target protein increases that protein's thermal stability. In this technical report, we describe the application of CETSA to platelets. We highlight CETSA as a quick and informative technique for confirming the direct binding of drugs to platelet protein targets, providing a platform for understanding the mechanism of action of drugs in platelets, and which will be a valuable tool for investigating platelet signaling and function.
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Affiliation(s)
| | - Matthew T Harper
- Department of Pharmacology, University of Cambridge, Cambridge, UK
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5
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Erickson JR, Walker SE, Arenas Gomez CM, Echeverri K. Sall4 regulates downstream patterning genes during limb regeneration. Dev Biol 2024; 515:151-159. [PMID: 39067503 PMCID: PMC11325254 DOI: 10.1016/j.ydbio.2024.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Many salamanders can completely regenerate a fully functional limb. Limb regeneration is a carefully coordinated process involving several defined stages. One key event during the regeneration process is the patterning of the blastema to inform cells of what they must differentiate into. Although it is known that many genes involved in the initial development of the limb are re-used during regeneration, the exact molecular circuitry involved in this process is not fully understood. Several large-scale transcriptional profiling studies of axolotl limb regeneration have identified many transcription factors that are up-regulated after limb amputation. Sall4 is a transcription factor that has been identified to play essential roles in maintaining cells in an undifferentiated state during development and also plays a unique role in limb development. Inactivation of Sall4 during limb bud development results in defects in anterior-posterior patterning of the limb. Sall4 has been found to be up-regulated during limb regeneration in both Xenopus and salamanders, but to date it function has been untested. We confirmed that Sall4 is up-regulated during limb regeneration in the axolotl using qRT-PCR and identified that it is present in the skin cells and also in cells within the blastema. Using CRISPR technology we microinjected gRNAs specific for Sall4 complexed with cas9 protein into the blastema to specifically knockout Sall4 in blastema cells only. This resulted in limb regenerate defects, including missing digits, fusion of digit elements, and defects in the radius and ulna. This suggests that during regeneration Sall4 may play a similar role in regulating the specification of anterior-proximal skeletal elements.
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Affiliation(s)
- J R Erickson
- Department of Genetics, Dell Biology and Development, Stell Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - S E Walker
- Marine Biological Laboratory, University of Chicago, Eugene Bell Center for Regeneration Biology and Tissue Engineering, Woods Hole, MA, USA
| | - C M Arenas Gomez
- Marine Biological Laboratory, University of Chicago, Eugene Bell Center for Regeneration Biology and Tissue Engineering, Woods Hole, MA, USA
| | - K Echeverri
- Department of Genetics, Dell Biology and Development, Stell Cell Institute, University of Minnesota, Minneapolis, MN, USA; Marine Biological Laboratory, University of Chicago, Eugene Bell Center for Regeneration Biology and Tissue Engineering, Woods Hole, MA, USA.
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6
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Li F, Bahr JN, Bierth FAL, Reshetniak S, Tetzlaff C, Fornasiero EF, Wichmann C, Rizzoli SO. Morphological correlates of synaptic protein turnover in the mouse brain. Life Sci Alliance 2024; 7:e202402793. [PMID: 39134363 PMCID: PMC11325198 DOI: 10.26508/lsa.202402793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/05/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
Synaptic proteins need to be replaced regularly, to maintain function and to prevent damage. It is unclear whether this process, known as protein turnover, relates to synaptic morphology. To test this, we relied on nanoscale secondary ion mass spectrometry, to detect newly synthesized synaptic components in the brains of young adult (6 mo old) and aged mice (24 mo old), and on transmission electron microscopy, to reveal synapse morphology. Several parameters correlated to turnover, including pre- and postsynaptic size, the number of synaptic vesicles and the presence of a postsynaptic nascent zone. In aged mice, the turnover of all brain compartments was reduced by ∼20%. The turnover rates of the pre- and postsynapses correlated well in aged mice, suggesting that they are subject to common regulatory mechanisms. This correlation was poorer in young adult mice, in line with their higher synaptic dynamics. We conclude that synapse turnover is reflected by synaptic morphology.
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Affiliation(s)
- Fengxia Li
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Julius N Bahr
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- Molecular Architecture of Synapses Group, Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
- Göttingen Graduate Center for Neurosciences, Biophysics and Molecular Biosciences (GGNB), University of Göttingen, Göttingen, Germany
| | - Felicitas A-L Bierth
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- Molecular Architecture of Synapses Group, Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
- Molecular Medicine Bachelor Programme, University Medical Center Göttingen, Göttingen, Germany
| | - Sofiia Reshetniak
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Christian Tetzlaff
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Carolin Wichmann
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- Molecular Architecture of Synapses Group, Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
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7
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Espinosa-Bustos C, Bertrand J, Villegas-Menares A, Guerrero S, Di Marcotullio L, Navacci S, Schulte G, Kozielewicz P, Bloch N, Villela V, Paulino M, Kogan MJ, Cantero J, Salas CO. New Smoothened ligands based on the purine scaffold as potential agents for treating pancreatic cancer. Bioorg Chem 2024; 151:107681. [PMID: 39106711 DOI: 10.1016/j.bioorg.2024.107681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/27/2024] [Accepted: 07/27/2024] [Indexed: 08/09/2024]
Abstract
Aberrant activation of the Hedgehog (Hh) signalling pathway has been associated with the development and progression of pancreatic cancer. For this reason, blockade of Hh pathway by inhibitors targeting the G protein-coupled receptor Smoothened (SMO) has been considered as a therapeutic target for the treatment of this cancer. In our previous work, we obtained a new SMO ligand based on a purine scaffold (compound I), which showed interesting antitumor activity in several cancer cell lines. In this work, we report the design and synthesis of 17 new purine derivatives, some of which showed high cytotoxic effect on Mia-PaCa-2 (Hh-dependent pancreatic cancer cell lines) and low toxicity on non-neoplastic HEK-293 cells compared with gemcitabine, such as 8f, 8g and 8h (IC50 = 4.56, 4.11 and 3.08 μM, respectively). Two of these purines also showed their ability to bind to SMO through NanoBRET assays (pKi = 5.17 for 8f and 5.01 for 8h), with higher affinities to compound I (pKi = 1.51). In addition, docking studies provided insight the purine substitution pattern is related to the affinity on SMO. Finally, studies of Hh inhibition for selected purines, using a transcriptional functional assay based on luciferase activity in NIH3T3 Shh-Light II cells, demonstrated that 8g reduced GLI activity with a IC50 = 6.4 μM as well as diminished the expression of Hh target genes in two specific Hh-dependent cell models, Med1 cells and Ptch1-/- mouse embryonic fibroblasts. Therefore, our results provide a platform for the design of SMO ligands that could be potential selective cytotoxic agents for the treatment of pancreatic cancer.
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Affiliation(s)
- Christian Espinosa-Bustos
- Departamento de Farmacia, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 702843 Santiago, Chile
| | - Jeanluc Bertrand
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 702843 Santiago, Chile
| | - Alondra Villegas-Menares
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 702843 Santiago, Chile
| | - Simón Guerrero
- Facultad de Medicina, Universidad de Atacama, 153601 Copiapó, Chile
| | - Lucia Di Marcotullio
- Department of Molecular Medicine, Faculty Pharmacy and Medicine, Sapienza University, 00161 Rome, Italy; Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University, 00161 Rome, Italy
| | - Shirin Navacci
- Department of Molecular Medicine, Faculty Pharmacy and Medicine, Sapienza University, 00161 Rome, Italy
| | - Gunnar Schulte
- Department of Physiology and Pharmacology, Karolinska Institute, 17165 Solna, Stockholm, Sweden
| | - Pawel Kozielewicz
- Department of Physiology and Pharmacology, Karolinska Institute, 17165 Solna, Stockholm, Sweden
| | - Nicolas Bloch
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 702843 Santiago, Chile
| | - Valentina Villela
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 702843 Santiago, Chile
| | - Margot Paulino
- Departamento DETEMA, Facultad de Química, Universidad de la República, 11800 Montevideo, Uruguay
| | - Marcelo J Kogan
- Departamento de Química Farmacológica y Toxicológica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, 8380492 Santiago, Chile; Advanced Center of Chronic Diseases (ACCDiS), Universidad de Chile, 8380492 Santiago, Chile
| | - Jorge Cantero
- Departamento DETEMA, Facultad de Química, Universidad de la República, 11800 Montevideo, Uruguay
| | - Cristian O Salas
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 702843 Santiago, Chile.
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8
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Brauer NR, Kempen AL, Hernandez D, Sintim HO. Non-kinase off-target inhibitory activities of clinically-relevant kinase inhibitors. Eur J Med Chem 2024; 275:116540. [PMID: 38852338 PMCID: PMC11243610 DOI: 10.1016/j.ejmech.2024.116540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/07/2024] [Accepted: 05/26/2024] [Indexed: 06/11/2024]
Abstract
Protein kinases are responsible for a myriad of cellular functions, such as cell cycle, apoptosis, and proliferation. Because of this, kinases make excellent targets for therapeutics. During the process to identify clinical kinase inhibitor candidates, kinase selectivity profiles of lead inhibitors are typically obtained. Such kinome selectivity screening could identify crucial kinase anti-targets that might contribute to drug toxicity and/or reveal additional kinase targets that potentially contribute to the efficacy of the compound via kinase polypharmacology. In addition to kinome panel screening, practitioners also obtain the inhibition profiles of a few non-kinase targets, such as ion-channels and select GPCR targets to identify compounds that might possess potential liabilities. Often ignored is the possibility that identified kinase inhibitors might also inhibit or bind to the other proteins (greater than 20,000) in the cell that are not kinases, which may be relevant to toxicity or even additional mode of drug action. This review highlights various inhibitors, which have been approved by the FDA or are currently undergoing clinical trials, that also inhibit other non-kinase targets. The binding poses of the drugs in the binding sites of the target kinases and off-targets are analyzed to understand if the same features of the compounds are critical for the polypharmacology.
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Affiliation(s)
- Nickolas R Brauer
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Allison L Kempen
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Delmis Hernandez
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Herman O Sintim
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA; Purdue Institute for Drug Discovery, 720 Clinic Drive, West Lafayette, IN, 47907, USA; Purdue Institute for Cancer Research, 201 S. University St., West Lafayette, IN, 47907, USA.
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9
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Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G. Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser. Proc Natl Acad Sci U S A 2024; 121:e2318527121. [PMID: 39190355 DOI: 10.1073/pnas.2318527121] [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: 11/06/2023] [Accepted: 07/23/2024] [Indexed: 08/28/2024] Open
Abstract
Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg2+, and, more importantly, a putative third (site C) Mg2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structures indicate that the third Mg2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/BH interactions induce conformational changes that could allow translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the T834P mutant reveal rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.
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Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Simon Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Jihnu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Artem Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
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10
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Ghavi Hossein-Zadeh N. An overview of recent technological developments in bovine genomics. Vet Anim Sci 2024; 25:100382. [PMID: 39166173 PMCID: PMC11334705 DOI: 10.1016/j.vas.2024.100382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024] Open
Abstract
Cattle are regarded as highly valuable animals because of their milk, beef, dung, fur, and ability to draft. The scientific community has tried a number of strategies to improve the genetic makeup of bovine germplasm. To ensure higher returns for the dairy and beef industries, researchers face their greatest challenge in improving commercially important traits. One of the biggest developments in the last few decades in the creation of instruments for cattle genetic improvement is the discovery of the genome. Breeding livestock is being revolutionized by genomic selection made possible by the availability of medium- and high-density single nucleotide polymorphism (SNP) arrays coupled with sophisticated statistical techniques. It is becoming easier to access high-dimensional genomic data in cattle. Continuously declining genotyping costs and an increase in services that use genomic data to increase return on investment have both made a significant contribution to this. The field of genomics has come a long way thanks to groundbreaking discoveries such as radiation-hybrid mapping, in situ hybridization, synteny analysis, somatic cell genetics, cytogenetic maps, molecular markers, association studies for quantitative trait loci, high-throughput SNP genotyping, whole-genome shotgun sequencing to whole-genome mapping, and genome editing. These advancements have had a significant positive impact on the field of cattle genomics. This manuscript aimed to review recent advances in genomic technologies for cattle breeding and future prospects in this field.
