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Su B, Palahnuk H, Harbaugh T, Rizk E, Hazard W, Chan A, Bernstein J, Weinsaft JW, Manning KB. Numerical Study on the Impact of Central Venous Catheter Placement on Blood Flow in the Cavo-Atrial Junction. Ann Biomed Eng 2024; 52:1378-1392. [PMID: 38407724 DOI: 10.1007/s10439-024-03463-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
An in silico study is performed to investigate fluid dynamic effects of central venous catheter (CVC) placement within patient-specific cavo-atrial junctions. Prior studies show the CVC infusing a liquid, but this study focuses on the placement without any liquid emerging from the CVC. A 7 or 15-French double-lumen CVC is placed virtually in two patient-specific models; the CVC tip location is altered to understand its effect on the venous flow field. Results show that the CVC impact is trivial on flow in the superior vena cava when the catheter-to-vein ratio ranges from 0.15 to 0.33. Results further demonstrate that when the CVC tip is directly in the right atrium, flow vortices in the right atrium result in elevated wall shear stress near the tip hole. A recirculation region characterizes a spatially variable flow field inside the CVC side hole. Furthermore, flow stagnation is present near the internal side hole corners but an elevated wall shear stress near the curvature of the side hole's exit. These results suggest that optimal CVC tip location is within the superior vena cava, so as to lower the potential for platelet activation due to elevated shear stresses and that CVC geometry and location depth in the central vein significantly influences the local CVC fluid dynamics. A thrombosis model also shows thrombus formation at the side hole and tip hole. After modifying the catheter design, the hemodynamics change, which alter thrombus formation. Future studies are warranted to study CVC design and placement location in an effort to minimize CVC-induced thrombosis incidence.
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Affiliation(s)
- Boyang Su
- Department of Biomedical Engineering, The Pennsylvania State University, 122 Chemical and Biomedical Engineering Building, University Park, PA, 16802-4400, USA
| | - Hannah Palahnuk
- Department of Biomedical Engineering, The Pennsylvania State University, 122 Chemical and Biomedical Engineering Building, University Park, PA, 16802-4400, USA
| | - Thaddeus Harbaugh
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
| | - Elias Rizk
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
| | - Will Hazard
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
| | - Angel Chan
- Department of Medicine (Cardiology), Weill Cornell College, New York, NY, USA
- Department of Medicine (Cardiology), Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan Bernstein
- Division of Pediatric Hematology/Oncology, Penn State Hershey Children's Hospital, Hershey, PA, USA
| | - Jonathan W Weinsaft
- Department of Medicine (Cardiology), Weill Cornell College, New York, NY, USA
- Department of Medicine (Cardiology), Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiology (Cardiothoracic Imaging), Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Keefe B Manning
- Department of Biomedical Engineering, The Pennsylvania State University, 122 Chemical and Biomedical Engineering Building, University Park, PA, 16802-4400, USA.
- Department of Surgery, Penn State College of Medicine, Hershey, PA, USA.
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2
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Capitaine A, Fajri ML, Sciacca B. Pushing the Limits of Capillary Assembly for the Arbitrary Positioning of Sub-50nm Nanocubes in Printable Plasmonic Surfaces. SMALL METHODS 2024; 8:e2300373. [PMID: 37391271 DOI: 10.1002/smtd.202300373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/15/2023] [Indexed: 07/02/2023]
Abstract
The fabrication of high quality nanophotonic surfaces for integration in optoelectronic devices remains a challenge because of the complexity and cost of top-down nanofabrication strategies. Combining colloidal synthesis with templated self-assembly emerged as an appealing low-cost solution. However, it still faces several obstacles before integration in devices can become a reality. This is mostly due to the difficulty in assembling small nanoparticles (<50 nm) in complex nanopatterns with a high yield. In this study, a reliable methodology is proposed to fabricate printable nanopatterns with an aspect ratio varying from 1 to 10 and a lateral resolution of 30 nm via nanocube assembly and epitaxy. Investigating templated assembly via capillary forces, a new regime was identified that was used to assemble 30-40 nm nanocubes in a patterned polydimethylsiloxane template with a high yield for both Au and Ag with multiple particles per trap. This new method relies on the generation and control of an accumulation zone at the contact line that is thin as opposed to dense, displaying higher versatility. This is in contrast with conventional wisdom, identifying a dense accumulation zone as a requirement for high-yield assembly. In addition, different formulations are proposed that can be used for the colloidal dispersion, showing that the standard water-surfactant solutions can be replaced by surfactant-free ethanol solutions, with good assembly yield. This allows to minimize the presence of surfactants that can affect electronic properties. Finally, it is shown that the obtained nanocube arrays can be transformed into continuous monocrystalline nanopatterns via nanocube epitaxy at near ambient temperature, and transferred to different substrates via contact printing. This approach opens new doors to the templated assembly of small colloids and could find potential applications in various optoelectronic devices ranging from solar cells to light-emitting diodes and displays.
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Affiliation(s)
- Anna Capitaine
- Aix-Marseille Univ, CNRS, CINaM, Campus de Luminy, Marseille, 13009, France
| | - Muhammad L Fajri
- Aix-Marseille Univ, CNRS, CINaM, Campus de Luminy, Marseille, 13009, France
| | - Beniamino Sciacca
- Aix-Marseille Univ, CNRS, CINaM, Campus de Luminy, Marseille, 13009, France
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3
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Wang Y, Guo X, Xu Y, Sun R, Cai X, Zhou Z, Qin T, Tao Y, Li B, Hou Y, Wang Q, Liu F. Genome-wide association study for boll weight in Gossypium hirsutum races. Funct Integr Genomics 2023; 23:331. [PMID: 37940771 DOI: 10.1007/s10142-023-01261-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
High yield has always been an essential target in almost all of the cotton breeding programs. Boll weight (BW) is a key component of cotton yield. Numerous linkage mapping and genome-wide association studies (GWAS) have been performed to understand the genetic mechanism of BW, but information on the markers/genes controlling BW remains limited. In this study, we conducted a GWAS for BW using 51,268 high-quality single-nucleotide polymorphisms (SNPs) and 189 Gossypium hirsutum accessions across five different environments. A total of 55 SNPs significantly associated with BW were detected, of which 29 and 26 were distributed in the A and D subgenomes, respectively. Five SNPs were simultaneously detected in two environments. For TM5655, TM8662, TM36371, and TM50258, the BW grouped by alleles of each SNP was significantly different. The ± 550 kb regions around these four key SNPs contained 262 genes. Of them, Gh_A02G1473, Gh_A10G1765, and Gh_A02G1442 were expressed highly at 0 to 1 days post-anthesis (dpa), - 3 to 0 dpa, and - 3 to 0 dpa in ovule of TM-1, respectively. They were presumed as the candidate genes for fiber cell differentiation, initiation, or elongation based on gene annotation of their homologs. Overall, these results supplemented valuable information for dissecting the genetic architecture of BW and might help to improve cotton yield through molecular marker-assisted selection breeding and molecular design breeding.
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Affiliation(s)
- Yuanyuan Wang
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xinlei Guo
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Runrun Sun
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Laboratory / National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Tengfei Qin
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ye Tao
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Baihui Li
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Qinglian Wang
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Institute of Science and Technology, Xinxiang, 453003, China.
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Hainan Yazhou Bay Seed Laboratory / National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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4
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Zhai Z, Zhang K, Fang Y, Yang Y, Cao X, Liu L, Tian Y. Systematically and Comprehensively Understanding the Regulation of Cotton Fiber Initiation: A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:3771. [PMID: 37960127 PMCID: PMC10648247 DOI: 10.3390/plants12213771] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023]
Abstract
Cotton fibers provide an important source of raw materials for the textile industry worldwide. Cotton fiber is a kind of single cell that differentiates from the epidermis of the ovule and provides a perfect research model for the differentiation and elongation of plant cells. Cotton fiber initiation is the first stage throughout the entire developmental process. The number of fiber cell initials on the seed ovule epidermis decides the final fiber yield. Thus, it is of great significance to clarify the mechanism underlying cotton fiber initiation. Fiber cell initiation is controlled by complex and interrelated regulatory networks. Plant phytohormones, transcription factors, sugar signals, small signal molecules, functional genes, non-coding RNAs, and histone modification play important roles during this process. Here, we not only summarize the different kinds of factors involved in fiber cell initiation but also discuss the mechanisms of these factors that act together to regulate cotton fiber initiation. Our aim is to synthesize a systematic and comprehensive review of different factors during fiber initiation that will provide the basics for further illustrating these mechanisms and offer theoretical guidance for improving fiber yield in future molecular breeding work.
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Affiliation(s)
- Zeyang Zhai
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Z.Z.); (K.Z.); (Y.F.); (Y.Y.); (X.C.); (L.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Kaixin Zhang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Z.Z.); (K.Z.); (Y.F.); (Y.Y.); (X.C.); (L.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Yao Fang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Z.Z.); (K.Z.); (Y.F.); (Y.Y.); (X.C.); (L.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Yujie Yang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Z.Z.); (K.Z.); (Y.F.); (Y.Y.); (X.C.); (L.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Xu Cao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Z.Z.); (K.Z.); (Y.F.); (Y.Y.); (X.C.); (L.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Li Liu
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Z.Z.); (K.Z.); (Y.F.); (Y.Y.); (X.C.); (L.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Yue Tian
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Z.Z.); (K.Z.); (Y.F.); (Y.Y.); (X.C.); (L.L.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
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5
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Bolden CT, Skibber MA, Olson SD, Zamorano Rojas M, Milewicz S, Gill BS, Cox CS. Validation and characterization of a novel blood-brain barrier platform for investigating traumatic brain injury. Sci Rep 2023; 13:16150. [PMID: 37752338 PMCID: PMC10522590 DOI: 10.1038/s41598-023-43214-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 09/21/2023] [Indexed: 09/28/2023] Open
Abstract
The Blood-Brain Barrier (BBB) is a highly-selective physiologic barrier responsible for maintaining cerebral homeostasis. Innovative in vitro models of the BBB are needed to provide useful insights into BBB function with CNS disorders like traumatic brain injury (TBI). TBI is a multidimensional and highly complex pathophysiological condition that requires intrinsic models to elucidate its mechanisms. Current models either lack fluidic shear stress, or neglect hemodynamic parameters important in recapitulating the human in vivo BBB phenotype. To address these limitations in the field, we developed a fluid dynamic novel platform which closely mimics these parameters. To validate our platform, Matrigel-coated Transwells were seeded with brain microvascular endothelial cells, both with and without co-cultured primary human astrocytes and bone-marrow mesenchymal stem cells. In this article we characterized BBB functional properties such as TEER and paracellular permeability. Our platform demonstrated physiologic relevant decreases in TEER in response to an ischemic environment, while directly measuring barrier fluid fluctuation. These recordings were followed with recovery, implying stability of the model. We also demonstrate that our dynamic platform is responsive to inflammatory and metabolic cues with resultant permeability coefficients. These results indicate that this novel dynamic platform will be a valuable tool for evaluating the recapitulating BBB function in vitro, screening potential novel therapeutics, and establishing a relevant paradigm to evaluate the pathophysiology of TBI.
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Affiliation(s)
- Christopher T Bolden
- Department of Pediatric Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA.
- Center for Translational Injury Research, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA.
| | - Max A Skibber
- Department of Pediatric Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Scott D Olson
- Department of Pediatric Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Miriam Zamorano Rojas
- Department of Pediatric Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Samantha Milewicz
- Department of Pediatric Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Brijesh S Gill
- Department of Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Charles S Cox
- Department of Pediatric Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA.
