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López-Pérez M, Aguirre-Garrido F, Herrera-Zúñiga L, Fernández FJ. Gene as a dynamical notion: An extensive and integrative vision. Redefining the gene concept, from traditional to genic-interaction, as a new dynamical version. Biosystems 2023; 234:105060. [PMID: 37844827 DOI: 10.1016/j.biosystems.2023.105060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/08/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
The current concept of gene has been very useful during the 20th and 21st centuries. However, recent advances in molecular biology and bioinformatics, which have further diversified the functional and adaptive profile of genetic information and its integration with cell physiology and environmental response, have contributed to focusing on additional new gene properties besides the traditional definition. Considering the inherent complexity of gene expression, whose adaptive objective must be referred to the Tortoise-Hare model, in which two tendencies converge, one focused on rapid adaptation to achieve survival, and the other that prevents an over-adaptation effect. In this context, a revision of the gene concept must be made, which must include these new mechanisms and approaches. In this paper, we propose a new conception of the idea of a gene that moves from a static and defined version of hereditary information to a dynamic idea that preponderates gene interaction (circumscribed to that established between protein-protein, protein-nucleic acid, and nucleic acid-nucleic acid) and the selection it exerts, as the irreducible element that works in a coordinated way in a genomic regulatory network (GRN).
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Affiliation(s)
- Marcos López-Pérez
- Environmental Sciences Department, Universidad Autónoma Metropolitana (Lerma Unit) Av. de las Garzas N° 10, Col. El Panteón, Municipio de Lerma de Villada, Estado de México, C.P. 52005, Mexico.
| | - Félix Aguirre-Garrido
- Environmental Sciences Department, Universidad Autónoma Metropolitana (Lerma Unit) Av. de las Garzas N° 10, Col. El Panteón, Municipio de Lerma de Villada, Estado de México, C.P. 52005, Mexico
| | - Leonardo Herrera-Zúñiga
- Chemistry Department, Universidad Autónoma Metropolitana (Iztapalapa Unit), C.P. 09340, Mexico City, Mexico
| | - Francisco J Fernández
- Biotechnology Department, Universidad Autónoma Metropolitana (Iztapalapa Unit), C.P. 09340, Mexico City, Mexico.
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Xu J, Pratt HE, Moore JE, Gerstein MB, Weng Z. Building integrative functional maps of gene regulation. Hum Mol Genet 2022; 31:R114-R122. [PMID: 36083269 PMCID: PMC9585680 DOI: 10.1093/hmg/ddac195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Every cell in the human body inherits a copy of the same genetic information. The three billion base pairs of DNA in the human genome, and the roughly 50 000 coding and non-coding genes they contain, must thus encode all the complexity of human development and cell and tissue type diversity. Differences in gene regulation, or the modulation of gene expression, enable individual cells to interpret the genome differently to carry out their specific functions. Here we discuss recent and ongoing efforts to build gene regulatory maps, which aim to characterize the regulatory roles of all sequences in a genome. Many researchers and consortia have identified such regulatory elements using functional assays and evolutionary analyses; we discuss the results, strengths and shortcomings of their approaches. We also discuss new techniques the field can leverage and emerging challenges it will face while striving to build gene regulatory maps of ever-increasing resolution and comprehensiveness.
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Affiliation(s)
- Jinrui Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
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Wells T, Carruthers T, Muñoz-Rodríguez P, Sumadijaya A, Wood JRI, Scotland RW. Species as a Heuristic: Reconciling Theory and Practice. Syst Biol 2022; 71:1233-1243. [PMID: 34672346 PMCID: PMC9366457 DOI: 10.1093/sysbio/syab087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 10/07/2021] [Accepted: 10/16/2021] [Indexed: 11/21/2022] Open
Abstract
Species are crucial to most branches of biological research, yet remain controversial in terms of definition, delimitation, and reality. The difficulty of resolving the "species problem" stems from the tension between their theoretical concept as groups of evolving and highly variable organisms and the practical need for a stable and comparable unit of biology. Here, we suggest that treating species as a heuristic can be consistent with a theoretical definition of what species are and with the practical means by which they are identified and delimited. Specifically, we suggest that theoretically species are heuristic since they comprise clusters of closely related individuals responding in a similar manner to comparable sets of evolutionary and ecological forces, whilst they are practically heuristic because they are identifiable by the congruence of contingent properties indicative of those forces. This reconciliation of the theoretical basis of species with their practical applications in biological research allows for a loose but relatively consistent definition of species based on the strategic analysis and integration of genotypic, phenotypic, and ecotypic data. [Cohesion; heuristic; homeostasis; lineage; species problem.].
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Affiliation(s)
- Tom Wells
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Tom Carruthers
- The Herbarium & ToL, Royal Botanic Garden, Kew, Richmond, UK
| | | | - Alex Sumadijaya
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Research Center for Biology National Research and Innovation Agency, Cibinong Science Center, Indonesia
| | - John R I Wood
- Department of Plant Sciences, University of Oxford, Oxford, UK
- The Herbarium & ToL, Royal Botanic Garden, Kew, Richmond, UK
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Roy B, Lee E, Li T, Rampersaud M. Role of miRNAs in Neurodegeneration: From Disease Cause to Tools of Biomarker Discovery and Therapeutics. Genes (Basel) 2022; 13:genes13030425. [PMID: 35327979 PMCID: PMC8951370 DOI: 10.3390/genes13030425] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 11/16/2022] Open
Abstract
Neurodegenerative diseases originate from neuronal loss in the central nervous system (CNS). These debilitating diseases progress with age and have become common due to an increase in longevity. The National Institute of Environmental Health Science’s 2021 annual report suggests around 6.2 million Americans are living with Alzheimer’s disease, and there is a possibility that there will be 1.2 million Parkinson’s disease patients in the USA by 2030. There is no clear-cut universal mechanism for identifying neurodegenerative diseases, and therefore, they pose a challenge for neurobiology scientists. Genetic and environmental factors modulate these diseases leading to familial or sporadic forms. Prior studies have shown that miRNA levels are altered during the course of the disease, thereby suggesting that these noncoding RNAs may be the contributing factor in neurodegeneration. In this review, we highlight the role of miRNAs in the pathogenesis of neurodegenerative diseases. Through this review, we aim to achieve four main objectives: First, we highlight how dysregulation of miRNA biogenesis led to these diseases. Second, we highlight the computational or bioinformatics tools required to identify the putative molecular targets of miRNAs, leading to biological molecular pathways or mechanisms involved in these diseases. Third, we focus on the dysregulation of miRNAs and their target genes leading to several neurodegenerative diseases. In the final section, we highlight the use of miRNAs as potential diagnostic biomarkers in the early asymptomatic preclinical diagnosis of these age-dependent debilitating diseases. Additionally, we discuss the challenges and advances in the development of miRNA therapeutics for brain targeting. We list some of the innovative strategies employed to deliver miRNA into target cells and the relevance of these viral and non-viral carrier systems in RNA therapy for neurodegenerative diseases. In summary, this review highlights the relevance of studying brain-enriched miRNAs, the mechanisms underlying their regulation of target gene expression, their dysregulation leading to progressive neurodegeneration, and their potential for biomarker marker and therapeutic intervention. This review thereby highlights ways for the effective diagnosis and prevention of these neurodegenerative disorders in the near future.
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Affiliation(s)
- Bidisha Roy
- Life Science Centre, Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07012, USA
- Correspondence:
| | - Erica Lee
- Department of Pathology, Icahn School of Medicine, New York, NY 10029, USA; (E.L.); (T.L.); (M.R.)
| | - Teresa Li
- Department of Pathology, Icahn School of Medicine, New York, NY 10029, USA; (E.L.); (T.L.); (M.R.)
| | - Maria Rampersaud
- Department of Pathology, Icahn School of Medicine, New York, NY 10029, USA; (E.L.); (T.L.); (M.R.)