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Affiliation(s)
- Navid Ghavi Hossein-Zadeh
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, 41635-1314, Iran
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11
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Jiang L, Yang S, Deng L, Luo J, Zhang X, Chen S, Dong Z. ARL13B promotes cell cycle through the sonic hedgehog signaling pathway to alleviate nerve damage during cerebral ischemia/reperfusion in rats. Biochem Pharmacol 2024; 227:116446. [PMID: 39038552 DOI: 10.1016/j.bcp.2024.116446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 07/24/2024]
Abstract
Cerebral ischemia/reperfusion (CIRI) is a leading cause of death worldwide. A small GTPase known as ADP-ribosylation factor-like protein 13B (ARL13B) is essential in several illnesses. The role of ARL13B in CIRI remains unknown, though. A middle cerebral artery occlusion/reperfusion (MCAO/R) in rats as well as an oxygen-glucose deprivation/reoxygenation (OGD/R) models in PC12 cells were constructed. The neuroprotective effects of ARL13B against MCAO/R were evaluated using neurological scores, TTC staining, rotarod testing, H&E staining, and Nissl staining. To detect the expression of proteins associated with the SHH pathway and apoptosis, western blotting and immunofluorescence were employed. Apoptosis was detected using TUNEL assays and flow cytometry. There was increased expression of ARL13B in cerebral ischemia/reperfusion models. However, ARL13B knockdown aggravated CIRI nerve injury by inhibiting the sonic hedgehog (SHH) pathway. In addition, the use of SHH pathway agonist (SAG) can increased ARL13B expression, reverse the effects of ARL13B knockdown exacerbating CIRI nerve injury. ARL13B alleviated cerebral infarction and pathological injury and played a protective role against MCAO/R. Furthermore, ARL13B significantly increased the expression of SHH pathway-related proteins and the anti-apoptotic protein BCL-2, while decreased the expression of pro-apoptotic protein BAX, thus reducing apoptosis. The results from the OGD/R model in PC12 cells were consistent with those obtained in vivo. Surprisingly, we demonstrated that ARL13B regulates the cell cycle to protect against CIRI nerve injury. Our findings indicate that ARL13B protects against CIRI by reducing apoptosis through SHH-dependent pathway activation, and suggest that ARL13B plays a crucial role in CIRI pathogenesis.
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Affiliation(s)
- Lu Jiang
- Department of Pharmacology, Chongqing Medical University, Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing 400016, China
| | - Shaonan Yang
- Department of Pharmacology, Chongqing Medical University, Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing 400016, China
| | - Ling Deng
- Department of Pharmacology, Chongqing Medical University, Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing 400016, China
| | - Jingjing Luo
- Department of Pharmacology, Chongqing Medical University, Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing 400016, China
| | - Xiaoling Zhang
- Department of Pharmacology, Chongqing Medical University, Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing 400016, China
| | - Sha Chen
- Department of Pharmacology, Chongqing Medical University, Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing 400016, China
| | - Zhi Dong
- Department of Pharmacology, Chongqing Medical University, Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing 400016, China.
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12
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Reyes JS, Cortés-Ríos J, Fuentes-Lemus E, Rodriguez-Fernandez M, Davies MJ, López-Alarcón C. Competitive oxidation of key pentose phosphate pathway enzymes modulates the fate of intermediates and NAPDH production. Free Radic Biol Med 2024; 222:505-518. [PMID: 38848786 DOI: 10.1016/j.freeradbiomed.2024.05.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/22/2024] [Accepted: 05/31/2024] [Indexed: 06/09/2024]
Abstract
The oxidative phase of the pentose phosphate pathway (PPP) involving the enzymes glucose-6-phosphate dehydrogenase (G6PDH), 6-phosphogluconolactonase (6PGL), and 6-phosphogluconate dehydrogenase (6PGDH), is critical to NADPH generation within cells, with these enzymes catalyzing the conversion of glucose-6-phosphate (G6P) into ribulose-5-phosphate (Ribu5-P). We have previously studied peroxyl radical (ROO•) mediated oxidative inactivation of E. coli G6PDH, 6PGL, and 6PGDH. However, these data were obtained from experiments where each enzyme was independently exposed to ROO•, a condition not reflecting biological reality. In this work we investigated how NADPH production is modulated when these enzymes are jointly exposed to ROO•. Enzyme mixtures (1:1:1 ratio) were exposed to ROO• produced from thermolysis of 100 mM 2,2'-azobis(2-methylpropionamidine) dihydrochloride (AAPH). NADPH was quantified at 340 nm, and protein oxidation analyzed by liquid chromatography with mass spectrometric detection (LC-MS). The data obtained were rationalized using a mathematical model. The mixture of non-oxidized enzymes, G6P and NADP+ generated ∼175 μM NADPH. Computational simulations showed a constant decrease of G6P associated with NADPH formation, consistent with experimental data. When the enzyme mixture was exposed to AAPH (3 h, 37 °C), lower levels of NADPH were detected (∼100 μM) which also fitted with computational simulations. LC-MS analyses indicated modifications at Tyr, Trp, and Met residues but at lower concentrations than detected for the isolated enzymes. Quantification of NADPH generation showed that the pathway activity was not altered during the initial stages of the oxidations, consistent with a buffering role of G6PDH towards inactivation of the oxidative phase of the pathway.
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Affiliation(s)
- Juan Sebastián Reyes
- Departamento de Química Física, Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Chile
| | - Javiera Cortés-Ríos
- Instituto de Ingeniería Biológica y Médica, Facultades de Ingeniería, Medicina y Ciencias Biológicas, Pontificia Universidad Católica de Chile, Chile
| | - Eduardo Fuentes-Lemus
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark
| | - Maria Rodriguez-Fernandez
- Instituto de Ingeniería Biológica y Médica, Facultades de Ingeniería, Medicina y Ciencias Biológicas, Pontificia Universidad Católica de Chile, Chile
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark.
| | - Camilo López-Alarcón
- Departamento de Química Física, Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Chile.
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13
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Pallarés S, Ortego J, Carbonell JA, Franco-Fuentes E, Bilton DT, Millán A, Abellán P. Genomic, morphological and physiological data support fast ecotypic differentiation and incipient speciation in an alpine diving beetle. Mol Ecol 2024; 33:e17487. [PMID: 39108249 DOI: 10.1111/mec.17487] [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: 03/08/2024] [Revised: 05/31/2024] [Accepted: 07/22/2024] [Indexed: 08/28/2024]
Abstract
An intricate interplay between evolutionary and demographic processes has frequently resulted in complex patterns of genetic and phenotypic diversity in alpine lineages, posing serious challenges to species delimitation and biodiversity conservation planning. Here we integrate genomic data, geometric morphometric analyses and thermal tolerance experiments to explore the role of Pleistocene climatic changes and adaptation to alpine environments on patterns of genomic and phenotypic variation in diving beetles from the taxonomically complex Agabus bipustulatus species group. Genetic structure and phylogenomic analyses revealed the presence of three geographically cohesive lineages, two representing trans-Palearctic and Iberian populations of the elevation-generalist A. bipustulatus and another corresponding to the strictly-alpine A. nevadensis, a narrow-range endemic taxon from the Sierra Nevada mountain range in southeastern Iberia. The best-supported model of lineage divergence, along with the existence of pervasive genetic introgression and admixture in secondary contact zones, is consistent with a scenario of population isolation and connectivity linked to Quaternary climatic oscillations. Our results suggest that A. nevadensis is an alpine ecotype of A. bipustulatus, whose genotypic, morphological and physiological differentiation likely resulted from an interplay between population isolation and local altitudinal adaptation. Remarkably, within the Iberian Peninsula, such ecotypic differentiation is unique to Sierra Nevada populations and has not been replicated in other alpine populations of A. bipustulatus. Collectively, our study supports fast ecotypic differentiation and incipient speciation processes within the study complex and points to Pleistocene glaciations and local adaptation along elevational gradients as key drivers of biodiversity generation in alpine environments.
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Affiliation(s)
- Susana Pallarés
- Department of Zoology, University of Seville, Seville, Spain
| | - Joaquín Ortego
- Department of Ecology and Evolution, Estación Biológica de Doñana, EBD-CSIC, Seville, Spain
| | | | | | - David T Bilton
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
- Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Andrés Millán
- Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
| | - Pedro Abellán
- Department of Zoology, University of Seville, Seville, Spain
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14
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Mackay TFC, Anholt RRH. Pleiotropy, epistasis and the genetic architecture of quantitative traits. Nat Rev Genet 2024; 25:639-657. [PMID: 38565962 PMCID: PMC11330371 DOI: 10.1038/s41576-024-00711-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/04/2024]
Abstract
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms affect the same trait) are fundamental aspects of the genetic architecture of quantitative traits. Recent advances in the ability to characterize the effects of polymorphic variants on molecular and organismal phenotypes in human and model organism populations have revealed the prevalence of pleiotropy and unexpected shared molecular genetic bases among quantitative traits, including diseases. By contrast, epistasis is common between polymorphic loci associated with quantitative traits in model organisms, such that alleles at one locus have different effects in different genetic backgrounds, but is rarely observed for human quantitative traits and common diseases. Here, we review the concepts and recent inferences about pleiotropy and epistasis, and discuss factors that contribute to similarities and differences between the genetic architecture of quantitative traits in model organisms and humans.
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Affiliation(s)
- Trudy F C Mackay
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| | - Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
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15
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Zhao Y, Wang G, Wei Z, Li D, Morshedi M. RETRACTED ARTICLE: Wnt, notch signaling and exercise: what are their functions? Hum Cell 2024; 37:1612. [PMID: 38386243 DOI: 10.1007/s13577-024-01036-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Affiliation(s)
- Yijie Zhao
- Ministry of Public Sports, Hebei North University, Zhangjiakou, 075000, Hebei, China
| | - Guangjun Wang
- Ministry of Public Sports, Hebei North University, Zhangjiakou, 075000, Hebei, China.
| | - Zhifeng Wei
- The First Affiliated Hospital of Hebei North University, Zhangjiakou, 075000, Hebei, China
| | - Duo Li
- The First Affiliated Hospital of Hebei North University, Zhangjiakou, 075000, Hebei, China
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16
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Frankish BP, Murphy RM. Does AMPK bind glycogen in skeletal muscle or is the relationship correlative? Essays Biochem 2024:EBC20240006. [PMID: 39192605 DOI: 10.1042/ebc20240006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 07/25/2024] [Accepted: 08/15/2024] [Indexed: 08/29/2024]
Abstract
Since its discovery over five decades ago, an emphasis on better understanding the structure and functional role of AMPK has been prevalent. In that time, the role of AMPK as a heterotrimeric enzyme that senses the energy state of various cell types has been established. Skeletal muscle is a dynamic, plastic tissue that adapts to both functional and metabolic demands of the human body, such as muscle contraction or exercise. With a deliberate focus on AMPK in skeletal muscle, this review places a physiological lens to the association of AMPK and glycogen that has been established biochemically. It discusses that, to date, no in vivo association of AMPK with glycogen has been shown and this is not altered with interventions, either by physiological or biochemical utilisation of glycogen in skeletal muscle. The reason for this is likely due to the persistent phosphorylation of Thr148 in the β-subunit of AMPK which prevents AMPK from binding to carbohydrate domains. This review presents the correlative data that suggests AMPK senses glycogen utilisation through a direct interaction with glycogen, the biochemical data showing that AMPK can bind carbohydrate in vitro, and highlights that in a physiological setting of rodent skeletal muscle, AMPK does not directly bind to glycogen.
