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Bagchi R, Tinker-Kulberg R, Salehin M, Supakar T, Chamberlain S, Ligaba-Osena A, Josephs EA. Polyvalent guide RNAs for CRISPR antivirals. iScience 2022; 25:105333. [PMID: 36325075 PMCID: PMC9618770 DOI: 10.1016/j.isci.2022.105333] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/13/2022] [Accepted: 10/10/2022] [Indexed: 11/29/2022] Open
Abstract
CRISPR effector Cas13 recognizes and degrades RNA molecules that are complementary to its guide RNA (gRNA) and possesses potential as an antiviral biotechnology because it can degrade viral mRNA and RNA genomes. Because multiplexed targeting is a critical strategy to improve viral suppression, we developed a strategy to design of gRNAs where individual gRNAs have maximized activity at multiple viral targets, simultaneously, by exploiting the molecular biophysics of promiscuous target recognition by Cas13. These "polyvalent" gRNA sequences ("pgRNAs") provide superior antiviral elimination across tissue/organ scales in a higher organism (Nicotiana benthamiana) compared to conventionally-designed gRNAs-reducing detectable viral RNA by >30-fold, despite lacking perfect complementarity with either of their targets and, when multiplexed, reducing viral RNA by >99.5%. Pairs of pgRNA-targetable sequences are abundant in the genomes of RNA viruses, and this work highlights the need for specific approaches to the challenges of targeting viruses in eukaryotes using CRISPR.
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Affiliation(s)
- Rammyani Bagchi
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
| | - Rachel Tinker-Kulberg
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
| | - Mohammad Salehin
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
| | - Tinku Supakar
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
| | - Sydney Chamberlain
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
| | - Ayalew Ligaba-Osena
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
| | - Eric A. Josephs
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
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Hetherington R, Toufique Hasan ABM, Khan A, Roy D, Salehin M, Wadud Z. Exposure risk analysis of COVID-19 for a ride-sharing motorbike taxi. Phys Fluids (1994) 2021; 33:113319. [PMID: 35002199 PMCID: PMC8726634 DOI: 10.1063/5.0069454] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/27/2021] [Indexed: 05/31/2023]
Abstract
A dominant mode of transmission for the respiratory disease COVID-19 is via airborne virus-carrying aerosols. As national lockdowns are lifted and people begin to travel once again, an assessment of the risk associated with different forms of public transportation is required. This paper assesses the risk of transmission in the context of a ride-sharing motorbike taxi-a popular choice of paratransit in South and South-East Asia and Sub-Saharan Africa. Fluid dynamics plays a significant role in understanding the fate of droplets ejected from a susceptible individual during a respiratory event, such as coughing. Numerical simulations are employed here using an Eulerian-Lagrangian approach for particles and the Reynolds-averaged Navier-Stokes method for the background air flow. The driver is assumed to be exhaling virus laden droplets, which are transported toward the passenger by the background flow. A single cough is simulated for particle sizes 1, 10, 50 μ m , with motorbike speeds 1 , 5 , 15 m / s . It has been shown that small and large particles pose different types of risk. Depending on the motorbike speed, large particles may deposit onto the passenger, while smaller particles travel between the riders and may be inhaled by the passenger. To reduce risk of transmission to the passenger, a shield is placed between the riders. The shield not only acts as a barrier to block particles, but also alters the flow field around the riders, pushing particles away from the passenger. The findings of this paper therefore support the addition of a shield potentially making the journey safer.
