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H. R C, L G. The Inside Scoop: What We Learnt About Getting into Academic Publishing During Our Editorial Internship. Med Sci Educ 2024; 34:439-444. [PMID: 38686168 PMCID: PMC11055811 DOI: 10.1007/s40670-023-01961-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 05/02/2024]
Abstract
The world of publication can seem intimidating and closed to the newcomer. How then does one even begin to get a foot in the door? In this paper, the authors draw from the literature and their recent lived experience as editorial interns to consider this challenge under the theme of access, and how it overlaps with the various components of academic publication. The main three components of the publication 'machine' are discussed in this article, authoring, reviewing, and editing. These are preceded by the first, and arguably foundational, interaction with academic journal publishing-reading. Without reading articles across different journals, and even in different disciplines, understanding the breadth of scholarship and its purpose is impossible. The subsequent components of authoring, reviewing, and editing, which are all enhanced by ongoing familiarity with current literature through further reading, are considered in further detail in the remainder of this article, with practical advice provided as to how to gain access and experience in each of these areas, for example, writing non-research article manuscripts, engaging in collaborative peer review, and applying for editorial opportunities (with perseverance) when the opportunity presents itself. Medical education publication can seem daunting and closed to entry-level academics. This article is written to dispel this view, and challenges the notion that the world of publication is reserved for experts only. On the contrary, newcomers to the field are essential for academic publications to retain relevance, dynamism, and innovation particularly in the face of the changing landscape of medical education.
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Affiliation(s)
- Church H. R
- Medical Education, University of Nottingham, Nottingham, UK
- Faculty of Medicine and Health Sciences, Medical School, University of Nottingham, Queen’s Medical Centre, Room B87, Nottingham, NG7 2UH UK
| | - Govender L
- Division of Anatomical Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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2
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Loeser J, Bauer J, Janßen K, Rockenbach K, Wachter A. A transient in planta editing assay identifies specific binding of the splicing regulator PTB as a prerequisite for cassette exon inclusion. Plant Mol Biol 2024; 114:22. [PMID: 38443687 PMCID: PMC10914923 DOI: 10.1007/s11103-024-01414-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/31/2023] [Indexed: 03/07/2024]
Abstract
The dynamic interaction of RNA-binding proteins (RBPs) with their target RNAs contributes to the diversity of ribonucleoprotein (RNP) complexes that are involved in a myriad of biological processes. Identifying the RNP components at high resolution and defining their interactions are key to understanding their regulation and function. Expressing fusions between an RBP of interest and an RNA editing enzyme can result in nucleobase changes in target RNAs, representing a recent addition to experimental approaches for profiling RBP/RNA interactions. Here, we have used the MS2 protein/RNA interaction to test four RNA editing proteins for their suitability to detect target RNAs of RBPs in planta. We have established a transient test system for fast and simple quantification of editing events and identified the hyperactive version of the catalytic domain of an adenosine deaminase (hADARcd) as the most suitable editing enzyme. Examining fusions between homologs of polypyrimidine tract binding proteins (PTBs) from Arabidopsis thaliana and hADARcd allowed determining target RNAs with high sensitivity and specificity. Moreover, almost complete editing of a splicing intermediate provided insight into the order of splicing reactions and PTB dependency of this particular splicing event. Addition of sequences for nuclear localisation of the fusion protein increased the editing efficiency, highlighting this approach's potential to identify RBP targets in a compartment-specific manner. Our studies have established the editing-based analysis of interactions between RBPs and their RNA targets in a fast and straightforward assay, offering a new system to study the intricate composition and functions of plant RNPs in vivo.
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Affiliation(s)
- Jorinde Loeser
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Julia Bauer
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Kim Janßen
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Kevin Rockenbach
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Andreas Wachter
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
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3
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Ayub N, Soto G. Multiple challenges in the development of commercial crops using CRISPR/Cas technology. Plant Sci 2023; 335:111809. [PMID: 37482301 DOI: 10.1016/j.plantsci.2023.111809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/25/2023]
Abstract
The CRISPR/Cas system is a highly efficient and versatile tool for editing plant genomes, with the potential to accelerate breeding programs and improve the sustainability of food production. Nevertheless, technical limitations delay the rapid spread of the CRISPR/Cas system benefits in agriculture. The natural features of plant species, including reproductive behavior, ploidy levels, genetic diversity, and generation times, can significantly impact the introgression of edited traits into elite germplasms. The production and selection of edited events require the same level of effort as those of their transgenic equivalents. Additionally, edited alleles tend to be recessive or not fully dominant, which differs from dominant transgenic events. To accelerate the introgression of edited events into conventional and transgenic varieties, we suggest utilizing edits on single-copy genes that induce dominant mutations. In the absence of new, simple traits that provide exceptional economic benefits for large companies, like herbicide tolerance in transgenic crops, we propose the emergence of particular public grants for edited variety productions, especially when the introgression shows a high level of technical feasibility. In the context of climate change, these public actions must be taken quickly to alleviate significant reductions in crop production.
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Affiliation(s)
- Nicolas Ayub
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO, CONICET-INTA), Argentina; Instituto de Genética (IGEAF, INTA), Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO, CONICET-INTA), Argentina; Instituto de Genética (IGEAF, INTA), Argentina.
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4
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Hwang SI, Lim JS, Lee RW, Matsui Y, Iguchi T, Hiraki T, Ahn H. Is ChatGPT a "Fire of Prometheus" for Non-Native English-Speaking Researchers in Academic Writing? Korean J Radiol 2023; 24:952-959. [PMID: 37793668 PMCID: PMC10550740 DOI: 10.3348/kjr.2023.0773] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 10/06/2023] Open
Abstract
Large language models (LLMs) such as ChatGPT have garnered considerable interest for their potential to aid non-native English-speaking researchers. These models can function as personal, round-the-clock English tutors, akin to how Prometheus in Greek mythology bestowed fire upon humans for their advancement. LLMs can be particularly helpful for non-native researchers in writing the Introduction and Discussion sections of manuscripts, where they often encounter challenges. However, using LLMs to generate text for research manuscripts entails concerns such as hallucination, plagiarism, and privacy issues; to mitigate these risks, authors should verify the accuracy of generated content, employ text similarity detectors, and avoid inputting sensitive information into their prompts. Consequently, it may be more prudent to utilize LLMs for editing and refining text rather than generating large portions of text. Journal policies concerning the use of LLMs vary, but transparency in disclosing artificial intelligence tool usage is emphasized. This paper aims to summarize how LLMs can lower the barrier to academic writing in English, enabling researchers to concentrate on domain-specific research, provided they are used responsibly and cautiously.
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Affiliation(s)
- Sung Il Hwang
- Department of Radiology, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Radiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Joon Seo Lim
- Scientific Publications Team, Clinical Research Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Ro Woon Lee
- Department of Radiology, Inha University Hospital, Incheon, Republic of Korea
| | - Yusuke Matsui
- Department of Radiology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Toshihiro Iguchi
- Department of Radiological Technology, Faculty of Health Sciences, Okayama University, Okayama, Japan
| | - Takao Hiraki
- Department of Radiology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Hyungwoo Ahn
- Department of Radiology, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
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5
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Park SH. Use of Generative Artificial Intelligence, Including Large Language Models Such as ChatGPT, in Scientific Publications: Policies of KJR and Prominent Authorities. Korean J Radiol 2023; 24:715-718. [PMID: 37500572 PMCID: PMC10400373 DOI: 10.3348/kjr.2023.0643] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023] Open
Affiliation(s)
- Seong Ho Park
- Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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6
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Whaley P, Roth N. How we promote rigour in systematic reviews and evidence maps at Environment International. Environ Int 2022; 170:107543. [PMID: 36280492 DOI: 10.1016/j.envint.2022.107543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
In 2016, Environment International became the first environmental health journal to adopt specialist policies for handling systematic review (SR) submissions. This included the appointment of a dedicated editor of SRs, the use of the CREST_Triage tool for transparent and consistent enforcement of editorial standards for SRs, the acceptance of SR protocols as full manuscripts, and the extension of SR handling policies to systematic evidence maps as a novel evidence synthesis methodology. Our data on triage decisions for SR submissions, gathered via CREST_Triage, indicates several ways in which researchers are challenged by SR methods, including problem formulation, critical appraisal methods, and certainty assessment. We recommend that author teams invest in developing protocols as a means to de-risk SR projects, arguing that the benefits outweigh the potential increase in time it may take to complete the research project. Finally, we present evidence that reliance among environmental health journals on informal peer-review and editorial checks for standards compliance and quality control is insufficient for ensuring the rigour of SR publications. This emphasises the importance of specialist editors using triage instruments for the effective enforcement of standards. Observing that Environment International appears to be one of few journals implementing effective quality control measures for SR publications, we suggest that adoption of our SR policies by other journals may be beneficial to the field at large.
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Affiliation(s)
- Paul Whaley
- Lancaster Environment Centre, Lancaster University, Lancaster, UK; Evidence-Based Toxicology Collaboration at Johns Hopkins Bloomberg School of Public Health, Baltimore, USA.
| | - Nicolas Roth
- Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland.
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7
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Smith J, Banerjee R, Weeks RJ, Chatterjee A. Editing of DNA Methylation Patterns Using CRISPR-Based Tools. Methods Mol Biol 2022; 2458:63-74. [PMID: 35103962 DOI: 10.1007/978-1-0716-2140-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
DNA methylation is an epigenetic modification with an established role in both normal cellular function and mammalian disease. Despite well-characterized associations between aberrant DNA methylation changes and gene expression, evidence for a causal relationship in this context has been difficult to obtain. Early techniques for interrogating the role of DNA methylation in the regulation of gene transcription lack specificity and, where more specific techniques such and ZNFs and TALEs have been developed, they are limited by their extensive cost and labor requirements. However, the recent advent of CRISPR-based technologies has revolutionized our potential for site-specific epigenomic editing. Here, we provide a detailed protocol for the design, construction, and utilization of a transient, CRISPR-based DNA methylation-editing system in mammalian cells.