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Affiliation(s)
- Barnaby P Frankish
- Sport, Exercise and Nutrition Sciences, School of Allied Health, Human Services and Sport, La Trobe University, Melbourne, VIC 3086, Australia
| | - Robyn M Murphy
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia Insert Affiliation Text Here
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17
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Tabuloc CA, Carlson CR, Ganjisaffar F, Truong CC, Chen CH, Lewald KM, Hidalgo S, Nicola NL, Jones CE, Sial AA, Zalom FG, Chiu JC. Transcriptome analysis of Drosophila suzukii reveals molecular mechanisms conferring pyrethroid and spinosad resistance. Sci Rep 2024; 14:19867. [PMID: 39191909 DOI: 10.1038/s41598-024-70037-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 08/09/2024] [Indexed: 08/29/2024] Open
Abstract
Drosophila suzukii lay eggs in soft-skinned, ripening fruits, making this insect a serious threat to berry production. Since its 2008 introduction into North America, growers have used insecticides, such as pyrethroids and spinosads, as the primary approach for D. suzukii management, resulting in development of insecticide resistance in this pest. This study sought to identify the molecular mechanisms conferring insecticide resistance in these populations. We sequenced the transcriptomes of two pyrethroid- and two spinosad-resistant isofemale lines. In both pyrethroid-resistant lines and one spinosad-resistant line, we identified overexpression of metabolic genes that are implicated in resistance in other insect pests. In the other spinosad-resistant line, we observed an overexpression of cuticular genes that have been linked to resistance. Our findings enabled the development of molecular diagnostics that we used to confirm persistence of insecticide resistance in California, U.S.A. To validate these findings, we leveraged D. melanogaster mutants with reduced expression of metabolic or cuticular genes that were found to be upregulated in resistant D. suzukii to demonstrate that these genes are involved in promoting resistance. This study is the first to characterize the molecular mechanisms of insecticide resistance in D. suzukii and provides insights into how current management practices can be optimized.
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Affiliation(s)
- Christine A Tabuloc
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, California, USA
| | - Curtis R Carlson
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, California, USA
| | - Fatemeh Ganjisaffar
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, California, USA
| | - Cindy C Truong
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, California, USA
| | - Ching-Hsuan Chen
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, California, USA
| | - Kyle M Lewald
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, California, USA
| | - Sergio Hidalgo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, California, USA
| | - Nicole L Nicola
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, California, USA
| | - Cera E Jones
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Ashfaq A Sial
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Frank G Zalom
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, California, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, California, USA.
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18
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Lavoie Smith EM, Von Ah D. Neurotoxicity in Cancer Survivorship: The Significance of Cancer-Related Cognitive Impairment and Chemotherapy-Induced Peripheral Neuropathy. Semin Oncol Nurs 2024:151724. [PMID: 39183088 DOI: 10.1016/j.soncn.2024.151724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 07/27/2024] [Accepted: 07/31/2024] [Indexed: 08/27/2024]
Affiliation(s)
- Ellen M Lavoie Smith
- Professor and Marie O'Koren Endowed Chair, Assistant Dean of Research and Scholarship, University of Alabama at Birmingham School of Nursing, Department of Acute, Chronic & Continuing Care, Birmingham, AL
| | - Diane Von Ah
- Mildred E. Newton Endowed Professor, Distinguished Professor of Cancer Research, The Ohio State University, College of Nursing, Columbus, OH.
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19
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Fernandez-Llimos F, Desselle S, Stewart D, Garcia-Cardenas V, Babar ZUD, Bond C, Dago A, Jacobsen R, Nørgaard LS, Polidori C, Sanchez-Polo M, Santos-Ramos B, Shcherbakova NG, Tonin FS. Improving the quality of publications in and advancing the paradigms of clinical and social pharmacy practice research: the Granada Statements. Eur J Hosp Pharm 2024; 31:483-488. [PMID: 36914239 PMCID: PMC11347197 DOI: 10.1136/ejhpharm-2023-003748] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 03/16/2023] Open
Abstract
Pharmacy and pharmaceutical sciences embrace a series of different disciplines. Pharmacy practice has been defined as 'the scientific discipline that studies the different aspects of the practice of pharmacy and its impact on healthcare systems, medicine use, and patient care'. Thus, pharmacy practice studies embrace both clinical pharmacy and social pharmacy elements. Like any other scientific discipline, clinical and social pharmacy practice disseminates research findings using scientific journals. Clinical pharmacy and social pharmacy journal editors have a role in promoting the discipline by enhancing the quality of the articles published. As has occurred in other healthcare areas (ie, medicine and nursing), a group of clinical and social pharmacy practice journal editors gathered in Granada, Spain to discuss how journals could contribute to strengthening pharmacy practice as a discipline. The result of that meeting was compiled in these Granada Statements, which comprise 18 recommendations gathered into six topics: the appropriate use of terminology, impactful abstracts, the required peer reviews, journal scattering, more effective and wiser use of journal and article performance metrics, and authors' selection of the most appropriate pharmacy practice journal to submit their work.
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Affiliation(s)
| | - Shane Desselle
- Research in Social and Administrative Pharmacy, Exploratory Research in Clinical and Social Pharmacy, Touro University California, Vallejo, California, USA
| | - Derek Stewart
- International Journal of Clinical Pharmacy, Qatar University College of Pharmacy, Doha, Qatar
| | - Victoria Garcia-Cardenas
- Research in Social and Administrative Pharmacy, University of Technology Sydney, Broadway, New South Wales, Australia
| | - Zaheer-Ud-Din Babar
- Journal of Pharmaceutical Policy and Practice, University of Huddersfield, Huddersfield, UK
| | - Christine Bond
- International Journal of Pharmacy Practice, University of Aberdeen, Aberdeen, UK
| | - Ana Dago
- Pharmaceutical Care España, Pharmaceutical Care España Foundation, Barcelona, Spain
| | - Ramune Jacobsen
- Exploratory Research in Clinical and Social Pharmacy, University of Copenhagen, Kobenhavn, Denmark
| | - Lotte Stig Nørgaard
- Research in Social and Administrative Pharmacy, University of Copenhagen, Kobenhavn, Denmark
| | - Carlo Polidori
- Experimental medicine and Public health, University of Camerino, Camerino, Italy
| | | | | | - Natalia G Shcherbakova
- Research in Social and Administrative Pharmacy, Western New England University, Springfield, Massachusetts, USA
| | - Fernanda S Tonin
- Pharmacy Practice, Instituto Politécnico de Lisboa, Lisboa, Portugal
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20
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Lamson DR, Tarpley M, Addo K, Ji X, Abu Rabe D, Ehe B, Hughes M, Smith GR, Daye LR, Musso DL, Zheng W, Williams KP. Identification of small molecule antagonists of sonic hedgehog/heparin binding with activity in hedgehog functional assays. Biochim Biophys Acta Gen Subj 2024; 1868:130692. [PMID: 39151833 DOI: 10.1016/j.bbagen.2024.130692] [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: 03/10/2024] [Revised: 07/30/2024] [Accepted: 08/07/2024] [Indexed: 08/19/2024]
Abstract
Sonic hedgehog (Shh) is a morphogen with important roles in embryonic development and in the development of a number of cancers. Its activity is modulated by interactions with binding partners and co-receptors including heparin and heparin sulfate proteoglycans (HSPG). To identify antagonists of Shh/heparin binding, a diverse collection of 34,560 chemicals was screened in single point 384-well format. We identified and confirmed twenty six novel small molecule antagonists with diverse structures including four scaffolds that gave rise to multiple hits. Nineteen of the confirmed hits blocked binding of the N-terminal fragment of Shh (ShhN) to heparin with IC50 values < 50 μM. In the Shh-responsive C3H10T1/2 cell model, four of the compounds demonstrated the ability to block ShhN-induced alkaline phosphatase activity. To demonstrate a direct and selective effect on ShhN ligand mediated activity, two of the compounds were able to block induction of Gli1 mRNA, a primary downstream marker for Shh signaling activity, in Shh-mediated but not Smoothened agonist (SAG)-mediated C3H10T1/2 cells. Direct binding of the two compounds to ShhN was confirmed by thermal shift assay and molecular docking simulations, with both compounds docking with the N-terminal heparin binding domain of Shh. Overall, our findings indicate that small molecule compounds that block ShhN binding to heparin and act to inhibit Shh mediated activity in vitro can be identified. We propose that the interaction between Shh and HSPGs provides a novel target for identifying small molecules that bind Shh, potentially leading to novel tool compounds to probe Shh ligand function.
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Affiliation(s)
- David R Lamson
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Michael Tarpley
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Kezia Addo
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Xiaojia Ji
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Dina Abu Rabe
- Biomanufacturing Research Institute and Technology Enterprise, USA; INBS PhD Program, USA
| | - Ben Ehe
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Mark Hughes
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Ginger R Smith
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Laura R Daye
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - David L Musso
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Weifan Zheng
- Biomanufacturing Research Institute and Technology Enterprise, USA; Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC 27707, USA
| | - Kevin P Williams
- Biomanufacturing Research Institute and Technology Enterprise, USA; Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC 27707, USA.
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21
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Margaritelis NV, Cobley JN, Nastos GG, Papanikolaou K, Bailey SJ, Kritsiligkou P, Nikolaidis MG. Evidence-based sports supplements: A redox analysis. Free Radic Biol Med 2024; 224:62-77. [PMID: 39147071 DOI: 10.1016/j.freeradbiomed.2024.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/30/2024] [Accepted: 08/09/2024] [Indexed: 08/17/2024]
Abstract
Despite the overwhelming number of sports supplements on the market, only seven are currently recognized as effective. Biological functions are largely regulated through redox reactions, yet no comprehensive analysis of the redox properties of these supplements has been compiled. Here, we analyze the redox characteristics of these seven supplements: bicarbonates, beta-alanine, caffeine, creatine, nitrates, carbohydrates, and proteins. Our findings suggest that all sports supplements exhibit some degree of redox activity. However, the precise physiological implications of these redox properties remain unclear. Future research, employing unconventional perspectives and methodologies, will reveal new redox pixels of the exercise physiology and sports nutrition picture.