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Affiliation(s)
- R. Hetherington
- School of Civil Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - A. B. M. Toufique Hasan
- Department of Mechanical Engineering, Bangladesh University of Engineering and Technology (BUET), Dhaka, Bangladesh
| | - A. Khan
- School of Civil Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - D. Roy
- Department of Mechanical Engineering, Bangladesh University of Engineering and Technology (BUET), Dhaka, Bangladesh
| | - M. Salehin
- Department of Mechanical Engineering, Bangladesh University of Engineering and Technology (BUET), Dhaka, Bangladesh
| | - Z. Wadud
- Institute for Transport Studies and School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
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Numan M, Khan AL, Asaf S, Salehin M, Beyene G, Tadele Z, Ligaba-Osena A. From Traditional Breeding to Genome Editing for Boosting Productivity of the Ancient Grain Tef [ Eragrostis tef (Zucc.) Trotter]. Plants (Basel) 2021; 10:628. [PMID: 33806233 PMCID: PMC8066236 DOI: 10.3390/plants10040628] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023]
Abstract
Tef (Eragrostis tef (Zucc.) Trotter) is a staple food crop for 70% of the Ethiopian population and is currently cultivated in several countries for grain and forage production. It is one of the most nutritious grains, and is also more resilient to marginal soil and climate conditions than major cereals such as maize, wheat and rice. However, tef is an extremely low-yielding crop, mainly due to lodging, which is when stalks fall on the ground irreversibly, and prolonged drought during the growing season. Climate change is triggering several biotic and abiotic stresses which are expected to cause severe food shortages in the foreseeable future. This has necessitated an alternative and robust approach in order to improve resilience to diverse types of stresses and increase crop yields. Traditional breeding has been extensively implemented to develop crop varieties with traits of interest, although the technique has several limitations. Currently, genome editing technologies are receiving increased interest among plant biologists as a means of improving key agronomic traits. In this review, the potential application of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR-Cas) technology in improving stress resilience in tef is discussed. Several putative abiotic stress-resilient genes of the related monocot plant species have been discussed and proposed as target genes for editing in tef through the CRISPR-Cas system. This is expected to improve stress resilience and boost productivity, thereby ensuring food and nutrition security in the region where it is needed the most.
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Affiliation(s)
- Muhammad Numan
- Laboratory of Molecular Biology and Biotechnology, Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (M.N.); (M.S.)
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, Biotechnology and OMICs Laboratory, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (S.A.)
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, Biotechnology and OMICs Laboratory, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (S.A.)
| | - Mohammad Salehin
- Laboratory of Molecular Biology and Biotechnology, Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (M.N.); (M.S.)
| | - Getu Beyene
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA;
| | - Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland;
| | - Ayalew Ligaba-Osena
- Laboratory of Molecular Biology and Biotechnology, Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (M.N.); (M.S.)
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Salehin M, Li B, Tang M, Katz E, Song L, Ecker JR, Kliebenstein DJ, Estelle M. Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels. Nat Commun 2019. [PMID: 31492889 DOI: 10.1038/s41467-019-12002-12001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
A detailed understanding of abiotic stress tolerance in plants is essential to provide food security in the face of increasingly harsh climatic conditions. Glucosinolates (GLSs) are secondary metabolites found in the Brassicaceae that protect plants from herbivory and pathogen attack. Here we report that in Arabidopsis, aliphatic GLS levels are regulated by the auxin-sensitive Aux/IAA repressors IAA5, IAA6, and IAA19. These proteins act in a transcriptional cascade that maintains expression of GLS levels when plants are exposed to drought conditions. Loss of IAA5/6/19 results in reduced GLS levels and decreased drought tolerance. Further, we show that this phenotype is associated with a defect in stomatal regulation. Application of GLS to the iaa5,6,19 mutants restores stomatal regulation and normal drought tolerance. GLS action is dependent on the receptor kinase GHR1, suggesting that GLS may signal via reactive oxygen species. These results provide a novel connection between auxin signaling, GLS levels and drought response.
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Affiliation(s)
- Mohammad Salehin
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, La Jolla CA., 92093, USA
| | - Baohua Li
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Michelle Tang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ella Katz
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Liang Song
- Genomic Analysis Laboratory, Howard Hughes Medical Institute and The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Howard Hughes Medical Institute and The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Mark Estelle
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, La Jolla CA., 92093, USA.