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Sari B, Isik M, Eylem CC, Kilic C, Okesola BO, Karakaya E, Emregul E, Nemutlu E, Derkus B. Omics Technologies for High-Throughput-Screening of Cell-Biomaterial Interactions. Mol Omics 2022; 18:591-615. [DOI: 10.1039/d2mo00060a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent research effort in biomaterial development has largely focused on engineering bio-instructive materials to stimulate specific cell signaling. Assessing the biological performance of these materials using time-consuming and trial-and-error traditional...
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García S. A, Casamayor JC. On how to generalize species-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome. BMC Bioinformatics 2021; 22:353. [PMID: 34592923 PMCID: PMC8482561 DOI: 10.1186/s12859-021-04237-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the genome, with all of its components and intrinsic relationships, is a great challenge. Conceptual modeling techniques have been used as a means to face this challenge. The heterogeneity and idiosyncrasy of genomic use cases mean that conceptual modeling techniques are used to generate conceptual schemes that focus on too specific scenarios (i.e., they are species-specific conceptual schemes). Our research group developed two different conceptual schemes. The first one is the Conceptual Schema of the Human Genome, which is intended to improve Precision Medicine and genetic diagnosis. The second one is the Conceptual Schema of the Citrus Genome, which is intended to identify the genetic cause of relevant phenotypes in the agri-food field. METHODS Our two conceptual schemes have been ontologically compared to identify their similarities and differences. Based on this comparison, several changes have been performed in the Conceptual Schema of the Human Genome in order to obtain the first version of a species-independent Conceptual Schema of the Genome. Identifying the different genome information items used in each genomic case study has been essential in achieving our goal. The changes needed to provide an expanded, more generic version of the Conceptual Schema of the Human Genome are analyzed and discussed. RESULTS This work presents a new CS called the Conceptual Schema of the Genome that is ready to be adapted to any specific working genome-based context (i.e., species-independent). CONCLUSION The generated Conceptual Schema of the Genome works as a global, generic element from which conceptual views can be created in order to work with any specific species. This first working version can be used in the human use case, in the citrus use case, and, potentially, in more use cases of other species.
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Affiliation(s)
- Alberto García S.
- PROS Research Center, Universitat Politècnica de València, Camino de Vera, Valencia, Spain
| | - Juan Carlos Casamayor
- PROS Research Center, Universitat Politècnica de València, Camino de Vera, Valencia, Spain
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Hasan N, Ma Z, Liu J, Li Z, Qian C, Liu Y, Chen M, Jiang H, Jia X, Ma Z. Selective Expression of a Carbazole-Phenothiazine Derivative Leads to Dual-mode AIEE, TADF and Distinctive Mechanochromism. Chemphyschem 2021; 22:2093-2098. [PMID: 34318995 DOI: 10.1002/cphc.202100435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/25/2021] [Indexed: 12/11/2022]
Abstract
In this article, we report a newly designed D-A-D' derivative (CNCzPTZ), which displays selective expression of chromophores. This enables CNCzPTZ with solvatochromism, rare dual-mode AIEE properties, solid-state dual-emissions with phosphorescence and distinctive mechanochromism.CNCzPTZ exhibits dual-mode AIEE properties, since the emission band abruptly shifts from 550 nm to 500 nm as the water fraction increases. In the crystalline state, CNCzPTZ demonstrated dual emission bands of 478 nm and 538 nm.CNCzPTZ shows distinctive mechanochromic property in the solid state due to the planarization.
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Affiliation(s)
- Numan Hasan
- Beijing State Key Laboratory of Organic-Inorganic Composites, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhimin Ma
- National high-tech industrial development zone in Jingdezhen, Jingdezhen, 333000, China
| | - Jianwei Liu
- Beijing State Key Laboratory of Organic-Inorganic Composites, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zewei Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and, Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Chen Qian
- Beijing State Key Laboratory of Organic-Inorganic Composites, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yan Liu
- Beijing State Key Laboratory of Organic-Inorganic Composites, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Mingxing Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and, Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Hong Jiang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and, Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Xinru Jia
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and, Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Zhiyong Ma
- Beijing State Key Laboratory of Organic-Inorganic Composites, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
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Szymanski E, Scher E. Models for DNA Design Tools: The Trouble with Metaphors Is That They Don't Go Away. ACS Synth Biol 2019; 8:2635-2641. [PMID: 31580653 DOI: 10.1021/acssynbio.9b00302] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Synthetic biology relies heavily on DNA design tools to enable manipulation of DNA in silico. Existing tools, however, are falling short of enabling aspirations for the field that emphasize efficient, automated design pipelines. We review existing DNA design tools, identify underlying similarities in how they model correlations between DNA structure and function, and suggest that iterating the existing model is unlikely to overcome limitations in matching software applications to design aspirations. The current model is predicated on metaphors conceptualizing DNA as linear text, accounting for relatively little of the known complexity of DNA function. New models that can account for more of that complexity and thus enable more ambitious DNA design goals are likely to call for new underlying metaphors-a need that may be addressed by rethinking DNA in terms of human rather than computer languages.
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Affiliation(s)
- Erika Szymanski
- Colorado State University, Department of English, Fort Collins, Colorado 80523, United States
| | - Emily Scher
- Informatics Forum, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, United Kingdom
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He Z, Yang Y, Liang HW, Liu JW, Yu SH. Nanowire Genome: A Magic Toolbox for 1D Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1902807. [PMID: 31566828 DOI: 10.1002/adma.201902807] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/07/2019] [Indexed: 06/10/2023]
Abstract
1D nanomaterials with high aspect ratio, i.e., nanowires and nanotubes, have inspired considerable research interest thanks to the fact that exotic physical and chemical properties emerge as their diameters approach or fall into certain length scales, such as the wavelength of light, the mean free path of phonons, the exciton Bohr radius, the critical size of magnetic domains, and the exciton diffusion length. On the basis of their components, aspect ratio, and properties, there may be imperceptible connections among hundreds of nanowires prepared by different strategies. Inspired by the heredity system in life, a new concept termed the "nanowire genome" is introduced here to clarify the relationships between hundreds of nanowires reported previously. As such, this approach will not only improve the tools incorporating the prior nanowires but also help to precisely synthesize new nanowires and even assist in the prediction on the properties of nanowires. Although the road from start-ups to maturity is long and fraught with challenges, the genetical syntheses of more than 200 kinds of nanostructures stemming from three mother nanowires (Te, Ag, and Cu) are summarized here to demonstrate the nanowire genome as a versatile toolbox. A summary and outlook on future challenges in this field are also presented.
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Affiliation(s)
- Zhen He
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Science Center of CAS, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Yuan Yang
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Science Center of CAS, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Hai-Wei Liang
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Science Center of CAS, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Jian-Wei Liu
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Science Center of CAS, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Shu-Hong Yu
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Science Center of CAS, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
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Wang X, Wang S, Song T. A Spectral Rotation Method with Triplet Periodicity Property for Planted Motif Finding Problems. Comb Chem High Throughput Screen 2019; 22:683-693. [PMID: 31782356 DOI: 10.2174/1386207322666191129112433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/18/2019] [Accepted: 08/07/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Genes are known as functional patterns in the genome and are presumed to have biological significance. They can indicate binding sites for transcription factors and they encode certain proteins. Finding genes from biological sequences is a major task in computational biology for unraveling the mechanisms of gene expression. OBJECTIVE Planted motif finding problems are a class of mathematical models abstracted from the process of detecting genes from genome, in which a specific gene with a number of mutations is planted into a randomly generated background sequence, and then gene finding algorithms can be tested to check if the planted gene can be found in feasible time. METHODS In this work, a spectral rotation method based on triplet periodicity property is proposed to solve planted motif finding problems. RESULTS The proposed method gives significant tolerance of base mutations in genes. Specifically, genes having a number of substitutions can be detected from randomly generated background sequences. Experimental results on genomic data set from Saccharomyces cerevisiae reveal that genes can be visually distinguished. It is proposed that genes with about 50% mutations can be detected from randomly generated background sequences. CONCLUSION It is found that with about 5 insertions or deletions, this method fails in finding the planted genes. For a particular case, if the deletion of bases is located at the beginning of the gene, that is, bases are not randomly deleted, then the tolerance of the method for base deletion is increased.