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Affiliation(s)
- Nikos V Margaritelis
- Department of Physical Education and Sports Science at Serres, Aristotle University of Thessaloniki, Serres, Greece.
| | - James N Cobley
- School of Life Sciences, The University of Dundee, Dundee, Scotland, UK
| | - George G Nastos
- Department of Physical Education and Sports Science at Serres, Aristotle University of Thessaloniki, Serres, Greece
| | | | - Stephen J Bailey
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Paraskevi Kritsiligkou
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Michalis G Nikolaidis
- Department of Physical Education and Sports Science at Serres, Aristotle University of Thessaloniki, Serres, Greece
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22
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Ruman T, Krupa Z, Nizioł J. Direct Three-Dimensional Mass Spectrometry Imaging with Laser Ablation Remote Atmospheric Pressure Photoionization/Chemical Ionization. Anal Chem 2024; 96:13326-13334. [PMID: 39077860 PMCID: PMC11325297 DOI: 10.1021/acs.analchem.4c03402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
The laser ablation remote atmospheric pressure photoionization/chemical ionization (LARAPPI/CI) platform coupled to an ultrahigh resolution quadrupole-time-of-flight (QToF) mass spectrometer was developed and employed for the first direct three-dimensional (3D) mass spectrometry imaging (MSI) of metabolites in human and plant tissues. Our solution for 3D MSI does not require sample modification or cutting into thin slices. Ablation characteristics of an optical system based on a diffraction optical element are studied and used for voxel stacking to directly remove layers of tissues. Agar gel, red radish, kiwi, human kidney cancer, and normal tissue samples were used for the tests of this new system. The 2D and 3D ion images vividly illustrate differences in the abundances of selected metabolites between cancerous and noncancerous regions of the kidney tissue and also between different parts of plant tissues. The LARAPPI/CI MSI setup is also the first example of the successful use of combined dopant-assisted atmospheric pressure photoionization (DA-APPI) and atmospheric pressure chemical ionization (APCI) ion source for mass spectrometry imaging.
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Affiliation(s)
- Tomasz Ruman
- Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, Rzeszów University of Technology, 6 Powstan ́ców Warszawy Ave., Rzeszów 35-959. Poland
| | - Zuzanna Krupa
- Doctoral School of Engineering and Technical Sciences at the Rzeszów University of Technology, 8 Powstan ́ców Warszawy Ave., Rzeszów 35-959, Poland
| | - Joanna Nizioł
- Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, Rzeszów University of Technology, 6 Powstan ́ców Warszawy Ave., Rzeszów 35-959. Poland
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23
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Lister NC, Milton AM, Patel HR, Waters SA, Hanrahan BJ, McIntyre KL, Livernois AM, Horspool WB, Wee LK, Ringel AR, Mundlos S, Robson MI, Shearwin-Whyatt L, Grützner F, Graves JAM, Ruiz-Herrera A, Waters PD. Incomplete transcriptional dosage compensation of chicken and platypus sex chromosomes is balanced by post-transcriptional compensation. Proc Natl Acad Sci U S A 2024; 121:e2322360121. [PMID: 39074288 PMCID: PMC11317591 DOI: 10.1073/pnas.2322360121] [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: 12/19/2023] [Accepted: 06/25/2024] [Indexed: 07/31/2024] Open
Abstract
Heteromorphic sex chromosomes (XY or ZW) present problems of gene dosage imbalance between sexes and with autosomes. A need for dosage compensation has long been thought to be critical in vertebrates. However, this was questioned by findings of unequal mRNA abundance measurements in monotreme mammals and birds. Here, we demonstrate unbalanced mRNA levels of X genes in platypus males and females and a correlation with differential loading of histone modifications. We also observed unbalanced transcripts of Z genes in chicken. Surprisingly, however, we found that protein abundance ratios were 1:1 between the sexes in both species, indicating a post-transcriptional layer of dosage compensation. We conclude that sex chromosome output is maintained in chicken and platypus (and perhaps many other non therian vertebrates) via a combination of transcriptional and post-transcriptional control, consistent with a critical importance of sex chromosome dosage compensation.
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Affiliation(s)
- Nicholas C. Lister
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales Sydney, Sydney, NSW2052, Australia
| | - Ashley M. Milton
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales Sydney, Sydney, NSW2052, Australia
| | - Hardip R. Patel
- John Curtin School of Medical Research, Australian National University, Canberra, ACT2600, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT2600, Australia
| | - Shafagh A. Waters
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW2052, Australia
| | - Benjamin J. Hanrahan
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales Sydney, Sydney, NSW2052, Australia
| | - Kim L. McIntyre
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales Sydney, Sydney, NSW2052, Australia
| | | | - William B. Horspool
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales Sydney, Sydney, NSW2052, Australia
| | - Lee Kian Wee
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales Sydney, Sydney, NSW2052, Australia
| | - Alessa R. Ringel
- Max Planck Institute for Molecular Genetics, Berlin14195, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin10117, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin14195, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin14195, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin10117, Germany
- Charité-Universitätsmedizin Berlin, Berlin Institute of Health Center for Regenerative Therapies, Berlin13353, Germany
| | - Michael I. Robson
- Max Planck Institute for Molecular Genetics, Berlin14195, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin10117, Germany
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EdinburghEH8 9YL, United Kingdom
| | | | - Frank Grützner
- School of Biological Sciences, University of Adelaide, Adelaide, SA5000, Australia
| | - Jennifer A. Marshall Graves
- Department of Environment and Genetics, La Trobe University, Melbourne, VIC3068, Australia
- Institute of Applied Ecology, University of Canberra, Canberra, ACT2601, Australia
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cellular, Fisiologia I Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès08193, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès08193, Spain
| | - Paul D. Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales Sydney, Sydney, NSW2052, Australia
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24
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Trivellin C, Torello Pianale L, Olsson L. Robustness quantification of a mutant library screen revealed key genetic markers in yeast. Microb Cell Fact 2024; 23:218. [PMID: 39098937 PMCID: PMC11298085 DOI: 10.1186/s12934-024-02490-2] [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: 12/22/2023] [Accepted: 07/24/2024] [Indexed: 08/06/2024] Open
Abstract
BACKGROUND Microbial robustness is crucial for developing cell factories that maintain consistent performance in a challenging environment such as large-scale bioreactors. Although tools exist to assess and understand robustness at a phenotypic level, the underlying metabolic and genetic mechanisms are not well defined, which limits our ability to engineer more strains with robust functions. RESULTS This study encompassed four steps. (I) Fitness and robustness were analyzed from a published dataset of yeast mutants grown in multiple environments. (II) Genes and metabolic processes affecting robustness or fitness were identified, and 14 of these genes were deleted in Saccharomyces cerevisiae CEN.PK113-7D. (III) The mutants bearing gene deletions were cultivated in three perturbation spaces mimicking typical industrial processes. (IV) Fitness and robustness were determined for each mutant in each perturbation space. We report that robustness varied according to the perturbation space. We identified genes associated with increased robustness such as MET28, linked to sulfur metabolism; as well as genes associated with decreased robustness, including TIR3 and WWM1, both involved in stress response and apoptosis. CONCLUSION The present study demonstrates how phenomics datasets can be analyzed to reveal the relationship between phenotypic response and associated genes. Specifically, robustness analysis makes it possible to study the influence of single genes and metabolic processes on stable microbial performance in different perturbation spaces. Ultimately, this information can be used to enhance robustness in targeted strains.
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Affiliation(s)
- Cecilia Trivellin
- Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Luca Torello Pianale
- Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Lisbeth Olsson
- Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
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25
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Al-Nuaimi DA, Rütsche D, Abukar A, Hiebert P, Zanetti D, Cesarovic N, Falk V, Werner S, Mazza E, Giampietro C. Hydrostatic pressure drives sprouting angiogenesis via adherens junction remodelling and YAP signalling. Commun Biol 2024; 7:940. [PMID: 39097636 PMCID: PMC11297954 DOI: 10.1038/s42003-024-06604-9] [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: 11/08/2023] [Accepted: 07/17/2024] [Indexed: 08/05/2024] Open
Abstract
Endothelial cell physiology is governed by its unique microenvironment at the interface between blood and tissue. A major contributor to the endothelial biophysical environment is blood hydrostatic pressure, which in mechanical terms applies isotropic compressive stress on the cells. While other mechanical factors, such as shear stress and circumferential stretch, have been extensively studied, little is known about the role of hydrostatic pressure in the regulation of endothelial cell behavior. Here we show that hydrostatic pressure triggers partial and transient endothelial-to-mesenchymal transition in endothelial monolayers of different vascular beds. Values mimicking microvascular pressure environments promote proliferative and migratory behavior and impair barrier properties that are characteristic of a mesenchymal transition, resulting in increased sprouting angiogenesis in 3D organotypic model systems ex vivo and in vitro. Mechanistically, this response is linked to differential cadherin expression at the adherens junctions, and to an increased YAP expression, nuclear localization, and transcriptional activity. Inhibition of YAP transcriptional activity prevents pressure-induced sprouting angiogenesis. Together, this work establishes hydrostatic pressure as a key modulator of endothelial homeostasis and as a crucial component of the endothelial mechanical niche.
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Affiliation(s)
| | - Dominic Rütsche
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Experimental Continuum Mechanics, Dübendorf, 8600, Switzerland
| | - Asra Abukar
- ETH Zürich, DMAVT, Experimental Continuum Mechanics, Zürich, 8092, Switzerland
| | - Paul Hiebert
- Department of Biology, ETH Zürich, Institute of Molecular Health Sciences, 8093, Zürich, Switzerland
- Centre for Biomedicine, Hull York Medical School, The University of Hull, Hull, HU6 7RX, UK
| | - Dominik Zanetti
- Department of Biology, ETH Zürich, Institute of Molecular Health Sciences, 8093, Zürich, Switzerland
| | - Nikola Cesarovic
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353, Berlin, Germany
- Department of Health Sciences and Technology, ETH Zürich, 8093, Zürich, Switzerland
| | - Volkmar Falk
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353, Berlin, Germany
- Department of Health Sciences and Technology, ETH Zürich, 8093, Zürich, Switzerland
| | - Sabine Werner
- Department of Biology, ETH Zürich, Institute of Molecular Health Sciences, 8093, Zürich, Switzerland
| | - Edoardo Mazza
- ETH Zürich, DMAVT, Experimental Continuum Mechanics, Zürich, 8092, Switzerland.
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Experimental Continuum Mechanics, Dübendorf, 8600, Switzerland.
| | - Costanza Giampietro
- ETH Zürich, DMAVT, Experimental Continuum Mechanics, Zürich, 8092, Switzerland.
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Experimental Continuum Mechanics, Dübendorf, 8600, Switzerland.
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26
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Barjesteh F, Heidari-Kalvani N, Alipourfard I, Najafi M, Bahreini E. Testosterone, β-estradiol, and hepatocellular carcinoma: stimulation or inhibition? A comparative effect analysis on cell cycle, apoptosis, and Wnt signaling of HepG2 cells. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:6121-6133. [PMID: 38421409 DOI: 10.1007/s00210-024-03019-5] [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: 11/09/2023] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
Unlike breast and prostate cancers, which are specifically affected by estrogens or androgens, hepatocellular carcinoma has been reported to be influenced by both sex hormones. Given the coincidental differences of hepatocellular carcinoma in men and women, we investigated the effects of β-estradiol and testosterone on the cell cycle, apoptosis, and Wnt signaling in a model of hepatocellular carcinoma to understand the sex hormone-related etiology. To determine the effective concentration of both hormones, an MTT assay was performed. The effects of β-estradiol and testosterone on cell proliferation and death were evaluated by specific staining and flow cytometry. In addition, gene expression levels of estimated factors involved in GPC3-Wnt survival signaling were analyzed using quantitative real-time polymerase chain reaction. Both hormones inhibited hepatic cell proliferation through arresting the cell cycle at S/G2 and increased the apoptosis rate in HepG2 cells. Both hormones dose-dependently decreased GPC3, Wnt, and DVL expression levels as activators of the Wnt-signaling pathway. In the case of Wnt-signaling inhibitors, the effects of both hormones on WIF were negligible, but they increased DKK1 levels in a dose-dependent manner. In each of the effects mentioned above, β-estradiol was notably more potent than testosterone. In contrast to the primary hypothesis of the project, in which testosterone was considered a stimulating carcinogenic factor in HCC pathogenesis, testosterone inhibited the occurrence of HCC similarly to β-estradiol. However, this inhibitory effect was weaker than that of β-estradiol and requires further study.