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Affiliation(s)
- Jim Smith
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Rakesh Banerjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Robert J Weeks
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
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8
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Amweg A, Tusup M, Cheng P, Picardi E, Dummer R, Levesque MP, French LE, Guenova E, Läuchli S, Kundig T, Mellett M, Pascolo S. The A to I editing landscape in melanoma and its relation to clinical outcome. RNA Biol 2022; 19:996-1006. [PMID: 35993275 PMCID: PMC9415457 DOI: 10.1080/15476286.2022.2110390] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
RNA editing refers to non-transient RNA modifications that occur after transcription and prior to translation by the ribosomes. RNA editing is more widespread in cancer cells than in non-transformed cells and is associated with tumorigenesis of various cancer tissues. However, RNA editing can also generate neo-antigens that expose tumour cells to host immunosurveillance. Global RNA editing in melanoma and its relevance to clinical outcome currently remain poorly characterized. The present study compared RNA editing as well as gene expression in tumour cell lines from melanoma patients of short or long metastasis-free survival, patients relapsing or not after immuno- and targeted therapy and tumours harbouring BRAF or NRAS mutations. Overall, our results showed that NTRK gene expression can be a marker of resistance to BRAF and MEK inhibition and gives some insights of candidate genes as potential biomarkers. In addition, this study revealed an increase in Adenosine-to-Inosine editing in Alu regions and in non-repetitive regions, including the hyperediting of the MOK and DZIP3 genes in relapsed tumour samples during targeted therapy and of the ZBTB11 gene in NRAS mutated melanoma cells. Therefore, RNA editing could be a promising tool for identifying predictive markers, tumour neoantigens and targetable pathways that could help in preventing relapses during immuno- or targeted therapies.
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Affiliation(s)
- Austeja Amweg
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Marina Tusup
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Phil Cheng
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Bari, Italy
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Lars E French
- Department of Dermatology and Allergy, University Hospital, LMU Munich, Munich, Germany.,Dr. Philip Frost, Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Emmanuella Guenova
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland.,Department of Dermatology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Severin Läuchli
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Thomas Kundig
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Mark Mellett
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
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9
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González B, Vazquez-Vilar M, Sánchez-Vicente J, Orzáez D. Optimization of Vectors and Targeting Strategies Including GoldenBraid and Genome Editing Tools: GoldenBraid Assembly of Multiplex CRISPR /Cas12a Guide RNAs for Gene Editing in Nicotiana benthamiana. Methods Mol Biol 2022; 2480:193-214. [PMID: 35616865 DOI: 10.1007/978-1-0716-2241-4_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
New breeding techniques, especially CRISPR/Cas, could facilitate the expansion and diversification of molecular farming crops by speeding up the introduction of new traits that improve their value as biofactories. One of the main advantages of CRISPR/Cas is its ability to target multiple loci simultaneously, a key feature known as multiplexing. This characteristic is especially relevant for polyploid species, as it is the case of Nicotiana benthamiana and other species of the same genus widely used in molecular farming. Here, we describe in detail the making of a multiplex DNA construct for genome editing in N. benthamiana using the GoldenBraid modular cloning platform. In this case, the procedure is adapted for the requirements of LbCas12a (Lachnospiraceae bacterium Cas12a), a nuclease whose cloning strategy differs from that of the more often used SpCas9 (Streptococcus pyogenes Cas9) enzyme. LbCas12a-mediated edition has several advantages, as its high editing efficiency, described for different plant species, and its T/A-rich PAM sequence, which expands the range of genomic loci that can be targeted by site-specific nucleases. The protocol also includes recommendations for the selection of protospacer sequences and indications for the analysis of editing results.
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10
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Nichols PJ, Henen MA, Vicens Q, Vögeli B. Solution NMR backbone assignments of the N-terminal Zα-linker-Zβ segment from Homo sapiens ADAR1p150. Biomol NMR Assign 2021; 15:273-279. [PMID: 33742389 PMCID: PMC9199369 DOI: 10.1007/s12104-021-10017-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
Adenosine-to-inosine (A-to-I) editing of a subset of RNAs in a eukaryotic cell is required in order to avoid triggering the innate immune system. Editing is carried out by ADAR1, which exists as short (p110) and long (p150) isoforms. ADAR1p150 is mostly cytoplasmic, possesses a Z-RNA binding domain (Zα), and is only expressed during the innate immune response. A structurally homologous domain to Zα, the Zβ domain, is separated by a long linker from Zα on the N-terminus of ADAR1 but its function remains unknown. Zβ does not bind to RNA in isolation, yet the binding kinetics of the segment encompassing Zα, Zβ and the 95-residue linker between the two domains (Zα-Zβ) are markedly different compared to Zα alone. Here we present the solution NMR backbone assignment of Zα-Zβ from H. Sapiens ADAR1. The predicted secondary structure of Zα-Zβ based on chemical shifts is in agreement with previously determined structures of Zα and Zβ in isolation, and indicates that the linker is intrinsically disordered. Comparison of the chemical shifts between the individual Zα and Zβ domains to the full Zα-Zβ construct suggests that Zβ may interact with the linker, the function of which is currently unknown.
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Affiliation(s)
- Parker J Nichols
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Morkos A Henen
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Quentin Vicens
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA.
| | - Beat Vögeli
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA.
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11
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Balzarotti S, Cavaletti F, D'Aloia A, Colombo B, Cardani E, Ciceri MR, Antonietti A, Eugeni R. The Editing Density of Moving Images Influences Viewers' Time Perception: The Mediating Role of Eye Movements. Cogn Sci 2021; 45:e12969. [PMID: 33844350 DOI: 10.1111/cogs.12969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 02/26/2021] [Accepted: 03/04/2021] [Indexed: 11/29/2022]
Abstract
The present study examined whether cinematographic editing density affects viewers' perception of time. As a second aim, based on embodied models that conceive time perception as strictly connected to the movement, we tested the hypothesis that the editing density of moving images also affects viewers' eye movements and that these later mediate the effect of editing density on viewers' temporal judgments. Seventy participants watched nine video clips edited by manipulating the number of cuts (slow- and fast-paced editing against a master shot, unedited condition). For each editing density, multiple video clips were created, representing three different kinds of routine actions. The participants' eye movements were recorded while watching the video, and the participants were asked to report duration judgments and subjective passage of time judgments after watching each clip. The results showed that participants subjectively perceived that time flew more while watching fast-paced edited videos than slow-paced or unedited videos; by contrast, concerning duration judgments, participants overestimated the duration of fast-paced videos compared to the master-shot videos. Both the slow- and the fast-paced editing generated shorter fixations than the master shot, and the fast-paced editing led to shorter fixations than the slow-paced editing. Finally, compared to the unedited condition, editing led to an overestimation of durations through increased eye mobility. These findings suggest that the editing density of moving images by increasing the number of cuts effectively altered viewers' experience of time and add further evidence to prior research showing that performed eye movement is associated with temporal judgments.
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Affiliation(s)
| | | | - Adriano D'Aloia
- Department of Letters, Philosophy, Communication, University of Bergamo
| | | | - Elisa Cardani
- Department of Psychology, Università Cattolica del Sacro Cuore
| | | | | | - Ruggero Eugeni
- Department of Communication and Performing Arts, Università Cattolica del Sacro Cuore
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12
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Hug F, Avrillon S, Del Vecchio A, Casolo A, Ibanez J, Nuccio S, Rossato J, Holobar A, Farina D. Analysis of motor unit spike trains estimated from high-density surface electromyography is highly reliable across operators. J Electromyogr Kinesiol 2021; 58:102548. [PMID: 33838590 DOI: 10.1016/j.jelekin.2021.102548] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 12/25/2022] Open
Abstract
There is a growing interest in decomposing high-density surface electromyography (HDsEMG) into motor unit spike trains to improve knowledge on the neural control of muscle contraction. However, the reliability of decomposition approaches is sometimes questioned, especially because they require manual editing of the outputs. We aimed to assess the inter-operator reliability of the identification of motor unit spike trains. Eight operators with varying experience in HDsEMG decomposition were provided with the same data extracted using the convolutive kernel compensation method. They were asked to manually edit them following established procedures. Data included signals from three lower leg muscles and different submaximal intensities. After manual analysis, 126 ± 5 motor units were retained (range across operators: 119-134). A total of 3380 rate of agreement values were calculated (28 pairwise comparisons × 11 contractions/muscles × 4-28 motor units). The median rate of agreement value was 99.6%. Inter-operator reliability was excellent for both mean discharge rate and time at recruitment (intraclass correlation coefficient > 0.99). These results show that when provided with the same decomposed data and the same basic instructions, operators converge toward almost identical results. Our data have been made available so that they can be used for training new operators.
