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Kreimendahl S, Pernas L. Metabolic immunity against microbes. Trends Cell Biol 2024; 34:496-508. [PMID: 38030541 DOI: 10.1016/j.tcb.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023]
Abstract
Pathogens, including viruses, bacteria, fungi, and parasites, remodel the metabolism of their host to acquire the nutrients they need to proliferate. Thus, host cells are often perceived as mere exploitable nutrient pools during infection. Mounting reports challenge this perception and instead suggest that host cells can actively reprogram their metabolism to the detriment of the microbial invader. In this review, we present metabolic mechanisms that host cells use to defend against pathogens. We highlight the contribution of domesticated microbes to host defenses and discuss examples of host-pathogen arms races that are derived from metabolic conflict.
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Affiliation(s)
| | - Lena Pernas
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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2
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Mei X, Wang X, Wu X, Liu G, Chen Y, Zhou S, Shang Y, Liu Z, Yang X, Sha W, Zhang H. Mitochondrial Genomic Evidence of Selective Constraints in Small-Bodied Terrestrial Cetartiodactyla. Animals (Basel) 2024; 14:1434. [PMID: 38791652 PMCID: PMC11117313 DOI: 10.3390/ani14101434] [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: 04/03/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Body size may drive the molecular evolution of mitochondrial genes in response to changes in energy requirements across species of different sizes. In this study, we perform selection pressure analysis and phylogenetic independent contrasts (PIC) to investigate the association between molecular evolution of mitochondrial genome protein-coding genes (mtDNA PCGs) and body size in terrestrial Cetartiodactyla. Employing selection pressure analysis, we observe that the average non-synonymous/synonymous substitution rate ratio (ω) of mtDNA PCGs is significantly reduced in small-bodied species relative to their medium and large counterparts. PIC analysis further confirms that ω values are positively correlated with body size (R2 = 0.162, p = 0.0016). Our results suggest that mtDNA PCGs of small-bodied species experience much stronger purifying selection as they need to maintain a heightened metabolic rate. On the other hand, larger-bodied species may face less stringent selective pressures on their mtDNA PCGs, potentially due to reduced relative energy expenditure per unit mass. Furthermore, we identify several genes that undergo positive selection, possibly linked to species adaptation to specific environments. Therefore, despite purifying selection being the predominant force in the evolution of mtDNA PCGs, positive selection can also occur during the process of adaptive evolution.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Honghai Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China; (X.M.)
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3
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van der Pouw Kraan D, Graham CT, Kavanagh F, Mirimin L. Development and validation of a DNA-based multi-species biomonitoring toolkit using a high-throughput qPCR platform: A case study of Irish shellfish species. Mol Ecol Resour 2024; 24:e13945. [PMID: 38429942 DOI: 10.1111/1755-0998.13945] [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: 07/18/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 03/03/2024]
Abstract
Biomonitoring of marine life has been enhanced in recent years by the integration of innovative DNA-based approaches, which offer advantages over more laborious techniques (e.g. microscopy). However, trade-offs between throughput, sensitivity and quantitative measurements must be made when choosing between the prevailing molecular methodologies (i.e. metabarcoding or qPCR/dPCR). Thus, the aim of the present study was to demonstrate the utility of a microfluidic-enabled high-throughput quantitative PCR platform (HTqPCR) for the rapid and cost-effective development and validation of a DNA-based multi-species biomonitoring toolkit, using larvae of 23 commercially targeted bivalve and crustacean species as a case study. The workflow was divided into three main phases: definition of (off-) target taxa and establishment of reference databases (PHASE 1); selection/development and assessment of molecular assays (PHASE 2); and protocol optimization and field validation (PHASE 3). 42 assays were eventually chosen and validated. Genetic signal not only showed good correlation with direct visual counts by microscopy but also showed the ability to provide quantitative data at the highest taxonomic resolution (species level) in a time- and cost-effective fashion. This study developed a biomonitoring toolkit, demonstrating the considerable advantages of this state-of-the-art technology in boosting the developmental testing and application of panels of molecular assays for the monitoring and management of natural resources. Once developed, this approach provides a cost and time-effective alternative compared to other multi-species approaches (e.g. metabarcoding). In addition, it is transferable to a wide range of species and will aid future monitoring programmes.
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Affiliation(s)
- Dennis van der Pouw Kraan
- Marine and Freshwater Research Centre, Department of Natural Resources and the Environment, Atlantic Technological University (ATU), Galway, Ireland
| | - Conor T Graham
- Marine and Freshwater Research Centre, Department of Natural Resources and the Environment, Atlantic Technological University (ATU), Galway, Ireland
| | - Fiona Kavanagh
- Marine and Freshwater Research Centre, Department of Natural Resources and the Environment, Atlantic Technological University (ATU), Galway, Ireland
| | - Luca Mirimin
- Marine and Freshwater Research Centre, Department of Natural Resources and the Environment, Atlantic Technological University (ATU), Galway, Ireland
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4
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Beyersdorf F. Innovation and disruptive science determine the future of cardiothoracic surgery. Eur J Cardiothorac Surg 2024; 65:ezae022. [PMID: 38243711 DOI: 10.1093/ejcts/ezae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/12/2024] [Indexed: 01/21/2024] Open
Abstract
One of the currently most asked questions in the field of medicine is how any specialty in the future will evolve to ensure better health for the patients by using current, unparalleled developments in all areas of science. This article will give an overview of new and evolving strategies for cardiothoracic (CT) surgery that are available today and will become available in the future in order to achieve this goal. In the founding era of CT surgery in the 1950s and 1960s, there was tremendous excitement about innovation and disruptive science, which eventually resulted in a completely new medical specialty, i.e. CT surgery. Entirely new treatment strategies were introduced for many cardiovascular diseases that had been considered incurable until then. As expected, alternative techniques have evolved in all fields of science during the last few decades, allowing great improvements in diagnostics and treatment in all medical specialties. The future of CT surgery will be determined by an unrestricted and unconditional investment in innovation, disruptive science and our own transformation using current achievements from many other fields. From the multitude of current and future possibilities, I will highlight 4 in this review: improvements in our current techniques, bringing CT surgery to low- and middle-income countries, revolutionizing the perioperative period and treating as yet untreatable diseases. These developments will allow us a continuation of the previously unheard-of treatment possibilities provided by ingenious innovations based on the fundamentals of CT surgery.
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Affiliation(s)
- Friedhelm Beyersdorf
- Department of Cardiovascular Surgery, University Hospital Freiburg, Freiburg, Germany
- Medical Faculty of the Albert-Ludwigs-University Freiburg, Germany
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5
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Yang M, Silverstein RL. Targeting Cysteine Oxidation in Thrombotic Disorders. Antioxidants (Basel) 2024; 13:83. [PMID: 38247507 PMCID: PMC10812781 DOI: 10.3390/antiox13010083] [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: 12/05/2023] [Revised: 12/29/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Oxidative stress increases the risk for clinically significant thrombotic events, yet the mechanisms by which oxidants become prothrombotic are unclear. In this review, we provide an overview of cysteine reactivity and oxidation. We then highlight recent findings on cysteine oxidation events in oxidative stress-related thrombosis. Special emphasis is on the signaling pathway induced by a platelet membrane protein, CD36, in dyslipidemia, and by protein disulfide isomerase (PDI), a member of the thiol oxidoreductase family of proteins. Antioxidative and chemical biology approaches to target cysteine are discussed. Lastly, the knowledge gaps in the field are highlighted as they relate to understanding how oxidative cysteine modification might be targeted to limit thrombosis.
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Affiliation(s)
- Moua Yang
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center, Harvard Medical School, 3 Blackfan Circle, CLS-924, Boston, MA 02115, USA
| | - Roy L. Silverstein
- Department of Medicine, Medical College of Wisconsin, Hub 8745, 8701 W Watertown Plank Rd., Milwaukee, WI 53226, USA
- Versiti Blood Research Institute, Milwaukee, WI 53226, USA
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6
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Baskerville R, Krijgsveld N, Esser P, Jeffery G, Poulton J. The Effect of Photobiomodulation on the Treatment of Hereditary Mitochondrial Diseases. J Lasers Med Sci 2023; 14:e41. [PMID: 38028882 PMCID: PMC10658120 DOI: 10.34172/jlms.2023.41] [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: 02/20/2023] [Accepted: 08/07/2023] [Indexed: 12/01/2023]
Abstract
Introduction: Despite a wide variety of clinical presentations in hereditary Mitochondrial Diseases, muscle fatigue is a common theme and impairs a patient's quality of life and ability to function. Current treatments are only supportive and include nutritional supplementation and physical therapy. Photobiomodulation therapy (PBMT) using low-intensity, narrow spectrum light in the red/near infrared (NIR) range, from a low-level laser or light-emitting diode sources, enhances mitochondrial function in preclinical and clinical studies on a range of conditions. However, little research has been done on the effectiveness of photobiomodulation in hereditary mitochondrial disorders. Methods: We performed a scoping review of the evidence of the beneficial effects of photobiomodulation for treating the muscle-related symptoms of hereditary mitochondrial disease. Results: No studies regarding photobiomodulation in hereditary mitochondrial disease were identified. However, in other clinical conditions featuring acquired mitochondrial impairment, we identified studies that suggested improved function, although sample sizes were small in number and statistical power. Conclusion: There is emerging evidence of efficacy for PBMT for diseases involving acquired mitochondrial insufficiency. We identified no published research on PBMT in hereditary mitochondrial disease, but this review confirms a theoretical rationale for a positive effect and suggests further research.
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Affiliation(s)
| | | | - Patrick Esser
- Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Glen Jeffery
- Institute of Ophthalmology, University College London, London, UK
| | - Joanna Poulton
- Hospital for Women and Reproductive Health, University of Oxford, Oxford, UK
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Andres KJ, Lodge DM, Andrés J. Environmental DNA reveals the genetic diversity and population structure of an invasive species in the Laurentian Great Lakes. Proc Natl Acad Sci U S A 2023; 120:e2307345120. [PMID: 37669387 PMCID: PMC10500163 DOI: 10.1073/pnas.2307345120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023] Open
Abstract
Environmental DNA (eDNA) has been established as a noninvasive and efficient approach to sample genetic material from aquatic environments. Although most commonly used to determine species presence and measure biodiversity, eDNA approaches also hold great potential to obtain population-level genetic information from water samples. In this study, we sequenced a panel of multiallelic microsatellite markers from filtered water and fish tissue samples to uncover patterns of intraspecific diversity in the freshwater Round Goby (Neogobius melanostomus) across their invaded range in the Laurentian Great Lakes region. Although we found that the concentration of nuclear eDNA is lower than mitochondrial eDNA, we nonetheless detected over two-thirds of all nuclear alleles identified from genotyped tissues in our eDNA samples, with the greatest recovery of common alleles in the population. Estimates of allele frequencies and genetic variability within and between populations were detected from eDNA in patterns that were consistent with individual tissue-based estimates of genetic diversity and differentiation. The strongest genetic differentiation in both eDNA and tissues exists in an isolation by distance pattern. Our study demonstrates the potential for eDNA-based approaches to characterize key population parameters required to effectively monitor, manage, or sustain aquatic species.