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Affiliation(s)
- Xun Wang
- School of Electrical Engineering and Automation, Tiangong University, Tianjin 300387, China
| | - Shudong Wang
- School of Electrical Engineering and Automation, Tiangong University, Tianjin 300387, China
| | - Tao Song
- School of Electrical Engineering and Automation, Tiangong University, Tianjin 300387, China.,Department of Artificial Intelligence, Faculty of Computer Science, Polytechnical University of Madrid, Campus de Montegancedo, Boadilla del Monte 28660, Madrid, Spain
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Hatje K, Mühlhausen S, Simm D, Kollmar M. The Protein-Coding Human Genome: Annotating High-Hanging Fruits. Bioessays 2019; 41:e1900066. [PMID: 31544971 DOI: 10.1002/bies.201900066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/07/2019] [Indexed: 12/19/2022]
Abstract
The major transcript variants of human protein-coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is considerable disagreement on the annotation of about 2000 genes-they can be protein-coding, noncoding, or pseudogenes-and on the annotation of most of the predicted alternative transcripts. Pure transcriptome mapping approaches seem to be limited in discriminating functional expression from noise. These limitations have partially been overcome by dedicated algorithms to detect alternative spliced micro-exons and wobble splice variants. Recently, knowledge about splice mechanism and protein structure are incorporated into an algorithm to predict neighboring homologous exons, often spliced in a mutually exclusive manner. Predicted exons are evaluated by transcript data, structural compatibility, and evolutionary conservation, revealing hundreds of novel coding exons and splice mechanism re-assignments. The emerging human pan-genome is necessitating distinctive annotations incorporating differences between individuals and between populations.
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Affiliation(s)
- Klas Hatje
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstr. 124, 4070, Basel, Switzerland
| | - Stefanie Mühlhausen
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Dominic Simm
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Goldschmidtstr. 7, 37077, Göttingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
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Abstract
A new paradigm for disease diagnosis and treatment is emerging that will bring about changes in health care delivery in and out of the hospital setting. Over the past several decades, genomic medicine has been one of the fastest growing fields in acute and chronic health care. This quick growth has created a lag in genomics knowledge and preparation among nurses and health care providers. Genomic medicine may lead to more precise evaluation, diagnosis, and management of selected acute care conditions. This article reviews the current state of genetic and genomics science and looks at the expanding field of genomic medicine's integration into precision medicine. The aim of this article is to raise awareness and spark further inquiry to the remarkable field of genomics and precision medicine.
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Affiliation(s)
- Christine Kessler
- Christine Kessler is an Endocrinology Nurse Practitioner and Founder, Metabolic Medicine Associates, 6315 Vista Court, King George, VA 22485
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Scherrer K. Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review. Exp Cell Res 2018; 373:1-33. [PMID: 30266658 DOI: 10.1016/j.yexcr.2018.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 12/15/2022]
Abstract
The main purpose of this review is to recall for investigators - and in particular students -, some of the early data and concepts in molecular genetics and biology that are rarely cited in the current literature and are thus invariably overlooked. There is a growing tendency among editors and reviewers to consider that only data produced in the last 10-20 years or so are pertinent. However this is not the case. In exact science, sound data and lucid interpretation never become obsolete, and even if forgotten, will resurface sooner or later. In the field of gene expression, covered in the present review, recent post-genomic data have indeed confirmed many of the earlier results and concepts developed in the mid-seventies, well before the start of the recombinant DNA revolution. Human brains and even the most powerful computers, have difficulty in handling and making sense of the overwhelming flow of data generated by recent high-throughput technologies. This was easier when low throughput, more integrative methods based on biochemistry and microscopy dominated biological research. Nowadays, the need for organising concepts is ever more important, otherwise the mass of available data can generate only "building ruins" - the bricks without an architect. Concepts such as pervasive transcription of genomes, large genomic domains, full domain transcripts (FDTs) up to 100 kb long, the prevalence of post-transcriptional events in regulating eukaryotic gene expression, and the 3D-genome architecture, were all developed and discussed before 1990, and are only now coming back into vogue. Thus, to review the impact of earlier concepts on later developments in the field, I will confront former and current data and ideas, including a discussion of old and new methods. Whenever useful, I shall first briefly report post-genomic developments before addressing former results and interpretations. Equally important, some of the terms often used sloppily in scientific discussions will be clearly defined. As a basis for the ensuing discussion, some of the issues and facts related to eukaryotic gene expression will first be introduced. In chapter 2 the evolution in perception of biology over the last 60 years and the impact of the recombinant DNA revolution will be considered. Then, in chapter 3 data and theory concerning the genome, gene expression and genetics will be reviewed. The experimental and theoretical definition of the gene will be discussed before considering the 3 different types of genetic information - the "Triad" - and the importance of post-transcriptional regulation of gene expression in the light of the recent finding that 90% of genomic DNA seems to be transcribed. Some previous attempts to provide a conceptual framework for these observations will be recalled, in particular the "Cascade Regulation Hypothesis" (CRH) developed in 1967-85, and the "Gene and Genon" concept proposed in 2007. A knowledge of the size of primary transcripts is of prime importance, both for experimental and theoretical reasons, since these molecules represent the primary units of the "RNA genome" on which most of the post-transcriptional regulation of gene expression occurs. In chapter 4, I will first discuss some current post-genomic topics before summarising the discovery of the high Mr-RNA transcripts, and the investigation of their processing spanning the last 50 years. Since even today, a consensus concerning the real form of primary transcripts in eukaryotic cells has not yet been reached, I will refer to the viral and specialized cellular models which helped early on to understand the mechanisms of RNA processing and differential splicing which operate in cells and tissues. As a well-studied example of expression and regulation of a specific cellular gene in relation to differentiation and pathology, I will discuss the early and recent work on expression of the globin genes in nucleated avian erythroblasts. An important concept is that the primary transcript not only embodies protein-coding information and regulation of its expression, but also the 3D-structure of the genomic DNA from which it was derived. The wealth of recent post-genomic data published in this field emphasises the importance of a fundamental principle of genome organisation and expression that has been overlooked for years even though it was already discussed in the 1970-80ties. These issues are addressed in chapter 5 which focuses on the involvement of the nuclear matrix and nuclear architecture in DNA and RNA biology. This section will make reference to the Unified Matrix Hypothesis (UMH), which was the first molecular model of the 3D organisation of DNA and RNA. The chapter on the "RNA-genome and peripheral memories" discusses experimental data on the ribonucleoprotein complexes containing pre-mRNA (pre-mRNPs) and mRNA (mRNPs) which are organised in nuclear and cytoplasmic spaces respectively. Finally, "Outlook " will enumerate currently unresolved questions in the field, and will propose some ideas that may encourage further investigation, and comprehension of available experimental data still in need of interpretation. In chapter 8, some propositions and paradigms basic to the authors own analysis are discussed. "In conclusion" the raison d'être of this review is recalled and positioned within the overall framework of scientific endeavour.
