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Kaur J, Tiwari N, Asif MH, Dharmesh V, Naseem M, Srivastava PK, Srivastava S. Integrated genome-transcriptome analysis unveiled the mechanism of Debaryomyces hansenii-mediated arsenic stress amelioration in rice. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133954. [PMID: 38484657 DOI: 10.1016/j.jhazmat.2024.133954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/22/2024] [Accepted: 03/02/2024] [Indexed: 04/07/2024]
Abstract
Globally, rice is becoming more vulnerable to arsenic (As) pollution, posing a serious threat to public food safety. Previously Debaryomyces hansenii was found to reduce grain As content of rice. To better understand the underlying mechanism, we performed a genome analysis to identify the key genes in D. hansenii responsible for As tolerance and plant growth promotion. Notably, genes related to As resistance (ARR, Ycf1, and Yap) were observed in the genome of D. hansenii. The presence of auxin pathway and glutathione metabolism-related genes may explain the plant growth-promoting potential and As tolerance mechanism of this novel yeast strain. The genome annotation of D. hansenii indicated that it contains a repertoire of genes encoding antioxidants, well corroborated with the in vitro studies of GST, GR, and glutathione content. In addition, the effect of D. hansenii on gene expression profiling of rice plants under As stress was also examined. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed 307 genes, annotated in D. hansenii-treated rice, related to metabolic pathways (184), photosynthesis (12), glutathione (10), tryptophan (4), and biosynthesis of secondary metabolite (117). Higher expression of regulatory elements like AUX/IAA and WRKY transcription factors (TFs), and defense-responsive genes dismutases, catalases, peroxiredoxin, and glutaredoxins during D. hansenii+As exposure was also observed. Combined analysis revealed that D. hansenii genes are contributing to stress mitigation in rice by supporting plant growth and As-tolerance. The study lays the foundation to develop yeast as a beneficial biofertilizer for As-prone areas.
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Affiliation(s)
- Jasvinder Kaur
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Nikita Tiwari
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Mehar Hasan Asif
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Varsha Dharmesh
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mariya Naseem
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Pankaj Kumar Srivastava
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suchi Srivastava
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Geng A, Lian W, Wang X, Chen G. Regulatory Mechanisms Underlying Arsenic Uptake, Transport, and Detoxification in Rice. Int J Mol Sci 2023; 24:11031. [PMID: 37446207 DOI: 10.3390/ijms241311031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/15/2023] Open
Abstract
Arsenic (As) is a metalloid environmental pollutant ubiquitous in nature that causes chronic and irreversible poisoning to humans through its bioaccumulation in the trophic chain. Rice, the staple food crop for 350 million people worldwide, accumulates As more easily compared to other cereal crops due to its growth characteristics. Therefore, an in-depth understanding of the molecular regulatory mechanisms underlying As uptake, transport, and detoxification in rice is of great significance to solving the issue of As bioaccumulation in rice, improving its quality and safety and protecting human health. This review summarizes recent studies on the molecular mechanisms of As toxicity, uptake, transport, redistribution, regulation, and detoxification in rice. It aims to provide novel insights and approaches for preventing and controlling As bioaccumulation in rice plants, especially reducing As accumulation in rice grains.
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Affiliation(s)
- Anjing Geng
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Wenli Lian
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Xu Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Guang Chen
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
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Mirza Z, Haque MM, Gupta M. WRKY transcription factors: a promising way to deal with arsenic stress in rice. Mol Biol Rep 2022; 49:10895-10904. [PMID: 35941412 DOI: 10.1007/s11033-022-07772-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022]
Abstract
Arsenic (As) is a global carcinogenic contaminant, and is one of the significant environmental constraints that limits the development and yield of crop plants. It is always tagged along with rice as rice takes up As and tends to accumulate it in grains. This amassment makes a way for As to get into the food chain that leads to unforeseen human health risks. Being viewed as parallel with toxicity, As in rice is an important global risk that calls for an urgent solution. WRKY Transcription Factors (TFs) seems to be promising in this area. The classical and substantial progress in the molecular mechanism of WRKY TFs, strengthened the understanding of innovative solutions for dealing with As in rice. Here, we review the potential of WRKY TFs under As stressed rice as a genetic solution and also provide insights into As and rice. Further, we develop an understanding of WRKY TF gene family and its regulation in rice. To date, studies on the role of WRKY TFs under As stressed rice are lacking. This area needs to be explored more so that this gene family can be utilized as an effective genetic tool that can break the As cycle to develop low or As free rice cultivar.