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Affiliation(s)
- Kara J. Andres
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY14853
- Department of Biology, Washington University in St. Louis, St. Louis, MO63130
- Living Earth Collaborative, Washington University in St. Louis, St. Louis, MO63130
| | - David M. Lodge
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY14853
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY14853
| | - Jose Andrés
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY14853
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Dunn KJ, Berger AJ. Three-dimensional angular scattering simulations inform analysis of scattering from single cells. JOURNAL OF BIOMEDICAL OPTICS 2023; 28:086501. [PMID: 37564163 PMCID: PMC10411915 DOI: 10.1117/1.jbo.28.8.086501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/16/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Significance Organelle sizes, which are indicative of cellular status, have implications for drug development and immunology research. At the single cell level, such information could be used to study the heterogeneity of cell response to drugs or pathogens. Aim Angularly resolved elastic light scattering is known to be sensitive to changes in organelle size distribution. We developed a Mie theory-based simulation of angular scattering from single cells to quantify the effects of noise on scattering and size estimates. Approach We simulated randomly sampled organelle sizes (drawn from a log normal distribution), interference between different organelles' scattering, and detector noise. We quantified each noise source's effect upon the estimated mean and standard deviation of organelle size distributions. Results The results demonstrate that signal-to-noise ratio in the angular scattering increased with the number of scatterers, cell area, and exposure time and decreased with the size distribution width. The error in estimating the mean of the size distributions remained below 5% for nearly all experimental parameters tested, but the widest size distribution tested (standard deviation of 600 nm) reached 20%. Conclusions The simulator revealed that sparse sampling of a broad size distribution can dominate the mismatch between actual and predicted size parameters. Alternative estimation strategies could reduce the discrepancy.
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Affiliation(s)
- Kaitlin J. Dunn
- University of Rochester, Institute of Optics, Rochester, New York, United States
| | - Andrew J. Berger
- University of Rochester, Institute of Optics, Rochester, New York, United States
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9
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Popov LD. Mitochondria as intracellular signalling organelles. An update. Cell Signal 2023:110794. [PMID: 37422005 DOI: 10.1016/j.cellsig.2023.110794] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/23/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023]
Abstract
Traditionally, mitochondria are known as "the powerhouse of the cell," responsible for energy (ATP) generation (by the electron transport chain, oxidative phosphorylation, the tricarboxylic acid cycle, and fatty acid ß-oxidation), and for the regulation of several metabolic processes, including redox homeostasis, calcium signalling, and cellular apoptosis. The extensive studies conducted in the last decades portray mitochondria as multifaceted signalling organelles that ultimately command cells' survival or death. Based on current knowledge, we'll outline the mitochondrial signalling to other intracellular compartments in homeostasis and pathology-related mitochondrial stress conditions here. The following topics are discussed: (i) oxidative stress and mtROS signalling in mitohormesis, (ii) mitochondrial Ca2+ signalling; (iii) the anterograde (nucleus-to-mitochondria) and retrograde (mitochondria-to-nucleus) signal transduction, (iv) the mtDNA role in immunity and inflammation, (v) the induction of mitophagy- and apoptosis - signalling cascades, (vi) the mitochondrial dysfunctions (mitochondriopathies) in cardiovascular, neurodegenerative, and malignant diseases. The novel insights into molecular mechanisms of mitochondria-mediated signalling can explain mitochondria adaptation to metabolic and environmental stresses to achieve cell survival.
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Affiliation(s)
- Lucia-Doina Popov
- Institute of Cellular Biology and Pathology "Nicolae Simionescu" of the Romanian Academy, 8, B.P. Hasdeu Street, 050568 Bucharest, Romania.
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10
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Endres K, Friedland K. Talk to Me-Interplay between Mitochondria and Microbiota in Aging. Int J Mol Sci 2023; 24:10818. [PMID: 37445995 DOI: 10.3390/ijms241310818] [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: 05/26/2023] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
The existence of mitochondria in eukaryotic host cells as a remnant of former microbial organisms has been widely accepted, as has their fundamental role in several diseases and physiological aging. In recent years, it has become clear that the health, aging, and life span of multicellular hosts are also highly dependent on the still-residing microbiota, e.g., those within the intestinal system. Due to the common evolutionary origin of mitochondria and these microbial commensals, it is intriguing to investigate if there might be a crosstalk based on preserved common properties. In the light of rising knowledge on the gut-brain axis, such crosstalk might severely affect brain homeostasis in aging, as neuronal tissue has a high energy demand and low tolerance for according functional decline. In this review, we summarize what is known about the impact of both mitochondria and the microbiome on the host's aging process and what is known about the aging of both entities. For a long time, bacteria were assumed to be immortal; however, recent evidence indicates their aging and similar observations have been made for mitochondria. Finally, we present pathways by which mitochondria are affected by microbiota and give information about therapeutic anti-aging approaches that are based on current knowledge.
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Affiliation(s)
- Kristina Endres
- Department of Psychiatry and Psychotherapy, University Medical Center of the Johannes Gutenberg-University, 55131 Mainz, Germany
| | - Kristina Friedland
- Department of Pharmacology and Toxicology, Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, 55128 Mainz, Germany
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11
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Udi Y, Zhang W, Stein ME, Ricardo-Lax I, Pasolli HA, Chait BT, Rout MP. A general method for quantitative fractionation of mammalian cells. J Cell Biol 2023; 222:213941. [PMID: 36920247 PMCID: PMC10040634 DOI: 10.1083/jcb.202209062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/11/2023] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Subcellular fractionation in combination with mass spectrometry-based proteomics is a powerful tool to study localization of key proteins in health and disease. Here we offered a reliable and rapid method for mammalian cell fractionation, tuned for such proteomic analyses. This method proves readily applicable to different cell lines in which all the cellular contents are accounted for, while maintaining nuclear and nuclear envelope integrity. We demonstrated the method's utility by quantifying the effects of a nuclear export inhibitor on nucleoplasmic and cytoplasmic proteomes.
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Affiliation(s)
- Yael Udi
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University , New York, NY, USA
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
| | - Inna Ricardo-Lax
- Laboratory of Virology and Infectious Disease, The Rockefeller University , New York, NY, USA
| | - Hilda A Pasolli
- Electron Microscopy Resource Center, The Rockefeller University , New York, NY, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University , New York, NY, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
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12
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Cotes-Perdomo AP, Nava S, Castro LR, Rivera-Paéz FA, Cortés-Vecino JA, Uribe JE. Phylogenetic relationships of the Amblyomma cajennense complex (Acari: Ixodidae) at mitogenomic resolution. Ticks Tick Borne Dis 2023; 14:102125. [PMID: 36806845 DOI: 10.1016/j.ttbdis.2023.102125] [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: 10/09/2022] [Revised: 11/28/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023]
Abstract
The genus Amblyomma is the third most diverse in the number of species within the Ixodidae, with practically half of its species distributed in the Americas, though there are also species occurring in Africa, Asia, and Australia. Within the genus, there are several species complexes with veterinary and public health importance. The Amblyomma cajennense complex, in the Americas, is represented by six species with a wide distribution, from Texas to northern Argentina. We combined two sequencing techniques to generate complete mitogenomes of species belonging to the Amblyomma cajennense complex: genome skimming and long-range PCRs sequencing methods. Thus, we generated seven new mitochondrial genomes for all species of the Amblyomma cajennense complex, except for Amblyomma interandinum. Genetic distances between the mitogenomes corroborate the clear differentiation between the five species of the Amblyomma cajennense complex. The phylogenetic relationships of these species had previously been evaluated by combining partial nuclear and mitochondrial genes and here these relationships are corroborated with a more robust framework of data, which demonstrates that the conjunction of mitochondrial and nuclear partial genes can resolve close relationships when entire genes or genomes are unavailable. The gene order, structure, composition, and length are stable across these mitogenomes, and they share the general characteristics of Metastriata. Future studies should increase the number of available mitogenomes for this genus, especially for those species from the Indo-Pacific region and Africa, by means of a better understanding of their relationships and evolutionary process.
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Affiliation(s)
- Andrea P Cotes-Perdomo
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain; Natural Sciences and Environmental Health Department, Natural Sciences and Maritime Sciences, Faculty of Technology, University of South-Eastern, Norway
| | - Santiago Nava
- Instituto de Investigación de la Cadena Láctea (IDICAL, INTA-CONICET), Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Rafaela (EEA Rafaela), Santa Fe, Argentina
| | - Lyda R Castro
- Grupo de investigación Evolución, Sistemática y Ecología Molecular (GIESEMOL), Facultad de Ciencias Básicas, Universidad del Magdalena, Santa Marta, Colombia
| | - Fredy A Rivera-Paéz
- Grupo de Investigación en Genética, Biodiversidad y Manejo de Ecosistemas (GEBIOME), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Calle 65 No. 26-10, Manizales, Caldas 170004, Colombia
| | - Jesús A Cortés-Vecino
- Grupo de Investigación Parasitología Veterinaria, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Juan E Uribe
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain; Invertebrate Zoology Department, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, United States of America.
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13
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Schank M, Zhao J, Wang L, Nguyen LNT, Zhang Y, Wu XY, Zhang J, Jiang Y, Ning S, El Gazzar M, Moorman JP, Yao ZQ. ROS-Induced Mitochondrial Dysfunction in CD4 T Cells from ART-Controlled People Living with HIV. Viruses 2023; 15:1061. [PMID: 37243148 PMCID: PMC10224005 DOI: 10.3390/v15051061] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
We have previously demonstrated mitochondrial dysfunction in aging CD4 T cells from antiretroviral therapy (ART)-controlled people living with HIV (PLWH). However, the underlying mechanisms by which CD4 T cells develop mitochondrial dysfunction in PLWH remain unclear. In this study, we sought to elucidate the mechanism(s) of CD4 T cell mitochondrial compromise in ART-controlled PLWH. We first assessed the levels of reactive oxygen species (ROS), and we observed significantly increased cellular and mitochondrial ROS levels in CD4 T cells from PLWH compared to healthy subjects (HS). Furthermore, we observed a significant reduction in the levels of proteins responsible for antioxidant defense (superoxide dismutase 1, SOD1) and ROS-mediated DNA damage repair (apurinic/apyrimidinic endonuclease 1, APE1) in CD4 T cells from PLWH. Importantly, CRISPR/Cas9-mediated knockdown of SOD1 or APE1 in CD4 T cells from HS confirmed their roles in maintaining normal mitochondrial respiration via a p53-mediated pathway. Reconstitution of SOD1 or APE1 in CD4 T cells from PLWH successfully rescued mitochondrial function as evidenced by Seahorse analysis. These results indicate that ROS induces mitochondrial dysfunction, leading to premature T cell aging via dysregulation of SOD1 and APE1 during latent HIV infection.
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Affiliation(s)
- Madison Schank
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Juan Zhao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Ling Wang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Lam Ngoc Thao Nguyen
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Yi Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Xiao Y. Wu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Jinyu Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Yong Jiang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Shunbin Ning
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Mohamed El Gazzar
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Jonathan P. Moorman
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
| | - Zhi Q. Yao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
- Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
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14
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He L, Tronstad KJ, Maheshwari A. Mitochondrial Dynamics during Development. NEWBORN (CLARKSVILLE, MD.) 2023; 2:19-44. [PMID: 37206581 PMCID: PMC10193651 DOI: 10.5005/jp-journals-11002-0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mitochondria are dynamic membrane-bound organelles in eukaryotic cells. These are important for the generation of chemical energy needed to power various cellular functions and also support metabolic, energetic, and epigenetic regulation in various cells. These organelles are also important for communication with the nucleus and other cellular structures, to maintain developmental sequences and somatic homeostasis, and for cellular adaptation to stress. Increasing information shows mitochondrial defects as an important cause of inherited disorders in different organ systems. In this article, we provide an extensive review of ontogeny, ultrastructural morphology, biogenesis, functional dynamics, important clinical manifestations of mitochondrial dysfunction, and possibilities for clinical intervention. We present information from our own clinical and laboratory research in conjunction with information collected from an extensive search in the databases PubMed, EMBASE, and Scopus.