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Affiliation(s)
- Klaus Scherrer
- Institute Jacques Monod, CNRS, University Paris Diderot, Paris, France.
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The Contributions of ‘Diet’, ‘Genes’, and Physical Activity to the Etiology of Obesity: Contrary Evidence and Consilience. Prog Cardiovasc Dis 2018; 61:89-102. [DOI: 10.1016/j.pcad.2018.06.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 06/10/2018] [Indexed: 12/12/2022]
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15
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Rangel-Chavez C, Galan-Vasquez E, Martinez-Antonio A. Consensus architecture of promoters and transcription units in Escherichia coli: design principles for synthetic biology. MOLECULAR BIOSYSTEMS 2017; 13:665-676. [PMID: 28256660 DOI: 10.1039/c6mb00789a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Genetic information in genomes is ordered, arranged in such a way that it constitutes a code, the so-called cis regulatory code. The regulatory machinery of the cell, termed trans-factors, decodes and expresses this information. In this way, genomes maintain a potential repertoire of genetic programs, parts of which are executed depending on the presence of active regulators in each condition. These genetic programs, executed by the regulatory machinery, have functional units in the genome delimited by punctuation-like marks. In genetic terms, these informational phrases correspond to transcription units, which are the minimal genetic information expressed consistently from initiation to termination marks. Between the start and final punctuation marks, additional marks are present that are read by the transcriptional and translational machineries. In this work, we look at all the experimentally described and predicted genetic elements in the bacterium Escherichia coli K-12 MG1655 and define a comprehensive architectural organization of transcription units to reveal the natural genome-design and to guide the construction of synthetic genetic programs.
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Affiliation(s)
- Cynthia Rangel-Chavez
- Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Campus Irapuato, Km. 9.6 Libramiento Norte Carr, Irapuato-León 36821, Irapuato Gto, Mexico.
| | - Edgardo Galan-Vasquez
- Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Campus Irapuato, Km. 9.6 Libramiento Norte Carr, Irapuato-León 36821, Irapuato Gto, Mexico.
| | - Agustino Martinez-Antonio
- Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Campus Irapuato, Km. 9.6 Libramiento Norte Carr, Irapuato-León 36821, Irapuato Gto, Mexico.
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16
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Orgogozo V, Peluffo AE, Morizot B. The "Mendelian Gene" and the "Molecular Gene": Two Relevant Concepts of Genetic Units. Curr Top Dev Biol 2017; 119:1-26. [PMID: 27282022 DOI: 10.1016/bs.ctdb.2016.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
We focus here on two prevalent meanings of the word gene in research articles. On one hand, the gene, named here "molecular gene," is a stretch of DNA that is transcribed and codes for an RNA or a polypeptide with a known or presumed function (as in "gene network"), whose exact spatial delimitation on the chromosome remains a matter of debate, especially in cases with alternative splicing, antisense transcripts, etc. On the other hand, the gene, called here "Mendelian gene," is a segregating genetic unit which is detected through phenotypic differences associated with different alleles at the same locus (as in "gene flow"). We show that the "Mendelian gene" concept is still extensively used today in biology research and is sometimes confused with the "molecular gene." We try here to clarify the distinction between both concepts. Efforts to delineate the beginning and the end of the DNA sequence corresponding to the "Mendelian gene" and the "molecular gene" reveal that both entities do not always match. We argue that both concepts are part of two relevant frameworks for explaining the biological world.
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Affiliation(s)
- V Orgogozo
- Institut Jacques Monod, UMR 7592, CNRS-Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
| | - A E Peluffo
- Institut Jacques Monod, UMR 7592, CNRS-Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - B Morizot
- Université Aix-Marseille, CNRS UMR 7304, Aix-en-Provence, France
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17
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Abstract
This paper presents a history of the changing meanings of the term "gene," over more than a century, and a discussion of why this word, so crucial to genetics, needs redefinition today. In this account, the first two phases of 20th century genetics are designated the "classical" and the "neoclassical" periods, and the current molecular-genetic era the "modern period." While the first two stages generated increasing clarity about the nature of the gene, the present period features complexity and confusion. Initially, the term "gene" was coined to denote an abstract "unit of inheritance," to which no specific material attributes were assigned. As the classical and neoclassical periods unfolded, the term became more concrete, first as a dimensionless point on a chromosome, then as a linear segment within a chromosome, and finally as a linear segment in the DNA molecule that encodes a polypeptide chain. This last definition, from the early 1960s, remains the one employed today, but developments since the 1970s have undermined its generality. Indeed, they raise questions about both the utility of the concept of a basic "unit of inheritance" and the long implicit belief that genes are autonomous agents. Here, we review findings that have made the classic molecular definition obsolete and propose a new one based on contemporary knowledge.
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Affiliation(s)
- Petter Portin
- Laboratory of Genetics, Department of Biology, University of Turku, 20014, Finland
| | - Adam Wilkins
- Institute of Theoretical Biology, Humboldt Universität zu Berlin, 10115, Germany
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18
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Griffiths DA. Queer Genes: Realism, Sexuality and Science. JOURNAL OF CRITICAL REALISM 2016; 15:511-529. [PMID: 28058037 PMCID: PMC5167250 DOI: 10.1080/14767430.2016.1210872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
What are 'gay genes' and are they real? This article looks at key research into these hypothesized gay genes, made possible, in part, by the Human Genome Project. I argue that the complexity of both genetics and human sexuality demands a truly critical approach: one that takes into account feminist epistemologies of science and queer approaches to the body, while putting into conversation resources from agential realism and critical realism. This approach is able to maintain the agential complexity of genetic materiality, while also critically challenging the seemingly stable relationships between sex, gender and sexuality.
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19
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Peterson T, Müller GB. Phenotypic Novelty in EvoDevo: The Distinction Between Continuous and Discontinuous Variation and Its Importance in Evolutionary Theory. Evol Biol 2016; 43:314-335. [PMID: 27512237 PMCID: PMC4960286 DOI: 10.1007/s11692-016-9372-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 01/29/2016] [Indexed: 10/25/2022]
Abstract
The introduction of novel phenotypic structures is one of the most significant aspects of organismal evolution. Yet the concept of evolutionary novelty is used with drastically different connotations in various fields of research, and debate exists about whether novelties represent features that are distinct from standard forms of phenotypic variation. This article contrasts four separate uses for novelty in genetics, population genetics, morphology, and behavioral science, before establishing how novelties are used in evolutionary developmental biology (EvoDevo). In particular, it is detailed how an EvoDevo-specific research approach to novelty produces insight distinct from other fields, gives the concept explanatory power with predictive capacities, and brings new consequences to evolutionary theory. This includes the outlining of research strategies that draw attention to productive areas of inquiry, such as threshold dynamics in development. It is argued that an EvoDevo-based approach to novelty is inherently mechanistic, treats the phenotype as an agent with generative potential, and prompts a distinction between continuous and discontinuous variation in evolutionary theory.
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Affiliation(s)
- Tim Peterson
- Department of Theoretical Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Gerd B. Müller
- Department of Theoretical Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
- The KLI Institute, Martinstrasse 12, 3400 Klosterneuburg, Austria
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20
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Xu B, Mu Y, Mao Z, Xie Z, Wu H, Zhang Y, Jin C, Chi Z, Liu S, Xu J, Wu YC, Lu PY, Lien A, Bryce MR. Achieving remarkable mechanochromism and white-light emission with thermally activated delayed fluorescence through the molecular heredity principle. Chem Sci 2016; 7:2201-2206. [PMID: 29910908 PMCID: PMC5975939 DOI: 10.1039/c5sc04155d] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/20/2015] [Indexed: 12/23/2022] Open
Abstract
Achieving high contrast mechanochromism (Δλem,max > 100 nm) and white-light emission under mild conditions from a single compound with a simple structure is a great challenge. Herein, we report a novel dual-emissive compound, namely SCP, with an asymmetric molecular structure that fully inherits the photophysical properties of the parent molecules SC2 and SP2. SCP shows high contrast, linearly tunable mechanochromism and bright white-light emission arising from a combination of traditional fluorescence and thermally activated delayed fluorescence (TADF). The origin of the dual-emission for SCP was demonstrated based on the analysis of the white-emitting single crystals. In addition, a mechanism of luminochromism for SCP driven by the application of mechanical force is proposed. These observations present a rational design strategy for the development of high performance multi-functional materials for white-light emission.