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Affiliation(s)
- Zainab Mirza
- Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, 25, New Delhi, India
| | - Mohammad Mahfuzul Haque
- Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, 25, New Delhi, India
| | - Meetu Gupta
- Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, 25, New Delhi, India.
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Khan MIR, Chopra P, Chhillar H, Ahanger MA, Hussain SJ, Maheshwari C. Regulatory hubs and strategies for improving heavy metal tolerance in plants: Chemical messengers, omics and genetic engineering. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 164:260-278. [PMID: 34020167 DOI: 10.1016/j.plaphy.2021.05.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/03/2021] [Indexed: 05/28/2023]
Abstract
Heavy metal (HM) accumulation in the agricultural soil and its toxicity is a major threat for plant growth and development. HMs disrupt functional integrity of the plants, induces altered phenological and physiological responses and slashes down qualitative crop yield. Chemical messengers such as phytohormones, plant growth regulators and gasotransmitters play a crucial role in regulating plant growth and development under metal toxicity in plants. Understanding the intricate network of these chemical messengers as well as interactions of genes/metabolites/proteins associated with HM toxicity in plants is necessary for deciphering insights into the regulatory circuit involved in HM tolerance. The present review describes (a) the role of chemical messengers in HM-induced toxicity mitigation, (b) possible crosstalk between phytohormones and other signaling cascades involved in plants HM tolerance and (c) the recent advancements in biotechnological interventions including genetic engineering, genome editing and omics approaches to provide a step ahead in making of improved plant against HM toxicities.
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Affiliation(s)
| | | | | | | | - Sofi Javed Hussain
- Department of Botany, Government Degree College, Kokernag, Jammu & Kashmir, India
| | - Chirag Maheshwari
- Agricultural Energy and Power Division, ICAR-Central Institute of Agricultural Engineering, Bhopal, India
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Yadav P, Srivastava S, Patil T, Raghuvanshi R, Srivastava AK, Suprasanna P. Tracking the time-dependent and tissue-specific processes of arsenic accumulation and stress responses in rice (Oryza sativa L.). JOURNAL OF HAZARDOUS MATERIALS 2021; 406:124307. [PMID: 33221079 DOI: 10.1016/j.jhazmat.2020.124307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/28/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
The present study analysed time (0.5 h to 24 h) and tissue [roots, old leaves (OL) and young leaves (YL)] dependent nature of arsenic (As) accumulation and ensuing responses in two contrasting varieties of rice (Oryza sativa L.); Pooja (tolerant) and CO-50 (moderately sensitive). Arsenic accumulation was 5.4-, 4.7- and 7.3-fold higher at 24 h in roots, OL and YL, respectively of var. CO-50 than that in var. Pooja. Arsenic accumulation in YL depicted a delayed accumulation; at 2 h onwards in var. Pooja (0.23 µg g-1 dw) while at 1 h onwards in var. CO50 (0.26 µg g-1 dw). The responses of oxidative stress parameters, antioxidant enzymes, metabolites and ions were also found to be tissue- and time-dependent and depicted differential pattern in the two varieties. Among hormone, salicylic acid and abscisic acid showed variable response in var. Pooja and var. CO-50. Metabolite analysis depicted an involvement of various metabolites in As stress responses of two varieties. In conclusion, an early sensing of the As stress, proper coordination of hormones, biochemical responses, ionic and metabolic profiles allowed var. Pooja to resist As stress and reduce As accumulation more effectively as compared to that of var. CO-50.