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Affiliation(s)
- Ling He
- Department of Pediatrics and Pharmacology, Johns Hopkins University, Baltimore, United States of America
| | | | - Akhil Maheshwari
- Founding Chairman, Global Newborn Society, Clarksville, Maryland, United States of America
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15
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Tan TCY, Dunning KR. Non-invasive assessment of oocyte developmental competence. Reprod Fertil Dev 2022; 35:39-50. [PMID: 36592982 DOI: 10.1071/rd22217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Oocyte quality is a key factor influencing IVF success. The oocyte and surrounding cumulus cells, known collectively as the cumulus oocyte complex (COC), communicate bi-directionally and regulate each other's metabolic function to support oocyte growth and maturation. Many studies have attempted to associate metabolic markers with oocyte quality, including metabolites in follicular fluid or 'spent medium' following maturation, gene expression of cumulus cells and measuring oxygen consumption in medium surrounding COCs. However, these methods fail to provide spatial metabolic information on the separate oocyte and cumulus cell compartments. Optical imaging of the autofluorescent cofactors - reduced nicotinamide adenine dinucleotide (phosphate) [NAD(P)H] and flavin adenine dinucleotide (FAD) - has been put forward as an approach to generate spatially resolved measurements of metabolism within individual cells of the COC. The optical redox ratio (FAD/[NAD(P)H+FAD]), calculated from these cofactors, can act as an indicator of overall metabolic activity in the oocyte and cumulus cell compartments. Confocal microscopy, fluorescence lifetime imaging microscopy (FLIM) and hyperspectral microscopy may be used for this purpose. This review provides an overview of current optical imaging techniques that capture the inner biochemistry within cells of the COC and discusses the potential for such imaging to assess oocyte developmental competence.
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Affiliation(s)
- Tiffany C Y Tan
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, SA, Australia
| | - Kylie R Dunning
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, SA, Australia
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16
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Zhu D, Wu F, Li H, Wang T, Bao L, Ge J, Wang H. Diet preferences based on sequence read count: the role of species interaction in tissue bias correction. Mol Ecol Resour 2022; 23:159-173. [PMID: 35980601 DOI: 10.1111/1755-0998.13700] [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: 01/01/2021] [Revised: 07/26/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022]
Abstract
High-throughput sequencing and metabarcoding techniques provide a unique opportunity to study predator-prey relationships. However, in animal dietary preference studies, how to properly correct tissue bias within the sequence read count and the role of interactions between co-occurring species in metabarcoding mixtures remain largely unknown. In this study, we proposed two categories of tissue bias correction indices: sequence read count number per unit tissue (SCN) and its ratio form (SCN ratio). By constructing plant mock communities with different numbers of co-occurring species in metabarcoding mixtures and conducting feeding trails on captive sika deer (Cervus nippon), we demonstrated the features of the SCN and SCN ratio, evaluated their correction effects, and assessed the role of species interactions during tissue bias correction. Tissue differences between species are defined as the differential ability in generating sequence counts. Our study suggests that pure tissue differences among species without species interaction is not an optimal correction index for many biomes with limited tissue differences among species. Species interactions in mixtures may amplify tissue differences, which is beneficial for tissue bias correction. However, caution must be taken because varied species interaction among communities may increase the risk of worse correction. Correction effects based on the SCN and SCN ratio are comparable, while the SCN is less influenced by control species than the SCN ratio. According to our study, several suggestions were provided for future animal diet studies or other high-throughput sequencing studies containing tissue bias.
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Affiliation(s)
- Di Zhu
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station.,College of Life Sciences, Beijing Normal University, Beijing
| | - Feng Wu
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station.,College of Life Sciences, Beijing Normal University, Beijing
| | - Hailong Li
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,College of Agriculture and Life Sciences, Seoul National University, Seoul.,College of Geography and Ocean Science, YanBian University, Hunchun
| | - Tianming Wang
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station.,College of Life Sciences, Beijing Normal University, Beijing
| | - Lei Bao
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station.,College of Life Sciences, Beijing Normal University, Beijing
| | - Jianping Ge
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station.,College of Life Sciences, Beijing Normal University, Beijing
| | - Hongfang Wang
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station.,College of Life Sciences, Beijing Normal University, Beijing
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17
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Chen X, Karmaker N, Cloutier P, Bass AD, Zheng Y, Sanche L. Low-Energy Electron Damage to Plasmid DNA in Thin Films: Dependence on Substrates, Surface Density, Charging, Environment, and Uniformity. J Phys Chem B 2022; 126:5443-5457. [PMID: 35834372 DOI: 10.1021/acs.jpcb.2c03664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of low-energy electrons (LEEs) with DNA plays a significant role in the mechanisms leading to biological damage induced by ionizing radiation, particularly in radiotherapy, and its sensitization by chemotherapeutic drugs and nanoparticles. Plasmids constitute the form of DNA found in mitochondria and appear as a suitable model of genomic DNA. In a search for the best LEE targets, damage was induced to plasmids, in thin films in vacuum, by 6, 10, and 100 eV electrons under single collision conditions. The yields of single- and double-strand breaks, other cluster damage, isolated base lesions, and crosslinks were measured by electrophoresis and enzyme treatment. The films were deposited on oriented graphite or polycrystalline tantalum, with or without DNA autoassembly via diaminopropane (Dap) intercalation. Yields were correlated with the influence of vacuum, film uniformity, surface density, substrates, and the DNA environment. Aided by surface potential measurements and scanning electron microscopy and atomic force microscopy images, the lyophilized Dap-DNA films were found to be the most practical high-quality targets. These studies pave the way to the fabrication of LEE target-films composed of plasmids intercalated with biomolecules that could mimic the cellular environment; for example, as a first step, by replacing Dap with an amino acid.
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Affiliation(s)
- Xingju Chen
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P. R. China
| | - Nanda Karmaker
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Pierre Cloutier
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Andrew D Bass
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P. R. China.,Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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18
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Zubaite G, Hindley JW, Ces O, Elani Y. Dynamic Reconfiguration of Subcompartment Architectures in Artificial Cells. ACS NANO 2022; 16:9389-9400. [PMID: 35695383 PMCID: PMC9245354 DOI: 10.1021/acsnano.2c02195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/27/2022] [Indexed: 06/01/2023]
Abstract
Artificial cells are minimal structures constructed from biomolecular building blocks designed to mimic cellular processes, behaviors, and architectures. One near-ubiquitous feature of cellular life is the spatial organization of internal content. We know from biology that organization of content (including in membrane-bound organelles) is linked to cellular functions and that this feature is dynamic: the presence, location, and degree of compartmentalization changes over time. Vesicle-based artificial cells, however, are not currently able to mimic this fundamental cellular property. Here, we describe an artificial cell design strategy that addresses this technological bottleneck. We create a series of artificial cell architectures which possess multicompartment assemblies localized either on the inner or on the outer surface of the artificial cell membrane. Exploiting liquid-liquid phase separation, we can also engineer spatially segregated regions of condensed subcompartments attached to the cell surface, aligning with coexisting membrane domains. These structures can sense changes in environmental conditions and respond by reversibly transitioning from condensed multicompartment layers on the membrane surface to a dispersed state in the cell lumen, mimicking the dynamic compartmentalization found in biological cells. Likewise, we engineer exosome-like subcompartments that can be released to the environment. We can achieve this by using two types of triggers: chemical (addition of salts) and mechanical (by pulling membrane tethers using optical traps). These approaches allow us to control the compartmentalization state of artificial cells on population and single-cell levels.
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Affiliation(s)
- Greta Zubaite
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- Department
of Chemical Engineering, Imperial College
London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - James W. Hindley
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, 82 Wood Lane, London W12
0BZ, United Kingdom
| | - Oscar Ces
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, 82 Wood Lane, London W12
0BZ, United Kingdom
| | - Yuval Elani
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- Department
of Chemical Engineering, Imperial College
London, Exhibition Road, London SW7 2AZ, United Kingdom
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19
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Production of Carotenoids and Phospholipids by Thraustochytrium sp. in Batch and Repeated-Batch Culture. Mar Drugs 2022; 20:md20070416. [PMID: 35877709 PMCID: PMC9325111 DOI: 10.3390/md20070416] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/07/2022] [Accepted: 06/21/2022] [Indexed: 02/06/2023] Open
Abstract
The carotenogenic thraustochytrid Thraustochytrium sp. RT2316-16 was grown in batch and repeated-batch cultures using different feeds containing glucose, or glycerol, and yeast extract, for the production of lipids, phospholipids and carotenoids. RT2316-16 produced canthaxanthin, astaxanthin and β-carotene. The effects of biotin, ascorbic acid, light and temperature were evaluated in some of the experiments. In 2-day-old batch cultures, the combined mass percentage of eicosapentaenoic acid and docosahexaenoic acid in total lipids was between 16.5% (glycerol-based medium in the dark; biomass concentration = 4.2 ± 1.1 g L−1) and 42.6% (glucose-based medium under light; biomass concentration = 3.3 ± 0.1 g L−1), decreasing to 3.8% and 6.1%, respectively, after day 4. In repeated-batch cultures, the total lipids in the biomass increased after glucose or glycerol was fed alone, whereas the total carotenoids (168 ± 7 μg g−1 dry weight (DW)) and phospholipids in the biomass increased after feeding with yeast extract. The biomass with the highest content of phospholipids (28.7 ± 4.3 mg g−1 DW) was obtained using a feed medium formulated with glycerol, yeast extract and ascorbic acid. Glycerol was the best carbon source for the production of a biomass enriched with total lipids (467 ± 45 mg g−1 DW). The composition of carotenoids depended strongly on the composition of the feed. Repeated-batch cultures fed with yeast extract contained canthaxanthin as the main carotenoid, whereas in the cultures fed only with glucose, the biomass contained mainly β-carotene.
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20
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Hanaford AR, Cho YJ, Nakai H. AAV-vector based gene therapy for mitochondrial disease: progress and future perspectives. Orphanet J Rare Dis 2022; 17:217. [PMID: 35668433 PMCID: PMC9169410 DOI: 10.1186/s13023-022-02324-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/09/2022] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial diseases are a group of rare, heterogeneous diseases caused by gene mutations in both nuclear and mitochondrial genomes that result in defects in mitochondrial function. They are responsible for significant morbidity and mortality as they affect multiple organ systems and particularly those with high energy-utilizing tissues, such as the nervous system, skeletal muscle, and cardiac muscle. Virtually no effective treatments exist for these patients, despite the urgent need. As the majority of these conditions are monogenic and caused by mutations in nuclear genes, gene replacement is a highly attractive therapeutic strategy. Adeno-associated virus (AAV) is a well-characterized gene replacement vector, and its safety profile and ability to transduce quiescent cells nominates it as a potential gene therapy vehicle for several mitochondrial diseases. Indeed, AAV vector-based gene replacement is currently being explored in clinical trials for one mitochondrial disease (Leber hereditary optic neuropathy) and preclinical studies have been published investigating this strategy in other mitochondrial diseases. This review summarizes the preclinical findings of AAV vector-based gene replacement therapy for mitochondrial diseases including Leigh syndrome, Barth syndrome, ethylmalonic encephalopathy, and others.
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Affiliation(s)
- Allison R Hanaford
- Center for Integrative Brain Research, Seattle Children's Reserach Institute, Seattle, WA, 98101, USA.
- Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Yoon-Jae Cho
- Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR, 97239, USA
- Division of Pediatric Neurology, Doernbecher Children's Hospital, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Hiroyuki Nakai
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Molecular Immunology and Microbiology, Oregon Health and Science University, Portland, OR, 97239, USA
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, 97006, USA
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21
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Lipko NB. Photobiomodulation: Evolution and Adaptation. Photobiomodul Photomed Laser Surg 2022; 40:213-233. [DOI: 10.1089/photob.2021.0145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Nancy B. Lipko
- Nancy B. Lipko, MD, MBA, Home Office, Beachwood, Ohio, USA
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22
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Duarte-Hospital C, Tête A, Brial F, Benoit L, Koual M, Tomkiewicz C, Kim MJ, Blanc EB, Coumoul X, Bortoli S. Mitochondrial Dysfunction as a Hallmark of Environmental Injury. Cells 2021; 11:cells11010110. [PMID: 35011671 PMCID: PMC8750015 DOI: 10.3390/cells11010110] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 02/07/2023] Open
Abstract
Environmental factors including diet, sedentary lifestyle and exposure to pollutants largely influence human health throughout life. Cellular and molecular events triggered by an exposure to environmental pollutants are extremely variable and depend on the age, the chronicity and the doses of exposure. Only a fraction of all relevant mechanisms involved in the onset and progression of pathologies in response to toxicants has probably been identified. Mitochondria are central hubs of metabolic and cell signaling responsible for a large variety of biochemical processes, including oxidative stress, metabolite production, energy transduction, hormone synthesis, and apoptosis. Growing evidence highlights mitochondrial dysfunction as a major hallmark of environmental insults. Here, we present mitochondria as crucial organelles for healthy metabolic homeostasis and whose dysfunction induces critical adverse effects. Then, we review the multiple mechanisms of action of pollutants causing mitochondrial toxicity in link with chronic diseases. We propose the Aryl hydrocarbon Receptor (AhR) as a model of “exposome receptor”, whose activation by environmental pollutants leads to various toxic events through mitochondrial dysfunction. Finally, we provide some remarks related to mitotoxicity and risk assessment.
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Affiliation(s)
- Carolina Duarte-Hospital
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, T3S, INSERM UMR-S 1124, F-75006 Paris, France; (C.D.-H.); (A.T.); (F.B.); (L.B.); (M.K.); (C.T.); (M.J.K.); (E.B.B.)
- Faculty of Sciences, Université de Paris, F-75006 Paris, France
| | - Arnaud Tête
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, T3S, INSERM UMR-S 1124, F-75006 Paris, France; (C.D.-H.); (A.T.); (F.B.); (L.B.); (M.K.); (C.T.); (M.J.K.); (E.B.B.)
- Faculty of Sciences, Université de Paris, F-75006 Paris, France
| | - François Brial
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, T3S, INSERM UMR-S 1124, F-75006 Paris, France; (C.D.-H.); (A.T.); (F.B.); (L.B.); (M.K.); (C.T.); (M.J.K.); (E.B.B.)
| | - Louise Benoit
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, T3S, INSERM UMR-S 1124, F-75006 Paris, France; (C.D.-H.); (A.T.); (F.B.); (L.B.); (M.K.); (C.T.); (M.J.K.); (E.B.B.)
- Faculty of Sciences, Université de Paris, F-75006 Paris, France
| | - Meriem Koual
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, T3S, INSERM UMR-S 1124, F-75006 Paris, France; (C.D.-H.); (A.T.); (F.B.); (L.B.); (M.K.); (C.T.); (M.J.K.); (E.B.B.)
- Faculty of Sciences, Université de Paris, F-75006 Paris, France
| | - Céline Tomkiewicz
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, T3S, INSERM UMR-S 1124, F-75006 Paris, France; (C.D.-H.); (A.T.); (F.B.); (L.B.); (M.K.); (C.T.); (M.J.K.); (E.B.B.)
- Faculty of Sciences, Université de Paris, F-75006 Paris, France
| | - Min Ji Kim
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, T3S, INSERM UMR-S 1124, F-75006 Paris, France; (C.D.-H.); (A.T.); (F.B.); (L.B.); (M.K.); (C.T.); (M.J.K.); (E.B.B.)
- Université Sorbonne Paris Nord, F-93000 Bobigny, France
| | - Etienne B. Blanc
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, T3S, INSERM UMR-S 1124, F-75006 Paris, France; (C.D.-H.); (A.T.); (F.B.); (L.B.); (M.K.); (C.T.); (M.J.K.); (E.B.B.)
- Faculty of Sciences, Université de Paris, F-75006 Paris, France
| | - Xavier Coumoul
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, T3S, INSERM UMR-S 1124, F-75006 Paris, France; (C.D.-H.); (A.T.); (F.B.); (L.B.); (M.K.); (C.T.); (M.J.K.); (E.B.B.)
- Faculty of Sciences, Université de Paris, F-75006 Paris, France
- Correspondence: (X.C.); (S.B.); Tel.: +33-1-76-53-43-70 (S.B.)
| | - Sylvie Bortoli
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, T3S, INSERM UMR-S 1124, F-75006 Paris, France; (C.D.-H.); (A.T.); (F.B.); (L.B.); (M.K.); (C.T.); (M.J.K.); (E.B.B.)
- Faculty of Sciences, Université de Paris, F-75006 Paris, France
- Correspondence: (X.C.); (S.B.); Tel.: +33-1-76-53-43-70 (S.B.)
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23
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Kelly S. The economics of organellar gene loss and endosymbiotic gene transfer. Genome Biol 2021; 22:345. [PMID: 34930424 PMCID: PMC8686548 DOI: 10.1186/s13059-021-02567-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/06/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The endosymbiosis of the bacterial progenitors of the mitochondrion and the chloroplast are landmark events in the evolution of life on Earth. While both organelles have retained substantial proteomic and biochemical complexity, this complexity is not reflected in the content of their genomes. Instead, the organellar genomes encode fewer than 5% of the genes found in living relatives of their ancestors. While many of the 95% of missing organellar genes have been discarded, others have been transferred to the host nuclear genome through a process known as endosymbiotic gene transfer. RESULTS Here, we demonstrate that the difference in the per-cell copy number of the organellar and nuclear genomes presents an energetic incentive to the cell to either delete organellar genes or transfer them to the nuclear genome. We show that, for the majority of transferred organellar genes, the energy saved by nuclear transfer exceeds the costs incurred from importing the encoded protein into the organelle where it can provide its function. Finally, we show that the net energy saved by endosymbiotic gene transfer can constitute an appreciable proportion of total cellular energy budgets and is therefore sufficient to impart a selectable advantage to the cell. CONCLUSION Thus, reduced cellular cost and improved energy efficiency likely played a role in the reductive evolution of mitochondrial and chloroplast genomes and the transfer of organellar genes to the nuclear genome.
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Affiliation(s)
- Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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24
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Groen J, Palanca A, Aires A, Conesa JJ, Maestro D, Rehbein S, Harkiolaki M, Villar AV, Cortajarena AL, Pereiro E. Correlative 3D cryo X-ray imaging reveals intracellular location and effect of designed antifibrotic protein-nanomaterial hybrids. Chem Sci 2021; 12:15090-15103. [PMID: 34909150 PMCID: PMC8612387 DOI: 10.1039/d1sc04183e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/17/2021] [Indexed: 12/20/2022] Open
Abstract
Revealing the intracellular location of novel therapeutic agents is paramount for the understanding of their effect at the cell ultrastructure level. Here, we apply a novel correlative cryo 3D imaging approach to determine the intracellular fate of a designed protein–nanomaterial hybrid with antifibrotic properties that shows great promise in mitigating myocardial fibrosis. Cryo 3D structured illumination microscopy (cryo-3D-SIM) pinpoints the location and cryo soft X-ray tomography (cryo-SXT) reveals the ultrastructural environment and subcellular localization of this nanomaterial with spatial correlation accuracy down to 70 nm in whole cells. This novel high resolution 3D cryo correlative approach unambiguously locates the nanomaterial after overnight treatment within multivesicular bodies which have been associated with endosomal trafficking events by confocal microscopy. Moreover, this approach allows assessing the cellular response towards the treatment by evaluating the morphological changes induced. This is especially relevant for the future usage of nanoformulations in clinical practices. This correlative super-resolution and X-ray imaging strategy joins high specificity, by the use of fluorescence, with high spatial resolution at 30 nm (half pitch) provided by cryo-SXT in whole cells, without the need of staining or fixation, and can be of particular benefit to locate specific molecules in the native cellular environment in bio-nanomedicine. A novel 3D cryo correlative approach locates designed therapeutic protein–nanomaterial hybrids in whole cells with high specificity and resolution. Detection of treatment-induced morphological changes, crucial for pre-clinical studies, are revealed.![]()
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Affiliation(s)
- J Groen
- MISTRAL Beamline, Experiments Division, ALBA Synchrotron Light Source Cerdanyola del Valles 08290 Barcelona Spain
| | - A Palanca
- Instituto de Biomedicina y Biotecnologia de Cantabria (IBBTEC), University of Cantabria, CSIC 39011 Santander Spain.,Department of Anatomy and Cell Biology, University of Cantabria 39011 Santander Spain
| | - A Aires
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 194 20014 Donostia San Sebastian Spain
| | - J J Conesa
- MISTRAL Beamline, Experiments Division, ALBA Synchrotron Light Source Cerdanyola del Valles 08290 Barcelona Spain .,National Center for Biotechnology CSIC (CNB-CSIC), Department of Macromolecular Structures Cantoblanco 28049 Madrid Spain
| | - D Maestro
- Instituto de Biomedicina y Biotecnologia de Cantabria (IBBTEC), University of Cantabria, CSIC 39011 Santander Spain
| | - S Rehbein
- Helmholtz-Zentrum Berlin für Materialien und Energie, Bessy II D-12489 Berlin Germany
| | - M Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - A V Villar
- Instituto de Biomedicina y Biotecnologia de Cantabria (IBBTEC), University of Cantabria, CSIC 39011 Santander Spain.,Department of Physiology and Pharmacology, University of Cantabria Avd. Herrera Oria s/n Santander Spain
| | - A L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 194 20014 Donostia San Sebastian Spain .,Ikerbasque, Basque Foundation for Science 48009 Bilbao Spain
| | - E Pereiro
- MISTRAL Beamline, Experiments Division, ALBA Synchrotron Light Source Cerdanyola del Valles 08290 Barcelona Spain
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25
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Fernandes Gyorfy M, Miller ER, Conover JL, Grover CE, Wendel JF, Sloan DB, Sharbrough J. Nuclear-cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:219-230. [PMID: 34309123 DOI: 10.1111/tpj.15436] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
The plant genome is partitioned across three distinct subcellular compartments: the nucleus, mitochondria, and plastids. Successful coordination of gene expression among these organellar genomes and the nuclear genome is critical for plant function and fitness. Whole genome duplication (WGD) events in the nucleus have played a major role in the diversification of land plants and are expected to perturb the relative copy number (stoichiometry) of nuclear, mitochondrial, and plastid genomes. Thus, elucidating the mechanisms whereby plant cells respond to the cytonuclear stoichiometric imbalance that follows WGDs represents an important yet underexplored question in understanding the evolutionary consequences of genome doubling. We used droplet digital PCR to investigate the relationship between nuclear and organellar genome copy numbers in allopolyploids and their diploid progenitors in both wheat and Arabidopsis. Polyploids exhibit elevated organellar genome copy numbers per cell, largely preserving the cytonuclear stoichiometry observed in diploids despite the change in nuclear genome copy number. To investigate the timescale over which cytonuclear stoichiometry may respond to WGD, we also estimated the organellar genome copy number in Arabidopsis synthetic autopolyploids and in a haploid-induced diploid line. We observed corresponding changes in organellar genome copy number in these laboratory-generated lines, indicating that at least some of the cellular response to cytonuclear stoichiometric imbalance is immediate following WGD. We conclude that increases in organellar genome copy numbers represent a common response to polyploidization, suggesting that maintenance of cytonuclear stoichiometry is an important component in establishing polyploid lineages.