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Affiliation(s)
- Fereshteh Barjesteh
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, 1449614525, Iran
| | - Nafiseh Heidari-Kalvani
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, 1449614525, Iran
| | - Iraj Alipourfard
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Mohammad Najafi
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, 1449614525, Iran
| | - Elham Bahreini
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, 1449614525, Iran.
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27
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Cecalev D, Viçoso B, Galupa R. Compensation of gene dosage on the mammalian X. Development 2024; 151:dev202891. [PMID: 39140247 DOI: 10.1242/dev.202891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show 'natural' differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species.
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Affiliation(s)
- Daniela Cecalev
- Molecular, Cellular and Developmental Biology (MCD) Unit, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Beatriz Viçoso
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg 3400, Austria
| | - Rafael Galupa
- Molecular, Cellular and Developmental Biology (MCD) Unit, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
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28
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Kültz D, Gardell AM, DeTomaso A, Stoney G, Rinkevich B, Rinkevich Y, Qarri A, Dong W, Luu B, Lin M. Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri). Proteomics 2024; 24:e2300628. [PMID: 38400697 DOI: 10.1002/pmic.202300628] [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: 12/02/2023] [Revised: 01/30/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024]
Abstract
Botryllus schlosseri, is a model marine invertebrate for studying immunity, regeneration, and stress-induced evolution. Conditions for validating its predicted proteome were optimized using nanoElute® 2 deep-coverage LCMS, revealing up to 4930 protein groups and 20,984 unique peptides per sample. Spectral libraries were generated and filtered to remove interferences, low-quality transitions, and only retain proteins with >3 unique peptides. The resulting DIA assay library enabled label-free quantitation of 3426 protein groups represented by 22,593 unique peptides. Quantitative comparisons of single systems from a laboratory-raised with two field-collected populations revealed (1) a more unique proteome in the laboratory-raised population, and (2) proteins with high/low individual variabilities in each population. DNA repair/replication, ion transport, and intracellular signaling processes were distinct in laboratory-cultured colonies. Spliceosome and Wnt signaling proteins were the least variable (highly functionally constrained) in all populations. In conclusion, we present the first colonial tunicate's deep quantitative proteome analysis, identifying functional protein clusters associated with laboratory conditions, different habitats, and strong versus relaxed abundance constraints. These results empower research on B. schlosseri with proteomics resources and enable quantitative molecular phenotyping of changes associated with transfer from in situ to ex situ and from in vivo to in vitro culture conditions.
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Affiliation(s)
- Dietmar Kültz
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
| | - Alison M Gardell
- School of Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, Washington, USA
| | - Anthony DeTomaso
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Goleta, California, USA
| | - Greg Stoney
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Goleta, California, USA
| | - Baruch Rinkevich
- Israel Oceanography & Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Yuval Rinkevich
- Helmholtz Zentrum München, Regenerative Biology and Medicine Institute, Munich, Germany
| | - Andy Qarri
- Israel Oceanography & Limnological Research, National Institute of Oceanography, Haifa, Israel
- Helmholtz Zentrum München, Regenerative Biology and Medicine Institute, Munich, Germany
| | - Weizhen Dong
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
| | - Brenda Luu
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
| | - Mandy Lin
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
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29
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Florido MHC, Ziats NP. Endothelial dysfunction and cardiovascular diseases: The role of human induced pluripotent stem cells and tissue engineering. J Biomed Mater Res A 2024; 112:1286-1304. [PMID: 38230548 DOI: 10.1002/jbm.a.37669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/07/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024]
Abstract
Cardiovascular disease (CVD) remains to be the leading cause of death globally today and therefore the need for the development of novel therapies has become increasingly important in the cardiovascular field. The mechanism(s) behind the pathophysiology of CVD have been laboriously investigated in both stem cell and bioengineering laboratories. Scientific breakthroughs have paved the way to better mimic cell types of interest in recent years, with the ability to generate any cell type from reprogrammed human pluripotent stem cells. Mimicking the native extracellular matrix using both organic and inorganic biomaterials has allowed full organs to be recapitulated in vitro. In this paper, we will review techniques from both stem cell biology and bioengineering which have been fruitfully combined and have fueled advances in the cardiovascular disease field. We will provide a brief introduction to CVD, reviewing some of the recent studies as related to the role of endothelial cells and endothelial cell dysfunction. Recent advances and the techniques widely used in both bioengineering and stem cell biology will be discussed, providing a broad overview of the collaboration between these two fields and their overall impact on tissue engineering in the cardiovascular devices and implications for treatment of cardiovascular disease.
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Affiliation(s)
- Mary H C Florido
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Nicholas P Ziats
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
- Departments of Biomedical Engineering and Anatomy, Case Western Reserve University, Cleveland, Ohio, USA
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30
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Liu A, Geraldes A, Taylor EB. Historical and contemporary processes driving the origin and structure of an admixed population within a contact zone between subspecies of a north temperate diadromous fish. Mol Ecol 2024; 33:e17459. [PMID: 38994921 DOI: 10.1111/mec.17459] [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: 11/30/2023] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 07/13/2024]
Abstract
Hybridization between divergent lineages can result in losses of distinct evolutionary taxa. Alternatively, hybridization can lead to increased genetic variability that may fuel local adaptation and the generation of novel traits and/or taxa. Here, we examined single-nucleotide polymorphisms generated using genotyping-by-sequencing in a population of Dolly Varden char (Pisces: Salmonidae) that is highly admixed within a contact zone between two subspecies (Salvelinus malma malma, Northern Dolly Varden [NDV] and S. m. lordi, Southern Dolly Varden [SDV]) in southwestern Alaska to assess the spatial distribution of hybrids and to test hypotheses on the origin of the admixed population. Ancestry analysis revealed that this admixed population is composed of advanced generation hybrids between NDV and SDV or advanced backcrosses to SDV; no F1 hybrids were detected. Coalescent-based demographic modelling supported the origin of this population about 55,000 years ago by secondary contact between NDV and SDV with low levels of contemporary gene flow. Ancestry in NDV and SDV varies within the watershed and ancestry in NDV was positively associated with distance upstream from the sea, contingent on habitat-type sampled, and negatively associated with the number of migrations that individual fish made to the sea. Our results suggest that divergence between subspecies over hundreds of thousands of years may not be associated with significant reproductive isolation, but that elevated diversity owing to hybridization may have contributed to adaptive divergence in habitat use and life history.
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Affiliation(s)
- Amy Liu
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Armando Geraldes
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric B Taylor
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Beaty Biodiversity Museum, University of British Columbia, Vancouver, British Columbia, Canada
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31
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Zhou J, Tian F, Hu J, Shi ZL, Godinez VG, Tsai DP, Liu Z. Eagle-Eye Inspired Meta-Device for Phase Imaging. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2402751. [PMID: 38816897 DOI: 10.1002/adma.202402751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/14/2024] [Indexed: 06/01/2024]
Abstract
The dual-focus vision observed in eagles' eyes is an intriguing phenomenon captivates scientists since a long time. Inspired by this natural occurrence, the authors' research introduces a novel bifocal meta-device incorporating a polarized camera capable of simultaneously capturing images for two different polarizations with slightly different focal distances. This innovative approach facilitates the concurrent acquisition of underfocused and overfocused images in a single snapshot, enabling the effective extraction of quantitative phase information from the object using the transport of intensity equation. Experimental demonstrations showcase the application of quantitative phase imaging to artificial objects and human embryonic kidney cells, particularly emphasizing the meta-device's relevance in dynamic scenarios such as laser-induced ablation in human embryonic kidney cells. Moreover, it provides a solution for the quantification during the dynamic process at the cellular level. Notably, the proposed eagle-eye inspired meta-device for phase imaging (EIMPI), due to its simplicity and compact nature, holds promise for significant applications in fields such as endoscopy and headsets, where a lightweight and compact setup is essential.
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Affiliation(s)
- Junxiao Zhou
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Fanglin Tian
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Jie Hu
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Zhixia Linda Shi
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, San Diego, CA, 92093, USA
| | - Veronica Gomez Godinez
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, San Diego, CA, 92093, USA
| | - Din Ping Tsai
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Zhaowei Liu
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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32
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Srour L, El Hajj N. The ribosome's comeback: new role in body weight regulation. Trends Genet 2024:S0168-9525(24)00172-0. [PMID: 39089934 DOI: 10.1016/j.tig.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
The recent discovery of an association between ribosomal DNA (rDNA) copy number and body mass index (BMI) by Law et al. sheds light on a possible role of 45S rDNA in body-weight regulation. This finding opens new avenues for further investigations into the effect of rDNA on various human phenotypes.
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Affiliation(s)
- Luma Srour
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Nady El Hajj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar; College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.
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33
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Rahiminejad S, De Sanctis B, Pevzner P, Mushegian A. Synthetic lethality and the minimal genome size problem. mSphere 2024; 9:e0013924. [PMID: 38904396 PMCID: PMC11288024 DOI: 10.1128/msphere.00139-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Gene knockout studies suggest that ~300 genes in a bacterial genome and ~1,100 genes in a yeast genome cannot be deleted without loss of viability. These single-gene knockout experiments do not account for negative genetic interactions, when two or more genes can each be deleted without effect, but their joint deletion is lethal. Thus, large-scale single-gene deletion studies underestimate the size of a minimal gene set compatible with cell survival. In yeast Saccharomyces cerevisiae, the viability of all possible deletions of gene pairs (2-tuples), and of some deletions of gene triplets (3-tuples), has been experimentally tested. To estimate the size of a yeast minimal genome from that data, we first established that finding the size of a minimal gene set is equivalent to finding the minimum vertex cover in the lethality (hyper)graph, where the vertices are genes and (hyper)edges connect k-tuples of genes whose joint deletion is lethal. Using the Lovász-Johnson-Chvatal greedy approximation algorithm, we computed the minimum vertex cover of the synthetic-lethal 2-tuples graph to be 1,723 genes. We next simulated the genetic interactions in 3-tuples, extrapolating from the existing triplet sample, and again estimated minimum vertex covers. The size of a minimal gene set in yeast rapidly approaches the size of the entire genome even when considering only synthetic lethalities in k-tuples with small k. In contrast, several studies reported successful experimental reductions of yeast and bacterial genomes by simultaneous deletions of hundreds of genes, without eliciting synthetic lethality. We discuss possible reasons for this apparent contradiction.IMPORTANCEHow can we estimate the smallest number of genes sufficient for a unicellular organism to survive on a rich medium? One approach is to remove genes one at a time and count how many of such deletion strains are unable to grow. However, the single-gene knockout data are insufficient, because joint gene deletions may result in negative genetic interactions, also known as synthetic lethality. We used a technique from graph theory to estimate the size of minimal yeast genome from partial data on synthetic lethality. The number of potential synthetic lethal interactions grows very fast when multiple genes are deleted, revealing a paradoxical contrast with the experimental reductions of yeast genome by ~100 genes, and of bacterial genomes by several hundreds of genes.
