1
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Grinde B. Consciousness makes sense in the light of evolution. Neurosci Biobehav Rev 2024:105824. [PMID: 39047928 DOI: 10.1016/j.neubiorev.2024.105824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/18/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
I believe consciousness is a property of advanced nervous systems, and as such a product of evolution. Thus, to understand consciousness we need to describe the trajectory leading to its evolution and the selective advantages conferred. A deeper understanding of the neurology would be a significant contribution, but other advanced functions, such as hearing and vision, are explained with a comparable lack of detailed knowledge of the brain processes responsible. In this paper, I try to add details and credence to a previously suggested, evolution-based model of consciousness. According to this model, the feature started to evolve in early amniotes (reptiles, birds, and mammals) some 320 million years ago. The reason was the introduction of feelings as a strategy for making behavioral decisions.
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Affiliation(s)
- Bjørn Grinde
- Professor Emeritus, University of Oslo, Problemveien 11, 0313 Oslo, Norway.
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2
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Hu C, Zhu XT, He MH, Shao Y, Qin Z, Wu ZJ, Zhou JQ. Elimination of subtelomeric repeat sequences exerts little effect on telomere essential functions in Saccharomyces cerevisiae. eLife 2024; 12:RP91223. [PMID: 38656297 DOI: 10.7554/elife.91223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
Telomeres, which are chromosomal end structures, play a crucial role in maintaining genome stability and integrity in eukaryotes. In the baker's yeast Saccharomyces cerevisiae, the X- and Y'-elements are subtelomeric repetitive sequences found in all 32 and 17 telomeres, respectively. While the Y'-elements serve as a backup for telomere functions in cells lacking telomerase, the function of the X-elements remains unclear. This study utilized the S. cerevisiae strain SY12, which has three chromosomes and six telomeres, to investigate the role of X-elements (as well as Y'-elements) in telomere maintenance. Deletion of Y'-elements (SY12YΔ), X-elements (SY12XYΔ+Y), or both X- and Y'-elements (SY12XYΔ) did not impact the length of the terminal TG1-3 tracks or telomere silencing. However, inactivation of telomerase in SY12YΔ, SY12XYΔ+Y, and SY12XYΔ cells resulted in cellular senescence and the generation of survivors. These survivors either maintained their telomeres through homologous recombination-dependent TG1-3 track elongation or underwent microhomology-mediated intra-chromosomal end-to-end joining. Our findings indicate the non-essential role of subtelomeric X- and Y'-elements in telomere regulation in both telomerase-proficient and telomerase-null cells and suggest that these elements may represent remnants of S. cerevisiae genome evolution. Furthermore, strains with fewer or no subtelomeric elements exhibit more concise telomere structures and offer potential models for future studies in telomere biology.
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Affiliation(s)
- Can Hu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Xue-Ting Zhu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Ming-Hong He
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Yangyang Shao
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Zhongjun Qin
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Zhi-Jing Wu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Jin-Qiu Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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3
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Mpamhanga CD, Kounatidis I. The utility of Drosophila melanogaster as a fungal infection model. Front Immunol 2024; 15:1349027. [PMID: 38550600 PMCID: PMC10973011 DOI: 10.3389/fimmu.2024.1349027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/27/2024] [Indexed: 04/02/2024] Open
Abstract
Invasive fungal diseases have profound effects upon human health and are on increase globally. The World Health Organization (WHO) in 2022 published the fungal priority list calling for improved public health interventions and advance research. Drosophila melanogaster presents an excellent model system to dissect host-pathogen interactions and has been proved valuable to study immunopathogenesis of fungal diseases. In this review we highlight the recent advances in fungal-Drosophila interplay with an emphasis on the recently published WHO's fungal priority list and we focus on available tools and technologies.
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Affiliation(s)
- Chengetai D Mpamhanga
- School of Life Health and Chemical Sciences, The Open University, Milton Keynes, United Kingdom
| | - Ilias Kounatidis
- School of Life Health and Chemical Sciences, The Open University, Milton Keynes, United Kingdom
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4
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Saha S, Chatterjee P, Basu S, Nasipuri M. EPI-SF: essential protein identification in protein interaction networks using sequence features. PeerJ 2024; 12:e17010. [PMID: 38495766 PMCID: PMC10944162 DOI: 10.7717/peerj.17010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/05/2024] [Indexed: 03/19/2024] Open
Abstract
Proteins are considered indispensable for facilitating an organism's viability, reproductive capabilities, and other fundamental physiological functions. Conventional biological assays are characterized by prolonged duration, extensive labor requirements, and financial expenses in order to identify essential proteins. Therefore, it is widely accepted that employing computational methods is the most expeditious and effective approach to successfully discerning essential proteins. Despite being a popular choice in machine learning (ML) applications, the deep learning (DL) method is not suggested for this specific research work based on sequence features due to the restricted availability of high-quality training sets of positive and negative samples. However, some DL works on limited availability of data are also executed at recent times which will be our future scope of work. Conventional ML techniques are thus utilized in this work due to their superior performance compared to DL methodologies. In consideration of the aforementioned, a technique called EPI-SF is proposed here, which employs ML to identify essential proteins within the protein-protein interaction network (PPIN). The protein sequence is the primary determinant of protein structure and function. So, initially, relevant protein sequence features are extracted from the proteins within the PPIN. These features are subsequently utilized as input for various machine learning models, including XGB Boost Classifier, AdaBoost Classifier, logistic regression (LR), support vector classification (SVM), Decision Tree model (DT), Random Forest model (RF), and Naïve Bayes model (NB). The objective is to detect the essential proteins within the PPIN. The primary investigation conducted on yeast examined the performance of various ML models for yeast PPIN. Among these models, the RF model technique had the highest level of effectiveness, as indicated by its precision, recall, F1-score, and AUC values of 0.703, 0.720, 0.711, and 0.745, respectively. It is also found to be better in performance when compared to the other state-of-arts based on traditional centrality like betweenness centrality (BC), closeness centrality (CC), etc. and deep learning methods as well like DeepEP, as emphasized in the result section. As a result of its favorable performance, EPI-SF is later employed for the prediction of novel essential proteins inside the human PPIN. Due to the tendency of viruses to selectively target essential proteins involved in the transmission of diseases within human PPIN, investigations are conducted to assess the probable involvement of these proteins in COVID-19 and other related severe diseases.
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Affiliation(s)
- Sovan Saha
- Department of Computer Science & Engineering (Artificial Intelligence & Machine Learning), Techno Main Salt Lake, Kolkata, West Bengal, India
| | - Piyali Chatterjee
- Department of Computer Science & Engineering, Netaji Subhash Engineering College, Kolkata, West Bengal, India
| | - Subhadip Basu
- Department of Computer Science & Engineering, Jadavpur University, Kolkata, West Bengal, India
| | - Mita Nasipuri
- Department of Computer Science & Engineering, Jadavpur University, Kolkata, West Bengal, India
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5
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Harshan P, Sukumaran S, Gopalakrishnan A. De novo transcriptome for Chiloscyllium griseum, a long-tail carpet shark of the Indian waters. Sci Data 2024; 11:285. [PMID: 38461175 PMCID: PMC10924892 DOI: 10.1038/s41597-024-03093-7] [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: 09/25/2023] [Accepted: 02/27/2024] [Indexed: 03/11/2024] Open
Abstract
Sharks have thrived in the oceans for 400 million years, experienced five extinctions and evolved into today's apex predators. However, enormous genome size, poor karyotyping and limited tissue sampling options are the bottlenecks in shark research. Sharks of the family Orectolobiformes act as model species in transcriptome research with exceptionally high reproductive fecundity, catch prominence and oviparity. The present study illustrates a de novo transcriptome for an adult grey bamboo shark, Chiloscyllium griseum (Chondrichthyes; Hemiscyllidae) using paired-end RNA sequencing. Around 150 million short Illumina reads were obtained from five different tissues and assembled using the Trinity assembler. 70,647 hits on Uniprot by BLASTX was obtained after the transcriptome annotation. The data generated serve as a basis for transcriptome-based population genetic studies and open up new avenues in the field of comparative transcriptomics and conservation biology.
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Affiliation(s)
- Pooja Harshan
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India.
- Cochin University of Science and Technology, South Kalamassery, Ernakulam, Kerala, 682022, India.
| | - Sandhya Sukumaran
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
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6
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Rees J, Sarangi G, Cheng Q, Floor M, Andrés AM, Oliva Miguel B, Villà-Freixa J, Arnér ESJ, Castellano S. Ancient Loss of Catalytic Selenocysteine Spurred Convergent Adaptation in a Mammalian Oxidoreductase. Genome Biol Evol 2024; 16:evae041. [PMID: 38447079 PMCID: PMC10958145 DOI: 10.1093/gbe/evae041] [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: 08/03/2023] [Revised: 02/14/2024] [Accepted: 02/22/2024] [Indexed: 03/08/2024] Open
Abstract
Selenocysteine, the 21st amino acid specified by the genetic code, is a rare selenium-containing residue found in the catalytic site of selenoprotein oxidoreductases. Selenocysteine is analogous to the common cysteine amino acid, but its selenium atom offers physical-chemical properties not provided by the corresponding sulfur atom in cysteine. Catalytic sites with selenocysteine in selenoproteins of vertebrates are under strong purifying selection, but one enzyme, glutathione peroxidase 6 (GPX6), independently exchanged selenocysteine for cysteine <100 million years ago in several mammalian lineages. We reconstructed and assayed these ancient enzymes before and after selenocysteine was lost and up to today and found them to have lost their classic ability to reduce hydroperoxides using glutathione. This loss of function, however, was accompanied by additional amino acid changes in the catalytic domain, with protein sites concertedly changing under positive selection across distant lineages abandoning selenocysteine in glutathione peroxidase 6. This demonstrates a narrow evolutionary range in maintaining fitness when sulfur in cysteine impairs the catalytic activity of this protein, with pleiotropy and epistasis likely driving the observed convergent evolution. We propose that the mutations shared across distinct lineages may trigger enzymatic properties beyond those in classic glutathione peroxidases, rather than simply recovering catalytic rate. These findings are an unusual example of adaptive convergence across mammalian selenoproteins, with the evolutionary signatures possibly representing the evolution of novel oxidoreductase functions.
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Affiliation(s)
- Jasmin Rees
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Division of Biosciences, University College London, London, UK
| | - Gaurab Sarangi
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Qing Cheng
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Martin Floor
- Department of Biosciences, Faculty of Sciences and Technology, Universitat de Vic—Universitat Central de Catalunya, Vic, Spain
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Aida M Andrés
- Division of Biosciences, University College London, London, UK
| | - Baldomero Oliva Miguel
- Department of Health and Experimental Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jordi Villà-Freixa
- Department of Biosciences, Faculty of Sciences and Technology, Universitat de Vic—Universitat Central de Catalunya, Vic, Spain
- Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central (IRIS-CC), Vic, Spain
| | - Elias S J Arnér
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Selenoprotein Research, National Institute of Oncology, Budapest, Hungary
| | - Sergi Castellano
- Great Ormond Street Institute of Child Health, University College London, London, UK
- UCL Genomics, University College London, London, UK
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7
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Wagener L, Nieder A. Conscious Experience of Stimulus Presence and Absence Is Actively Encoded by Neurons in the Crow Brain. J Cogn Neurosci 2024; 36:508-521. [PMID: 38165732 DOI: 10.1162/jocn_a_02101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
The emergence of consciousness from brain activity constitutes one of the great riddles in biology. It is commonly assumed that only the conscious perception of the presence of a stimulus elicits neuronal activation to signify a "neural correlate of consciousness," whereas the subjective experience of the absence of a stimulus is associated with a neuronal resting state. Here, we demonstrate that the two subjective states "stimulus present" and "stimulus absent" are represented by two specialized neuron populations in crows, corvid birds. We recorded single-neuron activity from the nidopallium caudolaterale of crows trained to report the presence or absence of images presented near the visual threshold. Because of the task design, neuronal activity tracking the conscious "present" versus "absent" percept was dissociated from that involved in planning a motor response. Distinct neuron populations signaled the subjective percepts of "present" and "absent" by increases in activation. The response selectivity of these two neuron populations was similar in strength and time course. This suggests a balanced code for subjective "presence" versus "absence" experiences, which might be beneficial when both conscious states need to be maintained active in the service of goal-directed behavior.