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Affiliation(s)
- François Hug
- Nantes University, Laboratory "Movement, Interactions, Performance" (EA 4334), Nantes, France; The University of Queensland, NHMRC Centre of Clinical Research Excellence in Spinal Pain, Injury and Health, School of Health and Rehabilitation Sciences, Brisbane, Australia; Institut Universitaire de France (IUF), Paris, France.
| | - Simon Avrillon
- Legs Walking AbilityLab, Shirley Ryan AbilityLab, Chicago, IL, USA; Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL, USA
| | - Alessandro Del Vecchio
- Department of Artificial Intelligence in Biomedical Engineering, Faculty of Engineering, Friedrich-Alexander University, Erlangen-Nuremberg, 91052 Erlangen, Germany
| | - Andrea Casolo
- Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Jaime Ibanez
- Department of Bioengineering, Faculty of Engineering, Imperial College London, UK; Department of Clinical and Movement Disorders, Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Stefano Nuccio
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy
| | - Julien Rossato
- Nantes University, Laboratory "Movement, Interactions, Performance" (EA 4334), Nantes, France
| | - Aleš Holobar
- Faculty of Electrical Engineering and Computer Science, University of Maribor, Slovenia
| | - Dario Farina
- Department of Bioengineering, Faculty of Engineering, Imperial College London, UK
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13
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Abstract
The innate immune receptors in higher organisms have evolved to detect molecular signatures associated with pathogenic infection and trigger appropriate immune response. One common class of molecules utilized by the innate immune system for self vs. nonself discrimination is RNA, which is ironically present in all forms of life. To avoid self-RNA recognition, the innate immune sensors have evolved sophisticated discriminatory mechanisms that involve cellular RNA metabolic machineries. Posttranscriptional RNA modification and editing represent one such mechanism that allows cells to chemically tag the host RNAs as "self" and thus tolerate the abundant self-RNA molecules. In this chapter, we discuss recent advances in our understanding of the role of RNA editing/modification in the modulation of immune signaling pathways, and application of RNA editing/modification in RNA-based therapeutics and cancer immunotherapies.
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Abstract
Aminoacyl-tRNA synthetases (aaRS) are ubiquitous enzymes responsible for aminoacyl-tRNA (aa-tRNA) synthesis. Correctly formed aa-tRNAs are necessary for proper decoding of mRNA and accurate protein synthesis. tRNAs possess specific nucleobases that promote selective recognition by cognate aaRSs. Selecting the cognate amino acid can be more challenging because all amino acids share the same peptide backbone and several are isosteric or have similar side chains. Thus, aaRSs can misactivate non-cognate amino acids and produce mischarged aa-tRNAs. If left uncorrected, mischarged aa-tRNAs deliver their non-cognate amino acid to the ribosome resulting in misincorporation into the nascent polypeptide chain. This changes the primary protein sequence and potentially causes misfolding or formation of non-functional proteins that impair cell survival. A variety of proofreading or editing pathways exist to prevent and correct mistakes in aa-tRNA formation. Editing may occur before the amino acid transfer step of aminoacylation via hydrolysis of the aminoacyl-adenylate. Alternatively, post-transfer editing, which occurs after the mischarged aa-tRNA is formed, may be carried out via a distinct editing site on the aaRS where the mischarged aa-tRNA is deacylated. In recent years, it has become clear that most organisms also encode factors that lack aminoacylation activity but resemble aaRS editing domains and function to clear mischarged aa-tRNAs in trans. This review focuses on these trans-editing factors, which are encoded in all three domains of life and function together with editing domains present within aaRSs to ensure that the accuracy of protein synthesis is sufficient for cell survival.
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Affiliation(s)
- Alexandra B Kuzmishin Nagy
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States.
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15
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Breton C, Clark PM, Wang L, Greig JA, Wilson JM. ITR-Seq, a next-generation sequencing assay, identifies genome-wide DNA editing sites in vivo following adeno-associated viral vector-mediated genome editing. BMC Genomics 2020; 21:239. [PMID: 32183699 PMCID: PMC7076944 DOI: 10.1186/s12864-020-6655-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Identifying nuclease-induced double-stranded breaks in DNA on a genome-wide scale is critical for assessing the safety and efficacy of genome editing therapies. We previously demonstrated that after administering adeno-associated viral (AAV) vector-mediated genome-editing strategies in vivo, vector sequences integrated into the host organism's genomic DNA at double-stranded breaks. Thus, identifying the genomic location of inserted AAV sequences would enable us to identify DSB events, mainly derived from the nuclease on- and off-target activity. RESULTS Here, we developed a next-generation sequencing assay that detects insertions of specific AAV vector sequences called inverted terminal repeats (ITRs). This assay, ITR-Seq, enables us to identify off-target nuclease activity in vivo. Using ITR-Seq, we analyzed liver DNA samples of rhesus macaques treated with AAV vectors expressing a meganuclease. We found dose-dependent off-target activity and reductions in off-target events induced by further meganuclease development. In mice, we identified the genomic locations of ITR integration after treatment with Cas9 nucleases and their corresponding single-guide RNAs. CONCLUSIONS In sum, ITR-Seq is a powerful method for identifying off-target sequences induced by AAV vector-delivered genome-editing nucleases. ITR-Seq will help us understand the specificity and efficacy of different genome-editing nucleases in animal models and clinical studies. This information can help enhance the safety profile of gene-editing therapies.
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Affiliation(s)
- Camilo Breton
- Gene Therapy Program, University of Pennsylvania Perelman School of Medicine, 125 South 31st Street, Suite 1200, Philadelphia, PA, 19104, USA
| | - Peter M Clark
- Gene Therapy Program, University of Pennsylvania Perelman School of Medicine, 125 South 31st Street, Suite 1200, Philadelphia, PA, 19104, USA
| | - Lili Wang
- Gene Therapy Program, University of Pennsylvania Perelman School of Medicine, 125 South 31st Street, Suite 1200, Philadelphia, PA, 19104, USA
| | - Jenny A Greig
- Gene Therapy Program, University of Pennsylvania Perelman School of Medicine, 125 South 31st Street, Suite 1200, Philadelphia, PA, 19104, USA
| | - James M Wilson
- Gene Therapy Program, University of Pennsylvania Perelman School of Medicine, 125 South 31st Street, Suite 1200, Philadelphia, PA, 19104, USA.
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Michno JM, Virdi K, Stec AO, Liu J, Wang X, Xiong Y, Stupar RM. Integration, abundance, and transmission of mutations and transgenes in a series of CRISPR/Cas9 soybean lines. BMC Biotechnol 2020; 20:10. [PMID: 32093670 PMCID: PMC7038615 DOI: 10.1186/s12896-020-00604-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 02/13/2020] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND As with many plant species, current genome editing strategies in soybean are initiated by stably transforming a gene that encodes an engineered nuclease into the genome. Expression of the transgene results in a double-stranded break and repair at the targeted locus, oftentimes resulting in mutation(s) at the intended site. As soybean is a self-pollinating species with 20 chromosome pairs, the transgene(s) in the T0 plant are generally expected to be unlinked to the targeted mutation(s), and the transgene(s)/mutation(s) should independently assort into the T1 generation, resulting in Mendellian combinations of transgene presence/absence and allelic states within the segregating family. This prediction, however, is not always consistent with observed results. RESULTS In this study, we investigated inheritance patterns among three different CRISPR/Cas9 transgenes and their respective induced mutations in segregating soybean families. Next-generation resequencing of four T0 plants and four T1 progeny plants, followed by broader assessments of the segregating families, revealed both expected and unexpected patterns of inheritance among the different lineages. These unexpected patterns included: (1) A family in which T0 transgenes and mutations were not transmitted to progeny; (2) A family with four unlinked transgene insertions, including two respectively located at paralogous CRISPR target break sites; (3) A family in which mutations were observed and transmitted, but without evidence of transgene integration nor transmission. CONCLUSIONS Genome resequencing provides high-resolution of transgene integration structures and gene editing events. Segregation patterns of these events can be complicated by several potential mechanisms. This includes, but is not limited to, plant chimeras, multiple unlinked transgene integrations, editing of intended and paralogous targets, linkage between the transgene integration and target site, and transient expression of the editing reagents without transgene integration into the host genome.
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Affiliation(s)
- Jean-Michel Michno
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN USA
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
| | - Kamaldeep Virdi
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
| | - Adrian O. Stec
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
| | - Junqi Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
| | - Xiaobo Wang
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
- School of Agronomy, Anhui Agricultural University, Hefei, China
| | - Yer Xiong
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
| | - Robert M. Stupar
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN USA
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
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Abstract
This chapter calls out the following contributed articles, and gives a sense of why the tRNA synthetases are an endless frontier for scientific research and the unveiling of a vast world of new biology.
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18
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Chan KL, Barker PB. Retrospective motion compensation for edited MR spectroscopic imaging. Neuroimage 2019; 202:116141. [PMID: 31479753 DOI: 10.1016/j.neuroimage.2019.116141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/23/2019] [Accepted: 08/28/2019] [Indexed: 12/12/2022] Open
Abstract
Edited magnetic resonance spectroscopic imaging (MRSI) is capable of mapping the distribution of low concentration metabolites such as gamma-aminobutyric acid (GABA) or and glutathione (GSH), but is prone to subtraction artifacts due to head motion or other instabilities. In this study, a retrospective motion compensation algorithm for edited MRSI is proposed. The algorithm identifies movement-affected signals by comparing residual water and lipid peaks between different transients recorded at the same point in k-space, and either phase corrects, replaces or removes affected spectra prior to spatial Fourier transformation. The method was tested on macromolecule-unsuppressed GABA-edited spin-echo MR spectroscopic imaging data acquired from 8 healthy adults scanned at 3T. Relative to non-motion compensated data sets, the motion compensated data had significantly less subtraction artifacts across subjects. The residual choline (Cho) peak in the spectrum (which is well resolved from as a different chemical shift from GABA and is completely absent in a spectrum without subtraction artifact) was used as a metric of motion artifact severity. The normalized Cho area was 5.14 times lower with motion compensation than without motion compensation. A 'removal-only' version of the technique is also shown to be promising in removing motion-corrupted artifacts in a GSH-edited MRSI acquisition acquired in 1 healthy subject. This study introduces a motion compensation technique and demonstrates that retrospective compensation in k-space is possible and significantly reduces the amount of subtraction artifacts in the resulting edited spectra.