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Affiliation(s)
- Bingjia Xu
- PCFM Lab , GD HPPC Lab , Guangdong Engineering Technology Research Center for High-performance Organic and Polymer Photoelectric Functional Films , State Key Laboratory of Optoelectronic Material and Technologies , School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , China . ; ; ; Tel: +86 20 84112712
- State Key Laboratory of Optoelectronic Material and Technologies , School of Physics and Engineering , Sun Yat-sen University , Guangzhou 510275 , China
| | - Yingxiao Mu
- PCFM Lab , GD HPPC Lab , Guangdong Engineering Technology Research Center for High-performance Organic and Polymer Photoelectric Functional Films , State Key Laboratory of Optoelectronic Material and Technologies , School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , China . ; ; ; Tel: +86 20 84112712
| | - Zhu Mao
- PCFM Lab , GD HPPC Lab , Guangdong Engineering Technology Research Center for High-performance Organic and Polymer Photoelectric Functional Films , State Key Laboratory of Optoelectronic Material and Technologies , School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , China . ; ; ; Tel: +86 20 84112712
| | - Zongliang Xie
- PCFM Lab , GD HPPC Lab , Guangdong Engineering Technology Research Center for High-performance Organic and Polymer Photoelectric Functional Films , State Key Laboratory of Optoelectronic Material and Technologies , School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , China . ; ; ; Tel: +86 20 84112712
| | - Haozhong Wu
- PCFM Lab , GD HPPC Lab , Guangdong Engineering Technology Research Center for High-performance Organic and Polymer Photoelectric Functional Films , State Key Laboratory of Optoelectronic Material and Technologies , School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , China . ; ; ; Tel: +86 20 84112712
| | - Yi Zhang
- PCFM Lab , GD HPPC Lab , Guangdong Engineering Technology Research Center for High-performance Organic and Polymer Photoelectric Functional Films , State Key Laboratory of Optoelectronic Material and Technologies , School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , China . ; ; ; Tel: +86 20 84112712
| | - Chongjun Jin
- State Key Laboratory of Optoelectronic Material and Technologies , School of Physics and Engineering , Sun Yat-sen University , Guangzhou 510275 , China
| | - Zhenguo Chi
- PCFM Lab , GD HPPC Lab , Guangdong Engineering Technology Research Center for High-performance Organic and Polymer Photoelectric Functional Films , State Key Laboratory of Optoelectronic Material and Technologies , School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , China . ; ; ; Tel: +86 20 84112712
| | - Siwei Liu
- PCFM Lab , GD HPPC Lab , Guangdong Engineering Technology Research Center for High-performance Organic and Polymer Photoelectric Functional Films , State Key Laboratory of Optoelectronic Material and Technologies , School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , China . ; ; ; Tel: +86 20 84112712
| | - Jiarui Xu
- PCFM Lab , GD HPPC Lab , Guangdong Engineering Technology Research Center for High-performance Organic and Polymer Photoelectric Functional Films , State Key Laboratory of Optoelectronic Material and Technologies , School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , China . ; ; ; Tel: +86 20 84112712
| | - Yuan-Chun Wu
- Shenzhen China Star Optoelectronics Technology Co., Ltd , Shenzhen 518107 , China
| | - Po-Yen Lu
- Shenzhen China Star Optoelectronics Technology Co., Ltd , Shenzhen 518107 , China
| | - Alan Lien
- Shenzhen China Star Optoelectronics Technology Co., Ltd , Shenzhen 518107 , China
| | - Martin R Bryce
- Department of Chemistry , Durham University , DH1 3LE , UK .
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21
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Sheshukova EV, Shindyapina AV, Komarova TV, Dorokhov YL. “Matreshka” genes with alternative reading frames. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416020149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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23
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Gupta S, Verma S, Mantri S, Berman NE, Sandhir R. Targeting MicroRNAs in Prevention and Treatment of Neurodegenerative Disorders. Drug Dev Res 2015; 76:397-418. [PMID: 26359796 DOI: 10.1002/ddr.21277] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Preclinical Research microRNAs (miRNAs) are small noncoding RNAs (ncRNAs) that are key regulators of gene expression. They act on wide range of targets by binding to mRNA via imperfect complementarity at 3' UTR. Evidence suggests that miRNAs regulate many biological processes including neuronal development, differentiation, and disease. Altered expression of several miRNAs has been reported in many neurodegenerative disorders (NDDs). Many miRNAs are altered in these diseases, but miRNA 15, miRNA 21, and miRNA 146a have been shown to play critical role in many neurodegenerative conditions. As these miRNAs regulate many genes, miRNA targeted approaches would allow concurrently targeting of multiple effectors of pathways that regulate disease progression. In this review, we describe the role of miRNAs in various NDDs and their potential as therapeutic tools in prevention and treatment of neurological conditions.
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Affiliation(s)
- Smriti Gupta
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Savita Verma
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Shrikant Mantri
- Computational Biology Laboratory, National Agri-Food Biotechnology Institute, Mohali, Punjab, 160071, India
| | - Nancy E Berman
- Department of Anatomy & Cell Biology, Kansas University Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Rajat Sandhir
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
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24
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Soberano EK, Kelty-Stephen DG. Demystifying cognitive science: explaining cognition through network-based modeling. Front Physiol 2015; 6:88. [PMID: 25852574 PMCID: PMC4365715 DOI: 10.3389/fphys.2015.00088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/04/2015] [Indexed: 11/13/2022] Open
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25
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Qian C, Siler T, Ozin GA. Exploring the possibilities and limitations of a nanomaterials genome. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:64-69. [PMID: 25244158 DOI: 10.1002/smll.201402197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/25/2014] [Indexed: 06/03/2023]
Abstract
What are we going to do with the cornucopia of nanomaterials appearing in the open and patent literature, every day? Imagine the benefits of an intelligent and convenient means of categorizing, organizing, sifting, sorting, connecting, and utilizing this information in scientifically and technologically innovative ways by building a Nanomaterials Genome founded upon an all-purpose Periodic Table of Nanomaterials. In this Concept article, inspired by work on the Human Genome project, which began in 1989 together with motivation from the recent emergence of the Materials Genome project initiated in 2011 and the Nanoinformatics Roadmap 2020 instigated in 2010, we envision the development of a Nanomaterials Genome (NMG) database with the most advanced data-mining tools that leverage inference engines to help connect and interpret patterns of nanomaterials information. It will be equipped with state-of-the-art visualization techniques that rapidly organize and picture, categorize and interrelate the inherited behavior of complex nanomatter from the information programmed in its constituent nanomaterials building blocks. A Nanomaterials Genome Initiative (NMGI) of the type imagined herein has the potential to serve the global nanoscience community with an opportunity to speed up the development continuum of nanomaterials through the innovation process steps of discovery, structure determination and property optimization, functionality elucidation, system design and integration, certification and manufacturing to deployment in technologies that apply these versatile nanomaterials in environmentally responsible ways. The possibilities and limitations of this concept are critically evaluated in this article.