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8
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Hebra T, Smrčková H, Elkatmis B, Převorovský M, Pluskal T. POMBOX: A Fission Yeast Cloning Toolkit for Molecular and Synthetic Biology. ACS Synth Biol 2024; 13:558-567. [PMID: 37991801 PMCID: PMC10877588 DOI: 10.1021/acssynbio.3c00529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
The fission yeast Schizosaccharomyces pombe is a popular model organism in molecular biology and cell physiology. With its ease of genetic manipulation and growth, supported by in-depth functional annotations in the PomBase database and genome-wide metabolic models,S. pombe is an attractive option for synthetic biology applications. However,S. pombe currently lacks modular tools for generating genetic circuits with more than 1 transcriptional unit. We developed a toolkit to address this gap. Adapted from the MoClo-YTK plasmid kit for Saccharomyces cerevisiae and using the same modular cloning grammar, our POMBOX toolkit is designed to facilitate fast, efficient, and modular construction of genetic circuits inS. pombe. It allows for interoperability when working with DNA sequences that are functional in bothS. cerevisiae and S. pombe (e.g., protein tags, antibiotic resistance cassettes, and coding sequences). Moreover, POMBOX enables the modular assembly of multigene pathways and increases the possible pathway length from 6 to 12 transcriptional units. We also adapted the stable integration vector homology arms to Golden Gate assembly and tested the genomic integration success rates depending on different sequence sizes, from 4 to 24 kb. We included 14 S. pombe promoters that we characterized using two fluorescent proteins, in both minimally defined (EMM2─Edinburgh minimal media) and complex (YES─yeast extract with supplements) media. Then, we examined the efficacy of 6 S. cerevisiae and 6 synthetic terminators in S. pombe. Finally, we used the POMBOX kit for a synthetic biology application in metabolic engineering and expressed plant enzymes in S. pombe to produce specialized metabolite precursors, namely, methylxanthine, amorpha-4,11-diene, and cinnamic acid from the purine, mevalonate, and aromatic amino acid pathways.
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Affiliation(s)
- Téo Hebra
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Helena Smrčková
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Büsra Elkatmis
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Martin Převorovský
- Department
of Cell Biology, Faculty of Science, Charles
University, 128 00 Prague, Czech
Republic
| | - Tomáš Pluskal
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
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9
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Alves-Pimenta S, Colaço B, Oliveira PA, Venâncio C. Development Features on the Selection of Animal Models for Teratogenic Testing. Methods Mol Biol 2024; 2753:67-104. [PMID: 38285334 DOI: 10.1007/978-1-0716-3625-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Today, the use of animal models from different species continues to represent a fundamental step in teratogenic testing, despite the increase in alternative solutions that provide an important screening to the enormous quantity of new substances that aim to enter the market every year. The maintenance of these models is due to the sharing of similar development processes with humans, and in this way they represent an important contribution to the safety in the use of the compounds tested. Furthermore, the application of advances in embryology to teratology, although hampered by the complexity of reproductive processes, continues to prove the importance of sensitivity during embryonic and fetal development to detect potential toxicity, inducing mortality/abortion and malformations.In this chapter, essential periods of development in different models are outlined, highlighting the similarities and differences between species, the advantages and disadvantages of each group, and specific sensitivities for teratogenic testing. Models can be divided into invertebrate species such as earthworms of the species Eisenia fetida/Eisenia andrei, Caenorhabditis elegans, and Drosophila melanogaster, allowing for rapid results and minor ethical concerns. Vertebrate nonmammalian species Xenopus laevis and Danio rerio are important models to assess teratogenic potential later in development with fewer ethical requirements. Finally, the mammalian species Mus musculus, Rattus norvegicus, and Oryctolagus cuniculus, phylogenetically closer to humans, are essential for the assessment of complex specialized processes, occurring later in development.Regulations for the development of toxicology tests require the use of mammalian species. Although ethical concerns and costs limit their use in large-scale screening. On the other hand, invertebrate and vertebrate nonmammalian species are increasing as alternative animal models, as these organisms combine low cost, less ethical requirements, and culture conditions compatible with large-scale screening. Their main advantage is to allow high-throughput screening in a whole-animal context, in contrast to the in vitro techniques, not dependent on the prior identification of a target. Better knowledge of the development pathways of animal models will allow to maximize human translation and reduce the number of animals used, leading to a selection of compounds with an improved safety profile and reduced time to market for new drugs.
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Affiliation(s)
- Sofia Alves-Pimenta
- Department of Animal Science, School of Agrarian and Veterinary Sciences (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Animal and Veterinary Research Centre (CECAV), Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Bruno Colaço
- Department of Animal Science, School of Agrarian and Veterinary Sciences (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Animal and Veterinary Research Centre (CECAV), Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Paula A Oliveira
- Animal and Veterinary Research Centre (CECAV), Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Institute for Innovation, Capacity Building and Sustainability of Agri-food Production (Inov4Agro), University of Trás-os Montes and Alto Douro (UTAD), Vila Real, Portugal
- Department of Veterinary Sciences, School of Agrarian and Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Carlos Venâncio
- Department of Animal Science, School of Agrarian and Veterinary Sciences (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.
- Animal and Veterinary Research Centre (CECAV), Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.
- Institute for Innovation, Capacity Building and Sustainability of Agri-food Production (Inov4Agro), University of Trás-os Montes and Alto Douro (UTAD), Vila Real, Portugal.
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10
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Nieder A. Convergent Circuit Computation for Categorization in the Brains of Primates and Songbirds. Cold Spring Harb Perspect Biol 2023; 15:a041526. [PMID: 38040453 PMCID: PMC10691494 DOI: 10.1101/cshperspect.a041526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2023]
Abstract
Categorization is crucial for behavioral flexibility because it enables animals to group stimuli into meaningful classes that can easily be generalized to new circumstances. A most abstract quantitative category is set size, the number of elements in a set. This review explores how categorical number representations are realized by the operations of excitatory and inhibitory neurons in associative telencephalic microcircuits in primates and songbirds. Despite the independent evolution of the primate prefrontal cortex and the avian nidopallium caudolaterale, the neuronal computations of these associative pallial circuits show surprising correspondence. Comparing cellular functions in distantly related taxa can inform about the evolutionary principles of circuit computations for cognition in distinctly but convergently realized brain structures.
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Affiliation(s)
- Andreas Nieder
- Animal Physiology Unit, Institute of Neurobiology, University of Tübingen, 72076 Tübingen, Germany
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11
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Gu H, Wen J, Zhao X, Zhang X, Ren X, Cheng H, Qu L. Evolution, Inheritance, and Strata Formation of the W Chromosome in Duck (Anas platyrhynchos). Genome Biol Evol 2023; 15:evad183. [PMID: 37931036 PMCID: PMC10630070 DOI: 10.1093/gbe/evad183] [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] [Accepted: 10/03/2023] [Indexed: 11/08/2023] Open
Abstract
The nonrecombining female-limited W chromosome is predicted to experience unique evolutionary processes. Difficulties in assembling W chromosome sequences have hindered the identification of duck W-linked sequences and their evolutionary footprint. To address this, we conducted three initial contig-level genome assemblies and developed a rigorous pipeline by which to successfully expand the W-linked data set, including 11 known genes and 24 newly identified genes. Our results indicate that the W chromosome expression may not be subject to female-specific selection; a significant convergent pattern of upregulation associated with increased female-specific selection was not detected. The genetic stability of the W chromosome is also reflected in the strong evolutionary correlation between it and the mitochondria; the complete consistency of the cladogram topology constructed from their gene sequences proves the shared maternal coevolution. By detecting the evolutionary trajectories of W-linked sequences, we have found that recombination suppression started in four distinct strata, of which three were conserved across Neognathae. Taken together, our results have revealed a unique evolutionary pattern and an independent stratum evolutionary pattern for sex chromosomes.
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Affiliation(s)
- Hongchang Gu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Junhui Wen
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiurong Zhao
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xinye Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xufang Ren
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huan Cheng
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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12
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Mammola S, Adamo M, Antić D, Calevo J, Cancellario T, Cardoso P, Chamberlain D, Chialva M, Durucan F, Fontaneto D, Goncalves D, Martínez A, Santini L, Rubio-Lopez I, Sousa R, Villegas-Rios D, Verdes A, Correia RA. Drivers of species knowledge across the tree of life. eLife 2023; 12:RP88251. [PMID: 37846960 PMCID: PMC10581686 DOI: 10.7554/elife.88251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023] Open
Abstract
Knowledge of biodiversity is unevenly distributed across the Tree of Life. In the long run, such disparity in awareness unbalances our understanding of life on Earth, influencing policy decisions and the allocation of research and conservation funding. We investigated how humans accumulate knowledge of biodiversity by searching for consistent relationships between scientific (number of publications) and societal (number of views in Wikipedia) interest, and species-level morphological, ecological, and sociocultural factors. Across a random selection of 3019 species spanning 29 Phyla/Divisions, we show that sociocultural factors are the most important correlates of scientific and societal interest in biodiversity, including the fact that a species is useful or harmful to humans, has a common name, and is listed in the International Union for Conservation of Nature Red List. Furthermore, large-bodied, broadly distributed, and taxonomically unique species receive more scientific and societal attention, whereas colorfulness and phylogenetic proximity to humans correlate exclusively with societal attention. These results highlight a favoritism toward limited branches of the Tree of Life, and that scientific and societal priorities in biodiversity research broadly align. This suggests that we may be missing out on key species in our research and conservation agenda simply because they are not on our cultural radar.