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Salehin M, Li B, Tang M, Katz E, Song L, Ecker JR, Kliebenstein DJ, Estelle M. Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels. Nat Commun 2019; 10:4021. [PMID: 31492889 PMCID: PMC6731224 DOI: 10.1038/s41467-019-12002-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/16/2019] [Indexed: 11/11/2022] Open
Abstract
A detailed understanding of abiotic stress tolerance in plants is essential to provide food security in the face of increasingly harsh climatic conditions. Glucosinolates (GLSs) are secondary metabolites found in the Brassicaceae that protect plants from herbivory and pathogen attack. Here we report that in Arabidopsis, aliphatic GLS levels are regulated by the auxin-sensitive Aux/IAA repressors IAA5, IAA6, and IAA19. These proteins act in a transcriptional cascade that maintains expression of GLS levels when plants are exposed to drought conditions. Loss of IAA5/6/19 results in reduced GLS levels and decreased drought tolerance. Further, we show that this phenotype is associated with a defect in stomatal regulation. Application of GLS to the iaa5,6,19 mutants restores stomatal regulation and normal drought tolerance. GLS action is dependent on the receptor kinase GHR1, suggesting that GLS may signal via reactive oxygen species. These results provide a novel connection between auxin signaling, GLS levels and drought response. Brassicaceae produce glucosinolates to protect against herbivory and pathogens. Here the authors show that auxin-sensitive Aux/IAA repressor proteins regulate aliphatic glucosinolate levels in Arabidopsis and this promotes stomatal closure via reactive oxygen species during drought stress.
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Affiliation(s)
- Mohammad Salehin
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, La Jolla CA., 92093, USA
| | - Baohua Li
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Michelle Tang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ella Katz
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Liang Song
- Genomic Analysis Laboratory, Howard Hughes Medical Institute and The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Howard Hughes Medical Institute and The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Mark Estelle
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, La Jolla CA., 92093, USA.
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Rahman M, Penny G, Mondal M, Zaman M, Kryston A, Salehin M, Nahar Q, Islam M, Bolster D, Tank J, Müller M. Salinization in large river deltas: Drivers, impacts and socio-hydrological feedbacks. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.wasec.2019.100024] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Bagchi R, Melnyk CW, Christ G, Winkler M, Kirchsteiner K, Salehin M, Mergner J, Niemeyer M, Schwechheimer C, Calderón Villalobos LIA, Estelle M. The Arabidopsis ALF4 protein is a regulator of SCF E3 ligases. EMBO J 2017; 37:255-268. [PMID: 29233834 DOI: 10.15252/embj.201797159] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 04/26/2017] [Revised: 11/10/2017] [Accepted: 11/16/2017] [Indexed: 12/21/2022] Open
Abstract
The cullin-RING E3 ligases (CRLs) regulate diverse cellular processes in all eukaryotes. CRL activity is controlled by several proteins or protein complexes, including NEDD8, CAND1, and the CSN Recently, a mammalian protein called Glomulin (GLMN) was shown to inhibit CRLs by binding to the RING BOX (RBX1) subunit and preventing binding to the ubiquitin-conjugating enzyme. Here, we show that Arabidopsis ABERRANT LATERAL ROOT FORMATION4 (ALF4) is an ortholog of GLMN The alf4 mutant exhibits a phenotype that suggests defects in plant hormone response. We show that ALF4 binds to RBX1 and inhibits the activity of SCFTIR1, an E3 ligase responsible for degradation of the Aux/IAA transcriptional repressors. In vivo, the alf4 mutation destabilizes the CUL1 subunit of the SCF Reduced CUL1 levels are associated with increased levels of the Aux/IAA proteins as well as the DELLA repressors, substrate of SCFSLY1 We propose that the alf4 phenotype is partly due to increased levels of the Aux/IAA and DELLA proteins.