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Affiliation(s)
- Chenxi Qian
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
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26
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Malhotra J. Molecular and Genetic Epidemiology of Cancer in Low- and Medium-Income
Countries. Ann Glob Health 2014; 80:418-25. [DOI: 10.1016/j.aogh.2014.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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27
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A million peptide motifs for the molecular biologist. Mol Cell 2014; 55:161-9. [PMID: 25038412 DOI: 10.1016/j.molcel.2014.05.032] [Citation(s) in RCA: 359] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/24/2014] [Accepted: 05/15/2014] [Indexed: 11/22/2022]
Abstract
A molecular description of functional modules in the cell is the focus of many high-throughput studies in the postgenomic era. A large portion of biomolecular interactions in virtually all cellular processes is mediated by compact interaction modules, referred to as peptide motifs. Such motifs are typically less than ten residues in length, occur within intrinsically disordered regions, and are recognized and/or posttranslationally modified by structured domains of the interacting partner. In this review, we suggest that there might be over a million instances of peptide motifs in the human proteome. While this staggering number suggests that peptide motifs are numerous and the most understudied functional module in the cell, it also holds great opportunities for new discoveries.
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28
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Coscia M. Average is boring: how similarity kills a meme's success. Sci Rep 2014; 4:6477. [PMID: 25257730 PMCID: PMC4175728 DOI: 10.1038/srep06477] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 07/28/2014] [Indexed: 11/16/2022] Open
Abstract
Every day we are exposed to different ideas, or memes, competing with each other for our attention. Previous research explained popularity and persistence heterogeneity of memes by assuming them in competition for limited attention resources, distributed in a heterogeneous social network. Little has been said about what characteristics make a specific meme more likely to be successful. We propose a similarity-based explanation: memes with higher similarity to other memes have a significant disadvantage in their potential popularity. We employ a meme similarity measure based on semantic text analysis and computer vision to prove that a meme is more likely to be successful and to thrive if its characteristics make it unique. Our results show that indeed successful memes are located in the periphery of the meme similarity space and that our similarity measure is a promising predictor of a meme success.
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Affiliation(s)
- Michele Coscia
- CID - Harvard University 79 JFK St, Cambridge MA, US 02138
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29
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Pervasive transcription: illuminating the dark matter of bacterial transcriptomes. Nat Rev Microbiol 2014; 12:647-53. [DOI: 10.1038/nrmicro3316] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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30
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Tan L, Yu JT, Tan L. Causes and Consequences of MicroRNA Dysregulation in Neurodegenerative Diseases. Mol Neurobiol 2014; 51:1249-62. [PMID: 24973986 DOI: 10.1007/s12035-014-8803-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/22/2014] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD) and amyotrophic lateral sclerosis (ALS), originate from a loss of neurons in the central nervous system (CNS) and are severely debilitating. The incidence of neurodegenerative diseases increases with age, and they are expected to become more common due to extended life expectancy. Because of no clear mechanisms, these diseases have become a major challenge in neurobiology. It is well recognized that these disorders become the culmination of many different genetic and environmental influences. Prior studies have shown that microRNAs (miRNAs) are pathologically altered during the inexorable course of some neurodegenerative diseases, suggesting that miRNAs may be the contributing factor in neurodegeneration. Here, we review what is known about the involvement of miRNAs in the pathogenesis of neurodegenerative diseases. The biogenesis of miRNAs and various functions of miRNAs that act as the chief regulators will be discussed. We focus in particular on dysregulation of miRNAs which leads to several neurodegenerative diseases from three aspects: miRNA-generating disorders, miRNA-targeting genes and epigenetic alterations. Furthermore, recent evidences have shown that circulating miRNA expression levels are changed in patients with neurodegenerative diseases. Circulating miRNA expression levels are reported in patients in order to evaluate their application as biomarkers of these diseases. A discussion is included with a potential diagnostic biomarker and the possible future direction in exploring the nexus between miRNAs and various neurodegenerative diseases.
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Affiliation(s)
- Lin Tan
- College of Medicine and Pharmaceutics, Ocean University of China, Qingdao, China
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31
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Wright LK, Fisk JN, Newman DL. DNA → RNA: What Do Students Think the Arrow Means? CBE LIFE SCIENCES EDUCATION 2014; 13:338-48. [PMID: 26086664 PMCID: PMC4041510 DOI: 10.1187/cbe.cbe-13-09-0188] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The central dogma of molecular biology, a model that has remained intact for decades, describes the transfer of genetic information from DNA to protein though an RNA intermediate. While recent work has illustrated many exceptions to the central dogma, it is still a common model used to describe and study the relationship between genes and protein products. We investigated understanding of central dogma concepts and found that students are not primed to think about information when presented with the canonical figure of the central dogma. We also uncovered conceptual errors in student interpretation of the meaning of the transcription arrow in the central dogma representation; 36% of students (n = 128; all undergraduate levels) described transcription as a chemical conversion of DNA into RNA or suggested that RNA existed before the process of transcription began. Interviews confirm that students with weak conceptual understanding of information flow find inappropriate meaning in the canonical representation of central dogma. Therefore, we suggest that use of this representation during instruction can be counterproductive unless educators are explicit about the underlying meaning.
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Affiliation(s)
- L Kate Wright
- Rochester Institute of Technology, Rochester, NY 14623
| | - J Nick Fisk
- Rochester Institute of Technology, Rochester, NY 14623
| | - Dina L Newman
- Rochester Institute of Technology, Rochester, NY 14623
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32
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Abstract
The last decade has seen tremendous effort committed to the annotation of the human genome sequence, most notably perhaps in the form of the ENCODE project. One of the major findings of ENCODE, and other genome analysis projects, is that the human transcriptome is far larger and more complex than previously thought. This complexity manifests, for example, as alternative splicing within protein-coding genes, as well as in the discovery of thousands of long noncoding RNAs. It is also possible that significant numbers of human transcripts have not yet been described by annotation projects, while existing transcript models are frequently incomplete. The question as to what proportion of this complexity is truly functional remains open, however, and this ambiguity presents a serious challenge to genome scientists. In this article, we will discuss the current state of human transcriptome annotation, drawing on our experience gained in generating the GENCODE gene annotation set. We highlight the gaps in our knowledge of transcript functionality that remain, and consider the potential computational and experimental strategies that can be used to help close them. We propose that an understanding of the true overlap between transcriptional complexity and functionality will not be gained in the short term. However, significant steps toward obtaining this knowledge can now be taken by using an integrated strategy, combining all of the experimental resources at our disposal.
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Affiliation(s)
- Jonathan M Mudge
- Department of Informatics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
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Meng J, Cui X, Rao MK, Chen Y, Huang Y. Exome-based analysis for RNA epigenome sequencing data. ACTA ACUST UNITED AC 2013; 29:1565-7. [PMID: 23589649 DOI: 10.1093/bioinformatics/btt171] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques. RESULT Through examining the connections of RNA epigenome sequencing data with two well-studied data types, ChIP-Seq and RNA-Seq, we unveiled the salient characteristics of this new data type. The computational strategies were discussed accordingly, and a novel data processing pipeline was proposed that combines several existing tools with a newly developed exome-based approach 'exomePeak' for detecting, representing and visualizing the post-transcriptional RNA modification sites on the transcriptome. AVAILABILITY The MATLAB package 'exomePeak' and additional details are available at http://compgenomics.utsa.edu/exomePeak/.
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Affiliation(s)
- Jia Meng
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, MA 02139, USA.