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Affiliation(s)
- Stefano Mammola
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of HelsinkiHelsinkiFinland
- National Biodiversity Future CenterPalermoItaly
| | - Martino Adamo
- National Biodiversity Future CenterPalermoItaly
- Department of Life Sciences and Systems Biology, University of TurinTorinoItaly
| | - Dragan Antić
- University of Belgrade - Faculty of BiologyBelgradeSerbia
| | - Jacopo Calevo
- Royal Botanic GardensLondonUnited Kingdom
- School of Molecular and Life Sciences, Curtin UniversityPerthAustralia
| | - Tommaso Cancellario
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of HelsinkiHelsinkiFinland
| | - Dan Chamberlain
- Department of Life Sciences and Systems Biology, University of TurinTorinoItaly
| | - Matteo Chialva
- National Biodiversity Future CenterPalermoItaly
- Department of Life Sciences and Systems Biology, University of TurinTorinoItaly
| | - Furkan Durucan
- Department of Aquaculture, Isparta University of Applied SciencesIspartaTurkey
| | - Diego Fontaneto
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
- National Biodiversity Future CenterPalermoItaly
| | - Duarte Goncalves
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of PortoMatosinhosPortugal
| | - Alejandro Martínez
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
| | - Luca Santini
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Iñigo Rubio-Lopez
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
| | - Ronaldo Sousa
- CBMA – Centre of Molecular and Environmental Biology, Department of Biology, University of MinhoMinhoPortugal
| | | | - Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias NaturalesMadridSpain
| | - Ricardo A Correia
- Helsinki Lab of Interdisciplinary Conservation Science (HELICS), Department of Geosciences and Geography, University of HelsinkiHelsinkiFinland
- Helsinki Institute of Sustainability Science (HELSUS), University of HelsinkiHelsinkiFinland
- CESAM – Centre for Environmental and Marine Studies, University of AveiroAveiroPortugal
- Biodiversity Unit, University of TurkuTurkuFinland
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13
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Sarkar P, Misra S, Ghosal A, Mukherjee S, Ghosh A, Sundaram G. Glucose to lactate shift reprograms CDK-dependent mitotic decisions and its communication with MAPK Sty1 in Schizosaccharomyces pombe. Biol Open 2023; 12:bio060145. [PMID: 37787465 PMCID: PMC10618596 DOI: 10.1242/bio.060145] [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: 09/08/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023] Open
Abstract
Cell cycle regulation in response to biochemical cues is a fundamental event associated with many diseases. The regulation of such responses in complex metabolic environments is poorly understood. This study reveals unknown aspects of the metabolic regulation of cell division in Schizosaccharomyces pombe. We show that changing the carbon source from glucose to lactic acid alters the functions of the cyclin-dependent kinase (CDK) Cdc2 and mitogen-activated protein kinase (MAPK) Sty1, leading to unanticipated outcomes in the behavior and fate of such cells. Functional communication of Cdc2 with Sty1 is known to be an integral part of the cellular response to aberrant Cdc2 activity in S. pombe. Our results show that cross-talk between Cdc2 and Sty1, and the consequent Sty1-dependent regulation of Cdc2 activity, appears to be compromised and the relationship between Cdc2 activity and mitotic timing is also reversed in the presence of lactate. We also show that the biochemical status of cells under these conditions is an important determinant of the altered molecular functions mentioned above as well as the altered behavior of these cells.
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Affiliation(s)
- Priyanka Sarkar
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India
| | - Susmita Misra
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India
| | - Agamani Ghosal
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India
| | | | - Alok Ghosh
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India
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14
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McCarthy M, Dodd WB, Lu X, Pritko DJ, Patel ND, Haskell CV, Sanabria H, Blenner MA, Birtwistle MR. Theory for High-Throughput Genetic Interaction Screening. ACS Synth Biol 2023; 12:2290-2300. [PMID: 37463472 PMCID: PMC10443530 DOI: 10.1021/acssynbio.2c00627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Indexed: 07/20/2023]
Abstract
Systematic, genome-scale genetic screens have been instrumental for elucidating genotype-phenotype relationships, but approaches for probing genetic interactions have been limited to at most ∼100 pre-selected gene combinations in mammalian cells. Here, we introduce a theory for high-throughput genetic interaction screens. The theory extends our recently developed Multiplexing using Spectral Imaging and Combinatorics (MuSIC) approach to propose ∼105 spectrally unique, genetically encoded MuSIC barcodes from 18 currently available fluorescent proteins. Simulation studies based on constraints imposed by spectral flow cytometry equipment suggest that genetic interaction screens at the human genome-scale may be possible if MuSIC barcodes can be paired to guide RNAs. While experimental testing of this theory awaits, it offers transformative potential for genetic perturbation technology and knowledge of genetic function. More broadly, the availability of a genome-scale spectral barcode library for non-destructive identification of single cells could find more widespread applications such as traditional genetic screening and high-dimensional lineage tracing.
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Affiliation(s)
- Madeline
E. McCarthy
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - William B. Dodd
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Xiaoming Lu
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Daniel J. Pritko
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Nishi D. Patel
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Charlotte V. Haskell
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Hugo Sanabria
- Department
of Physics and Astronomy, Clemson University, Clemson, South Carolina 29631, United States
| | - Mark A. Blenner
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Marc R. Birtwistle
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
- Department
of Bioengineering, Clemson University, Clemson, South Carolina 29631, United States
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15
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Yin Z, Shen D, Zhao Y, Peng H, Liu J, Dou D. Cross-kingdom analyses of transmembrane protein kinases show their functional diversity and distinct origins in protists. Comput Struct Biotechnol J 2023; 21:4070-4078. [PMID: 37649710 PMCID: PMC10463195 DOI: 10.1016/j.csbj.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023] Open
Abstract
Transmembrane kinases (TMKs) are important mediators of cellular signaling cascades. The kinase domains of most metazoan and plant TMKs belong to the serine/threonine/tyrosine kinase (S/T/Y-kinase) superfamily. They share a common origin with prokaryotic kinases and have diversified into distinct subfamilies. Diverse members of the eukaryotic crown radiation such as amoebae, ciliates, and red and brown algae (grouped here under the umbrella term "protists") have long diverged from higher eukaryotes since their ancient common ancestry, making them ideal organisms for studying TMK evolution. Here, we developed an accurate and high-throughput pipeline to predict TMKomes in cellular organisms. Cross-kingdom analyses revealed distinct features of TMKomes in each grouping. Two-transmembrane histidine kinases constitute the main TMKomes of bacteria, while metazoans, plants, and most protists have a large proportion of single-pass TM S/T/Y-kinases. Phylogenetic analyses classified most protist S/T/Y-kinases into three clades, with clades II and III specifically expanded in amoebae and oomycetes, respectively. In contrast, clade I kinases were widespread in all protists examined here, and likely shared a common origin with other eukaryotic S/T/Y-kinases. Functional annotation further showed that most non-kinase domains were grouping-specific, suggesting that their recombination with the more conserved kinase domains led to the divergence of S/T/Y-kinases. However, we also found that protist leucine-rich repeat (LRR)- and G-protein-coupled receptor (GPCR)-type TMKs shared similar sensory domain architectures with respective plant and animal TMKs, despite that they belong to distinct kinase subfamilies. Collectively, our study revealed the functional diversity of TMKomes and the distinct origins of S/T/Y-kinases in protists.
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Affiliation(s)
- Zhiyuan Yin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yaning Zhao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Peng
- USDA Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, USA
| | - Jinding Liu
- Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
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16
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Chian JS, Li J, Wang SM. Evolutionary Origin of Human PALB2 Germline Pathogenic Variants. Int J Mol Sci 2023; 24:11343. [PMID: 37511102 PMCID: PMC10379391 DOI: 10.3390/ijms241411343] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
PALB2 (Partner and localizer of BRCA2) is crucial for repairing DNA double-stranded breaks (DSBs) through homologous recombination (HR). Germline pathogenic variation in PALB2 disrupts DNA damage repair and increases the risk of Fanconi Anemia, breast cancer, and ovarian cancer. Determination of the evolutionary origin of human PALB2 variants will promote a deeper understanding of the biological basis of PALB2 germline variation and its roles in human diseases. We tested the evolution origin for 1444 human PALB2 germline variants, including 484 pathogenic and 960 benign variants. We performed a phylogenic analysis by tracing the variants in 100 vertebrates. However, we found no evidence to show that cross-species conservation was the origin of PALB2 germline pathogenic variants, but it is indeed a rich source for PALB2 germline benign variants. We performed a paleoanthropological analysis by tracing the variants in over 5000 ancient humans. We identified 50 pathogenic in 71 ancient humans dated from 32,895 to 689 before the present, of which 90.1% were dated within the recent 10,000 years. PALB2 benign variants were also highly shared with ancient humans. Data from our study reveal that human PALB2 pathogenic variants mostly arose in recent human history.
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Affiliation(s)
- Jia Sheng Chian
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
| | - Jiaheng Li
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
| | - San Ming Wang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
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17
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Van Etten J, Benites LF, Stephens TG, Yoon HS, Bhattacharya D. Algae obscura: The potential of rare species as model systems. JOURNAL OF PHYCOLOGY 2023; 59:293-300. [PMID: 36764681 DOI: 10.1111/jpy.13321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 05/28/2023]
Abstract
Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small fraction of extant biodiversity. Here, we present three examples of rare algae with unusual features that we refer to as "algae obscura." The Cyanidiophyceae (Rhodophyta), Glaucophyta, and Paulinella (rhizarian) lineages have all transitioned out of obscurity to become models for fundamental evolutionary research. Insights have been gained into the prevalence and importance of eukaryotic horizontal gene transfer, early Earth microbial community dynamics, primary plastid endosymbiosis, and the origin of Archaeplastida. By reviewing the research that has come from the exploration of these organisms, we demonstrate that underappreciated algae have the potential to help us formulate, refine, and substantiate core hypotheses and that such organisms should be considered when establishing future model systems.
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Affiliation(s)
- Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Luiz Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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18
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Brecht KF, Westendorff S, Nieder A. Neural correlates of cognitively controlled vocalizations in a corvid songbird. Cell Rep 2023; 42:112113. [PMID: 36821443 DOI: 10.1016/j.celrep.2023.112113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/13/2023] [Accepted: 01/28/2023] [Indexed: 02/24/2023] Open
Abstract
The neuronal basis of the songbird's song system is well understood. However, little is known about the neuronal correlates of the executive control of songbird vocalizations. Here, we record single-unit activity from the pallial endbrain region "nidopallium caudolaterale" (NCL) of crows that vocalize to the presentation of a visual go-cue but refrain from vocalizing during trials without a go-cue. We find that the preparatory activity of single vocalization-correlated neurons, but also of the entire population of NCL neurons, before vocal onset predicts whether or not the crows will produce an instructed vocalization. Fluctuations in baseline neuronal activity prior to the go-cue influence the premotor activity of such vocalization-correlated neurons and seemingly bias the crows' decision to vocalize. Neuronal response modulation significantly differs between volitional and task-unrelated vocalizations. This suggests that the NCL can take control over the vocal motor network during the production of volitional vocalizations in a corvid songbird.
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Affiliation(s)
- Katharina F Brecht
- Animal Physiology Unit, Institute of Neurobiology, University of Tübingen, 72076 Tübingen, Germany
| | - Stephanie Westendorff
- Animal Physiology Unit, Institute of Neurobiology, University of Tübingen, 72076 Tübingen, Germany
| | - Andreas Nieder
- Animal Physiology Unit, Institute of Neurobiology, University of Tübingen, 72076 Tübingen, Germany.
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19
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Banik SSR, Kushnir N, Doranz BJ, Chambers R. Breaking barriers in antibody discovery: harnessing divergent species for accessing difficult and conserved drug targets. MAbs 2023; 15:2273018. [PMID: 38050985 DOI: 10.1080/19420862.2023.2273018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/16/2023] [Indexed: 12/07/2023] Open
Abstract
To exploit highly conserved and difficult drug targets, including multipass membrane proteins, monoclonal antibody discovery efforts increasingly rely on the advantages offered by divergent species such as rabbits, camelids, and chickens. Here, we provide an overview of antibody discovery technologies, analyze gaps in therapeutic antibodies that stem from the historic use of mice, and examine opportunities to exploit previously inaccessible targets through discovery now possible in alternate species. We summarize the clinical development of antibodies raised from divergent species, discussing how these animals enable robust immune responses against highly conserved binding sites and yield antibodies capable of penetrating functional pockets via long HCDR3 regions. We also discuss the value of pan-reactive molecules often produced by these hosts, and how these antibodies can be tested in accessible animal models, offering a faster path to clinical development.