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Affiliation(s)
- Poonam Yadav
- Plant Stress Biology Laboratory, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi 221005, India
| | - Sudhakar Srivastava
- Plant Stress Biology Laboratory, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi 221005, India.
| | - Tanmayi Patil
- Centre for Cellular and Molecular Platforms, GKVK Post, Bengaluru 560065, India
| | - Rishiraj Raghuvanshi
- Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Ashish K Srivastava
- Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Penna Suprasanna
- Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
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Feng H, Li X, Sun D, Chen Y, Xu G, Cao Y, Ma LQ. Expressing Phosphate Transporter PvPht2;1 Enhances P Transport to the Chloroplasts and Increases Arsenic Tolerance in Arabidopsis thaliana. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2276-2284. [PMID: 33497189 DOI: 10.1021/acs.est.0c03316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Arsenic (As) contamination in soils is of great concerns due to its toxicity to plants. As an analogue, phosphorus plays an important role in protecting plants from As toxicity. In this study, we identified a new phosphate transporter 2 (PHT2), PvPht2;1, from As-hyperaccumulator Pteris vittata and analyzed its functions in As and P transport in a yeast mutant, and model plant Arabidopsis thalian. PvPht2;1 contained 12 transmembrane domains, sharing high identity with PHT2 genes in diverse plants. Further, independent of external P or As levels, PvPht2;1 was mainly expressed in P. vittata fronds with the expression being 3-4 folds higher than that in the roots and rhizomes. Localized to the chloroplasts based on GFP-fused PvPht2;1 in model plant tobacco, PvPht2;1 functioned as a low-affinity P transporter. Under As exposure, PvPht2;1 yeast transformants showed comparable growth with the control while high-affinity P transporter PvPht1;3 transformants showed better growth, suggesting that PvPht2;1 transported P but slower than PvPht1;3 transporter. Expressing PvPht2;1 in A. thaliana increased its shoot P concentration without influencing its As accumulation. Further, the chloroplasts' P content in transgenic A. thaliana increased by 37-59% than wild-type (WT) plants. Under As exposure, the photosynthesis of PvPht2;1-expressing A. thaliana remained stable but that of WT plants decreased. The data indicate that, under As stress, expressing PvPht2;1 in A. thaliana enhanced its P transport to the chloroplasts and protected its photosynthesis. In short, highly expressed in the fronds and not impacted by As exposure, chloroplast-located PvPht2;1 may have protected As-hyperaccumulator P. vittata from As toxicity by efficiently transporting only P to its chloroplasts.
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Affiliation(s)
- Huayuan Feng
- State Key Lab of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xinyuan Li
- State Key Lab of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Dan Sun
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Yanshan Chen
- School of the Environment, Nanjing Normal University, Nanjing, Jiangsu 210046, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yue Cao
- State Key Lab of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
- China School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Lena Q Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Shah S, Damare S. Cellular response of Brevibacterium casei #NIOSBA88 to arsenic and chromium-a proteomic approach. Braz J Microbiol 2020; 51:1885-1895. [PMID: 32729030 DOI: 10.1007/s42770-020-00353-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/25/2020] [Indexed: 11/25/2022] Open
Abstract
Cellular response against different heavy metal stress differs with the metal. Arsenic and chromium are heavy metals and toxic to living systems. The concentration of these metals in seawater is very low. However, due to their solubility in nature, they actively enter cells via various transport mechanisms and cause damage to the cells. Brevibacterium casei #NIOSBA88, a marine-derived, gram-positive isolate was multi-metal tolerant. Proteomic analysis of this isolate in response to arsenic and chromium resulted in the identification of total 2549 proteins, out of which 880 proteins were found to be commonly expressed at 750 mgL-1 arsenic and 100 mgL-1 chromium and in absence of both the metals. In contrast, 533, 212, and 270 proteins were found to be unique in the absence of any metal, 750 mgL-1 of arsenic and 100 mgL-1 of chromium respectively. Proteins such as antibiotic biosynthesis monooxygenase, ArsR family transcriptional regulator, cytochrome C oxidase subunit II, and thioredoxin reductase were exclusively expressed only in response to arsenic and chromium. Other proteins like superoxide dismutase, lipid hydroperoxide reductase, and thioredoxin-disulfide reductase were found to be upregulated in response to both the metals. Most of the proteins involved in the normal cell functioning were found to be downregulated. Major metabolic functions affected include amino acid metabolism, carbohydrate metabolism, translation, and energy metabolism. Peptide mass fingerprinting of Brevibacterium casei #NIOSBA88 exposed to arsenic and chromium respectively revealed the deleterious effect of these metals on the bacterium and its strategy to overcome the stress.