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Affiliation(s)
- Rammyani Bagchi
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA
| | | | - Gideon Christ
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Martin Winkler
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle, Germany.,Institute of Biology, Structural Biology/Biochemistry, Humboldt-University Berlin, Berlin, Germany
| | - Kerstin Kirchsteiner
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA
| | - Mohammad Salehin
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA
| | - Julia Mergner
- Plant Systems Biology, Technische Universität München, Freising, Germany
| | - Michael Niemeyer
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | | | | | - Mark Estelle
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA
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Shani E, Salehin M, Zhang Y, Sanchez SE, Doherty C, Wang R, Mangado CC, Song L, Tal I, Pisanty O, Ecker JR, Kay SA, Pruneda-Paz J, Estelle M. Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors. Curr Biol 2017; 27:437-444. [PMID: 28111153 DOI: 10.1016/j.cub.2016.12.016] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [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: 09/08/2016] [Revised: 11/02/2016] [Accepted: 12/08/2016] [Indexed: 10/20/2022]
Abstract
The Aux/IAA proteins are auxin-sensitive repressors that mediate diverse physiological and developmental processes in plants [1, 2]. There are 29 Aux/IAA genes in Arabidopsis that exhibit unique but partially overlapping patterns of expression [3]. Although some studies have suggested that individual Aux/IAA genes have specialized function, genetic analyses of the family have been limited by the scarcity of loss-of-function phenotypes [4]. Furthermore, with a few exceptions, our knowledge of the factors that regulate Aux/IAA expression is limited [1, 5]. We hypothesize that transcriptional control of Aux/IAA genes plays a central role in the establishment of the auxin-signaling pathways that regulate organogenesis, growth, and environmental response. Here, we describe a screen for transcription factors (TFs) that regulate the Aux/IAA genes. We identify TFs from 38 families, including 26 members of the DREB/CBF family. Several DREB/CBF TFs directly promote transcription of the IAA5 and IAA19 genes in response to abiotic stress. Recessive mutations in these IAA genes result in decreased tolerance to stress conditions, demonstrating a role for auxin in abiotic stress. Our results demonstrate that stress pathways interact with the auxin gene regulatory network (GRN) through transcription of the Aux/IAA genes. We propose that the Aux/IAA genes function as hubs that integrate genetic and environmental information to achieve the appropriate developmental or physiological outcome.
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Affiliation(s)
- Eilon Shani
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mohammad Salehin
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yuqin Zhang
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sabrina E Sanchez
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Colleen Doherty
- Department of Molecular and Structural Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Renhou Wang
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cristina Castillejo Mangado
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Liang Song
- Genome Analysis Laboratory, Howard Hughes Medical Institute and The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Iris Tal
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Odelia Pisanty
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Joseph R Ecker
- Genome Analysis Laboratory, Howard Hughes Medical Institute and The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Steve A Kay
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jose Pruneda-Paz
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Mark Estelle
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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Abstract
Ethylene regulates many aspects of plant growth and development. In the presence of ethylene, the C terminus of EIN2 (EIN2C) translocates into the nucleus and activates transcription. Li et al. and Merchante et al. show that EIN2C also regulates translation through an interaction with the 3' UTRs of transcripts.