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20
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Pasquier C, Robichon A. Evolutionary Divergence of Phosphorylation to Regulate Interactive Protein Networks in Lower and Higher Species. Int J Mol Sci 2022; 23:ijms232214429. [PMID: 36430905 PMCID: PMC9697241 DOI: 10.3390/ijms232214429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
The phosphorylation of proteins affects their functions in extensively documented circumstances. However, the role of phosphorylation in many interactive networks of proteins remains very elusive due to the experimental limits of exploring the transient interaction in a large complex of assembled proteins induced by stimulation. Previous studies have suggested that phosphorylation is a recent evolutionary process that differently regulates ortholog proteins in numerous lineages of living organisms to create new functions. Despite the fact that numerous phospho-proteins have been compared between species, little is known about the organization of the full phospho-proteome, the role of phosphorylation to orchestrate large interactive networks of proteins, and the intertwined phospho-landscape in these networks. In this report, we aimed to investigate the acquired role of phosphate addition in the phenomenon of protein networking in different orders of living organisms. Our data highlighted the acquired status of phosphorylation in organizing large, connected assemblages in Homo sapiens. The protein networking guided by phosphorylation turned out to be prominent in humans, chaotic in yeast, and weak in flies. Furthermore, the molecular functions of GO annotation enrichment regulated by phosphorylation were found to be drastically different between flies, yeast, and humans, suggesting an evolutionary drift specific to each species.
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Affiliation(s)
- Claude Pasquier
- I3S, Université Côte d’Azur, Campus SophiaTech, CNRS, 06903 Nice, France
- Correspondence:
| | - Alain Robichon
- INRAE, ISA, Université Côte d’Azur, Campus SophiaTech, CNRS, 06903 Nice, France
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21
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Holzhausen A, Stingl N, Rieth S, Kühn C, Schubert H, Rensing SA. Establishment and optimization of a new model organism to study early land plant evolution: Germination, cultivation and oospore variation of Chara braunii Gmelin, 1826. FRONTIERS IN PLANT SCIENCE 2022; 13:987741. [PMID: 36438147 PMCID: PMC9691404 DOI: 10.3389/fpls.2022.987741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
For studying land plant evolution, the establishment and optimization of model organisms representing streptophytic algae, sister to land plants, is essential. Long-term cultivation experiments with Chara braunii S276 were performed over 8 years, since 4 years (Nov. 2018) under constant conditions. Additionally, short-term experiments for optimization of culture conditions were performed with three strains of C. braunii (S276, NIES-1604 and Lausiger Teiche, LaT-2708). Germination success after application of sterilization agents, addition of gibberellic acid and under different incubation conditions with respect to pre-treatment, irradiance regime and substrate was investigated in order to develop protocols for generative cultivation of at least unialgal cultures. The resulting cultivation protocols for C. braunii S276, allowing maintenance of vegetative as well as generative cultures are presented in detail, including protocols for germination induction and growth of sterilized and unsterilized oospores.
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Affiliation(s)
- Anja Holzhausen
- Department of Biology, Plant Cell Biology, University of Marburg, Marburg, Germany
- Institute for Biosciences, Physiology of Plant Metabolism, University of Rostock, Rostock, Germany
| | - Nora Stingl
- Department of Biology, Plant Cell Biology, University of Marburg, Marburg, Germany
| | - Sophie Rieth
- Department of Biology, Plant Cell Biology, University of Marburg, Marburg, Germany
| | - Christine Kühn
- Department of Biology, Plant Cell Biology, University of Marburg, Marburg, Germany
- Institute for Biosciences, Ecology, University of Rostock, Rostock, Germany
| | - Hendrik Schubert
- Institute for Biosciences, Physiology of Plant Metabolism, University of Rostock, Rostock, Germany
| | - Stefan Andreas Rensing
- Department of Biology, Plant Cell Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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22
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Nieder A. In search for consciousness in animals: Using working memory and voluntary attention as behavioral indicators. Neurosci Biobehav Rev 2022; 142:104865. [PMID: 36096205 DOI: 10.1016/j.neubiorev.2022.104865] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/17/2022] [Accepted: 09/05/2022] [Indexed: 10/31/2022]
Abstract
Whether animals have subjective experiences about the content of their sensory input, i.e., whether they are aware of stimuli, is a notoriously difficult question to answer. If consciousness is present in animals, it must share fundamental characteristics with human awareness. Working memory and voluntary/endogenous attention are suggested as diagnostic features of conscious awareness. Behavioral evidence shows clear signatures of both working memory and voluntary attention as minimal criterium for sensory consciousness in mammals and birds. In contrast, reptiles and amphibians show no sign of either working memory or volitional attention. Surprisingly, some species of teleost fishes exhibit elementary working memory and voluntary attention effects suggestive of possibly rudimentary forms of subjective experience. With the potential exception of honeybees, evidence for conscious processing is lacking in invertebrates. These findings suggest that consciousness is not ubiquitous in the animal kingdom but also not exclusive to humans. The phylogenetic gap between animal taxa argues that evolution does not rely on specific neural substrates to endow distantly related species with basic forms of consciousness.
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Affiliation(s)
- Andreas Nieder
- Animal Physiology Unit, Institute of Neurobiology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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23
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Kachroo AH, Vandeloo M, Greco BM, Abdullah M. Humanized yeast to model human biology, disease and evolution. Dis Model Mech 2022; 15:275614. [PMID: 35661208 PMCID: PMC9194483 DOI: 10.1242/dmm.049309] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
For decades, budding yeast, a single-cellular eukaryote, has provided remarkable insights into human biology. Yeast and humans share several thousand genes despite morphological and cellular differences and over a billion years of separate evolution. These genes encode critical cellular processes, the failure of which in humans results in disease. Although recent developments in genome engineering of mammalian cells permit genetic assays in human cell lines, there is still a need to develop biological reagents to study human disease variants in a high-throughput manner. Many protein-coding human genes can successfully substitute for their yeast equivalents and sustain yeast growth, thus opening up doors for developing direct assays of human gene function in a tractable system referred to as 'humanized yeast'. Humanized yeast permits the discovery of new human biology by measuring human protein activity in a simplified organismal context. This Review summarizes recent developments showing how humanized yeast can directly assay human gene function and explore variant effects at scale. Thus, by extending the 'awesome power of yeast genetics' to study human biology, humanizing yeast reinforces the high relevance of evolutionarily distant model organisms to explore human gene evolution, function and disease.
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24
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Shan H, Peterson J, Conrad NJ, Tang Y, Zhu Y, Ghotbi S, Hathorn S, Chubykin AA, Mohammadi S. A 0.43 g Wireless Battery-Less Neural Recorder With On-Chip Microelectrode Array and Integrated Flexible Antenna. IEEE MICROWAVE AND WIRELESS COMPONENTS LETTERS : A PUBLICATION OF THE IEEE MICROWAVE THEORY AND TECHNIQUES SOCIETY 2022; 32:772-775. [PMID: 36338547 PMCID: PMC9635343 DOI: 10.1109/lmwc.2022.3167311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This work presents a single-chip battery-less neural recorder with 12 on-die microelectrodes. It can be powered wirelessly up to 16 cm away from a horn antenna at 915 MHz and only consumes 104 μW dc power for accessing 10 enabled recording sites simultaneously, transmitting at 5 Mbps. The implantable device integrated with a flexible antenna weighs only 0.43 gram. In vivo measurements on an unrestricted mouse have been successfully conducted, showing response to visual stimuli.
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Affiliation(s)
- Hengying Shan
- Purdue University, West Lafayette, IN 47907 USA; Amazon Lab126 in Sunnyvale, CA 94089, USA
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25
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Rafique F, Lauersen KJ, Chodasiewicz M, Figueroa NE. A New Approach to the Study of Plastidial Stress Granules: The Integrated Use of Arabidopsis thaliana and Chlamydomonas reinhardtii as Model Organisms. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111467. [PMID: 35684240 PMCID: PMC9182737 DOI: 10.3390/plants11111467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 05/16/2023]
Abstract
The field of stress granules (SGs) has recently emerged in the study of the plant stress response, yet these structures, their dynamics and importance remain poorly characterized. There is currently a gap in our understanding of the physiological function of SGs during stress. Since there are only a few studies addressing SGs in planta, which are primarily focused on cytoplasmic SGs. The recent observation of SG-like foci in the chloroplast (cpSGs) of Arabidopsis thaliana opened even more questions regarding the role of these subcellular features. In this opinion article, we review the current knowledge of cpSGs and propose a workflow for the joint use of the long-established model organisms Chlamydomonas reinhardtii and A. thaliana to accelerate the evaluation of individual plant cpSGs components and their impact on stress responses. Finally, we present a short outlook and what we believe are the significant gaps that need to be addressed in the following years.
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Affiliation(s)
- Fareena Rafique
- Plant Science Program, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (F.R.); (M.C.)
| | - Kyle J. Lauersen
- Bioengineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Monika Chodasiewicz
- Plant Science Program, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (F.R.); (M.C.)
| | - Nicolás E. Figueroa
- Plant Science Program, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (F.R.); (M.C.)
- Correspondence: ; Tel.: +966-128082834
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Datki Z, Sinka R, Galik B, Galik-Olah Z. Particle-dependent reproduction and exogenic biopolymer secretion of protozoa co-cultured rotifers. Int J Biol Macromol 2022; 211:669-677. [PMID: 35588974 DOI: 10.1016/j.ijbiomac.2022.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/24/2022] [Accepted: 05/03/2022] [Indexed: 11/30/2022]
Abstract
The rotifer-specific exogenic biopolymer, named Rotimer and its related molecular processes are affected by physical and chemical factors (e.g., temperature, pH or metal ions); however, the study of biological influences (e.g., the presence protozoa) concerning the particle-dependent reproduction (egg laying) and 'biopolymer producing capacity' (BPC) of rotifers is the objective of the present work. Non-planktonic rotifer species (Philodina acuticornis, Adineta vaga, Euchlanis dilatata, and Lecane bulla) were studied in paired micrometazoa-protozoa co-cultures involving Paramecium, Diplonema, and Amoeba. These protozoa can be beneficial food sources, enhancing reproduction, or even toxic factors for the above-mentioned animals, but can also function as particle-like mechanical stimulators. Furthermore, current studies reveal that bdelloids, similarly to monogonants, produce filamentous exudate; moreover, the body of bdelloids is covered by their exudate, unlike that of monogonants, especially in the case of A. vaga. A mathematical formula was developed as an improved version of a previously published viability marker to characterize the BPC and the relative amount of produced exudate in different conditions. Rotifer species secreting biopolymers appear to be a general trait indicating a common evolutionary background (e.g., calcium- and particle dependency) of such molecules; therefore, the BPC becomes an experiential sublethal influencing marker to these micrometazoans.