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Affiliation(s)
- Kimberly L Chan
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Peter B Barker
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
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Ding S, Liu XY, Wang HC, Wang Y, Tang JJ, Yang YZ, Tan BC. SMK6 mediates the C-to-U editing at multiple sites in maize mitochondria. J Plant Physiol 2019; 240:152992. [PMID: 31234031 DOI: 10.1016/j.jplph.2019.152992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/01/2019] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
The recently identified PPR-E+/NVWA/DYW2 RNA editing complex provides insights into the mechanism of RNA editing in higher plant organelles. However, whether the complex works together with the previously identified editing factors RIPs/MORFs is unclear. In this paper, we identified a maize Smk6 gene, which encodes a mitochondrion-targeted PPR-E+protein with E1 and E2 domains at the C terminus. Loss of Smk6 function affects the C-to-U editing at nad1-740, nad4L-110, nad7-739, and mttB-138,139 sites, impairs mitochondrial activity and blocks embryogenesis and endosperm development. Genetic and molecular analysis indicated that SMK6 is the maize ortholog of the Arabidopsis SLO2, which is a component of the PPR-E+/NVWA/DYW2 editing complex. However, yeast two-hybrid analyses did not detect any interaction between SMK6 and any of the mitochondrion-targeted RIPs/MORFs, suggesting that RIPs/MORFs may not be a component of PPR-E+/NVWA/DYW2 RNA editing complex. Further analyses are required to provide evidence that RIP/MORFs and SMK6 do not physically interact in vivo.
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Affiliation(s)
- Shuo Ding
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Xin-Yuan Liu
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Hong-Chun Wang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yong Wang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jiao-Jiao Tang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yan-Zhuo Yang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bao-Cai Tan
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China.
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20
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DeLisi LE. Successful publishing of research: An editor's view. Psychiatry Res 2019; 277:14-16. [PMID: 30717988 DOI: 10.1016/j.psychres.2019.01.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 11/16/2022]
Abstract
Authors often are frustrated by responses they receive from editors when their manuscripts are rejected and do not understand from an editor's view what is needed to successfully publish their work. Editors receive sometimes several manuscripts a day and have to develop methods to screen out the ones that are likely not to pass the review process. They also want papers to be able to be written in such a way that it is clear why the studies of which they report are important and novel and worth publishing. Thus, advice is given in the following article that begins with how to choose an appropriate journal, to the surprising importance of a title and ends with how one should conclude the manuscript.
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Affiliation(s)
- Lynn E DeLisi
- VA Boston Healthcare System, Harvard Medical School, 940 Belmont Avenue, Brockton, MA 02310, United States.
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21
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Malbert B, Rigaill G, Brunaud V, Lurin C, Delannoy E. Bioinformatic Analysis of Chloroplast Gene Expression and RNA Posttranscriptional Maturations Using RNA Sequencing. Methods Mol Biol 2018; 1829:279-94. [PMID: 29987729 DOI: 10.1007/978-1-4939-8654-5_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Sequencing of total RNA enables the study of the whole plant transcriptome resulting from the simultaneous expression of the three genomes of plant cells (located in the nucleus, mitochondrion and chloroplast). While commonly used for the quantification of the nuclear gene expression, this method remains complex and challenging when applied to organellar genomes and/or when used to quantify posttranscriptional RNA maturations. Here we propose a complete bioinformatical and statistical pipeline to fully characterize the differences in the chloroplast transcriptome between two conditions. Experimental design as well as bioinformatics and statistical analyses are described in order to quantify both gene expression and RNA posttranscriptional maturations, i.e., RNA splicing, editing, and processing, and identify statistically significant differences.
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Mikkelsen M, Rimbault DL, Barker PB, Bhattacharyya PK, Brix MK, Buur PF, Cecil KM, Chan KL, Chen DYT, Craven AR, Cuypers K, Dacko M, Duncan NW, Dydak U, Edmondson DA, Ende G, Ersland L, Forbes MA, Gao F, Greenhouse I, Harris AD, He N, Heba S, Hoggard N, Hsu TW, Jansen JFA, Kangarlu A, Lange T, Lebel RM, Li Y, Lin CYE, Liou JK, Lirng JF, Liu F, Long JR, Ma R, Maes C, Moreno-Ortega M, Murray SO, Noah S, Noeske R, Noseworthy MD, Oeltzschner G, Porges EC, Prisciandaro JJ, Puts NAJ, Roberts TPL, Sack M, Sailasuta N, Saleh MG, Schallmo MP, Simard N, Stoffers D, Swinnen SP, Tegenthoff M, Truong P, Wang G, Wilkinson ID, Wittsack HJ, Woods AJ, Xu H, Yan F, Zhang C, Zipunnikov V, Zöllner HJ, Edden RAE. Big GABA II: Water-referenced edited MR spectroscopy at 25 research sites. Neuroimage 2019; 191:537-548. [PMID: 30840905 PMCID: PMC6818968 DOI: 10.1016/j.neuroimage.2019.02.059] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 01/25/2023] Open
Abstract
Accurate and reliable quantification of brain metabolites measured in vivo using 1H magnetic resonance spectroscopy (MRS) is a topic of continued interest. Aside from differences in the basic approach to quantification, the quantification of metabolite data acquired at different sites and on different platforms poses an additional methodological challenge. In this study, spectrally edited γ-aminobutyric acid (GABA) MRS data were analyzed and GABA levels were quantified relative to an internal tissue water reference. Data from 284 volunteers scanned across 25 research sites were collected using GABA+ (GABA + co-edited macromolecules (MM)) and MM-suppressed GABA editing. The unsuppressed water signal from the volume of interest was acquired for concentration referencing. Whole-brain T1-weighted structural images were acquired and segmented to determine gray matter, white matter and cerebrospinal fluid voxel tissue fractions. Water-referenced GABA measurements were fully corrected for tissue-dependent signal relaxation and water visibility effects. The cohort-wide coefficient of variation was 17% for the GABA + data and 29% for the MM-suppressed GABA data. The mean within-site coefficient of variation was 10% for the GABA + data and 19% for the MM-suppressed GABA data. Vendor differences contributed 53% to the total variance in the GABA + data, while the remaining variance was attributed to site- (11%) and participant-level (36%) effects. For the MM-suppressed data, 54% of the variance was attributed to site differences, while the remaining 46% was attributed to participant differences. Results from an exploratory analysis suggested that the vendor differences were related to the unsuppressed water signal acquisition. Discounting the observed vendor-specific effects, water-referenced GABA measurements exhibit similar levels of variance to creatine-referenced GABA measurements. It is concluded that quantification using internal tissue water referencing is a viable and reliable method for the quantification of in vivo GABA levels.
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Affiliation(s)
- Mark Mikkelsen
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA.