- Center for Translational Injury Research, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA.
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6
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Dong Y, Li S, Wu H, Gao Y, Feng Z, Zhao X, Shan L, Zhang Z, Ren H, Liu X. Advances in understanding epigenetic regulation of plant trichome development: a comprehensive review. HORTICULTURE RESEARCH 2023; 10:uhad145. [PMID: 37691965 PMCID: PMC10483894 DOI: 10.1093/hr/uhad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 07/14/2023] [Indexed: 09/12/2023]
Abstract
Plant growth and development are controlled by a complex gene regulatory network, which is currently a focal point of research. It has been established that epigenetic factors play a crucial role in plant growth. Trichomes, specialized appendages that arise from epidermal cells, are of great significance in plant growth and development. As a model system for studying plant development, trichomes possess both commercial and research value. Epigenetic regulation has only recently been implicated in the development of trichomes in a limited number of studies, and microRNA-mediated post-transcriptional regulation appears to dominate in this context. In light of this, we have conducted a review that explores the interplay between epigenetic regulations and the formation of plant trichomes, building upon existing knowledge of hormones and transcription factors in trichome development. Through this review, we aim to deepen our understanding of the regulatory mechanisms underlying trichome formation and shed light on future avenues of research in the field of epigenetics as it pertains to epidermal hair growth.
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Affiliation(s)
- Yuming Dong
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Sen Li
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Haoying Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yiming Gao
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhongxuan Feng
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xi Zhao
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Li Shan
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhongren Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Huazhong Ren
- College of Horticulture, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya Hainan 572000, China
| | - Xingwang Liu
- College of Horticulture, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya Hainan 572000, China
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7
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Cobb SJ, Dharani AM, Oliveira AR, Pereira IAC, Reisner E. Carboxysome-Inspired Electrocatalysis using Enzymes for the Reduction of CO 2 at Low Concentrations. Angew Chem Int Ed Engl 2023; 62:e202218782. [PMID: 37078435 DOI: 10.1002/anie.202218782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/21/2023]
Abstract
The electrolysis of dilute CO2 streams suffers from low concentrations of dissolved substrate and its rapid depletion at the electrolyte-electrocatalyst interface. These limitations require first energy-intensive CO2 capture and concentration, before electrolyzers can achieve acceptable performances. For direct electrocatalytic CO2 reduction from low-concentration sources, we introduce a strategy that mimics the carboxysome in cyanobacteria by utilizing microcompartments with nanoconfined enzymes in a porous electrode. A carbonic anhydrase accelerates CO2 hydration kinetics and minimizes substrate depletion by making all dissolved carbon available for utilization, while a highly efficient formate dehydrogenase reduces CO2 cleanly to formate; down to even atmospheric concentrations of CO2 . This bio-inspired concept demonstrates that the carboxysome provides a viable blueprint for the reduction of low-concentration CO2 streams to chemicals by using all forms of dissolved carbon.
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Affiliation(s)
- Samuel J Cobb
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Azim M Dharani
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Erwin Reisner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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8
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Jo Y, Sarkar N, Bose S. In vitro biological evaluation of epigallocatechin gallate (EGCG) release from three-dimensional printed (3DP) calcium phosphate bone scaffolds. J Mater Chem B 2023; 11:5503-5513. [PMID: 36637404 PMCID: PMC11132590 DOI: 10.1039/d2tb02210a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Three-dimensional printed (3DP) tricalcium phosphate (TCP) scaffolds can guide bone regeneration, especially for patient-specific defect repair applications in low-load bearing sites. Epigallocatechin gallate (EGCG), a green tea compound, has gained attention as a safer alternative treatment for bone disorders. The 3DP TCP scaffold is designed for localized EGCG delivery, which can enhance in vitro osteogenic ability, anti-osteoclastogenic activity, vascularization formation, and chemoprevention. In the cocultures of human bone marrow-derived mesenchymal stem cells (hMSCs) and monocytes (THP-1), EGCG release enhances osteogenic differentiation of hMSCs at day 16 compared to the control; this is indicated by a 2.8- and 4.0-fold upregulation of Runt-related transcription factor 2 (Runx2) and bone gamma-carboxyglutamic acid-containing protein (BGLAP), the early and late osteoblast differentiation marker expressions. However, EGCG significantly downregulates the receptor activator of nuclear factor-κB ligand (RANKL) expression by 7.0-fold, indicating that EGCG suppresses RANKL-induced osteoclast maturation. EGCG also stimulates endothelial tube formation at as early as 3 hours when human umbilical vein endothelial cells (HUVECs) grow on Matrigel. It reduces human osteosarcoma MG-63 cell viability by 66% compared to the control at day 11. An in vitro release kinetics study demonstrates that EGCG shows a ∼64% release within a day followed by a sustained release in the physiological environment (pH 7.4) because its phenolic hydroxyl groups are easily deprotonated at physiological pH. These findings contribute to developing a multifunctional scaffold for the treatment of low load-bearing patient-specific bone defects after trauma and tumor excision.
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Affiliation(s)
- Yongdeok Jo
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, USA.
| | - Naboneeta Sarkar
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, USA.
| | - Susmita Bose
- School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, USA.
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9
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Wang Y, Guo X, Cai X, Xu Y, Sun R, Umer MJ, Wang K, Qin T, Hou Y, Wang Y, Zhang P, Wang Z, Liu F, Wang Q, Zhou Z. Genome-Wide Association Study of Lint Percentage in Gossypium hirsutum L. Races. Int J Mol Sci 2023; 24:10404. [PMID: 37373552 DOI: 10.3390/ijms241210404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/08/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Lint percentage is one of the most essential yield components and an important economic index for cotton planting. Improving lint percentage is an effective way to achieve high-yield in cotton breeding worldwide, especially upland cotton (Gossypium hirsutum L.). However, the genetic basis controlling lint percentage has not yet been systematically understood. Here, we performed a genome-wide association mapping for lint percentage using a natural population consisting of 189 G. hirsutum accessions (188 accessions of G. hirsutum races and one cultivar TM-1). The results showed that 274 single-nucleotide polymorphisms (SNPs) significantly associated with lint percentage were detected, and they were distributed on 24 chromosomes. Forty-five SNPs were detected at least by two models or at least in two environments, and their 5 Mb up- and downstream regions included 584 makers related to lint percentage identified in previous studies. In total, 11 out of 45 SNPs were detected at least in two environments, and their 550 Kb up- and downstream region contained 335 genes. Through RNA sequencing, gene annotation, qRT-PCR, protein-protein interaction analysis, the cis-elements of the promotor region, and related miRNA prediction, Gh_D12G0934 and Gh_A08G0526 were selected as key candidate genes for fiber initiation and elongation, respectively. These excavated SNPs and candidate genes could supplement marker and gene information for deciphering the genetic basis of lint percentage and facilitate high-yield breeding programs of G. hirsutum ultimately.
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Affiliation(s)
- Yuanyuan Wang
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xinlei Guo
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Hainan Yazhou Bay Seed Laboratory, National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya 572025, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Runrun Sun
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Tengfei Qin
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Pan Zhang
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Zihan Wang
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Hainan Yazhou Bay Seed Laboratory, National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya 572025, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Qinglian Wang
- Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
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Shaver A, Arroyo-Currás N. Expanding the Monolayer Scope for Nucleic Acid-Based Electrochemical Sensors Beyond Thiols on Gold: Alkylphosphonic Acids on ITO. ECS SENSORS PLUS 2023; 2:010601. [PMID: 37006966 PMCID: PMC10053865 DOI: 10.1149/2754-2726/acc4d9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/15/2023] [Indexed: 03/18/2023]
Abstract
Electrochemical biosensors are a powerful and rapidly evolving molecular monitoring technology. Evidenced by the success of the continuous glucose monitor in managing Type 1 Diabetes, these sensors are capable of precise, accurate measurements in unprocessed biological environments. Nucleic acid-based electrochemical sensors (NBEs) are a specific type of biosensor that employs the target binding and conformational dynamics of nucleic acids for signal transduction. Currently, the vast majority of NBEs are fabricated via self-assembly of alkylthiols on Au electrodes. However, this architecture is limited in scope, as Au electrodes are not universally deployable for all potential NBE applications. Here, to expand the repertoire of materials on which NBEs can be made, we describe the multistep procedure for creating sensing monolayers of alkylphosphonic acids on a conductive oxide surface. Using such monolayers on indium tin oxide (ITO)-coated glass slides, we couple redox reporter-modified nucleic acids and demonstrate signaling of procaine-binding NBE sensors in buffer and human serum. We investigate the operational stability of these NBE sensors to reveal faster signal loss relative to benchmark thiol-on-gold sensing layers, a result that arises due to poor stability of the underlying ITO. Finally, we discuss future directions to continue expansion of NBE sensor materials and applications.
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Affiliation(s)
- Alexander Shaver
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21202, United States of America
| | - Netzahualcóyotl Arroyo-Currás
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21202, United States of America
- Department of Chemical and Biomolecular Engineering and Institute for NanoBioTechnology, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States of America
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11
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Trocha G, Bonilla A, Romero C, Palacios J, Molano-Gonzalez N. Ultrasound measurement of optic nerve sheath diameter in a healthy adult Colombian population. BMC Neurol 2023; 23:16. [PMID: 36639617 PMCID: PMC9837461 DOI: 10.1186/s12883-023-03062-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/12/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Measurement of the optic nerve sheath diameter (ONSD) provides a rapid, safe, and easy method for detecting increased intracranial pressure (ICP). However, the normal mean and upper limit values may vary according to sex, age, ethnicity, and ultrasound technique. AIM We aimed to obtain the mean ONSD in a healthy Colombian adult population and to correlate it with demographic and anthropometric measures. METHODS In a prospective study using a 10-13 MHz linear ultrasound probe, eye transverse diameter (ETD) and ONSD in the transverse (ONSD-TP) and sagittal planes (ONSD-SP) were measured in healthy adult volunteers in Bogota, Colombia. RESULTS A total of 100 healthy subjects were included, with a mean age of 26,7 ± 8,3 years and 62 women. The mean ETD, ONSD-TP and ONSD-SP was 23.11 mm (95% confidence interval (CI): 22.90 mm-23.32 mm), 3.96 mm (95% CI: 3.85 mm-4.07 mm) and 4.0 mm (95% CI: 3.90 mm-4.11 mm), respectively. The ONSD in both planes ranged from 2.35 mm to 5.20 mm. There was a significant correlation between ONSD-SP and ONSD-TP (p < 0.0001) but no correlation between the ocular measures and demographic or anthropometric variables (p > 0.05). The intraclass correlation between the eyes was statistically significant. CONCLUSION Our study shows that ultrasound-measured ONSD in healthy adults in Colombia is similar to that found worldwide. An ONSD of 5.5 mm may be considered the upper limit for healthy adults in Colombia. ONSD can be measured in either plane; there is a good correlation between the two eyes; and ONSD is not modified by demographic or anthropometric characteristics.