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Affiliation(s)
- Sara Rahiminejad
- Department of Bioengineering, University of California—San Diego, La Jolla, California, USA
| | - Bianca De Sanctis
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Department of Ecology and Evolutionary Biology, University of California—Santa Cruz, Santa Cruz, California, USA
| | - Pavel Pevzner
- Department of Computer Science and Engineering, University of California—San Diego, La Jolla, California, USA
| | - Arcady Mushegian
- Molecular and Cellular Biosciences Division, National Science Foundation, Alexandria, Virginia, USA
- Clare Hall College, Cambridge, United Kingdom
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Melnik BC, Weiskirchen R, Stremmel W, John SM, Schmitz G. Risk of Fat Mass- and Obesity-Associated Gene-Dependent Obesogenic Programming by Formula Feeding Compared to Breastfeeding. Nutrients 2024; 16:2451. [PMID: 39125332 PMCID: PMC11314333 DOI: 10.3390/nu16152451] [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: 06/18/2024] [Revised: 07/21/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
It is the purpose of this review to compare differences in postnatal epigenetic programming at the level of DNA and RNA methylation and later obesity risk between infants receiving artificial formula feeding (FF) in contrast to natural breastfeeding (BF). FF bears the risk of aberrant epigenetic programming at the level of DNA methylation and enhances the expression of the RNA demethylase fat mass- and obesity-associated gene (FTO), pointing to further deviations in the RNA methylome. Based on a literature search through Web of Science, Google Scholar, and PubMed databases concerning the dietary and epigenetic factors influencing FTO gene and FTO protein expression and FTO activity, FTO's impact on postnatal adipogenic programming was investigated. Accumulated translational evidence underscores that total protein intake as well as tryptophan, kynurenine, branched-chain amino acids, milk exosomal miRNAs, NADP, and NADPH are crucial regulators modifying FTO gene expression and FTO activity. Increased FTO-mTORC1-S6K1 signaling may epigenetically suppress the WNT/β-catenin pathway, enhancing adipocyte precursor cell proliferation and adipogenesis. Formula-induced FTO-dependent alterations of the N6-methyladenosine (m6A) RNA methylome may represent novel unfavorable molecular events in the postnatal development of adipogenesis and obesity, necessitating further investigations. BF provides physiological epigenetic DNA and RNA regulation, a compelling reason to rely on BF.
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Affiliation(s)
- Bodo C. Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany;
| | - Wolfgang Stremmel
- Praxis for Internal Medicine, Beethovenstrasse 2, D-76530 Baden-Baden, Germany;
| | - Swen Malte John
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany
- Institute for Interdisciplinary Dermatological Prevention and Rehabilitation (iDerm), University of Osnabrück, D-49076 Osnabrück, Germany;
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital of Regensburg, D-93053 Regensburg, Germany;
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35
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Wu Y, Zhou D, Hu J. Reconstruction of gene regulatory networks for Caenorhabditis elegans using tree-shaped gene expression data. Brief Bioinform 2024; 25:bbae396. [PMID: 39133097 PMCID: PMC11318059 DOI: 10.1093/bib/bbae396] [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: 03/27/2024] [Revised: 06/11/2024] [Accepted: 08/07/2024] [Indexed: 08/13/2024] Open
Abstract
Constructing gene regulatory networks is a widely adopted approach for investigating gene regulation, offering diverse applications in biology and medicine. A great deal of research focuses on using time series data or single-cell RNA-sequencing data to infer gene regulatory networks. However, such gene expression data lack either cellular or temporal information. Fortunately, the advent of time-lapse confocal laser microscopy enables biologists to obtain tree-shaped gene expression data of Caenorhabditis elegans, achieving both cellular and temporal resolution. Although such tree-shaped data provide abundant knowledge, they pose challenges like non-pairwise time series, laying the inaccuracy of downstream analysis. To address this issue, a comprehensive framework for data integration and a novel Bayesian approach based on Boolean network with time delay are proposed. The pre-screening process and Markov Chain Monte Carlo algorithm are applied to obtain the parameter estimates. Simulation studies show that our method outperforms existing Boolean network inference algorithms. Leveraging the proposed approach, gene regulatory networks for five subtrees are reconstructed based on the real tree-shaped datatsets of Caenorhabditis elegans, where some gene regulatory relationships confirmed in previous genetic studies are recovered. Also, heterogeneity of regulatory relationships in different cell lineage subtrees is detected. Furthermore, the exploration of potential gene regulatory relationships that bear importance in human diseases is undertaken. All source code is available at the GitHub repository https://github.com/edawu11/BBTD.git.
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Affiliation(s)
- Yida Wu
- School of Mathematical Sciences, Xiamen University, Zengcuo'an West Road, Siming District, Xiamen 361000, China
| | - Da Zhou
- School of Mathematical Sciences, Xiamen University, Zengcuo'an West Road, Siming District, Xiamen 361000, China
| | - Jie Hu
- School of Mathematical Sciences, Xiamen University, Zengcuo'an West Road, Siming District, Xiamen 361000, China
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36
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Park S, Kim J, Lee J, Jung S, Pack SP, Lee JH, Yoon K, Woo SJ, Han JY, Seo M. RNA sequencing analysis of sexual dimorphism in Japanese quail. Front Vet Sci 2024; 11:1441021. [PMID: 39104546 PMCID: PMC11299063 DOI: 10.3389/fvets.2024.1441021] [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: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 08/07/2024] Open
Abstract
Introduction Japanese quail are of significant economic value, providing protein nutrition to humans through their reproductive activity; however, sexual dimorphism in this species remains relatively unexplored compared with other model species. Method A total of 114 RNA sequencing datasets (18 and 96 samples for quail and chicken, respectively) were collected from existing studies to gain a comprehensive understanding of sexual dimorphism in quail. Cross-species integrated analyses were performed with transcriptome data from evolutionarily close chickens to identify sex-biased genes in the embryonic, adult brain, and gonadal tissues. Results Our findings indicate that the expression patterns of genes involved in sex-determination mechanisms during embryonic development, as well as those of most sex-biased genes in the adult brain and gonads, are identical between quails and chickens. Similar to most birds with a ZW sex determination system, quails lacked global dosage compensation for the Z chromosome, resulting in directional outcomes that supported the hypothesis that sex is determined by the individual dosage of Z-chromosomal genes, including long non-coding RNAs located in the male hypermethylated region. Furthermore, genes, such as WNT4 and VIP, reversed their sex-biased patterns at different points in embryonic development and/or in different adult tissues, suggesting a potential hurdle in breeding and transgenic experiments involving avian sex-related traits. Discussion The findings of this study are expected to enhance our understanding of sexual dimorphism in birds and subsequently facilitate insights into the field of breeding and transgenesis of sex-related traits that economically benefit humans.
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Affiliation(s)
- Sinwoo Park
- Department of Computer and Information Science, Korea University, Sejong-si, Republic of Korea
| | - Jaeryeong Kim
- Department of Computer and Information Science, Korea University, Sejong-si, Republic of Korea
| | - Jinbaek Lee
- Department of Computer and Information Science, Korea University, Sejong-si, Republic of Korea
| | - Sungyoon Jung
- Department of Computer and Information Science, Korea University, Sejong-si, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-si, Republic of Korea
| | - Jin Hyup Lee
- Department of Food and Biotechnology, Korea University, Sejong-si, Republic of Korea
| | - Kyungheon Yoon
- Division of Genome Science, Department of Precision Medicine, National Institue of Health, Cheongju-si, Republic of Korea
| | - Seung Je Woo
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Minseok Seo
- Department of Computer and Information Science, Korea University, Sejong-si, Republic of Korea
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Bao L, Chen M, Dai B, Lei Y, Qin D, Cheng M, Song W, He W, Chen B, Shen H. Nanoengineered therapeutic strategies targeting SNHG1 for mitigating microglial ischemia-reperfusion injury implications for hypoxic-ischemic encephalopathy. SLAS Technol 2024:100167. [PMID: 39043303 DOI: 10.1016/j.slast.2024.100167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/05/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024]
Abstract
The purpose of this work is to investigate the function of SNHG1, a long non-coding RNA implicated in disease progression, apoptosis, and proliferation, in order to solve the problem of hypoxic-ischemic encephalopathy (HIE) in newborn care. We investigated the impact of overexpressing SNHG1 on hypoxia-induced apoptosis and studied its expression in BV2 microglial cells under hypoxic circumstances. As a result of modifying YY1 expression, SNHG1's overexpression prevents apoptosis, as our data demonstrate that it is considerably downregulated under hypoxia. We demonstrate that SNHG1 might potentially reduce microglial ischemia-reperfusion damage by using sophisticated nanoengineering drug delivery technologies to target it. This provides encouraging information for the therapy of ischemic epilepsy.
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Affiliation(s)
- Li Bao
- Department of Neonatology,Yixing Hospital Affiliated to Jiangsu University,Yixing 214200, Jiangsu Province, China
| | - Mingzhi Chen
- Department of Thoracic and Cardiovascular Surgery,Yixing Hospital Affiliated to Jiangsu University,Yixing 214200, Jiangsu Province, China
| | - Biao Dai
- Department of Science and Education,Yixing Hospital Affiliated to Jiangsu University,Yixing 214200, Jiangsu Province, China
| | - Yong Lei
- Department of Neonatology,Yixing Hospital Affiliated to Jiangsu University,Yixing 214200, Jiangsu Province, China
| | - Dani Qin
- Department of Pediatrics,Yixing Hospital Affiliated to Jiangsu University,Yixing 214200, Jiangsu Province, China
| | - Mengke Cheng
- Department of Neonatology,Yixing Hospital Affiliated to Jiangsu University,Yixing 214200, Jiangsu Province, China
| | - Wei Song
- Department of Neonatology,Yixing Hospital Affiliated to Jiangsu University,Yixing 214200, Jiangsu Province, China
| | - Wenxia He
- Department of Neonatology,Yixing Hospital Affiliated to Jiangsu University,Yixing 214200, Jiangsu Province, China
| | - Bingyu Chen
- Department of Pediatrics,Yixing Hospital Affiliated to Jiangsu University,Yixing 214200, Jiangsu Province, China
| | - Huiping Shen
- Department of Pediatrics,Yixing Hospital Affiliated to Jiangsu University,Yixing 214200, Jiangsu Province, China.
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38
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Lukhtanov VA, Dantchenko AV. Cryptic Taxa Revealed through Combined Analysis of Chromosomes and DNA Barcodes: The Polyommatus ripartii Species Complex in Armenia and NW Iran. INSECTS 2024; 15:545. [PMID: 39057277 PMCID: PMC11277131 DOI: 10.3390/insects15070545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024]
Abstract
The detection of cryptic species in complexes that have undergone recent speciation is often difficult, since many standard nuclear markers have not yet accumulated differences between closely related taxa, and differences in mitochondrial markers can be leveled out due to mitochondrial introgressions. In these cases, the use of derived chromosomal characters such as non-ancestral chromosomal numbers and/or unusual karyotype features may be a solution to the species delimitation problem. However, non-ancestral but similar karyotypes may arise secondarily as a result of homoplastic evolution, and their interpretation as homologies may lead to incorrect taxonomic conclusions. In our study, we show that the combined use of mitochondrial DNA barcodes and karyotypes helps to solve this problem and identifies cryptic species in situations where each of these markers does not work individually. Using this approach, we show that the fauna of Armenia and adjacent Iran includes the following cryptic taxa of the Polyommatus ripartii species complex (haploid chromosome number, n in parentheses): P. ripartii paralcestis (n = 90), P. ripartii kalashiani, subsp. nov (n close to 90), P. emmeli, sp. nov. (n = 77-79), P. keleybaricus, sp. nov. (n = 86), P. demavendi belovi (n = 73-75), P. demavendi antonius, subsp. nov. (n = 71-73), P. admetus anatoliensis (n = 79) and P. eriwanensis (n = 29-34). Polyommatus admetus yeranyani is synonymized with P. admetus anatoliensis.