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Affiliation(s)
| | - Emma R Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Daniel B Sloan
- Biology Department, Colorado State University, Fort Collins, CO, USA
| | - Joel Sharbrough
- Biology Department, Colorado State University, Fort Collins, CO, USA
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
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26
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Brown RB. Sodium Toxicity in the Nutritional Epidemiology and Nutritional Immunology of COVID-19. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:739. [PMID: 34440945 PMCID: PMC8399536 DOI: 10.3390/medicina57080739] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/17/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023]
Abstract
Dietary factors in the etiology of COVID-19 are understudied. High dietary sodium intake leading to sodium toxicity is associated with comorbid conditions of COVID-19 such as hypertension, kidney disease, stroke, pneumonia, obesity, diabetes, hepatic disease, cardiac arrhythmias, thrombosis, migraine, tinnitus, Bell's palsy, multiple sclerosis, systemic sclerosis, and polycystic ovary syndrome. This article synthesizes evidence from epidemiology, pathophysiology, immunology, and virology literature linking sodium toxicological mechanisms to COVID-19 and SARS-CoV-2 infection. Sodium toxicity is a modifiable disease determinant that impairs the mucociliary clearance of virion aggregates in nasal sinuses of the mucosal immune system, which may lead to SARS-CoV-2 infection and viral sepsis. In addition, sodium toxicity causes pulmonary edema associated with severe acute respiratory syndrome, as well as inflammatory immune responses and other symptoms of COVID-19 such as fever and nasal sinus congestion. Consequently, sodium toxicity potentially mediates the association of COVID-19 pathophysiology with SARS-CoV-2 infection. Sodium dietary intake also increases in the winter, when sodium losses through sweating are reduced, correlating with influenza-like illness outbreaks. Increased SARS-CoV-2 infections in lower socioeconomic classes and among people in government institutions are linked to the consumption of foods highly processed with sodium. Interventions to reduce COVID-19 morbidity and mortality through reduced-sodium diets should be explored further.
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Affiliation(s)
- Ronald B Brown
- School of Public Health Sciences, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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27
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Coppedè F. One-carbon epigenetics and redox biology of neurodegeneration. Free Radic Biol Med 2021; 170:19-33. [PMID: 33307166 DOI: 10.1016/j.freeradbiomed.2020.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022]
Abstract
One-carbon metabolism provides the methyl groups for both DNA and histone tail methylation reactions, two of the main epigenetic processes that tightly regulate the chromatin structure and gene expression levels. Several enzymes involved in one-carbon metabolism, as well as several epigenetic enzymes, are regulated by intracellular metabolites and redox cofactors, but their expression levels are in turn regulated by epigenetic modifications, in such a way that metabolism and gene expression reciprocally regulate each other to maintain homeostasis and regulate cell growth, survival, differentiation and response to environmental stimuli. Increasing evidence highlights the contribution of impaired one-carbon metabolism and epigenetic modifications in neurodegeneration. This article provides an overview of DNA and histone tail methylation changes in major neurodegenerative disorders, namely Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis, discussing the contribution of oxidative stress and impaired one-carbon and redox metabolism to their onset and progression.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Via Roma 55, 56126, Pisa, Italy.
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28
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Milane L, Dolare S, Jahan T, Amiji M. Mitochondrial nanomedicine: Subcellular organelle-specific delivery of molecular medicines. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 37:102422. [PMID: 34175455 DOI: 10.1016/j.nano.2021.102422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 04/21/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023]
Abstract
As mitochondria network together to act as the master sensors and effectors of apoptosis, ATP production, reactive oxygen species management, mitophagy/autophagy, and homeostasis; this organelle is an ideal target for pharmaceutical manipulation. Mitochondrial dysfunction contributes to many diseases, for example, β-amyloid has been shown to interfere with mitochondrial protein import and induce apoptosis in Alzheimer's Disease while some forms of Parkinson's Disease are associated with dysfunctional mitochondrial PINK1 and Parkin proteins. Mitochondrial medicine has applications in the treatment of an array of pathologies from cancer to cardiovascular disease. A challenge of mitochondrial medicine is directing therapies to a subcellular target. Nanotechnology based approaches combined with mitochondrial targeting strategies can greatly improve the clinical translation and effectiveness of mitochondrial medicine. This review discusses mitochondrial drug delivery approaches and applications of mitochondrial nanomedicines. Nanomedicine approaches have the potential to drive the success of mitochondrial therapies into the clinic.
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Affiliation(s)
- Lara Milane
- Northeastern University, Department of Pharmaceutical Sciences, Boston, MA.
| | - Saket Dolare
- Northeastern University, Department of Pharmaceutical Sciences, Boston, MA
| | - Tanjheela Jahan
- Northeastern University, Department of Pharmaceutical Sciences, Boston, MA
| | - Mansoor Amiji
- Northeastern University, Department of Pharmaceutical Sciences, Boston, MA
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29
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Fahimi P, Matta CF. On the power per mitochondrion and the number of associated active ATP synthases. Phys Biol 2021; 18. [PMID: 33853054 DOI: 10.1088/1478-3975/abf7d9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/14/2021] [Indexed: 11/12/2022]
Abstract
Recent experiments and thermodynamic arguments suggest that mitochondrial temperatures are higher than those of the cytoplasm. A "hot mitochondrion" calls for a closer examination of the energy balance that endows it with these claimed elevated temperatures. As a first step in this effort, we present here a semi-quantitative bookkeeping whereby, in one stroke, a formula is proposed that yields the rate of heat production in a typical mitochondrion and a formula for estimating the number of "active" ATP synthase molecules per mitochondrion. The number of active ATP synthase molecules is the equivalent number of ATP synthases operating at 100% capacity to maintain the rate of mitochondrial heat generation. Scaling laws are shown to determine the number of active ATP synthase molecules in a mitochondrion and mitochondrial rate of heat production, whereby both appear to scale with cell volume. Four heterotrophic protozoan cell types are considered in this study. The studied cells, selected to cover a wide range of sizes (volumes) fromca.100μm3to 1 millionμm3, are estimated to exhibit a power per mitochondrion ranging fromca.1 pW to 0.03 pW. In these cells, the corresponding number of active ATP synthases per mitochondrion ranges from 5000 to just about a hundred. The absolute total number of ATP synthase molecules per mitochondrion, regardless of their activity status, can be up to two orders of magnitudes higher.
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Affiliation(s)
- Peyman Fahimi
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, B3M2J6, Canada.,Département de Chimie, Université Laval, Québec, Québec, G1V0A6, Canada
| | - Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, B3M2J6, Canada.,Département de Chimie, Université Laval, Québec, Québec, G1V0A6, Canada.,Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, B3H3C3, Canada.,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H4J3, Canada
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30
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Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, Brown S, Capodiferro MR, Al-Ajli FO, Ambrosini R, Houde P, Koren S, Oliver K, Smith M, Skelton J, Betteridge E, Dolucan J, Corton C, Bista I, Torrance J, Tracey A, Wood J, Uliano-Silva M, Howe K, McCarthy S, Winkler S, Kwak W, Korlach J, Fungtammasan A, Fordham D, Costa V, Mayes S, Chiara M, Horner DS, Myers E, Durbin R, Achilli A, Braun EL, Phillippy AM, Jarvis ED. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. Genome Biol 2021; 22:120. [PMID: 33910595 PMCID: PMC8082918 DOI: 10.1186/s13059-021-02336-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/31/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. RESULTS As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. CONCLUSIONS Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.
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Affiliation(s)
- Giulio Formenti
- The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA.
- Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY, USA.
- The Howards Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Balacco
- The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA
| | - Bettina Haase
- The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA
| | | | - Olivier Fedrigo
- The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA
| | - Samara Brown
- Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY, USA
- The Howards Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Farooq O Al-Ajli
- Monash University Malaysia Genomics Facility, School of Science, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Qatar Falcon Genome Project, Doha, State of Qatar
| | - Roberto Ambrosini
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | - Iliana Bista
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | - Shane McCarthy
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology & Genetics, Dresden, Germany
| | | | | | | | - Daniel Fordham
- Oxford Nanopore Technologies Ltd, Oxford Science Park, Oxford, UK
| | - Vania Costa
- Oxford Nanopore Technologies Ltd, Oxford Science Park, Oxford, UK
| | - Simon Mayes
- Oxford Nanopore Technologies Ltd, Oxford Science Park, Oxford, UK
| | - Matteo Chiara
- Department of Biosciences, University of Milan, Milan, Italy
| | - David S Horner
- Department of Biosciences, University of Milan, Milan, Italy
| | - Eugene Myers
- Max Planck Institute of Molecular Cell Biology & Genetics, Dresden, Germany
| | - Richard Durbin
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erich D Jarvis
- The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA.
- Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY, USA.
- The Howards Hughes Medical Institute, Chevy Chase, MD, USA.
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31
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Abstract
Genetic diseases cause numerous complex and intractable pathologies. DNA sequences encoding each human's complexity and many disease risks are contained in the mitochondrial genome, nuclear genome, and microbial metagenome. Diagnosis of these diseases has unified around applications of next-generation DNA sequencing. However, translating specific genetic diagnoses into targeted genetic therapies remains a central goal. To date, genetic therapies have fallen into three broad categories: bulk replacement of affected genetic compartments with a new exogenous genome, nontargeted addition of exogenous genetic material to compensate for genetic errors, and most recently, direct correction of causative genetic alterations using gene editing. Generalized methods of diagnosis, therapy, and reagent delivery into each genetic compartment will accelerate the next generations of curative genetic therapies. We discuss the structure and variability of the mitochondrial, nuclear, and microbial metagenomic compartments, as well as the historical development and current practice of genetic diagnostics and gene therapies targeting each compartment.
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Affiliation(s)
- Theodore L Roth
- Medical Scientist Training Program, University of California, San Francisco, California 94143, USA; .,Department of Microbiology and Immunology and Diabetes Center, University of California, San Francisco, California 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.,Gladstone Institutes, San Francisco, California 94158, USA
| | - Alexander Marson
- Department of Microbiology and Immunology and Diabetes Center, University of California, San Francisco, California 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.,Gladstone Institutes, San Francisco, California 94158, USA.,Department of Medicine, University of California, San Francisco, California 94143, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, California 94129, USA.,Chan Zuckerberg Biohub, San Francisco, California 94158, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA
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32
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TP63 basal cells are indispensable during endoderm differentiation into proximal airway cells on acellular lung scaffolds. NPJ Regen Med 2021; 6:12. [PMID: 33674599 PMCID: PMC7935966 DOI: 10.1038/s41536-021-00124-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/01/2021] [Indexed: 12/24/2022] Open
Abstract
The use of decellularized whole-organ scaffolds for bioengineering of organs is a promising avenue to circumvent the shortage of donor organs for transplantation. However, recellularization of acellular scaffolds from multicellular organs like the lung with a variety of different cell types remains a challenge. Multipotent cells could be an ideal cell source for recellularization. Here we investigated the hierarchical differentiation process of multipotent ES-derived endoderm cells into proximal airway epithelial cells on acellular lung scaffolds. The first cells to emerge on the scaffolds were TP63+ cells, followed by TP63+/KRT5+ basal cells, and finally multi-ciliated and secretory airway epithelial cells. TP63+/KRT5+ basal cells on the scaffolds simultaneously expressed KRT14, like basal cells involved in airway repair after injury. Removal of TP63 by CRISPR/Cas9 in the ES cells halted basal and airway cell differentiation on the scaffolds. These findings suggest that differentiation of ES-derived endoderm cells into airway cells on decellularized lung scaffolds proceeds via TP63+ basal cell progenitors and tracks a regenerative repair pathway. Understanding the process of differentiation is key for choosing the cell source for repopulation of a decellularized organ scaffold. Our data support the use of airway basal cells for repopulating the airway side of an acellular lung scaffold.