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Affiliation(s)
- Zsolt Datki
- Micro-In Vivo Research Laboratory, Interdisciplinary Research, Development and Innovation Centre of Excellence, University of Szeged, Dugonics ter 13. H-6720 Szeged, Hungary.
| | - Rita Sinka
- Department of Genetics, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Hungary
| | - Bence Galik
- Bioinformatics Research Group, Bioinformatics and Sequencing Core Facility, Szentagothai Research Centre, University of Pecs, Ifjusag u. 20, H-7624 Pecs, Hungary; Department of Clinical Molecular Biology, Medical University of Bialystok, ul.Jana Kilinskiego 1, 15-089 Bialystok, Poland
| | - Zita Galik-Olah
- Micro-In Vivo Research Laboratory, Interdisciplinary Research, Development and Innovation Centre of Excellence, University of Szeged, Dugonics ter 13. H-6720 Szeged, Hungary
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Chiu SH, Ho WL, Sun YC, Kuo JC, Huang JR. Phase separation driven by interchangeable properties in the intrinsically disordered regions of protein paralogs. Commun Biol 2022; 5:400. [PMID: 35487971 PMCID: PMC9054762 DOI: 10.1038/s42003-022-03354-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/10/2022] [Indexed: 11/09/2022] Open
Abstract
Paralogs, arising from gene duplications, increase the functional diversity of proteins. Protein functions in paralog families have been extensively studied, but little is known about the roles that intrinsically disordered regions (IDRs) play in their paralogs. Without a folded structure to restrain them, IDRs mutate more diversely along with evolution. However, how the diversity of IDRs in a paralog family affects their functions is unexplored. Using the RNA-binding protein Musashi family as an example, we applied multiple structural techniques and phylogenetic analysis to show how members in a paralog family have evolved their IDRs to different physicochemical properties but converge to the same function. In this example, the lower prion-like tendency of Musashi-1's IDRs, rather than Musashi-2's, is compensated by its higher α-helical propensity to assist their assembly. Our work suggests that, no matter how diverse they become, IDRs could evolve different traits to a converged function, such as liquid-liquid phase separation.
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Affiliation(s)
- Shih-Hui Chiu
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Wen-Lin Ho
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Yung-Chen Sun
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Jean-Cheng Kuo
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Jie-Rong Huang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan. .,Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan. .,Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan.
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28
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Cell-type specific pallial circuits shape categorical tuning responses in the crow telencephalon. Commun Biol 2022; 5:269. [PMID: 35338240 PMCID: PMC8956685 DOI: 10.1038/s42003-022-03208-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/28/2022] [Indexed: 01/26/2023] Open
Abstract
The nidopallium caudolaterale (NCL), an integration centre in the telencephalon of birds, plays a crucial role in representing and maintaining abstract categories and concepts. However, the computational principles allowing pallial microcircuits consisting of excitatory and inhibitory neurons to shape the tuning to abstract categories remain elusive. Here we identified the major pallial cell types, putative excitatory projection cells and inhibitory interneurons, by characterizing the waveforms of action potentials recorded in crows performing a cognitively demanding numerical categorization task. Both cell types showed clear differences in their capacity to encode categorical information. Nearby and functionally coupled putative projection neurons generally exhibited similar tuning, whereas putative interneurons showed mainly opposite tuning. The results favour feedforward mechanisms for the shaping of categorical tuning in microcircuits of the NCL. Our findings help to decipher the workings of pallial microcircuits in birds during complex cognition and to compare them vis-a-vis neocortical processes in mammals. Neural recordings from the caudolateral nidopallium in crows during a numerosity task suggest there are two subsets of projection neurons and inhibitory interneurons involved in complex cognition.
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29
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Pyszko M, Němeček P, Horák O, Páral V, Kotrba R, Hoffman LC, Robovský J. Newly described anatomical opening on forelimb tendon in the artiodactyls and its relation to knee clicks. Sci Rep 2022; 12:4362. [PMID: 35288610 PMCID: PMC8921199 DOI: 10.1038/s41598-022-08303-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
To understand which morphological/anatomical parts may be responsible in artiodactyl ungulates for the clicking sound made when moving, this research focuses on the forelimb tendon apparatus where an undescribed opening in the fibrous cuff (manica flexoria), called hereafter for its shape as an “oval window” in the manica flexoria (OWMF), was detected. This oval window was found in 24 of the 25 species of four families (Camelidae, Giraffidae, Cervidae, and Bovidae) evaluated; the exception being in Bos taurus taurus (Domestic cattle). The length and width of the OWMF enabled correct species discrimination between the majority of species, but remained conservative intraspecifically, as it did not differ between the left and right side of the forelimb, third and fourth digits, or between sexes. When evaluating the shape of OWMF in individual species, and measuring its length and width, 18 out of the 24 species investigated had this window as an oval shape, the remaining 25% of species exhibited more oval-oblong shapes with either proximal or distal asymmetry. The function of the OWMF in the thoracic autopodium of most ruminant even-toed ungulates is not yet fully understood. Its most likely function is to help balance the pressure inside the ligament cuff and reduce the friction of the touching surfaces of the muscle tendons—thus facilitating the movement of the digits when walking. None of the absolute or relative OWMF parameters fit exclusively with the occurrence and distribution of knee-clicks produced by some bovids and cervids during movement, so the mechanism responsible for this sound remains cryptic from the present anatomical perspective.
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Affiliation(s)
- Martin Pyszko
- Department of Anatomy, Histology & Embryology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Palackého třída 1946/1, 612 42, Brno, Czech Republic
| | - Petr Němeček
- Jiří Orten Grammar School, Jaselská 932, 284 80, Kutná Hora, Czech Republic.
| | - Ondřej Horák
- Department of Anatomy, Histology & Embryology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Palackého třída 1946/1, 612 42, Brno, Czech Republic
| | - Václav Páral
- Department of Anatomy, Histology & Embryology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Palackého třída 1946/1, 612 42, Brno, Czech Republic
| | - Radim Kotrba
- Department of Ethology, Institute of Animal Science, 104 00, Prague 10 - Uhříněves, Czech Republic.,Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praha 6 - Suchdol, Czech Republic
| | - Louwrens C Hoffman
- Department of Animal Sciences, University of Stellenbosch, Matieland, Private Bag X1, Stellenbosch, 7602, South Africa.,Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Digital Agricultural Building, 8115, Office 110, Gatton, 4343, Australia
| | - Jan Robovský
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic. .,Liberec Zoo, Lidové sady 425/1, 460 01, Liberec, Czech Republic.
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30
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Cookson R, Winichayakul S, Xue H, Richardson K, Moraga R, Laugraud A, Biswas A, Bryan G, Roberts N. Evolution and conserved functionality of organ size and shape regulator PEAPOD. PLoS One 2022; 17:e0263928. [PMID: 35148336 PMCID: PMC8836299 DOI: 10.1371/journal.pone.0263928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/28/2022] [Indexed: 11/26/2022] Open
Abstract
Transcriptional regulator PEAPOD (PPD) and its binding partners comprise a complex that is conserved throughout many core eudicot plants with regard to protein domain sequence and the function of controlling organ size and shape. Orthologues of PPD also exist in the basal angiosperm Amborella trichopoda, various gymnosperm species, the lycophyte Selaginella moellendorffii and several monocot genera, although until now it was not known if these are functional sequences. Here we report constitutive expression of orthologues from species representing diverse taxa of plant phylogeny in the Arabidopsis Δppd mutant. PPD orthologues from S. moellendorffii, gymnosperm Picea abies, A. trichopoda, monocot Musa acuminata, and dicot Trifolium repens were able to complement the mutant and return it to the wild-type phenotype, demonstrating the conserved functionality of PPD throughout vascular plants. In addition, analysis of bryophyte genomes revealed potential PPD orthologues in model liverwort and moss species, suggesting a more primitive lineage for this conserved regulator. The Poaceae (grasses) lack the genes for the PPD module and the reason for loss of the complex from this economically significant family is unclear, given that grasses were the last of the flowering plants to evolve. Bioinformatic analyses identified putative PPD orthologues in close relatives of the Poaceae, indicating that the explanation for absence of PPD in the grasses may be more complex than previously considered. Understanding the mechanisms which led to loss of PPD from the grasses will provide insight into evolution of the Poaceae.
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Affiliation(s)
- Ruth Cookson
- Plant Biotechnology, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
- * E-mail: (RC); (NR)
| | - Somrutai Winichayakul
- Plant Biotechnology, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Hong Xue
- Plant Biotechnology, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Kim Richardson
- Plant Biotechnology, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Roger Moraga
- Bioinformatics and Statistics, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Aurelie Laugraud
- Bioinformatics and Statistics, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Ambarish Biswas
- Bioinformatics and Statistics, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Greg Bryan
- Plant Biotechnology, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Nick Roberts
- Plant Biotechnology, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
- * E-mail: (RC); (NR)
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31
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Stundl J, Soukup V, Franěk R, Pospisilova A, Psutkova V, Pšenička M, Cerny R, Bronner ME, Medeiros DM, Jandzik D. Efficient CRISPR Mutagenesis in Sturgeon Demonstrates Its Utility in Large, Slow-Maturing Vertebrates. Front Cell Dev Biol 2022; 10:750833. [PMID: 35223827 PMCID: PMC8867083 DOI: 10.3389/fcell.2022.750833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 01/17/2022] [Indexed: 11/14/2022] Open
Abstract
In the last decade, the CRISPR/Cas9 bacterial virus defense system has been adapted as a user-friendly, efficient, and precise method for targeted mutagenesis in eukaryotes. Though CRISPR/Cas9 has proven effective in a diverse range of organisms, it is still most often used to create mutant lines in lab-reared genetic model systems. However, one major advantage of CRISPR/Cas9 mutagenesis over previous gene targeting approaches is that its high efficiency allows the immediate generation of near-null mosaic mutants. This feature could potentially allow genotype to be linked to phenotype in organisms with life histories that preclude the establishment of purebred genetic lines; a group that includes the vast majority of vertebrate species. Of particular interest to scholars of early vertebrate evolution are several long-lived and slow-maturing fishes that diverged from two dominant modern lineages, teleosts and tetrapods, in the Ordovician, or before. These early-diverging or “basal” vertebrates include the jawless cyclostomes, cartilaginous fishes, and various non-teleost ray-finned fishes. In addition to occupying critical phylogenetic positions, these groups possess combinations of derived and ancestral features not seen in conventional model vertebrates, and thus provide an opportunity for understanding the genetic bases of such traits. Here we report successful use of CRISPR/Cas9 mutagenesis in one such non-teleost fish, sterlet Acipenser ruthenus, a small species of sturgeon. We introduced mutations into the genes Tyrosinase, which is needed for melanin production, and Sonic hedgehog, a pleiotropic developmental regulator with diverse roles in early embryonic patterning and organogenesis. We observed disruption of both loci and the production of consistent phenotypes, including both near-null mutants’ various hypomorphs. Based on these results, and previous work in lamprey and amphibians, we discuss how CRISPR/Cas9 F0 mutagenesis may be successfully adapted to other long-lived, slow-maturing aquatic vertebrates and identify the ease of obtaining and injecting eggs and/or zygotes as the main challenges.