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Affiliation(s)
- Guillermo Trocha
- grid.488756.0Department of Neurology, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá, Colombia
| | - Andrés Bonilla
- grid.488756.0Department of Neurology, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá, Colombia
| | - Camilo Romero
- grid.488756.0Department of Neurology, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá, Colombia
| | - Jonathan Palacios
- grid.488756.0Department of Critical Care Medicine, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá, Colombia
| | - Nicolas Molano-Gonzalez
- grid.412191.e0000 0001 2205 5940Clinical Research Group, School of Medicine and Health Science, Universidad del Rosario, Bogotá, Colombia
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12
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Naoumkina M, Thyssen GN, Fang DD, Florane CB, Li P. A deletion/duplication in the Ligon lintless-2 locus induces siRNAs that inhibit cotton fiber cell elongation. PLANT PHYSIOLOGY 2022; 190:1792-1805. [PMID: 35997586 PMCID: PMC9614481 DOI: 10.1093/plphys/kiac384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Most cultivated cotton (Gossypium hirsutum L.) varieties have two types of seed fibers: short fuzz fiber strongly adhered to the seed coat, and long lint fiber used in the textile industry. The Ligon lintless-2 (Li2) cotton mutant has a normal vegetative phenotype but produces very short lint fiber on the seeds. The Li2 mutation is controlled by a single dominant gene. We discovered a large structural rearrangement at the end of chromosome D13 in the Li2 mutant based on whole-genome sequencing and genetic mapping of segregating populations. The rearrangement contains a 177-kb deletion and a 221-kb duplication positioned as a tandem inverted repeat. The gene Gh_D13G2437 is located at the junction of the inverted repeat in the duplicated region. During transcription such structure spontaneously forms self-complementary hairpin RNA of Gh_D13G2437 followed by production of small interfering RNA (siRNA). Gh_D13G2437 encodes a Ran-Binding Protein 1 (RanBP1) that preferentially expresses during cotton fiber elongation. The abundance of siRNA produced from Gh_D13G2437 reciprocally corresponds with the abundance of highly homologous (68%-98% amino acid sequence identity) RanBP1 family transcripts during fiber elongation, resulting in a shorter fiber phenotype in the Li2. Overexpression of Gh_D13G2437 in the Li2 mutant recovered the long lint fiber phenotype. Taken together, our findings revealed that siRNA-induced silencing of a family of RanBP1s inhibit elongation of cotton fiber cells in the Li2 mutant.
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Affiliation(s)
- Marina Naoumkina
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), New Orleans, Louisiana 70124, USA
| | - Gregory N Thyssen
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), New Orleans, Louisiana 70124, USA
- Cotton Chemistry and Utilization Research Unit, USDA-ARS-SRRC, New Orleans, Louisiana 70124, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), New Orleans, Louisiana 70124, USA
| | - Christopher B Florane
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), New Orleans, Louisiana 70124, USA
| | - Ping Li
- Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), New Orleans, Louisiana 70124, USA
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13
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Upadhyay K, Alshareef A, Knutsen AK, Johnson CL, Carass A, Bayly PV, Pham DL, Prince JL, Ramesh KT. Development and validation of subject-specific 3D human head models based on a nonlinear visco-hyperelastic constitutive framework. J R Soc Interface 2022; 19:20220561. [PMCID: PMC9554734 DOI: 10.1098/rsif.2022.0561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Computational head models are promising tools for understanding and predicting traumatic brain injuries. Most available head models are developed using inputs (i.e. head geometry, material properties and boundary conditions) from experiments on cadavers or animals and employ hereditary integral-based constitutive models that assume linear viscoelasticity in part of the rate-sensitive material response. This leads to high uncertainty and poor accuracy in capturing the nonlinear brain tissue response. To resolve these issues, a framework for the development of subject-specific three-dimensional head models is proposed, in which all inputs are derived in vivo from the same living human subject: head geometry via magnetic resonance imaging (MRI), brain tissue properties via magnetic resonance elastography (MRE), and full-field strain-response of the brain under rapid head rotation via tagged MRI. A nonlinear, viscous dissipation-based visco-hyperelastic constitutive model is employed to capture brain tissue response. Head models are validated using quantitative metrics that compare spatial strain distribution, temporal strain evolution, and the magnitude of strain maxima, with the corresponding experimental observations from tagged MRI. Results show that our head models accurately capture the strain-response of the brain. Further, employment of the nonlinear visco-hyperelastic constitutive framework provides improvements in the prediction of peak strains and temporal strain evolution over hereditary integral-based models.
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Affiliation(s)
- Kshitiz Upadhyay
- Hopkins Extreme Materials Institute, Johns Hopkins University, Baltimore, MD 21218, USA,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ahmed Alshareef
- Hopkins Extreme Materials Institute, Johns Hopkins University, Baltimore, MD 21218, USA,Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew K. Knutsen
- Center for Neuroscience and Regenerative Medicine, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Curtis L. Johnson
- Department of Biomedical Engineering, University of Delaware, Newark, DE 19716, USA
| | - Aaron Carass
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Philip V. Bayly
- Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Dzung L. Pham
- Center for Neuroscience and Regenerative Medicine, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Jerry L. Prince
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - K. T. Ramesh
- Hopkins Extreme Materials Institute, Johns Hopkins University, Baltimore, MD 21218, USA,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Ma Y, Guo Z, Wang L, Wang B, Huang T, Tang B, Zhang G, Zhou Q. The genome of the rice planthopper egg parasitoid wasps Anagrus nilaparvatae casts light on the chemo- and mechanosensation in parasitism. BMC Genomics 2022; 23:541. [PMID: 35902811 PMCID: PMC9331105 DOI: 10.1186/s12864-022-08656-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mymaridae is an ancient insect group and is a basal lineage of the superfamily Chalcidoidea. Species of Mymaridae have great potential for biological control. Anagrus nilaparvatae, a representative species of Mymaridae, is ideal for controlling rice planthopper due to its high rate of parasitism and ability to find hosts efficiently in paddy ridges and fields. RESULTS Using both PacBio single-molecule real-time and Illumina sequencing, we sequenced and assembled the whole genome of A. nilaparvatae, a first for the family Mymaridae. The assembly consists of 394 scaffolds, totaling 488.8 Mb. The assembly is of high continuity and completeness, indicated by the N50 value of 25.4 Mb and 98.2% mapping rate of Benchmarking Universal Single-Copy Orthologs. In total, 16,894 protein-coding genes in the genome were annotated. A phylogenomic tree constructed for A. nilaparvatae and other 12 species of Hymenoptera confirmed that the family Mymaridae is sister to all remaining chalcidoids. The divergence time between A. nilaparvatae and the other seven Chalcidoidea species was dated at ~ 126.9 Mya. Chemoreceptor and mechanoreceptor genes are important in explaining parasitic behavior. We identified 17 odorant binding proteins, 11 chemosensory proteins, four Niemann-Pick type C2 proteins, 88 olfactory receptors, 12 gustatory receptors, 22 ionotropic receptors and 13 sensory neuron membrane proteins in the genome of A. nilaparvatae, which are associated with the chemosensory functions. Strikingly, there is only one pickpocket receptors and nine transient receptor potential genes in the genome that have a mechanosensory function. CONCLUSIONS We obtained a high-quality genome assembly for A. nilaparvatae using PacBio single-molecule real-time sequencing, which provides phylogenomic insights for its evolutionary history. The small numbers of chemo- and mechanosensory genes in A. nilaparvatae indicate the species-specific host detection and oviposition behavior of A. nilaparvatae might be regulated by relatively simple molecular pathways.
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Affiliation(s)
- Ying Ma
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,School of Agriculture, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zixiao Guo
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liyang Wang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Bingyang Wang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Tingfa Huang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Bingjie Tang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Guren Zhang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiang Zhou
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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15
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Bothe TL, Patzak A, Pilz N. The B-Score is a novel metric for measuring the true performance of blood pressure estimation models. Sci Rep 2022; 12:12173. [PMID: 35842524 PMCID: PMC9288457 DOI: 10.1038/s41598-022-16527-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
We aimed to develop and test a novel metric for the relative performance of blood pressure estimation systems (B-Score). The B-Score sets absolute blood pressure estimation model performance in contrast to the dataset the model is tested upon. We calculate the B-Score based on inter- and intrapersonal variabilities within the dataset. To test the B-Score for reliable results and desired properties, we designed generic datasets with differing inter- and intrapersonal blood pressure variability. We then tested the B-Score’s real-world functionality with a small, published dataset and the largest available blood pressure dataset (MIMIC IV). The B-Score demonstrated reliable and desired properties. The real-world test provided allowed the direct comparison of different datasets and revealed insights hidden from absolute performance measures. The B-Score is a functional, novel, and easy to interpret measure of relative blood pressure estimation system performance. It is easily calculated for any dataset and enables the direct comparison of various systems tested on different datasets. We created a metric for direct blood pressure estimation system performance. The B-Score allows researchers to detect promising trends quickly and reliably in the scientific literature. It further allows researchers and engineers to quickly assess and compare performances of various systems and algorithms, even when tested on different datasets.
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Affiliation(s)
- Tomas L Bothe
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Translational Physiology, Chariteplatz 1, 10117, Berlin, Germany.
| | - Andreas Patzak
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Translational Physiology, Chariteplatz 1, 10117, Berlin, Germany
| | - Niklas Pilz
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Translational Physiology, Chariteplatz 1, 10117, Berlin, Germany
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16
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Optimization of silk fibroin coating during storage using response surface methodology and its effect on the physicochemical properties of Solanum ferox (S. ferox). JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2022. [DOI: 10.1007/s11694-022-01448-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Barraza B, Olate-Moya F, Montecinos G, Ortega JH, Rosenkranz A, Tamburrino A, Palza H. Superhydrophobic SLA 3D printed materials modified with nanoparticles biomimicking the hierarchical structure of a rice leaf. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2022; 23:300-321. [PMID: 35557509 PMCID: PMC9090350 DOI: 10.1080/14686996.2022.2063035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 06/15/2023]
Abstract
The rice leaf, combining the surface properties of lotus leaves and shark skin, presents outstanding superhydrophobic properties motivating its biomimesis. We created a novel biomimetic rice-leaf superhydrophobic surface by a three-level hierarchical structure, using for a first time stereolithographic (SLA) 3D printed channels (100µm width) with an intrinsic roughness from the printing filaments (10µm), and coated with TiO2 nanoparticles (22 and 100nm). This structure presents a maximum advancing contact angle of 165° characterized by lower both anisotropy and hysteresis contact angles than other 3D printed surfaces, due to the presence of air pockets at the surface/water interface (Cassie-Baxter state). Dynamic water-drop tests show that the biomimetic surface presents self-cleaning, which is reduced under UV-A irradiation. The biomimetic surface further renders an increased floatability to 3D printed objects meaning a drag-reduction due to reduced water/solid contact area. Numerical simulations of a channel with a biomimetic wall confirm that the presence of air is essential to understand our results since it increases the average velocity and decreases the friction factor due to the presence of a wall-slip velocity. Our findings show that SLA 3D printing is an appropriate approach to develop biomimetic superhydrophobic surfaces for future applications in anti-fouling and drag-reduction devices.