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Abstract
Both theory and experimentation suggest that during development, the DNA of multicellular organisms, recognized as graced with a lifelong intrinsic stability, is instead target of several modifications (point mutations, larger structural variations, epigenetic marks) and partner of complex interactions with non-DNA moieties (RNAs and proteins). Some of these modifications probably affect a fraction of the genome larger than standard point mutations and are more likely to respond to environmental cues. Thus, the traditional concepts of gene and genome need revision: the structure serving as depository of the overall bioinformation of the cell is more dynamic and less homogeneous than allowed for by the Central Dogma, since in addition to DNA, it includes also RNA and proteins. Each of the individual contributors as well as their stoichiometry undergo modifications. Compared to the traditional unidimensional and static genome, the resulting dynamic aggregate could be more competent to cope with different regulatory requirements: its structural variations may respond to unscheduled macro- and microenvironmental stresses as well as to scheduled genetic programs. A detailed assessment of these variations in time and space should provide a basis for a deeper comprehension of the phenotypic changes punctuating the organism's physio-pathological development, aging and transgenerational transmission. The variations of such information storage-delivery system may interest also the germ cells: the inheritance of parental traits and hence their evolutionary transmission would be affected. For the structure featuring all these properties, we propose the term 'hypergenome' to underscore the dynamic composition of a complex nucleoprotein responsive to both unpredictable environmental stimuli and internal built-in programs.
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Affiliation(s)
- V Sgaramella
- Istituto Agrario di San Michele all'Adige, IT–38010 San Michele all'Adige, Italy.
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35
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Li Y, Zhao D. Basics of Molecular Biology. ADVANCED TOPICS IN SCIENCE AND TECHNOLOGY IN CHINA 2013. [PMCID: PMC7122053 DOI: 10.1007/978-3-642-34303-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Molecular biology is the study of biology on molecular level. The field overlaps with areas of biology and chemistry, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA (deoxyribonucleic acid), RNA (Ribonucleic acid) and protein biosynthesis as well as learning how these interactions are regulated[1].
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Ghelani HS, Rachchh MA, Gokani RH. MicroRNAs as newer therapeutic targets: A big hope from a tiny player. J Pharmacol Pharmacother 2012; 3:217-27. [PMID: 23129956 PMCID: PMC3487269 DOI: 10.4103/0976-500x.99416] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are a novel group of universally present small noncoding endogenous RNAs that regulate gene expression and protein coding by base pairing with the 3’ untranslated region (UTR) of target mRNAs. So they have been associated with several physiological processes and play an important role in the manifestation of diverse diseases. miRNAs expression is associated with the normal and diverse pathophysiological state including cardiac hypertrophy, neurodegenerative diseases, diabetes and its complication, and cancer because individual miRNAs are associated with the regulation of the expression of multiple target genes. Modulating the expression of a single miRNA can influence an entire gene network and thereby modify complex disease phenotypes. From recent studies, it has been confirmed that miRNA has a potential physiological role in various body systems. But in some specialized condition over expression of miRNA within the cytoplasm also leads to some pathological condition in the body. Here, we summarize the roles of miRNAs in various pathological conditions and consider the advantages and potential challenges of miRNA-based therapeutic approaches compared to conventional drug-based therapies.
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Affiliation(s)
- Hardik S Ghelani
- Department of Pharmacology, S.J. Thakkar Pharmacy College, Kalawad Road, Rajkot, Gujarat, India
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37
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Noble D. A biological relativity view of the relationships between genomes and phenotypes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2012; 111:59-65. [PMID: 23044397 DOI: 10.1016/j.pbiomolbio.2012.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 09/25/2012] [Accepted: 09/26/2012] [Indexed: 11/19/2022]
Abstract
This article explores the relativistic principle that there is no privileged scale of causality in biology to clarify the relationships between genomes and phenotypes. The idea that genetic causes are primary views the genome as a program. Initially, that view was vindicated by the discovery of mutations and knockouts that have large and specific effects on the phenotype. But we now know that these form the minority of cases. Many changes at the genome level are buffered by robust networks of interactions in cells, tissues and organs. The 'differential' view of genetics therefore fails because it is too restrictive. An 'integral' view, using reverse engineering from systems biological models to quantify contributions to function, can solve this problem. The article concludes by showing that far from breaking the supervenience principle, downward causation requires that it should be obeyed.
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Affiliation(s)
- Denis Noble
- Department of Physiology, Anatomy & Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK.
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38
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Gantt EE, Melling BS, Reber JS. Mechanisms or metaphors? The emptiness of evolutionary psychological explanations. THEORY & PSYCHOLOGY 2012. [DOI: 10.1177/0959354311434071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In recent decades, numerous psychological and sociological theories have been offered in the attempt to explain human cognition, motivation, and behavior in fundamentally evolutionary terms. Drawing inspiration from the Darwinian theory of natural selection, evolutionary approaches to social science argue that behavior arises primarily from underlying evolved psychological mechanisms and that the central task of social science is to identify and articulate the specific nature of such mechanisms. Much effort has been expended by evolutionary social scientists to definitively identify the various evolved psychological mechanisms that account for the diversity of human cognitive, emotional, and social behavior. We argue, however, that the search for evolved psychological mechanisms that adequately account for either the transmission of psychological entities (i.e., emotions, intentions, ideas, behaviors, etc.) across generations or the current existence of such entities cannot in principle succeed because evolutionary social science theorists have fundamentally mistaken their metaphors for mechanisms.
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Bochud M. Genetics for clinicians: from candidate genes to whole genome scans (technological advances). Best Pract Res Clin Endocrinol Metab 2012; 26:119-32. [PMID: 22498243 DOI: 10.1016/j.beem.2011.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Human genetics has progressed at an unprecedented pace during the past 10 years. DNA microarrays currently allow screening of the entire human genome with high level of coverage and we are now entering the era of high-throughput sequencing. These remarkable technical advances are influencing the way medical research is conducted and have boosted our understanding of the structure of the human genome as well as of disease biology. In this context, it is crucial for clinicians to understand the main concepts and limitations of modern genetics. This review will describe key concepts in genetics, including the different types of genetic markers in the human genome, review current methods to detect DNA variation, describe major online public databases in genetics, explain key concepts in statistical genetics and finally present commonly used study designs in clinical and epidemiological research. This review will therefore concentrate on human genetic variation analysis.
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Affiliation(s)
- Murielle Bochud
- Community Prevention Unit, Institute of Social and Preventive Medicine, Switzerland.
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40
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41
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Scherrer K. Regulation of gene expression and the transcription factor cycle hypothesis. Biochimie 2012; 94:1057-68. [PMID: 22234303 DOI: 10.1016/j.biochi.2011.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 12/09/2011] [Indexed: 11/26/2022]
Abstract
Post-genomic data show unexpected extent of the transcribed genome and the size of individual primary transcripts. Hence, most cis-regulatory modules (CRMs) binding transcription factors (TFs) at promotor, enhancer and other sites are actually transcribed within full domain transcripts (FDTs). The ensemble of these CRMs placed way upstream of exon clusters, downstream and in intronic or intergenic positions represent a program of gene expression which has been formally analysed within the Gene and Genon concept [1,2]. This concept has emphasised the necessity to separate product information from regulative information to allow information-theoretic analysis of gene expression. Classically, TFs have been assumed to act at DNA level exclusively but evidence has accumulated indicating eventual post-transcriptional functions. The transcription factor cycle (TFC) hypothesis suggests the transfer of DNA-bound factors to nascent RNA. Exerting downstream functions in RNA processing and transport, these factors would be liberated by RNA processing and cycle back to the DNA maintaining active transcription. Sequestered on RNA in absence of processing they would constitute a negative feedback loop. The TFC concept may explain epigenetic regulation in mitosis and meiosis. In mitosis control factors may survive as single proteins but also attached to FDTs as organised complexes. This process might perpetuate in cell division conditioning of chromatin for transcription. As observed on lampbrush chromosomes formed in avian and amphibian oogenesis, in meiosis the genome is fully transcribed and oocytes conserve high Mr RNA of high sequence complexity. When new interphase chromosomes form in daughter cells and early embryogenesis, TFs and other factors attached to RNA might be reinserted onto the DNA.
