Open Science: Challenges, Possible Solutions and the Way Forward

Everyone agrees that scientific communication should be free for all. Unfortunately, accessing publications from many reputed journals comes at a high cost—a cost that many researchers and institutions cannot afford. Although, open-access publication model is considered by many as a possible route to ensure that science is free for all; however, it is fraught with its own challenges. This review attempts at exploring the possibilities of keeping science accessible. Firstly, we re-visit the meaning of “open science” as a comprehensive concept which includes open source, data, access, resources, peer review etc. and not merely open access publication model. Next, we have discussed the global initiatives towards open access—the Budapest Open Access Initiative, Bethesda Statement on Open Access Publishing, Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities, cOAlition S and its Plan S initiative, UNESCO Recommendation on Open Science and the San Francisco Declaration on Research Assessment (DORA). Following this we have included the various open access initiatives from India. In the next part, we have focused on problems with dissemination of scientific outcomes and the challenges associated with existing publication models. Finally, we explore the possible solutions to the existing challenges, which include promotion of pre-print servers and other ideas that we have detailed in the manuscript. © 2022, Indian National Science Academy

CRISPR-Cas9 helps solve a piece of the puzzle of the biosynthesis of salicinoids and suggests a role in the growth-defense trade-off in poplar

Not AvailableWillow tree bark has been in use as a reliever of pain and fever for around 3,500 years (Desborough and Keeling, 2017). Unknown to our ancient ancestors, willow bark contains salicin, a salicinoid compound that is the original source of aspirin. Salicinoids are phenolic glycosides found only in willows and poplars. They are plant defense compounds and help willow and poplar trees to deter herbivores. Despite their medicinal value and importance in plant defense, salicinoid biosynthesis remains puzzling. Recent studies have provided a clue that a UDP-glycosyltransferase (UGT71L1) is essential for salicinoid biosynthesis in poplar (Fellenberg et al., 2020; Kulasekaran et al., 2021). In this issue, Harley Gordon and coauthors (Gordon et al., 2022) generated CRISPR-Cas9-mediated UGT71L1 knock-out mutants of poplar and revealed a central role of UGT71L1 in salicinoid biosynthesis and herbivore defense (see Figure).Not Availabl

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Not AvailableViruses are too small to be seen in a light microscope, yet they cause havoc in plants as well as animal communities. In the midst of a viral pandemic, who would know better than us how much damage this tiny invisible foe can cause. Viruses need to produce numerous proteins for replication, movement, and pathogenesis. Having a tiny genome, viruses use non-conventional strategies like initiating protein synthesis from un-annotated sites to increase their coding capacity (Ho et al., 2021). Accurate annotation of viral genes is crucial to developing antiviral strategies. However, deciphering a full set of viral genes is a great challenge as viruses use hidden open-reading frames (ORFs) with unanticipated translation initiation sites (TISs).Not Availabl

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Not AvailableThe CRISPR/Cas9-mediated base editing technology can efficiently generate point mutations in the genome without introducing a double-strand break (DSB) or supplying a DNA donor template for homology-directed repair (HDR). In this study, adenine base editors (ABEs) were used for rapid generation of precise point mutations in two distinct genes, OsWSL5, and OsZEBRA3 (Z3), in both rice protoplasts and regenerated plants. The precisely engineered point mutations were stably inherited to subsequent generations. These single nucleotide alterations resulted in single amino acid changes and associated wsl5 and z3 phenotypes as evidenced by white stripe leaf and light green/dark green leaf pattern, respectively. Through selfing and genetic segregation, transgene-free, base edited wsl5 and z3 mutants were obtained in a short period of time. We noticed a novel mutation (V540A) in Z3 locus could also mimic the phenotype of Z3 mutation (S542P). Furthermore, we observed unexpected non- A/G or T/C mutations in the ABE editing window in a few of the edited plants. The ABE vectors and the method from this study could be used to simultaneously generate point mutations in multiple target genes in a single transformation and serve as a useful base editing tool for crop improvement as well as basic studies in plant biology.Not Availabl