| | - Daniel L Rimbault
- Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | - Peter B Barker
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Pallab K Bhattacharyya
- Imaging Institute, Cleveland Clinic Foundation, Cleveland, OH, USA; Radiology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Maiken K Brix
- Department of Radiology, Haukeland University Hospital, Bergen, Norway
| | - Pieter F Buur
- Spinoza Centre for Neuroimaging, Amsterdam, the Netherlands
| | - Kim M Cecil
- Department of Radiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kimberly L Chan
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Y-T Chen
- Department of Radiology, Taipei Medical University Shuang Ho Hospital, New Taipei City, Taiwan
| | - Alexander R Craven
- Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway; NORMENT - Norwegian Center for Mental Disorders Research, University of Bergen, Bergen, Norway
| | - Koen Cuypers
- Movement Control & Neuroplasticity Research Group, Department of Movement Sciences, Group of Biomedical Sciences, KU Leuven, Leuven, Belgium; REVAL Rehabilitation Research Center, Hasselt University, Diepenbeek, Belgium
| | - Michael Dacko
- Department of Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Niall W Duncan
- Brain and Consciousness Research Centre, Taipei Medical University, Taipei, Taiwan
| | - Ulrike Dydak
- School of Health Sciences, Purdue University, West Lafayette, IN, USA; Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - David A Edmondson
- School of Health Sciences, Purdue University, West Lafayette, IN, USA; Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gabriele Ende
- Department of Neuroimaging, Central Institute of Mental Health, Mannheim, Germany
| | - Lars Ersland
- Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway; NORMENT - Norwegian Center for Mental Disorders Research, University of Bergen, Bergen, Norway; Department of Clinical Engineering, Haukeland University Hospital, Bergen, Norway
| | - Megan A Forbes
- Department of Clinical and Health Psychology, University of Florida, Gainesville, FL, USA; Center for Cognitive Aging and Memory, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Fei Gao
- Shandong Medical Imaging Research Institute, Shandong University, Jinan, China
| | - Ian Greenhouse
- Department of Human Physiology, University of Oregon, Eugene, OR, USA
| | - Ashley D Harris
- Department of Radiology, University of Calgary, Calgary, AB, Canada
| | - Naying He
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Stefanie Heba
- Department of Neurology, BG University Hospital Bergmannsheil, Bochum, Germany
| | - Nigel Hoggard
- Academic Unit of Radiology, University of Sheffield, Sheffield, UK
| | - Tun-Wei Hsu
- Department of Radiology, Taipei Veterans General Hospital, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Jacobus F A Jansen
- Department of Radiology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Alayar Kangarlu
- Department of Psychiatry, Columbia University, New York, NY, USA; New York State Psychiatric Institute, New York, NY, USA
| | - Thomas Lange
- Department of Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | | | - Yan Li
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Jy-Kang Liou
- Department of Radiology, Taipei Veterans General Hospital, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Jiing-Feng Lirng
- Department of Radiology, Taipei Veterans General Hospital, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Feng Liu
- New York State Psychiatric Institute, New York, NY, USA
| | - Joanna R Long
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA; National High Magnetic Field Laboratory, Gainesville, FL, USA
| | - Ruoyun Ma
- School of Health Sciences, Purdue University, West Lafayette, IN, USA; Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA
| | - Celine Maes
- Movement Control & Neuroplasticity Research Group, Department of Movement Sciences, Group of Biomedical Sciences, KU Leuven, Leuven, Belgium
| | | | - Scott O Murray
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Sean Noah
- Center for Mind and Brain, University of California, Davis, Davis, CA, USA
| | | | - Michael D Noseworthy
- Department of Electrical and Computer Engineering, McMaster University, Hamilton, ON, Canada
| | - Georg Oeltzschner
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Eric C Porges
- Department of Clinical and Health Psychology, University of Florida, Gainesville, FL, USA; Center for Cognitive Aging and Memory, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - James J Prisciandaro
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Nicolaas A J Puts
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Timothy P L Roberts
- Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Markus Sack
- Department of Neuroimaging, Central Institute of Mental Health, Mannheim, Germany
| | - Napapon Sailasuta
- Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada; Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Muhammad G Saleh
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Michael-Paul Schallmo
- Department of Psychology, University of Washington, Seattle, WA, USA; Department of Psychiatry and Behavioral Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas Simard
- School of Biomedical Engineering, McMaster University, Hamilton, ON, Canada
| | | | - Stephan P Swinnen
- Movement Control & Neuroplasticity Research Group, Department of Movement Sciences, Group of Biomedical Sciences, KU Leuven, Leuven, Belgium; Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Martin Tegenthoff
- Department of Neurology, BG University Hospital Bergmannsheil, Bochum, Germany
| | - Peter Truong
- Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Guangbin Wang
- Shandong Medical Imaging Research Institute, Shandong University, Jinan, China
| | - Iain D Wilkinson
- Academic Unit of Radiology, University of Sheffield, Sheffield, UK
| | - Hans-Jörg Wittsack
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich-Heine-University, Duesseldorf, Germany
| | - Adam J Woods
- Department of Clinical and Health Psychology, University of Florida, Gainesville, FL, USA; Center for Cognitive Aging and Memory, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Hongmin Xu
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fuhua Yan
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chencheng Zhang
- Department of Functional Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Vadim Zipunnikov
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Helge J Zöllner
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich-Heine-University, Duesseldorf, Germany; Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich-Heine-University, Duesseldorf, Germany
| | - Richard A E Edden
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
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Barroga E, Mitoma H. Critical Thinking and Scientific Writing Skills of Non-Anglophone Medical Students: a Model of Training Course. J Korean Med Sci 2019; 34:e18. [PMID: 30662384 PMCID: PMC6335120 DOI: 10.3346/jkms.2019.34.e18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/17/2018] [Indexed: 11/20/2022] Open
Abstract
There are currently very limited reports on the strengths and weaknesses of Japanese medical students in processing (i.e., searching, reading, synthesizing, writing, editing, refining) and presenting medical content based on scholarly journal articles. We developed and offered a 3-week group independent research course in English as a summer elective named "Improving Medical English Skills and Creating English Medical Content (PPT and video) Based on Medical Journal Articles" to our fourth-year Japanese medical students who follow a 6-year medical curriculum as the target audience. Herein, we describe the specific strengths and weaknesses of 6 students who chose and completed the course. Thereafter, we assessed the possible reasons underlying these weaknesses, pondered on the potential implications of such weaknesses on the critical thinking, logical reasoning, and communication skills of Japanese medical students, and suggested approaches to further enhance these skills. The assessments, implications, and suggestions given may provide medical educators new insights on how to newly organize educational and clinical programs to address such weaknesses, improve searching, reading, writing, editing, and presentation skills, enhance critical thinking and logical reasoning abilities, and gain in-depth knowledge essential for effectively appraising and communicating medical content.
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Affiliation(s)
- Edward Barroga
- Department of Medical Education, Tokyo Medical University, Tokyo, Japan
| | - Hiroshi Mitoma
- Department of Medical Education, Tokyo Medical University, Tokyo, Japan
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24
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Abstract
CRISPR/Cas9, an RNA-guided targeted genome editing system, can make precise, targeted modifications to the genome in living cells. Here we describe how this method can be used to efficiently edit the vaccinia virus genome enabling the insertion of transgene(s) specifically into a targeted site.
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Affiliation(s)
| | - Ming Yuan
- Barts Cancer Institute, Queen Mary University, London, UK
| | - Yaohe Wang
- Barts Cancer Institute, Queen Mary University, London, UK.
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25
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Abstract
m6A is the most abundant internal modification on mRNA. Recent improvements of high-throughput sequencing techniques enables its detection at the transcriptome level, even at the nucleotide resolution. However most current techniques require large amounts of starting material to detect the modification. Here, we describe a complementary technique of standard meRIP-seq/miCLIP-seq approaches to identify methylated RNA using a low amount of material. We believe this approach can be applied in vivo to identify methylated targets in specific tissues or subpopulations of cells.
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26
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Sagredo EA, Blanco A, Sagredo AI, Pérez P, Sepúlveda-Hermosilla G, Morales F, Müller B, Verdugo R, Marcelain K, Harismendy O, Armisén R. ADAR1-mediated RNA- editing of 3'UTRs in breast cancer. Biol Res 2018; 51:36. [PMID: 30290838 PMCID: PMC6172785 DOI: 10.1186/s40659-018-0185-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/09/2018] [Indexed: 12/22/2022] Open
Abstract
Background Whole transcriptome RNA variant analyses have shown that adenosine deaminases acting on RNA (ADAR) enzymes modify a large proportion of cellular RNAs, contributing to transcriptome diversity and cancer evolution. Despite the advances in the understanding of ADAR function in breast cancer, ADAR RNA editing functional consequences are not fully addressed. Results We characterized A to G(I) mRNA editing in 81 breast cell lines, showing increased editing at 3′UTR and exonic regions in breast cancer cells compared to immortalized non-malignant cell lines. In addition, tumors from the BRCA TCGA cohort show a 24% increase in editing over normal breast samples when looking at 571 well-characterized UTRs targeted by ADAR1. Basal-like subtype breast cancer patients with high level of ADAR1 mRNA expression shows a worse clinical outcome and increased editing in their 3′UTRs. Interestingly, editing was particularly increased in the 3′UTRs of ATM, GINS4 and POLH transcripts in tumors, which correlated with their mRNA expression. We confirmed the role of ADAR1 in this regulation using a shRNA in a breast cancer cell line (ZR-75-1). Conclusions Altogether, these results revealed a significant association between the mRNA editing in genes related to cancer-relevant pathways and clinical outcomes, suggesting an important role of ADAR1 expression and function in breast cancer. Electronic supplementary material The online version of this article (10.1186/s40659-018-0185-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eduardo A Sagredo
- Center of Excellence in Precision Medicine, Pfizer Chile, Obispo Arturo Espinoza Campos 2526, 7810305, Santiago, Chile.,Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Alejandro Blanco
- Center of Excellence in Precision Medicine, Pfizer Chile, Obispo Arturo Espinoza Campos 2526, 7810305, Santiago, Chile.,Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Alfredo I Sagredo
- Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Paola Pérez
- Center of Excellence in Precision Medicine, Pfizer Chile, Obispo Arturo Espinoza Campos 2526, 7810305, Santiago, Chile
| | - Gonzalo Sepúlveda-Hermosilla
- Center of Excellence in Precision Medicine, Pfizer Chile, Obispo Arturo Espinoza Campos 2526, 7810305, Santiago, Chile
| | - Fernanda Morales
- Center of Excellence in Precision Medicine, Pfizer Chile, Obispo Arturo Espinoza Campos 2526, 7810305, Santiago, Chile.,Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Bettina Müller
- Servicio de Oncología Médica, Instituto Nacional del Cáncer, Avenida Profesor Zañartu 1010, Santiago, Chile.,Grupo Oncológico Cooperativo Chileno de Investigación GOCCHI, Santiago, Chile
| | - Ricardo Verdugo
- Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.,Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.,Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Katherine Marcelain
- Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.,Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Olivier Harismendy
- Moores Cancer Center and Division of Biomedical Informatics, Department of Medicine, School of Medicine, University of California, San Diego, CA, USA.
| | - Ricardo Armisén
- Center of Excellence in Precision Medicine, Pfizer Chile, Obispo Arturo Espinoza Campos 2526, 7810305, Santiago, Chile. .,Centro de Investigación y Tratamiento del Cáncer, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile. .,Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile. .,Grupo Oncológico Cooperativo Chileno de Investigación GOCCHI, Santiago, Chile.
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Kuo J, Stirling F, Lau YH, Shulgina Y, Way JC, Silver PA. Synthetic genome recoding: new genetic codes for new features. Curr Genet 2018; 64:327-333. [PMID: 28983660 PMCID: PMC5849531 DOI: 10.1007/s00294-017-0754-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/20/2022]
Abstract
Full genome recoding, or rewriting codon meaning, through chemical synthesis of entire bacterial chromosomes has become feasible in the past several years. Recoding an organism can impart new properties including non-natural amino acid incorporation, virus resistance, and biocontainment. The estimated cost of construction that includes DNA synthesis, assembly by recombination, and troubleshooting, is now comparable to costs of early stage development of drugs or other high-tech products. Here, we discuss several recently published assembly methods and provide some thoughts on the future, including how synthetic efforts might benefit from the analysis of natural recoding processes and organisms that use alternative genetic codes.