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Affiliation(s)
- Jan Stundl
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Vladimír Soukup
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Roman Franěk
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Anna Pospisilova
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Viktorie Psutkova
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Martin Pšenička
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Robert Cerny
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Marianne E. Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Daniel Meulemans Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado in Boulder, Boulder, CO, United States
| | - David Jandzik
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
- *Correspondence: David Jandzik,
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32
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Agarwal I, Bauer AM, Gamble T, Giri VB, Jablonski D, Khandekar A, Mohapatra PP, Masroor R, Mishra A, Ramakrishnan U. The evolutionary history of an accidental model organism, the leopard gecko Eublepharis macularius (Squamata: Eublepharidae). Mol Phylogenet Evol 2022; 168:107414. [PMID: 35032646 DOI: 10.1016/j.ympev.2022.107414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/22/2022]
Abstract
The leopard gecko, Eublepharis macularius, is a widely used model organism in laboratory and experimental studies. The high phenotypic diversity in the pet trade, the fact that the provenance of different breeding lines is unknown, and that distinct Eublepharis species are known to hybridize, implies that the continued use of E. macularius as a model requires clarity on the origin of the lineages in the pet trade. We combine multi-locus sequence data and the first range-wide sampling of the genus Eublepharis to reconstruct the evolutionary history of the Eublepharidae and Eublepharis, with an updated time-tree for the Eublepharidae. Our sampling includes five of the six recognized species and additional nominal taxa of uncertain status comprising 43 samples from 34 localities plus 48 pet-trade samples. The Eublepharidae began diversifying in the Cretaceous. Eublepharis split from its sister genera in Africa in the Palaeocene-Eocene, and began diversifying in the Oligocene-Miocene, with late Miocene-Pliocene cladogenesis giving rise to extant species. The current species diversity within this group is moderately underestimated. Our species delimitation suggests 10 species with four potentially unnamed divergent lineages in Iran, India and Pakistan. All 30 individuals of E. macularius that we sampled from the pet trade, which include diverse morphotypes, come from a few shallow E. macularius clades, confirming that lab and pet trade strains are part of a single taxon. One of the wild-caught haplotypes of E. macularius, from near Karachi, Pakistan, is identical to (10) pet-trade samples and all other captive populations are closely related to wild-caught animals from central/southern Pakistan (0.1-0.5 % minimum pairwise uncorrected ND2 sequence divergence).
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Affiliation(s)
- Ishan Agarwal
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India; Thackeray Wildlife Foundation, Vaibhav Chambers, Bandra, Mumbai, 400051, India; Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, 800 Lancaster Avenue, Villanova, Pennsylvania, 19085, USA.
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, 800 Lancaster Avenue, Villanova, Pennsylvania, 19085, USA
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53233, USA; Milwaukee Public Museum, 800 W. Wells St., Milwaukee, WI 53233, USA; Bell Museum of Natural History, University of Minnesota, 2088 Larpenteur Ave. W., St. Paul, MN, 55113, USA
| | - Varad B Giri
- NIDUS, A1903, Shubh Kalyan, Nanded City, Pune, 411041, India
| | - Daniel Jablonski
- Department of Zoology, Ilkovičova 6, Mlynská dolina, Comenius University in Bratislava, 842 15 Bratislava, Slovakia
| | - Akshay Khandekar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India; Thackeray Wildlife Foundation, Vaibhav Chambers, Bandra, Mumbai, 400051, India
| | - Pratyush P Mohapatra
- Zoological Survey of India, Central Zone Regional Centre, Jabalpur, Madhya Pradesh, 482002, India
| | - Rafaqat Masroor
- Pakistan Museum of Natural History, Garden Avenue, Shakarparian, Islamabad-44000, Pakistan
| | - Anurag Mishra
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
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33
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Chin AF, Zheng Y, Hilser VJ. Phylogenetic convergence of phase separation and mitotic function in the disordered protein BuGZ. Protein Sci 2022; 31:822-834. [PMID: 34984754 DOI: 10.1002/pro.4270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 11/05/2022]
Abstract
Intrinsically disordered proteins (IDPs) effect biological function despite their sequence-encoded lack of preference for stable three-dimensional structure. Among their many functions, IDPs form membraneless cellular compartments through liquid-liquid phase separation (LLPS), also termed biomolecular condensation. The extent to which LLPS has been evolutionarily selected remains largely unknown, as the complexities of IDP evolution hamper progress. Unlike structured proteins, rapid sequence divergence typical of IDPs confounds inference of their biophysical or biological functions from comparative sequence analyses. Here, we leverage mitosis as a universal eukaryotic feature to interrogate condensate evolutionary history. We observe that evolution has conserved the ability for six homologs of the mitotic IDP BuGZ to undergo LLPS and to serve the same mitotic function, despite low sequence conservation. We also observe that cellular context may tune LLPS. The phylogenetic correlation of LLPS and mitotic function in one protein raises the possibility of an ancient evolutionary interplay between LLPS and biological function, dating back at least 1.6 billion years to the last common ancestor of plants and animals. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Alexander F Chin
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yixian Zheng
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, Maryland, USA
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.,T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland, USA
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Hao J, Xu X, Zhang L. Seasonal Dynamics of Photochemical Performance of PS II of Terrestrial Mosses from Different Elevations. PLANTS 2021; 10:plants10122613. [PMID: 34961084 PMCID: PMC8705637 DOI: 10.3390/plants10122613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022]
Abstract
Mosses are critical components of tropical forest ecosystems and have multiple essential ecological functions. The drying and rehydrating and often hot environments in tropical regions present some of the greatest challenges for their photosynthetic activities. There is limited knowledge available on the physiological responses to the changing environments such as temperature and water pattern changes for terrestrial mosses. We examined the seasonal dynamics of photochemical performance of PS II through the measuring of chlorophyll fluorescence of 12 terrestrial mosses in situ from five different elevations by Photosynthesis Yield Analyzer MINI-PAM-II, along with the seasonal changes of climatic factors (air temperature, dew point, relative humidity and rainfall), which were collected by local weather stations and self-deployed mini weather stations. The results showed a great seasonality during observing periods, which, mainly the changes of rainfall and relative humidity pattern, presented significant impacts on the photochemical performance of PS II of terrestrial mosses. All these tested moss species developed a suitable regulated and non-regulated strategy to avoid the detrimental effect of abiotic stresses. We found that only Hypnum plumaeforme, Pterobryopsis crassicaulis and Pogonatum inflexum were well adapted to the changes of habitat temperature and water patterns, even though they still experienced a lower CO2 assimilation efficiency in the drier months. The other nine species were susceptible to seasonality, especially during the months of lower rainfall and relative humidity when moss species were under physiologically reduced PS II efficiency. Anomobryum julaceum, Pogonatum neesii, Sematophyllum subhumile, Pseudotaxiphyllum pohliaecarpum and Leucobryum boninense, and especially Brachythecium buchananii, were sensitive to the changes of water patterns, which enable them as ideal ecological indicators of photosynthetic acclimation to stressed environments as a result of climate change.
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Affiliation(s)
- Jiewei Hao
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Correspondence: (J.H.); (L.Z.); Tel.: +86-199-8987-9261 (J.H.); +86-189-0768-2999 (L.Z.)
| | - Xueyan Xu
- Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, 58 Renmin Road, Haikou 570228, China;
- Center for Terrestrial Biodiversity of the South China Sea, Hainan University, 58 Renmin Road, Haikou 570228, China
| | - Lina Zhang
- Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, 58 Renmin Road, Haikou 570228, China;
- Center for Terrestrial Biodiversity of the South China Sea, Hainan University, 58 Renmin Road, Haikou 570228, China
- Correspondence: (J.H.); (L.Z.); Tel.: +86-199-8987-9261 (J.H.); +86-189-0768-2999 (L.Z.)
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35
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Benz R. Historical Perspective of Pore-Forming Activity Studies of Voltage-Dependent Anion Channel (Eukaryotic or Mitochondrial Porin) Since Its Discovery in the 70th of the Last Century. Front Physiol 2021; 12:734226. [PMID: 35547863 PMCID: PMC9083909 DOI: 10.3389/fphys.2021.734226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/24/2021] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic porin, also known as Voltage-Dependent Anion Channel (VDAC), is the most frequent protein in the outer membrane of mitochondria that are responsible for cellular respiration. Mitochondria are most likely descendants of strictly aerobic Gram-negative bacteria from the α-proteobacterial lineage. In accordance with the presumed ancestor, mitochondria are surrounded by two membranes. The mitochondrial outer membrane contains besides the eukaryotic porins responsible for its major permeability properties a variety of other not fully identified channels. It encloses also the TOM apparatus together with the sorting mechanism SAM, responsible for the uptake and assembly of many mitochondrial proteins that are encoded in the nucleus and synthesized in the cytoplasm at free ribosomes. The recognition and the study of electrophysiological properties of eukaryotic porin or VDAC started in the late seventies of the last century by a study of Schein et al., who reconstituted the pore from crude extracts of Paramecium mitochondria into planar lipid bilayer membranes. Whereas the literature about structure and function of eukaryotic porins was comparatively rare during the first 10years after the first study, the number of publications started to explode with the first sequencing of human Porin 31HL and the recognition of the important function of eukaryotic porins in mitochondrial metabolism. Many genomes contain more than one gene coding for homologs of eukaryotic porins. More than 100 sequences of eukaryotic porins are known to date. Although the sequence identity between them is relatively low, the polypeptide length and in particular, the electrophysiological characteristics are highly preserved. This means that all eukaryotic porins studied to date are anion selective in the open state. They are voltage-dependent and switch into cation-selective substates at voltages in the physiological relevant range. A major breakthrough was also the elucidation of the 3D structure of the eukaryotic pore, which is formed by 19 β-strands similar to those of bacterial porin channels. The function of the presumed gate an α-helical stretch of 20 amino acids allowed further studies with respect to voltage dependence and function, but its exact role in channel gating is still not fully understood.
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Nieder A. Consciousness without cortex. Curr Opin Neurobiol 2021; 71:69-76. [PMID: 34656051 DOI: 10.1016/j.conb.2021.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022]
Abstract
Sensory consciousness - the awareness and ability to report subjective experiences - is a property of biological nervous systems that has evolved out of unconscious processing over hundreds of millions of years. From which brain structures and based on which mechanisms can conscious experience emerge? Based on the body of work in human and nonhuman primates, the emergence of consciousness is intimately associated with the workings of the mammalian cerebral cortex with its specific cell types and layered structure. However, recent neurophysiological recordings demonstrate a neuronal correlate of consciousness in the pallial endbrain of crows. These telencephalic integration centers in birds originate embryonically from other pallial territories, lack a layered architecture characteristic for the cerebral cortex, and exhibit independently evolved pallial cell types. This argues that the mammalian cerebral cortex is not a prerequisite for consciousness to emerge in all vertebrates. Rather, it seems that the anatomical and physiological principles of the telencephalic pallium offer this structure as a brain substrate for consciousness to evolve independently across vertebrate phylogeny.
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Affiliation(s)
- Andreas Nieder
- Animal Physiology Unit, Institute of Neurobiology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
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Crapse J, Pappireddi N, Gupta M, Shvartsman SY, Wieschaus E, Wühr M. Evaluating the Arrhenius equation for developmental processes. Mol Syst Biol 2021; 17:e9895. [PMID: 34414660 PMCID: PMC8377445 DOI: 10.15252/msb.20209895] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/15/2022] Open
Abstract
The famous Arrhenius equation is well suited to describing the temperature dependence of chemical reactions but has also been used for complicated biological processes. Here, we evaluate how well the simple Arrhenius equation predicts complex multi-step biological processes, using frog and fruit fly embryogenesis as two canonical models. We find that the Arrhenius equation provides a good approximation for the temperature dependence of embryogenesis, even though individual developmental intervals scale differently with temperature. At low and high temperatures, however, we observed significant departures from idealized Arrhenius Law behavior. When we model multi-step reactions of idealized chemical networks, we are unable to generate comparable deviations from linearity. In contrast, we find the two enzymes GAPDH and β-galactosidase show non-linearity in the Arrhenius plot similar to our observations of embryonic development. Thus, we find that complex embryonic development can be well approximated by the simple Arrhenius equation regardless of non-uniform developmental scaling and propose that the observed departure from this law likely results more from non-idealized individual steps rather than from the complexity of the system.