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Affiliation(s)
- Mohammad Salehin
- Howard Hughes Medical Institute and Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark Estelle
- Howard Hughes Medical Institute and Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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Whitehead PG, Barbour E, Futter MN, Sarkar S, Rodda H, Caesar J, Butterfield D, Jin L, Sinha R, Nicholls R, Salehin M. Impacts of climate change and socio-economic scenarios on flow and water quality of the Ganges, Brahmaputra and Meghna (GBM) river systems: low flow and flood statistics. Environ Sci Process Impacts 2015; 17:1057-69. [PMID: 25736595 DOI: 10.1039/c4em00619d] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The potential impacts of climate change and socio-economic change on flow and water quality in rivers worldwide is a key area of interest. The Ganges-Brahmaputra-Meghna (GBM) is one of the largest river basins in the world serving a population of over 650 million, and is of vital concern to India and Bangladesh as it provides fresh water for people, agriculture, industry, conservation and for the delta system downstream. This paper seeks to assess future changes in flow and water quality utilising a modelling approach as a means of assessment in a very complex system. The INCA-N model has been applied to the Ganges, Brahmaputra and Meghna river systems to simulate flow and water quality along the rivers under a range of future climate conditions. Three model realisations of the Met Office Hadley Centre global and regional climate models were selected from 17 perturbed model runs to evaluate a range of potential futures in climate. In addition, the models have also been evaluated using socio-economic scenarios, comprising (1) a business as usual future, (2) a more sustainable future, and (3) a less sustainable future. Model results for the 2050s and the 2090s indicate a significant increase in monsoon flows under the future climates, with enhanced flood potential. Low flows are predicted to fall with extended drought periods, which could have impacts on water and sediment supply, irrigated agriculture and saline intrusion. In contrast, the socio-economic changes had relatively little impact on flows, except under the low flow regimes where increased irrigation could further reduce water availability. However, should large scale water transfers upstream of Bangladesh be constructed, these have the potential to reduce flows and divert water away from the delta region depending on the volume and timing of the transfers. This could have significant implications for the delta in terms of saline intrusion, water supply, agriculture and maintaining crucial ecosystems such as the mangrove forests, with serious implications for people's livelihoods in the area. The socio-economic scenarios have a significant impact on water quality, altering nutrient fluxes being transported into the delta region.
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Affiliation(s)
- P G Whitehead
- School of Geography and the Environment, University of Oxford, Oxford OX1 3QY, UK.
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Clarke D, Williams S, Jahiruddin M, Parks K, Salehin M. Projections of on-farm salinity in coastal Bangladesh. Environ Sci Process Impacts 2015; 17:1127-1136. [PMID: 25790459 DOI: 10.1039/c4em00682h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This paper quantifies the expected impacts of climate change, climate variability and salinity accumulation on food production in coastal Bangladesh during the dry season. This forms part of a concerted series of actions on agriculture and salinity in Bangladesh under the UK funded Ecosystems for Poverty Alleviation programme and the British Council INSPIRE scheme. The work was undertaken by developing simulation models for soil water balances, dry season irrigation requirements and the effectiveness of the monsoon season rainfall at leaching accumulated salts. Simulations were run from 1981 to 2098 using historical climate data and a daily climate data set based on the Met Office Hadley Centre HadRM3P regional climate model. Results show that inter-seasonal and inter-annual variability are key factors that affect the viability of dry season vegetable crop growing. By the end of the 21(st) century the dry season is expected to be 2-3 weeks longer than now (2014). Monsoon rainfall amounts will remain the same or possibly slightly increase but it will occur over a slightly shorter wet season. Expectations of sea level rise and additional saline intrusion into groundwater aquifers mean that dry season irrigation water is likely to become more saline by the end of the 21(st) century. A study carried out at Barisal indicates that irrigating with water at up to 4 ppt can be sustainable. Once the dry season irrigation water quality goes above 5 ppt, the monsoon rainfall is no longer able to leach the dry season salt deposits so salt accumulation becomes significant and farm productivity will reduce by as a much as 50%, threatening the livelihoods of farmers in this region.