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Affiliation(s)
- James Kuo
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Finn Stirling
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Yu Heng Lau
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Yekaterina Shulgina
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jeffrey C Way
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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28
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Habibzadeh F. Common Mistakes in Manuscripts Submitted to The IJOEM. Int J Occup Environ Med 2018; 9:61-62. [PMID: 29667642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
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29
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Mikkelsen M, Barker PB, Bhattacharyya PK, Brix MK, Buur PF, Cecil KM, Chan KL, Chen DYT, Craven AR, Cuypers K, Dacko M, Duncan NW, Dydak U, Edmondson DA, Ende G, Ersland L, Gao F, Greenhouse I, Harris AD, He N, Heba S, Hoggard N, Hsu TW, Jansen JFA, Kangarlu A, Lange T, Lebel RM, Li Y, Lin CYE, Liou JK, Lirng JF, Liu F, Ma R, Maes C, Moreno-Ortega M, Murray SO, Noah S, Noeske R, Noseworthy MD, Oeltzschner G, Prisciandaro JJ, Puts NAJ, Roberts TPL, Sack M, Sailasuta N, Saleh MG, Schallmo MP, Simard N, Swinnen SP, Tegenthoff M, Truong P, Wang G, Wilkinson ID, Wittsack HJ, Xu H, Yan F, Zhang C, Zipunnikov V, Zöllner HJ, Edden RAE. Big GABA: Edited MR spectroscopy at 24 research sites. Neuroimage 2017; 159:32-45. [PMID: 28716717 PMCID: PMC5700835 DOI: 10.1016/j.neuroimage.2017.07.021] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/20/2017] [Accepted: 07/11/2017] [Indexed: 12/14/2022] Open
Abstract
Magnetic resonance spectroscopy (MRS) is the only biomedical imaging method that can noninvasively detect endogenous signals from the neurotransmitter γ-aminobutyric acid (GABA) in the human brain. Its increasing popularity has been aided by improvements in scanner hardware and acquisition methodology, as well as by broader access to pulse sequences that can selectively detect GABA, in particular J-difference spectral editing sequences. Nevertheless, implementations of GABA-edited MRS remain diverse across research sites, making comparisons between studies challenging. This large-scale multi-vendor, multi-site study seeks to better understand the factors that impact measurement outcomes of GABA-edited MRS. An international consortium of 24 research sites was formed. Data from 272 healthy adults were acquired on scanners from the three major MRI vendors and analyzed using the Gannet processing pipeline. MRS data were acquired in the medial parietal lobe with standard GABA+ and macromolecule- (MM-) suppressed GABA editing. The coefficient of variation across the entire cohort was 12% for GABA+ measurements and 28% for MM-suppressed GABA measurements. A multilevel analysis revealed that most of the variance (72%) in the GABA+ data was accounted for by differences between participants within-site, while site-level differences accounted for comparatively more variance (20%) than vendor-level differences (8%). For MM-suppressed GABA data, the variance was distributed equally between site- (50%) and participant-level (50%) differences. The findings show that GABA+ measurements exhibit strong agreement when implemented with a standard protocol. There is, however, increased variability for MM-suppressed GABA measurements that is attributed in part to differences in site-to-site data acquisition. This study's protocol establishes a framework for future methodological standardization of GABA-edited MRS, while the results provide valuable benchmarks for the MRS community.
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Affiliation(s)
- Mark Mikkelsen
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Peter B Barker
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Pallab K Bhattacharyya
- Imaging Institute, Cleveland Clinic Foundation, Cleveland, OH, USA; Radiology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Maiken K Brix
- Department of Radiology, Haukeland University Hospital, Bergen, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Pieter F Buur
- Spinoza Centre for Neuroimaging, Amsterdam, The Netherlands
| | - Kim M Cecil
- Department of Radiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kimberly L Chan
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Y-T Chen
- Department of Radiology, Taipei Medical University Shuang Ho Hospital, New Taipei City, Taiwan
| | - Alexander R Craven
- Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway; NORMENT - Norwegian Center for Mental Disorders Research, University of Bergen, Bergen, Norway
| | - Koen Cuypers
- Department of Kinesiology, KU Leuven, Leuven, Belgium; REVAL Rehabilitation Research Center, Hasselt University, Diepenbeek, Belgium
| | - Michael Dacko
- Department of Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Niall W Duncan
- Brain and Consciousness Research Centre, Taipei Medical University, Taipei, Taiwan
| | - Ulrike Dydak
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | - David A Edmondson
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | - Gabriele Ende
- Department of Neuroimaging, Central Institute of Mental Health, Mannheim, Germany
| | - Lars Ersland
- Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway; NORMENT - Norwegian Center for Mental Disorders Research, University of Bergen, Bergen, Norway; Department of Clinical Engineering, Haukeland University Hospital, Bergen, Norway
| | - Fei Gao
- Shandong Medical Imaging Research Institute, Shandong University, Jinan, China
| | - Ian Greenhouse
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Ashley D Harris
- Department of Radiology, University of Calgary, Calgary, AB, Canada
| | - Naying He
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Stefanie Heba
- Department of Neurology, BG University Hospital Bergmannsheil, Bochum, Germany
| | - Nigel Hoggard
- Academic Unit of Radiology, University of Sheffield, Sheffield, UK
| | - Tun-Wei Hsu
- Department of Radiology, Taipei Veterans General Hospital, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Jacobus F A Jansen
- Department of Radiology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Alayar Kangarlu
- Department of Psychiatry, Columbia University, New York, NY, USA; New York State Psychiatric Institute, New York, NY, USA
| | - Thomas Lange
- Department of Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | | | - Yan Li
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Jy-Kang Liou
- Department of Radiology, Taipei Veterans General Hospital, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Jiing-Feng Lirng
- Department of Radiology, Taipei Veterans General Hospital, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Feng Liu
- New York State Psychiatric Institute, New York, NY, USA
| | - Ruoyun Ma
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | - Celine Maes
- Department of Kinesiology, KU Leuven, Leuven, Belgium
| | | | - Scott O Murray
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Sean Noah
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - Michael D Noseworthy
- Department of Electrical and Computer Engineering, McMaster University, Hamilton, ON, Canada
| | - Georg Oeltzschner
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - James J Prisciandaro
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Nicolaas A J Puts
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Timothy P L Roberts
- Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Markus Sack
- Department of Neuroimaging, Central Institute of Mental Health, Mannheim, Germany
| | - Napapon Sailasuta
- Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada; Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Muhammad G Saleh
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | | | - Nicholas Simard
- School of Biomedical Engineering, McMaster University, Hamilton, ON, Canada
| | - Stephan P Swinnen
- Department of Kinesiology, KU Leuven, Leuven, Belgium; Leuven Research Institute for Neuroscience & Disease (LIND), KU Leuven, Leuven, Belgium
| | - Martin Tegenthoff
- Department of Neurology, BG University Hospital Bergmannsheil, Bochum, Germany
| | - Peter Truong
- Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Guangbin Wang
- Shandong Medical Imaging Research Institute, Shandong University, Jinan, China
| | - Iain D Wilkinson
- Academic Unit of Radiology, University of Sheffield, Sheffield, UK
| | - Hans-Jörg Wittsack
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich-Heine-University, Duesseldorf, Germany
| | - Hongmin Xu
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fuhua Yan
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chencheng Zhang
- Department of Functional Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Vadim Zipunnikov
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Helge J Zöllner
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich-Heine-University, Duesseldorf, Germany; Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich-Heine-University, Duesseldorf, Germany
| | - Richard A E Edden
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA.
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Abstract
All types of nucleic acids in cells undergo naturally occurring chemical modifications, including DNA, rRNA, mRNA, snRNA, and most prominently tRNA. Over 100 different modifications have been described and every position in the purine and pyrimidine bases can be modified; often the sugar is also modified [1]. In tRNA, the function of modifications varies; some modulate global and/or local RNA structure, and others directly impact decoding and may be essential for viability. Whichever the case, the overall importance of modifications is highlighted by both their evolutionary conservation and the fact that organisms use a substantial portion of their genomes to encode modification enzymes, far exceeding what is needed for the de novo synthesis of the canonical nucleotides themselves [2]. Although some modifications occur at exactly the same nucleotide position in tRNAs from the three domains of life, many can be found at various positions in a particular tRNA and their location may vary between and within different tRNAs. With this wild array of chemical diversity and substrate specificities, one of the big challenges in the tRNA modification field has been to better understand at a molecular level the modes of substrate recognition by the different modification enzymes; in this realm RNA binding rests at the heart of the problem. This chapter will focus on several examples of modification enzymes where their mode of RNA binding is well understood; from these, we will try to draw general conclusions and highlight growing themes that may be applicable to the RNA modification field at large.