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Affiliation(s)
- Joseph Crapse
- Undergraduate Integrated Science CurriculumPrinceton UniversityPrincetonNJUSA
- Department of Molecular BiologyPrinceton UniversityPrincetonNJUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNJUSA
| | - Nishant Pappireddi
- Department of Molecular BiologyPrinceton UniversityPrincetonNJUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNJUSA
| | - Meera Gupta
- Department of Molecular BiologyPrinceton UniversityPrincetonNJUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNJUSA
- Department of Chemical and Biological EngineeringPrinceton UniversityPrincetonNJUSA
| | - Stanislav Y Shvartsman
- Undergraduate Integrated Science CurriculumPrinceton UniversityPrincetonNJUSA
- Department of Molecular BiologyPrinceton UniversityPrincetonNJUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNJUSA
- Center for Computational BiologyFlatiron InstituteSimons FoundationNew YorkNYUSA
| | - Eric Wieschaus
- Undergraduate Integrated Science CurriculumPrinceton UniversityPrincetonNJUSA
- Department of Molecular BiologyPrinceton UniversityPrincetonNJUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNJUSA
| | - Martin Wühr
- Undergraduate Integrated Science CurriculumPrinceton UniversityPrincetonNJUSA
- Department of Molecular BiologyPrinceton UniversityPrincetonNJUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNJUSA
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Abstract
Cell atlases are essential companions to the genome as they elucidate how genes are used in a cell type-specific manner or how the usage of genes changes over the lifetime of an organism. This review explores recent advances in whole-organism single-cell atlases, which enable understanding of cell heterogeneity and tissue and cell fate, both in health and disease. Here we provide an overview of recent efforts to build cell atlases across species and discuss the challenges that the field is currently facing. Moreover, we propose the concept of having a knowledgebase that can scale with the number of experiments and computational approaches and a new feedback loop for development and benchmarking of computational methods that includes contributions from the users. These two aspects are key for community efforts in single-cell biology that will help produce a comprehensive annotated map of cell types and states with unparalleled resolution.
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Affiliation(s)
| | - Bruno Tojo
- Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Aaron McGeever
- Chan Zuckerberg Biohub, San Francisco, California 94103, USA;
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Ohtsuka H, Shimasaki T, Aiba H. Response to sulfur in Schizosaccharomyces pombe. FEMS Yeast Res 2021; 21:6324000. [PMID: 34279603 PMCID: PMC8310684 DOI: 10.1093/femsyr/foab041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
Sulfur is an essential component of various biologically important molecules, including methionine, cysteine and glutathione, and it is also involved in coping with oxidative and heavy metal stress. Studies using model organisms, including budding yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe), have contributed not only to understanding various cellular processes but also to understanding the utilization and response mechanisms of each nutrient, including sulfur. Although fission yeast can use sulfate as a sulfur source, its sulfur metabolism pathway is slightly different from that of budding yeast because it does not have a trans-sulfuration pathway. In recent years, it has been found that sulfur starvation causes various cellular responses in S. pombe, including sporulation, cell cycle arrest at G2, chronological lifespan extension, autophagy induction and reduced translation. This MiniReview identifies two sulfate transporters in S. pombe, Sul1 (encoded by SPBC3H7.02) and Sul2 (encoded by SPAC869.05c), and summarizes the metabolic pathways of sulfur assimilation and cellular response to sulfur starvation. Understanding these responses, including metabolism and adaptation, will contribute to a better understanding of the various stress and nutrient starvation responses and chronological lifespan regulation caused by sulfur starvation.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
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Tanner RL, Grover N, Anderson ML, Crocker KC, Dutta S, Horner AM, Hough LE, Moore TY, Rosen GL, Whitney KS, Summers AP. Examining cultural structures and functions in biology. Integr Comp Biol 2021; 61:2282-2293. [PMID: 34151345 DOI: 10.1093/icb/icab140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/08/2021] [Accepted: 06/16/2021] [Indexed: 11/13/2022] Open
Abstract
Scientific culture and structure organize biological sciences in many ways. We make choices concerning the systems and questions we study. Our research then amplifies these choices into factors that influence the directions of future research by shaping our hypotheses, data analyses, interpretation, publication venues, and dissemination via other methods. But our choices are shaped by more than objective curiosity-we are influenced by cultural paradigms reinforced by societal upbringing and scientific indoctrination during training. This extends to the systems and data that we consider to be ethically obtainable or available for study, and who is considered qualified to do research, ask questions, and communicate about research. It is also influenced by the profitability of concepts like open-access-a system designed to improve equity, but which enacts gatekeeping in unintended but foreseeable ways. Creating truly integrative biology programs will require more than intentionally developing departments or institutes that allow overlapping expertise in two or more subfields of biology. Interdisciplinary work requires the expertise of large and diverse teams of scientists working together-this is impossible without an authentic commitment to addressing, not denying, racism when practiced by individuals, institutions, and cultural aspects of academic science. We have identified starting points for remedying how our field has discouraged and caused harm, but we acknowledge there is a long path forward. This path must be paved with field-wide solutions and institutional buy-in: our solutions must match the scale of the problem. Together, we can integrate-not reintegrate-the nuances of biology into our field.
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Affiliation(s)
- Richelle L Tanner
- Department of Animal Science, University of California at Davis, Davis CA 95616
| | - Neena Grover
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs CO 80903
| | | | | | - Shuchismita Dutta
- RCSB Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers University, New Brunswick NJ 08854
| | - Angela M Horner
- Department of Biology, California State University San Bernardino, San Bernardino CA 92407
| | - Loren E Hough
- BioFrontiers Institute, Department of Physics, University of Colorado Boulder, Boulder CO 80309
| | - Talia Y Moore
- Mechanical Engineering, Robotics Institute, Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor MI 48109
| | - Gail L Rosen
- Ecological & Evolutionary Signal Processing & Informatics Lab, Center for Biological Discovery from Big Data, Electrical, and Computer Engineering, Drexel University, Philadelphia PA 19104
| | - Kaitlin Stack Whitney
- Science, Technology, & Society Department, Rochester Institute of Technology, Rochester NY 14623
| | - Adam P Summers
- Friday Harbor Laboratories, University of Washington, Friday Harbor WA 98250
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Ferreira-Neto JRC, Borges ANDC, da Silva MD, Morais DADL, Bezerra-Neto JP, Bourque G, Kido EA, Benko-Iseppon AM. The Cowpea Kinome: Genomic and Transcriptomic Analysis Under Biotic and Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2021; 12:667013. [PMID: 34194450 PMCID: PMC8238008 DOI: 10.3389/fpls.2021.667013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/26/2021] [Indexed: 06/13/2023]
Abstract
The present work represents a pioneering effort, being the first to analyze genomic and transcriptomic data from Vigna unguiculata (cowpea) kinases. We evaluated the cowpea kinome considering its genome-wide distribution and structural characteristics (at the gene and protein levels), sequence evolution, conservation among Viridiplantae species, and gene expression in three cowpea genotypes under different stress situations, including biotic (injury followed by virus inoculation-CABMV or CPSMV) and abiotic (root dehydration). The structural features of cowpea kinases (VuPKs) indicated that 1,293 bona fide VuPKs covered 20 groups and 118 different families. The RLK-Pelle was the largest group, with 908 members. Insights on the mechanisms of VuPK genomic expansion and conservation among Viridiplantae species indicated dispersed and tandem duplications as major forces for VuPKs' distribution pattern and high orthology indexes and synteny with other legume species, respectively. K a /K s ratios showed that almost all (91%) of the tandem duplication events were under purifying selection. Candidate cis-regulatory elements were associated with different transcription factors (TFs) in the promoter regions of the RLK-Pelle group. C2H2 TFs were closely associated with the promoter regions of almost all scrutinized families for the mentioned group. At the transcriptional level, it was suggested that VuPK up-regulation was stress, genotype, or tissue dependent (or a combination of them). The most prominent families in responding (up-regulation) to all the analyzed stresses were RLK-Pelle_DLSV and CAMK_CAMKL-CHK1. Concerning root dehydration, it was suggested that the up-regulated VuPKs are associated with ABA hormone signaling, auxin hormone transport, and potassium ion metabolism. Additionally, up-regulated VuPKs under root dehydration potentially assist in a critical physiological strategy of the studied cowpea genotype in this assay, with activation of defense mechanisms against biotic stress while responding to root dehydration. This study provides the foundation for further studies on the evolution and molecular function of VuPKs.
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Affiliation(s)
| | | | - Manassés Daniel da Silva
- Laboratory of Molecular Genetics, Genetics Department, Federal University of Pernambuco, Recife, Brazil
| | | | - João Pacífico Bezerra-Neto
- Laboratory of Plant Genetics and Biotechnology, Genetics Department, Federal University of Pernambuco, Recife, Brazil
| | - Guillaume Bourque
- Génome Québec Innovation Centre, McGill University, Montréal, QC, Canada
| | - Ederson Akio Kido
- Laboratory of Molecular Genetics, Genetics Department, Federal University of Pernambuco, Recife, Brazil
| | - Ana Maria Benko-Iseppon
- Laboratory of Plant Genetics and Biotechnology, Genetics Department, Federal University of Pernambuco, Recife, Brazil
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Pointer MD, Gage MJG, Spurgin LG. Tribolium beetles as a model system in evolution and ecology. Heredity (Edinb) 2021; 126:869-883. [PMID: 33767370 PMCID: PMC8178323 DOI: 10.1038/s41437-021-00420-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 02/01/2023] Open
Abstract
Flour beetles of the genus Tribolium have been utilised as informative study systems for over a century and contributed to major advances across many fields. This review serves to highlight the significant historical contribution that Tribolium study systems have made to the fields of ecology and evolution, and to promote their use as contemporary research models. We review the broad range of studies employing Tribolium to make significant advances in ecology and evolution. We show that research using Tribolium beetles has contributed a substantial amount to evolutionary and ecological understanding, especially in the fields of population dynamics, reproduction and sexual selection, population and quantitative genetics, and behaviour, physiology and life history. We propose a number of future research opportunities using Tribolium, with particular focus on how their amenability to forward and reverse genetic manipulation may provide a valuable complement to other insect models.
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Affiliation(s)
- Michael D Pointer
- School of Biological Sciences, University of East Anglia, Norwich, UK.
| | - Matthew J G Gage
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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Mammola S, Lunghi E, Bilandžija H, Cardoso P, Grimm V, Schmidt SI, Hesselberg T, Martínez A. Collecting eco-evolutionary data in the dark: Impediments to subterranean research and how to overcome them. Ecol Evol 2021; 11:5911-5926. [PMID: 34141192 PMCID: PMC8207145 DOI: 10.1002/ece3.7556] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/25/2022] Open
Abstract
Caves and other subterranean habitats fulfill the requirements of experimental model systems to address general questions in ecology and evolution. Yet, the harsh working conditions of these environments and the uniqueness of the subterranean organisms have challenged most attempts to pursuit standardized research.Two main obstacles have synergistically hampered previous attempts. First, there is a habitat impediment related to the objective difficulties of exploring subterranean habitats and our inability to access the network of fissures that represents the elective habitat for the so-called "cave species." Second, there is a biological impediment illustrated by the rarity of most subterranean species and their low physiological tolerance, often limiting sample size and complicating laboratory experiments.We explore the advantages and disadvantages of four general experimental setups (in situ, quasi in situ, ex situ, and in silico) in the light of habitat and biological impediments. We also discuss the potential of indirect approaches to research. Furthermore, using bibliometric data, we provide a quantitative overview of the model organisms that scientists have exploited in the study of subterranean life.Our over-arching goal is to promote caves as model systems where one can perform standardized scientific research. This is important not only to achieve an in-depth understanding of the functioning of subterranean ecosystems but also to fully exploit their long-discussed potential in addressing general scientific questions with implications beyond the boundaries of this discipline.