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Affiliation(s)
- D Clarke
- Faculty of Engineering and the Environment, University of Southampton, Southampton, SO17 1BJ, UK
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Salehin M, Bagchi R, Estelle M. SCFTIR1/AFB-based auxin perception: mechanism and role in plant growth and development. Plant Cell 2015; 27:9-19. [PMID: 25604443 PMCID: PMC4330579 DOI: 10.1105/tpc.114.133744] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/14/2014] [Accepted: 12/26/2014] [Indexed: 05/18/2023]
Abstract
Auxin regulates a vast array of growth and developmental processes throughout the life cycle of plants. Auxin responses are highly context dependent and can involve changes in cell division, cell expansion, and cell fate. The complexity of the auxin response is illustrated by the recent finding that the auxin-responsive gene set differs significantly between different cell types in the root. Auxin regulation of transcription involves a core pathway consisting of the TIR1/AFB F-box proteins, the Aux/IAA transcriptional repressors, and the ARF transcription factors. Auxin is perceived by a transient coreceptor complex consisting of a TIR1/AFB protein and an Aux/IAA protein. Auxin binding to the coreceptor results in degradation of the Aux/IAAs and derepression of ARF-based transcription. Although the basic outlines of this pathway are now well established, it remains unclear how specificity of the pathway is conferred. However, recent results, focusing on the ways that these three families of proteins interact, are starting to provide important clues.
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Affiliation(s)
- Mohammad Salehin
- Howard Hughes Medical Institute and Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093
| | - Rammyani Bagchi
- Howard Hughes Medical Institute and Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093
| | - Mark Estelle
- Howard Hughes Medical Institute and Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093
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Salehin M, Huang YS, Bagchi R, Sherrier DJ, Dickstein R. Allelic differences in Medicago truncatula NIP/LATD mutants correlate with their encoded proteins' transport activities in planta. Plant Signal Behav 2013; 8:e22813. [PMID: 23154505 PMCID: PMC3656982 DOI: 10.4161/psb.22813] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 10/02/2012] [Revised: 11/06/2012] [Accepted: 11/06/2012] [Indexed: 05/18/2023]
Abstract
Medicago truncatula NIP/LATD gene, required for symbiotic nitrogen fixing nodule and root architecture development, encodes a member of the NRT1(PTR) family that demonstrates high-affinity nitrate transport in Xenopus laevis oocytes. Of three Mtnip/latd mutant proteins, one retains high-affinity nitrate transport in oocytes, while the other two are nitrate-transport defective. To further examine the mutant proteins' transport properties, the missense Mtnip/latd alleles were expressed in Arabidopsis thaliana chl1-5, resistant to the herbicide chlorate because of a deletion spanning the nitrate transporter AtNRT1.1(CHL1) gene. Mtnip-3 expression restored chlorate sensitivity in the Atchl1-5 mutant, similar to wild type MtNIP/LATD, while Mtnip-1 expression did not. The high-affinity nitrate transporter AtNRT2.1 gene was expressed in Mtnip-1 mutant roots; it did not complement, which could be caused by several factors. Together, these findings support the hypothesis that MtNIP/LATD may have another biochemical activity.
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Affiliation(s)
- Mohammad Salehin
- Department of Biological Sciences; University of North Texas; Denton, TX USA
| | - Ying-Sheng Huang
- Department of Biological Sciences; University of North Texas; Denton, TX USA
| | - Rammyani Bagchi
- Department of Biological Sciences; University of North Texas; Denton, TX USA
| | - D. Janine Sherrier
- Department of Plant and Soil Science; Delaware Biotechnology Institute; Newark, DE USA
| | - Rebecca Dickstein
- Department of Biological Sciences; University of North Texas; Denton, TX USA
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Bagchi R, Salehin M, Adeyemo OS, Salazar C, Shulaev V, Sherrier DJ, Dickstein R. Functional assessment of the Medicago truncatula NIP/LATD protein demonstrates that it is a high-affinity nitrate transporter. Plant Physiol 2012; 160:906-16. [PMID: 22858636 PMCID: PMC3461564 DOI: 10.1104/pp.112.196444] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 08/01/2012] [Indexed: 05/18/2023]
Abstract