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Eaton KA, Innes N, Balaji SM, Pugh C, Honkala E, Lynch CD. Don't be rejected, how can we help authors, reviewers and editors?: Report of a Symposium for Editors Publishers and Others with an Interest in Scientific Publication, Held in Boston on Wednesday, 11 March 2015, during the Annual Meeting of the International Association for Dental Research. J Dent 2017; 57:77-85. [PMID: 27894948 DOI: 10.1016/j.jdent.2016.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 11/24/2016] [Indexed: 11/23/2022] Open
Abstract
This satellite symposium was the fifth in a series for editors, publishers, reviewers and all those with an interest in scientific publishing. It was held on Wednesday, 11 March 2015 at the IADR meeting in Boston, Massachusetts. The symposium attracted more than 210 attendees. The symposium placed an emphasis on strategies to ensure that papers are accepted by peer reviewed journals. The speaker, representing the Journal of Dental Research gave a history of peer review and explained how to access material to advise new authors. The speaker from India outlined the problems that occur when there is no culture for dental research and it is given a low priority in dental education. He outlined remedies. The speaker from SAGE publications described the help that publishers and editors can provide authors. The final speaker suggested that in developing countries it was essential to create alliances with dental researchers in developed countries and that local conferences to which external speakers were invited, stimulated research both in terms of quantity and quality. A wide ranging discussion then took place.
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Saleh MG, Oeltzschner G, Chan KL, Puts NAJ, Mikkelsen M, Schär M, Harris AD, Edden RAE. Simultaneous edited MRS of GABA and glutathione. Neuroimage 2016; 142:576-582. [PMID: 27534734 DOI: 10.1016/j.neuroimage.2016.07.056] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/12/2016] [Accepted: 07/27/2016] [Indexed: 12/12/2022] Open
Abstract
Edited MRS allows the detection of low-concentration metabolites, whose signals are not resolved in the MR spectrum. Tailored acquisitions can be designed to detect, for example, the inhibitory neurotransmitter γ-aminobutyric acid (GABA), or the reduction-oxidation (redox) compound glutathione (GSH), and single-voxel edited experiments are generally acquired at a rate of one metabolite-per-experiment. We demonstrate that simultaneous detection of the overlapping signals of GABA and GSH is possible using Hadamard Encoding and Reconstruction of Mega-Edited Spectroscopy (HERMES). HERMES applies orthogonal editing encoding (following a Hadamard scheme), such that GSH- and GABA-edited difference spectra can be reconstructed from a single multiplexed experiment. At a TE of 80ms, 20-ms editing pulses are applied at 4.56ppm (on GSH),1.9ppm (on GABA), both offsets (using a dual-lobe cosine-modulated pulse) or neither. Hadamard combinations of the four sub-experiments yield GABA and GSH difference spectra. It is shown that HERMES gives excellent separation of the edited GABA and GSH signals in phantoms, and resulting edited lineshapes agree well with separate Mescher-Garwood Point-resolved Spectroscopy (MEGA-PRESS) acquisitions. In vivo, the quality and signal-to-noise ratio (SNR) of HERMES spectra are similar to those of sequentially acquired MEGA-PRESS spectra, with the benefit of saving half the acquisition time.
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Affiliation(s)
- Muhammad G Saleh
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Georg Oeltzschner
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Kimberly L Chan
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicolaas A J Puts
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Mark Mikkelsen
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Michael Schär
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ashley D Harris
- Department of Radiology, University of Calgary, Calgary, AB, Canada; Child and Adolescent Imaging Research Program, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Richard A E Edden
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; F. M. Kirby Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA.
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Shafik A, Schumann U, Evers M, Sibbritt T, Preiss T. The emerging epitranscriptomics of long noncoding RNAs. Biochim Biophys Acta 2015; 1859:59-70. [PMID: 26541084 DOI: 10.1016/j.bbagrm.2015.10.019] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/15/2015] [Accepted: 10/28/2015] [Indexed: 01/08/2023]
Abstract
The pervasive transcription of genomes into long noncoding RNAs has been amply demonstrated in recent years and garnered much attention. Similarly, emerging 'epitranscriptomics' research has shown that chemically modified nucleosides, thought to be largely the domain of tRNAs and other infrastructural RNAs, are far more widespread and can exert unexpected influence on RNA utilization. Both areas are characterized by the often-ephemeral nature of the subject matter in that few individual examples have been fully assessed for their molecular or cellular function, and effects might often be subtle and cumulative. Here we review available information at the intersection of these two exciting areas of biology, by focusing on four RNA modifications that have been mapped transcriptome-wide: 5-methylcytidine, N6-methyladenosine, pseudouridine as well as adenosine to inosine (A-to-I) editing, and their incidence and function in long noncoding RNAs. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Andrew Shafik
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Ulrike Schumann
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Maurits Evers
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Tennille Sibbritt
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia; Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst (Sydney), New South Wales 2010, Australia.
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Wong RG, Kazane K, Maslov DA, Rogers K, Aphasizhev R, Simpson L. U-insertion/deletion RNA editing multiprotein complexes and mitochondrial ribosomes in Leishmania tarentolae are located in antipodal nodes adjacent to the kinetoplast DNA. Mitochondrion 2015; 25:76-86. [PMID: 26462764 DOI: 10.1016/j.mito.2015.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 10/05/2015] [Accepted: 10/08/2015] [Indexed: 11/28/2022]
Abstract
We studied the intramitochondrial localization of several multiprotein complexes involved in U-insertion/deletion RNA editing in trypanosome mitochondria. The editing complexes are located in one or two antipodal nodes adjacent to the kinetoplast DNA (kDNA) disk, which are distinct from but associated with the minicircle catenation nodes. In some cases the proteins are in a bilateral sheet configuration. We also found that mitoribosomes have a nodal configuration. This type of organization is consistent with evidence for protein and RNA interactions of multiple editing complexes to form an ~40S editosome and also an interaction of editosomes with mitochondrial ribosomes.
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Affiliation(s)
- Richard G Wong
- Department of Gerontology, Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States; Department of Microbiology, Immunology and Molecular Genetics, Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States
| | - Katelynn Kazane
- Multispan Inc., Hayward, CA 94544, United States; Department of Microbiology, Immunology and Molecular Genetics, Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States
| | - Dmitri A Maslov
- Department of Biology, University of California - Riverside, Riverside, CA 92521, United States
| | - Kestrel Rogers
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, United States
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, United States
| | - Larry Simpson
- Department of Microbiology, Immunology and Molecular Genetics, Geffen School of Medicine at UCLA, Los Angeles, CA 90095, United States.
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Abstract
The primary objective of educational programs on biomedical writing, editing, and publishing is to nurture ethical skills among local and international researchers and editors from diverse professional backgrounds. The mechanics, essential components, and target outcomes of these programs are described in this article. The mechanics covers the objectives, design, benefits, duration, participants and qualifications, program formats, administrative issues, and mentorship. The essential components consist of three core schedules: Schedule I Basic aspects of biomedical writing, editing, and communications; Schedule II Essential skills in biomedical writing, editing, and publishing; and Schedule III Interactive lectures on relevant topics. The target outcomes of the programs comprise knowledge acquisition, skills development, paper write-up, and journal publication. These programs add to the prestige and academic standing of the host institutions.
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Affiliation(s)
- Edward Barroga
- Department of International Medical Communications, Tokyo Medical University, Tokyo, Japan
| | - Maya Vardaman
- Department of International Medical Communications, Tokyo Medical University, Tokyo, Japan
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Millar EL, Rennick LJ, Weissbrich B, Schneider-Schaulies J, Duprex WP, Rima BK. The phosphoprotein genes of measles viruses from subacute sclerosing panencephalitis cases encode functional as well as non-functional proteins and display reduced editing. Virus Res 2015; 211:29-37. [PMID: 26428304 DOI: 10.1016/j.virusres.2015.09.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 01/15/2023]
Abstract
Products expressed from the second (P/V/C) gene are important in replication and abrogating innate immune responses during acute measles virus (MV) infection. Thirteen clone sets were derived from the P/V/C genes of measles virus (MV) RNA extracted from brains of a unique collection of seven cases of subacute sclerosing panencephalitis (SSPE) caused by persistent MV in the central nervous system (CNS). Whether these functions are fully maintained when MV replicates in the CNS has not been previously determined. Co-transcriptional editing of the P mRNAs by non-template insertion of guanine (G) nucleotides, which generates mRNAs encoding the viral V protein, occurs much less frequently (9%) in the SSPE derived samples than during the acute infection (30-50%). Thus it is likely that less V protein, which is involved in combatting the innate immune response, is produced. The P genes in MV from SSPE cases were not altered by biased hypermutation but exhibited a high degree of variation within each case. Most but not all SSPE derived phospho-(P) proteins were functional in mini genome replication/transcription assays. An eight amino acid truncation of the carboxyl-terminus made the P protein non-functional while the insertion of an additional glycine residue by insertion of G nucleotides at the editing site had no effect on protein function.
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Affiliation(s)
- E L Millar
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, BT9 7BL Northern Ireland, UK
| | - L J Rennick
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, BT9 7BL Northern Ireland, UK; Department of Microbiology, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories, Boston University, 620 Albany Street, Boston, MA 02118, United States
| | - B Weissbrich
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Straβe 7, D-97078 Würzburg, Germany
| | - J Schneider-Schaulies
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Straβe 7, D-97078 Würzburg, Germany
| | - W P Duprex
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, BT9 7BL Northern Ireland, UK; Department of Microbiology, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories, Boston University, 620 Albany Street, Boston, MA 02118, United States
| | - B K Rima
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, BT9 7BL Northern Ireland, UK.