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Affiliation(s)
- Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe)Finnish Museum of Natural History (LUOMUS)University of HelsinkiHelsinkiFinland
- Dark‐MEG: Molecular Ecology GroupWater Research Institute (IRSA)National Research Council (CNR)VerbaniaItaly
| | - Enrico Lunghi
- Key Laboratory of the Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
- Museo di Storia Naturale dell'Università degli Studi di Firenze“La Specola”FirenzeItaly
| | - Helena Bilandžija
- Department of Molecular BiologyRudjer Boskovic InstituteZagrebCroatia
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe)Finnish Museum of Natural History (LUOMUS)University of HelsinkiHelsinkiFinland
| | - Volker Grimm
- Department of Ecological ModellingHelmholtz Centre for Environmental Research – UFZLeipzigGermany
- Plant Ecology and Nature ConservationUniversity of PotsdamPotsdamGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Susanne I. Schmidt
- Institute of HydrobiologyBiology Centre CASČeské BudějoviceCzech Republic
| | | | - Alejandro Martínez
- Dark‐MEG: Molecular Ecology GroupWater Research Institute (IRSA)National Research Council (CNR)VerbaniaItaly
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Campos TL, Korhonen PK, Young ND. Cross-Predicting Essential Genes between Two Model Eukaryotic Species Using Machine Learning. Int J Mol Sci 2021; 22:5056. [PMID: 34064595 PMCID: PMC8150380 DOI: 10.3390/ijms22105056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/24/2022] Open
Abstract
Experimental studies of Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular and cellular processes in metazoans at large. Since the publication of their genomes, functional genomic investigations have identified genes that are essential or non-essential for survival in each species. Recently, a range of features linked to gene essentiality have been inferred using a machine learning (ML)-based approach, allowing essentiality predictions within a species. Nevertheless, predictions between species are still elusive. Here, we undertake a comprehensive study using ML to discover and validate features of essential genes common to both C. elegans and D. melanogaster. We demonstrate that the cross-species prediction of gene essentiality is possible using a subset of features linked to nucleotide/protein sequences, protein orthology and subcellular localisation, single-cell RNA-seq, and histone methylation markers. Complementary analyses showed that essential genes are enriched for transcription and translation functions and are preferentially located away from heterochromatin regions of C. elegans and D. melanogaster chromosomes. The present work should enable the cross-prediction of essential genes between model and non-model metazoans.
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Affiliation(s)
- Tulio L. Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (T.L.C.); (P.K.K.)
- Bioinformatics Core Facility, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife 50740-465, PE, Brazil
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (T.L.C.); (P.K.K.)
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (T.L.C.); (P.K.K.)
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Adamo M, Chialva M, Calevo J, Bertoni F, Dixon K, Mammola S. Plant scientists' research attention is skewed towards colourful, conspicuous and broadly distributed flowers. NATURE PLANTS 2021; 7:574-578. [PMID: 33972712 DOI: 10.1038/s41477-021-00912-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Scientists' research interests are often skewed toward charismatic organisms, but quantifying research biases is challenging. By combining bibliometric data with trait-based approaches and using a well-studied alpine flora as a case study, we demonstrate that morphological and colour traits, as well as range size, have significantly more impact on species choice for wild flowering plants than traits related to ecology and rarity. These biases should be taken into account to inform more objective plant conservation efforts.
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Affiliation(s)
- Martino Adamo
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy.
| | - Matteo Chialva
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Jacopo Calevo
- Department of Biology, University of Napoli Federico II, Napoli, Italy
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Filippo Bertoni
- Humanities of Nature, Museum für Naturkunde, Berlin, Germany
| | - Kingsley Dixon
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Stefano Mammola
- Molecular Ecology Group, Water Research Institute (IRSA), National Research Council (CNR), Verbania Pallanza, Italy
- Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History (LUOMUS), University of Helsink, Helsinki, Finland
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46
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Lopes AM, Dahms HU, Converti A, Mariottini GL. Role of model organisms and nanocompounds in human health risk assessment. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:285. [PMID: 33876320 DOI: 10.1007/s10661-021-09066-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/11/2021] [Indexed: 06/12/2023]
Abstract
Safeguarding the environment is one of the most serious modern challenges, as increasing amounts of chemical compounds are produced and released into the environment, causing a serious threat to the future health of the Earth as well as organisms and humans on a global scale. Ecotoxicology is an integrative science involving different physical, chemical, biological, and social aspects concerned with the study of toxic effects caused by natural or synthetic pollutants on any constituents of ecosystems, including animals (including humans), plants, or microorganisms, in an integral context. In recent decades, this science has undergone considerable development by addressing environmental risk assessments through the biomonitoring of indicator species using biomarkers, model organisms, and nanocompounds in toxicological assays. Since a single taxon cannot be representative of complex ecotoxicological effects and mechanisms of action of a chemical, the use of test batteries is widely accepted in ecotoxicology. Test batteries include properly chosen organisms that are easy to breed, adapt easily to laboratory conditions, and are representative of the environmental compartment under consideration. One of the main issues of toxicological and ecotoxicological research is to gain a deeper understanding of how data should be obtained through laboratory and field approaches using experimental models and how they could be extrapolated to humans. There is a tendency to replace animal tests with in vitro systems and to perform them according to standardized analytical methods and the rules of the so-called good laboratory practice (GLP). This paper aims to review this topic to stimulate both efforts to understand the toxicological and ecotoxicological properties of natural and synthetic chemicals and the possible use of such data for application to humans.
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Affiliation(s)
- André Moreni Lopes
- Faculty of Pharmaceutical Sciences, University of Campinas - UNICAMP, Campinas, Brazil.
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100 Shin-Chuan 1st Road, Kaohsiung, 80708, Taiwan
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Attilio Converti
- Department of Civil, Chemical and Environmental Engineering, University of Genova, Genova, 16145, Italy
| | - Gian Luigi Mariottini
- Department of Earth, Environment and Life Sciences, University of Genova, Genova, 16132, Italy
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Zhang R, Li C, Yu M, Huang X, Zhang M, Liu S, Pan S, Xue W, Wang C, Mao C, Zhang H, Fan G. Chromosome-level genome assembly of the humpback puffer, Tetraodon palembangensis. GIGABYTE 2021; 2021:gigabyte17. [PMID: 36824331 PMCID: PMC9632004 DOI: 10.46471/gigabyte.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/31/2021] [Indexed: 11/09/2022] Open
Abstract
The humpback puffer, Tetraodon palembangensis, is a poisonous freshwater pufferfish species mainly distributed in Southeast Asia (Thailand, Laos, Malaysia and Indonesia). The humpback puffer has many interesting biological features, such as inactivity, tetrodotoxin production and body expansion. Here, we report the first chromosome-level genome assembly of the humpback puffer. The genome size is 362 Mb, with a contig N50 value of ∼1.78 Mb and a scaffold N50 value of ∼15.8 Mb. Based on this genome assembly, ∼61.5 Mb (18.11%) repeat sequences were identified, 19,925 genes were annotated, and the function of 90.01% of these genes could be predicted. Finally, a phylogenetic tree of ten teleost fish species was constructed. This analysis suggests that the humpback puffer and T. nigroviridis share a common ancestor 18.1 million years ago (MYA), and diverged from T. rubripes 45.8 MYA. The humpback puffer genome will be a valuable genomic resource to illustrate possible mechanisms of tetrodotoxin synthesis and tolerance.
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Affiliation(s)
- Rui Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Chang Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Mengjun Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | | | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Shanshan Pan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Weizhen Xue
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Congyan Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Chunyan Mao
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China,Department of Biology, Hong Kong Baptist University, Hong Kong, China, Corresponding authors. E-mail: ;
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, Corresponding authors. E-mail: ;
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48
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The Ecology of the Zebra Finch Makes It a Great Laboratory Model but an Outlier amongst Passerine Birds. BIRDS 2021. [DOI: 10.3390/birds2010004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Zebra Finches have become the most widely researched bird species outside of those used in agricultural production. Their adoption as the avian model of choice is largely down to a number of characteristics that make them easy to obtain and use in captivity. The main point of our paper is that the very characteristics that make the Zebra Finch a highly amenable laboratory model species mean that it is by definition different from many other passerine birds, and therefore not a good general model for many research areas. The Zebra Finch is likely to be particularly resilient to the effects of stress early in life, and is likely to show great flexibility in dealing with a wide variety of conditions later in life. Whilst it is tempting for researchers to turn to species such as the Zebra Finch, that can be the focus of manipulative work in the laboratory, we caution that the findings of such studies may confound our understanding of general avian biology. The Zebra Finch will remain an excellent species for laboratory work, and our paper should help to direct and interpret future work in the laboratory and the field.
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Adonin L, Drozdov A, Barlev NA. Sea Urchin as a Universal Model for Studies of Gene Networks. Front Genet 2021; 11:627259. [PMID: 33552139 PMCID: PMC7854572 DOI: 10.3389/fgene.2020.627259] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 12/10/2020] [Indexed: 01/06/2023] Open
Abstract
The purple sea urchin Strongylocentrotus purpuratus has been used for over 150 years as a model organism in developmental biology. Using this model species, scientists have been able to describe, in detail, the mechanisms of cell cycle control and cell adhesion, fertilization, calcium signaling, cell differentiation, and death. Massive parallel sequencing of the sea urchin genome enabled the deciphering of the main components of gene regulatory networks during the activation of embryonic signaling pathways. This knowledge helped to extrapolate aberrations in somatic cells that may lead to diseases, including cancer in humans. Furthermore, since many, if not all, developmental signaling pathways were shown to be controlled by non-coding RNAs (ncRNAs), the sea urchin organism represents an attractive experimental model. In this review, we discuss the main discoveries in the genetics, genomics, and transcriptomics of sea urchins during embryogenesis with the main focus on the role of ncRNAs. This information may be useful for comparative studies between different organisms, and may help identify new regulatory networks controlled by ncRNAs.
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Affiliation(s)
- Leonid Adonin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, Tyumen, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Anatoliy Drozdov
- Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Nickolai A Barlev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia.,Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
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50
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Abstract
Whereas scientists interested in subterranean life typically insist that their research is exciting, adventurous, and important to answer general questions, this enthusiasm and potential often fade when the results are translated into scientific publications. This is because cave research is often written by cave scientists for cave scientists; thus, it rarely “leaves the cave”. However, the status quo is changing rapidly. We analysed 21,486 articles focused on subterranean ecosystems published over the last three decades and observed a recent, near-exponential increase in their annual citations and impact factor. Cave research is now more often published in non-specialized journals, thanks to a number of authors who are exploiting subterranean habitats as model systems for addressing important scientific questions. Encouraged by this positive trend, we here propose a few personal ideas for improving the generality of subterranean literature, including tips for framing broadly scoped research and making it accessible to a general audience, even when published in cave-specialized journals. Hopefully, this small contribution will succeed in condensing and broadcasting even further the collective effort taken by the subterranean biology community to bring their research “outside the cave”.
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