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Affiliation(s)
- Belén Barraza
- Matemáticas, Universidad de ChileDepartamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y, Santiago, Chile
- Núcleo Milenio en Metamateriales Mecánicos Suaves e Inteligentes (Millennium Nucleus on Smart Soft Mechanical Metamaterials)
- Advanced Mining Technology Center, Universidad de Chile, Santiago, Chile
| | - Felipe Olate-Moya
- Matemáticas, Universidad de ChileDepartamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y, Santiago, Chile
- Núcleo Milenio en Metamateriales Mecánicos Suaves e Inteligentes (Millennium Nucleus on Smart Soft Mechanical Metamaterials)
| | - Gino Montecinos
- Departamento de Ingeniería Matemática, Universidad de la Frontera, Temuco, Chile
| | - Jaime H. Ortega
- Departamento de Ingeniería Matemática, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
- Centro de Modelamiento Matemático, IRL 2807 CNRS-UChile, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Andreas Rosenkranz
- Matemáticas, Universidad de ChileDepartamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y, Santiago, Chile
| | - Aldo Tamburrino
- Departamento de Ingeniería Civil, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Humberto Palza
- Matemáticas, Universidad de ChileDepartamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y, Santiago, Chile
- Núcleo Milenio en Metamateriales Mecánicos Suaves e Inteligentes (Millennium Nucleus on Smart Soft Mechanical Metamaterials)
- Advanced Mining Technology Center, Universidad de Chile, Santiago, Chile
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18
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Silicon mitigates nutritional stress of nitrogen, phosphorus, and calcium deficiency in two forages plants. Sci Rep 2022; 12:6611. [PMID: 35459764 PMCID: PMC9033876 DOI: 10.1038/s41598-022-10615-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/11/2022] [Indexed: 11/09/2022] Open
Abstract
Forages are one of the most cultivated crops in the world. However, nutritional deficiency is common, specifically in N, P, and Ca in many forage-growing regions. Silicon (Si) can attenuate the stress caused by nutritional deficiency, but studies on Si supply's effects on forage plants are still scarce. This research was carried out to evaluate whether the Si supply can mitigate the effects of N, P, and Ca deficiencies of two forages and the physiological and nutritional mechanisms involved. Two experiments were carried out with two forage species (Urochloa brizantha cv. Marandu and Megathyrsus maximum cv. Massai). We used nutrient solution under balanced nutrition conditions and nutritional stress due to the lack of N, P, and Ca combined with the -Si and +Si. The deficiencies of N, P, and Ca in both forages' cultivation caused damage to physiological and nutritional variables, decreasing the plant dry matter. However, in both forage species, the Si addition to the nutrient solution decreased the extravasation of cellular electrolytes and increased the content of phenolic compounds, the green colour index, the quantum efficiency of photosystem II, the efficiencies of use of N, P and Ca and the production of shoot dry matter. The beneficial effects of Si were evidenced in stressed and non-stressed plants. The research emphasised the advantage of using Si to grow U. brizantha and M. maximum under N, P, and Ca deficiency, contributing to their sustainable cultivation.
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Luikham S, Mavani A, Bhattacharyya J. Deciphering binding affinity, energetics, and base specificity of plant alkaloid Harmane with AT & GC hairpin duplex DNA. LUMINESCENCE 2022; 37:691-701. [DOI: 10.1002/bio.4210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Soching Luikham
- Department of Chemistry National Institute of Technology Nagaland Chumukedima Dimapur Nagaland India
| | - A. Mavani
- Department of Chemistry National Institute of Technology Nagaland Chumukedima Dimapur Nagaland India
| | - Jhimli Bhattacharyya
- Department of Chemistry National Institute of Technology Nagaland Chumukedima Dimapur Nagaland India
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20
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Zou X, Ali F, Jin S, Li F, Wang Z. RNA-Seq with a novel glabrous-ZM24fl reveals some key lncRNAs and the associated targets in fiber initiation of cotton. BMC PLANT BIOLOGY 2022; 22:61. [PMID: 35114937 PMCID: PMC8815142 DOI: 10.1186/s12870-022-03444-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/24/2022] [Indexed: 06/12/2023]
Abstract
BACKGROUND Cotton fiber is an important natural resource for textile industry and an excellent model for cell biology study. Application of glabrous mutant cotton and high-throughput sequencing facilitates the identification of key genes and pathways for fiber development and cell differentiation and elongation. LncRNA is a type of ncRNA with more than 200 nt in length and functions in the ways of chromatin modification, transcriptional and post-transcriptional modification, and so on. However, the detailed lncRNA and associated mechanisms for fiber initiation are still unclear in cotton. RESULTS In this study, we used a novel glabrous mutant ZM24fl, which is endowed with higher somatic embryogenesis, and functions as an ideal receptor for cotton genetic transformation. Combined with the high-throughput sequencing, fatty acid pathway and some transcription factors such as MYB, ERF and bHLH families were identified the important roles in fiber initiation; furthermore, 3,288 lncRNAs were identified, and some differentially expressed lncRNAs were also analyzed. From the comparisons of ZM24_0 DPA vs ZM24_-2 DPA and fl_0 DPA vs ZM24_0 DPA, one common lncRNA MSTRG 2723.1 was found that function upstream of fatty acid metabolism, MBY25-mediating pathway, and pectin metabolism to regulate fiber initiation. In addition, other lncRNAs MSTRG 3390.1, MSTRG 48719.1, and MSTRG 31176.1 were also showed potential important roles in fiber development; and the co-expression analysis between lncRNAs and targets showed the distinct models of different lncRNAs and complicated interaction between lncRNAs in fiber development of cotton. CONCLUSIONS From the above results, a key lncRNA MSTRG 2723.1 was identified that might mediate some key genes transcription of fatty acid metabolism, MYB25-mediating pathway, and pectin metabolism to regulate fiber initiation of ZM24 cultivar. Co-expression analysis implied that some other important lncRNAs (e.g., MSTRG 3390.1, MSTRG 48719.1, and MSTRG 31176.1) were also showed the different regulatory model and interaction between them, which proposes some valuable clues for the lncRNAs associated mechanisms in fiber development.
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Affiliation(s)
- Xianyan Zou
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Faiza Ali
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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21
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Bruno C, Sauvage E, Simcock I, Redaelli A, Schievano S, Shroff R, Capelli C. Computational investigation of the haemodynamics shows criticalities of central venous lines used for chronic haemodialysis in children. Front Pediatr 2022; 10:1055212. [PMID: 36389366 PMCID: PMC9659647 DOI: 10.3389/fped.2022.1055212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/10/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Haemodialysis is a life-saving treatment for children with kidney failure. The majority of children have haemodialysis through central venous lines (CVLs). The use of CVLs in pediatric patients is often associated to complications which can lead to their replacement. The aim of this study is to investigate haemodynamics of pediatric CVLs to highlight the criticalities of different line designs. METHODS Four models of CVLs for pediatric use were included in this study. The selected devices varied in terms of design and sizes (from 6.5 Fr to 14 Fr). Accurate 3D models of CVLs were reconstructed from high-resolution images including venous and arterial lumens, tips and side holes. Computational fluid dynamics (CFD) analyses were carried out to simulate pediatric working conditions of CVLs in ideal and anatomically relevant conditions. RESULTS The arterial lumens of all tested CVLs showed the most critical conditions with the majority of blood flowing through the side-holes. A zone of low flow was identified at the lines' tip. The highest shear stresses distribution (>10 Pa) was found in the 8 Fr line while the highest platelet lysis index in the 10 Fr model. The analysis on the anatomical geometry showed an increase in wall shear stress measured in the 10 F model compared to the idealised configuration. Similarly, in anatomical models an increased disturbance and velocity of the flow was found inside the vein after line placement. CONCLUSION This study provided a numerical characterization of fluid dynamics in pediatric CVLs highlighting performance criticalities (i.e. high shear stresses and areas of stagnation) associated to specific sizes (8 Fr and 10 Fr) and conditions (i.e. anatomical test).
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Affiliation(s)
- Claudia Bruno
- Institute of Child Health, University College London, London, United Kingdom
| | - Emilie Sauvage
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Ian Simcock
- Great Ormond Street Hospital for Children, NHS Foundation Trust, London, United Kingdom
| | - Alberto Redaelli
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy
| | - Silvia Schievano
- Institute of Cardiovascular Science, University College London, London, United Kingdom.,Great Ormond Street Hospital for Children, NHS Foundation Trust, London, United Kingdom
| | - Rukshana Shroff
- Institute of Child Health, University College London, London, United Kingdom.,Great Ormond Street Hospital for Children, NHS Foundation Trust, London, United Kingdom
| | - Claudio Capelli
- Institute of Cardiovascular Science, University College London, London, United Kingdom.,Great Ormond Street Hospital for Children, NHS Foundation Trust, London, United Kingdom
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22
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Feng X, Cheng H, Zuo D, Zhang Y, Wang Q, Lv L, Li S, Yu JZ, Song G. Genome-wide identification and expression analysis of GL2-interacting-repressor (GIR) genes during cotton fiber and fuzz development. PLANTA 2021; 255:23. [PMID: 34923605 DOI: 10.1007/s00425-021-03737-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/20/2021] [Indexed: 06/14/2023]
Abstract
GL2-interacting-repressor (GIR) family members may contribute to fiber/fuzz formation via a newly discovered unique pathway in Gossypium arboreum. There are similarities between cotton fiber development and the formation of trichomes and root hairs. The GL2-interacting-repressors (GIRs) are crucial regulators of root hair and trichome formation. The GaFzl gene, annotated as GaGIR1, is negatively associated with trichome development and fuzz initiation. However, there is relatively little available information regarding the other GIR genes in cotton, especially regarding their effects on cotton fiber development. In this study, 21 GIR family genes were identified in the diploid cotton species Gossypium arboreum; these genes were divided into three groups. The GIR genes were characterized in terms of their phylogenetic relationships, structures, chromosomal distribution and evolutionary dynamics. These GIR genes were revealed to be unequally distributed on 12 chromosomes in the diploid cotton genome, with no GIR gene detected on Ga06. The cis-acting elements in the promoter regions were predicted to be responsive to light, phytohormones, defense activities and stress. The transcriptomic data and qRT-PCR results revealed that most GIR genes were not differentially expressed between the wild-type control and the fuzzless mutant line. Moreover, 14 of 21 family genes were expressed at high levels, indicating these genes may play important roles during fiber development and fuzz formation. Furthermore, Ga01G0231 was predominantly expressed in root samples, suggestive of a role in root hair formation rather than in fuzz initiation and development. The results of this study have enhanced our understanding of the GIR genes and their potential utility for improving cotton fiber through breeding.
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Affiliation(s)
- Xiaoxu Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Plant Genetics, Gembloux Agro Bio-Tech, University of Liège, 5030, Gembloux, Belgium
| | - Hailiang Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Dongyun Zuo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Youping Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qiaolian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Limin Lv
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Shuyan Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - John Z Yu
- Southern Plains Agricultural Research Center, USDA-ARS, Crop Germplasm Research Unit, 2881 F&B Road, College Station, Texas, 77845, USA.
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Ryu B, Yoo S, Kim S, Choi J. Thirty-day hospital readmission prediction model based on common data model with weather and air quality data. Sci Rep 2021; 11:23313. [PMID: 34857799 PMCID: PMC8639801 DOI: 10.1038/s41598-021-02395-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/29/2021] [Indexed: 12/03/2022] Open
Abstract
Although several studies have attempted to develop a model for predicting 30-day re-hospitalization, few attempts have been made for sufficient verification and multi-center expansion for clinical use. In this study, we developed a model that predicts unplanned hospital readmission within 30 days of discharge; the model is based on a common data model and considers weather and air quality factors, and can be easily extended to multiple hospitals. We developed and compared four tree-based machine learning methods: decision tree, random forest, AdaBoost, and gradient boosting machine (GBM). Above all, GBM showed the highest AUC performance of 75.1 in the clinical model, while the clinical and W-score model showed the best performance of 73.9 for musculoskeletal diseases. Further, PM10, rainfall, and maximum temperature were the weather and air quality variables that most impacted the model. In addition, external validation has confirmed that the model based on weather and air quality factors has transportability to adapt to other hospital systems.