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Affiliation(s)
- Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia
| | - Alexander V. Dantchenko
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia
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39
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Zhu Z, Younas L, Zhou Q. Evolution and regulation of animal sex chromosomes. Nat Rev Genet 2024:10.1038/s41576-024-00757-3. [PMID: 39026082 DOI: 10.1038/s41576-024-00757-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2024] [Indexed: 07/20/2024]
Abstract
Animal sex chromosomes typically carry the upstream sex-determining gene that triggers testis or ovary development and, in some species, are regulated by global dosage compensation in response to functional decay of the Y chromosome. Despite the importance of these pathways, they exhibit striking differences across species, raising fundamental questions regarding the mechanisms underlying their evolutionary turnover. Recent studies of non-model organisms, including insects, reptiles and teleosts, have yielded a broad view of the diversity of sex chromosomes that challenges established theories. Moreover, continued studies in model organisms with recently developed technologies have characterized the dynamics of sex determination and dosage compensation in three-dimensional nuclear space and at single-cell resolution. Here, we synthesize recent insights into sex chromosomes from a variety of species to review their evolutionary dynamics with respect to the canonical model, as well as their diverse mechanisms of regulation.
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Affiliation(s)
- Zexian Zhu
- Evolutionary and Organismal Biology Research Center and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lubna Younas
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Qi Zhou
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
- State Key Laboratory of Transvascular Implantation Devices, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
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40
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Lin XQ, Quan YL, He HL, Peng J. [ NFIX gene mutation causes Marshall-Smith syndrome in a pair of identical twins and literature review]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2024; 26:750-756. [PMID: 39014953 DOI: 10.7499/j.issn.1008-8830.2401047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
This article reports on the clinical and genetic characteristics of monozygotic twins with Marshall-Smith syndrome (MRSHSS) due to a mutation in the NFIX gene, along with a review of related literature. Both patients presented with global developmental delays, a prominent forehead, shallow eye sockets, and pectus excavatum. Genetic testing revealed a heterozygous splicing site mutation c.697+1G>A in both children, with parents showing wild-type at this locus. According to the guidelines of the American College of Medical Genetics and Genomics, this mutation is considered likely pathogenic and has not been previously reported in the literature. A review of the literature identified 32 MRSHSS patients with splicing/frameshift mutations. Accelerated bone maturation and moderate to severe global developmental delay/intellectual disability are the primary clinical manifestations of patients with MRSHSS. Genetic testing results are crucial for the diagnosis of this condition.
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Affiliation(s)
- Xue-Qin Lin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yu-Lin Quan
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Hai-Lan He
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha 410008, China
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41
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Zhao H. Structural Basis of Conformational Dynamics in the PROTAC-Induced Protein Degradation. ChemMedChem 2024; 19:e202400171. [PMID: 38655701 DOI: 10.1002/cmdc.202400171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024]
Abstract
Pronounced conformational dynamics is unveiled upon analyzing multiple crystal structures of the same proteins recruited to the same E3 ligases by PROTACs, and yet, is largely permissive for targeted protein degradation due to the intrinsic mobility of E3 assemblies creating a large ubiquitylation zone. Mathematical modelling of ternary dynamics on ubiquitylation probability confirms the experimental finding that ternary complex rigidification need not correlate with enhanced protein degradation. Salt bridges are found to prevail in the PROTAC-induced ternary complexes, and may contribute to a positive cooperativity and prolonged half-life. The analysis highlights the importance of presenting lysines close to the active site of the E2 enzyme while constraining ternary dynamics in PROTAC design to achieve high degradation efficiency.
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Affiliation(s)
- Hongtao Zhao
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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42
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Sin WC, Liu J, Zhong JY, Lam HM, Lim BL. Comparative proteomics analysis of root and nodule mitochondria of soybean. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39007421 DOI: 10.1111/pce.15026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024]
Abstract
Legumes perform symbiotic nitrogen fixation through rhizobial bacteroids housed in specialised root nodules. The biochemical process is energy-intensive and consumes a huge carbon source to generate sufficient reducing power. To maintain the symbiosis, malate is supplied by legume nodules to bacteroids as their major carbon and energy source in return for ammonium ions and nitrogenous compounds. To sustain the carbon supply to bacteroids, nodule cells undergo drastic reorganisation of carbon metabolism. Here, a comprehensive quantitative comparison of the mitochondrial proteomes between root nodules and uninoculated roots was performed using data-independent acquisition proteomics, revealing the modulations in nodule mitochondrial proteins and pathways in response to carbon reallocation. Corroborated our findings with that from the literature, we believe nodules preferably allocate cytosolic phosphoenolpyruvates towards malate synthesis in lieu of pyruvate synthesis, and nodule mitochondria prefer malate over pyruvate as the primary source of NADH for ATP production. Moreover, the differential regulation of respiratory chain-associated proteins suggests that nodule mitochondria could enhance the efficiencies of complexes I and IV for ATP synthesis. This study highlighted a quantitative proteomic view of the mitochondrial adaptation in soybean nodules.
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Affiliation(s)
- Wai-Ching Sin
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Jinhong Liu
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Jia Yi Zhong
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Hon-Ming Lam
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Boon Leong Lim
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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Liu L, Zhang W, Wang Y, Wu J, Fan Q, Chen W, Zhou L, Li J, Li Y. Radiomics combined with clinical and MRI features may provide preoperative evaluation of suboptimal debulking surgery for serous ovarian carcinoma. Abdom Radiol (NY) 2024:10.1007/s00261-024-04343-3. [PMID: 39003651 DOI: 10.1007/s00261-024-04343-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 07/15/2024]
Abstract
PURPOSE To develop and validate a model for predicting suboptimal debulking surgery (SDS) of serous ovarian carcinoma (SOC) using radiomics method, clinical and MRI features. METHODS 228 patients eligible from institution A (randomly divided into the training and internal validation cohorts) and 45 patients from institution B (external validation cohort) were collected and retrospectively analyzed. All patients underwent abdominal pelvic enhanced MRI scan, including T2-weighted imaging fat-suppressed fast spin-echo (T2FSE), T1-weighted dual-echo magnetic resonance imaging (T1DEI), diffusion weighted imaging (DWI), and T1 with contrast enhancement (T1CE). We extracted, selected and eliminated highly correlated radiomic features for each sequence. Then, Radiomic models were made by each single sequence, dual-sequence (T1CE + T2FSE), and all-sequence, respectively. Univariate and multivariate analyses were performed to screen the clinical and MRI independent predictors. The radiomic model with the highest area under the curve (AUC) was used to combine the independent predictors as a combined model. RESULTS The optimal radiomic model was based on dual sequences (T2FSE + T1CE) among the five radiomic models (AUC = 0.720, P < 0.05). Serum carbohydrate antigen 125, the relationship between sigmoid colon/rectum and ovarian mass or mass implanted in Douglas' pouch, diaphragm nodules, and peritoneum/mesentery nodules were considered independent predictors. The AUC of the radiomic-clinical-radiological model was higher than either the optimal radiomic model or the clinical-radiological model in the training cohort (AUC = 0.908 vs. 0.720/0.854). CONCLUSIONS The radiomic-clinical-radiological model has an overall algorithm reproducibility and may help create individualized treatment programs and improve the prognosis of patients with SOC.
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Affiliation(s)
- Li Liu
- Department of Radiology, The People's Hospital of Yubei District of Chongqing City, No. 23 ZhongyangGongyuanBei Road, Yubei District, Chongqing, 401120, China
- Department of Radiology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, China
| | - Wenfei Zhang
- Department of Radiology, The People's Hospital of Yubei District of Chongqing City, No. 23 ZhongyangGongyuanBei Road, Yubei District, Chongqing, 401120, China
| | - Yudong Wang
- Institute of Clinical Algorithms, InferVision, Ocean International Center, Chaoyang District, Beijing, 100020, China
| | - Jiangfen Wu
- Institute of Clinical Algorithms, InferVision, Ocean International Center, Chaoyang District, Beijing, 100020, China
| | - Qianrui Fan
- Institute of Clinical Algorithms, InferVision, Ocean International Center, Chaoyang District, Beijing, 100020, China
| | - Weidao Chen
- Institute of Clinical Algorithms, InferVision, Ocean International Center, Chaoyang District, Beijing, 100020, China
| | - Linyi Zhou
- Department of Radiology, Daping Hospital, Army Medical Center, Army Medical University, 10# Changjiangzhilu, Chongqing, 40024, China
| | - Juncai Li
- Department of Surgery, The People's Hospital of Yubei District of Chongqing City, No. 23 ZhongyangGongyuanBei Road, Yubei District, Chongqing, 401120, China.
| | - Yongmei Li
- Department of Radiology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, China.
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Gupta M, Johnson ANT, Cruz ER, Costa EJ, Guest RL, Li SHJ, Hart EM, Nguyen T, Stadlmeier M, Bratton BP, Silhavy TJ, Wingreen NS, Gitai Z, Wühr M. Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation. Nat Commun 2024; 15:5890. [PMID: 39003262 PMCID: PMC11246515 DOI: 10.1038/s41467-024-49920-8] [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: 07/05/2023] [Accepted: 06/25/2024] [Indexed: 07/15/2024] Open
Abstract
Protein turnover is critical for proteostasis, but turnover quantification is challenging, and even in well-studied E. coli, proteome-wide measurements remain scarce. Here, we quantify the turnover rates of ~3200 E. coli proteins under 13 conditions by combining heavy isotope labeling with complement reporter ion quantification and find that cytoplasmic proteins are recycled when nitrogen is limited. We use knockout experiments to assign substrates to the known cytoplasmic ATP-dependent proteases. Surprisingly, none of these proteases are responsible for the observed cytoplasmic protein degradation in nitrogen limitation, suggesting that a major proteolysis pathway in E. coli remains to be discovered. Lastly, we show that protein degradation rates are generally independent of cell division rates. Thus, we present broadly applicable technology for protein turnover measurements and provide a rich resource for protein half-lives and protease substrates in E. coli, complementary to genomics data, that will allow researchers to study the control of proteostasis.
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Affiliation(s)
- Meera Gupta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Alex N T Johnson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Edward R Cruz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Eli J Costa
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Randi L Guest
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Elizabeth M Hart
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Thao Nguyen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael Stadlmeier
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Benjamin P Bratton
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Vanderbilt Institute of Infection, Immunology and Inflammation, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ned S Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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Hu L, Xiao X, Huang W, Zhou T, Chen W, Zhang C, Ying QL. A novel chemical genetic approach reveals paralog-specific role of ERK1/2 in mouse embryonic stem cell fate control. Front Cell Dev Biol 2024; 12:1415621. [PMID: 39071800 PMCID: PMC11272557 DOI: 10.3389/fcell.2024.1415621] [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: 04/10/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024] Open
Abstract
Introduction: Mouse embryonic stem cell (ESC) self-renewal can be maintained through dual inhibition of GSK3 and MEK kinases. MEK has two highly homologous downstream kinases, extracellular signal-regulated kinase 1 and 2 (ERK1/2). However, the exact roles of ERK1/2 in mouse ESC self-renewal and differentiation remain unclear. Methods: We selectively deleted or inhibited ERK1, ERK2, or both using genetic and chemical genetic approaches combined with small molecule inhibitors. The effects of ERK paralog-specific inhibition on mouse ESC self-renewal and differentiation were then assessed. Results: ERK1/2 were found to be dispensable for mouse ESC survival and self-renewal. The inhibition of both ERK paralogs, in conjunction with GSK3 inhibition, was sufficient to maintain mouse ESC self-renewal. In contrast, selective deletion or inhibition of only one ERK paralog did not mimic the effect of MEK inhibition in promoting mouse ESC self-renewal. Regarding ESC differentiation, inhibition of ERK1/2 prevented mesendoderm differentiation. Additionally, selective inhibition of ERK1, but not ERK2, promoted mesendoderm differentiation. Discussion: These findings suggest that ERK1 and ERK2 have both overlapping and distinct roles in regulating ESC self-renewal and differentiation. This study provides new insights into the molecular mechanisms of ERK1/2 in governing ESC maintenance and lineage commitment, potentially informing future strategies for controlling stem cell fate in research and therapeutic applications.