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Affiliation(s)
- Shruti Shah
- Biological Oceanography Division, CSIR- National Institute of Oceanography, Dona Paula, Goa, India
| | - Samir Damare
- Biological Oceanography Division, CSIR- National Institute of Oceanography, Dona Paula, Goa, India.
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Viana VE, Pegoraro C, Busanello C, Costa de Oliveira A. Mutagenesis in Rice: The Basis for Breeding a New Super Plant. FRONTIERS IN PLANT SCIENCE 2019; 10:1326. [PMID: 31781133 PMCID: PMC6857675 DOI: 10.3389/fpls.2019.01326] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/24/2019] [Indexed: 05/28/2023]
Abstract
The high selection pressure applied in rice breeding since its domestication thousands of years ago has caused a narrowing in its genetic variability. Obtaining new rice cultivars therefore becomes a major challenge for breeders and developing strategies to increase the genetic variability has demanded the attention of several research groups. Understanding mutations and their applications have paved the way for advances in the elucidation of a genetic, physiological, and biochemical basis of rice traits. Creating variability through mutations has therefore grown to be among the most important tools to improve rice. The small genome size of rice has enabled a faster release of higher quality sequence drafts as compared to other crops. The move from structural to functional genomics is possible due to an array of mutant databases, highlighting mutagenesis as an important player in this progress. Furthermore, due to the synteny among the Poaceae, other grasses can also benefit from these findings. Successful gene modifications have been obtained by random and targeted mutations. Furthermore, following mutation induction pathways, techniques have been applied to identify mutations and the molecular control of DNA damage repair mechanisms in the rice genome. This review highlights findings in generating rice genome resources showing strategies applied for variability increasing, detection and genetic mechanisms of DNA damage repair.
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Affiliation(s)
| | | | | | - Antonio Costa de Oliveira
- Centro de Genômica e Fitomelhoramento, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Rio Grande do Sul, Brazil
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Amitai Y, Koren G. High risk for neural tube defects; the role of arsenic in drinking water and rice in Asia. Med Hypotheses 2018; 119:88-90. [PMID: 30122498 DOI: 10.1016/j.mehy.2018.07.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/24/2018] [Accepted: 07/21/2018] [Indexed: 11/30/2022]
Abstract
BACKGROUND Neural tube defects (NTDs) affect >300,000 children annually worldwide. The incidence of NTDs in Northern India (7.7/1000), is tenfold higher than in the US (0.7/1000). Higher rates were previously reported in Northern China. The causes of these trends have not been elucidated. Arsenic is a teratogen shown in animals to induce NTDs. The main potential sources for environmental arsenic exposure, groundwater and rice as a staple food, are high in India and China. OBJECTIVES To discuss the possible association between high environmental arsenic exposure through drinking water and rice with the high NTDs rates in these regions. DISCUSSION Arsenic contamination of groundwater is the main source of environmental arsenic exposure. The locations of toxic arsenic regions in China and India correspond in most cases to the northern regions where the NTDs rates were high. Rice, the staple food in India and China, can absorb up to 10 times more arsenic than other crops, such as wheat and might further increase arsenic exposure. CONCLUSIONS We hypothesize that this NTD-arsenic in drinking water and rice association may explain why these areas in the northern regions of both countries have the highest incidence of NTDs. If proven true, this has major public health implications.
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Affiliation(s)
- Yona Amitai
- Department of Management, Public Health and Health Management, Bar Ilan University, Ramat Gan, Israel
| | - Gideon Koren
- Maccabi-Kahn Institute of Research and Innovation, Tel Aviv, Israel; Motherisk Israel Program, Tel Aviv University, Israel.
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