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Affiliation(s)
- Borim Ryu
- Office of eHealth Research and Business, Seoul National University Bundang Hospital, 172, Dolma-ro, Bundang-gu, Seongnam-si, 13605, Gyeonggi-do, Republic of Korea.,Department of Biomedical Engineering, College of Medicine, Seoul National University, 28 Yongon-Dong Chongro-Gu, Seoul, 110-799, Korea
| | - Sooyoung Yoo
- Office of eHealth Research and Business, Seoul National University Bundang Hospital, 172, Dolma-ro, Bundang-gu, Seongnam-si, 13605, Gyeonggi-do, Republic of Korea.
| | - Seok Kim
- Office of eHealth Research and Business, Seoul National University Bundang Hospital, 172, Dolma-ro, Bundang-gu, Seongnam-si, 13605, Gyeonggi-do, Republic of Korea
| | - Jinwook Choi
- Department of Biomedical Engineering, College of Medicine, Seoul National University, 28 Yongon-Dong Chongro-Gu, Seoul, 110-799, Korea. .,Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University, Seoul, South Korea.
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24
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Volarić J, Szymanski W, Simeth NA, Feringa BL. Molecular photoswitches in aqueous environments. Chem Soc Rev 2021; 50:12377-12449. [PMID: 34590636 PMCID: PMC8591629 DOI: 10.1039/d0cs00547a] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Indexed: 12/17/2022]
Abstract
Molecular photoswitches enable dynamic control of processes with high spatiotemporal precision, using light as external stimulus, and hence are ideal tools for different research areas spanning from chemical biology to smart materials. Photoswitches are typically organic molecules that feature extended aromatic systems to make them responsive to (visible) light. However, this renders them inherently lipophilic, while water-solubility is of crucial importance to apply photoswitchable organic molecules in biological systems, like in the rapidly emerging field of photopharmacology. Several strategies for solubilizing organic molecules in water are known, but there are not yet clear rules for applying them to photoswitchable molecules. Importantly, rendering photoswitches water-soluble has a serious impact on both their photophysical and biological properties, which must be taken into consideration when designing new systems. Altogether, these aspects pose considerable challenges for successfully applying molecular photoswitches in aqueous systems, and in particular in biologically relevant media. In this review, we focus on fully water-soluble photoswitches, such as those used in biological environments, in both in vitro and in vivo studies. We discuss the design principles and prospects for water-soluble photoswitches to inspire and enable their future applications.
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Affiliation(s)
- Jana Volarić
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Department of Radiology, Medical Imaging Center, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Nadja A Simeth
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Institute for Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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Arora S, Chaudhary B. Global expression dynamics and miRNA evolution profile govern floral/fiber architecture in the modern cotton (Gossypium). PLANTA 2021; 254:62. [PMID: 34459999 DOI: 10.1007/s00425-021-03711-3] [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: 06/08/2021] [Accepted: 08/23/2021] [Indexed: 05/15/2023]
Abstract
Majority of differentially expressed miRNAs with functional attributes have been recruited independently and parallelly during allopolyploidy followed by the millennia of human selection of both domesticated G. hirsutum and G. barbadense. The genus Gossypium is a marvelous evolutionary model for studying allopolyploidy and morpho-evolution of long-spinnable fibers from the ancestral wild-fuzz. Many genes, transcription factors, and notably, the regulatory miRNAs essentially govern such remarkable modern fiber phenotypes. To comprehend the impact of allopolyploidy on the evolutionary selection of transcriptional dynamicity of key miRNAs, comparative transcriptome profiling of vegetative and fiber tissues of domesticated diploid G. arboreum (A2) and allopolyploid cotton species G. hirsutum (AD1), and G. barbadense (AD2) identified > 300 differentially expressed miRNAs (DEmiRs) within or between corresponding tissues of A2, AD1 and AD2 species. Up to 49% and 32% DEmiRs were up- and down-regulated at fiber initiation stage of AD1 and AD2 species, respectively, whereas 50% and 18% DEmiRs were up- and down-regulated at fiber elongation stage of both the allopolyploid species. Interestingly, A-subgenome-specific DEmiRs exhibit expression dominance in the allopolyploid genetic backgrounds. Comparative spatio-temporal expression analyses of AD1 and AD2 species discovered that a majority of DEmiRs were recruited independently under millennia of human selection during domestication. Functional annotations of these DEmiRs revealed selection of associated molecular functions such as hormone-signaling, calcium-signaling and reactive oxygen species (ROS) signaling during fiber initiation and elongation. To validate the functional attributes of annotated DEmiRs, we demonstrated for the first time that the target-mimicry-based constitutive diminution of auxin-signaling associated miR167 directly affected the differentiation of floral and fiber tissues of transgenic cotton. These results strongly suggested that the evolutionarily favored DEmiRs including miR167 were involved in the transcriptional regulation of numerous genes during cotton evolution for enhanced fiber-associated agronomic traits.
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Affiliation(s)
- Sakshi Arora
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201310, India
| | - Bhupendra Chaudhary
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201310, India.
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26
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Campese N, Beatino MF, Del Gamba C, Belli E, Giampietri L, Del Prete E, Galgani A, Vergallo A, Siciliano G, Ceravolo R, Hampel H, Baldacci F. Ultrasensitive techniques and protein misfolding amplification assays for biomarker-guided reconceptualization of Alzheimer's and other neurodegenerative diseases. Expert Rev Neurother 2021; 21:949-967. [PMID: 34365867 DOI: 10.1080/14737175.2021.1965879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION The clinical validation and qualification of biomarkers reflecting the complex pathophysiology of neurodegenerative diseases (NDDs) is a fundamental challenge for current drug discovery and development and next-generation clinical practice. Novel ultrasensitive detection techniques and protein misfolding amplification assays hold the potential to optimize and accelerate this process. AREAS COVERED Here we perform a PubMed-based state of the art review and perspective report on blood-based ultrasensitive detection techniques and protein misfolding amplification assays for biomarkers discovery and development in NDDs. EXPERT OPINION Ultrasensitive assays represent innovative solutions for blood-based assessments during the entire Alzheimer's disease (AD) biological and clinical continuum, for contexts of use (COU) such as prediction, detection, early diagnosis, and prognosis of AD. Moreover, cerebrospinal fluid (CSF)-based misfolding amplification assays show encouraging performance in detecting α-synucleinopathies in prodromal or at-high-risk individuals and may serve as tools for patients' stratification by the presence of α-synuclein pathology. Further clinical research will help overcome current methodological limitations, also through exploring multiple accessible bodily matrices. Eventually, integrative longitudinal studies will support precise definitions for appropriate COU across NDDs.
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Affiliation(s)
- Nicole Campese
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | | | - Claudia Del Gamba
- Neurology Unit, Nuovo Ospedale Santo Stefano, Via Suor Niccolina Infermiera 20, Prato, Italy
| | - Elisabetta Belli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Linda Giampietri
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Eleonora Del Prete
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Alessandro Galgani
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Andrea Vergallo
- Sorbonne University, GRC N° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié- Salpêtrière Hospital, Boulevard De L'hôpital, Paris, France
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Roberto Ceravolo
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Harald Hampel
- Sorbonne University, GRC N° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié- Salpêtrière Hospital, Boulevard De L'hôpital, Paris, France
| | - Filippo Baldacci
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,Sorbonne University, GRC N° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié- Salpêtrière Hospital, Boulevard De L'hôpital, Paris, France
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27
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Lodzinska J, Munro E, Shaw DJ, Suñol A. MRI of the optic nerve sheath and globe in cats with and without presumed intracranial hypertension. J Feline Med Surg 2021; 23:751-758. [PMID: 33252305 PMCID: PMC10812188 DOI: 10.1177/1098612x20976106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVES The study aimed to: (1) test MRI repeatability of measurements of optic nerve sheath diameter (ONSD), optic nerve diameter (OND) and eye globe transverse diameter (ETD); (2) investigate the associations between the OND, ONSD and ETD; (3) assess whether these measurements are affected by age or body weight; and (4) test the association between ONSD, OND, ETD and ONSD:ETD ratio with presumed intracranial pressure (ICP) status. METHODS This was a retrospective and blinded study where patients were allocated to presumed normal or intracranial hypertension groups based on MRI findings. The ONSD and ETD were measured and recorded. Interclass correlation coefficient (ICC) was calculated to investigate interobserver agreement. Data were analysed using the Pearson correlation coefficient, two-sample t-test and general linear model ANOVA. RESULTS Seventy-seven cats were included, 62 with presumed normal ICP and 15 with presumed intracranial hypertension. The ICC showed moderate-to-good reliability for all measurements. Positive correlations were identified for: (1) ETD and weight; (2) ONSD and age; (3) OND and age; (4) ONSD and ETD; (5) ONSD:ETD ratio and presumed ICP status; and (6) ONSD and presumed ICP status. No difference was detected between the presumed normal and intracranial hypertension groups and ONSD, as well as ONSD:ETD ratio and presumed ICP status when patient age was considered. CONCLUSIONS AND RELEVANCE The measurement of the ONSD and the ONSD:ETD ratio on T2-weighted MRI might not be reliable as non-invasive tests for diagnosing intracranial hypertension in cats.
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Affiliation(s)
- Joanna Lodzinska
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Roslin, UK
| | - Elizabeth Munro
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Roslin, UK
| | - Darren J Shaw
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Roslin, UK
| | - Anna Suñol
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Roslin, UK
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da Cruz ADSE, Puydinger Dos Santos MV, Campanelli RB, Pagliuso PG, Bettini J, Pirota KR, Béron F. Low-temperature electronic transport of manganese silicide shell-protected single crystal nanowires for nanoelectronics applications. NANOSCALE ADVANCES 2021; 3:3251-3259. [PMID: 36133655 PMCID: PMC9419286 DOI: 10.1039/d0na00809e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 04/15/2021] [Indexed: 05/12/2023]
Abstract
Recently, core-shell nanowires have been proposed as potential electrical connectors for nanoelectronics components. A promising candidate is Mn5Si3 nanowires encapsulated in an oxide shell, due to their low reactivity and large flexibility. In this work, we investigate the use of the one-step metallic flux nanonucleation method to easily grow manganese silicide single crystal oxide-protected nanowires by performing their structural and electrical characterization. We find that the fabrication method yields a room-temperature hexagonal crystalline structure with the c-axis along the nanowire. Moreover, the obtained nanowires are metallic at low temperature and low sensitive to a strong external magnetic field. Finally, we observe an unknown electron scattering mechanism for small diameters. In conclusion, the one-step metallic flux nanonucleation method yields intermetallic nanowires suitable for both integration in flexible nanoelectronics as well as low-dimensionality transport experiments.