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Abstract
This review discusses gene editing and its potential in oncology. Gene editing has not evolved faster towards clinical application because of its difficulty in implementation. There have been many limitations of the tools thought to be useful in therapeutic gene editing. However, recently the combinatorial use of multiple biological tools appears to have broken the barrier impending clinical development. This review gives a short primer on gene editing followed by some of the foundational work in gene editing and subsequently a discussion of programmable nucleases leading to a description of Zinc Finger Nuclease, TALENs and CRISPRs. Gene editing tools are now being used routinely to re-engineer the human genome. Theoretically, any gene or chromosomal sequence for which a targeting site can be identified could be rendered nonfunctional by the chromosomal breakage activity of Zinc Finger Nucleases, TALENs or a CRISPR/Cas9 system. Since the initial work started on the mechanism and regulation of gene editing, investigators have been searching for a way to develop these technologies as a treatment for cancer. The issue is finding a practical application of gene editing in oncology. However, progressive ideas are working their way through the research arena which may have an impact on cancer treatment.
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Affiliation(s)
- Eric B Kmiec
- Gene Editing Institute, Center for Translational Cancer Research, Helen F. Graham Cancer Center and Research Institute, 4701 Ogletown-Stanton Road, Suite 4300, Newark, DE, 19713, USA.
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Greif G, Rodriguez M, Reyna-Bello A, Robello C, Alvarez-Valin F. Kinetoplast adaptations in American strains from Trypanosoma vivax. Mutat Res 2015; 773:69-82. [PMID: 25847423 DOI: 10.1016/j.mrfmmm.2015.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/06/2015] [Accepted: 01/17/2015] [Indexed: 05/24/2023]
Abstract
The mitochondrion role changes during the digenetic life cycle of African trypanosomes. Owing to the low abundance of glucose in the insect vector (tsetse flies) the parasites are dependent upon a fully functional mitochondrion, capable of performing oxidative phosphorylation. Nevertheless, inside the mammalian host (bloodstream forms), which is rich in nutrients, parasite proliferation relies on glycolysis, and the mitochondrion is partially redundant. In this work we perform a comparative study of the mitochondrial genome (kinetoplast) in different strains of Trypanosoma vivax. The comparison was conducted between a West African strain that goes through a complete life cycle and two American strains that are mechanically transmitted (by different vectors) and remain as bloodstream forms only. It was found that while the African strain has a complete and apparently fully functional kinetoplast, the American T. vivax strains have undergone a drastic process of mitochondrial genome degradation, in spite of the recent introduction of these parasites in America. Many of their genes exhibit different types of mutations that are disruptive of function such as major deletions, frameshift causing indels and missense mutations. Moreover, all but three genes (A6-ATPase, RPS12 and MURF2) are not edited in the American strains, whereas editing takes place normally in all (editable) genes from the African strain. Two of these genes, A6-ATPase and RPS12, are known to play an essential function during bloodstream stage. Analysis of the minicircle population shows that its diversity has been greatly reduced, remaining mostly those minicircles that carry guide RNAs necessary for the editing of A6-ATPase and RPS12. The fact that these two genes remain functioning normally, as opposed to that reported in Trypanosoma brucei-like trypanosomes that restrict their life cycle to the bloodstream forms, along with other differences, is indicative that the American T. vivax strains are following a novel evolutionary pathway.
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Affiliation(s)
- Gonzalo Greif
- Unidad de Biología Molecular, Institut Pasteur de Montevideo, Uruguay
| | - Matías Rodriguez
- Sección Biomatemática, Facultad de Ciencias, Universidad de la Republica, Uruguay
| | - Armando Reyna-Bello
- Departamento de Ciencias de la Vida, Carrera en Ingeniería en Biotecnología, Universidad de las Fuerzas Armadas, Ecuador; Centro de Estudios Biomédicos y Veterinarios, Universidad Nacional Experimental Simón Rodríguez-IDECYT, Caracas, Venezuela
| | - Carlos Robello
- Unidad de Biología Molecular, Institut Pasteur de Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República Uruguay
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Gasparyan AY, Akazhanov NA, Voronov AA, Kitas GD. Systematic and open identification of researchers and authors: focus on open researcher and contributor ID. J Korean Med Sci 2014; 29:1453-6. [PMID: 25408574 PMCID: PMC4234910 DOI: 10.3346/jkms.2014.29.11.1453] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 10/06/2014] [Indexed: 11/20/2022] Open
Abstract
Unique identifiers of researchers and authors can help all stakeholders of scientific communications improve their workflows. There have been several attempts to establish professional networks of scholars and list their scholarly achievements on digital platforms. Some of these platforms such as Google Scholar, Web of Knowledge and PubMed are searched to pick relevant peer reviewers, assess authors' publication history or choose suitable candidates for research and academic projects. However, each of these hubs has its specific applications, limiting the universal use for permanent tagging of researcher profiles. The Open Researcher and Contributor ID (ORCID) initiative, launched in 2012, is aimed at registering scholarly contributors and averting the persistent ambiguity of recorded author names. The ORCID registry is growing fast and integrating with other ID-generating platforms, thereby increasing the functionality of the integrated systems. ORCID identifiers are increasingly used for selecting peer reviewers and acknowledging various scholarly contributions (e.g., published articles, reviewer comments, conference presentations). The initiative offers unique opportunities for transparent disclosures of author contributions and competing interests and improving ethical standards of research, editing, and publishing.
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Affiliation(s)
- Armen Yuri Gasparyan
- Department of Rheumatology and Research and Development, Dudley Group NHS Foundation Trust (A Teaching Trust of the University of Birmingham, UK), Russells Hall Hospital, Dudley, West Midlands, United Kingdom
| | - Nurbek A. Akazhanov
- Department of Internship and Residency for General Practitioners N3, Kazakh National Medical University, Almaty, Kazakhstan
| | - Alexander A. Voronov
- Department of Marketing and Trade Deals, Kuban State University, Krasnodar, Russian Federation
| | - George D. Kitas
- Department of Rheumatology and Research and Development, Dudley Group NHS Foundation Trust (A Teaching Trust of the University of Birmingham, UK), Russells Hall Hospital, Dudley, West Midlands, United Kingdom
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester, United Kingdom
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40
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Bitzer J. Standing on the shoulders of giants, and looking ahead. EUR J CONTRACEP REPR 2014; 19:227-30. [PMID: 25039757 DOI: 10.3109/13625187.2014.943979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Johannes Bitzer
- Editor-in-Chief, The European Journal of Contraception and Reproductive Health Care
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Martin CB, Hamon M, Lanfumey L, Mongeau R. Controversies on the role of 5-HT(2C) receptors in the mechanisms of action of antidepressant drugs. Neurosci Biobehav Rev 2014; 42:208-23. [PMID: 24631644 DOI: 10.1016/j.neubiorev.2014.03.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 01/22/2014] [Accepted: 03/02/2014] [Indexed: 01/08/2023]
Abstract
Evidence from the various sources indicates alterations in 5-HT2C receptor functions in anxiety, depression and suicide, and other stress-related disorders treated with antidepressant drugs. Although the notion of a 5-HT2C receptor desensitization following antidepressant treatments is rather well anchored in the literature, this concept is mainly based on in vitro assays and/or behavioral assays (hypolocomotion, hyperthermia) that have poor relevance to anxio-depressive disorders. Our objective herein is to provide a comprehensive overview of the studies that have assessed the effects of antidepressant drugs on 5-HT2C receptors. Relevant molecular (second messengers, editing), neurochemical (receptor binding and mRNA levels), physiological (5-HT2C receptor-induced hyperthermia and hormone release), behavioral (5-HT2C receptor-induced changes in feeding, anxiety, defense and motor activity) data are summarized and discussed. Setting the record straight about drug-induced changes in 5-HT2C receptor function in specific brain regions should help to determine which pharmacotherapeutic strategy is best for affective and anxiety disorders.
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42
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Abstract
The transcriptome changes hugely during development of the brain. Whole genes, alternate exons, and single base pair changes related to RNA editing all show differences between embryonic and mature brain. Collectively, these changes control proteomic diversity as the brain develops. Additionally, there are many changes in noncoding RNAs (miRNA and lncRNA) that interact with mRNA to influence the overall transcriptional landscape. Here, we will discuss what is known about such changes in brain development, particularly focusing on high-throughput approaches and how those can be used to infer mechanisms by which gene expression is controlled in the brain as it matures.
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Affiliation(s)
- Allissa A Dillman
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Mark R Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA.
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43
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Vinken L, Megens S, Schrooten Y, Vandamme AM, Van Laethem K. Evaluation of the automatic editing tool RECall for HIV-1 pol and V3 loop sequences. J Virol Methods 2013; 193:135-9. [PMID: 23748120 DOI: 10.1016/j.jviromet.2013.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 05/14/2013] [Accepted: 05/28/2013] [Indexed: 11/24/2022]
Abstract
Genotypic drug resistance testing is routine practice in HIV-1 clinical care. The visual interpretation of sequencing electropherograms is labour-intensive and subject to intra- and inter-assay variability because decisions are based on operators' judgments. In this study the performance of the automatic editing tool RECall was compared to the current standard of editing manually and editing using the tool ViroSeq. Using RECall a consensus sequence could be generated for 97% of the V3 loop and for 79% of the pol experiments. By comparison, using manual editing a consensus sequence could be reached for 87% of the V3 and 87% of the pol experiments. Using ViroSeq, a consensus sequence was generated for 68% of the pol experiments. On a predefined dataset, manual editing displayed the highest probability to accurately assign mixtures (0.91 vs. 0.88 by ViroSeq vs. 0.76 by RECall) and the lowest probability to inaccurately assign a mixture to a pure base call (0.002 vs. 0.019 by ViroSeq vs. 0.002 by RECall). As differences in base calling have little impact on drug resistance interpretation and hands-on-time could be substantially reduced, RECall could be a valuable tool for the standardization and acceleration of the editing process.
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Affiliation(s)
- Lore Vinken
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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