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Not AvailableThis second volume provides new and updated methods detailing advancements in CRISPR-Cas technical protocols. Chapters guide readers through protocols on prime editing, base editing, multiplex editing, editing in cell-free extract, in silico analysis of gRNA secondary structure and CRISPR-diagnosis. Authoritative and cutting-edge, CRISPR-Cas Methods, Volume 2 aims to serves as a laboratory manual providing scientists with a holistic view of CRISPR-Cas methodologies and its practical application for the editing of crop plants, cell lines, nematode and microorganism. The chapter “CRISPR/Cas9-mediated gene editing in human induced pluripotent stem cells” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.”Not Availabl

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Not AvailableThe discovery and subsequent repurposing of the CRISPR (clustered regularly interspaced short palindromic repeats) and Cas proteins (CRISPR-associated proteins) has revolutionized our ability to manipulate DNA and RNA sequences in vitro, ex vivo, and in vivo. In this introductory chapter, we present a brief overview of basics of CRISPR-Cas-mediated genome editing and different orthologues and engineered versions of Cas protein with altered specificity and expanded targetability. More importantly, we comprehensively portray the advances made by developing diverse CRISPR-Cas-based genome modification tools and their application in basic biology, agriculture, and medicine.Not Availabl

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Not AvailableRice, a key staple food crop in the world and India, offers food and nutrition security to millions of the global population. Abiotic (water, soil, atmospheric) stresses affect yield and quality of rice. This necessitates stressresilient rice production technologies sufficiently fortified by novel stress mitigation and adaptation strategies. Recent crop improvement strategy has partially managed to resolve the challenges presented by abiotic stresses such as high temperature, drought, salinity, alkalinity, waterlogging and mineral deficiency. The complication and multiplicity of abiotic stresses necessitate the use of extensive, integrative and multi-disciplinary techniques to achieve resilience. Crop improvement, along with the agronomic interventions, is essential to stabilise the productivity and profitability of rice production. This article gives an overview of the potential impacts of abiotic stress on rice and suggests the adaptation and mitigation strategies.Not Availabl

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Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the expertsThis volume details the fundamentals of the CRISPR-Cas system, and its protocols illustrate advances in CRISPR-Cas techniques for efficient genome editing. Introductory chapters provide a wide horizon of CRISPR/Cas-based methods and applications. Additional chapters guide readers through HDR-mediated editing, sgRNA design, the step-by-step procedure of multiplex adenine base editing experiments in rice, generating mutants for rice, wheat, Brachypodium, Barley, Flax, and Phytophthora, visual screening of mutants, gene deletion (knock-out), tagging (knock-in) in mammalian cells, the cloning-free (DNA-free) technique, cell-penetrating peptides, generating a genome-edited banana, and nuclear genome editing of Chlamydomonas employing CRISPR-Cpf1 combined with a single-stranded DNA (ssODN) repair template. Authoritative and cutting-edge, CRISPR-Cas Methods aims to assist researchers who are new to the field and are aiming to learn how best to adopt this technology for a particular organism.Not Availabl

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Not AvailableThe development of CRISPR–Cas systems has sparked a genome editing revolution in plant genetics and breeding. These sequence-specific RNA-guided nucleases can induce DNA double-stranded breaks, resulting in mutations by imprecise non-homologous end joining (NHEJ) repair or precise DNA sequence replacement by homology-directed repair (HDR). However, HDR is highly inefficient in many plant species, which has greatly limited precise genome editing in plants. To fill the vital gap in precision editing, base editing and prime editing technologies have recently been developed and demonstrated in numerous plant species. These technologies, which are mainly based on Cas9 nickases, can introduce precise changes into the target genome at a single-base resolution. This Review provides a timely overview of the current status of base editors and prime editors in plants, covering both technological developments and biological applications.Not Availabl