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33
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Mitochondrial Homeostasis Mediates Lipotoxicity in the Failing Myocardium. Int J Mol Sci 2021; 22:ijms22031498. [PMID: 33540894 PMCID: PMC7867320 DOI: 10.3390/ijms22031498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 01/17/2023] Open
Abstract
Heart failure remains the most common cause of death in the industrialized world. In spite of new therapeutic interventions that are constantly being developed, it is still not possible to completely protect against heart failure development and progression. This shows how much more research is necessary to understand the underlying mechanisms of this process. In this review, we give a detailed overview of the contribution of impaired mitochondrial dynamics and energy homeostasis during heart failure progression. In particular, we focus on the regulation of fatty acid metabolism and the effects of fatty acid accumulation on mitochondrial structural and functional homeostasis.
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34
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Ambers A, Elwick K, Cropper ER, Brandhagen MD, Jones B, Durst J, Gilmore KK, Bruseth JE, Gill-King H. Mitochondrial DNA analysis of the putative skeletal remains of Sieur de Marle: Genetic support for anthropological assessment of biogeographic ancestry. Forensic Sci Int 2021; 320:110682. [PMID: 33461005 DOI: 10.1016/j.forsciint.2021.110682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 12/02/2020] [Accepted: 01/04/2021] [Indexed: 10/22/2022]
Abstract
In 1932, seven burials were discovered on a Texas plantation that was originally the site of a 17th-century Caddo Indian village. Of the seven excavated graves, one set of remains (an adult male) was notably buried in a manner inconsistent with traditional Caddoan burial practices and has long been purported to be the remains of Sieur de Marle (a member of the French explorer La Salle's last expedition). Diary accounts of La Salle's expedition scribe report that Sieur de Marle died along a river near an Indian village during a trek to Canada to find help for colonists left behind at the ill-fated Fort St. Louis. Additionally, two lead projectiles recovered from the grave were ballistically analyzed and determined to be consistent with ammunition used in 17th-century weaponry. In the 1980s, anthropologists requested access to the remains for study, but the skull was missing. Cranial measurements recorded in 1940 and 1962 (by two independent anthropologists) were used to investigate the ancestry of this individual; and the Giles-Elliot (G-E) discriminant function was calculated to be 18.1, within the Anglo-European range. Dietary isotope testing on non-cranial skeletal elements determined that this unknown male's diet was rich in animal/marine protein sources, which differs appreciably from Caddo Indian populations of that time period. In order to genetically assess this individual's biogeographic ancestry and to provide further support that this individual is of European descent, mitochondrial DNA (mtDNA) sequencing was performed using the Applied Biosystems™ Precision ID mtDNA Whole Genome Panel. mtDNA sequencing of multiple sections from two different long bones yielded compiled results consistent with either Haplogroup H or R, both predominantly European mtDNA haplogroups. Further anthropological calculations were conducted using cranial measurements, FORDISC™ software, and discriminant function analysis. Two-way, four-way, and multigroup discriminant function analyses further classify this set of unidentified remains as being White (European) in origin, with posterior probabilities of 0.999, 0.881 and 0.986, respectively. Combined with historical records of Sieur de Marle's death, as well as overlays of historical and contemporary maps which demonstrate that the plantation site aligns with Joutel's diary accounts of de Marle's burial, these collective results support that these remains are of a European male and may possibly belong to this prominent member of La Salle's expedition team.
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Affiliation(s)
- Angie Ambers
- Center for Human Identification, Research and Development Unit, University of North Texas Health Science Center, Fort Worth, TX, USA; Forensic Science Department, Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT, USA; Henry C. Lee Institute of Forensic Science, West Haven, CT, USA.
| | - Kyleen Elwick
- Federal Bureau of Investigation Laboratory Division, Research and Support Unit, Visiting Scientist Program, Quantico, VA, USA
| | - Emily R Cropper
- Federal Bureau of Investigation Laboratory Division, Research and Support Unit, Visiting Scientist Program, Quantico, VA, USA
| | - Michael D Brandhagen
- Federal Bureau of Investigation Laboratory Division, DNA Support Unit, Quantico, VA, USA
| | - Bradford Jones
- Texas Historical Commission, Archaeology Division, Austin, TX, USA
| | - Jeffrey Durst
- Texas Historical Commission, Archaeology Division, Austin, TX, USA
| | | | - James E Bruseth
- Texas Historical Commission, Archaeology Division, Austin, TX, USA
| | - Harrell Gill-King
- Center for Human Identification, Forensic Anthropology Unit, University of North Texas Health Science Center, Fort Worth, TX, USA
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35
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Ramos-Ibeas P, Gimeno I, Cañón-Beltrán K, Gutiérrez-Adán A, Rizos D, Gómez E. Senescence and Apoptosis During in vitro Embryo Development in a Bovine Model. Front Cell Dev Biol 2020; 8:619902. [PMID: 33392207 PMCID: PMC7775420 DOI: 10.3389/fcell.2020.619902] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/01/2020] [Indexed: 12/15/2022] Open
Abstract
According to the World Health Organization, infertility affects up to 14% of couples under reproductive age, leading to an exponential rise in the use of assisted reproduction as a route for conceiving a baby. In the same way, thousands of embryos are produced in cattle and other farm animals annually, leading to increased numbers of individuals born. All reproductive manipulations entail deviations of natural phenotypes and genotypes, with in vitro embryo technologies perhaps showing the biggest effects, although these alterations are still emerging. Most of these indications have been provided by animal models, in particular the bovine species, due to its similarities to human early embryo development. Oocytes and embryos are highly sensitive to environmental stress in vivo and in vitro. Thus, during in vitro culture, a number of stressful conditions affect embryonic quality and viability, inducing subfertility and/or long-term consequences that may reach the offspring. A high proportion of the embryos produced in vitro are arrested at a species-specific stage of development during the first cell divisions. These arrested embryos do not show signs of programmed cell death during early cleavage stages. Instead, defective in vitro produced embryos would enter a permanent cell cycle arrest compatible with cellular senescence, in which they show active metabolism and high reactive oxygen species levels. Later in development, mainly during the morula and blastocyst stages, apoptosis would mediate the elimination of certain cells, accomplishing both a physiological role in to balancing cell proliferation and death, and a pathological role preventing the transmission of damaged cells with an altered genome. The latter would acquire relevant importance in in vitro produced embryos that are submitted to stressful environmental stimuli. In this article, we review the mechanisms mediating apoptosis and senescence during early embryo development, with a focus on in vitro produced bovine embryos. Additionally, we shed light on the protective role of senescence and apoptosis to ensure that unhealthy cells and early embryos do not progress in development, avoiding long-term detrimental effects.
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Affiliation(s)
- Priscila Ramos-Ibeas
- Department of Animal Reproduction, National Institute for Agriculture and Food Research and Technology (INIA), Madrid, Spain
| | - Isabel Gimeno
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Gijón, Spain
| | - Karina Cañón-Beltrán
- Department of Animal Reproduction, National Institute for Agriculture and Food Research and Technology (INIA), Madrid, Spain
| | - Alfonso Gutiérrez-Adán
- Department of Animal Reproduction, National Institute for Agriculture and Food Research and Technology (INIA), Madrid, Spain
| | - Dimitrios Rizos
- Department of Animal Reproduction, National Institute for Agriculture and Food Research and Technology (INIA), Madrid, Spain
| | - Enrique Gómez
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Gijón, Spain
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36
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Schlieben LD, Prokisch H. The Dimensions of Primary Mitochondrial Disorders. Front Cell Dev Biol 2020; 8:600079. [PMID: 33324649 PMCID: PMC7726223 DOI: 10.3389/fcell.2020.600079] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/06/2020] [Indexed: 12/19/2022] Open
Abstract
The concept of a mitochondrial disorder was initially described in 1962, in a patient with altered energy metabolism. Over time, mitochondrial energy metabolism has been discovered to be influenced by a vast number of proteins with a multitude of functional roles. Amongst these, defective oxidative phosphorylation arose as the hallmark of mitochondrial disorders. In the premolecular era, the diagnosis of mitochondrial disease was dependent on biochemical criteria, with inherent limitations such as tissue availability and specificity, preanalytical and analytical artifacts, and secondary effects. With the identification of the first mitochondrial disease-causing mutations, the genetic complexity of mitochondrial disorders began to unravel. Mitochondrial dysfunctions can be caused by pathogenic variants in genes encoded by the mitochondrial DNA or the nuclear DNA, and can display heterogenous phenotypic manifestations. The application of next generation sequencing methodologies in diagnostics is proving to be pivotal in finding the molecular diagnosis and has been instrumental in the discovery of a growing list of novel mitochondrial disease genes. In the molecular era, the diagnosis of a mitochondrial disorder, suspected on clinical grounds, is increasingly based on variant detection and associated statistical support, while invasive biopsies and biochemical assays are conducted to an ever-decreasing extent. At present, there is no uniform biochemical or molecular definition for the designation of a disease as a “mitochondrial disorder”. Such designation is currently dependent on the criteria applied, which may encompass clinical, genetic, biochemical, functional, and/or mitochondrial protein localization criteria. Given this variation, numerous gene lists emerge, ranging from 270 to over 400 proposed mitochondrial disease genes. Herein we provide an overview of the mitochondrial disease associated genes and their accompanying challenges.
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Affiliation(s)
- Lea D Schlieben
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
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37
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Lefèvre E, Gardner CM, Gunsch CK. A novel PCR-clamping assay reducing plant host DNA amplification significantly improves prokaryotic endo-microbiome community characterization. FEMS Microbiol Ecol 2020; 96:5850752. [PMID: 32490528 DOI: 10.1093/femsec/fiaa110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/01/2020] [Indexed: 11/12/2022] Open
Abstract
Due to the sequence homology between the bacterial 16S rRNA gene and plant chloroplast and mitochondrial DNA, the taxonomic characterization of plant microbiome using amplicon-based high throughput sequencing often results in the overwhelming presence of plant-affiliated reads, preventing the thorough description of plant-associated microbial communities. In this work we developed a PCR blocking primer assay targeting the taxonomically informative V5-V6 region of the 16S rRNA gene in order to reduce plant DNA co-amplification, and increase diversity coverage of associated prokaryotic communities. Evaluation of our assay on the characterization of the prokaryotic endophytic communities of Zea mays, Pinus taeda and Spartina alternifora leaves led to significantly reducing the proportion of plant reads, yielded 20 times more prokaryotic reads and tripled the number of detected OTUs compared to a commonly used V5-V6 PCR protocol. To expand the application of our PCR-clamping assay across a wider taxonomic spectrum of plant hosts, we additionally provide an alignment of chloroplast and mitochondrial DNA sequences encompassing more than 200 terrestrial plant families as a supporting tool for customizing our blocking primers.
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Affiliation(s)
- Emilie Lefèvre
- Department of Civil and Environmental Engineering, Duke University, 127 Hudson Hall, Box 90287, Durham, NC 27708, USA
| | - Courtney M Gardner
- Department of Civil and Environmental Engineering, Washington State University, 405 Spokane street, Sloan 101, Box 642910, Pullman, WA 99164, USA
| | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, 127 Hudson Hall, Box 90287, Durham, NC 27708, USA
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38
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Mitochondrial Sequencing of Missing Persons DNA Casework by Implementing Thermo Fisher's Precision ID mtDNA Whole Genome Assay. Genes (Basel) 2020; 11:genes11111303. [PMID: 33158032 PMCID: PMC7692767 DOI: 10.3390/genes11111303] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/31/2022] Open
Abstract
The advent of massively parallel sequencing (MPS) in the past decade has opened the doors to mitochondrial whole-genome sequencing. Mitochondrial (mt) DNA is used in forensics due to its high copy number per cell and maternal mode of inheritance. Consequently, we have implemented the Thermo Fisher Precision ID mtDNA Whole Genome panel coupled with the Ion Chef™ and Ion S5™ for MPS analysis in the California Department of Justice, Missing Persons DNA Program. Thirty-one mostly challenging samples (degraded, inhibited, low template, or mixed) were evaluated for this study. The majority of these samples generated single source full or partial genome sequences with MPS, providing information in cases where previously there was none. The quantitative and sensitive nature of MPS analysis was beneficial, but also led to detection of low-level contaminants. In addition, we found Precision ID to be more susceptible to inhibition than our legacy Sanger assay. Overall, the success rate (full single source hypervariable regions I and II (HVI/HVII) for Sanger and control region for MPS result) for these challenging samples increased from 32.3% with Sanger sequencing to 74.2% with the Precision ID assay. Considering the increase in success rate, the simple workflow and the higher discriminating potential of whole genome data, the Precision ID platform is a significant improvement for the CA Department of Justice Missing Persons DNA Program.