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Affiliation(s)
| | | | - Raul B Campanelli
- Institute of Physics Gleb Wataghin (IFGW), University of Campinas (UNICAMP) Campinas 13083-859 São Paulo Brazil
| | - Pascoal G Pagliuso
- Institute of Physics Gleb Wataghin (IFGW), University of Campinas (UNICAMP) Campinas 13083-859 São Paulo Brazil
| | - Jefferson Bettini
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Nanotechnology National Laboratory (LNNano) Campinas 13085-903 São Paulo Brazil
| | - Kleber R Pirota
- Institute of Physics Gleb Wataghin (IFGW), University of Campinas (UNICAMP) Campinas 13083-859 São Paulo Brazil
| | - Fanny Béron
- Institute of Physics Gleb Wataghin (IFGW), University of Campinas (UNICAMP) Campinas 13083-859 São Paulo Brazil
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Raghavendra KP, Das J, Kumar R, Gawande SP, Santosh HB, Sheeba JA, Kranthi S, Kranthi KR, Waghmare VN. Genome-wide identification and expression analysis of the plant specific LIM genes in Gossypium arboreum under phytohormone, salt and pathogen stress. Sci Rep 2021; 11:9177. [PMID: 33911097 PMCID: PMC8080811 DOI: 10.1038/s41598-021-87934-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 03/30/2021] [Indexed: 11/09/2022] Open
Abstract
Asiatic cotton (Gossypium arboreum) cultivated as ‘desi cotton’ in India, is renowned for its climate resilience and robustness against biotic and abiotic stresses. The genome of G. arboreum is therefore, considered as a valued reserve of information for discovering novel genes or gene functions for trait improvements in the present context of cotton cultivation world-wide. In the present study, we carried out genome-wide analysis of LIM gene family in desi cotton and identified twenty LIM domain proteins (GaLIMs) which include sixteen animals CRP-like GaLIMs and four plant specific GaLIMs with presence (GaDA1) or absence (GaDAR) of UIM (Ubiquitin Interacting Motifs). Among the sixteen CRP-like GaLIMs, eleven had two conventional LIM domains while, five had single LIM domain which was not reported in LIM gene family of the plant species studied, except in Brassica rapa. Phylogenetic analysis of these twenty GaLIM proteins in comparison with LIMs of Arabidopsis, chickpea and poplar categorized them into distinct αLIM1, βLIM1, γLIM2, δLIM2 groups in CRP-like LIMs, and GaDA1 and GaDAR in plant specific LIMs group. Domain analysis had revealed consensus [(C-X2-C-X17-H-X2-C)-X2-(C-X2-C-X17-C-X2-H)] and [(C-X2-C-X17-H-X2-C)-X2-(C-X4-C-X15-C-X2-H)] being conserved as first and/or second LIM domains of animal CRP-like GaLIMs, respectively. Interestingly, single LIM domain containing GaLIM15 was found to contain unique consensus with longer inter-zinc-motif spacer but shorter second zinc finger motif. All twenty GaLIMs showed variable spatio-temporal expression patterns and accordingly further categorized into distinct groups of αLIM1, βLIM1, γLIM2 δLIM2 and plant specific LIM (DA1/DAR). For the first time, response of GaDA1/DAR under the influence of biotic and abiotic stresses were studied in cotton, involving treatments with phytohormones (Jasmonic acid and Abscisic acid), salt (NaCl) and wilt causing pathogen (Fusarium oxysporum). Expressions patterns of GaDA1/DAR showed variable response and identified GaDA2 as a probable candidate gene for stress tolerance in G. arboreum.
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Affiliation(s)
- K P Raghavendra
- Division of Crop Improvement, ICAR - Central Institute for Cotton Research (CICR), Nagpur, Maharashtra, India.
| | - J Das
- Division of Crop Improvement, ICAR - Central Institute for Cotton Research (CICR), Nagpur, Maharashtra, India
| | - R Kumar
- Division of Crop Improvement, ICAR - Central Institute for Cotton Research (CICR), Nagpur, Maharashtra, India
| | - S P Gawande
- Division of Crop Protection, ICAR - Central Institute for Cotton Research (CICR), Nagpur, Maharashtra, India
| | - H B Santosh
- Division of Crop Improvement, ICAR - Central Institute for Cotton Research (CICR), Nagpur, Maharashtra, India
| | - J A Sheeba
- Division of Crop Production, ICAR - Central Institute for Cotton Research (CICR), Nagpur, Maharashtra, India
| | - S Kranthi
- Division of Crop Protection, ICAR - Central Institute for Cotton Research (CICR), Nagpur, Maharashtra, India
| | - K R Kranthi
- Technical Information Section, International Cotton Advisory Committee (ICAC), Washington, DC, USA
| | - V N Waghmare
- Division of Crop Improvement, ICAR - Central Institute for Cotton Research (CICR), Nagpur, Maharashtra, India
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Palladino C, Ezeonwumelu IJ, Mate-Cano I, Borrego P, Martínez-Román P, Arca-Lafuente S, Resino S, Taveira N, Briz V. Epidemic history and baseline resistance to NS5A-specific direct acting drugs of hepatitis C virus in Spain. Sci Rep 2020; 10:13024. [PMID: 32747734 PMCID: PMC7398927 DOI: 10.1038/s41598-020-69692-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/07/2020] [Indexed: 11/29/2022] Open
Abstract
Hepatitis C virus (HCV) infection remains a global health problem. Previously, the prevalence of NS5A resistance-associated substitutions (RASs) to elbasvir, a new direct-acting antiviral (DAA) against the NS5A viral protein was assessed by our group before its introduction into clinical use in Spain. However, the origin, epidemic history, transmission dynamics, diversity and baseline RASs to NS5A direct-acting agents of HCV-GT1a in Spain remain unknown. A nationwide cross-sectional survey of individuals chronically-infected with HCV-G1a and DAAs-naïve was performed. HCV population sequencing, phylogenetic analysis and Bayesian methods were used. GT1a clade II was more prevalent than clade I (82.3% vs. 17.7%; P < 0.001) and older (estimated origin in 1912 vs. 1952). Clade II epidemic is currently declining whereas clade I epidemic has reached equilibrium. A total of 58 single RASs were identified, which account for the moderate level (10%) of baseline resistance observed. When considering the regional data, marked differences were observed, with thirteen regions showing an intermediate level (5–15%) and one a high level (20%) of resistance. Current HCV-GT1a epidemic in Spain is driven by clade I which seem to have different dissemination routes relative to clade II. A moderate level of baseline RASs to NS5A-DAAs with marked differences among regions was observed. Close surveillance of response to treatment with DAAs will be important.
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Affiliation(s)
- Claudia Palladino
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisbon, Portugal.
| | - Ifeanyi Jude Ezeonwumelu
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisbon, Portugal
| | - Irene Mate-Cano
- Laboratory of Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Carretera Majadahonda-Pozuelo km 2.2, Majadahonda, 28220, Madrid, Spain
| | - Pedro Borrego
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisbon, Portugal
| | - Paula Martínez-Román
- Laboratory of Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Carretera Majadahonda-Pozuelo km 2.2, Majadahonda, 28220, Madrid, Spain
| | - Sonia Arca-Lafuente
- Laboratory of Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Carretera Majadahonda-Pozuelo km 2.2, Majadahonda, 28220, Madrid, Spain
| | - Salvador Resino
- Laboratory of Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Carretera Majadahonda-Pozuelo km 2.2, Majadahonda, 28220, Madrid, Spain
| | - Nuno Taveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisbon, Portugal.,Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, Portugal
| | - Verónica Briz
- Laboratory of Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Carretera Majadahonda-Pozuelo km 2.2, Majadahonda, 28220, Madrid, Spain.
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Cheng LC, Simonaitis JW, Gadelrab KR, Tahir M, Ding Y, Alexander-Katz A, Ross CA. Imparting Superhydrophobicity with a Hierarchical Block Copolymer Coating. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905509. [PMID: 31808616 DOI: 10.1002/smll.201905509] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/10/2019] [Indexed: 06/10/2023]
Abstract
A robust and transparent silica-like coating that imparts superhydrophobicity to a surface through its hierarchical multilevel self-assembled structure is demonstrated. This approach involves iterative steps of spin-coating, annealing, and etching of polystyrene-block-polydimethylsiloxane block copolymer thin films to form a tailored multilayer nanoscale topographic pattern with a water contact angle up to 155°. A model based on the hierarchical topography is developed to calculate the wetting angle and optimize the superhydrophobicity, in agreement with the experimental trends, and explaining superhydrophobicity arising through the combination of roughness at different lengthscales. Additionally, the mechanical robustness and optically passive properties of the resulting hydrophobic surfaces are demonstrated.
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Affiliation(s)
- Li-Chen Cheng
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - John W Simonaitis
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Karim R Gadelrab
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mukarram Tahir
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yi Ding
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Caroline A Ross
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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Abstract
As the nanotechnological applications have taken over in different fields, their applications for water and wastewater treatment is also surfacing as a fast-developing and very promising area. Recent advancements in nanotechnological science and engineering advise that many of the waterborne pathogens could be culminated or debilitated using nanobiosorbents, nanocatalysts, bioactive nanoparticles, nanostructured catalytic membranes, nanobioreactors, nanoparticle-enhanced filtration among other products, and processes resulting from the development of nanotechnology. A detailed insight has been provided for advanced techniques such as photochemical (photocatalytic and advanced oxidation processes) applications of metal oxide nanoparticles, nanomembrane technology, bioinspired nanomaterials, and nanotechnological innovations (nano-Ag, fullerenes, nanotubes, and molecularly imprinted polymers, etc.), which prove to be highly potential as well as promising and cost-effective. However, there are still some shortcomings and challenges that must be overcome which will be looked upon in this chapter.
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Liu F, Tang Y, Guo Q, Chen J. Identification and characterization of microRNAs in phloem and xylem from ramie (Boehmeria nivea). Mol Biol Rep 2019; 47:1013-1020. [PMID: 31820312 DOI: 10.1007/s11033-019-05193-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 11/12/2019] [Indexed: 11/28/2022]
Abstract
Ramie (Boehmeria nivea) is a widely cropped species in southern China due to its high economic value of natural fiber for industry. Development of phloem and xylem is key evidence for generating fiber. However, the MicroRNA (miRNA) profiles of phloem and xylem in ramie have not been reported yet. miRNA belong to a small RNA family which has been recognized as an important regulator for various biological processes. In the present study, we aimed to identify differently expressed miRNAs between phloem and xylem in adult ramie. The results showed that 137 and 122 unique conserved miRNAs were identified from phloem and xylem libraries, respectively. Meanwhile, 4 novel miRNAs were identified from ramie by miRDeep2. Of these miRNAs, 77 conserved miRNAs in ramie were differentially expressed. Among the differentially expressed miRNAs, 44 miRNAs and 33 miRNAs were up-regulated and down-regulated in phloem compared to that in xylem, respectively. The functions of differentially expressed miRNAs were associated with regulating the development and differentiation of phloem and xylem. The present study provides a glance of miRNA profiles for further understanding of miRNA role in ramie development.
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Affiliation(s)
- Fang Liu
- Department of Biotechnology and Environmental Science, Changsha University, Hongshan Road 98#, Changsha, 410003, Hunan, China
| | - Yinghong Tang
- Department of Biotechnology and Environmental Science, Changsha University, Hongshan Road 98#, Changsha, 410003, Hunan, China
| | - Qingquan Guo
- Department of Biotechnology and Environmental Science, Changsha University, Hongshan Road 98#, Changsha, 410003, Hunan, China
| | - Jianrong Chen
- Department of Biotechnology and Environmental Science, Changsha University, Hongshan Road 98#, Changsha, 410003, Hunan, China.