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Affiliation(s)
- Klaus Scherrer
- Inst. J. Monod, CNRS and University Paris Diderot, 9, rue Larrey, 75005 Paris, France
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42
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Frías-Lasserre D. Non coding RNAs and viruses in the framework of the phylogeny of the genes, epigenesis and heredity. Int J Mol Sci 2012; 13:477-490. [PMID: 22312265 PMCID: PMC3269699 DOI: 10.3390/ijms13010477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 12/22/2011] [Accepted: 12/23/2011] [Indexed: 01/21/2023] Open
Abstract
The origin of genes is one of the most enigmatic events in the origin of life. It has been suggested that noncoding (nc) RNA was probably a precursor in the formation of the first polypeptide, and also at the origin of the first manifestation of life and genes. ncRNAs are also becoming central for understanding gene expression and silencing. Indeed, before the discovery of ncRNAs, proteins were viewed as the major molecules in the regulation of gene expression and gene silencing; however, recent findings suggest that ncRNA also plays an important role in gene expression. Reverse transcription of RNA viruses and their integration into the genome of eukaryotes and also their relationship with the ncRNA suggest that their origin is basal in genome evolution, and also probably constitute the first mechanism of gene regulation. I am to review the different roles of ncRNAs in the framework of gene evolution, as well as the importance of ncRNAs and viruses in the epigenesis and in the non-Mendelian model of heredity and evolution.
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Affiliation(s)
- Daniel Frías-Lasserre
- Institute of Entomology, Metropolitan University of Educational Sciences, Avenue J.P. Alessandri 774 Ñuñoa, Código Postal 7760197, Santiago, Chile; E-Mail: ; Tel.: +56-2-2412457; Fax: +56-2-2412699
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43
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Transcriptional noise as a driver of gene evolution. J Theor Biol 2012; 293:27-33. [DOI: 10.1016/j.jtbi.2011.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 09/16/2011] [Accepted: 10/03/2011] [Indexed: 01/09/2023]
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44
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Newman DL, Catavero CM, Wright LK. Students fail to transfer knowledge of chromosome structure to topics pertaining to cell division. CBE LIFE SCIENCES EDUCATION 2012; 11:425-36. [PMID: 23222838 PMCID: PMC3516798 DOI: 10.1187/cbe.12-01-0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Cellular processes that rely on knowledge of molecular behavior are difficult for students to comprehend. For example, thorough understanding of meiosis requires students to integrate several complex concepts related to chromosome structure and function. Using a grounded theory approach, we have unified classroom observations, assessment data, and in-depth interviews under the theory of knowledge transfer to explain student difficulties with concepts related to chromosomal behavior. In this paper, we show that students typically understand basic chromosome structure but do not activate cognitive resources that would allow them to explain macromolecular phenomena (e.g., homologous pairing during meiosis). To improve understanding of topics related to genetic information flow, we suggest that instructors use pedagogies and activities that prime students for making connections between chromosome structure and cellular processes.
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Affiliation(s)
- Dina L Newman
- School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA.
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45
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Machado JAT, Costa AC, Quelhas MD. Analysis and visualization of chromosome information. Gene 2012; 491:81-7. [PMID: 22001546 DOI: 10.1016/j.gene.2011.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 09/07/2011] [Accepted: 09/14/2011] [Indexed: 11/15/2022]
Abstract
This paper analyzes the DNA code of several species in the perspective of information content. For that purpose several concepts and mathematical tools are selected towards establishing a quantitative method without a priori distorting the alphabet represented by the sequence of DNA bases. The synergies of associating Gray code, histogram characterization and multidimensional scaling visualization lead to a collection of plots with a categorical representation of species and chromosomes.
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Affiliation(s)
- J A Tenreiro Machado
- Institute of Engineering of Porto, Dept. of Electrical Engineering, Rua Dr. António Bernardino de Almeida, 431, 4200-072 Porto, Portugal.
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46
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47
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Sun F, Zhu L. Citation genetic genealogy: a novel insight for citation analysis in scientific literature. Scientometrics 2011. [DOI: 10.1007/s11192-011-0588-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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48
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Nowacki M, Shetty K, Landweber LF. RNA-Mediated Epigenetic Programming of Genome Rearrangements. Annu Rev Genomics Hum Genet 2011; 12:367-89. [PMID: 21801022 DOI: 10.1146/annurev-genom-082410-101420] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
RNA, normally thought of as a conduit in gene expression, has a novel mode of action in ciliated protozoa. Maternal RNA templates provide both an organizing guide for DNA rearrangements and a template that can transport somatic mutations to the next generation. This opportunity for RNA-mediated genome rearrangement and DNA repair is profound in the ciliate Oxytricha, which deletes 95% of its germline genome during development in a process that severely fragments its chromosomes and then sorts and reorders the hundreds of thousands of pieces remaining. Oxytricha's somatic nuclear genome is therefore an epigenome formed through RNA templates and signals arising from the previous generation. Furthermore, this mechanism of RNA-mediated epigenetic inheritance can function across multiple generations, and the discovery of maternal template RNA molecules has revealed new biological roles for RNA and has hinted at the power of RNA molecules to sculpt genomic information in cells.
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Affiliation(s)
- Mariusz Nowacki
- Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland.
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49
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Machado JAT, Costa AC, Quelhas MD. Wavelet analysis of human DNA. Genomics 2011; 98:155-63. [PMID: 21672622 DOI: 10.1016/j.ygeno.2011.05.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 05/21/2011] [Accepted: 05/27/2011] [Indexed: 10/18/2022]
Abstract
This paper studies the human DNA in the perspective of signal processing. Six wavelets are tested for analyzing the information content of the human DNA. By adopting real Shannon wavelet several fundamental properties of the code are revealed. A quantitative comparison of the chromosomes and visualization through multidimensional and dendograms is developed.
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Affiliation(s)
- J A Tenreiro Machado
- Institute of Engineering of Porto, Dept. of Electrical Engineering, Rua Dr. António Bernardino de Almeida, 431, 4200-072 Porto, Portugal.
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50
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Costa AM, Machado JT, Quelhas MD. Histogram-based DNA analysis for the visualization of chromosome, genome and species information. Bioinformatics 2011; 27:1207-14. [PMID: 21398672 DOI: 10.1093/bioinformatics/btr131] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION We describe a novel approach to explore DNA nucleotide sequence data, aiming to produce high-level categorical and structural information about the underlying chromosomes, genomes and species. RESULTS The article starts by analyzing chromosomal data through histograms using fixed length DNA sequences. After creating the DNA-related histograms, a correlation between pairs of histograms is computed, producing a global correlation matrix. These data are then used as input to several data processing methods for information extraction and tabular/graphical output generation. A set of 18 species is processed and the extensive results reveal that the proposed method is able to generate significant and diversified outputs, in good accordance with current scientific knowledge in domains such as genomics and phylogenetics. AVAILABILITY AND IMPLEMENTATION Source code freely available for download at http://www4.dei.isep.ipp.pt/etc/dnapaper2010, implemented in Free Pascal and UNIX scripting tools. Study input data available online for download at University of California at Santa Cruz Genome Bioinformatics, http://hgdownload.cse.ucsc.edu/downloads.html.
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Affiliation(s)
- António M Costa
- Department of Informatics Engineering, Department of Electrotechnical Engineering, ISEP, Rua Dr Bernardino Almeida 431, Porto, Portugal.
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