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39
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Bagheri HS, Bani F, Tasoglu S, Zarebkohan A, Rahbarghazi R, Sokullu E. Mitochondrial donation in translational medicine; from imagination to reality. J Transl Med 2020; 18:367. [PMID: 32977804 PMCID: PMC7517067 DOI: 10.1186/s12967-020-02529-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023] Open
Abstract
The existence of active crosstalk between cells in a paracrine and juxtacrine manner dictates specific activity under physiological and pathological conditions. Upon juxtacrine interaction between the cells, various types of signaling molecules and organelles are regularly transmitted in response to changes in the microenvironment. To date, it has been well-established that numerous parallel cellular mechanisms participate in the mitochondrial transfer to modulate metabolic needs in the target cells. Since the conception of stem cells activity in the restoration of tissues’ function, it has been elucidated that these cells possess a unique capacity to deliver the mitochondrial package to the juxtaposed cells. The existence of mitochondrial donation potentiates the capacity of modulation in the distinct cells to achieve better therapeutic effects. This review article aims to scrutinize the current knowledge regarding the stem cell’s mitochondrial transfer capacity and their regenerative potential.
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Affiliation(s)
- Hesam Saghaei Bagheri
- School of Medicine, Biophysics Department, Koç University, Rumeli Fener, Sarıyer, Istanbul, Turkey.,Koç University Translational Medicine Research Center (KUTTAM) Rumeli Feneri, Sarıyer, Istanbul, Turkey
| | - Farhad Bani
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Savas Tasoglu
- Koç University Translational Medicine Research Center (KUTTAM) Rumeli Feneri, Sarıyer, Istanbul, Turkey.,Faculty of Engineering, Mechanical Engineering Department, Koç University, Rumeli Feneri Yolu, Sarıyer, Istanbul, Turkey
| | - Amir Zarebkohan
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Rahbarghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Imam Reza St., Daneshgah St., 51666-14756, Tabriz, Iran.
| | - Emel Sokullu
- School of Medicine, Biophysics Department, Koç University, Rumeli Fener, Sarıyer, Istanbul, Turkey. .,Koç University Translational Medicine Research Center (KUTTAM) Rumeli Feneri, Sarıyer, Istanbul, Turkey.
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40
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Baerwald MR, Goodbla AM, Nagarajan RP, Gootenberg JS, Abudayyeh OO, Zhang F, Schreier AD. Rapid and accurate species identification for ecological studies and monitoring using CRISPR-based SHERLOCK. Mol Ecol Resour 2020; 20:961-970. [PMID: 32396992 PMCID: PMC7497203 DOI: 10.1111/1755-0998.13186] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/17/2020] [Accepted: 04/23/2020] [Indexed: 12/26/2022]
Abstract
One of the most fundamental aspects of ecological research and monitoring is accurate species identification, but cryptic speciation and observer error can confound phenotype‐based identification. The CRISPR‐Cas toolkit has facilitated remarkable advances in many scientific disciplines, but the fields of ecology and conservation biology have yet to fully embrace this powerful technology. The recently developed CRISPR‐Cas13a platform SHERLOCK (Specific High‐sensitivity Enzymatic Reporter unLOCKing) enables highly accurate taxonomic identification and has all the characteristics needed to transition to ecological and environmental disciplines. Here we conducted a series of “proof of principle” experiments to characterize SHERLOCK’s ability to accurately, sensitively and rapidly distinguish three fish species of management interest co‐occurring in the San Francisco Estuary that are easily misidentified in the field. We improved SHERLOCK’s ease of field deployment by combining the previously demonstrated rapid isothermal amplification and CRISPR genetic identification with a minimally invasive and extraction‐free DNA collection protocol, as well as the option of instrument‐free lateral flow detection. This approach opens the door for redefining how, where and by whom genetic identifications occur in the future.
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Affiliation(s)
| | - Alisha M Goodbla
- Department of Animal Science, University of California Davis, Davis, CA, USA
| | - Raman P Nagarajan
- Department of Animal Science, University of California Davis, Davis, CA, USA
| | - Jonathan S Gootenberg
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,McGovern Institute for Brain Research, MIT, Cambridge, MA, USA.,Department of Brain and Cognitive Science, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA.,Department of Systems Biology, Harvard University, Boston, MA, USA
| | - Omar O Abudayyeh
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,McGovern Institute for Brain Research, MIT, Cambridge, MA, USA.,Department of Brain and Cognitive Science, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA.,Department of Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Feng Zhang
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,McGovern Institute for Brain Research, MIT, Cambridge, MA, USA.,Department of Brain and Cognitive Science, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Andrea D Schreier
- Department of Animal Science, University of California Davis, Davis, CA, USA
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41
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Mitochondrial Inheritance in Phytopathogenic Fungi-Everything Is Known, or Is It? Int J Mol Sci 2020; 21:ijms21113883. [PMID: 32485941 PMCID: PMC7312866 DOI: 10.3390/ijms21113883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022] Open
Abstract
Mitochondria are important organelles in eukaryotes that provide energy for cellular processes. Their function is highly conserved and depends on the expression of nuclear encoded genes and genes encoded in the organellar genome. Mitochondrial DNA replication is independent of the replication control of nuclear DNA and as such, mitochondria may behave as selfish elements, so they need to be controlled, maintained and reliably inherited to progeny. Phytopathogenic fungi meet with special environmental challenges within the plant host that might depend on and influence mitochondrial functions and services. We find that this topic is basically unexplored in the literature, so this review largely depends on work published in other systems. In trying to answer elemental questions on mitochondrial functioning, we aim to introduce the aspect of mitochondrial functions and services to the study of plant-microbe-interactions and stimulate phytopathologists to consider research on this important organelle in their future projects.
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42
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Abstract
Tracing cell lineages is fundamental for understanding the rules governing development in multicellular organisms and delineating complex biological processes involving the differentiation of multiple cell types with distinct lineage hierarchies. In humans, experimental lineage tracing is unethical, and one has to rely on natural-mutation markers that are created within cells as they proliferate and age. Recent studies have demonstrated that it is now possible to trace lineages in normal, noncancerous cells with a variety of data types using natural variations in the nuclear and mitochondrial DNA as well as variations in DNA methylation status. It is also apparent that the scientific community is on the verge of being able to make a comprehensive and detailed cell lineage map of human embryonic and fetal development. In this review, we discuss the advantages and disadvantages of different approaches and markers for lineage tracing. We also describe the general conceptual design for how to derive a lineage map for humans.
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Affiliation(s)
- Alexej Abyzov
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA;
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, Connecticut 06520, USA;
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43
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Diroma MA, Varvara AS, Attimonelli M, Pesole G, Picardi E. Investigating Human Mitochondrial Genomes in Single Cells. Genes (Basel) 2020; 11:genes11050534. [PMID: 32403285 PMCID: PMC7290567 DOI: 10.3390/genes11050534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/18/2022] Open
Abstract
Mitochondria host multiple copies of their own small circular genome that has been extensively studied to trace the evolution of the modern eukaryotic cell and discover important mutations linked to inherited diseases. Whole genome and exome sequencing have enabled the study of mtDNA in a large number of samples and experimental conditions at single nucleotide resolution, allowing the deciphering of the relationship between inherited mutations and phenotypes and the identification of acquired mtDNA mutations in classical mitochondrial diseases as well as in chronic disorders, ageing and cancer. By applying an ad hoc computational pipeline based on our MToolBox software, we reconstructed mtDNA genomes in single cells using whole genome and exome sequencing data obtained by different amplification methodologies (eWGA, DOP-PCR, MALBAC, MDA) as well as data from single cell Assay for Transposase Accessible Chromatin with high-throughput sequencing (scATAC-seq) in which mtDNA sequences are expected as a byproduct of the technology. We show that assembled mtDNAs, with the exception of those reconstructed by MALBAC and DOP-PCR methods, are quite uniform and suitable for genomic investigations, enabling the study of various biological processes related to cellular heterogeneity such as tumor evolution, neural somatic mosaicism and embryonic development.
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Affiliation(s)
- Maria Angela Diroma
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola 118, 70126 Bari, Italy; (M.A.D.); (G.P.)
| | - Angelo Sante Varvara
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70125 Bari, Italy; (A.S.V.); (M.A.)
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70125 Bari, Italy; (A.S.V.); (M.A.)
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola 118, 70126 Bari, Italy; (M.A.D.); (G.P.)
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70125 Bari, Italy; (A.S.V.); (M.A.)
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola 118, 70126 Bari, Italy; (M.A.D.); (G.P.)
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70125 Bari, Italy; (A.S.V.); (M.A.)
- Correspondence: ; Tel.: +39-0805442179
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44
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Guo X, Zhang X, Qin Y, Liu YX, Zhang J, Zhang N, Wu K, Qu B, He Z, Wang X, Zhang X, Hacquard S, Fu X, Bai Y. Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome. PLANT COMMUNICATIONS 2020; 1:100003. [PMID: 33404537 PMCID: PMC7747982 DOI: 10.1016/j.xplc.2019.100003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/09/2019] [Accepted: 07/29/2019] [Indexed: 05/08/2023]
Abstract
Plant-associated microbes are critical for plant growth and survival under natural environmental conditions. To date, most plant microbiome studies involving high-throughput amplicon sequencing have focused on the relative abundance of microbial taxa. However, this technique does not assess the total microbial load and the abundance of individual microbes relative to the amount of host plant tissues. Here, we report the development of a host-associated quantitative abundance profiling (HA-QAP) method that can accurately examine total microbial load and colonization of individual root microbiome members relative to host plants by the copy-number ratio of microbial marker gene to plant genome. We validate the HA-QAP method using mock experiments, perturbation experiments, and metagenomic sequencing. The HA-QAP method eliminates the generation of spurious outputs in the classical method based on microbial relative abundance, and reveals the load of root microbiome to host plants. Using the HA-QAP method, we found that the copy-number ratios of microbial marker genes to plant genome range from 1.07 to 6.61 for bacterial 16S rRNA genes and from 0.40 to 2.26 for fungal internal transcribed spacers in the root microbiome samples from healthy rice and wheat. Furthermore, using HA-QAP we found that an increase in total microbial load represents a key feature of changes in root microbiome of rice plants exposed to drought stress and of wheat plants with root rot disease, which significantly influences patterns of differential taxa and species interaction networks. Given its accuracy and technical feasibility, HA-QAP would facilitate our understanding of genuine interactions between root microbiome and plants.