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Zhu L, Zheng B, Song W, Tao C, Jin X, Li H. Comparative Proteomic Analysis of Molecular Differences between Leaves of Wild-Type Upland Cotton and Its Fuzzless- Lintless Mutant. Molecules 2019; 24:molecules24203769. [PMID: 31635060 PMCID: PMC6832260 DOI: 10.3390/molecules24203769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/13/2019] [Accepted: 10/16/2019] [Indexed: 01/01/2023] Open
Abstract
Fuzzless-lintless mutant (fl) ovules of upland cotton have been used to investigate cotton fiber development for decades. However, the molecular differences of green tissues between fl and wild-type (WT) cotton were barely reported. Here, we found that gossypol content, the most important secondary metabolite of cotton leaves, was higher in Gossypium hirsutum L. cv Xuzhou-142 (Xu142) WT than in fl. Then, we performed comparative proteomic analysis of the leaves from Xu142 WT and its fl. A total of 4506 proteins were identified, of which 103 and 164 appeared to be WT- and fl-specific, respectively. In the 4239 common-expressed proteins, 80 and 74 were preferentially accumulated in WT and fl, respectively. Pathway enrichment analysis and protein–protein interaction network analysis of both variety-specific and differential abundant proteins showed that secondary metabolism and chloroplast-related pathways were significantly enriched. Quantitative real-time PCR confirmed that the expression levels of 12 out of 16 selected genes from representative pathways were consistent with their protein accumulation patterns. Further analyses showed that the content of chlorophyll a in WT, but not chlorophyll b, was significantly increased compared to fl. This work provides the leaf proteome profiles of Xu142 and its fl mutant, indicating the necessity of further investigation of molecular differences between WT and fl leaves.
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Affiliation(s)
- Liping Zhu
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
| | - Bowen Zheng
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
| | - Wangyang Song
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
| | - Chengcheng Tao
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
| | - Xiang Jin
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Hongbin Li
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
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Salih H, Gong W, He S, Xia W, Odongo MR, Du X. Long non-coding RNAs and their potential functions in Ligon-lintless-1 mutant cotton during fiber development. BMC Genomics 2019; 20:661. [PMID: 31426741 PMCID: PMC6700839 DOI: 10.1186/s12864-019-5978-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 07/16/2019] [Indexed: 01/28/2023] Open
Abstract
Background Long non-coding RNAs (LncRNAs) are part of genes, which are not translated into proteins and play a vital role in plant growth and development. Nevertheless, the presence of LncRNAs and how they functions in Ligon-lintless-1 mutant during the early cessation of cotton fiber development are still not well understood. In order to investigate the function of LncRNAs in cotton fiber development, it is necessary and important to identify LncRNAs and their potential roles in fiber cell development. Results In this work, we identified 18,333 LncRNAs, with the proportion of long intergenic noncoding RNAs (LincRNAs) (91.5%) and anti-sense LncRNAs (8.5%), all transcribed from Ligon-lintless-1 (Li1) and wild-type (WT). Expression differences were detected between Ligon-lintless-1 and wild-type at 0 and 8 DPA (day post anthesis). Pathway analysis and Gene Ontology based on differentially expressed LncRNAs on target genes, indicated fatty acid biosynthesis and fatty acid elongation being integral to lack of fiber in mutant cotton. The result of RNA-seq and RT-qPCR clearly singles out two potential LncRNAs, LNC_001237 and LNC_017085, to be highly down-regulated in the mutant cotton. The two LncRNAs were found to be destabilized or repressed by ghr-miR2950. Both RNA-seq analysis and RT-qPCR results in Ligon-lintless-1 mutant and wild-type may provide strong evidence of LNC_001237, LNC_017085 and ghr-miR2950 being integral molecular elements participating in various pathways of cotton fiber development. Conclusion The results of this study provide fundamental evidence for the better understanding of LncRNAs regulatory role in the molecular pathways governing cotton fiber development. Further research on designing and transforming LncRNAs will help not only in the understanding of their functions but will also in the improvement of fiber quality. Electronic supplementary material The online version of this article (10.1186/s12864-019-5978-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haron Salih
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.,Zalingei University, Central Darfur, Sudan
| | - Wenfang Gong
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Shoupu He
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Wang Xia
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Magwanga Richard Odongo
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Xiongming Du
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.
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Feng X, Cheng H, Zuo D, Zhang Y, Wang Q, Liu K, Ashraf J, Yang Q, Li S, Chen X, Song G. Fine mapping and identification of the fuzzless gene GaFzl in DPL972 (Gossypium arboreum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2169-2179. [PMID: 30941465 PMCID: PMC6647196 DOI: 10.1007/s00122-019-03330-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/14/2018] [Indexed: 05/15/2023]
Abstract
The fuzzless gene GaFzl was fine mapped to a 70-kb region containing a GIR1 gene, Cotton_A_11941, responsible for the fuzzless trait in Gossypium arboreum DPL972. Cotton fiber is the most important natural textile resource. The fuzzless mutant DPL972 (Gossypium arboreum) provides a useful germplasm resource to explore the molecular mechanism underlying fiber and fuzz initiation and development. In our previous research, the fuzzless gene in DPL972 was identified as a single dominant gene and named GaFzl. In the present study, we fine mapped this gene using F2 and BC1 populations. By combining traditional map-based cloning and next-generation sequencing, we mapped GaFzl to a 70-kb region containing seven annotated genes. RNA-Sequencing and re-sequencing analysis narrowed these candidates to two differentially expressed genes, Cotton_A_11941 and Cotton_A_11942. Sequence alignment uncovered no variation in coding or promoter regions of Cotton_A_11942 between DPL971 and DPL972, whereas two single-base mutations in the promoter region and a TTG insertion in the coding region were detected in Cotton_A_11941 in DPL972. Cotton_A_11941 encoding a homologous gene of GIR1 (GLABRA2-interacting repressor) in Arabidopsis thaliana is thus the candidate gene most likely responsible for the fuzzless trait in DPL972. Our findings should lead to a better understanding of cotton fuzz formation, thereby accelerating marker-assisted selection during cotton breeding.
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Affiliation(s)
- Xiaoxu Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Plant Genetics, Gembloux Agro Bio Tech, University of Liège, Gembloux, Belgium
| | - Hailiang Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Dongyun Zuo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Youping Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qiaolian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Ke Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Javaria Ashraf
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qiuhong Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Simin Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiaoqin Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Nozaka A, Nishiwaki A, Nagashima Y, Endo S, Kuroki M, Nakajima M, Narukawa M, Kamisuki S, Arazoe T, Taguchi H, Sugawara F, Kamakura T. Chloramphenicol inhibits eukaryotic Ser/Thr phosphatase and infection-specific cell differentiation in the rice blast fungus. Sci Rep 2019; 9:9283. [PMID: 31243315 PMCID: PMC6594944 DOI: 10.1038/s41598-019-41039-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/25/2019] [Indexed: 01/23/2023] Open
Abstract
Chloramphenicol (Cm) is a broad-spectrum classic antibiotic active against prokaryotic organisms. However, Cm has severe side effects in eukaryotes of which the cause remains unknown. The plant pathogenic fungus Magnaporthe oryzae, which causes rice blast, forms an appressorium to infect the host cell via single-cell differentiation. Chloramphenicol specifically inhibits appressorium formation, which indicates that Cm has a novel molecular target (or targets) in the rice blast fungus. Application of the T7 phage display method inferred that MoDullard, a Ser/Thr-protein phosphatase, may be a target of Cm. In animals Dullard functions in cell differentiation and protein synthesis, but in fungi its role is poorly understood. In vivo and in vitro analyses showed that MoDullard is required for appressorium formation, and that Cm can bind to and inhibit MoDullard function. Given that human phosphatase CTDSP1 complemented the MoDullard function during appressorium formation by M. oryzae, CTDSP1 may be a novel molecular target of Cm in eukaryotes.
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Affiliation(s)
- Akihito Nozaka
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Ayaka Nishiwaki
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Yuka Nagashima
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Shogo Endo
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Misa Kuroki
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Masahiro Nakajima
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Megumi Narukawa
- Osaka University, Research Institute for Microbial Diseases, Department of Molecular Microbiology, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shinji Kamisuki
- Azabu University, Department of Veterinary Science, Laboratory of Basic Education, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa, 252-5201, Japan
| | - Takayuki Arazoe
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Hayao Taguchi
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Fumio Sugawara
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Takashi Kamakura
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan.
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Zhao T, Xu X, Wang M, Li C, Li C, Zhao R, Zhu S, He Q, Chen J. Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application. BMC Genomics 2019; 20:421. [PMID: 31138116 PMCID: PMC6537205 DOI: 10.1186/s12864-019-5760-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 05/02/2019] [Indexed: 12/18/2022] Open
Abstract
Background Cotton is the most essential textile crop worldwide, and phytohormones are critical for cotton fiber development. One example is the role of auxin in fiber initiation, but we know little molecular basis. MicroRNAs (miRNAs) have a significant function in cotton development; nevertheless their role in fiber initiation remains unclear. Here, exogenous IAA was applied to cotton plant before anthesis. Utilizing small RNA sequencing, the mechanism underlying miRNA-mediated regulation of fiber initiation under exogenous IAA treatment was investigated. Results With exogenous IAA application, the endogenous IAA and GA contents of IAA treated (IT) ovules were higher than control (CK) ovules at the fiber initiation stage, while endogenous ABA content was lower in IT than CK. Using scanning electron microscopy, we found the fiber number and size were significantly promoted in IT at 0 DPA. Fiber quality analysis showed that fiber length, uniformity, strength, elongation, and micronaire of IT were higher than CK, though not statistically significant, while lint percent was significantly higher in IT. We generated six small RNA libraries using − 3, 0, and 3 DPA ovules of IT and CK, and identified 58 known miRNAs and 83 novel miRNAs together with the target genes. The differential expressed miRNAs number between IT and CK at − 3, 0, 3 DPA was 34, 16 and 24, respectively. Gene ontology and KEGG pathway enrichment analyses for the target genes of the miRNAs expressed in a differential manner showed that they were significantly enriched in 30 terms and 8 pathways. QRT-PCR for those identified miRNAs and the target genes related to phytohormones and fiber development was performed, and results suggested a potential role of these miRNAs in fiber initiation. Conclusions The exogenous IAA application affected the relative phytohormone contents in ovule and promoted fiber initiation in cotton. Identification and profiling of miRNAs and their targets at the fiber initiation stage provided insights for miRNAs’ regulation function of fiber initiation. These findings not only shed light on the regulatory network of fiber growth but also offer clues for cotton fiber amelioration strategies in cotton. Electronic supplementary material The online version of this article (10.1186/s12864-019-5760-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tianlun Zhao
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Xiaojian Xu
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Min Wang
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Cheng Li
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Cong Li
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Rubing Zhao
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Shuijin Zhu
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Qiuling He
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, Zhejiang Sci-Tech University, Zhejiang, 310018, Hangzhou, China.
| | - Jinhong Chen
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China.
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miR-363-3p is activated by MYB and regulates osteoporosis pathogenesis via PTEN/PI3K/AKT signaling pathway. In Vitro Cell Dev Biol Anim 2019; 55:376-386. [PMID: 31025251 DOI: 10.1007/s11626-019-00344-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/26/2019] [Indexed: 12/17/2022]
Abstract
Osteoporosis results from the imbalance between osteogenesis and bone resorption mediated by osteoblasts and osteoclasts. During the disease process of osteoporosis, the alteration of gene expression occurs, which lead to the disease progression. MicroRNAs (miRNAs) have been previously demonstrated to be modulators for bone metabolism via regulation of osteoblast and osteoclast differentiation. In the present study, we detected the expression levels of five osteoporosis-related miRNAs in bone and serum samples of patient with or without osteoporosis. The downstream molecular mechanism of miR-363-3p was analyzed and detected by using bioinformatics analysis and mechanism experiment. The upstream transcription factor of miR-363-3p was analyzed by applying bioinformatics analysis and ChIP assay and luciferase reporter assay. The role of this pathway in osteoclastogenesis was demonstrated by functional assays. MiR-363-3p was significantly highly expressed in osteoporotic samples. Mechanistically, miR-363-3p promotes osteoclastogenesis and inhibits osteogenic differentiation by targeting PTEN and therefore activating PI3K/AKT signaling pathway. MiR-363-3p was activated by its upstream transcription activator MYB. This study revealed that MYB-induced upregulation of miR-363-3p regulates osteoporosis pathogenesis via PTEN/PI3K/AKT signaling pathway.