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Affiliation(s)
- Liang Hu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Xiong Xiao
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Wesley Huang
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Tao Zhou
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Weilu Chen
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Chao Zhang
- Loker Hydrocarbon Research Institute and Department of Chemistry, University of Southern California, Los Angeles, CA, United States
| | - Qi-Long Ying
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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46
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Smiles WJ, Ovens AJ, Kemp BE, Galic S, Petersen J, Oakhill JS. New developments in AMPK and mTORC1 cross-talk. Essays Biochem 2024:EBC20240007. [PMID: 38994736 DOI: 10.1042/ebc20240007] [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: 05/09/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024]
Abstract
Metabolic homeostasis and the ability to link energy supply to demand are essential requirements for all living cells to grow and proliferate. Key to metabolic homeostasis in all eukaryotes are AMPK and mTORC1, two kinases that sense nutrient levels and function as counteracting regulators of catabolism (AMPK) and anabolism (mTORC1) to control cell survival, growth and proliferation. Discoveries beginning in the early 2000s revealed that AMPK and mTORC1 communicate, or cross-talk, through direct and indirect phosphorylation events to regulate the activities of each other and their shared protein substrate ULK1, the master initiator of autophagy, thereby allowing cellular metabolism to rapidly adapt to energy and nutritional state. More recent reports describe divergent mechanisms of AMPK/mTORC1 cross-talk and the elaborate means by which AMPK and mTORC1 are activated at the lysosome. Here, we provide a comprehensive overview of current understanding in this exciting area and comment on new evidence showing mTORC1 feedback extends to the level of the AMPK isoform, which is particularly pertinent for some cancers where specific AMPK isoforms are implicated in disease pathogenesis.
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Affiliation(s)
- William J Smiles
- Metabolic Signalling Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Research Program for Receptor Biochemistry and Tumour Metabolism, Department of Paediatrics, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Ashley J Ovens
- Protein Engineering in Immunity and Metabolism, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Bruce E Kemp
- Protein Chemistry and Metabolism, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Department of Medicine, University of Melbourne, Parkville, VIC 3010, Australia
- Mary Mackillop Institute for Health Research, Australian Catholic University, Fitzroy, Vic 3065, Vic. Australia
| | - Sandra Galic
- Department of Medicine, University of Melbourne, Parkville, VIC 3010, Australia
- Metabolic Physiology, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Janni Petersen
- Flinders Health and Medical Research Institute, Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, SA 5042, Australia
- Nutrition and Metabolism, South Australia Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Jonathan S Oakhill
- Metabolic Signalling Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Department of Medicine, University of Melbourne, Parkville, VIC 3010, Australia
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47
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Nagakura T, Morono Y, Ito M, Mangelsdorf K, Pötz S, Schnabel E, Kallmeyer J. Microbial anabolic and catabolic utilization of hydrocarbons in deep subseafloor sediments of Guaymas Basin. FEMS Microbiol Ecol 2024; 100:fiae093. [PMID: 38955392 PMCID: PMC11250447 DOI: 10.1093/femsec/fiae093] [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: 02/26/2024] [Revised: 06/02/2024] [Accepted: 07/01/2024] [Indexed: 07/04/2024] Open
Abstract
Guaymas Basin, located in the Gulf of California, is a hydrothermally active marginal basin. Due to steep geothermal gradients and localized heating by sill intrusions, microbial substrates like short-chain fatty acids and hydrocarbons are abiotically produced from sedimentary organic matter at comparatively shallow depths. We analyzed the effect of hydrocarbons on uptake of hydrocarbons by microorganisms via nano-scale secondary ion mass spectrometry (NanoSIMS) and microbial sulfate reduction rates (SRR), using samples from two drill sites sampled by IODP Expedition 385 (U1545C and U1546D). These sites are in close proximity of each other (ca. 1 km) and have very similar sedimentology. Site U1546D experienced the intrusion of a sill that has since then thermally equilibrated with the surrounding sediment. Both sites currently have an identical geothermal gradient, despite their different thermal history. The localized heating by the sill led to thermal cracking of sedimentary organic matter and formation of potentially bioavailable organic substrates. There were low levels of hydrocarbon and nitrogen uptake in some samples from both sites, mostly in surficial samples. Hydrocarbon and methane additions stimulated SRR in near-seafloor samples from Site U1545C, while samples from Site U1546D reacted positively only on methane. Our data indicate the potential of microorganisms to metabolize hydrocarbons even in the deep subsurface of Guaymas Basin.
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Affiliation(s)
- Toshiki Nagakura
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Yuki Morono
- JAMSTEC Japan Agency for Marine-Earth Science and Technology, Kochi Institute for Core Sample Research, 200 Monobe Otsu, 783-8502 Nankoku, Kochi, Japan
| | - Motoo Ito
- JAMSTEC Japan Agency for Marine-Earth Science and Technology, Kochi Institute for Core Sample Research, 200 Monobe Otsu, 783-8502 Nankoku, Kochi, Japan
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, Telegrafenberg, 14473 Potsdam, Germany
| | - Stefanie Pötz
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, Telegrafenberg, 14473 Potsdam, Germany
| | - Ellen Schnabel
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
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48
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Spealman P, de Santana C, De T, Gresham D. Multilevel gene expression changes in lineages containing adaptive copy number variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.20.563336. [PMID: 37961325 PMCID: PMC10634702 DOI: 10.1101/2023.10.20.563336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Copy-number variants (CNVs) are an important class of recurrent variants that mediate adaptive evolution. While CNVs can increase the relative fitness of the organism, they can also incur a cost. We previously evolved populations of Saccharomyces cerevisiae over hundreds of generations in glutamine-limited (Gln-) chemostats and observed the recurrent evolution of CNVs at the GAP1 locus. To understand the role that expression plays in adaptation, both in relation to the adaptation of the organism to the selective condition, and as a consequence of the CNV, we measured the transcriptome, translatome, and proteome of 4 strains of evolved yeast, each with a unique CNV, and their ancestor in Gln- conditions. We find CNV-amplified genes correlate with higher RNA abundance; however, this effect is reduced at the level of the proteome, consistent with post-transcriptional dosage compensation. By normalizing each level of expression by the abundance of the preceding step we were able to identify widespread divergence in the efficiency of each step in the gene in the efficiency of each step in gene expression. Genes with significantly different translational efficiency were enriched for potential regulatory mechanisms including either upstream open reading frames, RNA binding sites for SSD1, or both. Genes with lower protein expression efficiency were enriched for genes encoding proteins in protein complexes. Taken together, our study reveals widespread changes in gene expression at multiple regulatory levels in lineages containing adaptive CNVs highlighting the diverse ways in which adaptive evolution shapes gene expression.
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Affiliation(s)
- Pieter Spealman
- Center for Genomics and Systems Biology, Department of Biology, New York University
| | - Carolina de Santana
- Laboratório de Microbiologia Ambiental e Saúde Pública - Universidade Estadual de Feira de Santana (UEFS), Bahia
| | - Titir De
- Center for Genomics and Systems Biology, Department of Biology, New York University
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University
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49
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Calvanese AL, Cecconi V, Stäheli S, Schnepf D, Nater M, Pereira P, Gschwend J, Heikenwälder M, Schneider C, Ludewig B, Silina K, van den Broek M. Sustained innate interferon is an essential inducer of tertiary lymphoid structures. Eur J Immunol 2024:e2451207. [PMID: 38980268 DOI: 10.1002/eji.202451207] [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: 04/19/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024]
Abstract
Tertiary lymphoid structures (TLS) resemble follicles of secondary lymphoid organs and develop in nonlymphoid tissues during inflammation and cancer. Which cell types and signals drive the development of TLS is largely unknown. To investigate early events of TLS development in the lungs, we repeatedly instilled p(I:C) plus ovalbumin (Ova) intranasally. This induced TLS ranging from lymphocytic aggregates to organized and functional structures containing germinal centers. We found that TLS development is independent of FAP+ fibroblasts, alveolar macrophages, or CCL19 but crucially depends on type I interferon (IFN-I). Mechanistically, IFN-I initiates two synergistic pathways that culminate in the development of TLS. On the one hand, IFN-I induces lymphotoxin (LT)α in lymphoid cells, which stimulate stromal cells to produce the B-cell-attracting chemokine CXCL13 through LTβR-signaling. On the other hand, IFN-I is sensed by stromal cells that produce the T-cell-attracting chemokines CXCL9, CXCL10 as well as CCL19 and CCL21 independently of LTβR. Consequently, B-cell aggregates develop within a week, whereas follicular dendritic cells and germinal centers appear after 3 weeks. Thus, sustained production of IFN-I together with an antigen is essential for the induction of functional TLS in the lungs.
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Affiliation(s)
| | - Virginia Cecconi
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Severin Stäheli
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Daniel Schnepf
- Institute of Virology, Medical Center University of Freiburg, Freiburg im Breisgau, Germany
| | - Marc Nater
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Paulo Pereira
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Julia Gschwend
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
- M3 Research Institute, Eberhard Karls University Tübingen, Tübingen, Germany
| | | | - Burkhard Ludewig
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Karina Silina
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
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50
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Elguweidi A, Crease T. Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing. G3 (BETHESDA, MD.) 2024; 14:jkae105. [PMID: 38771699 PMCID: PMC11228840 DOI: 10.1093/g3journal/jkae105] [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: 02/17/2024] [Revised: 02/17/2024] [Accepted: 05/10/2024] [Indexed: 05/23/2024]
Abstract
Ribosomal DNA (rDNA) has a vital role in ribosome biogenesis as it contains the genes that encode ribosomal RNA (rRNA) separated by intergenic spacers (IGSs). The rRNA genes occur in hundreds to tens of thousands of copies per haploid genome in eukaryotes and are generally highly conserved with low variation within species. Due to the repetitive nature and large size of rDNA arrays, detecting intraindividual variation can be difficult. In this study, we use whole-genome sequences of 169 Daphnia pulex individuals from 10 natural populations to measure the copy number and sequence variation in rDNA. This revealed that variation in rDNA copy number between individuals spans an order of magnitude. We further observed a substantial level of sequence variation within individual genomes. As expected, single-nucleotide polymorphisms occurred in regions of lower functional constraint such as the IGS and expansion segments of the rRNA genes. The presence of strong linkage disequilibrium among variants facilitated identification of haplotypes within each population. Although there was evidence of recombination among haplotypes from different populations, it is insufficient to eliminate linkage disequilibrium within populations. Estimating copy number and haplotype diversity within individuals revealed that the level of intraindividual sequence variation is not strongly correlated with copy number. The observed patterns of variation highlight a complex evolutionary history of rDNA in D. pulex. Future research should explore the functional implications of rDNA copy number and sequence variation on organismal phenotypes.
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Affiliation(s)
- Abir Elguweidi
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Teresa Crease
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
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