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Affiliation(s)
- Xiaoxuan Guo
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Xiaoning Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yuan Qin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yong-Xin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Na Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Kun Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoyuan Qu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Zishan He
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xin Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Xinjian Zhang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Stéphane Hacquard
- Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Corresponding author
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
- Corresponding author
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45
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Pucker B, Rückert C, Stracke R, Viehöver P, Kalinowski J, Weisshaar B. Twenty-Five Years of Propagation in Suspension Cell Culture Results in Substantial Alterations of the Arabidopsis Thaliana Genome. Genes (Basel) 2019; 10:E671. [PMID: 31480756 PMCID: PMC6770967 DOI: 10.3390/genes10090671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/23/2019] [Accepted: 08/29/2019] [Indexed: 01/16/2023] Open
Abstract
Arabidopsis thaliana is one of the best studied plant model organisms. Besides cultivation in greenhouses, cells of this plant can also be propagated in suspension cell culture. At7 is one such cell line that was established about 25 years ago. Here, we report the sequencing and the analysis of the At7 genome. Large scale duplications and deletions compared to the Columbia-0 (Col-0) reference sequence were detected. The number of deletions exceeds the number of insertions, thus indicating that a haploid genome size reduction is ongoing. Patterns of small sequence variants differ from the ones observed between A. thaliana accessions, e.g., the number of single nucleotide variants matches the number of insertions/deletions. RNA-Seq analysis reveals that disrupted alleles are less frequent in the transcriptome than the native ones.
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Affiliation(s)
- Boas Pucker
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany.
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
| | - Ralf Stracke
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
| | - Prisca Viehöver
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
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46
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Knudsen C, Gallage NJ, Hansen CC, Møller BL, Laursen T. Dynamic metabolic solutions to the sessile life style of plants. Nat Prod Rep 2019; 35:1140-1155. [PMID: 30324199 PMCID: PMC6254060 DOI: 10.1039/c8np00037a] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plants are sessile organisms. To compensate for not being able to escape when challenged by unfavorable growth conditions, pests or herbivores, plants have perfected their metabolic plasticity by having developed the capacity for on demand dynamic biosynthesis and storage of a plethora of phytochemicals.
Covering: up to 2018 Plants are sessile organisms. To compensate for not being able to escape when challenged by unfavorable growth conditions, pests or herbivores, plants have perfected their metabolic plasticity by having developed the capacity for on demand synthesis of a plethora of phytochemicals to specifically respond to the challenges arising during plant ontogeny. Key steps in the biosynthesis of phytochemicals are catalyzed by membrane-bound cytochrome P450 enzymes which in plants constitute a superfamily. In planta, the P450s may be organized in dynamic enzyme clusters (metabolons) and the genes encoding the P450s and other enzymes in a specific pathway may be clustered. Metabolon formation facilitates transfer of substrates between sequential enzymes and therefore enables the plant to channel the flux of general metabolites towards biosynthesis of specific phytochemicals. In the plant cell, compartmentalization of the operation of specific biosynthetic pathways in specialized plastids serves to avoid undesired metabolic cross-talk and offers distinct storage sites for molar concentrations of specific phytochemicals. Liquid–liquid phase separation may lead to formation of dense biomolecular condensates within the cytoplasm or vacuole allowing swift activation of the stored phytochemicals as required upon pest or herbivore attack. The molecular grid behind plant plasticity offers an endless reservoir of functional modules, which may be utilized as a synthetic biology tool-box for engineering of novel biological systems based on rational design principles. In this review, we highlight some of the concepts used by plants to coordinate biosynthesis and storage of phytochemicals.
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Affiliation(s)
- Camilla Knudsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.
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47
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Braukmann TWA, Ivanova NV, Prosser SWJ, Elbrecht V, Steinke D, Ratnasingham S, de Waard JR, Sones JE, Zakharov EV, Hebert PDN. Metabarcoding a diverse arthropod mock community. Mol Ecol Resour 2019; 19:711-727. [PMID: 30779309 PMCID: PMC6850013 DOI: 10.1111/1755-0998.13008] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/13/2019] [Indexed: 12/31/2022]
Abstract
Although DNA metabarcoding is an attractive approach for monitoring biodiversity, it is often difficult to detect all the species present in a bulk sample. In particular, sequence recovery for a given species depends on its biomass and mitome copy number as well as the primer set employed for PCR. To examine these variables, we constructed a mock community of terrestrial arthropods comprised of 374 species. We used this community to examine how species recovery was impacted when amplicon pools were constructed in four ways. The first two protocols involved the construction of bulk DNA extracts from different body segments (Bulk Abdomen, Bulk Leg). The other protocols involved the production of DNA extracts from single legs which were then merged prior to PCR (Composite Leg) or PCR‐amplified separately (Single Leg) and then pooled. The amplicons generated by these four treatments were then sequenced on three platforms (Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5). The choice of sequencing platform did not substantially influence species recovery, although the Miseq delivered the highest sequence quality. As expected, species recovery was most efficient from the Single Leg treatment because amplicon abundance varied little among taxa. Among the three treatments where PCR occurred after pooling, the Bulk Abdomen treatment produced a more uniform read abundance than the Bulk Leg or Composite Leg treatment. Primer choice also influenced species recovery and evenness. Our results reveal how variation in protocols can have substantial impacts on perceived diversity unless sequencing coverage is sufficient to reach an asymptote.
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Affiliation(s)
| | - Natalia V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Vasco Elbrecht
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | | | - Jeremy R de Waard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.,School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Jayme E Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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48
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Serrage HJ, Joanisse S, Cooper PR, Palin W, Hadis M, Darch O, Philp A, Milward MR. Differential responses of myoblasts and myotubes to photobiomodulation are associated with mitochondrial number. JOURNAL OF BIOPHOTONICS 2019; 12:e201800411. [PMID: 30701682 PMCID: PMC7065641 DOI: 10.1002/jbio.201800411] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/22/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
OBJECTIVE Photobiomodulation (PBM) is the application of light to promote tissue healing. Current indications suggest PBM induces its beneficial effects in vivo through upregulation of mitochondrial activity. However, how mitochondrial content influences such PBM responses have yet to be evaluated. Hence, the current study assessed the biological response of cells to PBM with varying mitochondrial contents. METHODS DNA was isolated from myoblasts and myotubes (differentiated myoblasts), and mitochondrial DNA (mtDNA) was amplified and quantified using a microplate assay. Cells were seeded in 96-wellplates, incubated overnight and subsequently irradiated using a light-emitting diode array (400, 450, 525, 660, 740, 810, 830 and white light, 24 mW/cm2 , 30-240 seconds, 0.72-5.76J/cm2 ). The effects of PBM on markers of mitochondrial activity including reactive-oxygen-species and real-time mitochondrial respiration (Seahorse XFe96) assays were assessed 8 hours post-irradiation. Datasets were analysed using general linear model followed by one-way analysis of variance (and post hoc-Tukey tests); P = 0.05). RESULTS Myotubes exhibited mtDNA levels 86% greater than myoblasts (P < 0.001). Irradiation of myotubes at 400, 450 or 810 nm induced 53%, 29% and 47% increases (relative to non-irradiated control) in maximal respiratory rates, respectively (P < 0.001). Conversely, irradiation of myoblasts at 400 or 450 nm had no significant effect on maximal respiratory rates. CONCLUSION This study suggests that mitochondrial content may influence cellular responses to PBM and as such explain the variability of PBM responses seen in the literature.
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Affiliation(s)
- Hannah J. Serrage
- School of DentistryCollege of Medical and Dental Sciences, Institute of Clinical Sciences, University of BirminghamBirminghamUK
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
- Philips ResearchEindhovenThe Netherlands
| | - Sophie Joanisse
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
| | - Paul R. Cooper
- School of DentistryCollege of Medical and Dental Sciences, Institute of Clinical Sciences, University of BirminghamBirminghamUK
| | - William Palin
- School of DentistryCollege of Medical and Dental Sciences, Institute of Clinical Sciences, University of BirminghamBirminghamUK
| | - Mohammed Hadis
- School of DentistryCollege of Medical and Dental Sciences, Institute of Clinical Sciences, University of BirminghamBirminghamUK
| | - Owen Darch
- Philips ResearchEindhovenThe Netherlands
| | - Andrew Philp
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
- Garvan Institute of Medical ResearchDarlinghurstNew South WalesAustralia
| | - Mike R. Milward
- School of DentistryCollege of Medical and Dental Sciences, Institute of Clinical Sciences, University of BirminghamBirminghamUK
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49
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Weinhardt V, Chen JH, Ekman A, McDermott G, Le Gros MA, Larabell C. Imaging cell morphology and physiology using X-rays. Biochem Soc Trans 2019; 47:489-508. [PMID: 30952801 PMCID: PMC6716605 DOI: 10.1042/bst20180036] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/02/2019] [Accepted: 01/09/2019] [Indexed: 02/07/2023]
Abstract
Morphometric measurements, such as quantifying cell shape, characterizing sub-cellular organization, and probing cell-cell interactions, are fundamental in cell biology and clinical medicine. Until quite recently, the main source of morphometric data on cells has been light- and electron-based microscope images. However, many technological advances have propelled X-ray microscopy into becoming another source of high-quality morphometric information. Here, we review the status of X-ray microscopy as a quantitative biological imaging modality. We also describe the combination of X-ray microscopy data with information from other modalities to generate polychromatic views of biological systems. For example, the amalgamation of molecular localization data, from fluorescence microscopy or spectromicroscopy, with structural information from X-ray tomography. This combination of data from the same specimen generates a more complete picture of the system than that can be obtained by a single microscopy method. Such multimodal combinations greatly enhance our understanding of biology by combining physiological and morphological data to create models that more accurately reflect the complexities of life.
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Affiliation(s)
- Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Anatomy, University of California San Francisco, San Francisco, California, U.S.A
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Axel Ekman
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Gerry McDermott
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Mark A Le Gros
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Anatomy, University of California San Francisco, San Francisco, California, U.S.A
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.
- Department of Anatomy, University of California San Francisco, San Francisco, California, U.S.A
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50
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Rahman MH, Xiao Q, Zhao S, Qu F, Chang C, Wei AC, Ho YP. Demarcating the membrane damage for the extraction of functional mitochondria. MICROSYSTEMS & NANOENGINEERING 2018; 4:39. [PMID: 31057927 PMCID: PMC6311452 DOI: 10.1038/s41378-018-0037-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/11/2018] [Accepted: 10/19/2018] [Indexed: 05/02/2023]
Abstract
Defective mitochondria have been linked to several critical human diseases such as neurodegenerative disorders, cancers and cardiovascular disease. However, the detailed characterization of mitochondria has remained relatively unexplored, largely due to the lack of effective extraction methods that may sufficiently retain the functionality of mitochondria, particularly when limited amount of sample is considered. In this study, we explore the possibility of modulating hydrodynamic stress through a cross-junction geometry at microscale to selectively disrupt the cellular membrane while mitochondrial membrane is secured. The operational conditions are empirically optimized to effectively shred the cell membranes while keeping mitochondria intact for the model mammalian cell lines, namely human embryonic kidney cells, mouse muscle cells and neuroblastoma cells. Unsurprisingly, the disruption of cell membranes with higher elastic moduli (neuroblastoma) requires elevated stress. This study also presents a comparative analysis of total protein yield and concentrations of extracted functional mitochondria with two commercially available mitochondria extraction approaches, the Dounce Homogenizer and the Qproteome® Mitochondria Isolation Kit, in a range of cell concentrations. Our findings show that the proposed "microscale cell shredder" yields at least 40% more functional mitochondria than the two other approaches and is able to preserve the morphological integrity of extracted mitochondria, particularly at low cell concentrations (5-20 × 104 cells/mL). Characterized by its capability of rapidly processing a limited quantity of samples (200 μL), demarcating the membrane damage through the proposed microscale cell shredder represents a novel strategy to extract subcellular organelles from clinical samples.
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Affiliation(s)
- Md Habibur Rahman
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Qinru Xiao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Shirui Zhao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Fuyang Qu
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Chen Chang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University,
| | - An-Chi Wei
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University,
| | - Yi-Ping Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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