The Medicago truncatula NIP/LATD (for Numerous Infections and Polyphenolics/Lateral root-organ Defective) gene encodes a protein found in a clade of nitrate transporters within the large NRT1(PTR) family that also encodes transporters of dipeptides and tripeptides, dicarboxylates, auxin, and abscisic acid. Of the NRT1(PTR) members known to transport nitrate, most are low-affinity transporters. Here, we show that M. truncatula nip/latd mutants are more defective in their lateral root responses to nitrate provided at low (250 μm) concentrations than at higher (5 mm) concentrations; however, nitrate uptake experiments showed no discernible differences in uptake in the mutants. Heterologous expression experiments showed that MtNIP/LATD encodes a nitrate transporter: expression in Xenopus laevis oocytes conferred upon the oocytes the ability to take up nitrate from the medium with high affinity, and expression of MtNIP/LATD in an Arabidopsis chl1(nrt1.1) mutant rescued the chlorate susceptibility phenotype. X. laevis oocytes expressing mutant Mtnip-1 and Mtlatd were unable to take up nitrate from the medium, but oocytes expressing the less severe Mtnip-3 allele were proficient in nitrate transport. M. truncatula nip/latd mutants have pleiotropic defects in nodulation and root architecture. Expression of the Arabidopsis NRT1.1 gene in mutant Mtnip-1 roots partially rescued Mtnip-1 for root architecture defects but not for nodulation defects. This suggests that the spectrum of activities inherent in AtNRT1.1 is different from that possessed by MtNIP/LATD, but it could also reflect stability differences of each protein in M. truncatula. Collectively, the data show that MtNIP/LATD is a high-affinity nitrate transporter and suggest that it could have another function.
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Affiliation(s)
| | | | - O. Sarah Adeyemo
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 (R.B., M.S., O.S.A., C.S., V.S., R.D.); Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711 (D.J.S.)
| | - Carolina Salazar
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 (R.B., M.S., O.S.A., C.S., V.S., R.D.); Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711 (D.J.S.)
| | - Vladimir Shulaev
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 (R.B., M.S., O.S.A., C.S., V.S., R.D.); Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711 (D.J.S.)
| | - D. Janine Sherrier
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 (R.B., M.S., O.S.A., C.S., V.S., R.D.); Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711 (D.J.S.)
| | - Rebecca Dickstein
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 (R.B., M.S., O.S.A., C.S., V.S., R.D.); Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711 (D.J.S.)
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Yendrek CR, Lee YC, Morris V, Liang Y, Pislariu CI, Burkart G, Meckfessel MH, Salehin M, Kessler H, Wessler H, Lloyd M, Lutton H, Teillet A, Sherrier DJ, Journet EP, Harris JM, Dickstein R. A putative transporter is essential for integrating nutrient and hormone signaling with lateral root growth and nodule development in Medicago truncatula. Plant J 2010; 62:100-12. [PMID: 20088899 DOI: 10.1111/j.1365-313x.2010.04134.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Legume root architecture involves not only elaboration of the root system by the formation of lateral roots but also the formation of symbiotic root nodules in association with nitrogen-fixing soil rhizobia. The Medicago truncatula LATD/NIP gene plays an essential role in the development of both primary and lateral roots as well as nodule development. We have cloned the LATD/NIP gene and show that it encodes a member of the NRT1(PTR) transporter family. LATD/NIP is expressed throughout the plant. pLATD/NIP-GFP promoter-reporter fusions in transgenic roots establish the spatial expression of LATD/NIP in primary root, lateral root and nodule meristems and the surrounding cells. Expression of LATD/NIP is regulated by hormones, in particular by abscisic acid which has been previously shown to rescue the primary and lateral root meristem arrest of latd mutants. latd mutants respond normally to ammonium but have defects in responses of the root architecture to nitrate. Taken together, these results suggest that LATD/NIP may encode a nitrate transporter or transporter of another compound.
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Affiliation(s)
- Craig R Yendrek
- Department of Plant Biology, University of Vermont, Burlington, VT 05405-0086, USA
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