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Morais A, Egger J, Alves V. Automated Computer-aided Design of Cranial Implants Using a Deep Volumetric Convolutional Denoising Autoencoder. ADVANCES IN INTELLIGENT SYSTEMS AND COMPUTING 2019. [DOI: 10.1007/978-3-030-16187-3_15] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Kumar V, Singh B, Singh SK, Rai KM, Singh SP, Sable A, Pant P, Saxena G, Sawant SV. Role of GhHDA5 in H3K9 deacetylation and fiber initiation in Gossypium hirsutum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1069-1083. [PMID: 29952050 DOI: 10.1111/tpj.14011] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 05/28/2023]
Abstract
Cotton fibers are single-celled trichomes that initiate from the epidermal cells of the ovules at or before anthesis. Here, we identified that the histone deacetylase (HDAC) activity is essential for proper cotton fiber initiation. We further identified 15 HDACs homoeologs in each of the A- and D-subgenomes of Gossypium hirsutum. Few of these HDAC homoeologs expressed preferentially during the early stages of fiber development [-1, 0 and 6 days post-anthesis (DPA)]. Among them, GhHDA5 expressed significantly at the time of fiber initiation (-1 and 0 DPA). The in vitro assay for HDAC activity indicated that GhHDA5 primarily deacetylates H3K9 acetylation marks. Moreover, the reduced expression of GhHDA5 also suppresses fiber initiation and lint yield in the RNA interference (RNAi) lines. The 0 DPA ovules of GhHDA5RNAi lines also showed alterations in reactive oxygen species homeostasis and elevated autophagic cell death in the developing fibers. The differentially expressed genes (DEGs) identified through RNA-seq of RNAi line (DEP12) and their pathway analysis showed that GhHDA5 modulates expression of many stress and development-related genes involved in fiber development. The reduced expression of GhHDA5 in the RNAi lines also resulted in H3K9 hyper-acetylation on the promoter region of few DEGs assessed by chromatin immunoprecipitation assay. The positively co-expressed genes with GhHDA5 showed cumulative higher expression during fiber initiation, and gene ontology annotation suggests their involvement in fiber development. Furthermore, the predicted protein interaction network in the positively co-expressed genes indicates HDA5 modulates fiber initiation-specific gene expression through a complex involving reported repressors.
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Affiliation(s)
- Verandra Kumar
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, India
| | - Babita Singh
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI, Lucknow, India
| | - Sunil K Singh
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
| | - Krishan M Rai
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
| | - Surendra P Singh
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, India
| | - Anshulika Sable
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
| | - Poonam Pant
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI, Lucknow, India
| | - Gauri Saxena
- Department of Botany, University of Lucknow, Lucknow, India
| | - Samir V Sawant
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI, Lucknow, India
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Palladino C, Ezeonwumelu IJ, Marcelino R, Briz V, Moranguinho I, Serejo F, Velosa JF, Marinho RT, Borrego P, Taveira N. Epidemic history of hepatitis C virus genotypes and subtypes in Portugal. Sci Rep 2018; 8:12266. [PMID: 30116054 PMCID: PMC6095915 DOI: 10.1038/s41598-018-30528-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/27/2018] [Indexed: 12/15/2022] Open
Abstract
Any successful strategy to prevent and control HCV infection requires an understanding of the epidemic behaviour among the different genotypes. Here, we performed the first characterization of the epidemic history and transmission dynamics of HCV subtypes in Portugal. Direct sequencing of NS5B was performed on 230 direct-acting antiviral drugs (DAA)-treatment naïve patients in Lisbon. Phylogenetic analysis was used for subtyping and transmission cluster identification. Bayesian methods were used to reconstruct the epidemic history of HCV subtypes. Sequences were analysed for resistance-associated substitutions (RAS). The majority of strains were HCV-GT1 (62.6%), GT3 (18.3%, all subtype 3a) and GT4 (16.1%). Among GT1, the most frequent were subtypes 1a (75.5%) and 1b (24.5%). Polyphyletic patterns were found in all but 12 lineages suggesting multiple introductions of the different subtypes in this population. Five distinct epidemics were identified. The first significant HCV epidemic in Portugal occurred between 1930s and 1960s, was caused almost exclusively by GT1b and was likely associated with blood transfusions. Rapid expansion of GT3a occurred in the 1960s and GT1a in the 1980s, associated with intravenous drug use. The most recent epidemics were caused by GT4a and GT4d and seem to be associated with the resurgence of opioid use. The C316N substitution was found in 31.4% of GT1b-patients. Close surveillance of patients bearing this mutation and undergoing dasabuvir-based regimens will be important to determine its impact on treatment outcome.
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Affiliation(s)
- Claudia Palladino
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
| | - Ifeanyi Jude Ezeonwumelu
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Rute Marcelino
- Global Health and Tropical Medicine (GHTM), Unit of Medical Microbiology, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisbon, Portugal
| | - Verónica Briz
- Laboratory of Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - Inês Moranguinho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Fátima Serejo
- Department of Gastroenterology and Hepatology, Santa Maria Hospital, Universidade de Lisboa, Lisbon, Portugal
| | - José Fernando Velosa
- Department of Gastroenterology and Hepatology, Santa Maria Hospital, Universidade de Lisboa, Lisbon, Portugal
| | - Rui Tato Marinho
- Department of Gastroenterology and Hepatology, Santa Maria Hospital, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro Borrego
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Centro de Administração e Políticas Públicas (CAPP), Instituto Superior de Ciências Sociais e Políticas, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno Taveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, Portugal.
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Moss DK, Surge D, Khaitov V. Lifespan and growth of Astarte borealis (Bivalvia) from Kandalaksha Gulf, White Sea, Russia. Polar Biol 2018. [DOI: 10.1007/s00300-018-2290-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pan X, Nichols RL, Li C, Zhang B. MicroRNA-target gene responses to root knot nematode (Meloidogyne incognita) infection in cotton (Gossypium hirsutum L.). Genomics 2018; 111:383-390. [PMID: 29481843 DOI: 10.1016/j.ygeno.2018.02.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 01/23/2023]
Abstract
MicroRNAs (miRNAs) are a large class of small regulatory RNA molecules, however no study has been performed to elucidate the role of miRNAs in cotton (Gossypium hirsutum) response to the root knot nematode (RKN, Meloidogyne incognita) infection. We selected 28 miRNAs and 8 miRNA target genes to investigate the miRNA-target gene response to M. incognita infection. Our results show that RKN infection significantly affected the expression of several miRNAs and their targeted genes. After 10 days of RKN infection, expression fold changes on miRNA expressions ranged from down-regulated by 33% to upregulated by 406%; meanwhile the expression levels of miRNA target genes were 45.8% to 231%. Three miRNA-target pairs, miR159-MYB, miR319-TCP4 and miR167-ARF8, showed inverse expression patterns between gene targets and their corresponded miRNAs, suggesting miRNA-mediated gene regulation in cotton roots in response to RKN infection.
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Affiliation(s)
- Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
| | | | - Chao Li
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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Dong Z, Zhang J, Zhu Q, Zhao L, Sui S, Li Z, Zhang Y, Wang H, Tian D, Zhao Y. Identification of microRNAs involved in drought stress responses in early-maturing cotton by high-throughput sequencing. Genes Genomics 2017; 40:305-314. [PMID: 29892798 DOI: 10.1007/s13258-017-0637-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/15/2017] [Indexed: 01/19/2023]
Abstract
Drought stress is one of the most important abiotic stresses. Cotton is classified as drought tolerant crop but the regulatory mechanism is unknown. MicroRNAs (miRNAs) have been implicated important roles in stress responses in many plants. However, the study of miRNAs in cotton responsive to drought stress is limited, especially in early-maturing cotton. In this study, we performed deep sequencing of small RNAs to identify known and novel miRNAs involved in the regulation of drought stress and understand the expression profile of miRNAs in early-maturing cotton. Three cotton small RNA libraries: non-stressed Shizao1 (early-maturing cotton variety) library (NSS), drought-stressed Shizao1 library (DSS) and non-stressed Jimian958 (medium-maturing cotton variety) library (NSJ) were constructed for deep sequencing. As a result, we identified a total of 64 known and 67 novel miRNAs in the 3 libraries and 88 of them were dramatically differentially expressed (greater than twofold) during drought stress. In addition, we found the expression of 41 miRNAs increased or reduced more than twofold in early-maturing cotton variety compared with that in medium-maturing cotton variety. Our results significantly increased the number of miRNAs in cotton and revealed for the first time the expression profile of miRNAs for early-maturing cotton.
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Affiliation(s)
- Zhanghui Dong
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China.
| | - Jianhong Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 598 Heping Road, Shijiazhuang, 050051, Hebei, China
| | - Qingzhu Zhu
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Lifen Zhao
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Shuxiang Sui
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Zengshu Li
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Yanli Zhang
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Hu Wang
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Dongliang Tian
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Yankun Zhao
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
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Ghobadi A, Dereshgi SA, Butun B, Ozbay E. Ultra-broadband Asymmetric Light Transmission and Absorption Through The Use of Metal Free Multilayer Capped Dielectric Microsphere Resonator. Sci Rep 2017; 7:14538. [PMID: 29109475 PMCID: PMC5674040 DOI: 10.1038/s41598-017-15248-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 10/24/2017] [Indexed: 11/08/2022] Open
Abstract
In this paper, we propose a simple design with an excellent performance to obtain high contrast in transmission asymmetry based on dielectric microspheres. Initially, we scrutinize the impact of the sphere radius on forward and backward transmissions. Afterward, by introducing a capping layer on top of the sphere, transmission response for the backward illuminated light will be blocked. In the next step, in order to replace the reflecting metal cap with a metal free absorbing design, we adopt a modeling approach based on the transfer matrix method (TMM) to explore an ideal material to achieve metal free perfect absorption in a multilayer configuration of material-insulator-material-insulator (MIMI). As a result of our investigations, it is found that Titanium Nitride (TiN) is an excellent alternative to replace metal in a MIMI multilayer stack. Setting this stack as the top capping coating, we obtain a high contrast between forward and backward light transmission where in an ultra-broadband range of 400 nm-1000 nm, forward transmission is above 0.85 while its backward response stays below 0.2. Moreover, due to the existence of multilayer stack, a high asymmetry is also observed for absorption profiles. This design has a relatively simple and large scale compatible fabrication route.
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Affiliation(s)
- Amir Ghobadi
- NANOTAM-Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey.
- Department of Electrical and Electronics Engineering, Bilkent University, 06800, Ankara, Turkey.
| | - Sina Abedini Dereshgi
- NANOTAM-Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey
- Department of Electrical and Electronics Engineering, Bilkent University, 06800, Ankara, Turkey
| | - Bayram Butun
- NANOTAM-Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey
| | - Ekmel Ozbay
- NANOTAM-Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey.
- Department of Electrical and Electronics Engineering, Bilkent University, 06800, Ankara, Turkey.
- Department of Physics, Bilkent University, 06800, Ankara, Turkey.
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara, Turkey.
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